2012 Summer Symposium Program - Middlebury College

Summer 

Research Symposium 

Student Research Abstracts 

Thursday, August 2, 2012 | 2:00–4:00 p.m. 

McCardell Bicentennial Hall

The Summer Research Symposium is an annual event where students present posters of their 

summer research projects for faculty, staff, and other students. It is a great opportunity to 

write an abstract, produce a poster and then explain the project to prepare for a professional 

conference. 

Most of the students are Summer Research Assistants who receive stipends to work with a 

faculty mentor during the summer. Faculty benefit by having quality research assistance that 

can bridge the academic year and span multiple summers. Students benefit from the in-depth 

learning that is possible over the focused summer weeks. Research has been shown to be one of 

the high impact educational practices that students benefit from most in higher education. 

Summer assistants are supported by multiple funding sources such as faculty and institutional 

grants and Middlebury College endowments. Funding sources are noted on the left column of 

the abstracts. 

Statistics at the time of the symposium show over 100 students were Summer Research 

Assistants in 2012 in the following general departments or programs: 

Athletics (1) 

Biology (14) 

Center for Teaching, Learning and Research (1) 

Chemistry (15) 

Computer Science (7) 

Economics (14) 

English & American Literatures (3) 

Environmental Studies (3) 

Geography (6) 

Geology (11) 

Music (1) 

Philosophy (1) 

Physics (7) 

Political Science (6) 

Psychology (5) 

Sociology & Anthropology (1) 

Spanish (1) 

Students worked an average of 36 hours and 8.5 weeks contributing over 29,000 hours 

of research time to the college in the summer of 2012! 

Thank you to all the faculty, staff, and students for all your hard work and enthusiasm. 

