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Hosted by 

BIOENGINEERING 

INSTITUTE OF 

CALIFORNIA 

10 th Annual UC Systemwide 

Bioengineering Symposium 

June 19-21, 2009 

SCHOOL OF ENGINEERING

Campus Map

Welcome to 

Merced!

In October 2003, the Bioengineering Institute of California 

(BIC) was approved as a Multicampus Research Unit. Under 

the MRU, all 10 UC campuses will establish a modern 

information infrastructure with facilities and staffing for 

broadband inter-campus transmission, thus forming a network 

for research and teaching system-wide. It will make possible 

the sharing of database, broadcasting of teaching materials, 

teleoperation of specialized instruments, video conferencing, 

and telecommunication. The MRU will provide seed funds 

for inter-campus collaboration for high-risk, high payoff 

research, establish graduate student fellowships and facilitate 

intercampus joint training, set up a Traveling Seminar 

Program, and attract the participation of large industrial 

companies to facilitate academia-industry collaboration and 

technology transfer. The MRU will establish state-of-the-art 

research core facilities for shared usage by the participating 

campuses. The activities of the MRU will synergize with 

other units in the UC system, including the three new 

California Institutes for Science and Innovation.

10 th Annual Systemwide 

Bioengineering Symposium 

UC Merced 

19-21 June 2009 

Dear Colleagues (Faculty, Students, and Others): 

It is a great pleasure for me to welcome you to the 10 th UC System-wide 

Bioengineering Symposium to be held on the UC Merced campus on June 19-21, 

2000. This Symposium has special significance in that it will be held in the newest of 

our ten UC campuses and that it will mark the 10 th Anniversary of the System-wide 

Symposium to complete the first decade of a wonderful tradition that has brought 

together faculty and students from all ten campuses. The symposia have served the 

important purpose of fostering exchange and collaboration on bioengineering 

research performed on the ten campuses of the University of California, which have 

strong representations in many different areas and offers almost limitless 

opportunities for new interactions. 

On behalf of the System-wide Bioengineering Institute in California, I would like to 

express our sincere thanks to Dr. Kara McCloskey and the other members of the 

Organizing Committee at UC Merced for their tremendous efforts in organizing this 

10 th Symposium, with an outstanding program. I am certain that this Symposium will 

be very successful in achieving our goal of uniting our ten campuses as one, learning 

and growing together. 

I would like to express my sincere thanks for your participation, best wishes for your 

enjoyment, and warmest anticipation of the great success of this epical Symposium 

that marks the first decade of our joint efforts. 

Sincerely yours, 

Shu Chien, M.D., Ph.D. 

Director 

Bioengineering Institute of California

Partners & Sponsers

Program Organizing & Logistics Chair 

Kara McCloskey 

Scientific Program Chair 

Michelle Khine 

Fundraising Director 

Ron Durbin 

Financial Director 

Christina Christensen 

Organizing & Logistics Subcommittee 

Jonathan Pegan 

Maureen Long 

Drew Glaser 

Booklet Photography 

Anthony Grimes 

Special Thanks to BIC Staff 

Shu Chien, Director 

Jennifer Griffin 

Rowella Garcia

The goal of this symposium is to increase the synergistic 

interaction of the University of California’s vast biomedical 

engineering research expertise with the practical medical and 

healthcare engineering undertaken by biomedical firms and a 

number of agencies in the government.

Table of Contents 

WELCOME .................................................................... P. 1-2 

ACKNOWLEDGEMENTS ............................................ P. 3-4 

SYMPOSIUM INFORMATION ................................. P. 7-12 

KEYNOTE SPEAKERS ................................................................. P. 7-8 

TATRC PARTNER ........................................................................... P. 9 

WELCOME MAP .......................................................................... P. 10 

PROGRAM SCHEDULE ............................................................ P. 11-12 

SCIENTIFIC SESSIONS ........................................... P. 13–33 

SATURDAY, JUNE 20 TH .......................................................... P. 13–25 

Podium Session I ...................................................................... P. 13–17 

Poster Session ............................................................................ P. 30–33 

Podium Session II ...................................................................... P. 18-21 

Podium Session III .................................................................... P. 22-25 

SUNDAY, JUNE 21 ST ................................................................ P. 26-29 

Podium Session IV .................................................................... P. 26-29 

PROGRAM ABSTRACTS ....................................... P. 24-140 

ORAL ABSTRACTS .................................................................P. 24-123 

POSTER ABSTRACTS ............................................................ P. 124-140

Distinguished Keynote Presenters 

Robert M. Nerem, PhD 

Professor and Director, Parker H. Petit Institute for Bioengineering 

and Bioscience, Georgia Institute of Technology 

Robert Nerem has been active in bioengineering for more than thirty-five 

years. He now is director of the Georgia Tech/Emory Center for the 

Engineering of Living Tissues (GTEC), an Engineering Research Center 

established in 1998 and funded by the National Science Foundation. 

Friday, June 19, 2009 

6:00pm – 7:00pm 

In recognition of his work, he was elected to the National Academy of 

Engineering in 1988 and to the Institute of Medicine of the National 

Academy of Sciences in 1992. He was elected a fellow of the American 

Academy of Arts and Sciences in 1998. Nerem is past president of the 

International Federation for Medical and Biological Engineering and past 

president of the International Union for Physical and Engineering Sciences 

in Medicine. He was also the founding president of the American Institute 

of Medical and Biological Engineering and he served on the Science Board 

of the Food and Drug Administration from 2000 to 2003. In 2008 he 

received the Founders Award from the National Academy of Engineering. 

William L. Ditto, PhD 

Chair, Harrington Department of Bioengineering, Arizona State 

University 

Dr. William Ditto is the new chairman for the Harrington Department of 

Bioengineering in the Ira A. Fulton School of Engineering at Arizona State 

University's Bioengineering school. He comes arrived at ASU from the 

University of Florida, where he was the founding chairman of the J. 

Crayton Pruitt Family Department of Biomedical Engineering and the J. 

Crayton Pruitt Family Eminent Scholar Endowed Chair. Dr. Ditto's 

visionary and charismatic leadership provide a foundation for the 

department's innovative approach to research and academics. 

In recognition of his achievements, Dr. Ditto recently was named a fellow 

of the American Physical Society and a fellow of the American Institute for 

Medical and Biological Engineering. 

Saturday, June 20, 2009 

8:30am – 9:30am

Distinguished Keynote Presenters 

Buddy Ratner, PhD 

University of Washington Engineered Biomaterials (UWEB) 

Professor of Bioengineering and Chemical Engineering, University 

of Washington 

Buddy Ratner became director of UWEB in 1996. He is also the Darland 

Endowed Chair in Technology Commercialization and professor of 

bioengineering and chemical engineering at the University of Washington. 

He has launched two companies and three others have resulted from his 

research. His research interests include biomaterials, tissue engineering, 

polymers, biocompatibility, surface analysis of organic materials, self 

assembly, nanobiotechnology, and RF-plasma thin film deposition. He has 

written more than 400 scholarly works and holds 17 patents. 


6:00pm – 7:00pm 

Buddy Ratner was elected a member of the National Academy of 

Engineering (USA) in 2002 and president of the Tissue Engineering Society 

of North America in 2003. He is on the council of the Tissue Engineering 

and Regenerative Medicine International Society and is an associate editor 

of the Journal of Biomedical Materials Research. He is on the advisory 

board of the journal Biointerphases, and is on the editorial boards of 10 

other journals. 

Jack Lloyd 

Founder, Alere Medical and Nellcor Inc. 

Jack Lloyd has been a founder, officer, and director of many medical and 

high technology companies since 1970, including Nellcor, Aradigm, and 

Alere Medical. From 1974 to 1981, Mr. Lloyd was founder and President of 

Humphrey Instruments (acquired by Carl Zeiss Meditec). Mr. Lloyd served 

as founder, president and CEO of Nellcor from 1981-1990, during which 

time he built Nellcor from a start-up, based on his development of the Pulse 

Oximeter, to a company with $150 million in annual sales, now owned by 

Covidian Medical. He was also Chairman and President of Aradigm, a 

developer of aerosol drug delivery systems to deliver insulin; he is a founder 

of Alere Medical, and developed a system to monitor patients with 

congestive heart failure at home. Alere was sold to Inverness Medical in 

2007. Mr. Lloyd holds 29 U.S. Patents. 

Sunday, June 21, 2009 

8:30am – 9:30am 

Jack Lloyd currently serves on the boards of directors of several medical 

companies. Mr. Lloyd earned his bachelor's degree in mechanical 

engineering from the University of California, Berkeley and now serves on 

the Engineering Advisory Board of the UC Berkeley School of Engineering 

and is a trustee of the U.C. Berkeley Foundation.

TATRC Sponsor 

Chuck Peterson, MD 

Telemedicine and Advanced Technology Research Center 

Saturday, June 20, 2009, 11:30am – 12:00pm 

The Telemedicine and Advanced Technology Research Center (TATRC), a subordinate element of 

the U.S. Army and Medical Research and Materiel Command, has as its mission to explore science 

and engineering technologies ahead of programmed research, leveraging other programs to 

maximize benefits to military medicine. Specifically, TATRC is charged with managing core 

research, development, test and evaluation (RDT&E) and congressionally mandated projects in 

telemedicine and advanced medical technologies. To support its research and development effort, 

TATRC maintains a productive mix of partnerships with federal, academic, and commercial 

organizations. TATRC also provides short-duration technical support to federal and defense 

agencies, and develops, evaluates, and demonstrates new technologies and concepts. In addition, 

TATRC conducts market surveillance with a focus on leveraging emerging technologies in 

healthcare and ancillary services. Ultimately, TATRC aims to be the government model of 

opportunity-driven research agility. TATRC strives to make medical care and services more 

accessible to military personnel, and to reduce costs, thereby enhancing the overall quality of 

military healthcare.

CIRM Sponsor 

The California Institute for Regenerative Medicine ("The Institute" or 

"CIRM") was established in early 2005 following the passage of Proposition 71, the 

California Stem Cell Research and Cures Initiative. The statewide ballot measure, 

which provided $3 billion in funding for stem cell research at California 

universities and research institutions, was approved by California voters on 

November 2, 2004, and called for the establishment of a new state agency to make 

grants and provide loans for stem cell research, research facilities and other vital 

research opportunities. 

The mission of CIRM is to support and advance stem cell research and regenerative 

medicine under the highest ethical and medical standards for the discovery and 

development of cures, therapies, diagnostics and research technologies to relieve 

human suffering from chronic disease and injury.

Symposium Schedule 

Time and Date 

Friday, June 19, 2009 

4:00pm – 6:00pm 

6:00pm – 9:00pm 

Event 

Check–In and Registration (Housing) 

Keynote: Dr. Robert Nerem followed by Dinner 

Keynote: COB 105 

Dinner: Cat Quad between Housing and Dining 


7:15 am – 8:30am Bioengineering Institute of California Steering Committee Meeting 

COB 263 

7:30am – 8:30am 

Breakfast in COB lobby(2 nd floor) 

7:30am – 8:30am 

Check–In and Registration (COB lobby) 

Exhibitor Set-Up (Lantern) 

7:30am – 8:30am 

8:30am – 9:30am 

All Posters Set-Up (Lantern) 

Welcome Address and 

Plenary speaker: Dr. William Ditto 

COB 102 

9:30am – 11:15am 

Podium Session I (2 nd floor COB) 

Track 1 Track 2 Track 3 

Bioinformatics & 

Biosystems Modeling 

Biomedical Imaging I 

Biomaterials 

11:15am – 11:30am 

11:30am – 12:00pm 

12:00pm – 2:00pm 

2:00pm – 3:45pm 

Coffee Break and Poster Review 

Plenary Speaker: Dr. Charles Peterson, TATRC 

COB 102 

Lunch wih Poster Session - Lantern 

Podium Session II (2 nd floor COB) 


Computation, in Silico Tissue Engineering Nanotechnology & 

BioMEMS 

3:45pm – 4:00pm 

Coffee Break and Poster Review 

11 | 10 th Annual UC Systemwide Bioengineering Symposium | Bioengineering Institute of California

4:00pm – 5:45pm 

5:45pm – 6:00pm 

6:00pm – 7:00 pm 

7:00pm – 10:30pm 


7:30am – 8:30am 

8:30am - 9:30am 

9:30am - 9:45am 

9:45am – 11:30am 

Podium Session III (2 nd floor COB) 


Stem Cells 

Drug Delivery & 

Targeting 

Poster Removal 

Reception with Keynote: Dr. Buddy Ratner 

10 th Annual Gala Celebration Dinner 

Breakfast in COB lobby (2 nd floor) 

Plenary Speaker: John Lloyd 

COB 102 

Coffee Break 

Podium Session IV (2 nd floor COB) 

Biomechanics 


Molecular & Cellular Biophysics 

New Frontiers 

Engineering 

11:30 am – 12:00 pm Judges Meeting COB 263/Check-out in Housing 

12:00 pm – 2:00pm Lunch and Award Ceremony 

Dining Commons 

10 th Annual UC Systemwide Bioengineering Symposium | Bioengineering Institute of California | 12

Podium Session I 


9:30am – 11:15am 

Track 1 

Bioinformatics and 

Genomics 

COB 279 

Session Chair 

J. Liao, UCR 

Track 2 

Biomaterials 

COB 263 

Session Chair 

K. Leach, UCD 

Track 3 

Biomedical Imaging 

COB 267 

Session Chairs 

X. Li, UCSF 

X. Zhang, UCSF 

Track 1 - Bioinformatics and Genomics 

Session Chair 

Jiayu Liao 

UC Riverside 

Time Title and Speaker Page 

9:30 AM Introduction to Bioinformatics and Genomics. Jiayu Liao, UCR 

9:50 AM 

10:02 AM 

10:14 AM 

Molecular Interactions between GATA-3 and Notch-1 That Regulate T 

Cell Commitment. Mufadhal M. Al-Kuhlani, Jesús Ciriza, Joseph H. 

Ramos, Tanya Carroll, Harshani Peiris, and Marcos E. García-Ojeda. 

UCM 

Signaling model of cell death shows cell-to-cell stochastic fluctuations are 

linked to apoptosis related diseases. Marin Djendjinovic, Kavya 

Katipally, and Subhadip Raychaudhuri. UCD 

CHIP-Seq experiments reveal global shift of protein coding RNA and 

intergenic non-coding RNA transcription in primary macrophages by 

Kdo2-Lipid A. Lana Garmire, Josh Stender, Shankar Subramaniam, 

Christopher Glass. UCSD 

32 

33 

34 


10:26 AM 

Selective PPARγ Ligand Modulation of Metabolic Pathways in Obese 

Zucker fa/fa Rats. Gene Hsiao, Dr. Shankar Subramaniam, and Dr. 

Dorothy D. Sears. UCSD 

35 

10:38 AM 

Energy based Monte Carlo Simulation of B-cell Receptor Clustering. A. 

Srinivas Reddy, Sandeep Chilukuri, and Subhadip Raychaudhuri. UCD 

36 

10:50 AM 

Computational Analysis of Feedback Regulation in Signaling Networks. 

Sean Kim, Arnold Kim, Jian Qiao Sun, and Henry Foreman. UCM 

37 

Track 2 - Biomaterials 

Session Chair 

Kent Leach 

UC Davis 


9:30 AM Indroduction to Biomaterials. Kent Leach, UCD 

9:50 AM 

10:02 AM 

10:14 AM 

10:26 AM 

10:38 AM 

Investigating the Properties of Block Copolypeptide Vesicles. Uh-Joo 

Choe, April R. Rodriguez, Zhibo Li, Howard Dai, Sophia Lin, 

Timothy J. Deming, and Daniel T. Kamei. UCLA 

Decellularized Solubilized Extracellular Matrix Coatings for Cell 

Culture. Jessica A. DeQuach, Amar Miglani, and Karen L. Christman. 

UCSD 

Controllable Biomimetic Hydrogel Scaffolds to Study Pulmonary 

Fibroblast Mechanotransduction. HN Chia and AM Kasko. UCLA 

Nanotopographical Effects on Vascular Endothelial and Smooth Muscle 

Cells. Matthew L. Eltgroth, Lily Peng, and Tejal A. Desai. UCSF 

Synthesis of Photoreactive Linkers with Varying Degradation Rates for 

use in Biomedical Applications. RD Griffin, DY Wong, and AM Kasko. 

UCLA 

38 

39 

40 

41 

42 


10:50 AM 

11:02 AM 

Capsule Thickness Surrounding Titanium Oxide Nanotube Implants. 

Garrett C. Smith, Seunghan Oh, Linda Fauxius, Kristian Kolind, Adam 

Bohr, Sungho Jin, and Lars M. Bjursten. UCSD 

Towards methodology to characterize fibrillar collagen assembled in 

vitro under different initial parameters.Yu-Jer Hwang, and Julia 

Lyubovitsky. UCR 

43 

44 

Track 3 - Biomedical Imaging 

Session Chair 

Xiaojuan Li 

UC San Francisco 

Session Chair 

Xiaoliang Zhang 



9:30 AM 

Introduction to Biomedical Imaging. Xiaojuan Li and Xiaoliang Zhang UCSF 

9:50 AM 

10:02 AM 

10:14 AM 

10:26 AM 

10:38 AM 

10:50 AM 

Integrated Microfluidic Platform with Surface-Plasmonic Aptasensor for 

On-chip Label-free Detection of Cancer Markers from Cells. Hansang 

Cho, Yolanda Zhang, Brian R. Baker, and Luke P. Lee. UCBerkeley 

Measuring Error of Diffusion MRI-based Brain Connectivity Matrices 

with Residual Bootstrap. C.T. Nguyen, SW Chung, and Roland G. 

Henry. UCSF 

Endoscopic Fluorescence Lifetime Imaging for the Characterization of 

Human Atherosclerotic Plaques. Jennifer Phipps, Nisa Hatami, Yinghua 47 

Sun, Ramez Saroufeem, and Laura Marcu. UCD 

Magnetic Resonance Thermal Imaging in Combination with Parallel MRI 

in Phantom Experiments in the Presence of Motion. Youngseob Seo and 48 

Jeffrey H. Walton. UCD 

Simulation tool for theoretical modeling of hyperpolarized 13 C metabolic 

imaging. Peter J. Shin, Simon Hu, Peder E.Z. Larson, and Daniel B. 

49 

Vigneron. UCSF 

Quantitative assessment of peripheral nerve damage using polarizationsensitive 

optical coherence tomography. Yan Wang and Hyle Park. UCR 50 

45 

46 

11:02 AM 

Using Diffusion Tensor Imaging to Highlight White Matter Relevant to 

Deep Brain Stimulation. Christine M. Zwart, Josef P. Debbins, 

Guillermo Moguel-Cabos, and Peter N. Steinmetz. Arizona State 

University, Tempe, Arizona. 

51 


Podium Session II 


2:00pm – 3:45pm 

Track 4 

Computation, in Silico 

COB 279 

Session Chair 

S. Raychaudhuri, UCD 

L. Davila, UCM 

Track 5 

Tissue Engineering 

COB 263 


K. McCloskey, UCM 

A. Kasko, UCLA 

Track 6 

Nanotechnology and 

BioMEMS 

COB 267 


E. Hui, UCI 

A. Revzin, UCD 

Track 4 –Computation, in Silico 

Session Chair 

Subhadip Raychaudhuri 

UC Davis 

Session Chair 

Lilian Davila 



2:00 PM 

Introduction to Computation, in Silico. Subhadip Raychaudhuri, UCD 

and Lilian Davila, UCM 

2:20 PM 

2:32 PM 

2:44 PM 

The Role of Regulatory Light Chain Phosphorylation in Murine Left 

Ventricular Function: A Multi-Scale Modeling Approach. Stuart G. 

Campbell, Farah Sheikh, Ju Chen, Roy C. P. Kerckhoffs, and Andrew 

D. McCulloch. UCSD 

Electrostatic Exploration of Complement Receptor 1 using 

Computational Alanine Scan and Experimental Mutagenesis Data. 

Gabrielle N. Goodman, Chris A. Kieslich, Richard Hauhart, Thomas 

Allen, John P. Atkinson, and Dimitrios Morikis. UCR 

Electrostatic Analysis of C3d/Efb-C Interaction. Ronald D. 

Gorham, Christopher A. Kieslich, and Dimitrios Morikis. UCR 

10 th Annual UC Systemwide Bioengineering Symposium | Bioengineering Institute of California | 16 

52 

53 

54

2:56 PM 

3:08 PM 

3:20 PM 

3:32 PM 

Lipid peroxidation in living cells promotes membrane 

electropermeabilization. Zachary A. Levine, Yu-Hsuan Wu, Matthew J. 

Ziegler, Martin A. Gundersen, D. Peter Tieleman, and P. Thomas 

Vernier. University of Southern California, Los Angeles, California 

Clustering of Sequences and Electrostatic Potentials of HIV-1 Subtypes. 

Aliana López De Victoria, Chris A. Kieslich, and Dimitrios Morikis. 

UCR 

Computational Modeling of Immunological Synapse Formation Shows 

That Cytoskeletal Transport of Receptor Molecules Is a Potential 

Formation Mechanism. Philippos K. Tsourkas, and Subhadip 

Raychaudhuri. UCD 

The Impact of Mass Transfer of AMPK Signaling Pathways. Prashanthi 

Vandrangi, John Shyy, and V. G. J. Rodgers. UCR 

55 

56 

57 

58 

Track 5 - Tissue Engineering and Regenerative Medicine 

Session Chair 



Session Chair 

Andrea Kasko 

UC Los Angeles 


Introduction to Tissue Engineering and Regenerative Medicine. Kara 

2:00 PM McCloskey , UCM and Andrea Kasko, UCLA 

2:20 PM 

2:32 PM 

2:44 PM 

Morphology of the Embryonic Stem Cell Cultures: Testimony of the 

Integrins and Cadherins. Alicia A. Blancas, Chi-Shuo Chen , Sarah E. 

Stolberg, and Kara E. McCloskey. UCM 

Electric Field Induces Plasticity on Cortical Neurons In Vitro. Addie 

Hicks, Alyssa Panitch, Michael Caplan, and James D. Sweeney. Arizona 

State University, Tempe, Arizone 

Cultivating Liver Cells on Growth Factor Microarrays. Caroline N. 

Jones, Nazgul Tuleuova1, Ji Youn Lee, Erlan Ramanculov, A. Hari 

Reddi, Mark A. Zern, and Alexander Revzin. UCD 

59 

60 

61 


2:56 PM 

3:08 PM 

3:20 PM 

3:32 PM 

Wrinkled microtopography to induce cell alignment and maintain 

contractibility of cardiac myocytes. Jesus Isaac Luna, Jesus Ciriza, 

Marcos E. García-Ojeda, and Michelle Khine. UCM 

Contribution of Bioceramic Towards Osteogenic Response and 

Mechanical Properties of Composite Scaffolds. Diana G. Morales and J. 

Kent Leach. UCD 

Cartilage Regeneration: A Macrodesigned, Acellular Scaffold Promotin 

Endogenous Cell Influx and Chondrogenesis. Stephanie Reed, Dr. Bill 

Tawil, and Dr. Benjamin Wu. UCLA 

Injectable myocardial matrix for cardiac tissue engineering. Jennifer M. 

Singelyn, Jessica A. DeQuach, Sonya B. Seif-Naraghi, Robert B. 

Littlefield, Pamela J. Schup-Magoffin, Karen L. Christman. UCSD 

62 

63 

64 

65 

Track 6- Nanotechnology and BioMEMs 


2:00 PM 

Session Chair 

Elliot Hui 

UC Irvine 

Session Chair 

Alexander Revzin 

UC Davis 

Introduction to Nanotechnology and BioMEMS. Elliot Hui, UCI and 

Alexander Revzin, UCD 

2:20 PM 

Fabrication of Photopatternable Superhydrophobic Nanosurfaces. Hailin 

Cong, Lingfei Hong, and Tingrui Pan. UCD 

66 

2:32 PM 

Characterization of kinetics, sensitivity and affinity of label-free 

electrochemical immunosensor. Aaron Fairchild, Ugur Demirok, and 

Jeffrey La Belle. Arizona State University, Tempe, Arizona 

67 


2:44 PM 

Metal nanowrinkles and nanopetals for surface enhanced sensing in 

microfluidic devices. Chi-Cheng Fu, Maureen Long, Anthony Grimes, 

Christopher G.L. Ferri, Brent D. Rich, Somnath Ghosh, Ajay 

Gopinathan, Sayantini Ghosh, Luke P. Lee, and Michelle Khine. UCM 

68 

2:56 PM 

3:08 PM 

3:20 PM 

3:32 PM 

Engineering dynamic surfaces of single molecule DNA structures. Eric 

Josephs, Jingru Shao, Janice Lianne Cosio, Tao Ye. UCM 

On-Cue Detachment of Cell-Containing Heparin Hydrogels from a 

Conductive Substrate. Mihye Kim, Ji Youn Lee, Sunny Shah, Alexander 

Revzin, and Giyoong Tae. UCD 

Frequency Domain Analysis of an Artificial Reflex Device Derived from 

Response Characteristics of a Wireless Accelerometer Reflex Quantification 

System. R. C. Lemoyne, C. Coroian, T. Mastroianni, and W. S. Grundfest. 

UCLA 

Do-It-Yourself Three-Dimensional Microfabrication: Direct Projection- 

Lithography On Dry-Film Photoresist. Siwei Zhao, Hailin Cong, and 

Tingrui Pan. UCD 

69 

70 

71 

72 


Podium Session III 


4:00pm – 5:45pm 

Track 7 

Stem Cells 

COB 263 


K. McCloskey, UCM 

S. Simon, UCD 

Track 8 

Drug Delivery and 

Targeting 

COB 267 


J. Lu, UCM 

V. Rogers, UCR 

Track 9 

Biomechanics 

COB 279 


C. Viney, UCM 

T. Pan, UCD 

Track 7—Stem Cell Engineering 

Session Chair 



Session Chair 

Scott Simon 

UC Davis 


4:00 PM 

Introduction to Stem Cell Engineering. Kara McCloskey, UCM and 

Scott Simon, UCD 

4:20 PM 

Investigations into the Angiogenic Potential of Prostrate Tumor Stem 

Cells. Jane Frimodig, Hongwei Li, Jianqun Han, Rita Finones, Laura 

Restrepo, Martin Haas, Ruijuan Xiu, David Gough. UCSD 

73 

4:32 PM 

Directing Hepatic Differentiation of Embryonic Stem Cells With 

Protein-Microarray-Based Co-Cultures. Ji Youn Lee, Nazgul Tuleuova, 

Caroline N. Jones, and Alexander Revzin. UCD 

74 


4:44 PM 

Synergistic Effects of Biomineralization and Inductive Signals on 

Osteogenic Differentiation of Human Mesenchymal Stem Cells. S. 

Lauren Miller, Erin M. Case, Hillary E. Davis, J. Kent Leach. UCD 

75 

4:56 PM 

Age related dynamics of committed T cell progenitors in mice. T. 

Harshani Peiris, Jesús Ciriza, Mufadhal Al-Kulhani, Tanya Carroll, and 

Marcos E. García-Ojeda. UCM 

76 

5:08 PM 

Honeywell Microchip for Efficient and Controlled Generation of 

Embryoid Bodies for Cardiomyocyte Differentiation. Silin Sa, Diep 

Nuyenen, Michelle Khine, and Kara McCloskey. UCM 

77 

5:20 PM 

Adhesion Molecules Direct Hematopoietic and Endothelial 

Commitment of Murine Embryonic Stem Cells. Basha Stankovich, 

Esmeralda Aguayo, Fatima Barragan, Aniket Sharma, and Maria 

Pallavicini. UCM 

78 

5:32 PM 

The in vitro response of human adipose-derived stem cells to biomimetic 

apatite microstructure. Eric Tsang, Chris Arakawa, Benjamin Wu, and 

Patricia Zuk. UCLA 

79 

Track 8—Drug Delivery and Targetting 

Session Chair 

Jennifer Lu 


Session Chair 

Victor Rogers 

UC Riverside 


4:00 PM 

Introduction to Drug Delivery and Targetting. Jennifer Liu, UCM and 

Victor Rogers, UCR 

4:20 PM 

Imaging of regulable expression of matriptase, a marker for cancer 

progression in a mouse model for human breast cancer with PET. Julia 

C. Choi, Sven H. Hausner, M. Karen J. Gagnon, David L. Kukis, 

Chen-Yong Lin, Michael D. Johnson, and Julie L. Sutcliffe. UCD 

80 


4:32 PM 

Honeycomb Microwell Assay Platform for Generation and Culture of 

Embryoid Bodies from Human Embryonic Stem Cells. Diep Nguyen, 

Guangxin Xiang, Jon Pegan, Jason S. Park, Kenta Nakamura, Jennifer 

Manilay, Bruce R. Conklin, and Michelle Khine. UCM 

81 

4:44 PM 

4:56 PM 

5:08 PM 

5:20 PM 

5:32 PM 

Steric Stabilization of Liposomes for Drug Delivery: Impact Membrane 

Fluidity and Diffusion.Raquel Orozco-Alcaraz and Tonya Kuhl. UC 

Davis 

Controlling supramolecular architecture of poly(glutamyl-glutamate) 

Paclitaxel nanoparticles by selective hydrophilic/hydrophobic 

patterning: A coarse-grained modeling study. Lili X. Peng, Anthony 

Ivetac, Sang Van, Lei Yu, J. Andrew McCammon, and David A. Gough. 

UCSD 

Microfluidic Solvent Extraction Method for poly(lactide-co-glycolide) 

Particle Formation. Shia-Yen Teh, Lung-Hsin Hung, and Abraham P. 

Lee. UCI 

Engineering transferrin-diphtheria toxin conjugates for the treatment of 

glioblastoma multiforme.Dennis J. Yoon, Byron H. Kwan, Felix C. 

Chao, 

Anne B. Mason, and Daniel T. Kamei. UCLA 

Microneedle Drug Delivery System for Skin Diseases. Kevin Zhang, 

Benjamin Wu. UCLA 

82 

83 

84 

85 

86 


Track 9 – Biomechanics and Biodevices 

Session Chair 

Christopher Viney 


Session Chair 

Tangrui Pan 

UC Davis 


4:00 PM 

Introduction to Biomechanics and Biodevices. Christophery Viney, UCM 

and Tangrui Pan, UCD 

4:20 PM 

4:32 PM 

4:44 PM 

4:56 PM 

The Effects of Coil Packing Density on Cerebral Aneurysm Inflow: In 

Vitro Assessment with Particle Image Velocimetry. Haithem Babiker, L. 

Fernando Gonzalez, Arius Elvikis, Dan Collins, Felipe Albuquerque, 

andDavid Frakes. Arizona State University, Tempe, Arizona 

Open-Surface Microfluidics Using Photosensitive Superhydrophobic 

Nanocomposite. Lingfei Hong, Hailin Cong, and Tingrui Pan. UCD 

Carbon Nanotubes lead to early Onset of Electrical Activity in Developing 

Hippocampal Neurons Cultured on Silicon Microelectrodes. Massoud L 

Khraiche, Nathan Jackson, and Jit Muthuswamy. Arizona State University, 

Tempe, Arizona 

Long-Term Oxygen Sensor Implantation in the Porcine Subcutaneous 

Environment. L.S. Kumosa, J. Lin, T. Routh, J. Lucisano, and D.A. Gough. 

UC San Diego 

87 

88 

89 

90 

5:08 PM 

A simple three-dimensional vortex micromixer. Maureen Long, Michael A. 

Sprague. Anthony A. Grimes, Brent D. Rich, and Michelle Khine. UCM 

91 

5:20 PM 

Immobilization of Lactate Oxidase for Stability and High Loading in a 

Lactate Sensor. Adam Strobl, Henry Tse, and David Gough. UCSF 

92 

5:32 PM 

A Smart Contact-Lens Sensor for Dynamic Measurement of Intraocular 

Flow Resistance. Chaoqi Zhang and Tingrui Pan. UCD 

93 


Podium Session IV 


9:45am – 11:30am 

Track 10 

Molecular and Cellular 

Engineering 

COB 263 


S. Li, UCB 

D. Kamei, UCLA 

Track 11 

Biophysics 

COB 267 


Y. Seo, UCSF 

Jane P. Bearinger, LLNL 

Track 12 

New Frontiers 

COB 279 


D. DiCarlo, UCLA 

M. Khine, UCM 

Track 10-Molecular and Cellular Engineering 

Session Chair 

Song Li 

UC Berkeley 

Session Chair 

Dan Kamei 



9:45 AM 

10:05 AM 

10:17 AM 

Introduction to Molecular and Cellular Engineering. Song Li, UCB and 

Dan Kamei, UCLA 

Postprandial up-regulation of monocyte integrin CD11c/CD18 increases 

firm arrest to vascular cell adhesion molecule-1. R Michael Gower, Anne A 

Knowlton, and Scott I Simon. UCD 

Engineered proteolytic antibody fragments as therapeutics for Alzheimer’s 

disease. Srinath Kasturirangan, and Michael Sierks. Arizona State 

University, Tempe, Arizona 

94 

95 


10:29 AM 

10:41 AM 

10:53 AM 

11:05 AM 

11:17 AM 

Sudden death from gut ischemia may result from a neurogenic shock 

mechanism. Alexander Hayes Penn, and Geert W. Schmid-Schönbein. 