Undergraduate Research Office 

Middlebury College 

Bob Cluss, Dean of Curriculum and Faculty Development 

Kathy Skubikowski, Director of the Center for Teaching, Learning, and Research 

Colleen Norden, Administrative Assistant 

go.middlebury.edu/uro

Middlebury Summer Research Symposium 2012 

Abstract Title Page 

1 Does Context Matter in Lexical Simplification? 4 

Patrick Adelstein, Edward Pendergast, and David Kauchak 

2 Substrate effect on periphyton composition and abundance in the New Haven River 4 

Meg Anderson and Sallie Sheldon 

3 Characterizing aquatic macroinvertebrate communities along an elevational gradient in 5 

Vermont rivers following tropical storm Irene 

Samouel Beguin and Sallie Sheldon 

4 Assessing the Source of Uranium and Alpha Radiation in Northwestern Vermont: 5 

The Role of Depositional Environment 

Kevin Chu and Peter Ryan 

5 Identifying Critical Nucleotides for the SloR:SRE Interaction in S. mutans 6 

Lou Cornacchione and Grace Spatafora 

6 Colonization of Leaf Pack Microhabitats by Macro-invertebrates in the New Haven River 7 

Nicholas Dragone and Sallie Sheldon 

7 Implications for Low-Temperature Geothermal Resources in Vermont: 8 

A Bedrock Mapping and Geochemical Perspective from Northeastern Addison County 

Julia Favorito and Peter Ryan 

8 Electromagnetic Scattering: Modeling Asymmetric Dielectrics 9 

Aden Forrow, Bjorn Kjellstrand and Noah Graham 

9 Mutational Analysis of SloR Amino Acid Residues: Finding their Respective Roles in 9 

SloR-DNA Binding 

Clark Hatheway and Grace Spatafora 

10 Attentional Biases to Trauma Relevant Stimuli in Motor Vehicle Accident Survivors 10 

and Veterans of the Iraq War: An Eye Tracking Study 

Patrick Hebble, Hugh Randall, and Matthew Kimble 

11 Manipulating Beam Polarization for Laser Cooling 11 

Jacob Hobbie and Anne Goodsell 

12 Effects of the Cognitive Interview on Children’s Dietary Recalls 11 

Kelsi Morgan, Nora Keathley and Michelle McCauley 

Page 1

Page 2 


13 Surfactant Modification of Montmorillonite for Environmental Contaminant 12 

Remediation 

Malcolm Littlefield, Annie Mejaes, and Molly Costanza-Robinson 

14 Utilization of Academic Support Services at the Center for Teaching, Learning, 12 

and Research 

Adrienne Matunas and Yonna McShane 

15 Preparing a Proper Environment for Cooling Atoms 13 

Poomirat Nawarat and Anne Goodsell 

16 3D Capture of Complex Real-World Scenes 14 

Nera Nesic, Xi Wang, and Daniel Scharstein 

17 An Atlas of Stars Past: Supernova Remnants in the Optical Spectrum 15 

Lucia Perez, Teddy Smyth and Frank Winkler 

18 Phosphorus Abundance and Reactivity in Champlain Valley Sediments: Implications 16 

for Nutrient Transport to Lake Champlain 

Lauren Pincus and Peter Ryan 

19 Characterization of 4- and 5-coordinate Co(II) Model Complexes by Magnetic 16 

Circular Dichroism Spectroscopy 

Nathan Rudd and Jim Larrabee 

20 Origin of the Moretown Formation, Vermont: A Detrital Zircon Study 17 

Juliet Ryan-Davis, Ray Coish, and Will Amidon 

21 Comparative MCD study of DapE-Encoded N-Succinyl-l,l-Diaminopimelic Acid 18 

Desuccinylase (DapE) from Haemophilus influenza and Neisseria meningitides 

Wisath Sae-Lee (Momo) and Jim Larrabee 

22 Constructing mutant variants of the S. mutans SloR metalloregulatory protein: 19 

A crystal structure on the horizon 

Garron Sanchez and Grace Spatafora 

23 Mapping Natural Communities for the Nature Conservancy/ Vermont Natural 20 

Heritage Program 

Avery Shawler and Bill Hegman 

24 The Effect of Metamorphic Grade on Arsenic in Bedrock and Groundwater: 20 

An Analysis of Shales, Slates, Phyllites and Schists from the Champlain Valley Sequence 

in Quebec and Vermont 

Annika Silverman and Peter Ryan


25 The Effect of SloR on Streptococcus mutans susceptibility to chlorhexidine digluconate 21 

Meghan Stang and Grace Spatafora 

26 Expression and purification of the enzyme methionine aminopeptidase for magnetic 22 

circular dichroism and equilibrium dialysis studies 

Matthew Thomas Stanley and Jim Larrabee 

27 Glycation Inhibits Cytochrome c’s Ability to Induce Apoptosis 23 

Karl Wetterhorn, Emily Martine and Roger Sandwick 

28 The Production of Molecular Wires through Acyclic Diene Metathesis (ADMET) and 24 

Ring Opening Metathesis Polymerization (ROMP) of Chromium Organometallic Arenes 

Peter Hetzler, Mark Isbell, Rachel Fowler and Jeff Byers 

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1 

Patrick Adelstein ‘14 

Major: CSCI, MATH 

Bicentennial Fund 

Edward Pendergast ‘13 

Major: CSCI 


David Kauchak 

Assistant Professor of Computer 

Science 

2 

Meg Anderson ‘14 

Major: BIOL 

VT EPSCoR/RACC 

Sallie Sheldon 

Professor of Biology 


Does Context Matter in Lexical Simplification? 

Patrick Adelstein, Edward Pendergast, and David Kauchak 

Department of Computer Science, Middlebury College, Middlebury VT 05753 

Lexical Simplification is the task of replacing a target word or phrase in a sentence 

to make the sentence simpler. Lexical simplification is a sub-problem of the full 

text simplification problem which can benefit children, second language learners, 

and people with cognitive disabilities. In this paper we investigate whether the 

textual context surrounding the word to be replaced is important in identifying and 

selecting substitutions. Starting with a corpus of sentence-aligned English Wikipedia 

and Simple English Wikipedia data we generated lexical simplification examples. 

These examples consist of a sentence, a target word to replace, and a list of candidate 

substitutes solicited from users on Amazon’s Mechanical Turk service. We compare 

data collected both with and without the sentence context and utilize a variety of 

metrics including frequency, entropy, and similarity of the collected substitutes. We 

find that for some words context does matter for the simplification task, however not 

for all words. 

Substrate effect on periphyton composition and 

abundance in the New Haven River 

Meg Anderson and Sallie Sheldon 

Department of Biology, Middlebury College, Middlebury VT 05753 

This study focused on the relationship between rock size and the algae covering the 

rock surface (periphyton). Glass microscope slides were installed in three different 

substrate types (sand/gravel, coarse gravel and cobble/boulder) in a small section of 

the New Haven River in Bristol, Vermont. Slides were collected over the course 

of three weeks to assess species composition, and after three and a half weeks, 

periphyton on the cement blocks was dried and weighed. Species composition was 

similar between substrate types, and periphyton density increased over time in the 

stream. Periphyton abundance was directly related to substrate size with very little 

periphyton accruing on cement blocks in sand/gravel. The results from this study 

suggest that while the composition of periphyton in streams may not be related 

to substrate type, the abundance of periphyton is affected. Further research using 

cement blocks and natural substrates will lead to better understanding of which 

abiotic factors have the greatest effect on periphyton in streams.

3 

Samouel Beguin ‘13 

Major: ENVS, Biology 

VT EPSCoR 



4 

Kevin Chu ‘14 

Major: ENVS, GEOL 

Baldwin/Coney Fund 

Peter Ryan 

Professor of Geology 


Characterizing aquatic macroinvertebrate 

communities along an elevational gradient in 

Vermont rivers following tropical storm Irene 

Samouel Beguin and Sallie Sheldon 


In August 2011, tropical storm Irene struck the Northeastern United States. The 

state of Vermont in particular experienced damaging rainfall and flooding. In order 

to assess the impact of this large-scale disturbance on Vermont’s river ecosystems, 

we studied stream macroinvertebrate communities along an elevational gradient. 

Macroinvertebrates were sampled at sites along each river by rubbing stream rocks 

smooth and agitating streambed gravel. The number and proportions of different 

types of macroinvertebrates were recorded and used to calculate several metrics 

describing the composition, taxa richness, and functional feeding groups at each 

site. Preliminary results for two rivers in the western region of the state revealed 

clear biological gradients corresponding to decreasing elevation, with certain 

macroinvertebrate groups found mainly at high elevation sites and others found 

mainly at low elevation sites. Several significant relationships were also found 

between physical stream characteristics (e.g. canopy cover, dominant substrate type) 

and various macroinvertebrate metrics, indicating that physical gradients influence 

biological gradients. By combining these results with physical and macroinvertebrate 

data from four other Vermont rivers and future Geographic Information Systems 

(GIS) analysis, this research will improve understanding of the impacts of both 

large-scale disturbance and watershed land use on macroinvertebrate assemblages at a 

variety of spatial scales and across a range of storm severity regions. 

Assessing the Source of Uranium and Alpha 

Radiation in Northwestern Vermont: The Role of 

Depositional Environment 

Kevin Chu and Peter Ryan 

Department of Geology and Environmental Studies, Middlebury College, Middlebury VT 05753 

Jonathan Kim, Geologist/Environmental Scientist, Vermont Geologic Survey 

From 2000–2002, the Vermont Geological Survey (VGS) found that ~35% of private 

wells in Milton and Colchester, VT contain alpha radiation above the VT and EPA 

MCL of 15 pCi/L. The source was identified as black chips within the Clarendon 

Springs Formation (CSF). Jonathan Kim and colleagues from the VGS speculated 

that the black chips were rich in organic material and uranium and hypothesized 

that the black chips were evidence for ancient cave collapse breccias; however, 

they did not perform geochemical or mineralogical analyses of the black chips. 