UCSD 

Development of FRET-based high-throughput screening to discover small 

chemical inhibitors targeting protein-protein interaction in the 

SUMOylation network. Yang Song, Vipul Madahar, Yan Liu, and Jiayu 

Liao. UCR 

Cellular Uptake of Polyarginine-Polyleucine Block Copolymer Vesicles. 

Victor Z. Sun, Zhibo Li, Timothy J. Deming, and Daniel T. Kamei. UCLA 

Design of an Aptamer Beacon for Real-Time Detection of Interferon- 

Gamma. Nazgul Tuleuova, Caroline N. Jones, Jun Yan, and Erlan 

Ramanculov, 

Alexander Revzin. UCD 

Solid-Phase Peptide Synthesis of Bioinspired Electrets Based on Non- 

Traditional Amino Acids: Synthesizing oligo-ortho-anthranilic acids for 

improved Charge-Transfer properties in photovoltaic cells. Srigokul 

Upadhyayula, Duoduo Bao, David Bui, and Valentine I. Vullev. UCR 

96 

97 

98 

99 

100 

Track 11—Biophysics 

Session Chair 

Youngho Seo 


Session Chair 

Jane P. Bearinger 

Lawrence Livermore National Laboratories 


9:45 AM 

10:05 AM 

Introducton Biophysics. Youngho Seo, UCSF and Jane P. Bearinger, 

LLNL. 

The Rehm-Weller Equation in View of Bioengineering. Duoduo Bao, 

Antonio Contreras, and Valentine I. Vullev. UCR 

101 


10:17 AM 

10:29 AM 

10:41 AM 

10:53 AM 

11:05 AM 

Ca 2+ depletion of sarcoplasmic reticulum during reperfusion after ischemia. 

Marcela Ferreiro, Dmytro Kornyeyev, Carlos A. Valverde, Alicia 

Mattiazzi, and Ariel L. Escobar. UCM 

Mapping the Position of DNA Polymerase-Bound DNA Templates in a 

Nanopore at 5Å Resolution. Daniel R. Garalde, Brett Gyarfas, Felix 

Olasagasti, Seico Benner, William Dunbar, Kate R. Lieberman, and Mark 

Akeson. UCSC 

Concentrating DNA Using Two-Phase Aqueous Micellar Systems. Foad 

Mashayekhi, Aaron S. Meyer, Stacey A. Shiigi, and Daniel T. Kamei. 

UCLA 

Fluorescence Lifetime Imaging Microscopy (FLIM) for Cancer 

Demarcation during Medical Surgery. Yinghua Sun, Jennifer Phipps, 

Daniel S. Elson, Jeremy Meier, Nisa Hatami, Frank S. Chuang, Rudolph J. 

Schrot, D. Gregory Farwell, and Laura Marcu. UC Davis 

Multi-photon optical microscopy of actin filaments and mitochondrial 

bioenergetics of ACBT human grade IV glioblastoma cells migrating within 

3-D collagen-based hydrogels. Miso Yang, Yu-Jer Hwang, Edgar Sanchez, 

Chung-ho Sun, Tatiana B. Krasieva, Bruce J. Tromberg, and Julia G. 

Lyubovitsky. UCR 

102 

103 

104 

105 

106 

11:17 AM 

Optical Model of Human Skin for Biomedical Reflectance and 

Fluorescence Spectroscopy. Dmitry Yudovsky and Laurent Pilon. UCLA 

107 


Track 12 - New Frontiers in Bioengineering 

Session Chair 

Dino DiCarlo 


Session Chair 

Michelle Khine 



9:45 AM 

Introduction to New Frontiers in Bioengineering. Dino DiCarlo, 

UCLA and Michelle Khine, UCM 

10:05 AM 

10:17 AM 

10:29 AM 

Bench Scale Electroenzymatic Biosensor for the Rapid Detection of 

Pyruvate. Lorenzo D’Amico, Andrew Basilio, Si Luo, Justin Yeap, and 

Dale A. Baker. UCSD 

Effects of coating material on cellular uptake of nanocapsules 

loaded with indocyanine green.Bongsu Jung and Bahman Anvari. 

UCR 

Novel Dielectrophoretic Device for Cancer Cell, Stem Cell and DNA 

Biomarker Isolation and Detection. Rajaram Krishnan, Joaquim 

Teixeira, Jennifer Y. Marciniak, Mark Mercola, Sadik C. Esener, and 

Michael J. Heller. UCSD 

108 

109 

110 

10:41 AM 

10:53 AM 

11:05 AM 

Detection of Enzymatic Biomarkers Directly in Whole Blood for Point- 

Of-Care Diagnostics. Roy B. Lefkowitz, Jennifer Y. Marciniak, Che- 

Ming Hu, Geert W. Schmid-Schönbein, and Michael J. Heller. UCSD 

The Deposition and Fate of Ultra-fine Pollutants in Normal and 

Asthmatic Mice using Positron Emission Tomography. Heather A. 

Palko and Angelique Y. Louie. UCD 

Dual-Beam Optical Fiber Trapping Platform for Biophotonics 

Applications. Tessa Piñón and Jay Sharping. UCM 

111 

112 

113 


Poster Session 


12:00pm – 2:00pm 

Poster 

Number 

1 

2 

3 

4 

5 

6 

7 

Title and Speaker 

Solid Lipid Nanoparticles as Vehicles for Delivering Imaging Probes 

across In Vitro Models of the Blood Brain Barrier (BBB). Erica Andreozzi, 

Benjamin Jarrett, and Angelique Louie. UCD 

Implementation of a Shack-Hartmann Wavefront Sensor for the 

measurement of embryo induced aberrations using fluorescent 

microscopy. Oscar Azucena, Joel Kubby, Justin Crest, Jian Cao, William 

Sullivan, Peter Kner, Donald Gavel, Daren Dillon, and Scot Olivier. 

UCSC 

A Hybrid Assistive System for Upper-Extremity Stroke 

Rehabilitation. Sivakumar Balasubramanian, and Jiping He. 

Arizona State University, Tempe, Arizona 

Digestive Protease Transport and Mechanisms for Disruption of the 

Epithelial Barrier in Early Stages of Shock. Marisol Chang and Geert 

Schmid-Schönbein. UCSD 

Characterization of Chymotrypsin’s single-molecule Kinetics using an 

Array of Microwells. Angela Y. Chen and James P. Brody. UCI 

Modification of intracellular Ca 2+ release in cardiac myocytes of intact 

beating mouse hearts upon application of an exogenous buffer. Ariel L. 

Escobar and Dmytro Kornyeyev. UCM 

Generation of a Novel Duel Reporting Embryonic Stem Cell Line for 

Endothelial and Smooth Muscle Expression. Drew Elizabeth Glaser, 

Alicia Blancas, and Kara McCloskey. UCM 

Page 

114 

115 

116 

117 

118 

119 

120 


8 

9 

Quantitative Conversion of Alcohols to Aldehydes Using Alcohol 

Dehydrogenase. Sean Guthrie and Valentine Vullev. UCR 

Evaluation of collagen and matrix metalloproteinase content in human 

carotid plaque by time-resolved fluorescence spectroscopy. Nisa 

Hatami, Jennifer E. Phipps, Michael C. Fishbein, and Laura Marcu. 

UCD 

121 

122 

10 

11 

12 

13 

14 

15 

16 

17 

Highly Accelerated Hyperpolarized 13 C 3D-MRSI and Time-Resolved 

3D-MRSI Using Compressed Sensing and Multiband Pulses with In 

Vivo Applications. Simon Hu, Peder E.Z. Larson, Michael Lustig, 

Adam B. Kerr, Asha Balakrishnan, Robert Bok, John Kurhanewicz, 

Sarah J. Nelson, Andrei Goga, John M. Pauly, and Daniel B. Vigneron. 

UCB and UCSF 

Equilibrium and Pre Steady-State Kinetics of DNA Binding to DNA 

Polymerase Characterized with a Nanopore. Nicholas Hurt, Hongyun 

Wang, Brett Gyarfas, and William Dunbar. UCSC 

A Wearable Electronic Mobility Aide for the Blind. Brant 

Jameson, and Roberto Manduchi. UCSC 

Feasibility of Using Radioactive Bone Cement to Treat Vertebral 

Metastases. Tadashi S. Kaneko, Varun Sehgal, Harry B. Skinner, 

Muthana S. Al-Ghazi, Bang H. Hoang, Nilam S. Ramsinghani, and 

Joyce H. Keyak. UCI 

Effects of Cholesterol on Plasma Membrane Mechanics. N. 

Khatibzadeh, S. Gupta, W. E. Brownell, and B. Anvari. UCR 

Effect of Ultraviolet Light Crosslinking on Mechanical Stiffness of 

Fibrin Scaffolds. Soma Esmailian Lari, Haison Duong, Benjamin Wu, 

and Bill Tawil. UCLA 

Serum Free Derivation of Embryonic Stem Cells Towards Functional 

Cardiomyocytes with Electrical Stimulation. Nicholas E Lauer and Kara 

McCloskey. UCM 

Peptide Arrays for the Evaluation of Chemical Conjugation and 

Enzyme-Substrate Interaction. Yan Liu, Yongfeng Zhao, Yang Song, 

and Jiayu Liao. UCR 

123 

125 

126 

127 

128 

129 

130 

131 


18 

Ariadne’s Thread: A Wayfinding Tool for the Visually Impaired Based 

on Camera Cell Phones. Roberto Manduchi and James Coughlan. 

UCSC 

132 

19 

Theoretical Significance of Ion Binding on Observed Non-idealities in 

Osmotic Pressure in Crowded Macromolecular Environments. Devin 

W. McBride and Victor G. J. Rodgers. UCR 

133 

20 

In vivo Optical Microscopy of Axonal Myelination of a Multiple 

Sclerosis Disease Model with Polarization Sensitive-Optical Coherence 

Tomography. Christian Oh and Hyle Park. UCR 

134 

21 

Cascaded Microconcentration Cells. Oxana S. Pantchenko, Javad 

Shavani, Mona Zebrajadi, Howard Young, Mehrdad Mahomoodi, 

Michail Isaacson, Ali Shakouri. UCSC 

135 

22 

23 

Inhibition of the sodium/calcium exchanger by lithium in intact mouse 

hearts modifies cardiac alternans. Azadé Petrosky, Dmytro Kornyeyev, 

and Ariel L. Escobar. UCM 

On Calibrating the Power of a Microwave Oven. Emily J. Reed and 

Christopher Viney. UCM 

136 

137 

24 Optimizing qNano: Characterizing a resizable nanopore. Jessie Rucker, 

Asma Uz-Zaman, David Deamer, and William Dunbar. UCSC 

25 

In Vitro Culturing of the Ovarian Follicle: Alginate Encapsulation and 

Evaluation of the Nutrients Environment. Noriko Sausman, P. Talbot, 

and V. G. J. Rodgers. UCR 

138 

139 

26 

A Microdevice for Detecting Cytokine Production from Individual 

Immune Cells. Jaime Silangcruz, Gulnaz Stybayeva, He Zhu, and 


140 

27 

Kinetics of Staining: Flourescence Enhancement Induced By Escerichia 

Coli. Marlon S. Thomas, Elizabeth T. Zielins, Duoduo Bao, Baharak 

Bahmni, Vicente Numez and Valentine I. Vullev. UCR 

141 

28 

Fluorescence Enhancement of Warfarin Induced by Interaction with β- 

Cyclodextrin. Jacob M. Vasquez, Andrew Vu, Jerome S. Schultz, and 

Valentine I. Vullev. UCR 

142 

29 

Luminal Ca 2+ Regulation of Single RyR2 Channels by Cardiac 

Calsequestrin. Patricio Vélez, Dmytro Kornyeyev, Marcia Cortés- 

Gutiérrez, Björn C. Knollmann, and Ariel L. Escobar. UCM 

143 


30 

31 

32 

33 

34 

Electrotactile Inducement of the Cutaneous Rabbit Effect (CRE) Across 

Human Fingertips. Jay P Warren, Marco Santello, and Stephen I Helms 

Tillery. Arizona State University, Tempe, Arizona 

Fluorescent Lifetime Changes as Function of Divalent Cations Ca 2+ and 

Mg 2+ Ions. Stephanie Wong and Ariel L. Escobar. UCM 

Alternate Reception for Coil Array Elements. Bing Wu, Chunsheng 

Wang, Yong Pang, and Xiaoliang Zhang. UCSF. 

Lab-on-a-Chip Characterization of Cellular Media using Electrical 

Impedance Spectroscopy. John Yan and Tingrui Pan. UCD 

Miniature Electrochemical Biosensors for Detection of Extracellular 

Metabolites. Jun Yan, Valber D. Pedrosa, Aleksandr L. Simonian, and 


144 

145 

146 

147 

148 


Molecular Interactions between GATA-3 and Notch-1 That Regulate T Cell Commitment 

Mufadhal M. Al-Kuhlani, Jesús Ciriza, Joseph H. Ramos, Tanya Carroll, Harshani Peiris, and 

Marcos E. García-Ojeda 

School of Natural Sciences, University of California, Merced 

Hematopoietic stem cells (HSC) differentiate into all mature blood cells, including 

lymphoid progenitors (LPs) that can give rise to NK, dendritic, B and T cells. The final fate of 

these LPs depends on the signals and growth factors received during development. The 

transmembrane receptor Notch-1 and the transcription factor GATA-3 are two of the signals that 

regulate the commitment of LPs towards the T cell lineage. Notch-1 instructs lymphocyte 

progenitors to differentiate into T cells but not B cells. However, the role that GATA-3 plays in 

early T cell development in relation to Notch-1 is poorly characterized. Our studies show that 

GATA-3 deficient progenitors initiate a normal T cell development program, but become 

arrested at an early CD44 + CD25 + double negative (DN2) stage, and generate aberrantly B cells 

in the presence of Notch-1 signals. The gene expression profile of GATA-3 deficient DN2 cells 

showed elevated expression of Deltex-1, a Notch-1 regulator known to induce B cell 

development while inhibiting T cell differentiation. To elucidate the molecular mechanism 

exerted by GATA-3 on Notch-1 signaling, we will transduce fetal liver HSC with GATA-3-GFP 

shRNA retrovirus followed by a co-culture on OP9DL-1 stroma, which expresses the Notch-1 

ligand Delta-like-1. After two weeks of culture, the transduced cells are sorted on the basis of 

GFP expression. Molecular analysis for the expression of three of Notch-1 regulators, Deltex-1, 

Mint and Numb, is evaluated via q-PCR. Understanding the mechanisms of interaction between 

GATA-3 and Notch-1, as well as other genes involved in T cell commitment is very crucial. 

Such understanding will allow us to reveal how early lymphocyte precursors commit to the T cell 

fate, and lead to the development of new stem cell-based therapeutic approaches to treat 

diseases related to impaired T cells. 


Signaling Model of Cell Death Shows Cell-to-Cell Stochastic Fluctuations are Linked to 

Apoptosis Related Diseases 

Marin Djendjinovic, Kavya Katipally, Subhadip Raychaudhuri 

Biomedical Engineering Department, University of California, Davis 

We have developed a detailed computational model of apoptotic cell death signaling to 

study the system level behavior of the apoptotic pathway that is mediated through two major 

pathways (type 1 and type 2). One advantage of our Monte Carlo model is that we could study 

the behavior of the type 1 and type 2 apoptosis separately by setting the appropriate kinetic 

constants to zero, as well as the combined behavior of the two pathways, as we vary the 

strength of the apoptotic stimulus. Our initial results show how apoptosis signaling can be slow 

(~ 10 hours) under weak stimulus due to large cell-to-cell stochastic fluctuations through the 

type 2 pathway of signaling and thus explains slow apoptotic death under certain conditions 

such as oxidative stress conditions. Very recent single-cell experiments on apoptosis, where cell 

death was induced by death ligands TNF or TRAIL, showed large cell-to-cell fluctuations as 

predicted by our computational model. We use a minimal model of a stochastic signaling 

network along with a novel set of stochastic differential equations to elucidate that cell-to-cell 

stochastic fluctuations in apoptosis signaling is cell-type independent. However, apoptosis 

signaling and diseases that arise from aberrant apoptosis signaling are often cell-type specific. 

We propose apoptosis related diseases, such as degenerative disorders and cancer, arise due 

to aberrant signaling through the stochastic type 2 pathway and depends on the cell-type and 

other details of the system. We discuss such aberrant apoptotic signaling through two signaling 

inhibitors of the type 2 pathway: (a) B cell lymphoma protein 2 (Bcl2) and (b) Neuroglobin. A 

generalized reaction function based Monte Carlo algorithm is currently being developed to study 

apoptosis related diseases. 


CHIP-Seq experiments reveal global shift of protein coding RNA and intergenic noncoding 

RNA transcription in primary macrophages by Kdo 2 -Lipid A 

Lana Garmire 1 , Josh Stender 2 , Shankar Subramaniam 1,2 , Christopher Glass 2 

1 Department of Bioengineering, University of California, San Diego 

2 Department of Cellular and Molecular Medicine, University of California, San Diego 

Macrophages respond both acutely and chronically to Kdo 2 -Lipid A, a homogeneous 

lipopolysaccharide (LPS) sub-structure that has endotoxin activity. The immune-response 

related global gene expression shift in macrophages has been shown under Kdo 2 treatment at 

the mRNA transcripts level, using the microarray platform. However, direct transcription events 

occurring at the genome level, and the degree of correlation to mature mRNAs are not known. 

Recently, chromatin immunoprecipitation in conjugation with next generation sequencing 

technology (CHIP-Seq) enables the determination of protein binding on genomes directly. 

Towards this goal, we recently conducted primary macrophage CHIP-Seq experiments of 

polymerase II (polII) and histone H3 lysine 4 trimethylation sites (H3K4me3) with and without 

Kdo 2 treatment at 1h. Unexpectedly, we found more genes having significantly fewer pol II tags 

intragenically in CHIP-Seq after normalization, opposite to the pattern that more mRNAs are upregulated 

in microarray experiments at the same time point. This apparent discrepancy can be 

explained by the time delay from transcription to mRNA maturation for a subgroup of genes. 

The overall correlations between logarithm change of pol II tag counts in Chip-Seq and 

logarithm change of intensity in microarray are 0.44 and 0.27 for 1h and 12h microarray 

respectively. We found stalled pol II in the promoter regions. For the genes with significant 

change of intragenic pol II tags, the ratios of (Kdo 2 / no treatment) pol II tags in the promoters 

are well correlated (corr=0.5) to those in the intragenic regions. Kdo 2 treatment caused about 

50% drop of overall genes that have pol II tags. However, proportionally Kdo 2 treatment only 

caused dramatic (~40%) increase of pol II peaks in the intergenic region, but not in 

distal/proximal transcription starting/ending sites. Finally, we identified nearly one thousand 

putative intergenic non-coding RNA species that are enriched by pol II- H3K4me3 domains. 


Selective PPARγ Ligand Modulation of Metabolic Pathways in Obese Zucker fa/fa Rats 

Gene Hsiao 1 , Dr. Shankar Subramaniam 1 , Dr. Dorothy D. Sears 2 


2 Department of Medicine, University of California, San Diego 

PPARγ ligands, which include the thiazolidinedione drug class, are known to activate 

and repress hundreds of genes. However, little is known about PPARγ ligand-specific 

modulation of cellular mechanisms that lead to insulin sensitization. We characterized lean and 

insulin resistant obese (fa/fa) Zucker rats treated with or without one of four PPARγ ligands, 

pioglitazone, rosiglitazone, troglitazone, and AG035029. Each PPARγ ligand treatment 

improved whole-body and tissue-associated insulin sensitivity in the obese rats, albeit to varying 

degrees. We transcriptionally profiled skeletal muscle, adipose tissue, and liver from the rats to 

determine whether the physiological insulin sensitizing potency of the ligands was related to 

altered functional pathways in these tissues. We employed a microarray variance-modeled 

statistical analysis suite to identify differentially expressed genes and subjected these genes to 

biochemical pathway analysis. Skeletal muscle profiles showed that insulin resistance is 

associated with increased adipocyte markers and slow-twitch fiber genes, a pattern that 

invariantly increased after treatment with each PPARγ ligand. PPARγ ligand-treated adipose 

tissue profiles revealed variable modulation of inflammatory and branched chain amino acid 

metabolic pathways which coincided with compound-specific potency. In liver, PPARγ-ligands 

invariantly repressed the elevated de novo lipogenesis associated with insulin resistance. 

Together, these results highlight common mechanisms associated with PPARγ ligand-induced 

insulin sensitization and elucidate functional pathway changes that correlate with ligand insulinsensitizing 

potency. 


Energy based Monte Carlo Simulation of B-cell Receptor Clustering 

A. Srinivas Reddy 1 , Sandeep Chilukuri 2,1 Subhadip Raychaudhuri 1 

1 Department of Biomedical Engineering, University of California-Davis, Davis, California 

2 Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India 

Antigens in solution are known to trigger B-cell receptor (BCR) clustering which in turn 

leads to B-cell activation. Such clustering is thought to be organized as a two-step process: (a) 

early-time micro-clustering where a number of micro-clusters form that typically contain a few 

BCR (~10) molecules, (b) followed by a large macroscopic clustering of B cell receptors. Little 

is known about the molecular mechanics that prompt the BCR clustering and how such 

clustering leads to B-cell activation. We develop an energy based Monte Carlo model to 

elucidate the mechanism of B-cell receptor clustering. We propose a model of B cell receptor 

clustering due to intrinsic attractions among the receptor molecules. Such mutual attractions 

may also arise indirectly due to cross-linking by soluble antigens among other possibilities. At 

the outset, micro-clusters of receptor molecules are formed due to mutual BCR-BCR attractions, 

however, such mutual interactions are not enough to create a large macro-cluster at a later 

time. A simple model of biased diffusion where BCR molecules experience a biased directed 

motion towards the largest cluster is then applied, resulting in a single macro cluster of receptor 

molecules. The various types of clusters are analyzed using network-based metrics such as the 

average distance between any pairs of receptors. 


Computational Analysis of Feedback Regulation in Signaling Networks 

Sean Kim 1, * , Arnold Kim 2 , Jian Qiao Sun 3 , Henry Forman 1, * 

1 

Quantitative and Systems Biology, University of California, Merced 

2 

Applied Mathematics, University of California, Merced 

3 

Mechanical Engineering, University of California, Merced 

* 

Atmospheric Aerosol and Health Lead Program. UC TSR&TP 

Signal transduction networks contain complex interconnections that regulate their 

properties over the spatiotemporal domain. One general class of such interconnections is 

feedback regulation that can confers positive and/or negative effects on the components of 

signaling networks. Based on Michaelis-Menten kinetic formalism, feedback regulation can be 

represented as nonlinear ordinary differential equations (ODEs) that allow emergence of a rich 

class of behaviors such as hysteresis, bifurcation, oscillations, and robustness, some of which 

have been verified experimentally in the literature. (1) 

In this work, we apply various ways to study the feedback regulation such as 

autonomous linear ODEs, controlled nonlinear ODEs, and non-autonomous nonlinear ODEs to 

test if the systems can produce expected behaviors in stable and robust manner. When 

feedback systems are represented as a system of linear ODEs, we can capture the main 

expected behaviors such as oscillation and exponential growth for negative and positive 

feedback, respectively; however, it lacks complexity necessary to confer behaviors like 

bifurcation seen in nonlinear systems. We also show that positive feedback, on its own, is 

uncontrollable and unstabilizable; whereas, interlinked positive and negative feedback 

regulations form a control circuit, and systems become controllable and stabilizable as 

expected. (2) We also present the signaling network as a non-autonomous system that has 

explicit time-dependent parameters and study the stability and the robustness. We also show 

that the behavior of the signaling networks is perturbed by electrophilic aldehydes generated 

during normal signaling by reactive oxygen species. 

1. J. J. Tyson, K. C. Chen, B. Novak, Curr. Opin. Cell Biol. 15, 221 (2003) 

2. T. Y. Tsai, Y. S. Choi, W. Ma, J.R. Pomerening, C. Tang, J.E. Ferrell Jr. Science Vol. 321. 

no. 5885, 126 (2008) 


Investigating the Properties of Block Copolypeptide Vesicles 

Uh-Joo Choe, April R. Rodriguez, Zhibo Li, Howard Dai, Sophia Lin, 

Timothy J. Deming, and Daniel T. Kamei 

Department of Bioengineering, University of California, Los Angeles 

Investigation of polymeric vesicles as novel drug delivery vehicles is an emerging area of 

research and shows great promise. With respect to this field, our focus has been on developing 

amino acid-based nanomaterials for drug delivery. We previously developed vesicles composed 

of lysine-leucine (poly(L-lysine) 60 -block-poly(L-leucine) 20 , K 60 L 20 ), glutamate-leucine (poly(Lglutamic 

acid) 60 -block-poly(L-leucine) 20 , E 60 L 20 ), and arginine-leucine (poly(L-arginine) 60 -blockpoly(L-leucine) 

20 , R 60 L 20 ) block copolypeptides. These block copolypeptides formed vesicles in 

aqueous solutions that were stable up to 80°C, could encapsulate polar molecules with 

negligible leakage, and could be prepared with diameters ranging from 50 nm to 1 μm. In the 

case of the R 60 L 20 vesicles, they were also shown to be able to deliver hydrophilic cargo into 

both endothelial and epithelial cells. We recently performed studies to further characterize and 

optimize the vesicles as potential drug delivery vehicles. The vesicle extrusion process was 

optimized to control the size distribution of the vesicles. The toxicity of K 60 L 22 vesicles extruded 

to different sizes was investigated in HeLa cells with the MTS assay. To study the leakage 

properties of the vesicles, fluroescein was encapsulated in R 60 L 20 vesicles. These 

characterization studies are currently being extended to polypeptides with varying lengths. 


Decellularized Solubilized Extracellular Matrix Coatings for Cell Culture 

Jessica A. DeQuach, Amar Miglani, and Karen L. Christman 

Department of Bioengineering, University of California, San Diego 

The use of biomaterials in conjunction with cells is important for many bioengineering 

applications. For these cellular-based therapies, the extracellular matrix (ECM) used plays an 

important role as it has been shown that the matrix composition and matrix mechanical 

properties can affect cell behavior and function. It is hypothesized that the best growth 

environment for cells would be the same ECM as found in vivo. The aim of this present study is 

to test whether native ECM would demonstrate better properties for cell culture when compared 

to conventional coatings. To test this hypothesis, various porcine tissue was decellularized, and 

then solubilized using a pepsin digestion to be used as cell culture coatings. These coatings 

were characterized using SDS-PAGE, and were found to be more complex than collagen I and 

laminin, as indicated by a mixture of different sized peptides. Glycosaminoglycan content was 

quantified using a Blyscan assay, where frontal lobe coating had the highest content of GAG at 

35.95±1.45 ug/mg ECM, followed by cardiac 27.77±1.20 ug/mg ECM, cortex 12.80±0.43 ug/mg 

ECM, and skeletal muscle at 2.99±0.11 μg/mg ECM. GAG content was thought to be important 

as several other decellularization techniques have not shown to retain the GAG content. C2C12 

cells plated on the skeletal muscle matrix at day 3 were shown to have increased myotube width 

and percent differentiation when compared to collagen coating (myotube 17.6±1.8 m vs. 

14.2±1.7 m; p~0.0001) (differentiation 16.3±0.2 vs. 13.1±0.1; p=0.018). The study 

demonstrates that the ECM component for biomaterials has an important effect on cell behavior, 

and consideration should be taken when selecting an ECM coating for any biomaterial 

application. The more solubilized, decellularized ECM demonstrated an increase on 

differentiation and structure for C2C12 myoblasts, and following studies are being performed on 

the other tissue coatings. 


Controllable Biomimetic Hydrogel Scaffolds to Study Pulmonary Fibroblast 

Mechanotransduction 

Chia HN, Kasko AM 

Department of Bioengineeirng, UCLA, Los Angeles, CA 

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disease. While the cause is not 

well-understood, IPF is thought to be the result of an abnormal wound-healing process in the 

lungs. Many chemical cues have been identified as effectors in fibrosis, but the effect of 

mechanical environment in the development of IPF is poorly understood. Fibroblast 

differentiation into the myofibroblast phenotype is a critical event in the wound healing process, 

and when this differentiation is not ―turned off‖, fibrosis occurs. We are developing a two- and 

three-dimensional hydrogel cell scaffolds with varying stiffness and biochemical composition 

that will enable us to answer important questions about the effects of cell-matrix interactions on 

the differentiation of pulmonary fibroblasts. Poly(ethylene glycol) macromers are copolymerized 

with peptide-based crosslinking agents that mimic extracellular matrix adhesive fragments to 

produce hydrogels where the chemistry and gel structure can be independently controlled. 

Human pulmonary fibroblasts show good adhesion to hydrogels containing the adhesion 

peptide sequence CRGDSC (cysteines are reactive with the PEG macromers), and little 

adhesion on hydrogels without RGDS. Increasing the crosslinking density of the hydrogel (via 

decreasing macromer length) increases the compressive modulus of elasticity. Pulmonary 

fibroblasts seeded on to soft hydrogels (E= 67 kPa, [RGDS]=2 mM) express no alpha-smooth 

muscle actin (-SMA), a marker of the myofibroblast phenotype. On more rigid hydrogels 

(E=585 kPa, [RGDS]=2 mM) cells express significant amount of -SMA, indicating the 

myofibroblast phenotype. Pulmonary fibroblasts encapsulated into a 3D hydrogel construct are 

viable after 72 hours, but persist in a non-native rounded morphology. We are currently 

optimizing 3D culture conditions in this biomimetic matrix to allow fibroblasts to adopt their 

native morphology. This synthetic, biomimetic cell culture system allows the chemistry of the 

cellular environment to be decoupled from the mechanical environment, and provides a 

universal synthetic platform for cell culture. 


Nanotopographical Effects on Vascular Endothelial and Smooth Muscle Cells 

Matthew L. Eltgroth, Lily Peng, Tejal A. Desai 

Department of Bioengineering and Therapeutic Sciences and Department of Physiology, 

University of California, San Francisco 

The nanotopographical cues provided by biomaterial surfaces are known to have an 

important influence on the behavior of cells they interact with. In addition, specific cell types 

have been shown to exhibit different responses depending on nanotube diameter. This study 

was aimed at investigating the effects that nanotubular titania (TiO 2 ) surfaces have on vascular 

endothelial and vascular smooth muscle cells. Using a variety of microscopic techniques and 

biochemical assays, we showed that nanotubular TiO 2 surfaces promoted vascular endothelial 

cell proliferation and production of anti-thrombotic factors, while inhibiting proliferation of 

vascular smooth muscle cells and causing them to assume a more differentiated phenotype. 

Additional work has been performed using gene expression analysis to lend further support to 

these observations. These results support prior findings that nanotubular TiO 2 surfaces may 

promote cellular responses that would make them favorable for use in endovascular 

applications, such as stents. 


Synthesis of Photoreactive Linkers with Varying Degradation Rates for use in Biomedical 

Applications 

Griffin DR 1 , Wong DY 2 , Kasko AM 1,2 

1 Biomedical Engineering Interdepartmental Program, UCLA, Los Angeles, CA 

2 Department of Bioengineering, UCLA, Los Angeles, CA 

A critical aspect of designing biomaterial carriers for cells and drug delivery is tuning and 

controlling the material‘s degradation behavior. Most synthetic biomaterials degrade via 

hydrolysis or enzymolysis. The rate of hydrolysis is pre-engineered and cannot be modified 

after the scaffold is fabricated under physiologically relevant conditions. The rate of enzymatic 

degradation is cell-mediated and is normally limited to local degradation. In the last decade, 

there has been considerable interest in using photochemistry to produce biomaterials because 

of the ability to form scaffolds in situ under physiological conditions 1 . Integrating photochemistry 

as a degradation mechanism should be equally biocompatible, affording spatial and temporal 

control over the chemical, mechanical, and physical properties of the biomaterial, and allowing 

for the controlled and triggerable release of therapeutic agents. We have designed a series of 

five photodegradable linkers based on nitrobenzylether to provide a range of degradation rates 

upon exposure to long-wave UV light 2 (365 nm, biocompatible 1 ). We developed three separate 

synthesis schemes, each using high yield reactions and inexpensive starting materials. We 

followed the photodegradation of the linkers by 1 H NMR and found that the rate of degradation 

increases as the number of aryl ether groups decreases. Additionally, compounds with a 

secondary benzyl ether group degrade at a faster rate than those with a primary benzyl ether. 