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5 

Lou Cornacchione ‘13 

Major: MBBC 

Ostro Family Molecular Biology 

and Biochemistry Research 

Fund 

Grace Spatafora 

Given Professor of Biology & 

Pre-Medical Sciences 


Follow-up research in 2011–2012 by Emily McDonald was prompted by concerns 

of citizens in Highgate, VT where the CSF outcrops. Field work consisting of well 

and bedrock sampling, followed up with lab analyses, led to the development of 

a model in which fluoroapatite incorporates U into its mineral structure on the 

ancient seafloor. During marine upwelling, U +4 co-precipitates in place of Ca +2 in 

the structure of Ca 5 (PO 4 ) 3 F. It is authigenic but can be re-mobilized by bottom 

currents and redeposited as rip-up clasts, possibly explaining the breccias throughout 

the CSF. Bedrock samples from Colchester and Milton, VT are being analyzed 

using a combination of XRD, SEM-WDS SEM-WDS, ICP-AES, ICP-MS, and 

gamma ray spectrometry to interpret geochemistry, mineralogy, and distribution of 

breccias and other lithologies in the CSF. Early XRD results have yielded positive 

results for fluoroapatite at a site in Colchester where high radioactivity had been 

confirmed using gamma ray spectrometry. Fluoroapatite hosts high uranium content 

(80-300 ppm) in black chip breccias farther north in Highgate (crustal average 

is 3 ppm). Distinctive X-ray diffraction peaks at 0.281, 0.270, 0.244, 0.277, 0.317, 

and 0.263 nm provided the positive identification of fluoroapatite. XRD was also 

useful in differentiating fluoroapatite in sample 061412-1 and 061412-3 at the highradioactivity 

site from chert in sample 061412-14 at Thompson Farm that is not a 

source of U. Further analysis will include ICP-AES at Middlebury College, ICP-MS 

at a contract lab (for uranium and thorium content as well as other trace elements), 

and SEM-EDS and SEM-WDS for analysis of the micron-scale spatial distribution of 

P, U, and other elements. 

Identifying Critical Nucleotides for the SloR:SRE 

Interaction in S. mutans 

Lou Cornacchione and Grace Spatafora 


Streptococcus mutans is considered to be the most cariogenic bacterial species among 

those resident in the human oral cavity. S. mutans-induced dental caries have 

been implicated in a variety of health risks and are associated with substantial 

economic costs. Researchers in the Spatafora laboratory previously demonstrated 

that a multitude of virulence genes in S. mutans are regulated by a 25-kDa 

metalloregulatory protein called SloR. SloR is known to bind to palindromic 

recognition elements (SREs) at promoter-proximal or -distal regions in a 

manganese-dependent manner to either repress or activate downstream genes, 

respectively. The sloA gene with a promoter-proximal SRE that is repressed in the 

presence of elevated manganese concentrations belongs to a sloABC operon, which 

encodes an important manganese transporter involved in metal ion homeostasis. 

Importantly, a SloR-deficient strain of S. mutans, GMS584, has been demonstrated 

to be hyper-cariogenic in a germ-free rat model, and to de-repress virulence 

genes in qRT-PCR experiments. The goal of the present study is to further our

6 

Nicholas Dragone ‘14 

Major: BIOL 

Vermont EPSCOR 




understanding of the SloR:SRE interaction, by introducing point mutations 

into the SRE that precedes the sloABC operon. We based our rationale for SRE 

mutagenesis on a probability matrix that we generated previously, and that includes 

an interrupted palindrome of 22bp. Specifically, we generated T-to-C transitions 

at positions 15, 16, and 19 within the sloA SRE using an OE-PCR and a markerless 

mutagenesis approach. In addition, we monitored sloABC expression in both 

GMS615 and GMS616, S. mutans strains harboring transitions at SRE positions 15 

and 16 respectively, in qRT-PCR experiments. Expression in GMS616 was derepressed 

relative to the UA159 wild-type progenitor strain, whereas expression in 

GMS615 was not significantly different from that of UA159. These findings implicate 

thymidine-16 as important for the SloR:SRE binding and subsequent repression 

of the sloABC transcript. Interestingly, previous DNA footprinting experiments 

that we performed with SloR revealed an additional region of protection between 

two and twelve base pairs upstream of the SRE. To confirm that these upstream 

nucleotides are involved in the SloR:SRE interaction, we are targeting eight 

additional nucleotides, mainly thymidine residues, for mutation by OE-PCR. Gel 

mobility shift experiments are planned with these mutated SRE variants to assess 

their relative binding affinities with SloR. The identification of critical nucleotide 

bases for SloR binding in this important oral pathogen is significant because it could 

inform rational drug design for anti-caries therapeutics. 

Colonization of Leaf Pack Microhabitats by 

Macro-invertebrates in the New Haven River 

Nicholas Dragone and Sallie Sheldon 


Stream Macro-invertebrate communities consist of different guilds based on feeding 

behavior. The presence of a guild in a stream microhabitat depends on the food 

source available at the site, and the substrate structure. Leaf Packs are an important 

stream microhabitat for invertebrates. In this study, artificially created leaf packs were 

placed in the field to determine whether invertebrate guilds colonize based on the 

presence of the food source, or of the structure the leaves provide. An experiment 

using sugar maple leaves, red oak leaves, and plastic leaves, was set out in the New 

Haven River. Leaf packs were collected after 1 week, 2 weeks, or 4 weeks, to 

determine whether macro-invertebrate colonization and utilization changed as the 

leaves broke down. Sugar maple leaves and oak leaves had the highest abundance of 

invertebrate while plastic leaves had the lowest abundance. There was no difference 

in the presence of guilds among the three leaf treatments although filterers and 

gatherers were the most abundant on all three treatments. This result suggests that 

leaf packs in streams are primarily used for structure, and not food. 

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7 

Julia Favorito ‘12 

Major: GEOL 

Vermont Geological Survey 

Peter Ryan 



Implications for Low-Temperature Geothermal 

Resources in Vermont: A Bedrock Mapping and 

Geochemical Perspective from Northeastern 

Addison County 

Julia Favorito and Peter Ryan 

Department of Geology, Middlebury College, Middlebury VT 05753 

Research into the low-temperature geothermal energy potential in Vermont is 

currently being carried out by the Vermont Geological Survey (VGS) in conjunction 

with student researchers from Middlebury College and UVM. Some of the interest 

in geothermal potential is based on the discovery of groundwater wells with elevated 

uranium and thorium in metasedimentary rocks of the western Green Mountains 

as well as granites in central and eastern Vermont. In the vicinity of Bristol and 

Starksboro (northeastern Addison County, VT), early Cambrian metasedimentary 

rocks of the Pinnacle Formation and Cheshire Quartzite are the target of this 

current project. Previous work by the Vermont Geological Survey and Middlebury 

College (e.g. theses of Katharine North, 2005; Leland Davis, 2008; Jared Bean, 

2009) in Hinesburg indicates that metamorphosed sandstones and mudstones of the 

Pinnacle and Fairfield Pond formations as well as the Cheshire Quartzite commonly 

contain U and Th which are elevated ~3–5 times above background levels. Although 

these elevated levels of U and Th cause issues with water quality, they also may have 

a potential benefit in that deep wells may contain water that is warmer than normal 

ambient groundwater. This would be caused by radioactive decay of U and Th 

and their daughter products. Examining data from the theses cited above indicates 

that average water temperature in wells drilled into the metasedimentary rocks is 

11.5 o C; by comparison, wells drilled into unmetamorphosed carbonate rocks in 

the same area is 10.0 o C. This provides impetus to analyze water temperatures and 

bedrock U and Th concentrations in an area (Bristol, Starksboro) where these rocks 

are particularly thick and well-exposed. My research to date includes a considerable 

amount of field work with Jon Kim of the VGS mapping out fractures and bedrock 

in Bristol. Fractures play a major role in the movement of water and bedrock type 

likely will strongly control geothermal potential, so both of these factors must be 

closely mapped out in order to move ahead with a geothermal project. In addition 

to field mapping and fracture analysis, I have also researched types of geothermal 

energy systems that might be appropriate for the climate and bedrock types in an 

area like Vermont. In th next two weeks I will begin to focus on the chemical 

analysis of rock compositions as well as borehole temperature analysis. In my 

presentation at the symposium I will be presenting my findings on the possibilities 

for geothermal energy in Vermont based on the research and field work I have done 

so far this summer.