We incorporated each linker into PEG macromers with bifunctional acrylate groups and created 

photodegradable hydrogels by combining the macromers with a multi-functional thiol using a 

pseudo-Michael addition. Through this approach, we have developed a sophisticated material 

platform suitable for cell encapsulation and drug delivery with real-time external control. 


Capsule Thickness Surrounding Titanium Oxide Nanotube Implants 

Garrett C. Smith, 1* Seunghan Oh, 2 Linda Fauxius, 3 Kristian Kolind, 4 Adam Bohr, 4 Sungho Jin 2 

and Lars M. Bjursten 1, 3 


2 Materials Science and Engineering Program, Department of Aerospace and Mechanical 

Engineering, University of California, San Diego 

3 Clinical Sciences, Lund University, Malmö, Sweden 

4 Department of Biomedical Engineering, Technical University of Denmark, Copenhagen, 

Denmark 

Titanium is a widely used biomaterial for oral implants, although it is susceptible to intraoral 

bacteria and inflammatory reactions. 1 In this project we explored the soft tissue response of 

titanium dioxide (TiO 2 ) nanotubes which represent new possibilities to influence tissue 

response, and compared with a mesoscale structured surface. Vertically-aligned nanotubes 

with a ~70nm inner diameter and ~250nm height were fabricated by electrochemical 

anodization on Ti disks (5mm Ø by 1.5mm height). Gritblasted implants with a typical 

roughness depth of ~2um were used as reference. Twenty rats received each implant type in 

the abdominal wall as previously described. 2 Tissues were removed en bloc after one or six 

weeks of healing. Histological evaluation showed that foreign body capsule thickness was 

significantly lower for the nanotube surface at one week (p=0.002) and six weeks (p=0.046) 

compared to gritblasted surface. Higher amounts of ED1 positive macrophages were observed 

at one week compared with six weeks for both implant types. Significantly lower NO activity, 

measured by presence of nitrotyrosine, (p=0.05) was found on the nanotube surface at one 

week. The reduced numbers of recruited macrophages, and less developed fibrotic capsule 

suggests that the nanotube-modified surface is beneficial for implants in contact with soft 

tissues. This may be due to the NO scavenging properties of TiO surfaces 3 that is greatly 

increased by the nanotube structure. These findings may be significant for the interaction 

between titanium implants in soft tissue as well as bone tissue 4 and provide a mechanism to 

improve future clinical implants. 

1. Myshin, J. of Prosthetic Dentistry 94, 5, 440-444 

2. Rosengren Biomaterials. 18(14):979-87 

3. Sahlin, H, J Biomed Mater Res A.;77(1):43-9 

4. Bjursten, J. Biomed. Mater Res. In press 2009 


Towards methodology to characterize fibrillar collagen assembled in vitro under different 

initial parameters 

Yu-Jer Hwang 1 , Julia Lyubovitsky 2 

1 Cell, Molecular, and Developmental Biology Graduate Program, University of California, 

Riverside 

2 Department of Bioengineering, University of California, Riverside 

We developed a combination of methods to systematically identify the relationship 

between the collagen nanostructures formed and their scattering properties on the micrometer 

scale when sample are assembled under different initial protein concentrations and incubation 

temperatures. From the turbidity curves measured at 450 nm, we obtained the kinetic 

parameters of fibrillogenesis which indicated faster polymerization rate at 37°C, however, higher 

final optical density at 27°C. Transmission electron microscopy (TEM) had revealed fibrillar 

morphologies. For example, incubated at both 27°C and 37°C, spindle-shaped fibrils appeared 

at the concentrations of 1, 2, 2.5 and 4 g/l and the spiral-shaped fibrils prevailed at the 

concentrations of 2 and 2.5 g/l. The reflectance multiphoton optical microscopy (MPM) 

evaluations demonstrated a nonlinear increase in scattering from structures formed from higher 

initial collagen concentrations. The approach and the knowledge obtained can be applied in the 

future developments to tissue engineer extracellular matrices that use collagen as a substrate 

material. 


Integrated Microfluidic Platform with Surface-Plasmonic Aptasensor for On-chip Labelfree 

Detection of Cancer Markers from Cells 

Hansang Cho 1,2 , Yolanda Zhang 1 , Brian R. Baker 2 , and Luke P. Lee 1 

1 Biomolecular Nanotechnology Center, Berkeley Sensor & Actuator Center 

Department of Bioengineering, University of California, Berkeley 

2 BioSecurity and NanoSciences Laboratory, Lawrence Livermore National Laboratory 

Although there are many hypotheses from clinical and laboratory data on the mechanism 

of growth factors in angiogenesis, there is not yet any definitive and quantitative evidence for 

their efficacy. In this paper, we propose an integrated nanoplasmonic aptasensor within a 

microfluidic device for on-chip and label-free detection of secreted growth factor under the 

spatial and temporal control of a simulated tumor microenvironment. The sensor is applicable to 

culturing conditions owing to the stability of the aptamer at 37°C for a week. The integrated 

platform achieved the label-free detection of vascular endothelial growth factor (VEGF) down to 

1 nM in buffer solution and also VEGF secreted from MCF-7 (human breast cancer) cells upon 

continuous stimulation with 0.1 mM estrodiole for 37 hrs. Additionally, there was no discernible 

signal change in the absence of VEGF in buffer or in the absence of the estrodiole stimulus in 

cells. 

In the absence of targets, Cy3-conjugated VEGF binding aptamer is immobilized on gold 

nanoparticle (GNP) surfaces by an electrostatic force and baseline intensity is observed as local 

surface plasmon resonance (LSPR) induces surface enhanced fluorescence of Cy3. Secreted 

VEGF, induced by estrodiole, interacts with the aptamer resulting in displacement of the 

aptamer from the GNP surface and a subsequent decrease in fluorescence intensity by 

displacing Cy3 from the LSPR region. The signal decrease reached a saturation level within 20 

min at 100 nM VEGF. Furthermore the integrated platform could monitor VEGF present in 

culturing media containing 10% FBS and detect additional VEGF secreted from MCF-7 cells 

stimulated by estrodiole at 0.1 mM after culturing for 37 hrs. 

The integrated microfluidic platform may be useful for future studies on angiogenesis 

under chemical stimulus and for high-throughput screening of drug candidates that inhibit VEGF 

secretion. 


Measuring Error of Diffusion MRI-based Brain Connectivity Matrices with Residual 

Bootstrap 

C.T. Nguyen 1,2 , SW Chung 1,3 , Roland G. Henry 1,3 

1 Center for Molecular and Functional Imaging, Department of Radiology and Biomedical 

Imaging, University of California, San Francisco 

2 Department of Bioengineering, University of California, Berkeley 

3 Graduate Group in Bioengineering, University of California, San Francisco 

Brain connectivity matrices are highly resourceful representations of network 

connectivity relating specific regions of the brain to function. Recently, noninvasive techniques 

using diffusion MRI were used to construct in-vivo connectivity matrices and networks. However 

with the existence of numerous fiber tracking techniques, using diffusion MRI to construct 

connectivity networks leads to ambiguity in interpreting results. We propose a method to 

measure error in obtaining connectivity matrices allowing for greater confidence in interpreting 

results. We constructed a connectivity matrix that examines the number of streamlines between 

pairs of 63 Brodmann regions of interest (ROIs) of a normal control subject. We chose to use a 

simple FACT algorithm but any fiber tracking algorithm can be used. Residual bootstrap, an 

empirical non-parametric statistical resampling technique, was performed to yield standard 

errors of the number of tracks between the pairs of ROIs. We present the connectivity matrix of 

number of streamlines and a useful fractional error (FE) matrix in which we normalize the 

standard error with the number of streamlines. The fractional error matrix reveals that for the 

majority of pair of ROIs there exists large error. Observing a particular pair of ROIs, the cuneus 

(occipital lobe) and superior parietal, the FE matrix shows high variability in the number of 

streamlines. Our results illustrate the error that may exist in constructing connectivity matrices 

and the need to quantify variability that may result in choosing a particular fiber tracking 

algorithm. In choosing FACT, we found significant variability (FE>0.05) in most connections 

between the pairs of ROIs. This is consistent with previous literature in which FACT fails to 

resolve crossing fibers that may exist between these ROIs. As a result of quantifying this 

variability, connectivity matrices constructed with different fiber tracking algorithms can be 

compared and interpreted. 


Endoscopic Fluorescence Lifetime Imaging for the Characterization of Human 

Atherosclerotic Plaques 

Jennifer Phipps 1 , Nisa Hatami 1 , Yinghua Sun 1, 2 , Ramez Saroufeem 3 , and Laura Marcu 1,2 

1 Department of Biomedical Engineering, University of California, Davis 

2 NSF Center for Biophotonics, University of California, Davis 

3 Department of Medical Pathology and Laboratory Medicine, University of California, Davis 

Atherosclerotic plaque composition has been associated with plaque instability and 

rupture. This study investigates the use of a fluorescence lifetime imaging microscopy (FLIM) 

system for assessing features of plaque vulnerability, particularly lipid accumulation, 

macrophage infiltration, and collagen degradation. Me asurements were conducted in 

atherosclerotic human aortic and carotid plaque samples using a new endoscopic FLIM system 

(spatial resolution of 35 µm; temporal resolution 200 ps) developed in our lab. Chemical 

composition of the samples is mapped within a volume of 4 mm diameter x 250 µm depth with 

each pixel in the images representing a corresponding fluorescence lifetime value. 

Fluorescence images are formed through a flexible 0.6 mm imaging bundle (10,000 coherent 

fibers with a GRIN objective lens and 90 degree prism for side-viewing) which allows for further 

intravascular applications. Based on previously recorded spectra of human atherosclerotic 

plaque, fluorescence emission was collected through three filters: F1: 377/50, F2: 460/60 and 

F3: 510/84 nm (center wavelength/bandwidth), which together provides optimum discrimination 

of intrinsic fluorophores related to plaque vulnerability. The lifetime images were retrieved using 

a Laguerre expansion deconvolution technique and correlated with the histopathological 

analysis of the plaque. 

Current average fluorescence lifetime results demonstrate discrimination between 

compositional features of plaque. For example, discrimination is seen between elastin-rich 

(2.14 +/- 0.07 ns) and collagen-rich (2.51 +/- 0.11 ns) regions when using F1 and between 

collagen-rich (2.21 +/- 0.06 ns) and lipid-rich (1.94 +/- 0.07 ns) regions when using F2. These 

results correlate with earlier reported data from human atherosclerotic plaques obtained using 

time-resolved fluorescence-spectroscopy measurements and demonstrate the potential of this 

system for implementation as an intravascular diagnostic modality. 


Magnetic Resonance Thermal Imaging in Combination with Parallel MRI 

in Phantom Experiments in the Presence of Motion 

Youngseob Seo 1 and Jeffrey H. Walton 2 


2 Department of Biomedical Engineering Graduate Group, University of California, Davis 

MR thermal imaging has been used to generate real-time in vivo temperature maps for 

monitoring thermal therapies such as radiofrequency (RF) ablation, laser ablation, focused 

ultrasound, and cryotherapy. In this way, the treatment can be tailored to meet very specific 

endpoints for individual patients with immediate feedback-ensuring the coagulation of tumor 

margins and protecting adjacent normal tissue. 

MR temperature maps, however, are easily corrupted by motion, meaning these 

techniques are limited to static organs. Previous methods of reducing motion artifacts have 

drawbacks that prevent them from being optimal for the application of thermal MRI. We want to 

apply recently developed motion detection and correction technique based on parallel MRI 

concepts. The combination of thermal ablation and parallel MRI will enable monitoring and 

controlling the heat distribution and temperature change in the dynamic tumor tissue under 

thermal therapies, and will be a very important tool for cancer treatment in mobile organs. 

The main purpose of this research is to develop and optimize an MR thermometry 

method combined with parallel MRI techniques in phantom experiments with respect to 

detecting and correcting motion artifacts from a phantom. 

We simulated an in vivo liver motion as a simple, linear harmonic motion using a motor 

system and the phantom was heated by hot water at 60°C. MR thermal imaging based on the 

modified proton resonance frequency (PRF) shift method combined with SMASH navigator 

technique resulted in accurate temperature maps of the heated phantom in the presence of 

motion 


Simulation tool for theoretical modeling of hyperpolarized 13 C metabolic imaging 

Peter J. Shin 1 , Simon Hu 1,2 , Peder E.Z. Larson 2 , Daniel B. Vigneron 1,2 

1 Joint Graduate Group in Bioengineering, University of California at San Francisco & Berkeley 

2 Department of Radiology, University of California at San Francisco 

Hyperpolarized 13 C magnetic resonance spectroscopy and imaging (MRSI) has recently 

emerged as a means for real-time monitoring of metabolic processes in vivo. In this method, 13 C 

labeled metabolic substrates (such as pyruvate) are highly polarized through dynamic nuclear 

polarization (DNP) and injected in vivo for time resolved spectroscopic imaging of the substrate 

and its metabolites. Careful data acquisition schemes must be used as the magnetization 

achieved through hyperpolarization undergoes T 1 relaxation to thermal equilibrium within the 

time window of 1-2 minutes. In addition, each RF excitation irreversibly destroys some portion of 

this non-thermal magnetization. The goal of this project is to develop a simulation package for 

theoretical modeling of hyperpolarized 13 C MRSI. Users could simulate various data acquisition 

schemes including different phase-encoding trajectories and arbitrary RF excitation flip angles. 

Evaluation on signal-to-noise ratio (SNR) and blurring effect in data can provide useful insight 

and optimization before the users do actual experiments in vivo. The simulation tool is 

developed with MATLAB (The Mathworks, Natick, MA, USA). A flexible software object model is 

created to simulate physical phantom objects used in 3D-MRSI. The users will be able to 

specify different 13 C compounds in different locations and test their pulse sequence schemes. 

With physical and chemical conditions taken into account, 4D data set composed of object‘s 

spectral-spatial information will be calculated and, in turn, reconstructed (Fourier transform) into 

user interpretable information. So far, point-spread-function (PSF) analysis of variable flip angle 

(VFA) RF excitation with different phase encoding schemes has been tested. From the result, 

non-uniform weighting in excitation k-space has been observed. This is due to the signal loss in 

the later stages of data acquisition which reflects the T 1 relaxation of the longitudinal 

magnetization. As a consequence, severe reduction in SNR and blurring could occur in 

reconstructed data unless the acquisition parameters are optimized. Initial results have been 

very encouraging and more functionality for the tool and new RF excitation with T 1 compensated 

VFA is under development. 

1 Klaes Golman, et al., PNAS 2006, 103, 11270-11275. 

2 Peder E.Z. Larson, et al., J Magn Reson 2008, 194, 121-127 


Quantitative assessment of peripheral nerve damage using polarization-sensitive optical 

coherence tomography 

Yan Wang, Hyle Park 

Department of Bioengineering, University of California, Riverside 

The necessity for surgical intervention for peripheral nerve damage often depends on the 

severity of the injury. Neurapraxic and axonotmesic injuries preserve enough surrounding 

connective tissue for axonal regeneration, whereas the disruption of these tissues in 

neurotmesis requires surgery to re-establish continuity of the nerve. The overall length of the 

repaired nerve is critical, and so such surgeries often involve differentiation of viable from 

damaged nerve by observation of scar formation, intraoperative electrophysiology, or imaging 

modalities such as computed tomography and magnetic resonance myelography. While these 

well-established techniques have led to great improvements in the field of acute nerve repair, 

they are not without flaw; waiting for scar formation introduces a delay before surgical 

intervention, intraoperative electrophysiology yields only bulk conduction properties of a nerve 

bundle with no cross-sectional differentiation, and CT and MR myelography can image only 

gross morphologies. Polarization-sensitive optical coherence tomography (PS-OCT) can 

provide rapid volumetric imaging of nerve microstructure with a resolution on the order of 2-5 

microns. We present results of an animal study using data acquired from rat sciatic nerve that 

demonstrate the ability to non-destructively assess the viability of the peripheral nervous system 

through examination of structural features and quantitative assessment of nerve myelination. 


Using Diffusion Tensor Imaging to Highlight White Matter Relevant to Deep Brain 

Stimulation 

Christine M. Zwart 1,2 , Josef P. Debbins 2 , Guillermo Moguel-Cabos 2 , Peter N. Steinmetz2 

1 Arizona State University,Tempe, AZ 

2 Barrow Neurological Institute (BNI), St. Joseph's Hospital, Phoenix, AZ 

Studies of optimum placements for deep brain stimulators (DBS) typically rely on 

atlases for defining the regional anatomy. As a result, implantation decisions are made with 

distant landmarks that are defined in structural images and templates registered to patient 

anatomy. We are developing imaging based techniques to highlight patient anatomy in the 

region of potential stimulation during DBS of the subthalamic nucleus (STN). The zona incerta 

(ZI), fields of Forel (FF), and the internal capsule (IC) are highly anisotropic structures within this 

region that we aim to identify with diffusion tensor imaging and tractography. 

Our method relies on the T2 hypointensity of the STN, RN, and the lentiform nucleus. 

By seeding tractography on the horizontal plane between the STN and the RN (roughly the ZI), 

a stereotypical looping of the white matter through FF and into the lentiform nucleus can be 

observed leaving a hollow region containing the IC, (integration with the IC occurs in higher 

slices). To summarize our approach: the FMRIB Software Library (FSL) is used for preliminary 

processing, the ZI is identified based on the gradient of the intensity of a thresholded version of 

the T2 weighted image using custom MATLAB code, tractography is performed using FSL's 

probabilistic tractography package, and the subregions representing the relevant structures are 

isolated within the results based on a weighted consideration of the tract probability and 

collinearity using custom MATLAB code. 

Initial results (five patients) with clinical protocols (GE Signa 3T, 24 cm field of view, 128 

x 128 matrix, 2.6 cm slices spaced 1.5 cm apart) show identification of the ZI and tractography 

results that include the desired structures in all patients. Some cases yielded IC connections in 

the same plane as connections through the lentiform nucleus suggesting the inter-slice spaces 

in the imaging protocol should be reduced. 


The Role of Regulatory Light Chain Phosphorylation in 

Murine Left Ventricular Function: A Multi-Scale Modeling Approach 

Stuart G. Campbell 1 , Farah Sheikh 2 , Ju Chen 2 , Roy C. P. Kerckhoffs 1 , and Andrew D. 

McCulloch 1 


2 Department of Medicine, University of California, San Diego 

We have combined computational models at several biological scales to study the 

effects of region-dependent protein phosphorylation on heart function. Several mutations 

altering phosphorylation of myosin regulatory light chain (RLC) have been found in patients with 

familial hypertrophic cardiomyopathy (FHC), however the precise role of RLC phosphorylation in 

the heart is not well understood. Spatial gradients of RLC phosphorylation have been reported 

in the murine ventricular wall, suggesting that its role is region-dependent. We proposed that 

altered myosin kinetics induced by RLC phosphorylation act in concert with ventricular gradients 

in phosphorylation to create a physiological pattern of left ventricular torsion. Additionally, we 

hypothesized that the abolishment of the gradient and molecular-level effects of 

phosphorylation, as is caused by certain FHC mutations, results in substantial losses to cardiac 

output. We tested these hypotheses by representing molecular-scale effects of phosphorylation 

in a model of myofilament force generation. This model was integrated within a finite-element 

model of left ventricular tissue mechanics, which was in turn coupled to a lumped-parameter 

model of the circulatory system. Simulations performed with the combined model revealed that 

the transmural gradient in phosphorylation contributed substantially to ventricular torsion during 

ejection when compared with a model in which phosphorylation was uniform. Simulations in 

which phosphorylation was completely eliminated displayed a further decrease in peak systolic 

torsion as well as reduced ejection fraction. These results suggest an important role for both 

RLC phosphorylation and its spatial distribution in normal ventricular function. 


Electrostatic Exploration of Complement Receptor 1 using Computational Alanine Scan 

and Experimental Mutagenesis Data 

Gabrielle N. Goodman 1 , Chris A. Kieslich 1 , Richard Hauhart 2 , Thomas Allen 2 , John P. Atkinson 2 , 

Dimitrios Morikis 1 


2 Division of Rheumatology, Department of Medicine, Washington University School of 

Medicine 

Complement Receptor 1 (CR1/CD35) is approximately a 220kDa single chain 

glycoprotein consisting of 30 complement control protein (CCP) modules and exists within the 

human immune system as both a complement immune adherence receptor and membranebound 

regulator. Whether as a receptor or regulator, CR1 functions mainly by binding 

complement proteins C3b and C4b. Without proper regulation via CR1, multiple autoimmune 

diseases may develop as a result. Our goal is to contribute to the physicochemical 

understanding of the binding interaction that occurs between Binding Site 2 of CR1 (CCP 

modules 15-17) and C3b/C4b at atomic resolution. In previous studies, we have determined 

that electrostatic properties, derived from intrinsic protein charges, mediate the processes of 

recognition and binding between excessively-charged regulators of the complement system and 

their target proteins. In this study, we altered the electrostatic properties of CR1 Site 2 using a 

high-throughput computational protocol to generate three datasets of theoretical mutants. In 

two datasets, mutants were generated based on our computational alanine scan method in 

which we mutated all charged residues within CR1 Site 2 to alanine. The rationale behind the 

alanine scan is to quantify the relative contribution of each charged residue to the overall spatial 

distribution of the electrostatic potential and, according to our model, to recognition and binding. 

In the third dataset, mutants were generated based on previously determined experimental 

mutagenesis data. In all cases, we present correlations between the similarities of the 

electrostatic potentials, binding properties, and related immunological activities for mutants of 

CR1 Site 2. Our goal is to understand the underlying electrostatic properties of existing 

experimental data and to provide an integrated database of mutants which may serve as a 

predictive set to guide future experimental mutagenesis studies. These studies may form the 

basis for development of regulators of the immune system with tailored properties. 


Electrostatic Analysis of C3d/Efb-C Interaction 

Ronald D. Gorham, Christopher A. Kieslich, Dimitrios Morikis 


The complement system serves as a link between innate and adaptive immunities, 

participating in removal of pathogens from the body. The C-terminal fragment of the 

Staphylococcus aureus extracellular fibrinogen binding protein (Efb-C) is a potent inhibitor of 

complement system activation. Efb-C is excessively charged, possessing a net charge of +7e. 

The protein binds to its complement target C3d at an acidic interface. Within a 2-step model of 

association, which separates recognition from binding, the excess charge in Efb-C is expected 

to play a significant role in recognition with C3d. In addition, charge localization at the interface 

of Efb-C with C3d implies that electrostatic interactions also contribute to binding. Using a highthroughput 

computational approach, the C3d/Efb-C complex was theoretically mutated through 

an alanine scan of ionizable residues, and electrostatic potentials were calculated using 

Poisson-Boltzmann electrostatics. Based on these calculations, similarity indices were utilized 

to cluster mutants according to their respective electrostatic properties. Additionally, free 

energies of association and solvation were calculated for each mutant. The results showed that 

electrostatic free energies of association are strongly correlated to the clustering analysis, 

indicating the importance of clustering in determining which mutants have similar 

characteristics. Mutations that significantly reduced the electrostatic free energy of association 

were mostly located within the binding interface, although several mutations located >10 Å from 

the interface affected binding as well. This indicates that not only are electrostatic interactions 

at the interface are crucial for binding, but the global electrostatic contributions are important as 

well. This study serves as the foundation for future work in two areas: (1) development of an 

inhibitor of the C3d/Efb-C interaction to combat bacterial evasion of the complement system and 

(2) design of a therapeutic inhibitor of complement activation using Efb-C as a model, which 

may serve as a treatment for certain autoimmune diseases. 


Lipid peroxidation in living cells promotes membrane electropermeabilization 

Zachary A. Levine 1,2 , Yu-Hsuan Wu 3 , Matthew J. Ziegler 1,3 , Martin A. Gundersen 2,3,4 , D. Peter 

Tieleman 5 , P. Thomas Vernier 1,4 

1 MOSIS, Information Sciences Institute, University of Southern California 

2 Department of Physics and Astronomy, University of Southern California 

3 Mork Family Department of Chemical Engineering and Materials Science, University of 

Southern California 

4 Ming Hsieh Department of Electrical Engineering, University of Southern California 

5 Department of Biological Sciences, University of Calgary 

Nanosecond, megavolt-per-meter, pulsed electric field (nanoelectropulse) technology — 

a low-energy, nondestructive means for perturbing the intracellular environment and for 

transiently electropermeabilizing cell membranes — is used in cancer therapy, genetic 

engineering, and cell biology. In order to optimize pulsing protocols, a better understanding of 

the mechanisms of membrane permeabilization and of the factors affecting the susceptibility of 

cells to nanoelectropulse exposure is needed. Molecular dynamics (MD) studies have shown 

that oxidized lipids increase the frequency of water defects in phospholipid bilayers and suggest 

that the presence of oxidized lipids in a bilayer will also increase the sensitivity of the bilayer to 

electropermeabilization. To investigate this possibility we applied external electric fields during 

MD simulations of lipid bilayers using varying concentrations of oxidized lipids. Systems with 

higher concentrations of oxidized lipids form hydrophilic electropores in significantly shorter 

times than do systems with lower oxidized lipid concentrations, and at lower electric fields. Sites 

of water defect formation and subsequent electroporation appear to coincide with local 

clustering of oxidized lipids in the bilayer. In large-area simulations containing localized high 

oxidized lipid concentrations, pores formed preferentially in these oxidized regions. The 

presence of aldehyde and hydroperoxy oxygens on an otherwise nonpolar lipid tail appears to 

facilitate the penetration of water into the bilayer interior. To validate these simulations, in vitro 

cell experiments were carried out using human T lymphoblasts. After peroxidation, cell 

suspensions were exposed to pulsed electric fields in a medium containing YO-PRO-1, a 

membrane-impermeant dye that fluoresces only when the cell membrane becomes 

permeabilized. The results confirm the simulation results — peroxidation significantly increases 

pulse-induced membrane permeabilization. 


Clustering of Sequences and Electrostatic Potentials of HIV-1 Subtypes 

Aliana López De Victoria, Chris A. Kieslich, Dimitrios Morikis 


HIV infection involves binding of its envelope glycoprotein gp120 to CD4 receptor and 

coreceptors CCR5 or CXCR4 in the host cell. The third variable region of gp120 forms a loop, 

called the V3-loop, which is composed of 31-39 residues. Previous studies have demonstrated 

that the V3-loop interacts with the N-terminal extra-cellular domain of CCR5 (CCR5-Nt) and that 

electrostatics plays the dominant role in this interaction. The electrostatic attraction involves a 

highly positive V3-loop and a highly negative CCR5-Nt. The V3-loop is responsible for 

determining HIV tropism and plays an important role in viral entry by selecting the appropriate 

coreceptor. HIV-1 is divided into three distinct genetic groups: M, N, and O; with the M group 

being responsible for the majority of the infected population. This group is further divided based 

on the sequence variability of its env and gag genes into 10 subtypes. A consensus sequence 

for the V3-loop of several subtypes was obtained from Los Alamos National Laboratory. 1 

Modeling of the V3-loop for each subtype was performed using the two available crystal 

structures with an intact V3-loop as templates. We have applied our high-throughput 

computational methodology to cluster the various subtypes according to similarities or 

dissimilarities of the spatial distributions of electrostatic potential generated by the V3-loop 

charges. The resulting clusters have been analyzed to determine correlations between the 

electrostatic potentials and net charge, global prevalence, geographical distribution, and 

coreceptor selection. This work is important for design of potential therapeutics targeting the 

electrostatic properties of the interaction between the V3-loop of gp120 with CCR5. 

1 Myers G, Kober B, Foley B, Jeang KT, Mellers JW, Wain-Hubson S. (1996). Human 

retroviruses and AIDS 1996: A Compilation and Analysis of Nucleic Acid and Amino Acid 

Sequences. Los Alamos National Laboratory. Los Alamos, New Mexico. 


Computational Modeling of Immunological Synapse Formation Shows That Cytoskeletal 

Transport of Receptor Molecules Is a Potential Formation Mechanism 

Philippos K. Tsourkas * , Subhadip Raychaudhuri *†‡§ 

* Dept. of Biomedical Engineering, † Biophysics Graduate Group, 

‡ Graduate Group in Immunology, § Graduate Group in Applied Mathematics 

University of California, Davis 

The formation of the protein segregation structure known as the ―immunological 

synapse‖ in the contact region between B cells and antigen presenting cells (APCs) appears to 

precede antigen (Ag) uptake by B cells. The mature B cell synapse consists of a central cluster 

of B cell receptor/Antigen (BCR/Ag) complexes surrounded by a ring of LFA-1/ICAM-1 

complexes. In this study, we developed an in silico model to investigate whether cytoskeletallydriven 

transport of molecules towards the center of the contact zone is a potential mechanism of 

immunological synapse formation in B cells. We modeled cytoskeletally-driven transport in an 

effective manner, by biasing the diffusion of molecules towards the center of the contact zone. 

Our results clearly show that biased diffusion of BCR/Ag complexes on the B cell surface is 

sufficient to produce patterns similar to experimentally observed immunological synapses. This 

is true even in the presence of significant membrane deformation as a result of receptor-ligand 

binding, which in previous work we showed has a detrimental effect on synapse formation for 

high affinity antigens. Comparison of our model‘s results to those of experiments shows that 

our model produces synapses for realistic length, time, and affinity scales. Our results also 

show that strong biased diffusion of integrin molecules has a negative effect on synapse 

formation by excluding BCR/Ag complexes from the center of the contact zone. However, 

synapses may still form provided the bias in diffusion of integrins is an order-of-magnitude 

weaker than that of BCR/Ag complexes. We also show how diffusion trajectories obtained from 

recent single-molecule tracking experiments can generate insight into the cytoskeletally-driven 

transport mechanism of synapse formation. 


The Impact of Mass Transfer of AMPK Signaling Pathways 

Prashanthi Vandrangi 1 , John Shyy 2 , and V. G. J. Rodgers 1 

1 Department of Bioengineering, University of California Riverside 

2 Department of Biomedical Sciences, University of California Riverside 

AMP-activated protein kinase (AMPK) plays an important role in regulating the 

metabolism of the body. AMPK signalling pathway is correlated to a myriad of processes such 

as fatty acid oxidation, synthesis and transport of glucose, glycolysis, apoptosis, protein 

synthesis, vascular shear stress, ischemia, and activation of ion channels. [1] At the vascular bed, 

AMPK phosphorylation triggers endothelial nitric oxide synthase (eNOS) and the production of 

nitric oxide (NO). In fatty acid synthesis, AMPK phosphorylation inhibits the rate-limiting step of 

cholesterol and the assembly of low density lipoproteins (LDL). In this study, we explore the role 

of NO and LDL mass transfer at the arterial vasculature in response to altering blood flow 

parameters. 

Physiologically, endothelial cells, the inner most layer of the vascular system, 

experience blood flow. The mechanism by which vascular blood flow elicits AMPK signalling in 

the endothelial cells remains vague. Mechanotransduction of hemodynamic forces into AMPK 

cascading has been extensively studied during the past decade. [2] Along with hemodynamic 

forces such as shear stress, endothelial cells might be triggered by a biochemical response 

such as mass transfer. However, vascular shear stress might modify the gradients of molecules 

such as NO and LDL at the endothelium surface. The subsequent role of mass transfer in 

arteriosclerosis, arrhythmias, and other diseased states has, however, received relatively little 

attention. [3] 

We mathematically simulate a 2-D parallel flow chamber experiment to simulate the 

biochemical or mass transfer response of the vascular endothelium to varying blood flow 

parameters. The corresponding effect of amplitude and frequency of pulsatile and oscillatory 

blood flow on mass flux is studied. Our research also investigates the impact of coupling 

viscosity and diffusivity to shear field gradients. We also investigate the significance of mass flux 

of molecules, such as NO and LDL, decoupled from mechanical shear stress in the 

phosphorylation of AMPK and evaluate their effects. 