8 

Aden Forrow ‘13 

Major: PHYS, MATH 

National Science Foundation 

(Graham) 

Bjorn Kjellstrand ‘13 

Major: PHYS 

Noah Graham 

Associate Professor of Physics 

9 

Clark Hatheway ‘13 

Major: MBBC 

NIH Summer Research 

Fellowship 





Electromagnetic Scattering: Modeling 

Asymmetric Dielectrics 

Aden Forrow, Bjorn Kjellstrand and Noah Graham 

Department of Physics, Middlebury College, Middlebury VT 05753 

What happens when light interacts with an object? The relationship between 

the light that went in to the object and the light that comes out gives important 

information about the object itself. Knowing the shape of the object and the 

differential equations governing electromagnetism should let us calculate this 

relationship; the equations, however, are too complicated to solve analytically except 

in the simplest cases. We are developing numerical techniques in Mathematica that 

do not rely on specific symmetries of the object and are therefore useful in many 

more situations. 

Mutational Analysis of SloR Amino Acid 

Residues: Finding their Respective Roles in 

SloR-DNA Binding 

Clark Hatheway and Grace Spatafora 


Streptococcus mutans is a gram-positive bacterium normally present along with other 

microbes in the microflora of the oral cavity. It plays a principal role in cariogenesis, 

as acidic byproducts of its metabolism lower the pH of the plaque environment, 

resulting in demineralization of the dental enamel. Of particular interest to the 

Spatafora laboratory is a metalloregulatory protein called SloR, which regulates 

transcription by binding to short palindromic SloR Recognition Elements (SRE) 

present distal or proximal to various genes that have been implicated in S. mutans 

virulence. SloR has been shown to repress expression of the sloABC gene cassette, 

which codes for an essential manganese ion transport system. SloR does so by 

binding to a SRE located upstream of the sloABC genes and proximal to the sloABC 

promoter. Previous studies in our laboratory have focused on mutational analysis of 

the SloR protein within each of three different functional domains to identify amino 

acid residues that are essential for SRE binding. In this study we expanded upon this 

work by generating additional mutations in the DNA binding, dimerization, and 

FeoA domains. Specifically, we used OE-PCR site-directed mutagenesis to generate 

SloR variants with conservative substitutions in sites previously identified to be 

important for the SloR-SRE interaction, as well as non-conservative substitutions 

in additional sites that we believe are important. We subsequently cloned the 

SloR variant amplicons into the pDL277 shuttle vector for transformation into 

a SloR-deficient S. mutans strain called GMS182. This strain harbors a fusion of 

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10 

Patrick Hebble ‘13 

Major: NSCI 

NIH AREA Grant (R15 

MH081276) 

Hugh Randall ‘14 

Major: PSYC at UVM 

NIH AREA Grant (R15 

MH081276) 

Matthew Kimble 

Associate Professor of 

Psychology 


the sloA promoter to a cat reporter gene within the bacterial chromosome. Future 

experiments will assess the putative effect(s) of these mutations on SloR binding 

to the promoter-proximal SRE at the sloABC locus. Residues identified as being 

important to the SloR-SRE interaction could be potential therapeutic targets. 

Treatments could be developed that would interfere with or enhance this interaction 

with the aim of controlling S. mutans virulence and cariogenicity. 

Attentional Biases to Trauma Relevant Stimuli in 

Motor Vehicle Accident Survivors and Veterans of 

the Iraq War: An Eye Tracking Study 

Patrick Hebble, Hugh Randall, and Matthew Kimble 

Department of Psychology, Middlebury College, Middlebury VT 05753 

Attentional impairment is one of the symptoms most often associated with posttraumatic 

stress disorder (PTSD). Yet, the manifestation of these impairments is 

complex and still not completely understood. The DSM-IV lists that both avoidance 

of stimuli associated with trauma and hyper-arousal/vigilance are symptoms of 

PTSD (APA, 2000). While many studies have used event related potentials to study 

these attentional biases in PTSD, relatively few have used eye tracking technology 

to do the same. Our research is a follow up to one such study (Kimble et. al., 2010). 