[1] D., Carling, 'The AMP-activated protein kinase cascade – a unifying system for energy 

control', Trends in Biochemical Sciences, Vol. 29(1):18-24, 2004. 

[2] Y Zhang, T. S., Lee, E. M., Kolb, K. Sun, X. Lu, F. M., Sladek, G. S., Kassab, T. Jr., Graland, 

J. Y., Shyy, 'AMP-activated protein kinase is involved in endothelial NO synthase activation in 

response to shear stress', Arteriosclerosis, Thrombosis, and Vascular Biology, Vol. 26(6):1281- 

7, 2006. 

[3] M. U., Nollert, S. L., Diamond, and L. V., McIntire, "Hydrodynamic Shear Stress and Mass 

Transport Modulation of Endothelial Cell Metabolism," Biotechnology and Bioengineering, 

38:588-602, 1991. 


Morphology of the Embryonic Stem Cell Cultures: Testimony of the Integrins and 

Cadherins 

Alicia A. Blancas 1 , Chi-Shuo Chen 2 , Sarah E. Stolberg 1 , Kara E. McCloskey 1,2,3 

1 Graduate Group in Quantitative and Systems Biology, University of California, Merced 

2 Graduate Group in Biological Engineering and Small Scale Technology, University of 

California, Merced 

3 School of Engineering, University of California, Merced 

In vitro studies employing mouse and/or human embyronic stem cells (ESC) are 

becoming widely popular due to their ability to differentiate into all tissue-specific cell types. The 

pluripotent property of these cells, coupled with their proliferative capabilities, makes them an 

attractive in vitro system for studying cell fate and applications in regenerative medicine. 

Compared with many tissue cell culture systems that classically grow as contact-inhibited 

monolayers, the ESC form tightly packed three-dimensional (3-D) colonies and readily form cell 

aggregates, called embryoid bodies (EB) that partially mimic the spatio- and temporal processes 

of the developing embryo. The cells‘ adhesion strength to two-dimensional (2-D) extracellular 

matrix (ECM), ESC-to-ECM, or mouse embryonic fibroblasts (MEF)-coated tissue culture 

dishes, ESC-to-MEF, is precariously balanced by their adhesion to one another, ESC-to-ESC, 

forming a spherical-like structure. Here we model and estimate the adhesive forces of cell-cell 

and cell-ECM of ESC which, at least in part, supports the observed spherical 3-D nature of ESC 

colonies. 


Electric Field Induces Plasticity on Cortical Neurons In Vitro 

Addie Hicks 1 , Alyssa Panitch 2 , Michael Caplan 1 , James D. Sweeney 3* 

1 Harrington Department of Bioengineering, Arizona State University 

2 Weldon School of Biomedical Engineering, Purdue University 

3 U.A. Whitaker School of Engineering, Florida Gulf Coast University 

Endogenous electric fields (naturally occurring) are present during development and 

regeneration of tissue. Studies suggest that they provide a signal for cell migration, affect 

cellular alignment, and enhance growth. They may also play a role in neuronal pathfinding of 

target tissue. Our study seeks to determine the responses of existing fibers of mammalian 

cortical neurons to an applied DC electric field (EF) in vitro, and the feasibility of using electrical 

stimulation as a therapeutic mechanism after spinal cord injury. Cells with in tact fibers were 

obtained from partially dissociated embryonic (day 18) rat cortical neurons. The cells were 

cultured for 12 to 20 hours prior to applying electric fields ranging from 37.75 to 226 mV/mm. 

Neurite length, alignment, and response variations to the anode and cathode were observed for 

stimulated and control cultures. Our results suggest that an imposed electric field can induce 

the fibers of cortical neurons to realign and appears to also enhance their growth. 


Cultivating Liver Cells on Growth Factor Microarrays 

Caroline N. Jones 1 , Nazgul Tuleuova 1† , Ji Youn Lee 1 , Erlan Ramanculov † , A. Hari Reddi 2 , Mark 

A. Zern ‡ and Alexander Revzin 1 

1 Department of Biomedical Engineering, University of California. Davis 

2 Department Orthopaedic Surgery, Center for Tissue Regeneration and Repair, University of 

California, Davis 

‡ 

Department of Medicine, Transplant Research Institute, University of California, Davis 

† 

National Center for Biotechnology, Astana, Republic of Kazakhstan 

Growth factors are commonly present in soluble form during in vitro cell cultivation 

experiments in order to provide signals for cellular proliferation or differentiation. This study 

investigates solid-phase presentation of hepatocyte growth factor (HGF), a protein important in 

liver development and regeneration, on microarrays of extracellular matrix (ECM) proteins. In 

our experiments, HGF was mixed in solution with ECM proteins (collagen (I), (IV) or laminin) 

and robotically printed onto silane-modified glass slides. Primary rat hepatocytes were seeded 

onto HGF/ECM protein microarrays and formed cellular clusters that corresponded in size to the 

dimensions of individual protein spots (500 m diameter). Analysis of liver specific products, 

albumin and 1-antitrypsin, revealed several fold higher levels of expression of these proteins in 

hepatocytes cultured on HGF/ECM microarrays compared to cells cultivated on ECM proteins 

alone. In addition, cultivation of hepatocytes on HGF/ECM protein spots led to spontaneous 

reorganization of cellular clusters from a monolayer into three-dimensional spheroids. We also 

investigated the effects of surface-tethered HGF on hepatocytes co-cultivated with stromal cells 

such as hepatic stellate cells and observed a significantly higher level of albumin in co-cultures 

where hepatocytes were stimulated by HGF/ECM spots compared to co-cultures created on 

ECM protein islands without the growth factor. In summary, our study suggests that 

incorporation of HGF into ECM protein microarrays has a profound and long-lasting effect on 

the morphology and phenotype of primary hepatocytes. Current studies are focused on using 

the platform developed in this study to investigate the therapeutic potential of multiple growth 

factors during acute alcohol injury. 


Wrinkled microtopography to induce cell alignment and maintain contractibility of 

cardiac myocytes 

Jesus Isaac Luna 1 , Jesus Ciriza 2 , Marcos E. García-Ojeda 2 , and Michelle Khine 1 


2 School of Natural Sciences, University of California, Merced 

Ventricular cardiac myocytes in the native tissue are arranged in such a way that allows 

them to electrically and mechanically synchronize. Commonly used cardiac myocyte culture 

methods do not provide the proper environmental factors that allow these cells to physiologically 

nor morphologically respond as they do in the native tissue. Here we present a rapid method to 

tunably fabricate a bio-mimetic substrate patterned with wrinkled microtopographies to align and 

culture murine neonatal cardiac myocytes (NNCM). Notably, this wrinkled substrate resembles 

more the fibrous environment provided by the cardiac tissue. The generated metal wrinkles 

serve as a soft lithography mold to fabricate polydimethylsiloxane (PDMS) substrate. Coating 

the PDMS wrinkled substrate with a combination of laminin and fibronectin at high 

concentrations induces NNCM to align within days and contract for weeks. This protein matrix 

provides anchorage where cells establish focal adhesions that allow them to align with respect 

to the wrinkles direction and to beat. Cell alignment was examined by staining cytoskeletal 

elements. We demonstrated that our microtextured substrates induce cells to synchronize and 

form cardiac tissue. In addition, gap junction and cell adhesion proteins were examined by 

immunostaining to analyze cell to cell interactions. Finally, we observed sarcomere 

development over time which indicates cardiac myocyte maturation on our substrate. 


Contribution of Bioceramic Towards Osteogenic Response and Mechanical Properties of 

Composite Scaffolds 

Diana G. Morales and J. Kent Leach 

Department of Biomedical Engineering, University of California, Davis 

Bone defects resulting from trauma or degenerative bone diseases are a significant 

clinical problem, and implants formed of polymers and bioceramics are under investigation to fill 

these defects. Synthetic polymers such as poly(lactide-co-glycolide) [PLG] provide space for 

cells to reside but lack sufficient mechanical properties for treating many bone defects. 

Alternatively, implants formed of bioceramics (e.g., hydroxyapatite [HA] and bioactive glass 

[BG]) exhibit increased strength and osteoconductivity and can promote osteogenic 

differentiation in vivo. However, these lack appropriate porosity to support cell viability within the 

substrate. Composite biomaterials represent a promising alternative to bone grafts and other 

materials and capitalize on the beneficial aspects of individual components. We hypothesized 

that the mechanical properties and osteogenic potential of composite scaffolds is dependent 

upon biomineral selection. We fabricated 3-dimensional composite scaffolds at a 2.5:1 mass 

ratio of bioceramic (either HA or BG) to polymer (PLG) using the gas foaming/particulate 

leaching method. MC3T3-E1 preosteoblasts were seeded on composite scaffolds or scaffolds 

lacking mineral and cultured for 21 days in media containing osteogenic supplements. 

Mechanical properties were determined by measuring the compressive moduli. The osteogenic 

response of cells to each material was assessed by quantifying intracellular alkaline 

phosphatase activity (ALP), while metabolic activity was monitored with an AlamarBlue assay. 

Compared to control scaffolds (1.4+0.156 MPa), HA containing composite scaffolds possessed 

significantly increased mechanical strength exhibiting higher compressive moduli (12.2+3.4 

MPa) than BG-containing scaffolds (0.482+0.25 MPa). We observed significant increases in 

ALP for MC3T3s on control scaffolds compared to composite scaffolds at both 7 and 21 days, 

with no significant differences detected for cells on composite substrates. However, cells 

cultured on composite scaffolds possessed greater metabolic activity compared to control 

scaffolds. Our results demonstrate that the inclusion of various biominerals in composite 

scaffolds enables enhanced control over mechanical properties while maintaining a comparable 

osteogenic response. 


Cartilage Regeneration: A Macrodesigned, Acellular Scaffold Promotin 

Endogenous Cell Influx and Chondrogenesis 

Stephanie Reed 1 , Dr. Bill Tawil 1 , Dr. Benjamin Wu 1,2 

1 Biomedical Engineering, University of California, Los Angeles 

2 Division of Advanced Prosthodontics, Biomaterials, and Hospital Dentistry, University of 

California, Los Angeles 

While many tissue-engineered constructs aimed to treat cartilage defects are being 

researched, most involve chondrocytes or stem cells seeded on a scaffold and provided with 

proper signaling molecules to maintain phenotype and function. Various cell-loaded scaffolds in 

conjunction with delivered growth factors are being studied both in vitro and in vivo in animals, 

but the clinical application of these techniques is limited due to the cost of maintaining cellular 

constructs on the shelf, the potential immune response to allogeneic cell lines, and autologous 

cell sources requiring biopsy from already diseased, scarce tissue. Thus an acellular scaffold 

that can induce the endogenous influx of native cells holds great promise for cartilage 

regeneration. An ideal scaffold would encourage migration of surrounding chondrocytes and 

also effortlessly allow access to the underlying bone marrow for mesenchymal stem cell influx. If 

the subchondral bone is exposed during cartilage resurfacing, a tissue engineered construct 

that quickly absorbs blood and its contained stem cells could accelerate regeneration without 

the need for exogenously seeded cells. Chitosan-alginate scaffolds are highly wetting because 

of their porous structure and the hydrophilicity of chitosan. However, incorporating macroscopic 

channels into the microscopic porous scaffold architecture drastically increases the wetting 

speed. This system of capillary action and porous absorption allows for a much greater uptake 

flow rate than porous absorption alone. Wetting speed in chitosan-alginate scaffolds with 

channels was three fold faster than scaffolds without channels. Further, swelling ratio and 

equilibrium water uptake were also increased in scaffolds with channels compared to those 

without, and these parameters reached their peaks within 1 minute of wetting. Finally, 

channeled chitosan-alginate scaffolds imbibing a concentrated cell solution demonstrated 

homogeneously distributed chondrocytes throughout the entire scaffold height and diameter. All 

of these results indicate that macrodesigned chitosan-alginate scaffolds are good candidates for 

endogenous cell-based cartilage regeneration. 


Injectable myocardial matrix for cardiac tissue engineering 

Jennifer M. Singelyn 1 , Jessica A. DeQuach 1 , Sonya B. Seif-Naraghi 1 , Robert B. Littlefield 2 , 

Pamela J. Schup-Magoffin 1 , Karen L. Christman 1 

1 Department of Bioengineering, University of California San Diego, La Jolla, CA, USA 

2 Department of Biomedical Engineering, Bucknell University, Lewisburg, PA, USA. 

Heart failure remains one of the leading causes of death in the United States, and is only 

curable by a total heart transplant. Cardiac tissue engineering has thus emerged as an 

important field to prevent heart failure following a myocardial infarction. Several materials have 

been examined as injectable scaffolds; however none have been specifically designed to mimic 

the natural myocardial extracellular environment. Injectable materials offer the unique 

advantage of minimally invasive delivery. Herein, we evaluate in vitro properties and in vivo 

feasibility of a naturally derived myocardial matrix. Decellularized and solubilized porcine 

myocardial tissue was able to gel at 37C in vitro, as well as in vivo, when injected into the left 

ventricular (LV) free wall in a rat model. Characterization of the matrix demonstrated its 

complexity, including nanofibers 100-150 nm in diameter, and 23.2 ± 4.63 g of 

glycosaminoglycans per mg of matrix. An in vitro assay revealed migration of human coronary 

artery endothelial cells and rat aortic smooth muscle cells towards the myocardial matrix. 

Migration of endothelial and smooth muscle cells into the myocardial matrix was also seen in 

vivo, at 11 days post injection into the LV myocardium, with a significant increase in arteriole 

formation. To determine the potential of the myocardial matrix to be delivered minimally 

invasively, it was pushed through a small gauge catheter, currently used for cellular delivery into 

the myocardium. In this study, we have demonstrated that the myocardial matrix selfassembles 

to form a nanofibrous scaffold both in vitro and in situ, promotes cell infiltration and 

neovascularization, and is able to be pushed through a small gauge catheter for minimally 

invasive delivery into the myocardium. Thus, we have demonstrated the potential of this 

material, developed specifically as a myocardial mimic, to be used as an injectable scaffold for 

cardiac tissue engineering. 


Fabrication of Photopatternable Superhydrophobic Nanosurfaces 

Hailin Cong 1 , Lingfei Hong 2 , Tingrui Pan 1 


2 Department of Instrument Science and Optoelectronic Engineering, Beihang University 

Micro-nanoengineered surfaces with desired superhydrophobicity have attracted 

considerable interest in recent years. To define the selected superhydrophoic patterns on the 

surface, a number of approaches have been demonstrated, including microcontact printing, 

chemical vapor deposition, layer by layer self-assembly, TiO 2 based photochemistry, 

mechanical manipulation, laser etching, plasma chemical patterning and so on. However, all the 

aforementioned techniques either involve lengthy preparation/generation of superhydrophobic 

surfaces, or require special microfabrication equipment or dedicated molding templates. In this 

paper, we first report on direct fabrication of photodefinable superhydrophobic surfaces by 

mixing and spray coating nanocomposite methods, combining the superhydrophobicity of 

polytetrafluoroethylene (PTFE) nanoparticles and photopatternability of SU-8 photoresist. By the 

mixing nanocomposite method, the superhydrophobic PTFE/SU-8 nanocomposite surface can 

be reliably achieved on transparent substrates (e.g., glass) with a 150° contact angle of water 

and minimal feature resolution of 50 µm, the transparency of the formed nanocomposites by this 

method is about 20 %. While by the spray coating nanocomposite method, thermally 

immobilized PTFE nanosurface on SU-8 can be well controlled from 1 µm to 14 µm in thickness 

with corresponding transparency from 91% to 43 %, the superhydrophobic nanocomposite 

surface can be reliably achieved on various substrates (e.g., glass, silicon, and plastics) with a 

more than 165° contact angle of water and minimal feature resolution of 10 µm. Additionally, the 

superhydrophobic nanosurface made by both methods exhibits excellent adherence to the 

underlining substrates under prolonged high-pressure water and air streams. The novel 

PTFE/SU-8 nanocomposite surface provides unique combination of superhydrophobicity, optical 

transparency, and photopatternability along with excellent adaptability and simple processability, 

which offers great extension to the rapid-evolving micro-nanoengineering applications including 

micro-nanofluidics, self-cleaning coatings and textiles, non-fogging surfaces, oil-water 

separation, friction-drag reduction, molecular assembly and biochemical manipulation, as well 

as biological and medical investigations. 


Characterization of kinetics, sensitivity and affinity of label-free electrochemical 

immunosensor. 

Aaron Fairchild 1,2 , Ugur Demirok 2,3 , Jeffrey La Belle 1,2 


2 Biodesign Institute, Arizona State University 

3 Chemical Engineering Department, Arizona State University 

A printed circuit board (PCB) based Electrochemical Impedance Spectroscopy (EIS) 

immunosensor quantifying the cytokine IL-12 in physiologically relevant ranges has been 

described previously (La Belle et al 2007). Here, the sensor is deployed for multiplexing, 

multimarker detection of cytokines. These markers could be useful in research such as the 

development of point of care technologies for disease including cancer, Multiple Sclerosis and 

pathogenic infection. This arrangement is characterized for individualized optimal detection 

frequency for each cytokine with an aim towards time-based EIS on a sensor array. On-sensor 

antibody-antigen affinity is determined via fluorescent imaging then correlate to the impedance 

over time measurement. Finally, the limit of detection for each cytokine is determined and 

compared with commercial immunoassays. The goal of this work is to develop a rapid, 

reproducible and scalable sensor platform for screening of proteomic markers of disease. 


Metal nanowrinkles and nanopetals for surface enhanced sensing in microfluidic devices 

Chi-Cheng Fu, 1 Maureen Long, 1 Anthony Grimes, 1 Christopher G.L. Ferri, 2 Brent D. Rich, 1 

Somnath Ghosh, 2 Ajay Gopinathan, Sayantini Ghosh, 2 Luke P. Lee 3 and Michelle Khine 1 



3 Department of Bioengineering, University of California, Berkeley 

A simple two-step (metal deposition and subsequent heating) approach to fabricate 

controllable biaxial and uniaxial nanowrinkles and nanopetals based on shape memory polymer 

(pre-stressed polystyrene) sheets is presented. Wavelengths of wrinkles and size of petals can 

be controlled by varying thickness of deposited metal. We demonstrate utility of these 

nanostructures with ready integration into microchannels and effectiveness in surface enhanced 

sensing. 

Metal wrinkles, thin films of metal on polymer substrates, have promise for a variety of 

applications. Previous demonstrations of metal wrinkles exhibited relatively large wrinkle 

wavelengths, and the process requires a microfabricated mold and several hours to create. 

Here, we present a novel fabrication based on Shrinky-Dinks technique. For biaxial wrinkles, 

after sputtering a nanometer thickness of gold on a Shrinky-Dinks sheet, heating induces the 

substrate to retract and causes the stiffer, non-shrinkable metal film to buckle. For uniaxial 

wrinkles, before heating two short-edges of a gold-coated sheet are clamped by clips to make it 

only can retract in the other direction. Both bi- and uni-axial wrinkles can be controllably tuned 

from 300nm to 800nm by adjusting the thickness of deposited gold. To create nanopetals, 

bimetallic wrinkles (with 40nm thickness of silver and gold films) are fabricated. Wrinkling 

induced cracks make it possible to fabricate both bi-and uniaxial nanopetals. 

To widen applications, these metal nanostructure are integrated into microchannel and 

demonstrated as substrates for surface enhanced sensing. A significant enhancement on 

fluorescence intensity, together with the high throughput of lab-on-chip technique, makes these 

novel materials promising low-cost substrates for ultra-sensitive and -fast detection for 

biomedical applications. In addition, such nanoscale features, along with ease of surface 

functionalization, render the gold-wrinkle a potential useful substrate for studying cell membrane 

dynamics 


Engineering dynamic surfaces of single molecule DNA structures 

Eric Josephs 1 , Jingru Shao 2 , Janice Lianne Cosio 2 , Tao Ye 2 



DNA is generally thought of solely as a biological information carrier, but precise control 

of its topology has allowed for the engineering of DNA assemblies as structurally well-defined 

tools for cell biology. Chemical patterning of these nanotechnologies would integrate them as 

active components on surfaces and allow for the creation of dynamic substrates with 

unprecedented chemical, spatial, and temporal control of the cell-surface interface. Here we 

report our nanometer-resolution patterning, observation, and manipulation of single DNA 

molecules on a chemically well-defined surface by combining electrochemical atomic force 

microscopy (EC-AFM) and nanolithography. We can control DNA location and density over 

micrometer areas by replacing select nanometer-scale regions in a neutral surface monolayer 

with a layer of single, negatively-charged DNA molecules that are covalently linked to the gold 

substrate and diluted with surface-bound, positively-charged molecules. We demonstrate 

electrochemical switching of the strong resulting surface confinement of the chemisorbed DNA. 

The versatility and availability of DNA and its ability to hybridize on surfaces have allowed for 

our patterning of a variety of DNA forms, from flexible single-stranded DNA to catalytic 

DNAzymes to longer strands suitable for in situ folding of large-scale, ‗origami‘ structures. 

These results suggest that we can combine lithographic techniques with compatible ‗bottom-up' 

molecular self-assembly to create complex and dynamic biotechnological surfaces with control 

over multiple, biologically-relevant length-scales. 


On-Cue Detachment of Cell-Containing Heparin Hydrogels from a Conductive Substrate 

Mihye Kim 1 , Ji Youn Lee 2 , Sunny Shah 2 , Alexander Revzin 2 and Giyoong Tae 1 

1 Research Center for Biomolecular Nanotechnology and Department of Materials Science and 

Engineering, Gwangju Institute of Science and Technology (GIST) 


We developed a novel method of controlling the detachment of a bioactive, heparinbased 

hydrogels from optically transparent indium tin oxide (ITO) electrode surfaces. The 

hydrogel elements, patterned on individually addressable ITO electrodes, could be detached 

with both spatial and temporal control by applying reductive potential to the desired electrode. 

First, micropattern of ITO electrodes was fabricated on glass substrates by using 

photolithography, and the surface of ITO electrodes was further modified with vinylfunctionalized 

silane. Then, heparin-based hydrogels, which are crosslinked by a Michael-type 

addition reaction between thiolated heparin and diacrylated poly (ethylene glycol), were formed 

on the micropatterned ITO using a PDMS stencil. Vinyl groups on the ITO pattern enabled a 

stable binding of the hydrogel on ITO surface. Application of a reductive potential (-1.8 V) 

resulted in detaching heparin-based hydrogels from the microelectrodes. Thus, the specific 

location and the time point of detachment of hydrogel from micropattern could be modulated by 

an electrical signal. Effective and complete removal of hydrogel from ITO electrodes was 

verified by optical microscopy and scanning electron microscopy (SEM), as well as cyclic 

voltammetry. In addition, this electrochemical release method was used to detach heparin 

hydrogels with encapsulated cells and was found to cause minimal damage to the cells. 

Therefore, the present approach of controlling detachment of cell-containing hydrogel structures 

represents a novel means of sampling and sorting of cells from a complex cell culture substrate. 


Frequency Domain Analysis of an Artificial Reflex Device Derived from Response 

Characteristics of a Wireless Accelerometer Reflex Quantification System 

R. C. Lemoyne 1 , C. Coroian 2 , T. Mastroianni 3 , W. S. Grundfest 1 

1 Department of Biomedical Engineering IDP, 

2 David Geffen School of Medicine, UCLA, Los Angeles, CA; 

3 Cognition Engineering, Pittsburgh, PA 

The deep tendon reflex is a fundamental aspect of the neurological examination. Reflex 

response is a particular parameter for the deep tendon evaluation, which can augment the 

classification of recovery from central nervous system trauma. For instance, the recovery status 

for traumatic brain injury and spinal cord trauma can be assessed with tendon reflex evaluation. 

Other neurodegenerative diseases, such as Parkinson‘s disease and Multiple Sclerosis, can be 

assessed with respect to tendon reflex examination. Essential to the association between 

central nervous system trauma and tendon reflex is the descending supraspinal influence to the 

modulation of the reflex, which subsequent to central nervous system trauma can be perturbed 

from nominal functionality. Response can be quantified through the incorporation of ordinal 

scales. The NINDS Myotatic Reflex Scale is widely used. The capacity of such ordinal scales 

to provide accurate reflex quantification is a subject of dispute. The ordinal scales lack the 

capacity to characterize temporal data of the reflex response. A device incorporating a potential 

energy derived reflex input, with a wireless MEMS accelerometer to quantify reflex response is 

tested and evaluated as an advance relative to qualitative evaluation based on the existing 

ordinal scales. Testing and evaluation of the wireless reflex quantification system is conducted 

using an artificial reflex device, which lacks the inherent variability of the neurological reflex 

loop. Previous test and evaluation of the quantified wireless reflex system has demonstrated 

the capacity to evaluate the extreme bounds of the reflex response acceleration waveform. 

Further testing and evaluation is extended into the evaluation of the frequency domain of the 

reflex response acceleration waveform. Initial evaluation indicates that the analysis of the 

frequency domain could provide further insight and classification as to the status of a trauma to 

the central nervous system. 


Do-It-Yourself Three-Dimensional Microfabrication: Direct Projection-Lithography On 

Dry-Film Photoresist 

Siwei Zhao, Hailin Cong, Tingrui Pan 

Department of Biomedical Engineering, University of California, Davis, CA 

Benefiting from modern microfabrication techniques, the emerging miniature lab-on-achip 

systems for biological and chemical applications have drawn increasing attention over the 

past years 1, 2 . Recently, numerous rapid prototyping techniques for fabricating lab-on-a-chip 

devices have been explored 3, 4 , among which soft lithography demonstrates the superior 

potential to reduce multiple complications of the cleanroom-based fabrication 5 . Although these 

techniques greatly simplify the existing microfabrication procedures, none of them offers a 

combinational solution of flexible pattern design and transfer, high feature resolution, multilayer 

alignment and packaging in a self-sustaining process. Therefore, in this abstract, we present 

the first completely out-of-cleanroom micromachining technique of three-dimensional multilayer 

microstructures with a 10 µm resolution, named as Direct Projection on Dry-film Photoresist 

(DP 2 ) 6 . The photolithography setup employs a DLP projector, a camera lens and a digital 

microscope. The projector serves as both the mask-generation tool and photoexposure unit. 

The camera lens is in place of the original projector lens, which provides a tunable magnification 

from the DLP chip to projection plane. An easy-processing dry-film photoresist, a negative-tone 

photosensitive film for PCB, is utilized as both the photopatternable layer as well as the 

structural film to construct three-dimensional microfluidic chips because of its superb 

mechanical and biological properties 7, 8 . Moreover, the alignment between patterned dry-film 

layers has been successfully addressed by a novel software alignment scheme with 5 µm 

precision. The digital microscope is to oversee the projected image and then its position is 

adjusted according to the alignment mark in the layout software directly instead of using any 

mechanical motion stage. The plasma-assisted thermal bonding between different layers of dry 

film offers an easy implementation for suspended multilayer microstructures. Development of a 

complex microfluidic chip from computer layout can thus be accomplished within an hour in a 

regular chemical or biological lab environment using this approach. 

1. G. M. Whitesides, Nature, 2006, 442, 368-373. 

2. D. J. Beebe, G. A. Mensing and G. M. Walker, Annual Review of Biomedical 

Engineering, 2002, 4, 261-286. 

3. H. C. W. Wang, Z. Qiu, S. Zhao, H. Zhu, A. Revzin, and T. Pan, in Hilton Head 2008, 

130 Shipyard Drive, Hilton Head Island, SC 29928, 2008. 

4. W. Wang, S. Zhao and T. Pan, Lab on a Chip, 2009, DOI: 10.1039/b816287e. 

5. Y. N. Xia and G. M. Whitesides, Angewandte Chemie-International Edition, 1998, 37, 

551-575. 

6. S. Zhao, H. Cong and T. Pan, Lab on a Chip, 2009, DOI: 10.1039/b817925e. 

7. P. Vulto, N. Glade, L. Altomare, J. Bablet, L. Del Tin, G. Medoro, I. Chartier, N. 

Manaresi, M. Tartagni and R. Guerrieri, Lab on a Chip, 2005, 5, 158-162. 

8. L. C. Adarsh D. Radadia, Hae-Kwon Jeong, Mark A. Shannon, and Richard I. Masel, in 

IEEE 20th International Conference on Micro Electro Mechanical Systems, Kobe, Japan, 

2007. 


Investigations into the Angiogenic Potential of Prostrate Tumor Stem Cells 

Jane Frimodig 1 , Hongwei Li 2 , Jianqun Han 2 , Rita Finones 1 , Laura Restrepo 4 , Martin Haas 3 , 

Ruijuan Xiu 2 , David Gough 5 

1 Department of Materials Science and Engineering, University of California San Diego 

2 Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical 

College 

3 Department of Biology, University of California San Diego 

4 Department of Bioengineering, Antioquia School of Engineering, Columbia 

5 

Department of Bioengineering, University of California San Diego 

One in every six men in the United States will get prostate cancer in his lifetime; one in 

every 34 men will die of metastatic prostate cancer (American Cancer Society). There is 

currently no successful therapy available for prostate cancer that has progressed to the 

androgen-deprivation-resistant metastatic stage. It is believed that after androgen-deprivation 

ablation of the bulk of differentiated cells that make up the tumor, the hormone-deprivation 

resistant tumor regrows from a subpopulation of prostate epithelial cells that do not have 

androgen receptors. The role of these prostate tumor stem cells (PrTuSC) in neovascularization 

is of primary interest, due to the direct correlation of angiogenesis with metastasis. However, the 

cells are difficult to study because they senesce in culture. To overcome this problem, PrTuSC 

isolated from early human prostate tumors were immortalized. In vitro analyses examined the 

angiogenic potential of the PrTuSC cells. These included an angiogenic antibody array assay of 

medium conditioned by the cells to discover which angiogenic proteins they expressed. Proteins 

expressed at high levels in vitro were Tissue Inhibitor of Metalloproteinases (TIMP-1) and 

Interleukin 8 (Il-8). Next, the functional angiogenic properties of these proteins were verified by a 

migration assay. ELISA was done to quantify protein levels. Since hypoxia is known to promote 

angiogenesis in tumors, cells were cultured in hypoxia and normoxia and the expression of 

TIMP-1 and Il-8 under these conditions was compared. Development of an in vivo methodology 

to study paracrine effects of PrTuSC on neovascularization has been undertaken. This 

methodology entails encapsulation of the PrTuSC in alginate disks, followed by implantation in 

the dorsal skin-fold window chamber of nude mice. 


Directing Hepatic Differentiation of Embryonic Stem Cells With Protein-Microarray-Based 

Co-Cultures 

Ji Youn Lee, Nazgul Tuleuova, Caroline N. Jones, Alexander Revzin 


Embryonic stem cells hold considerable promise in tissue engineering and regenerative 

medicine as a source of tissue-specific cells. However, realizing this promise requires novel 

methods for guiding lineage-specific differentiation of stem cells. In this study, we developed a 

micropatterned co-culture platform for stimulating hepatic differentiation of mouse embryonic 

stem cells (mESCs). Studies of mESC and hepatic cell adhesion preferences revealed that 

mESC required fibronectin for attachment while hepatic cells (HepG2) preferred collagen (I) 

substrate and did not adhere to fibronectin. Printing columns of collagen (I) and fibronectin spots 

(300 or 500 μm diameter) followed by sequential seeding of the two cell types allowed to 

position clusters of mESCs adjacent to groups of hepatic cells within the same microarray. 

These micropatterned co-cultures were maintained for up to 2 weeks in differentiation media 

supplemented with insulin and dexamethasone. To examine the differentiation, mESCs were 

selectively extracted from the co-culture using laser microdissection and analyzed using realtime 

RT-PCR. These analyses revealed that mESCs co-cultured with HepG2 cells showed a 

decrease in pluripotency gene expression concomitant with upregulation of endodermal genes. 

In addition, the co-culture format induced a significant increase in the expression of liver genes 

compared to mESCs cultured alone. In conclusion, micropatterned co-cultures of mESCs and 

hepatic cells showed a significant promise in driving stem cell differentiation towards hepatic 

phenotype. In the future, this cell culture platform will be further enhanced to enable efficient 

conversion of mouse and human ESCs to hepatocytes. 