In this study a group of veterans of the Iraq war (n=19) were presented with a 

series of 20 slides containing two images: one negatively valenced picture and one 

neutral. Negatively valenced pictures varied in terms of trauma relevance [Iraq War 

vs. Motor Vehicle Accident (MVA) images]. Participants were told to look at the 

images as they interested them while their eye movements were being tracked. The 

study found that veterans with comparatively higher levels of PTSD symptomology 

spent more time looking at the negatively valenced imaged (regardless of trauma 

relevance) than participants who reported lower levels of PTSD symptoms. In 

addition, the veterans reporting higher levels of PTSD symptoms also tended to look 

towards Iraq images first, suggesting that PSTD is associated with hyper-vigilance 

rather than avoidant behavior when processing trauma relevant stimuli. In this study, 

we collected data from MVA survivors (n=17) using Kimble et al.’s (2010) methods 

and compared it to their combat veteran sample. All subjects tended to look first and 

longest at negatively valenced images. However, regardless of PTSD levels, veterans 

looked at the negative images significantly longer than the MVA survivors. Veterans 

also looked at the negative images first significantly more than the MVA survivors 

regardless of PTSD symptoms. Finally, while not statistically significant, veterans 

looked at trauma relevant images longer than MVA survivors. These findings suggest 

that trauma type plays a key role in post-traumatic pathology, and that the levels of 

vigilance and avoidance in persons with PTSD may be dependent on the type of 

trauma one experienced.

11 

Jacob Hobbie ‘15 

Major: PHYS 

Elizabeth Miller Palen ‘40 Fund 

Anne Goodsell 

Assistant Professor of Physics 

12 

Kelsi Morgan ‘14 

Major: LITS 

Vermont Genetics Network 

Michelle McCauley 

Professor of Psychology 


Manipulating Beam Polarization for Laser 

Cooling 

Jacob Hobbie and Anne Goodsell 


In the Goodsell lab, we are constructing an apparatus to trap and laser cool 

Rubidium atoms. To perform this, we are using a laser that is tuned to emit light at 

a precise frequency. Using mirrors to direct the path of the beam, we send our laser 

through various pieces of optical equipment, each with a specific function. Devices 

such as lenses allow us to reshape the laser beam, while others such as wave plates 

allow us to alter the polarization, or the orientation of the oscillations of the light 

wave. The polarization of light is crucial for the central part of our experiment: 

laser cooling of atoms. Light that is polarized circularly, that is to say the orientation 

of the oscillations rotates as the light travels, is used to cool and trap atoms inside a 

vacuum chamber and hold them in a very small region. With three intersecting laser 

beams, atoms are prevented from escaping in any direction. Laser cooled atoms are 

particularly useful to perform experiments on because they have minimal initial 

velocity. When we entered the lab this summer, the laser only passed through several 

optical components on a small section of the table. Currently, the laser is split into 

three beams that now pass through the vacuum chamber which we assembled. We 

also installed a second “repump” laser that will perform a slightly different function 

from the original laser. This also required installing many of the optical components 

also placed in the path of the first laser. 

Effects of the Cognitive Interview on Children’s 

Dietary Recalls 

Kelsi Morgan, Nora Keathley and Michelle McCauley 

Department of Psychology, Middlebury College, Middlebury VT 05753 

This study examined whether children interviewed with the Enhanced Cognitive 

Interview (ECI) would perform better on a dietary recall task compared to those 

interviewed with the multiple-pass protocol (MPP), and if so, which type(s) of 

fact recall the ECI improves, and where in the interview these facts are found. 

Fifty-seven children (average age 7 years) participated in an after-school event that 

involved eating snacks. After an average two-day delay, the children were asked to 

recall the foods they had seen and eaten at the event with either the ECI or MPP. 

The ECI allowed for a higher recall of overall facts without compromising accuracy. 