Synergistic Effects of Biomineralization and Inductive Signals on Osteogenic 

Differentiation of Human Mesenchymal Stem Cells 

S. Lauren Miller 1 , Erin M. Case 1 , Hillary E. Davis 1,2 , J. Kent Leach 1 


2 School of Medicine, University of California, Davis 

The repair of slow-healing fractures and non-unions requires biomaterials-based 

interventions to facilitate bone regeneration. The addition of bone-like mineral (apatite) can 

increase the osteoconductivity of synthetic polymers, yet previous data by our group and others 

suggest this mineral can impair osteogenic differentiation. Growth factors, such as bone 

morphogenic proteins (BMPs), induce differentiation of progenitor cells. However, the effects of 

BMP-2 in combination with apatite-coated scaffolds on progenitor differentiation are unknown. 

Three-dimensional poly(lactide-co-glycolide) scaffolds were fabricated using a gas 

foaming/particulate leaching method. Apatite coating was accomplished by soaking the 

scaffolds in modified simulated body fluid (mSBF). Nonmineralized scaffolds served as our 

control material. Scaffolds were then seeded with human mesenchymal stem cells (hMSC) and 

cultured in media containing osteogenic supplements in the presence or absence of BMP-2 

(100 ng/mL) for 4 weeks. Osteogenic differentiation was determined by quantifying alkaline 

phosphatase (ALP) activity, DNA content, and cell-secreted calcium. As expected, hMSC on 

nonmineralized scaffolds yielded increased ALP activity in the presence of BMP-2, yet cells on 

mineralized scaffolds exhibited similar ALP activity in the presence or absence of the growth 

factor. Furthermore, calcium secretion was impaired for hMSC on mineralized scaffolds with 

BMP-2 compared to osteogenic media alone. These results demonstrate that the presence of 

multiple signals, both substrate and chemically-mediated, can have varied effects on osteogenic 

differentiation of human progenitor cell populations. These data necessitate the need for further 

investigation of the role of apatite in current bone regeneration strategies. 


Age Related Dynamics of Committed T cell Progenitors in Mice 

T. Harshani Peiris, Jesús Ciriza, Mufadhal Al-Kulhani, Tanya Carroll, Marcos E. García-Ojeda. 


Immunosenescence is the reduced ability of the body to mediate an adaptive immune 

response. Multiple factors contribute to immunosenescence, including age-related changes in 

hematopoietic stem cell (HSC) phenotype, its niche, and the tissues responsible for lymphocyte 

development, such as the bone marrow and the thymus. Therefore, understanding lymphocyte 

development in the aged is fundamental to enhance the immune response capacity of the aging 

immune system. Here, we investigate the age-related dynamics of committed T cell progenitors 

(CTP), an HSC-derived bone marrow population capable of generating functional T cells via 

both thymic and extrathymic pathways. Specifically, we will examine the CTP‘s frequency and 

absolute numbers in the bone marrow of young (1 month) and old (12 and 18 months) C57BL/6 

mice using flow cytometry. Moreover, we will compare the capability of young and aged CTP to 

generate T cells in vitro and in vivo following transplantation into irradiated young and old hosts. 

Understanding the biology of CTP in relationship to aging could have important clinical 

applications in the treatment of diseases related to immune deficiencies and cancer by 

hematopoietic stem cell transplantation, as CTP derived T cells protect against viral infections 

without inducing graft vs. host disease. This work could pave the way to studies related to 

human CTP populations and their therapeutic potential. 


Honeywell Microchip for Efficient and Controlled Generation of Embryoid Bodies for 

Cardiomyocyte Differentiation 

Silin Sa 1,2 , Diep Nuyenen 1,2 , Michelle Khine 1,2 , and Kara McCloskey 1,2 


2 Graduate Program in Biological Engineering and Small-scale Technologies, University of 


Many cell types have been shown to engraft in areas of myocardial damage and partially 

repair cardiac function, suggesting cardiac/stem cell transplantation to be a promising treatment 

for cardiomyopathy. However, full cardiac tissue regeneration will only become possible when 

technologies allow the generation of a sustainable, purified source of mature functional cardiac 

progenitors. Human embryonic stem cells (hESC) are an exciting potential cell source for 

cardiac repair due their proliferative potential, pluripotency, and scale-up capabilities. 

Conventional EB formation approaches for initial induction of hESC use hanging drops 

that often results in inhomogeneous environments that result in diverse EB sizes. In order to 

address this problem, we employ a new micro-technology that captures hESC into microwells 

for controlling the EB sizes. In these chips, our hESC generate embryoid bodies up to 300 um 

in diameter. After plating on gelatin, approximately 60% of these EB will express beta myosin 

heavy chain by day 13 increasing to 85% by day 15, and 30% will begin to spontaneously beat 

by day 15. 


Adhesion Molecules Direct Hematopoietic and Endothelial Commitment of Murine 

Embryonic Stem Cells 

Basha Stankovich, Esmeralda Aguayo, Fatima Barragan, Aniket Sharma, Maria Pallavicini 


Embryonic stem cells (ESC) have therapeutic potential due to their ability to differentiate 

into any cell type. Understanding the mechanism driving differentiation along a specific lineage 

is important in a tissue engineering platform. Mouse ESC collect information from their 

environment and make cell fate decisions based on intrinsic and extrinsic factors, including cellcell 

contact or cell-environment interactions. However, the molecular mechanisms underlying 

modulation of ESC fate decisions by cell-environmental interactions are incompletely 

understood. Adhesion molecules influence proliferation and differentiation in multiple 

developing and adult tissues. We hypothesize that adhesion molecule interactions have a 

critical role in guiding ESC commitment to hematopoietic and endothelial lineages. Quantitative 

RT-PCR was used to establish the relative levels of adhesion molecule expression during EB 

formation and early hematopoietic differentiation. Adhesion molecules differentially expressed 

under these conditions were primarily representative of adherens junction, tight junction and gap 

junction pathways. Differential regulation of molecules in the junction pathways during 

hematopoietic and endothelial development supports the hypothesis that cell-cell interactions 

are important for ESC fate decisions. Stable ESC lines constitutively knocking down expression 

of E-cadherin, Connexin-43, Claudin-4, ZO-1 and ZO-2 were generated using lentiviral 

transductions with shRNA constructs. Expression of CD45, an extracellular protein found on 

most hematopoietic cells, is decreased in cell lines with decreased expression in each of these 

genes. A parallel increase in endothelial differentiation is observed in these knockdown lines as 

indicated by VE-cadherin expression and functional assays of endothelial sprouting EB. 

Functional and molecular assays are ongoing to determine the consequence of manipulation of 

adhesion molecule expression levels on transitional states of hematopoietic and endothelial 

differentiation. 


The in vitro response of human adipose-derived stem cells to biomimetic apatite 

microstructure 

Eric Tsang 1 , Chris Arakawa 1 , Benjamin Wu 1 , Patricia Zuk 2 

1 Department of Bioengineering, University of California, Los Angeles 

2 Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles 

Biomimetic apatites and other calcium phosphate materials have been shown to play an 

important role in bone tissue engineering. Coating substrates with apatite by immersion in 

solutions that have similar ionic composition as blood plasma, or simulated body fluid (SBF), 

may promote osteogenic activity by improving the in vivo bone-bonding ability of non-bioactive 

materials, as well as by enhancing the proliferation and differentiation of human osteoblasts, 

murine osteoblasts, and mesenchymal stem cells. The effect of apatite coatings on human 

adipose-derived stem cells (hASCs), however, is less well understood. Here, various 

biomimetic apatite microstructure coatings were created by altering simulated body fluid 

formulation to evaluate in vitro the effect of apatite architecture on the viability, proliferation, and 

differentiation of hASCs. Furthermore, the ability of apatite to manipulate cell signal 

transduction pathways for promoting osteogenesis in hASCs, such as the MAPK signaling 

pathway, was investigated. Tissue culture treated polystyrene culture dishes were immersed in 

various SBF solutions to create uniform coatings of amorphous/nano-crystalline precursor 

apatite spheres, polycrystalline small plate-like apatite, or single crystalline large plate-like 

apatite. Human ASCs were cultured on the apatite-coated substrates and were examined for 

osteogenic differentiation after 1, 3, 7, 14, 21, 28 and 35 days by real-time PCR, ELISA, 

Western blot analysis and by assessment of alkaline phosphatase activity. Similar methods 

were used to determine the ability of apatite to influence activity of ERK signaling in the MAPK 

transduction pathway. Preliminary data suggests that ALP activity is augmented in hASCs 

cultured on large plate-like apatite coatings compared to non-coated TCPS controls. 

Additionally, examination of ERK pathway activity shows trends of decreasing ERK and MEK 

phosphorylation in hASCs cultured on apatite in osteogenic media versus hASCs cultured on 

non-coated TCPS by 21 days in culture. 


Imaging of regulable expression of matriptase, a marker for cancer progression in a 

mouse model for human breast cancer with PET 

Julia C. Choi 1 , Sven H. Hausner 1 , M. Karen J. Gagnon 1 , David L. Kukis 2 , 

Chen-Yong Lin 3 , Michael D. Johnson 4 , Julie L. Sutcliffe 1,3 


2 Center for Molecular and Genomic Imaging, University of California, Davis 

3 School of Medicine, University of Maryland 

4 Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University 

The serine protease matriptase has been implicated in many epithelial cancers. We 

propose to develop radioimmunoconjugates to image in vivo expression of both the activated 

and total states of matriptase using microPET. The radioimmunoconjugates 64 Cu-TETA-M69 

(against activated matriptase) and 64 Cu-TETA-M32 (against total matriptase) were synthesized 

and evaluated in vivo. Briefly, female nude mice were implanted with a tetracycline (dox)- 

regulable cell line (3E6 cells), and fed dox chow for matriptase-positive expressing tumors or 

standard chow for control tumors. Mice were injected with 64 Cu-TETA-M69 or 64 Cu-TETA-M32 

(50-150 μCi, 20 μg) and imaged using microPET at 24, 48, 72 and 96h; corresponding 

biodistribution studies were also performed. Biodistribution and image values were evaluated 

for statistical significance with general linear model testing. 

64 Cu-labeled 

radioimmunoconjugates were >95% radiochemically pure and immunoreactive. PET images 

showed specific accumulation of both immunoconjugates in target positive tumors. 

Biodistribution revealed a two-fold increase in tumor activity from dox-fed mice over those fed 

normal chow for 64 Cu-TETA-M32 at 96 h, with a more modest uptake for 64 Cu-TETA-M69. We 

have developed two radioimmunoconjugates for imaging activated matriptase in vivo. We have 

demonstrated that tet-regulable matriptase expression can be monitored in vivo using PET. 

While faster tumor targeting was observed for the total state, activated matriptase is the more 

relevant target for future clinical development. We observed an upward trend of specific tumor 

uptake at 96h; longer-lived isotopes may be required for improved detection of activated 

matriptase. This approach has the potential for imaging metastasis, the primary cause of 

mortality in breast cancer patients. 


Honeycomb Microwell Assay Platform for Generation and Culture of Embryoid Bodies 

from Human Embryonic Stem Cells 

Diep Nguyen 1 , Guangxin Xiang 1 , Jon Pegan 2 , Jason S. Park 3 , Kenta Nakamura 3 , Jennifer 

Manilay 4 , Bruce R. Conklin 3 Michelle Khine 1, 2 

1 Biological Engineering & Small-scale Technologies, School of Engineering, University of 


2 School of Engineering, University of California, Merced, 

3 Department of Medicine, University of California, San Francisco, 

4 School of Natural Sciences, University of California, Merced. 

Embryoid body (EB) formation and lineage commitment closely recapitulates early 

embryonic development and is greatly affected by cell-cell interactions. Studies have shown the 

preferential commitment of EBs towards specific lineages based on the initial size of cell 

aggregates [1]. Thus the ability to control the initial number of cell aggregates in addition to 

providing a hydrophobic substrate are crucial parameters for inducing uniform EB formation [2]. 

Here we report and ultra-rapid fabrication method utilizing a laser-jet printer to generate closely 

arrayed microwells (honeycomb microwells) of tunable sizes for the induction of uniform 

embryoid body from single cell suspensions of human embryonic stem cells. Through heatinduced 

shrinking of this pre-stressed polymer, high aspect micromolds are generated [3]. By 

staggering the well design and spacing the wells such as to minimize free surface area, upon 

heat-induced shrinking, the wells are pulled together forming closely packed honeycomb 

shapes. To produce the microwells, polydimethylsiloxane (PDMS) can then be molded on to 

the micromolds. Notably, we achieve rounded bottom wells not easily achievable with standard 

microfabrication methods but critical to achieve spherical EBs. Through the curvature of the 

microwells, single cell hESCs are forced into cell aggregates, facilitating the rapid formation of 

uniform EBs. In addition, the microwell arrayed system can be adapted to most standard well 

plates and is easily integrated into commercial liquid handling systems, thus potentially 

providing an inexpensive high throughput drug screening platform. 


Steric Stabilization of Liposomes for Drug Delivery: Impact Membrane Fluidity and 

Diffusion 

Raquel Orozco-Alcaraz and Tonya Kuhl 

Department of Chemical Engineering and Materials Science, University of California, Davis 

The interaction between bilayers coated with PEG polymers is important for drug 

delivery applications as PEG functionalized bilayers are commonly used to extend the 

circulation time of liposomes. Here we investigate the impact of liposome phase state on the 

interaction forces using the Surface Force Apparatus. The force-distance profiles show the 

presence of electrostatic and steric repulsion due to the PEG chains and negatively charged 

PEG-lipid. Similar behavior has been observed with solid phase bilayers containing PEG-lipid. 

The much greater lateral diffusivity in the fluid phase relative to gel phase, allows exclusion of 

the PEG-lipid upon compression and may be used to achieve better liposome targeting. 

However a quantitative comparison between fluid and gel phases demonstrates a reduced rate 

of diffusion for PEG functionalized lipids. These findings suggest that the reduced diffusion of 

PEG-lipids results from lateral friction and entanglements between the polymer chains in 

restricted geometries and provides new information to better tailor drug delivery vehicles. 


Controlling supramolecular architecture of poly(glutamyl-glutamate) Paclitaxel 

nanoparticles by selective hydrophilic/hydrophobic patterning: 

A coarse-grained modeling study 

Lili X. Peng 1 , Anthony Ivetac 2 , Sang Van 3 , Lei Yu 3 , J. Andrew McCammon 2 , and David A. 

Gough 1 


2 Department of Chemistry and Biochemistry, University of California, San Diego 

3 Nitto Denko Technical Corporation (Oceanside, CA) 

Polymers are of particular interest as drug carriers due to their ability of targeting drugs 

to tumors while simultaneously decreasing drug exposure to normal tissues. The classical 

method of designing polymer-drug conjugates invokes trial-and-error testing of chemical 

substances on animals and subsequently matching apparent effects to treatments. While 

effective, this procedure can be time-consuming and expensive. In our study, we use an ab 

initio approach to elucidate physicochemical properties of polymer-drug therapeutics that cannot 

as readily determined by traditional experimental methods: bottom-up atomistic-to-mesoscale 

modeling. 

Our polymeric nanoparticle is poly-L-glutamyl-glutamate (PGG) covalently bound to 

Paclitaxel, a widely-used yet hydrophobic anticancer therapeutic. Physicochemical properties of 

polymer-drug conjugates that have been shown to potentially affect the delivery and targeting of 

drugs to tumors are particle size and shape. The size and shape of polymer-drug conjugates 

have been shown to affect their abilities of adhering to tumor endothelium, being taken up by 

tumor cells, and diffusing through fenestrations of tumor vasculature. We hypothesize that an 

intricate balance of hydrophobic vs. hydrophilic molecules of an amphiphilic nanoparticle 

ultimately determines its supramolecular morphology. Thus, we have developed all-atom 

models of PGG Paclitaxel varying in the mass fraction of Paclitaxels vs. PGG (f phob = 0.18, 0.24, 

and 0.37) and spatial positioning of Paclitaxels on PGG (even, random, clusters, middle, side, 

ends). Atomistic MD simulations were run on the PGG Paclitaxel systems until they reached 

equilibrium. Coarse-grained parameterization was accomplished by using extracting the target 

observables, intramolecular bond distances and angles, according to the MARTINI force field 

and employing the Boltzmann inversion method. Using GROMACS, simulations were then run 

in explicit water in 310 K until self-assembly of PGG Paclitaxels into micelles were observed. 

Finally, to validate our model, we use dynamic light scattering and transmission electron 

microscopy to confirm the size and morphology of PGG Paclitaxel. 


Microfluidic Solvent Extraction Method for poly(lactide-co-glycolide) Particle 

Formation 

Shia-Yen Teh, Lung-Hsin Hung, Abraham P. Lee 

University of California, Irvine 

We present a novel approach for the synthesis of monodispersed poly(lactide-coglycolide) 

(PLGA) nanoparticles for therapeutic delivery using a droplet-based microfluidic 

solvent extraction platform. The solvent extraction formation process consists of two main steps: 

First, PLGA is dissolved in a water-soluble solvent and emulsified by an immiscible liquid phase 

as shown in figure 1. We use dimethyl sulfoxide (DMSO) as the solvent, and mineral oil as the 

continuous phase. Then extraction of the solvent from PLGA is accomplished by fusion of the 

PLGA/DMSO droplet with a water droplet. Due to the higher solubility of the DMSO and low 

solubility of PLGA in water, PLGA is precipitated out of solution, resulting in the production of 

nanoparticles. Selection of the water-soluble solvent is key, since the use of a strongly watersoluble 

liquid is necessary to properly precipitate out and form the PLGA particles. We chose 

DMSO because it dissolves PLGA well, but has a higher affinity for water than that of PLGA. 

After solvent removal, the nanoparticles are collected and the oil is removed by centrifuge. It is 

advantageous to use droplet microfluidics to perform solvent extraction since the small reaction 

volume enables precise control and high reproducibility of the microenvironment. This in turn 

produces large numbers of monodispersed particles. Determination of particle size was done 

with dynamic light scattering (DLS) and image analysis to show less than little variation in 

particle size. Sizes of the PLGA microspheres were controlled by the PLGA concentration in 

solvent and by the relative flowrates of oil and aqueous phases in the system to achieve 50- 

1000nm particles. A penetration imaging assay will be performed to determine the depth of 

diffusion of a model drug molecule fluorescein, out of the PLGA nanoparticles into corneal 

tissue. With the ability to prepare high quality, monodisperse, biodegradable particles, our 

method has great potential to benefit drug delivery applications. 

Figure 1. Schematic of solvent extraction platform. Water and 

PLGA/DMSO droplets are formed by T-junction and fused to 

allow solvent extraction 

Figure 2 Solvent extraction sequence. a) water (upper channel) and 

PLGA/DMSO (lower channel) droplets are formed, b) the two droplets 

merge in the fusion chamber, c) droplets fuse to spontaneously form 

PLGA particles, d) sequence is repeated again 


Engineering Transferrin-Diphtheria Toxin Conjugates for the Treatment of Glioblastoma 

Multiforme 

Dennis J. Yoon 1 , Byron H. Kwan 1 , Felix C. Chao 1 , 

Anne B. Mason 2 and Daniel T. Kamei 1 

1 Department of Bioengineering, University of California, Los Angeles 

2 Department of Biochemistry, University of Vermont College of Medicine 

Glioblastoma multiforme (GBM) is a highly aggressive form of primary brain tumors with 

a median survival rate less than a year post-diagnosis. To develop more effective treatments 

for GBM, ligands, such as transferrin (Tf), for receptors naturally overexpressed in cancer cells 

have been utilized as targeting moieties for cancer therapeutics, such as diphtheria toxin (DT). 

Though Tf-DT conjugates have shown promise, the short association time of Tf with cancer 

cells can limit its drug-carrier efficacy. Therefore, we have developed Tf mutants using 

mathematical modeling and site-directed mutagenesis with greater cellular association times 

and have shown that DT conjugates of these Tf mutants exhibit a greater cytotoxicity against 

HeLa cells than native Tf-DT. Additionally, we have applied our mutant Tf-DT conjugates to the 

treatment of GBM by performing in vitro cytotoxicity experiments on U87 and U251 human 

glioma cells. Results have shown a significant increase in cytotoxicity with our mutant Tf-DT 

conjugates compared to the native counterpart. We also investigated the mechanism of our Tf- 

DT conjugate‘s mode of action by performing a protein synthesis inhibition assay. 


Microneedle Drug Delivery System for Skin Diseases 

Kevin Zhang, Benjamin Wu. 

Biomedical Engineering IDP, University of California, Los Angeles 

Current methods for treating many skin diseases rely on passive diffusion of topically 

applied drugs on the skin surface. The stratum corneum layer, however, provides an efficient 

physical barrier to such technique due to the lack of vasculatures and innervations to carry 

drugs across the skin into the blood stream. As a result, drugs often are required to be applied 

multiple times at high dosage to set up high concentration gradient for effective drug diffusion. 

More importantly, drug molecules must be small and lipophilic so that diffusion of such species 

is more favorable. For many skin conditions, larger drug molecules, for instance growth factors 

and enzymes, provide more effective treatments for diseases such as scleroderma and skin 

burn, but the diffusion of these drugs is significantly limited. A patch of microneedles loaded 

with desired drug molecules can be utilized to overcome the stratum corneum barrier and 

increase efficiency of drug delivery. In this study, microneedles, which are fabricated from lowmolecular-weight 

carboxymethycellulose (CMC), can be rapidly dissolved in the presence of 

water in the skin and release drug-encapsulated polycarprolactone (PCL) microspheres and 

nano-silver particles. PCL micospheres allow sustained release of drugs to maximize drug 

effectiveness while minimizing the required doses and the number of drug applications, which is 

highly desirable and convenient. The presence of nano-silver particles provides anti-microbial 

property. CMC microneedles have shown to possess high Young‘s Modulus and can 

successfully puncture the stratum corneum layer without distortion. Because of the micro-scale 

size of these microneedles, the microneedles only reach to the least innervated region of the 

skin, causing minimal or no pain. The materials used to construct the delivery system are 

chemically inert, dissolvable, and biodegradable. Therefore, such an innovative system shows 

potentials to become low cost, minimally invasive, and highly efficient drug delivery method to 

target a variety of skin conditions 


The Effects of Coil Packing Density on Cerebral Aneurysm Inflow: In Vitro Assessment 

with Particle Image Velocimetry 

Haithem Babiker 1 , L. Fernando Gonzalez 2 , Arius Elvikis 3 , Dan Collins 3 , Felipe Albuquerque 2 , 

David Frakes 1,4 


2 Barrow Neurological Institute, St. Joseph‘s Hospital and Medical Center 

3 Partnership for Research in Spatial Modeling, Arizona State University 

4 Department of Electrical Engineering, Arizona State University 

Ruptured cerebral aneurysms cause an estimated 80% of fatal subarachnoid 

hemorrhages. Over the past decade, coil embolization has emerged as the endovascular 

treatment of choice for cerebral aneurysms. Nevertheless, current understanding of posttreatment 

aneurysm inflow and recurrence is both limited and highly qualitative. We present an 

in vitro study that quantifies the relationship between coil packing density and aneurysm inflow. 

Idealized models of basilar tip aneurysms with variable neck sizes were constructed from 

transparent silicon elastomer. A blood analog solution was circulated through the models at 

steady flow rates spanning a range of physiologic conditions. Aneurysms were embolized with 

bare platinum coils. Volumetric 3D flow velocity data were acquired at the aneurysm necks 

before and after each stage of multi-coil deployments using particle image velocimetry. Results 

showed a strong correlation between increased packing density and decreased aneurysm 

inflow. Specifically, aneurysm inflow in the narrowest neck model was reduced by 41.7% at a 

packing density of 36.5% for a parent vessel flow rate of 3 ml/s. Under the same parent vessel 

flow conditions, aneurysm inflow in the widest neck model was reduced by 65.8% at a packing 

density of 28.4%. To assess inter-deployment inflow variation, one of the aneurysm models 

was coiled repeatedly with different coils of the same model and size. At identical packing 

density, an average inflow discrepancy of 6.75% was observed over 6 repeat data acquisitions. 

Overall, the relative effects of coiling on aneurysm inflow were found to be more significant at 

lower parent vessel flow rates and for wider neck aneurysms. Marginal decreases in aneurysm 

inflow were also found to be greater at higher packing densities. Our in vitro study provides 

novel quantitative evidence to support clinical findings that high packing density contributes to 

decreased aneurysm recurrence rates through more complete embolization. 


Open-Surface Microfluidics Using Photosensitive Superhydrophobic Nanocomposite 

Lingfei Hong 1, 2 , Hailin Cong 1 , Tingrui Pan 1 

1 Department of Biomedical Engineering, University of California, Davis, USA 

2 School of Instrument Science and Optoelectronic Engineering, Beihang University, Beijing, 

China 

Open-Surface microfluidics present unique opportunities to address the insurmountable 

challenges in the conventional microfluidic systems, including hydrodynamic cavitation and 

optical obstruction. In this abstract, we present the recently developed photosensitive 

superhydrophobic nanocomposite combining superhydrophobicity of polytetrafluoroethylene 

(PTFE) nanoparticles and photopatternability and transparency of SU-8 photoresist for 

microfabrication of the open-surface microfluidic devices. General adaptability and simple 

processability of the superhydrophobic nanocomposite enable its excellent applicability in opensurface 

microfluidic devices for chemical and biomedical applications. In order to power the 

device two simple passive pumping mechanics have been investigated. In the first design, we 

utilize the Laplace pressure gradient generated by the surface tension on the different 

curvatures of the inlet and outlet droplets. [1-3] Therefore, the flow rates primarily dependent on 

the curvatures/shapes of the droplets, surface tension of the fluid, as well as the geometry and 

the resistance of the photo-defined open-surface microchannels [4-5] . Alternatively, an absorption 

pumping is constructed based on absorption and swelling property of the microfabricated 

structure (i.e., hydrogel) at the outlet. In comparison with the previous surface tension pump, 

the absorption pump offers more maneuver over the pump rate and volume by control of the 

geometry and diffusion of the absorption media, and thereby, high flow rates and high pump 

volume can be implemented in the miniature device. 


Carbon Nanotubes lead to early Onset of Electrical Activity in Developing Hippocampal 

Neurons Cultured on Silicon Microelectrodes 

Massoud L Khraiche 1 , Nathan Jackson 1 , Jit Muthuswamy 1 

1 Harintgton‘s Department of Bioengineering, Arizona State University 

In this study, we test the hypothesis that increased surface roughness resulting from 

carbon nanotubes (CNTs) modification enhances neuronal adhesion and consequently 

electrical excitability of single neurons. Primary hippocampal neurons (embryonic day 18) are 

grown on CNT modified silicon microelectrode arrays (MEAs). Electrophysiology revealed 

initiation of multi-unit activity as early as 4 days after seeding compared to 7 days in control 

cultures grown on microelectrodes without CNTs. Progressive maturation of single neuronal 

action potentials as manifested by increasing peak-to-peak amplitudes and firing rate, were 

observed days 4-7 on microelectrodes with immobilized CNTs. The results overall, demonstrate 

earlier onset and significantly higher level of electrical activity in neurons seeded on CNT 

modified MEAs compared to non-modified control MEAs. We conclude that CNTs on 

microelectrodes enhance electrical excitability of single neurons in culture. 


Long-Term Oxygen Sensor Implantation in the Porcine Subcutaneous Environment 

L.S. Kumosa † , J. Lin ‡ , T. Routh ‡ , J. Lucisano ‡ , D.A. Gough †‡ 

† Biosensors Lab, Department of Bioengineering, UCSD 

‡ Glysens, Inc., San Diego, CA 

The effect of long-term implantation on metabolically active devices is of utmost 

importance for not only the success of implanted glucose sensors used in diabetic therapy, but 

also for the development of artificial tissues and encapsulated cell devices. Such devices are 

also dependent on the constant, predictable supply of metabolites from the local vasculature. 

Long-term implantation leads to the formation of a foreign body capsule whose purpose is the 

protection of the host and isolation of the foreign material from local tissue resources. While this 

encapsulation is successful in protecting tissues from invading agents, metabolite flow 

continues, albeit at greatly reduced levels. The understanding of this encapsulation process is 

critical for the design and successful implementation of active implants dependent on metabolite 

supply. 

The project goal is to utilize implantable wireless telemeters designed and manufactured by 

Glysens, Inc. to understand changes in oxygen levels of the surrounding subcutaneous tissues 

over the course of implantation in pigs. This is performed in three distinct, yet interrelated parts, 

namely: the analysis of oxygen signals collected from the long-term implantation of telemeters, 

the histological analysis of serial tissue samples collected from regions adjacent to the 

telemeters over the course of implantation, and the development of an accurate model for the 

dynamics of metabolite supply to implanted devices over the long-term. The successful 

completion of this project will lead to better understanding of the tissue changes that occur 

during the foreign body reaction and the improved design and implementation of devices that 

require constant tissue-supplied metabolites. 


A simple three-dimensional vortex micromixer 

Maureen Long 1 , Michael A. Sprague 2 , Anthony A. Grimes 1 , Brent D. Rich 1 , and Michelle 

Khine 1 



We demonstrate rapid homogenous micromixing at low Reynolds numbers in an easily 

fabricated and geometrically simple three-dimensional polystyrene vortex micromixer. 

Micromixing is critically important for miniaturized analysis systems. However, rapid and 

effective mixing at these small scales remains a persistent challenge. We compare our 

micromixer's performance against a two-dimensional square-wave design by examining its 

effectiveness in mixing solutions of dissimilar concentration as well as suspension solutions 

comprised of microparticles. Numerical simulations confirm our experimental observations and 

provide insights on the self-rotational mixing dynamics achieved with our simple geometry at low 

Reynolds numbers. This rapid, robust, and easily fabricated micromixer is amenable readily to 

large scale integration. 


Immobilization of Lactate Oxidase for Stability and High Loading in a Lactate Sensor 

Adam Strobl, Henry Tse, David Gough 


Knowledge of metabolic state is the cornerstone of treatment for diabetic patients. The 

current standard of care relies on infrequent discrete measurements of one metabolite, glucose. 

Knowledge of other important variables such as lactic acid would help form a more complete 

picture of the patient‘s metabolism. In addition, continuous sensors allow the gathering of 

dynamic information so that all metabolic excursions can be tracked and treated. Other patients 

suffering from pulmonary or cardiac impairments would also benefit from continuous lactate 

information. In comparison with continuous glucose sensors in development, lactate sensors 

have a short lifespan due to the instability of the enzyme lactate oxidase (LOx). Past results 

show a lifespan on the order of three weeks for continuous lactate sensors; this is unacceptable 

in a subcutaneous implant since frequent surgeries would be necessitated. 

Enzyme immobilization is necessary for the construction of a successful implantable 

sensor. We have characterized LOx in immobilized form in order to understand how 

immobilization affects sensor lifespan. In particular, the effect of process parameters on the 

resulting activity and stability of LOx in an enzyme-loaded membrane have been studied. A 

chemical immobilization procedure utilizing glutaraldehyde was developed and optimized to give 

maximum enzymatic yield and stability at physiological conditions. Results were analyzed 

through a reaction/diffusion model to calculate the effects of diffusion on the spectrophotometric 

assay utilized. In addition, we are developing methods for immobilization based on electrostatic 

interaction. There is evidence that this processing technique can lead to higher activity yields, 

and literature also indicates the possibility of increased stability. Finally, the loading levels and 

stabilization achieved in vitro are used to estimate the lifetime of an in vivo sensor based on a 

previously developed model. Using parameter results achieved in the lab, sensor lifetime is 

expected to be four to five months. 


A Smart Contact-Lens Sensor for Dynamic Measurement of Intraocular Flow Resistance 

Chaoqi Zhang, Tingrui Pan 


Worldwide more than 60 million people suffer from glaucoma, a leading cause of the 

irreversible blindness due to the optic nerve damage. [1-4] Although the tonometry-based 

intraocular pressure (IOP) measurement has been used as the gold standard to monitor the 

glaucoma for over a century, a new diagnostic device for early glaucoma detection is highly in 

demand, due to the indirect correlation, imprecise measurement principle, operation-sensitive 

assessment of the current tonometry. In this abstract, we proposed a new dynamic 

measurement principle to assess intraocular flow resistance, a direct indication of ocular flow 

circulation. Analogous to the circuit analysis, ocular volume is altered through a coupled 

contact-lens device while the IOP change is continuously tracked. Such a smart contact-lens 

measurement device has been fabricated using soft lithography on polymer materials. In 

addition, an artificial ocular model is constructed for evaluation and calibration of the dynamic 

measurement system. 


Postprandial up-regulation of monocyte integrin CD11c/CD18 increases firm arrest to 

vascular cell adhesion molecule-1 

R Michael Gower 1 , Anne A Knowlton 2 , Scott I Simon 1 

1 Biomedical Engineering Department, 

2 Molecular & Cellular Cardiology and Cardiovascular Division, Department of Medicine, 

3 Department of Medical Pharmacology, University of California, Davis 

Monocyte activation and migration into the arterial wall are key events in atherogenesis. 

Monocyte integrin CD11c/CD18 mediates adhesion to vascular cell adhesion molecule (VCAM)- 

1 and knocking out CD11c in hypercholesterolemic mice lowers the incidence of 

atherosclerosis. Both suggest CD11c may be an attractive therapeutic target for cardiovascular 

disease (CVD). We demonstrate that monocyte CD11c expression and function can be 

efficiently screened in whole blood. Flow cytometric analysis of fasting and postprandial blood 

samples from 37 healthy human donors revealed that a high fat meal induces a 10% increase in 

monocyte CD11c expression. Plasma triglyceride concentration significantly correlated with the 

increase in CD11c (P < 0.0001; Pearson r = 0.6419; 95% CI: 0.4013 to 0.7996). When donors 

were grouped by plasma triglyceride, those above 160 mg/dL experienced a 30% increase in 

CD11c postprandial, while those below 90 mg/dL exhibited no increase. Monocyte inflammatory 

potential following the meal was measured by recruitment to VCAM-1 in shear flow. Cover slips 

coated with recombinant VCAM-1 were incorporated into a microfluidic device and blood was 

perfused over these cover slips at a shear force of 4 dynes/cm 2 . Firmly arrested monocytes 

were enumerated by cover slip staining. The fraction of monocytes among total leukocytes 

firmly arrested on VCAM-1 increased 50% postprandial. Firm arrest could be decreased 40% 

with an antibody that inhibits CD11c or increased 55% with a CD11c agonist. We conclude that 

following a high fat meal the systemic circulation exerts pro-inflammatory effects on monocytes 

and activation can be sensitively monitored by changes in CD11c expression. Thus CD11c is a 

functional biomarker that correlates with known risk factors of CVD and is important for 

monocyte adhesion to VCAM-1. 


Engineered proteolytic antibody fragments as therapeutics for Alzheimer’s disease 

Srinath Kasturirangan 1 , Michael Sierks 2 


2 Department of Chemical Engineering, Arizona State University 

Deposition of beta-amyloid (Aβ) is considered an important early event in the 

pathogenesis of Alzheimer's Disease (AD) and reduction of Aβ levels in the brain can be a 

viable therapeutic approach. A potentially non-inflammatory approach to facilitate clearance and 

reduce toxicity is to hydrolyze Aβ at its -secretase site using single chain antibody fragments 

(scFvs). We have previously identified antibody light chain mk18 having -secretase-like 

catalytic activity producing the 1-16 and 17-40 amino acid fragments of Aβ40. To improve the 

specific activity of the recombinant antibody by affinity maturation, we constructed a yeast 

surface displayed scFv library by mutating the CDR3 heavy chain region responsible for antigen 

recognition. A biotinylated covalently reactive analog mimicking -secretase site cleavage site 

was synthesized, immobilized on streptavidin beads, and used to select scFvs with increased 

specificity for Aβ. Following bio-panning, a fluorescently labeled A substrate was used to 

further screen isolated clones for improved activity. Two clones which showed the highest 

increase in proteolytic activity compared to the parent mk18 were selected for further analysis. 

Kinetic analyses using purified soluble scFvs showed a 3- and 6-fold increase in catalytic 

activity (k cat /K M ) toward the synthetic Aβ substrate compared to the original scFv primarily due to 

an expected decrease in K M rather than an increase in k cat . Affinity maturation strategy resulted 

in highly stable scFv with improved affinity and activity towards A. These clones prevented 

aggregation of Ain-vitro as determined by atomic force microscopy (AFM) and reduced A 

induced cytotoxicity towards SHSY5Y neuroblastoma cells. The ability of the proteolytic scFv to 

cleave pre-formed Aoligomers, the predominant toxic species, as well as their capacity to 

cleave the amyloid precursor protein (APP), producing the neuroprotective sAPP fragment, are 

also being studied. These proteolytic scFvs could have potential therapeutic applications for AD 

by decreasing soluble Aβ levels in vivo. 


Sudden death from gut ischemia may result from a neurogenic shock mechanism 

Alexander Hayes Penn, Geert W. Schmid-Schönbein 


Hemorrhagic shock is a life-threatening event. Splanchnic arterial occlusion (SAO) 

followed by reperfusion is an established model for physiologic shock. Even without 

reperfusion, SAO is highly lethal. We show here that death is either associated with gradual 

drops in mean arterial blood pressure (MABP) over 80 mmHg) over 1 to 6 minutes. The rapid drop 

occurs after ~ 75-150 min of ischemia. We observed that a 10% glucose solution added to the 

lumen of the small intestine significantly decreases the onset of the fatal drop and significantly 

increases its rate of occurrence (from 29% to 63%). As gut ischemia stimulates the sympathetic 

nervous system and afferent neurons in the gut can detect hyperglycemia, our objective was to 

determine whether a total subdiaphragmatic vagotomy (TSV), could prevent the rapid drop in 

MABP by interfering with the autonomic nervous system. We found that survival time was 

increased by TSV (P

Development of FRET-Based High-Throughput Screening to Discover Small Chemical 

Inhibitors Targeting Protein-Protein Interaction in the SUMOylation Network 

Yang Song, Vipul Madahar, Yan Liu, Jiayu Liao 

Department of Bioengineering at University of California, Riverside 

Covalent modifications of proteins are general mechanisms to alter protein functions in 

most cells, especially in eukaryotic cells. SUMO (Small Ubiquitin-like MOdifier) is a well-known 

small protein family which is attached to proteins involved in diverse cellular processes by the 

catalytic enzyme cascade, E1, E2 and E3. However, the investigations of SUMOylation in 

different cellular processes are limited by the difficulties in determining the interaction between 

SUMO, SUMO E1-E3 enzymes and the substrates as well as the lethality of gene knockout 

studies given the importance roles of SUMO in vivo. Using sensitive fluorescence proteins by 

genetic labeling techniques, our lab is currently developing FRET-based methods to test the in 

vivo interactions between different proteins involved in the SUMOylation network. We are also 

developing these methods into high-throughput screening assays for novel small chemical 

inhibitor screening, which can disrupt the protein-protein interactions between SUMO and its E1, 

E2 and E3 enzymes. Once discovered, these small chemical compounds will not only serve as 

unique tools for the functional studies of SUMOylation, but also can have great potentials in the 

treatment of diseases related to the dysregulation of SUMOylation network. 


Cellular Uptake of Polyarginine-Polyleucine Block Copolymer Vesicles 

Victor Z. Sun, Zhibo Li, Timothy J. Deming, and Daniel T. Kamei 


We previously reported the preparation of vesicles composed of lysine-leucine (K 60 L 20 ) 

block copolypeptides. These vesicles were stable in an aqueous environment, and could be 

processed to different sizes. They could also be prepared in large quantities, and were found to 

be able to encapsulate water-soluble contents. These vesicles, however, were not able to cross 

the plasma membrane of cells for intracellular delivery of a payload. To engineer this added 

feature, we investigated the literature, and found that the arginine-rich HIV-1 Tat peptide 

(GRKKRRQRRRAP 59 ) and oligomers of arginine can transport molecules into cells. We 

therefore reasoned that the lysine residues in our copolypeptides could be replaced with 

arginine without disrupting their ability to form vesicles while also enabling them to enter cells. 

Subsequent experiments confirmed our hypothesis, as R 60 L 20 block copolypeptides could form 

vesicles with similar properties as the K 60 L 20 vesicles, while additionally being able to deliver 

water-soluble Texas-Red dextran into various mammalian cell lines. In the current study, we 

examined the endocytosis and intracellular trafficking pathways of the R 60 L 20 vesicles. 

Specifically, we investigated the mechanism by which the R 60 L 20 vesicles could enter cells by 

preparing 100 nm diameter FITC-labeled vesicles and incubating them with cells in the 

presence of different drugs that inhibit various endocytosis pathways. To investigate the fate of 

the R 60 L 20 polypeptide vesicles inside the cell, we performed immunofluorescence labeling of 

the endosomes and lysosomes in cells loaded with FITC-labeled R 60 L 20 vesicles. The ability of 

these vesicles to deliver bioactive therapeutic agents is also currently being tested. 


Design of an Aptamer Beacon for Real-Time Detection of Interferon-Gamma 

Nazgul Tuleuova 1,2 , Caroline N. Jones 1 , Jun Yan 1 , Erlan Ramanculov, 2 

Alexander Revzin 1 


2 National Center for Biotechnology, Astana, Kazakhstan 

Aptamers are nucleic acid ligands, either RNA or DNA, that have been selected to bind a 

huge variety of targets ranging from whole cells to metal ions. The aptamers nucleic acid 

structure ensures chemical and thermal stability of these molecules making them real rivals to 

antibodies and also allows to develop novel sensing strategies. Aptamer beacons represent 

one such sensing strategy where is an aptamer and shorter complimentary oligonucleotide 

conjugated with fluorophore-quencher pairs and where fluorescence signal changes as the 

function of hybridization/dehybridization due to the analyte binding. The goal of the present 

study was to develop an aptamer beacon for detection of interferon-gamma (IFN-) – an 

important inflammatory cytokine commonly monitored in clinical setting and basic research. For 

testing we immobilized biotinylated aptamers with different orientation (immobilization via 3‘-end 

or 5‘-end) and distance to the surface (incorporation of a spacer at the ends) onto avidin-coated 

surfaces and were examined using surface plasmon resonance (SPR) and fluorescence 

microscopy. SPR studies of IFN- - aptamer interactions revealed the equilibrium constant for 

the best scenario was 3.44 nM for immobilization via 3‘-end. In addition, SPR was employed to 

characterize interaction IFN- a double-stranded DNA construct comprised of fluorophorelabeled 

aptamer and a complementary sequence containing a quencher. These SPR studies 

revealed that cytokine binding occurred rapidly within 30 mins – pointing to the possibility of 

dynamic replacement of quencher-complementary strand with IFN- molecules. Importantly, 

these results where corroborated by fluorescence microscopy experiments where a shift in 

fluorescence intensity was observed from low fluorescence due to the quencher-complementary 

strand hybridized with fluorophore-aptamer to high fluorescence after introduction of IFN- into 

the system. This change in signal was observed in real-time and was dependent on IFN- 

concentration. This aptamer beacon had a detection limit of 10 nM which is sufficient to monitor 

physiological levels of this cytokine. In conclusion, we designed an aptamer beacon for realtime 

monitoring of IFN-. In the future, this sensing strategy will be employed to monitor in realtime 

cytokine production by the immune cells. 


Solid-Phase Peptide Synthesis of Bioinspired Electrets Based on Non-Traditional Amino 

Acids: Synthesizing oligo-ortho-anthranilic Acids for Improved Charge-Transfer 

Properties in Photovoltaic Cells 

Srigokul Upadhyayula 1,2 , Duoduo Bao 1 , David Bui 1 , Valentine I. Vullev 1 


2 Department of Biochemistry, University of California, Riverside 

As of 2008, fossil fuels account for 77.88% of energy production; while only 0.02% is 

generated using renewable energy sources (Science 2007, 315, 798-801). The cost of solar 

energy conversion technology is the main drawback in the primary widespread use of 

photovoltaic devices (Nature Materials 2006, 5, 161-164; PNAS 2006, 103, 5251-5255). 

Conversion of fossil fuels to electricity costs approximately 0.05 kWh -1 , whereas converting solar 

energy cost approximately 5 times higher (Monthly Energy Review, DOE/EIA-0035, Janary 

2009). The gap between energy generated via fossil fuels vs. photovoltaics exists solely due to 

price and can be bridged either by an increase in the efficiency of solar cells made of 

inexpensive materials, or by lowering the cost of the materials used for the fabrication of highly 

efficient photovoltaic devices. Utilizing de novo macromolecular design and engineering, we aim 

at bioinspired electrets that can mediate efficiently long-range charge transfer and at the same 

time, suppress the undesired charge recombination that is responsible for energy loss. We 

demonstrated that, similar to protein -helices, oligo-anthranilamides possess considerable 

intrinsic dipole moments making them highly promising macromolecular electrets (Ashraf et al. 

Biotech. Progress 2009, in press). Although others and we currently prepare 

oligoanthranilamides using conventional solution-phase coupling, it is highly inconvenient for 

exploring a broad range of such conjugates. Moreover, others and we have observed that 

traditional solid-phase synthetic procedures (which can be automated and conducted in parallel) 

do not yield coupling between anthranilic residues, and hence, solid-phase synthesis has never 

been used for making such conjugates. Our experimental analysis indicated that the steric 

hindrance was the principal reason for the observed failure of the ―traditional‖ approaches. 

Utilizing small-size active acid intermediates allowed us for the first time to prepare largemolecular 

weight oligoanthranilamides using automated solid-phase synthesis. We explored in 

situ and ex situ activation. We believe that these procedures for preparation of bioinspired 

macromolecular electrets can be immensely beneficial for the facile automated parallel 

synthesis of a large range of biomaterials of non-traditional amino acids. 


The Rehm-Weller Equation in View of Bioengineering 

Duoduo Bao, Antonio Contreras, and Valentine I. Vullev 

Bioengineering Department, University of California, Riverside 

Charge transfer is a key process for all redox functionalities in biological systems. The 

Rehm-Weller equation allows for etimation of the driving force of photoinduced charge-transfer 

processes. A term, based on the Born equation for solvation energy of ions, is introduced in the 

Rehm-Weller equation to correct for the differences measuring media. The Born correction term, 

however, requires a prior knowledge of the dielectric constants of the electrolyte solutions used 

for the redox measurements and the radii of the donor and acceptor molecules. Because of 

limited information for such dielectrics, the values for the dielectric constants of electrolyte 

solutions are approximated to the values of the dielectric constants of the corresponding neat 

solvents. We determined that this approximation can lead to significant errors in the calculated 

values of photoinduced charge transfer [1] , as well as to discrepancies between the measured 

and estimated charge-separation kinetics [2] . We demonstrated the use of non-linear 

extrapolation for elimination of the dielectric-constant approximation [1] . The other key 

component for estimation the kinetics and thermodynamics of charge transfer is the ionic radii of 

the donor and the acceptor. Usually, the ionic radii are estimated from to the van der Waals 

dimensions of the redox species. This estimation assumes that the charges are delocalized over 

the whole molecule, which for a range of biologically active redox species is wrong. Recently, 

we reported a discrepancy that implied that the ionic radius of acridinium is smaller than its 

molecular radius [3] . Extending our extrapolation cyclic-voltammetry methodology to non-polar 

media allowed us to determine the ionic radii of electron donors and acceptors, which are not 

necessarily their van der Waals radii. We believe that our advances will allow for improved 

characterization of biological redox process and of redox species with biological activity. 

1 Bao et al. J. Phys. Chem. A 2009, 113, 1259-1267 

2 Wan et al., J. Photochem. Biotobiol. A: Chem. 2008, 197, 364-374 

3 Hu et al., J. Phys. Chem. A 2009, 113; 3096–3107 


Ca 2+ Depletion of Sarcoplasmic Reticulum during Reperfusion after Ischemia 

Marcela Ferreiro 1 , Dmytro Kornyeyev 1 , Carlos A. Valverde 2 , Alicia Mattiazzi 2 and Ariel L. 

Escobar 2 


2 School of Medicine, Universidad Nacional de La Plata, Argentina 

One of the negative consequences of myocardial infarction is cytosolic Ca 2+ overload 

occurring shortly after the restoration of the blood flow through coronary arteries. In order to 

investigate this phenomenon we conducted ischemia-reperfusion experiments on intact mouse 

hearts. Our hypothesis was that the cytosolic Ca 2+ overload is associated with the redistribution 

of intracellular Ca 2+ from sarcoplasmic reticulum (SR) to cytosol. To address this issue, we 

performed 12 min of global no-flow ischemia followed by reperfusion in the isovolumic 

Langendorff perfused mouse heart positioned on a Pulsed Local Field Fluorescence microscope 

and loaded with fluorescent dyes (Rhod-2 or Mag-Fluo-4 to assess cytosolic or SR Ca 2+ , 

respectively) or membrane potential (di-8-ANNEPS). The results indicated there is an initial 

increase in diastolic Ca 2+ during early reperfusion that gradually returned to pre-ischemic levels. 

This increase was associated with a decrease in SR Ca 2+ content that recovered within 10 min, 

as a mirror image of the diastolic Ca 2+ profile. Additionally, experiments in which caffeine pulses 

(20 mM) were applied, confirmed that SR Ca 2+ content was greatly diminished at the onset of 

reperfusion. Moreover, both Ca 2+ release and Ca 2+ reuptake slowed down significantly during 

the ischemia and restored during reperfusion. Action potentials recorded during ischemia were 

shorter (no normal spike-and-dome morphology) probably due to the inhibition of Ca 2+ release. 

This is in agreement with the decrease in Ca 2+ content in SR during reperfusion. Interestingly, 

similar changes occurred when a pulse of caffeine was applied. The present findings indicate 

that the increase in diastolic Ca 2+ that occurs upon reperfusion is due to a SR Ca 2+ release and 

not just because of the Ca 2+ entry through the reverse NCX mode, as has been previously 

thought. Supported NIH R01-HL-084487 to AE. 


Mapping the Position of DNA Polymerase-Bound DNA Templates in a Nanopore at 5Å 

Resolution 

Daniel R. Garalde 1 , Brett Gyarfas 1 , Felix Olasagasti 2 , Seico Benner 2 , William Dunbar 1 , Kate R. 

Lieberman 2 , Mark Akeson 2 

1 Department of Computer Engineering, Baskin School of Engineering, University of California, 

Santa Cruz 

2 Department of Biomolecular Engineering, Baskin School of Engineering, University of 

California, Santa Cruz 

Nanopores have emerged as a method for single molecule analysis of DNA, RNA, and 

protein complexes formed with these polymers. In this study, we used the α-hemolysin 

nanopore to study complexes of DNA and the Klenow fragment of Escherichia coli DNA 

polymerase I (KF) or T7 DNA polymerase (T7 DNA pol). Ionic current flows through the 

nanopore as a result of an applied electrical potential and the current is obstructed when DNA is 

drawn into the nanopore by electrophoresis. A block of abasic (1‘,2‘-dideoxy) residues within a 

DNA template can be detected if the abasic residues are positioned within a restricted region of 

the nanopore because they cause less obstruction of ion flow than standard nucleotides. We 

mapped the sensitivity of the α-hemolysin nanopore to abasic residue position by designing a 

series of DNA template-primer hybrids, each with a block of three abasic residues placed at a 

different position along the template DNA. We measured ionic current blockades during 

nanopore capture of these DNA hybrids bound in complexes with either KF or T7 DNA pol. A 

single nucleotide displacement of the abasic block position could be clearly distinguished. Maps 

of ionic current as a function of the position of abasic residues for templates bound to KF or T7 

DNA pol were nearly identical, indicating with single nucleotide resolution that when captured 

atop the nanopore, both enzymes hold the DNA in a similar position 


Concentrating DNA Using Two-Phase Aqueous Micellar Systems 

Foad Mashayekhi, Aaron S. Meyer, Stacey A. Shiigi, Daniel T. Kamei 


The concentration of cancer biomarkers, such as DNA, prior to a subsequent detection 

step may facilitate the early detection of cancer, which could significantly increase chances for 

survival. In this study, the partitioning behavior of mammalian genomic DNA fragments, as well 

as oligonucleotides, were experimentally and theoretically investigated in a two-phase aqueous 

micellar system. The micellar system was generated using the nonionic surfactant Triton X-114 

and phosphate-buffered saline. Partition coefficients were measured under a variety of 

conditions and compared with our theoretical predictions, demonstrating that the partitioning 

behavior of DNA fragments in this system is primarily driven by repulsive, steric, excludedvolume 

interactions that operate between the micelles and the DNA fragments, but is limited by 

the entrainment of micelle-poor, DNA-rich domains in the macroscopic micelle-rich phase. 

Furthermore, the volume ratio, that is, the volume of the top, micelle-poor phase divided by that 

of the bottom, micelle-rich phase, was manipulated to concentrate DNA fragments in the top 

phase. Specifically, by decreasing the volume ratio from 1 to 1/10, we demonstrated proof-ofprinciple 

that the concentration of DNA fragments in the top phase could be increased 2- to 9- 

fold in a predictive manner. 


Fluorescence Lifetime Imaging Microscopy (FLIM) for Cancer Demarcation during 

Medical Surgery 

Yinghua Sun 1,2 , Jennifer Phipps 1 , Daniel S. Elson 3 , Jeremy Meier 4 , Nisa Hatami 1 , Frank S. 

Chuang 2 , Rudolph J. Schrot 5 , D. Gregory Farwell 4 , and Laura Marcu 1,2 


2 NSF Center for Biophotonics Science & Technology, University of California, Davis 

3 Imperial College London, London, U. K. 

4 Department of Otolaryngology, University of California, Davis 

5 Department of Neurological Surgery, University of California, Davis 

A compact endoscopic fluorescence lifetime imaging microscopy (FLIM) system was 

developed for intraoperative disease diagnosis in clinics. By extracting multiple parameters 

including fluorescence intensity, spectrum, and lifetime, FLIM has the inherent advantages for in 

vivo application because the time-resolved analysis is minimally affected by the irregular tissue 

surface, the non-uniform illumination, and the presence of endogenous absorbers. The 

endoscopic design in this system allowed for the remote image collection via a flexible fiber 

imaging bundle (2 m long, 0.6 mm outer diameter, 10,000 optical fibers) cemented with a 

gradient index lens (0.5 mm diameter) as the objective. Tissue autofluorescence was induced 

with 337 nm, 700 ps pulsed laser. Fluorescence images were recorded using a compact gated 

ICCD camera with the temporal resolution up to 200 ps. The spatial resolution of the imaging 

system was examined as 35 μm in the field of view with a 4 mm diameter. Pertinent emission 

wavelengths were selected by bandpass filters in a motorized filter wheel. The system 

performance and imaging processing were calibrated with standard fluorophores. A hamster 

model was used to validate the system in vivo for carcinoma characterization. A significant drop 

of fluorescence lifetime from 2.5±0.36 ns to 1.77±0.26 ns at 450/65 nm and an 81% intensity 

decrease at 390 nm were observed in tumor regions compared with normal healthy tissue. 

Finally the portable FLIM system was installed on a mobile cart for clinical applications in 

operating room. 10 patients were studied for tumor delineation during head and neck surgery 

and 4 patients were examined for glioblastoma. This work demonstrates the potential of FLIM 

as a non-invasive intraoperative diagnostic technique. 


Multi-photon Optical Microscopy of Actin Filaments and Mitochondrial Bioenergetics of 

ACBT Human Frade IV Flioblastoma Cells Migrating within 3-D Collagen-based Hydrogels 

Miso Yang 1 , Yu-Jer Hwang 1 , Edgar Sanchez 2 , Chung-ho Sun 2 , Tatiana B. Krasieva 2 , 

Bruce J. Tromberg 2, 3 , Julia G. Lyubovitsky 1 

1 Bioengineering Department, University of California, Riverside 

2 Laser Microbeam and Medical Program, Beckman Laser Institute, University of California, 

Irvine 

3 Biomedical Engineering, University of California, Irvine 

Multi-photon optical microscopy (MPM) that combines second harmonic generation 

(SHG) and two-photon fluorescence (TPF) signals to allow many opportunities to nondestructive 

probing of molecular processes in tissue with high spatial resolution and contrast in 

real time. In this study, we created 3-D mitochondial metabolic state maps of ACBT human 

grade IV glioblastoma cells migrating within 3-D collagen-based hydrogels using the multiphoton 

ratiometric redox fluorometry method. The average mitochondrial metabolic state 

number was 0.9, which indicates that for the majority of mitochondria, the fluorescence was 

equally distributed between reduced nicotinamide adenine dinucleotide (NADH) and oxidized 

flavin adenine dinucleotide (FAD). Apoptosis and aging are strongly associated with the 

interactions of mitochondria with actin cytoskeleton. Therefore, we established protocols to 

probe the distribution of F-actin filaments in ACBT glioblastoma cells that migrate within 3-D 

collagen-based hydrogels. Specifically, we both stained and transiently transfected ACBT cells 

with green fluorescent protein (GFP)-actin to follow actin reorganization during cell migration in 

real time. 


Optical Model of Human Skin for Biomedical Reflectance and Fluorescence 

Spectroscopy 

Dmitry Yudovsky and Laurent Pilon 

Inter-Departmental Biomedical Engineering Program, University of California, Los Angeles 

Biomedical fluorescence spectroscopy has been used in many applications, including 

detection of malignant tissue, feedback during ablative laser therapy, non-invasive monitoring of 

drug delivery, and real-time non-invasive glucose monitoring. Human skin is the largest and 

most accessible organ of the body. Furthermore, changes in its reflective and fluorescence 

properties are known to correlate with pathological and normal bodily function. Therefore, there 

is a great interest in developing optical methods and algorithms for analyzing the reflectance 

and fluorescence of skin for non-invasive health-monitoring. 

Analysis of light transfer through biological tissue is complicated by tissue heterogeneity. 

Skin is made of several layers which absorb and scatter incident and fluorescent light. The top 

layer (the epidermis) is characterized by strong absorption due to melanin and fluorescence by 

tryptophan, keratin, and tyrosine. Beneath the epidermis is the dermis whose optical properties 

are affected by the presence of blood, collagen, NADH, pepsin, and tryptophan. Blood has 

drastically different absorptive and scattering characteristics that vary with oxygen saturation. 

Spectroscopic analysis of skin has been based on approximate models of light transfer 

such as Beer-Lambert‘s law or the diffusion approximation. Then, skin is treated as a semiinfinite 

and homogenous medium. Unfortunately, these methods provide an incomplete and 

often inaccurate assessment of light transfer through biological tissue. More complex, 

multilayered Monte Carlo models have been developed, but are too slow and computer 

intensive to use in real-time spectroscopy or in inverse method for non-invasive monitoring of 

skin. 

In this study, a model of light transfer through skin, treated as a two-layer medium, is 

developed that is both realistic and computationally efficient. Skin reflectance and fluorescence 

as well as the distribution of excitation and fluorescence irradiances through the tissue are 

modeled taking into account optical and geometric properties of the epidermis and dermis. 


Bench Scale Electroenzymatic Biosensor for the Rapid Detection of Pyruvate 

Lorenzo D‘Amico, Andrew Basilio, Si Luo, Justin Yeap, and Dale A. Baker, Ph.D. 


A bench-scale electrochemical biosensor was developed for the rapid detection of 

pyruvate. The design is based on the enzyme, pyruvate oxidase, which is entrapped in a 

membrane in contact with a Clark-type oxygen sensor. During the reaction catalyzed by 

pyruvate oxidase, pyruvate and oxygen are consumed in a one-to-one ratio. Utilizing this ratio, 

the concentration of pyruvate can be related to the amount of oxygen that is consumed while a 

sample of pyruvate diffuses across the enzyme membrane. The sensor has been shown to 

respond to a step in pyruvate within 5 minutes and to pyruvate concentrations, between 50 and 

1500 μM, which covers a wide physiological range. This amperometric sensor was operated at 

37 o C to assess its potential for an implantable sensor design. The bench-top sensor was build 

to be an alternative to the standard spectrophotometric method for determining pyruvate from 

blood samples, a method which usually requires perchloric acid treatment for deproteinizing the 

samples, and thus, centrifugation as well. So to avoid this pre-treatment inconvenience, we 

have developed a simple, inexpensive and reliable electrochemical method for determining 

pyruvate. The concentration level of lactate to pyruvate or L/P ratio is used to assess ischemia, 

circulatory shock and hypoxia. The L/P ratio has at times been shown to be a better indicator 

than just the lactate concentration in some forms of ischemia, hypoxia and concomitant cellular 

dysfunction .A person at rest typically has a blood L/P ratio of 10-15:1. When experiencing 

hypo-perfusion, ischemia or hypoxia, the L/P ratio increases, which indicate an abnormality. 

Elevated levels are considered to be L/P ratio greater than 20. The severity of the abnormality 

as indicated by the ratio depends on the specific ischemic, hypoxic or shock situation. Pyruvate 

levels are also helpful in the evaluation of novel oxygen therapeutics and their role in 

resuscitation. 


Effects of Coating Material on Cellular Uptake of Nanocapsules Loaded with Indocyanine 

Green 

Bongsu Jung, Bahman Anvari 

Department of Bioengineering, University of California Riverside 

Indocyanine green (ICG) is an FDA-approved near-infrared (NIR) fluorescent dye used 

in ophthalmic angiography and assessment of liver function angiography. However, clinical 

applications of ICG remain very limited due to its rapid clearance from general circulation and 

unstable optical properties. To overcome these limitations, we have encapsulated ICG within 

nanoscale biopolymers. Nanoencapsulation of ICG can be potentially applied for tumortargeting 

purposes by further surface coating and or functionalization of the capsule surface. 

ICG containing nanocapsules offer a dual ability for optical imaging and optical therapy in that 

the same nanocapsule system can be irradiated with laser light to elicit a thermal or chemical 

response that will lead to destruction of the targeted structures. Our preliminary results 

demonstrate that ICG containing nanocapsules coated with the composite magnetite and 

polyethylene glycol (PEG) material deposit in greater amounts within the lungs of healthy mice 

than nanocapsules coated with polylysine or dextran. To understand the effects of coating 

materials on the cellular distribution of the nanocapsules, we measure the uptake of ICG 

containing nanocapsules coated with various materials by different cells including peripheral 

blood monocytes, and normal and cancerous bronchial epithelial cells. Results of these studies 

will provide important information for subsequent applications of ICG containing nanocapsules 

that can be used for targeted optical vascular and tissue imaging as well laser therapy. 


Novel Dielectrophoretic Device for Cancer Cell, Stem Cell and DNA Biomarker Isolation 

and Detection 

Rajaram Krishnan 1 , Joaquim Teixeira 2 , Jennifer Y. Marciniak 1 , Mark Mercola 2 , Sadik C. Esener 3 

and Michael J. Heller 1,3 

1 Department of Bioengeering, University of California, San Diego 

2 Burnham Institute for Medical Research, San Diego 

3 Department of Nanoengeering, University of California, San Diego 

The goal for our NCI NanoTumor Center project is the development of new 

dielectrophoretic (DEP) technology that allows cancer cells, high molecular weight (hmw) DNA 

nanoparticulates and other cancer biomarkers to be isolated and detected directly in whole 

blood or plasma. Achieving this goal required overcoming the basic limitation of DEP to low 

conductance (ionic strength) samples. Last year, we demonstrated the separation and detection 

of DNA nanoparticles in high-conductance solutions (Electrophoresis 2008). Now, we have 

been able to demonstrate that DEP can be used for the separation of nanoparticles and hmw 

DNA biomarkers directly from whole blood. Both fluorescent nanoparticles and fluorescentstained 

hmw DNA in undiluted whole blood samples were separated and held in DEP high field 

regions and then detected after the blood cells were removed by a fluidic wash. In buffy coat 

blood, 40nm nanoparticles concentrated into the DEP high field regions while the blood cells 

concentrated into the DEP low field regions. A fluidic wash then selectively removed the cells 

while the nanoparticles remained trapped. We further showed that unlabeled hmw DNA could 

first be separated by DEP, and then stained with a fluorescent dye for subsequent detection. 

This was an important result that demonstrated both the intrinsic advantage of DEP for 

separating unlabeled analytes and the potential for using the technology in a seamless sample 

to answer process. In the area of stem cells, we have been able to use DEP to carry out the 

separation of cardiomyocytes from fibroblasts and endothelial cells. Currently, we are 

constructing a new generation of diagnostic systems, where specific analytes are rapidly 

concentrated from a complex sample onto microscopic locations and subsequently detected. 

Such DEP systems will allow biological samples such as blood, plasma etc. to be rapidly 

analyzed for a variety of disease related biomarkers. 


Detection of Enzymatic Biomarkers Directly in Whole Blood for Point-Of-Care 

Diagnostics 

Roy B. Lefkowitz 1 , Jennifer Y. Marciniak 1 , Che-Ming Hu 1 , Geert W. Schmid-Schönbein 1 , and 

Michael J. Heller 1,2 

1 Bioengineering Department, University of California San Diego 

2 Nanoengineering Department, University of California San Diego 

Rapidly progressing high-mortality diseases and medical conditions such as 

physiological shock (52% hospital mortality) and pancreatic cancer (1-year survival rate of 24%) 

require rapid early-stage Point-of-Care (POC) diagnostics in order to facilitate immediate 

intervention and maximize patient survival. Several studies have shown that that degradative 

enzymes (e.g. pancreatic proteases) are potential biomarkers for these and several other major 

diseases. Unfortunately, POC testing of these enzymes is often limited by the requirement for 

costly time-consuming sample preparation. To overcome this fundamental limitation, we need to 

detect these disease biomarkers directly in unprocessed plasma and whole blood. Our goal is to 

facilitate the development of POC diagnostics by creating technology that can rapidly measure 

degradative enzymes directly in plasma and whole blood. Toward this end, we have developed 

charge-changing substrates that produce positively charged fluorescent cleavage products upon 

cleavage by the target enzyme. These products can readily be separated from the 

predominantly negatively charged components of whole blood by electrophoresis and then 

quantified with a fluorescent detector. We developed a charge changing substrate for detection 

of pancreatic α-chymotrypsin and trypsin activity. After a 1-hour reaction of substrate and 

enzyme and then 30 minutes of agarose gel electrophoresis, the detection limit for both 

enzymes is 2 nM in human plasma and 20 nM in whole rat blood. The Michaelis Menten kinetics 

parameter, kcat/Km, is 2000 s-1 M-1 for α-chymotrypsin and 800 s-1 M-1 for trypsin. The 

substrate is specific toward α-chymotrypsin and trypsin, with no significant cross-reactivity with 

trypsin-like protease thrombin, plasmin, and kallikrein. We have also developed substrates 

specific to α-chymotrypsin, trypsin, elastase, MMP-2, and MMP-9. This simple assay overcomes 

a major limitation in developing viable, cost effective POC diagnostics because it can measure 

disease biomarkers directly in clinical samples, without sample preparation. 


The Deposition and Fate of Ultra-fine Pollutants in Normal and Asthmatic Mice using 

Positron Emission Tomography 

Heather A. Palko 1 and Angelique Y. Louie 2 

1 Department of Chemistry, University of California, Davis, CA 95616 

2 Department of Biomedical Engineering, University of California, Davis, CA 95616 

Air pollution of all types is now understood to be detrimental to human health. It has been shown 

that there is a connection between air pollution and serious health effects. These effects include 

problems with lung function and cardiovascular complications. There is great interest in studying the 

bio-distribution of particulate matter (PM) after delivery to the lung to look for correlation between sites 

of particle accumulation and abnormal conditions known to be associated with PM exposure. The aim 

of this work is to use Positron Emission Tomography (PET) to track the deposition and fate of model 

ultra-fine particles in vivo after delivery to the lungs in both normal and asthmatic mice. Amine 

terminated polystyrene nanoparticles conjugated to DOTA- 64 Cu were used as a model of ultra-fine 

particles. In these studies it has been shown that the polystyrene nanoparticles are capable of 

translocating out of the lungs in both mouse models. Future work will focus on how surface charge 

affects translocation out of the lung into other target organs. 


Dual-Beam Optical Fiber Trapping Platform for Biophotonics Applications 

Tessa Piñón, Jay Sharping 

Biological Engineering and Small-Scale Technologies, University of California, Merced 

Optical fiber trapping is a technique utilized for manipulating micron-sized dielectric 

particles such as microspheres and biological cells. In this submission, we describe the 

fabrication and particle trapping performance of a compact and inexpensive optical trapping 

system. The system is constructed using one or more pairs of single-mode optical fibers 

arranged in a counter-propagating configuration with a small space between the cleaved fiber 

ends. Particles are trapped by a combination of optical scattering and optical gradient forces 

from a 980 nm laser, where proper alignment of the fibers is essential for stable performance. 

Uniform fiber alignment channels are burned into cast acrylic ―plexiglass‖ using resistive wire. 

The optical fibers are introduced from the sides, stabilized using alignment rods, and glued into 

place. Proper alignment is verified by observing the system through a microscope and 

monitoring laser light coupled through the trapping space. The resulting system can be scaled to 

support numerous independent optical traps, and it is small enough to fit into a standard 

microscope for trapped particle observation. 

We investigate the light force dynamics acting on polystyrene microspheres in such a 

counter-propagating beam trap. Polystyrene particle measurements are a necessary foundation 

for future studies involving optical cell manipulation and sorting within a microlaboratory 

environment. To characterize the trapping forces of the system, we modulate the optical power 

in the trap in order to displace the microsphere from its equilibrium position. The subsequent 

motion of the particle allows us to calculate the effective spring constant of the trap from which 

trapping forces can be estimated. We observe spring constants over the range of 100-500 

nN/m. As an extension of this work, we plan to scale the system into a multi-fiber array of traps. 

This project sets the stage for simple and consumable microfluidic optical trapping technology. 


Solid Lipid Nanoparticles as Vehicles for Delivering Imaging Probes across In Vitro 

Models of the Blood Brain Barrier (BBB) 

Erica Andreozzi 1 , Benjamin Jarrett 2 , Angelique Louie 1 


Activated microglia, macrophage-lineage cells located in the central nervous system 

(CNS), are known to play an important role in the neuroinflammatory response that is 

associated with progression of Alzheimer‘s Disease (AD). 1 Although the role of microglia in the 

pathogenesis of AD is still unknown, regions with high microglia content tend to be correlated 

with greater neurotoxicity. 2 We propose to develop novel imaging probes that are targeted to 

activated microglia through a type of scavenger receptor, SRA, that are highly expressed by 

microglia in AD but not by normal microglia. We propose to deliver these imaging probes 

across the blood brain barrier (BBB) with nanoparticle transport systems such as solid lipid 

nanoparticles (SLNs). SLNs constitute an attractive colloidal drug carrier system that has 

previously shown effective transport across the BBB, resulting in increased drug loading 

efficiencies to the brain. 4, 5, 6 To validate our proposed delivery methods, we have encapsulated 

fluorescently-labeled bovine serum albumin (i.e. TAMRA-BSA) probes into SLNs and employed 

these encapsulated probes in cell studies of BBB transport. Using established in vitro BBB 

models comprised of human primary brain endothelial cells (HPBECs) and human primary 

astrocytes (HPAs) in a Transwell co-culture system, the transport efficiency of SLNencapsulated 

TAMRA-BSA was evaluated using optical methods. SLN were introduced to the 

upper chamber of the Transwell system and transport of probes across the HPBEC monolayer 

was assessed by collecting media from the lower chamber at various time-points and measuring 

fluorescence of TAMRA. Unencapsulated probes (i.e. free TAMRA-BSA) were tested in parallel 

wells as a control. Our preliminary data from these in vitro BBB model studies lend strong 

support that our imaging probes can be encapsulated in SLN carriers for effective BBB transport 

in animal models, and that therefore high resolution in vivo imaging is possible using these 

encapsulated contrast agents. 

1. D. Giulian, "Microglia and the immune pathology of Alzheimer disease", American 

Journal of Human Genetics 65 (1), 13 (1999), 

2. H. L. Weiner and D. Frenkel, "Immunology and immunotherapy of Alzheimer's disease.‖ 

Nature Reviews Imm 6 (6), 490 (2006) 

3. P. Blasi, S. Glovagnoli, A. Schoubben et al., "Solid lipid nanoparticles for targeted brain drug 

delivery", Advanced Drug Delivery Reviews 59 (6), 454 (2007). 

4. RH Muller, "Lipid nanoparticles: recent advances", Adv. Drug. Delivery Reviews 59, 375 

(2007). 

5. I Kaur, R Bhandari, S Bhandari et al., "Potential of solid lipid nanoparicles in brain targeting", 

J Controlled Release 127 (2), 97 (2008) 


Implementation of a Shack-Hartmann Wavefront Sensor for the measurement of embryo 

induced aberrations using fluorescent microscopy 

Oscar Azucena, 1 Joel Kubby, 1 Justin Crest, 2 Jian Cao, 2 William Sullivan, 2 Peter Kner, 3 Donald 

Gavel, 4 Daren Dillon, 4 Scot Olivier 5 

1 Jack Baskin School of Engineering, University of California, Santa Cruz 

2 Molecular, Cell, and Developmental Biology, University of California, Santa Cruz 

3 Department of Biochemistry and Biophysics, University of California, San Francisco 

4 Laboratory for Adaptive Optics, University of California, Santa Cruz 

5 Physics and Advanced Technologies, Lawrence Livermore National Laboratory 

Adaptive optics (AO) improves the quality of astronomical imaging systems by using real 

time measurement of the turbulent medium in the optical path using a guide star (natural or 

artificial) as a point source reference beacon. AO has also been applied to vision science to 

improve the current view of the human eye. This paper will address our current research 

focused on the improvement of fluorescent microscopy for biological imaging utilizing current 

AO technology. A Shack-Hartmann wavefront sensor (SHWS) was used to measure the 

aberration introduced by a Drosophila Melanogaster embryo with an implanted 1 micron 

fluorescent bead that serves as a point source reference beacon. The measurements show an 

average peak-to-valley and root-mean-square (RMS) wavefront error of 0.77 micrometers and 

0.15 micrometers, respectively. The Zernike coefficients have been measured for these 

aberrations which indicate that the correction of the first 14 Zernike coefficients should be 

sufficient to correct the aberrations we have obtained. These results support the utilization of 

SHWS for biological imaging applications and that a MEMS deformable mirror with 1 micron of 

stroke and 100 actuators will be sufficient to correct these aberrations. The design, assembly 

and initial results for the use of a MEMS deformable mirror, SHWS and implanted fluorescent 

reference beacon for wavefront correction will also be discussed. 


A Hybrid Assistive System for Upper-Extremity Stroke Rehabilitation 

Sivakumar Balasubramanian 1 , Jiping He 1 

1 Harrington Department of Bioengineering, Arizona State University, Tempe, Arizona 

Recent developments in the stroke rehabilitation arena with the use of robotic devices 

and functional electrical therapy (FET) for delivering of intense task-oriented therapy for the 

upper-extremity (UE) demonstrate potential for targeted functional recovery. However, several 

challenges remain to be overcome. Present-day robotic and FET devices mainly focus on the 

isolated training of the proximal and distal sections of the UE, respectively. Although these 

isolated trainings of different sections are useful, most of the UE movements in day-to-day 

activities involve the use of the entire UE. A recent preliminary study showed that training the 

whole UE can result in better outcomes than training parts of the UE in isolation. And, this 

approach of training the entire UE as single entity might be a good approach even from a taskoriented 

therapy point-of-view. 

In our current study, we propose the development of a rehabilitation device that combines a 

rehabilitation robot for the assisting the arm movements, and a simple surface FES system for 

assisting hand movements. Such a device that combines a robotic component with an electrical 

stimulation component is defined as a hybrid assistive system (HAS). The HAS is mainly used 

for training whole UE tasks such as a reach-and-grasp task, which is an important task for 

performing activities-of-daily living. 

The proposed HAS uses RUPERT III (Robotic UPper-Extremity Repetitive Trainer, Version III), 

a wearable exoskeleton robot developed by our group for assisting arm movements, and a 

computer controller 4-channel surface electrical stimulator (OctoStim, Freiler Corp) for assisting 

hand movements. The device also uses a system consisting of bend sensors for sensing finger 

movements; these sensors along with the ones in RUPERT III will allow the HAS to operate in 

an active-assist therapy mode that takes into account volitional effort from the patient. 

Additionally, a simple biofeedback environment that can be used for training whole UE tasks 

has also been developed. 

: 


Digestive Protease Transport and Mechanisms for Disruption of the Epithelial Barrier in 

Early Stages of Shock 

Marisol Chang and Geert Schmid-Schönbein 

Department of Bioengineering, Institute for Engineering in Medicine, University of California San 

Diego 

Physiological shock is an important clinical problem that is associated with high 

mortality. During early states of shock the integrity of the intestinal mucosa becomes irreversibly 

compromised, making epithelial cells and the multiple layers of the intestinal wall accessible to 

digestive enzymes in the lumen of the intestine including those of the family of serine proteases. 

Increased permeability of the intestinal mucosal layer results also in the generation and leakage 

of inflammatory mediators causing cellular dysfunction, multiple organ failure and death due to 

autodigestion. However, the mechanism by which these events take place is not understood. 

We hypothesize that pancreatic digestive proteases disrupt the epithelial barrier at early stages 

of shock by enzymatic cleavage of epithelial adhesion molecules, e.g. E-cadherin. In this study 

we occlude the superior mesentery artery as a model to study the pathophysiologic breakdown 

of the intestinal barrier. We use tissue zymography for quantification and visualization of the 

serine proteases activity along the intestinal wall and immunohistochemistry to determine the 

extent to which both the cellular and mechanical barriers are disrupted during early stages of 

intestinal ischemia. The results show the entry of chymotrypsin within minutes of ischemia from 

the lumen of the intestine across the epithelium into the intestinal mucosa; in addition to an early 

loss of the extracellular domain of E-cadherin, blocking the ability for tight junction formation. 

These results indicate that the powerful pancreatic digestive proteases disrupt the epithelial 

barrier as soon as intestinal ischemia starts to take place. Supported by HL 76180. 


Characterization of Chymotrypsin’s Single-Molecule Kinetics Using an Array of 

Microwells. 

Angela Y. Chen and James P. Brody 

Department of Biomedical Engineering, University of California, Irvine 

The isolation of a population of enzymes into individual molecules is a key step in 

observing single-enzyme activity. To uncover the single-molecule kinetics hidden by the 

ensemble average, we describe a simple method that allows simultaneous observation of 

hundreds of individual chymotrypsin molecules. Each enzyme molecule is enclosed in a 

cylindrical well that is 2µm in diameter and 1.35µm in height. An array of these identical wells 

comprises the reaction chambers whose intensity we track via fluorescence imaging. We 

fabricate the wells by using electron-beam lithography, metal evaporation, and deep reactive ion 

etching (DRIE). Fluorescence images of the microwells containing single enzymes are captured 

every 3min for a total duration of 1 hour by using a charge-coupled device (CCD). We calibrate 

and analyze the images by using the software ImageJ. The enzyme to substrate ratio for a 

given well enclosing a single enzyme is 1:1,000. We use orange fluorescent microspheres 

(540/560nm) as a reference standard. In addition, the photobleaching rate of the BODIPY 

Texas Red dye conjugated to the substrate is determined by exposing the dye to the mercury 

lamp and recording fluorescence changes over time. Our results show that the product 

formation rate of individual molecules of chymotrypsin not only differs from one another, but 

they are also stable over time, confirming static inhomogeneity. 


Modification of intracellular Ca 2+ release in cardiac myocytes of intact beating mouse 

hearts upon application of an exogenous buffer 

Ariel L. Escobar and Dmytro Kornyeyev 

School of Engineering, University of California, Merced 

The investigation of the mechanism of Ca 2+ -induced Ca 2+ release (CICR) is vital to 

understand normal the function of ventricular cardiac myocytes as well as some pathological 

conditions. Two likely major factors contributing to the regulation of CICR are the free Ca 2+ 

concentration in cytosol and the Ca 2+ content of the sarcoplasmic reticulum (SR). We explored 

the possibility of regulating CICR in the myocytes through Ca 2+ buffering with EGTA AM, a highaffinity 

slow association rate Ca 2+ chelator. Pulsed Local-Field Fluorescence microscopy was 

employed to measure both cytosolic and the SR luminal Ca 2+ signals from the intact mouse 

hearts using Ca 2+ -sensitive fluorescent dyes rhod-2 AM and mag-fluo-4 AM at different 

temperatures. Analysis of the Ca 2+ transients recorded at two different temperatures 21 and 

37 o C implies that the presence of EGTA shortens the refractory period and accelerates the 

restitution of Ca 2+ release. These changes were not induced by alterations in the refractoriness 

of the epicardial action potentials or the Ca 2+ influx through L-Type channels. Additionally, the 

frequency dependence of alternans in Ca 2+ release (cyclic beat-to-beat variations in the 

amplitude of Ca 2+ release) was shifted toward higher frequency in response to the treatment 

with EGTA AM. These results are consistent with the hypotheses that the addition of a high 

affinity exogenous Ca 2+ buffers can modify the luminal Ca 2+ content by decreasing the uptake 

through the SERCa pump and that Ca 2+ release from the SR is a rate limiting step defining the 

refractoriness of ventricular contractility. Supported NIH R01-HL-084487 to AE. 


Generation of a Novel Duel Reporting Embryonic Stem Cell Line for Endothelial and 

Smooth Muscle Expression 

Drew E. Glaser 1 , Alicia A. Blancas 2 and Kara E. McCloskey 1,2* 

1 Biological Engineering and Small-scale Technologies, University of California, Merced 

2 Graduate Program in Quantitative and Systems Biology, University of California, Merced 

Embryonic stem cells offer a vast range of possible therapeutic applications for a 

multitude of diseases. In order to further understand the differentiation process, fluorescent 

reporters (i.e. green fluorescent protein, GFP) linked with specific promoters are often used to 

visualize and quantify the expression of various proteins. Using this technology, we are 

generating a novel murine embryonic stem cell line that will express GFP when Tie-2, an 

endothelial gene, is expressed and red fluorescent protein (RFP) when α-smooth muscle actin 

is expressed as the cells differentiate into smooth muscle cells. In order to generate this cell 

line, a mouse carrying a Tie-2 GFP reporter has been crossed with a mouse with α-smooth 

muscle actin RFP reporter. Delayed blastocysts are recovered from the pregnant mouse 

between days 6-8 and cultivated on a mouse embryonic fibroblast feeder layer for 4 days. The 

embryonic inner cell mass (i.e. embryonic stem cells) will then be dissected from each embryo 

and transferred to separate dishes. For verification of the cell line with both reporters, the cells 

will be allowed to differentiate into embryoid bodies for 7 days and observed via fluorescence 

microscopy. 


Quantitative Conversion of Alcohols to Aldehydes Using Alcohol Dehydrogenase 

Sean Guthrie and Valentine Vullev 


Due to their reactivity, aliphatic aldehydes are important precursors for a range of 

coupling reactions broadly used in organic and bioorganic synthetic procedures. We 

demonstrated utilization of surface-anchored aldehydes for the engineering of non-fouling 

bioactive interfaces (Wan et al., Annals of Biomedical Engineering 2009, in press). Polyethylene 

glycol is a versatile material for preparation of bioinert (i.e., non-fouling) interfaces. Thus, we 

utilize PEG for assurance that the proteins, covalently attached to substrates surfaces, preserve 

their activity. Aldehydes, essential for such surface-engineering procedures, are usually 

prepared by selective chemical oxidation of the corresponding alcohol derivatives. Such 

chemical procedures, however, can readily lead to overoxidation and formation of carboxylic 

acids, decreasing the yield of aldehyde production. Furthermore, PEGs are susceptible to 

oxidation, placing high demands on the types of reaction used for their chemical 

transformations. Enzyme catalysis, on the other hand, allows for highly selective control of 

chemical transformation under mild conditions in aqueous media. We utilized alcohol 

dehydrogenase (AD) for the development of homogeneous and heterogeneous procedures for 

quantitative transformation of aliphatic alcohols into the corresponding aldehydes. We 

demonstrated the AD-catalyzed conversion of hydroxyl-terminated polyethylene glycol (PEG) 

into PEG-aldehyde conjugates. This conversion is supported by enzyme kinetic measurements 

and characterization of the enzymatic reaction progress using high performance liquid 

chromatography. The selective oxidation of this family of hydroxyl-terminated polymers conveys 

the utility of our enzyme-catalyzed conversion methodology. 


Evaluation of collagen and matrix metalloproteinase content in human carotid 

plaque by time-resolved fluorescence spectroscopy 

Nisa Hatami 1 , Jennifer E. Phipps 1 , Michael C. Fishbein 2 , Laura Marcu 1 

1 Department of Biomedical Engineering, University of California Davis 

2 Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, 

University of California Los Angeles 

Matrix metalloproteinases (MMPs) play a major role in the pathogenesis of atherosclerosis, 

degrading the collagen cross-links within the plaque and disrupting the fibrous cap. The goal of 

this study is to design an algorithm to quantify collagen content from picrosirius red (PSR) 

stained slides and show the correlation between collagen and MMP content. In addition we will 

determine whether using time-resolved laser-induced fluorescence spectroscopy (TR-LIFS), a 

technique that is sensitive to the fluorescence of collagen and collagen cross-links, can be used 

to detect levels of MMP-2 and -9 in human carotid plaques. TR-LIFS measurements were 

obtained from 78 carotid plaque samples (29 patients undergoing carotid endarterectomy) using 

a 337 nm pulsed nitrogen laser as an excitation source. Spectroscopic parameters, such as 

average fluorescence lifetime, were analyzed and correlated with the specific cellular and 

biological content of plaque. An algorithm was designed to use digitized images of the PSR 

slides (viewed under circularly polarized light) to quantify collagen content by segmenting the 

image into three layers (hue, saturation and value), thresholding for known hues of thick and 

thin collagen fibers, and counting the number of pixels of each type. Using ANOVA, a significant 

correlation was found between the algorithm quantification of collagen content and the 

pathologist assessment from the trichrome stain, thus verifying the accuracy of the algorithm. 

Also, we found that as levels of MMP-2 and -9 increased, the average lifetime at 550 nm 

significantly decreased from 1.62 ns to 1.44 ns, and from 1.65 ns to 1.47 ns, respectively. In 

summary, we successfully developed an algorithm to quantify collagen content from PSR 

stained slides and correlated collagen and MMP levels with spectroscopic parameters. This 

further supports the potential of this method as a novel tool for evaluating the chemical 

composition of vulnerable plaques. 


Highly Accelerated Hyperpolarized 13 C 3D-MRSI and Time-Resolved 3D-MRSI Using 

Compressed Sensing and Multiband Pulses with 

In Vivo Applications 

Simon Hu 1,2 , Peder E.Z. Larson 1 , Michael Lustig 3 , Adam B. Kerr 3 , Asha Balakrishnan 4 , Robert 

Bok 1 , John Kurhanewicz 1,2 , Sarah J. Nelson 1,2 , 

Andrei Goga 4 , John M. Pauly 3 , Daniel B. Vigneron 1,2 

1 Dept. of Radiology and Biomedical Imaging, University of California, San Francisco, CA 2 

UCSF & UCB Joint Graduate Group in Bioengineering 

3 Dept. of Electrical Engineering, Stanford University, Stanford, CA 4 Dept. of Medicine, Division 

of Hematology/Oncology, University of California, San Francisco, CA 

High polarization of nuclear spins in liquid state through hyperpolarized technology utilizing DNP 

has enabled the direct monitoring of 13 C metabolites in vivo at very high SNR [1]. Acquisition 

time limitations due to T1 decay of the hyperpolarized signal make accelerated imaging 

methods, such as compressed sensing, very important. Compressed sensing is an approach 

that combines random undersampling with a non-linear reconstruction [2-3]. Previously, we 

developed a compressed sensing scheme applied in one dimension to achieve 2-fold 

acceleration to obtain 2 times better spatial resolution without increasing scan time [4]. In this 

project, we developed new techniques and applications. We developed a 7.5-fold accelerated 

sequence for 3D spectroscopic imaging, which we validated with simulations, phantom testing, 

and in vivo experiments. In addition, we combined compressed sensing with a multiband 

excitation approach [5] to achieve a time-resolved 3D spectroscopic imaging sequence. Finally, 

we acquired in vivo compressed sensing data from transgenic liver cancer mice [6-7], a new 

animal model for hyperpolarized studies. Our new accelerated pulse sequences extend our 

previous designs by employing both x and y gradient blips (Figure 1) to achieve random 

undersampling in the spectral dimension and two spatial dimensions. In the case of 3D-MRSI, 

this meant undersampling in k f -k x -k y with k z fully sampled. In time-resolved 3D-MRSI, multiple 

3D-MRSI datasets were acquired over time with each having a different k f -k x -k y undersampling 

pattern. In addition, for time-resolved 3D-MRSI, spectrally selective multiband excitation pulses 

were used instead of standard SLR pulses in order to place a smaller flip angle on pyruvate, the 

injected substrate, which has a much higher concentration and signal intensity, and larger flip 

angles on the metabolic products lactate and alanine, with the metabolically inactive pyruvatehydrate 

not excited at all. This allowed for efficient use and preservation of the hyperpolarized 

magnetization over the many flips required for time-resolved 3D-MRSI. The reconstruction 

iteratively filled in missing k-space data using a non-linear conjugate gradient implementation [8] 

that included a wavelet transform in the spectral dimension and a total variation penalty. Animal 

imaging of transgenic mice was performed on a GE 3T system using the double spin-echo 

sequence [4-5] shown in Figure 1. Acquisition parameters were: 1) phantom 3D-MRSI: 10 

degree flip angle, TE = 140 ms, TR = 2 s, FOV = 8x8 cm, and 5x5x10 mm spatial resolution 2) 

animal 3D-MRSI: variable flip angle, centric phase encoding order, TE = 140 ms, TR = 215 ms, 

FOV = 4x4 cm, 2.5x2.5x5.4 mm spatial resolution 3) animal time-resolved 3D-MRSI: TE = 

160ms, TR = 250ms, FOV = 6x6 cm, 5x5x5.4 mm spatial resolution, and 6 s time resolution. 


Figure 2 shows simulation and phantom validation of a x7.53 accelerated 3D-MRSI sequence. 

The simulations, in which peaks were perfect lorentzians, showed that as expected the x7.53 

undersampled compressed sensing reconstructed data set matched the fully sampled data set 

extremely well. The error in the magnitude reconstruction was uniformly 1/50 of the original 

signal throughout all the slices. The phantom experiments also showed excellent agreement 

between the accelerated and normal acquisitions. Finally, the in vivo data in Figure 2, which 

show a factor-of-4 resolution enhancement in approximately half the acquisition time, 

demonstrated good spectral quality and the preservation of small peaks. Figure 3 shows 3D- 

MRSI compressed sensing data acquired from normal and liver cancer mice in which a x3.37 

accelerated sequence was used to achieve a factor-of-4 resolution enhancement without 

increasing scan time. These spectra and color overlays demonstrate the feasibility of performing 

hyperpolarized liver cancer studies in vivo, showing the elevated lactate in tumor compared with 

normal tissue that is characteristic of hyperpolarized cancer studies. Also of prominence was 

elevation of the alanine biomarker in tumors, which is linked to unique ALT activity in the liver 

and thus has not been observed in other tumor models. Finally, Figure 4 shows metabolite color 

overlays generated from a x6 accelerated time-resolved 3D-MRSI acquisition of a prostate 

cancer mouse. Figure 4 demonstrates that dynamic images can be acquired in 3 spatial 

dimensions (liver, kidney, and tumor slices are shown in Figure 4). 

Figure 1: Blipped compressed sensing 

pulse sequence. The multiband pulse was 

used for time-resolved 3D-MRSI. Blip 

areas were multiples of the area in a 

phase encode step. 

Figure 2: Slices from simulation/phantom validation of a x7.53 

sequence and an in vivo example from a prostate cancer 

mouse. The simulated and phantom grids show the central 

portions from the full 16x16. 

Figure 3: Representative hyperpolarized 

spectroscopic data from normal and liver 

cancer mice. Individual spectra as well as 

metabolite color overlays are shown. 

Figure 4: Selected slices and time points from a full 3D 

dynamic acquisition showing metabolites and their 

kinetics. 


Equilibrium and Pre Steady-State Kinetics of DNA Binding to DNA Polymerase 

Characterized with a Nanopore 

Nicholas Hurt 1 , Hongyun Wang 2 , Brett Gyarfas 3 , William Dunbar 3 , 

1 Department of Chemistry and Biochemistry, University of Calfornia, Santa Cruz 

2 Department of Mathematics and Applied Statistics, University of California, Santa Cruz 

3 Department of Biomolecular Engineering, University of California, Santa Cruz 

The nanopore is emerging as an important tool to study single molecule biophysical interactions. 

Under an applied voltage, charged biomolecules can be captured from solution in an alpha-hemolysin 

nanopore. This results in a characteristic current blockade signature which contains information about 

the identity and state of the captured molecule. In this study, we exploit the capability of the pore to 

distinguish between single molecules of Klenow Fragment (KF) bound and unbound primer/template 

DNA to directly observe binding kinetics. Equilibrium binding probabilities were determined under 

varying concentrations of Klenow Fragment. A 1:1 equilibrium binding model fit to the data gives us a 

K d of 66.56nM. Saturation of this binding curve at 73.8% enzyme bound events at high KF 

concentration suggests that there are one or more binding modes of KF to DNA that are not observed 

in the nanopore, but which inhibit the observed binding state. Pre-steady state binding kinetics were 

examined using feedback control and a technique called ‗fishing‘, in which the accessibility of the 

primer-template junction to free Klenow Fragment can be precisely temporally voltage-controlled. From 

this method, we determined the k on for KF binding to DNA to be 13s -1 uM -1 . 


A Wearable Electronic Mobility Aide for the Blind 

Brant Jameson, Roberto Manduchi 

University of California at Santa Cruz 

It is estimated that over 250,000 Americans are blind or have only some light perception, 

many of whom rely on guide dogs or long canes to ambulate autonomously. Guide dogs and 

long canes, while providing excellent protection at ground level, do not provide adequate 

coverage of one's torso and head. Head level collisions are known to occur during independent 

excursions, causing injury and possibly reducing one's confidence in their travel skills. While 

many Electronic Travel Aids (ETAs) have been designed for the blind, few have been 

considered successful. It is speculated that previous ETAs have not gained widespread 

acceptance due to poor performance, cosmetics and difficulty of use. 

We propose a new ETA, a miniaturized, wearable ultrasonic system that complements 

the user's primary mobility device. This device relies on ultrasonic multi-lateration to locate, 

discriminate and track hazards at head level. An accelerometer is used to detect the user's 

movements, thereby reducing the occurrence of annoying and uninformative alarms. Novel 

signal processing schemes enable a form-factor and power consumption that was 

unachievable in previous systems. Excellent performance in terms of detection accuracy and 

range resolution is demonstrated by experimental results. 


Dose (Gy) 

Feasibility of Using Radioactive Bone Cement to Treat Vertebral Metastases 

Tadashi S. Kaneko 1,A , Varun Sehgal 1,A , Harry B. Skinner 1,2,A , 

Muthana S. Al-Ghazi 1 , Bang H. Hoang 1 , Nilam S. Ramsinghani 1 , Joyce H. Keyak 1,A 

1 University of California, Irvine 

2 St. Jude Heritage Medical Group, Fullerton, CA 

A Stock held in Bone-Rad Therapeutics, Inc. 

To evaluate the feasibility of using radioactive bone cement to deliver therapeutic 

radiation to the vertebral body without undue risk to the spinal cord, i.e. vertebral brachytherapy. 

CT-scan based Monte Carlo N-Particle radiation transport models, consisting of a threedimensional 

rectangular lattice of 0.625×0.625×1.25-mm voxels, were created of a T-12 human 

cadaveric vertebra. Trabecular and cortical bone were both represented by a spectrum of thirty 

complementary volume fractions of solid cortical bone and bone marrow, and all soft tissue was 

represented as a single material. A cylindrical volume of radioactive bone cement was simulated 

within the model, and two candidate radioisotopes were studied: P-32 and Sr-89. Thirty million 

particle histories were simulated (MCNPX v.2.5.0) to characterize the dose distribution within 

the vertebral body. The dose distributions for both radioisotopes were axisymmetric about the 

cement implant and rapidly decreased with increasing distance from the cement (Fig. 1). Initial 

activities of 0.94 mCi and 0.51 mCi for P-32 and Sr-89, respectively, would deliver >300 Gy to 

bone within 1.6 mm of the cement implant and >80 Gy to bone within 2.8 mm, while keeping the 

dose at 3.4 mm under 45 Gy. The predicted dose distributions show that a therapeutic radiation 

dose would be delivered to all bone within ~3 mm of the cement without undue risk to tissue 

beyond 3.4 mm (such as the spinal cord), indicating preliminary feasibility of this technique. With 

further development, this technology may yield a clinically-feasible procedure that would 

eliminate the need for 10 radiotherapy sessions, making it convenient for the patient, while 

potentially improving the clinical outcome by delivering a higher dose to the tumor and a lower 

dose to the spinal cord than conventional radiotherapy. This study was funded by DOD BCRP 

W81XWH-07-1-0397 

1600 

1400 

1200 

P-32 

Sr-89 

1000 

800 

600 

400 

200 

0 

0 1 2 3 4 5 6 7 8 

Radial Distance from Cement Boundary (mm) 

Figure 1. Lifetime dose distribution in 

vertebral body, with 45 Gy delivered 

to bone at 3.4 mm 


Effects of Cholesterol on Plasma Membrane Mechanics 

N. Khatibzadeh 1 , S. Gupta 2 , W. E. Brownell 3 , and B. Anvari 2 

1 

Department of Mechanical Engineering, University of California, Riverside 

2 


3 Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of 

Medicine, Houston, TX 

Cholesterol is an important factor in determining the biophysical properties of the cell 

membrane, and plays an important role in the regulation of the membrane proteins. In this 

study, effects of cholesterol on viscoelastic properties of the plasma membrane are 

investigated. We use optical tweezers to extract nanotubes (tethers) under various pulling rates 

from the plasma membrane of human embryonic kidney (HEK) cells under cholesterol depleted 

and cholesterol enriched conditions. Threshold tether formation force, and the elastic and 

viscous parameters are quantified and correlated to the changes in the membrane cholesterol 

level. 


Effect of Ultraviolet Light Crosslinking on Mechanical Stiffness of Fibrin Scaffolds 

Soma Esmailian Lari, Haison Duong, Benjamin Wu, Bill Tawil 

University of California, Los Angeles, Department of Bioengineering 

Fibrin has been recognized as a good biomaterial because it is biocompatible, 

bioresorbable, and biodegradable. It has been shown that the mechanical and structural 

properties of fibrin scaffolds are determined by its compositions; namely, fibrinogen and 

thrombin. The interactions between fibrin monomers and thrombin form a stable network 

comprising of noncovalent bonding between the monomers .This bonding process defines the 

mechanical stiffness of the fibrin network. Fibrin have been extensively used in tissue 

engineered applications: from sealants to hydrogels and tissue constructs; however, the 

downside of using fibrin is that it has low mechanical stiffness and it rapidly degrades in vivo 

which is not sufficient for many tissue engineered structures. Thus, in order to optimize fibrin‘s 

potential as a bioscaffold, its mechanical stiffness and resistance to degradation should be 

improved. The purpose of this study is to enhance the overall mechanical stiffness as well as to 

modify the rate of degradation by thermal treatment and UV- irradiation of the fibrin network. 

The results show that upon heat treatment the mechanical stiffness of fibrin matrices increased, 

and this increase is most significant in the lower fibrin concentration .Upon UV-irradiation with 

4000 µW/cm 2 intensity the stiffness was increased by as much as 150% for all the fibrin 

matrices with different fibrinogen and thrombin concentration. Similarly the crosslinked fibrin 

matrices showed a slower rate of degradation (as indicated by a decrease in the modulus) when 

incubated in either serum or serum free medium. 


Serum Free Derivation of Embryonic Stem Cells Towards Functional Cardiomyocytes 

with Electrical Stimulation 

Nicholas E Lauer 1 , Kara McCloskey 1 

1 Graduate Program in Biological Engineering and Small-scale Technologies, University of 


In 2005 coronary heart disease killed more than 7.6 million people worldwide. Many 

forms of heart disease leads to the progressive apoptosis of cardiomyocytes (CM) within the 

heart from myocardial infarctions, ischemia, heart failures, and other cardiomyopathies. Human 

embryonic stem cells (hESC) could potentially serve as a vast source for a variety of therapeutic 

applications, including heart tissue repair. The differentiation and purification of hESC into 

functional CM is a first step towards using hESC for heart repair. Our laboratory is exploring the 

physical, electrical, and biochemical cues required for the differentiation of hESC towards CM. 

Using a C-Pace EP multi-channel stimulation device, electrical stimulation of primary isolated 

CM has shown to help maintain consistent contractility for 6-7 days [1, 2]. Pacing hESC at 

different stages of CM differentiation may increase the percentage of contractile cells, and is 

expected to coordinate pacing frequency. The stages of differentiation studied include: 

undifferentiated hESC in monolayer cultures, embryoid bodies (EBs) in suspension, and beating 

CM progenitors manually selected from EB outgrowths. Characterization includes cardiac 

specific protein markers cardiac troponin-T, GATA4, Nkx2.5, and brachyury, and stem cell 

marker, SSEA4, to test for undifferentiated hESC. 

1. Shimizu, T., et al., Electrically communicating three-dimensional cardiac tissue mimic 

fabricated by layered cultured cardiomyocyte sheets. J Biomed Mater Res, 2002. 60(1): 

p. 110-7. 

2. Shimizu, T., et al., Fabrication of pulsatile cardiac tissue grafts using a novel 3- 

dimensional cell sheet manipulation technique and temperature-responsive cell culture 

surfaces. Circ Res, 2002. 90(3): p. e40. 


Peptide Arrays for the Evaluation of Chemical Conjugation and Enzyme-Substrate 

Interation 

Yan Liu, Yongfeng Zhao, Yang Song, Jiayu Liao 


Microarrays have become a widely used tool for biological research in last decade. One 

crucial step in microarrays fabrication is the covalently immobilization of biological samples on a 

solid surface. We have successfully developed two chemical strategies to immobilize peptides 

onto glass surface using either amine- or keto- reactive groups. An engineered peptide with a 

specific cleavage site for SENP2 (SUMO1 specific peptidase 2) and fluorofores at the end of 

peptide was immobilized on glass surface by chemical conjugation. The peptide arrays can be 

utilized to characterize the efficiencies of different chemical conjugations methods. Moreover, 

measuring the changes of emitted fluorescent intensity can show the cleavage efficiency of 

SENP2. This technology can be developed into high-throughput peptide array which can be 

used to studying enzyme catalytic activity, including characterizing inhibition effect of small 

compounds or molecules, which can be used in drug screening in the future. 


Ariadne’s Thread: 

A Wayfinding Tool for the Visually Impaired Based on Camera Cell Phones 

Roberto Manduchi, Department of Computer Engineering, UC Santa Cruz 

James Coughlan, Smith-Kettlewell Eye Research Institute, San Francisco 

The ability to move independently in a new environment is an essential component of 

any person‘s active life. Visiting a shopping mall, finding a room in a hotel, negotiating a terminal 

transfer in an airport, are all activities that require orientation and wayfinding skills. 

Unfortunately, many individuals are impeded from such basic under takings due to physical, 

cognitive, or visual impairments. In particular, these tasks are dauntingly challenging for those 

who cannot see, and thus cannot make use of the visual information that sighted individuals rely 

on. 

We have developed a wayfinding system based on special color markers that can be 

easily detectable by a regular camera cell phone. Our color markers are passive and 

inexpensive, and the user is not required to purchase and carry any other device than his or her 

own cell phone. In a sense, color markers behave as ―beacons‖, which can be placed at key 

locations in the environment. Additional information in the form of text or bar code can be 

placed nearby and decoded by the cell phone after the marker has been detected. Whereas 

detecting a bar code or text in the scene may require considerable computation time, detecting 

our proposed marker and estimating its distance with a camera cell phone is a very fast and 

robust operation. 

We conducted a number of experiments using color markers in indoor and outdoor 

environments with the help of three blind subjects. The broader goals of these tests were: (1) to 

validate the effectiveness of color markers for labeling specific locations; and (2) to investigate 

different search strategies for marker detection, depending on the type of marker placement and 

the layout of the environment. All of the subjects in our experiments were able to quickly localize 

and reach for the markers in a variety of fairly realistic environments with a relatively small 

amount of training. 

Fig. 1: Marker detection and 

segmentation (shown in yellow) 

on the cell phone. 

Fig. 2: Indoor wayfinding 

experiments. 


Theoretical Significance of Ion Binding on Observed Non-idealities in Osmotic Pressure 

in Crowded Macromolecular Environments 

Devin W. McBride and Victor G. J. Rodgers 


Previous studies have shown that, in crowded macromolecular environments, protein-ion 

binding is a significant factor for the observed non-idealities in osmotic pressure and can be 

captured by a free-solvent model 1 . This work will address the specifics for protein-ion binding 

and protein hydration using in vitro and in silico studies; the equilibrium dialysis method will be 

used in the in vitro studies, while an electrostatic potential map of the surface will be used in the 

in silico studies. The binding of NaCl to Bovine Serum Albumin (BSA), for varying ionic 

strengths and pH, will be used as a model system; ionic strengths ranged from 0 M to 0.15 M 

and pH ranged from 4.5 to 10. Human Serum Albumin (HSA) will be compared to determine the 

specifics for the slight differences in ion binding observed. For the in silico studies, a homology 

model was developed for BSA from Human Serum Albumin (PDB code: 1BM0). Protein-ion 

binding and protein hydration was determined for BSA and HSA; ions and water were added to 

the proteins using Visual Molecular Dynamics (VMD); Molecular Dynamics (MD) simulations 

were run to determine the number of bound ions and water. In addition to the MD simulations, 

the electrostatic potential maps for BSA and HSA, under each condition, were compared and 

the sites of ion binding were determined; the regions in which electrostatic potential changes 

were observed were near those residues in which charge was altered, such as become 

negatively charged (aspartate, glutamate, cysteine) or uncharged (histidine), in the pH range 

studied. The in silico protein-ion binding and protein hydration, by BSA and HSA, were 

compared to the experimental data and the predicted ion-binding results of the free-solvent 

model. 


In vivo Optical Microscopy of Axonal Myelination of a Multiple Sclerosis Disease Model 

with Polarization Sensitive-Optical Coherence Tomography 

Christian Oh 1 and Hyle Park 1 

1 Bourns College of Engineering, Bioengineering Department, University of California, Riverside 

Encephalomyelitis disseminata, commonly known as multiple sclerosis, is an incurable 

autoimmune condition in which the immune system attacks the central nervous system. This 

causes demyelination of nerves and progressive levels of physical and cognitive disability. 

Early detection of demyelination may provide preventable measures for the affected population. 

Myelin exhibits birefringence, and thus, using polarization-sensitive optical coherence 

tomography (PS-OCT), we are capable of imaging nerves and quantitatively assessing the 

degree of myelination. Preliminary results indicate a direct correlation of histological parameters 

with birefringence values obtained from PS-OCT images which allows for a statistically 

significant method of quantifying axonal myelination. We will apply this approach to imaging 

rats in which multiple sclerosis has been induced. By means of direct histological correlation, 

the ability of PS-OCT to evaluate and quantify axonal myelination/demyelination in a nondestructive, 

in vivo manner will be assessed for this disease model. 


Cascaded Micro Concentration Cells 

Oxana S. Pantchenko 1 , Javad Shavani 1 , Mona Zebarjadi 1 , Howard Young 1 , Mehrdad 

Mahmoodi 1 , Michael Isaacson 1 , Ali Shakouri 1 

1 Department of Electrical Engineering, University of California, Santa Cruz 

For generations, electric fish, electrophorus electricushas, have been a subject of 

interest for studying the property of the membrane of electrogenic cell, electrocyte, etc. A few 

have designed mathematical models for mimicking such a complex system while others have 

focused their attention on studying individual types of ionic pumps. We report on the cascading 

of micro concentration cells, the scaling factor, as well as, the resulting power dissipation of 

such system. 


Inhibition of the sodium/calcium exchanger by lithium in intact mouse hearts modifies 

cardiac alternans 

Azadé Petrosky, Dmytro Kornyeyev, Ariel L. Escobar 

School of Engineering, University of California, Merced 

The Na/Ca 2+ exchanger (NCX) plays an important role in the regulation of the cardiac 

function. The aim of our research was to study the effect of impairing NCX with various 

concentrations of LiCl (by replacing Na + with Li + in normal Tyrode solution). We hypothesized 

that the inhibition of the exchanger would lead to the accumulation of Ca 2+ in the cytosol and 

consequently to the enhancement of Ca 2+ release from the sacroplasmic reticulum. Elevation of 

the amplitude of the release can affect the amplitude of cardiac alternans, a beat-to-beat 

oscillation in the various functional characteristics of the heart. The measurements were 

conducted using the Pulsed Local-Field Fluorescence microscopy on Langendorff-perfused 

mouse hearts that were loaded with fluorescent dyes sensitive to Ca 2+ (rhod-2, AM) and 

membrane potential (DI-8ANEPPS). The presence of LiCl was found to slow down the 

restitution of Ca 2+ release as well as to augment Ca 2+ alternans that occur at high stimulation 

frequency (14 Hz, 37˚C). Additionally, LiCl induce a dramatic increase in the diastolic Ca 2+ 

levels. Action potentials were measured to verify the effects of LiCl on the NCX. The maximum 

rate of phase 0 depolarization (dV/dt) of the action potentials and the duration of phase 2 were 

reduced with increasing concentration of LiCl in Tyrode solution. Similar to Ca 2+ alternans, 

action potential alternans was more pronounced in the presence of LiCl. These results suggest 

that in the epicardial layer of the ventricular wall the repolarization of the action potential is 

partially defined by the influx of Na + through NCX. Supported NIH R01-HL-084487 to AE. 


On Calibrating the Power of a Microwave Oven 

Emily J. Reed 1 , Christopher Viney 1 

1 School of Engineering, University of California at Merced 

Commercially available microwave ovens are a convenient source of electromagnetic 

waves that are useful not only for heating food but also as an aid in materials processing. In 

both contexts, it becomes necessary to consider the power output of the microwave source, in 

order to determine the appropriate microwave exposure time for a given application. We use 

beakers of water to investigate how sample volume affects the apparent power as determined 

by a calibration procedure. As a general rule, we find that smaller samples do not accumulate 

energy as effectively as larger samples do, leading to an erroneously low measure of 

microwave power (in some cases, 600 watts too low). We also observe points of deviation from 

this general relationship; these points are considered in view of previously published 

observations on microwave heating of small samples. In addition, marshmallows are used to 

map out the distribution of ‗hot spots‘ in the microwave oven, verifying that sample placement in 

the chamber is important for obtaining consistent results in experiments. Our results 

demonstrate relationships of practical consequence, and suggest directions for further study. 


Optimizing qNano: Characterizing a resizable nanopore 

Jessie Rucker, Asma Uz-Zaman, David Deamer, William Dunbar 

Department of Computer Engineering , University of California, Santa Cruz 

Our goal is to realize the potential of the qNano instrument (developed by IZON) for accurate 

pore characterization and particle analysis. The ability to detect, count and identify nanoscale 

particles in real time would significantly advance 

on-site particle analysis platforms critical to a wide range of quality control and technical 

development applications such as bio-detection in research, pharmaceutical, and hospital 

laboratories. The portable and inexpensive qNano instrument is ideally suited to meet these 

unique particle detection requirements. 

The qNano is a resizable nanopore, electrical characterization is attained by means of 

electrophoresis 2 of charged polystyrene beads 3 . We will model the ionic current through the 

pore as a function of ion concentration, voltage, and pore size. The qNano allows real-time 

control of the nanopore size and applied voltage. Modeling the characteristics of the pore using 

MATLAB, we conclude that although we can detect and count translocation events, 

identification of particle size, concentration, and composition is not possible with only the 

amplifier built into the qNano. We propose for future research interfacing the qNano with an 

AXIOPATCH amplifier to compensate for amplifier deficiencies in qNano. IZON is currently 

designing a custom chip to replace the existing amplifier. Our studies will help identify optimal 

pore geometries and derive the conditions necessary for detection and analysis of particles 

ranging is size from 40 to 800nm. 

2 

(movement of suspended particles carrying a charge through an applied electric field) 

3 

(charged with carboxyl groups, 4 atoms present in carboxylic acid, and DNA) 


In Vitro Culturing of the Ovarian Follicle: Alginate Encapsulation and Evaluation of the 

Nutrients Environment 

Noriko Sausman 1 , P. Talbot 2 , V. G. J. Rodgers 1 


2 Stem Cell Center, University of California, Riverside 

Traditional in vitro culturing methods carried out in a 2-D culture plate do not maintain 

the structural integrity of ovarian follicles, often resulting in the degradation of follicles and 

limited success rate of the in vitro maturation (IVM). To improve culturing methods, it is 

necessary to determine growth conditions that simulate the in vivo environment so that the 

follicles retain their complex 3-D structure and have natural growth and maturation. Here, both 

experimental and computational techniques were used to elucidate the suitable culturing 

condition as well as provide a quantitative understanding of nutrient transport to the follicle for 

improved IVM techniques. 

Experimentally, we propose to use biocompatible alginate hydrogels to encapsulate 

follicles to provide uniform structural supports. To analyze particle preparation parameters, 

maintain encapsulation consistency, we have developed an adjustable concentric needle 

device, a coaxial gas flow extrusion device. The inner needle (18 gauge) carries the alginate 

solution and the outer needle (13 gauge) conducts nitrogen gas, which shears off the extruding 

alginate solution into a droplet size. The adjustable inner needle is varied to alter the gas and 

liquid exit distance. Alginate beads prepared by this concentric needle device were quantified 

and analyzed. In summary, the gas pressure and relative tip locations significantly affected 

overall microparticle morphology or development of particles. The gas pressure was most 

significant for the size and shape of microparticles when formed. 

In order to understand the nutrient environments in which follicles are matured, the 

nutrient transport, mainly glucose, across the alginate layer into the follicle is computationally 

analyzed in COMSOL ® . An asymmetrical 3-D model that reflects the shape and size of the 

alginate bead prepared by the concentric needle is evaluated. 


A Microdevice for Detecting Cytokine Production from Individual Immune Cells 

Jaime Silangcruz, Gulnaz Stybayeva, He Zhu, and Alexander Revzin 

Department of Biomedical Engineering, University of California, Davis, CA 

The high throughput analysis of immune cells at the single cell level is crucial in 

understanding cellular function in response to viral and bacterial infection. In particular, the 

analysis of cytokines produced by immune cells in the presence of pathogens provides 

significant diagnostic value. The present study describes the development of a microfabricated 

cytometry platform used to determine the interferon (IFN)-γ cytokine production of individual 

CD4 + T-lymphocytes (T-cells) isolated from human blood. A mixture of cell and cytokine-specific 

antibodies was co-printed onto a poly(ethylene glycol) (PEG) hydrogel coated glass slide and 

superimposed with an array of PEG microwells via photolithography. This engineered surface 

was then enclosed in a microfluidic device to minimize blood volume requirement. Introduction 

of red blood cell (RBC) depleted whole human blood into the microfluidic chamber followed by 

washing at a pre-defined shear stress resulted in the isolation of individual CD4 + T-cells in PEG 

microwells. Mitogenic activation of the captured T-cells followed by immunofluorescent staining 

in the microfluidic chamber revealed a localized IFN-γ cytokine signal around individual cells. 

Significantly, IFN-γ secretion profiles for hundreds of CD4 T-cells could be characterized at 

single cell resolution. The device and process presented herein marks the first step towards 

functional analysis of immune cells organized into high density single cell arrays. 


Fluorescence Enhancement of Warfarin Induced by Interaction with β-Cyclodextrin 

Jacob M. Vasquez †, ‡ , Andrew Vu † , Jerome S. Schultz † , Valentine I. Vullev †, * 

Department of Bioengineering and Department of Biochemistry and Molecular Biology, 

University of California, Riverside 

Warfarin is the most common agent used for control and prevention of venous as well as 

arterial thromboembolism (blood clots). In aqueous media, warfarin forms inclusion complexes 

with a family of cyclic oligosaccharides, α, β, γ-cyclodextrins (CD). The formation of these 

complexes results in enhancement of the fluorescence of warfarin. Such spectroscopic changes 

offer a venue for the development of bioanalytical methodologies for warfarin quantification in 

biological liquids. We characterized the photophysical properties of warfarin in solvents with 

varying polarity and viscosity. The fluorescence quantum yield of warfarin correlated: (1) 

strongly with the solvent viscosity (R=0.979) and (2) weakly with the solvent polarity (R=0.118). 

These findings indicate that it is the change of the viscosity, rather than polarity, of the 

microenvironment that causes the fluorescence enhancement of warfarin upon binding to β-CD. 

Utilizing the observed fluorescence enhancement in fluorescence titration measurements, the 

binding constants of warfarin to β-CD were obtained (2.610 2 M –1 -3.710 2 M –1 ). Using 

multivariable linear analysis, we extracted the stoichiometry of warfarin-b-CD interaction (1:1). 


Kinetics of Staining: Fluorescence Enhancement Induced by Escherichia Coli 

Marlon S. Thomas, Elizabeth R. Zielins, Duoduo Bao, Baharak Bahmni, Vicente Nunez and 

Valentine I. Vullev 


For more than a century, colorimetric and fluorescence staining has been the foundation 

of a broad range of key bioanalytical techniques and methodologies. The dynamics of such 

staining processes, however, still remains largely unexplored. We investigated the kinetics of 

fluorescence staining of a Gram-negative bacterium, Escherichia coli (E. coli) TOP10, with a 

cyanine dye, 3,3‘-diethylthiacyanine iodide (THIA). The observed fluorescence staining resulted 

from an orders-of-magnitude increase in the emission quantum yield of THIA upon binding to 

the bacterial cells. The kinetics of fluorescence enhancement did not manifest statistically 

significant dependence neither on the dye concentration, nor on the cell density (within the 

investigated concentration ranges). We utilized ANOVA analysis to demonstrate that within a 

95% confidence, the time constants for E. coli are not random. Our findings suggest that this 

assay can provide a very rapid, species specific, fingerprint for bacterial cells. 


Luminal Ca 2+ Regulation of Single RyR2 Channels by Cardiac Calsequestrin 

Patricio Vélez 1,2 , Dmytro Kornyeyev 1 , Marcia Cortés-Gutiérrez 1 , Björn C. Knollmann 3 , Ariel L. 

Escobar 1 


2 Faculty of Sciences, University of Valparaiso, Chile 

3 Department of Medicine, Vanderbilt University Medical Center, Nashville 

Intracellular Ca 2+ measurements in whole hearts show that ablation of Calsequestrin 

(Casq2) causes faster relaxation of intra-SR and cytosolic Ca 2+ transients, accelerated recovery 

of Ca 2+ release and less pronounced Ca 2+ alternans. These changes may be related to Ca 2+ 

buffering by Casq2 but also to luminal control of RyR2 gating by Casq2. We examined this later 

hypothesis combining single channel electrophysiology and lanthanide resonance energy 

transfer. Under steady-state, open probability (Po) of RyR2 of cardiac SR fractions from wildtype 

mice is modulated by luminal [Ca 2+ ]. Po increased from 0.1 to 0.8 when luminal [Ca 2+ ] was 

increased from 6 µM to 8 mM at a fixed cytosolic [Ca 2+ ] of 2 µM. The apparent K D for this 

luminal Ca 2+ modulation was ~1 mM. This effect on RyR2 appears to be mediated by luminal 

sites since it was observed under conditions that precluded Ca 2+ feed-through on cytosolic sites. 

This effect of luminal Ca 2+ was not observed in RyR2 obtained from Casq2 KO mice indicating 

that luminal Ca 2+ regulation of RyR2 requires Casq2. To gain mechanistic insights on the 

Casq2-mediated luminal regulation, we used Tb +3 as a sensitive probe. Fluorescence of purified 

dog SR Casq2 (6 nM) increased in the presence of Tb +3 . This fluorescence was reduced as 

[Ca 2+ ] in the solution increased suggesting that Ca 2+ binds to purified Casq2 (apparent K D ~ 800 

µM) by displacing tightly bound Tb +3 from a common binding site. At fixed cytosolic [Ca 2+ ] of 2 

µM, Po of single RyR2 from dog microsomes increased as a function of luminal [Tb +3 ], 

approaching saturating Po when [Tb +3 ] reached 1 µM (K D ~ 500 nM, Hill coeff. ~5.7). These 

results are consistent with Casq2 acting as luminal sensor detecting intra-SR [Ca 2+ ] and 

translating it into changes in RyR2 gating. Supported by NIH R01-HL-084487 to AE. Supported 

NIH R01-HL-084487 to AE. 


Electrotactile Inducement of the Cutaneous Rabbit Effect (CRE) Across Human 

Fingertips 

Jay P Warren 1 , Marco Santello 1,2 , Stephen I Helms Tillery 1,2 


2 Department of Kinesiology, Arizona State University 

A new electrotactile stimulus (ETS) paradigm was developed to determine if saltatory 

stimuli spanning the fingertips could elicit the CRE. Consistent with work by other groups, our 

previous research indicates that two ETS timing sequences can elicit the CRE on the forearm. 

Both timing sequences consist of two 5 ms electrical pulses delivered to a stimulation site. In the 

first ETS timing sequence, two electrical stimuli are delivered to the same stimulus site, here a 

fingertip, with an inter-stimulus interval (ISI) of 10 ms and are delivered to the next stimulation 

site, the next fingertip, with an inter-digit interval (IDI) of 150 ms. The second ETS timing 

sequence consists of 25 ms ISI and 100 ms IDI. We designed a train of stimuli, the order in 

which the fingertips were stimulated, to induce the CRE across the fingertips. We then 

compared this ―illusory train‖ to three distinctive control trains; tap, motion bias, and a negative 

control. Subjects reported that their middle fingertip (the location of the CRE/illusion) had been 

stimulated in 90 % of tap trials, 40 % of illusory trials, 25 % of motion bias trials, and 15 % of 

negative control trials. In most cases, the presence of stimuli on the middle fingertip was 

reported significantly more often under illusory trains compared to motion bias trains. Alternately 

subjects were asked to, ‗Indicate the order of the preceding stimulus train,‘ the order their 

fingertips were stimulated, and their responses were analyzed for reports of middle fingertip 

stimulation. The data here were very similar to the previous question type. These results 

suggest that saltatory stimuli delivered across the fingertips can generate a cutaneous rabbit 

effect. This is the first time that the CRE has been shown to ‗jump‘ across non-continuous body 

segments that can independently assume different spatial configurations. 


Fluorescent Lifetime Changes as Function of Divalent Cations Ca 2+ and Mg 2+ Ions 

Stephanie Wong 1 , Ariel L. Escobar 1 


The measurement of intracellular Ca 2+ or Mg 2+ concentrations using non-ratiometric 

fluorescent dyes in living cells is a challenging process due to possible experimental artifacts. 

Changes in the measured fluorescence can be attributed not only to changes in the divalent 

concentration, but also in dye concentration, excitation light intensity and illumination/detection 

volumes. These fluorescent indicators showed dramatic changes in the dye‘s quantum 

efficiency between the free and bound form of the dye. These changes in quantum efficiency 

are associated with the time the dye stayed in the excited state before returning to the ground 

state. The development of fluorescence lifetime measurements has proven to be a useful 

method in analyzing the dynamics of fluorescent dye relaxations as functions for Ca 2+ or Mg 2+ . 

Here, we evaluated the steady state and dynamic behavior of three different dyes as functions 

for Ca 2+ or Mg 2+ . Mag-Fluo 4 showed a large change in the quantum efficiency as function of the 

free divalent concentration, and no change in lifetime. Interestingly, Magnesium-Green and 

OGB-5N both displayed a quantum efficiency change and a large fluorescence lifetime 

increase. This approach can be used to measure divalent concentrations in intracellular 

organelles as the sarcoplasmic reticulum of intact beating mouse hearts. Supported NIH R01- 

HL-084487 to AE. 


Alternate Reception for Coil Array Elements 

Bing Wu 1 , Chunsheng Wang 2 , Yong Pang 1 , Xiaoliang Zhang 1,2 

1 Department of Radiology and Biomedical Imaging, University of California San Francisco 

2 UCSF/UC Berkeley Joint Graduate Group in Bioengineering, San Francisco & Berkeley, CA, 

United States 

Phased array coils with densely placed coil elements have been used for magnetic 

resonance imaging to pursue high signal-to-noise ratio or fast imaging acquisitions. Recently 

many companies and research groups reported their array coils with more than 64 channels for 

human torso, head and other applications. However, the coil array with large number of coil 

elements raises a high demand for MRI system in which the large number of receive channels is 

necessary. In this work, we study the possibility to apply array coils to MRI system with less 

receive channels. In such manner, the coil with high number of elements is applicable for MRI 

systems equipped with any receive channels. A general multiple reception technique by using 

alternate reception of coil elements is discussed. A 16-ch head array was then applied to a MRI 

system with 8 receive channels. The result shows that the decoupling between coil elements 

was optimized. Noise correlation is much improved. 

This principle of the alternative reception method is straight-forward and is demonstrated 

in Fig.1. 16 coil elements were divided into two groups, and two continuous receptions were 

conducted for those groups. Images were then combined with sum-of-square method. 

Compared with 8-ch array with NEX2, the image qualities have no much difference. Fig.2 

illustrates the improvements of noise correlation matrix with this alternative reception method. In 

Fig2a, noise correlation is calculated from 16-ch array with 16 receive channels. After grouping, 

noise coefficients were relocated in the matrix (Fig.2b), and after twice receptions (Fig.2c), the 

final noise matrix in Fig.2d has much smaller mean value than the case shown in Fig.2a, which 

indicates the improvements of coil isolations. 

A general method is applied for array coil with less receive channels by using alternative 

reception. Thus the number of array elements and receive channels can be variance. 

FIG.1 

FIG.1 FIG.21 


Lab-on-a-Chip Characterization of Cellular Media using Electrical Impedance 

Spectroscopy 

John Yan 1 , Tingrui Pan 2 

1 Department of Electrical and Computer Engineering, University of California, Davis 


Recent advances in the lab-on-a-chip technologies offer new opportunities for biological 

investigations, which typically require minimal analytes to facilitate the biochemical reactions 

and thereby to improve sensitivity and precision [1]. Several electrical detection strategies, 

including electrical impedance spectroscopy (EIS) techniques, have been demonstrated in the 

lab-on-a-chip systems for high-throughput cellular and biomolecular interrogation recently [2,3]. 

In this abstract, we reported a lab-on-a-chip system incorporating miniature label-free detection 

electrodes into a PDMS-based microfluidics for cellular media characterization. A variety of 

cellular contents, including bacterial and mammalian cell media, have been fully characterized 

in the system. Furthermore, an electrical circuit model with noise considerations has been 

developed to interpret the biological findings from these electrical measurements. 

[1] J. El-Ali, P. K. Sorger and K. F. Jensen, Nature, 2006, 442, 403–411. 

[2] K. Cheung, S. Gawad and P. Renaud, Cytometry, Part A, 2005, 65, 124–132. 

[3] K. Ahn, C. Kerbage, T. P. Hunt, R. M. Westervelt, D. R. Link and D. A. Weitz, Appl. Phys. 

Lett., 2006, 88(2), 024104. 


Miniature Electrochemical Biosensors for Detection of Extracellular Metabolites 

Jun Yan 1 , Valber D. Pedrosa 2 , Aleksandr L. Simonian 2 , Alexander Revzin 1 


2 Materials Research and Education Center, Department of Chemical Engineering, Auburn 

University, Auburn 

Seamless integration of biological and electrochemical sensing components is critical for 

successful development of BioMEMS. In this presentation, we will propose a platform that 

integrates small group of cancer cells with miniature glucose electrochemical biosensors in a 

microfabricated device where cellular microenvironment can be precisely defined and easily 

modulated. The juxtaposing of miniature sensing elements with cells is achieved through 

photolithographic patterning of glucose oxidase (GOX)-containing poly (ethylene glycol) (PEG) 

hydrogel microstructures on silane modified glass substrates. Gold microelectrode array is 

fabricated onto regular glass slide using standard semiconductor process of photolithography. 

The ability to deposit enzyme-containing hydrogel microstructures onto gold microelectrodes is 

very critical for the development of electrochemical bisosensors. PEG patterning process is 

very similar to the traditional photoresist lithography so that enzyme containing PEG can be 

fabricated on top of existing gold microelectrodes. Enzyme GOX is entrapped inside PEG 

hydrogel. To facilitate electron transfer through PEG hydrogel and wire GOX, redox polymer 

vinylferrocene is also added to PGE precursor solution and covalently bound to PEG polymer 

during UV exposure. Importantly, enzyme-entrapping hydrogel micropatterns do not support 

protein or cell deposition and allowed to guide attachment of small group of cells next to the 

sensing elements. The determination of glucose generation by stimulated cells is accomplished 

using three-electrode electrochemical system. In addition, the PEG hydrogel lithography also 

allows us to deposit second enzyme such as lactate oxidase (LOX) next to GOX using the same 

method, realizing simultaneous detection of two analytes. A microfluidic device is developed to 

enclose cells and sensing hydrogel elements inside a confined volume of ~ 2 µl, thus increasing 

sensitivity of the biosensor and allowing to dynamically change the extracellular 

microenvironment. This novel electrochemical dual biosensor integrated with cell cultivation 

element is envisioned as an in vitro model of metabolism study of cancer cells. 


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