The findings also show an increase in accurate fact recall with the ECI without an 

increase in inaccurate or intrusive information. The study also found that these facts 

are not evenly distributed throughout the interview: by splitting each interview’s 

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13 

Malcolm Littlefield ‘13 

Major: ENVS, CHEM 


(Costanza-Robinson) 

Annie Mejaes ‘13 

Major: ENVS, CHEM 


(Costanza-Robinson) 

Molly Costanza-Robinson 


Chemistry and Environmental 

Studies 

14 

Adrienne Matunas ‘13 

Major: RELI, PHIL 

Undergraduate Collaborative 

Research Fund 

Yonna McShane 

Director of Learning Resources 

for CTLR 


substantive section into thirds, we found that accurate, inaccurate, intrusive facts 

occur in differing patterns by time, as does the proportion of accurate facts for each 

interview. These findings have important implications for health professionals who 

interview children. 

Surfactant Modification of Montmorillonite for 

Environmental Contaminant Remediation 

Malcolm Littlefield, Annie Mejaes, and Molly Costanza-Robinson 

Department of Chemistry & Biochemistry, Middlebury College, Middlebury VT 05753 

Surfactant-modified clay minerals (organoclays) are increasingly being examined 

as a cost-effective, sorbent for environmental contaminants (e.g., for groundwater 

remediation). However, few studies have examined the relationship between the 

microstructure and chemistry of the organoclay and its capacity to adsorb various 

contaminants. Our work this summer involved preparing and characterizing 

a Na-montmorillonite that we modified with the cationic surfactant myristyl 

trimethylammonium bromide. The organomontmorillonite was prepared at various 

surfactant surface coverages (% of cation exchange capacity, CEC). X-ray diffraction 

revealed the basal spacing of 100 % CEC montmorillonite to be 17.8 Å, significantly 

larger than that for unmodified montmorillonite (12.5 Å). An expanded basal spacing 

may increase the clay’s adsorption capacity for larger contaminants. No uptake of 

aniline, a model contaminant, was observed for unmodified montorillonite, whereas 

1.2 mg/g of aniline was adsorbed by the 100% CEC modified montorillonite. We 

attribute these findings to the increased hydrophobicity of the modified clay surface, 

as well as the increased basal spacing. These preliminary findings, along with 

additional data, will greatly increase our ability to optimize clays for contaminant 

uptake. 

Utilization of Academic Support Services at the Center for Teaching, 

Learning, and Research 

Adrienne Matunas and Yonna McShane 

Center for Teaching, Learning, and Research, Middlebury College, Middlebury VT 05753 

The Center for Teaching, Learning, and Research offers an array of academic 

support services to Middlebury students, including peer and professional tutoring 

in writing, quantitative disciplines, languages, oral presentation skills, study skills, 

and time management. Literature reviews about postsecondary academic support 

reveal the widespread belief that learning centers at 4-year institutions serve a 

small segment of the student body, predominantly first-year students and students 

experiencing academic crises. At institutions like Middlebury where student 

achievement is very high, it is often assumed that few students seek tutoring, or that

15 

Poomirat Nawarat ‘14 

Major: PHYS, CSCI 


Anne Goodsell 

Assistant Professor of Physics 


only first-year students or students with serious academic needs utilize academic 

support services. Data collected from AccuTrack, the CTLR’s tutoring database, 

challenge these assumptions. Over 44% of the Middlebury student body met with a 

CTLR tutor over the course of the 2011–2012 academic year, and more than half of 

visits to professional tutors, peer content tutors, and peer writing tutors were made 

by sophomore, junior, and senior students. In addition, many of the students who 

met with tutors had high grade point averages, up to and including 4.0. Continued 

research will focus on academic outcomes for students who took advantage of 

CTLR services in order to understand more precisely the impact of tutoring and 

academic support on student achievement at Middlebury. 

Preparing a Proper Environment for Cooling 

Atoms 

Poomirat Nawarat and Anne Goodsell 


The ultimate goal of our project is to perform laser cooling on a dilute gas of neutral 

atoms, which is Rubidium in our case. In order to achieve this goal one needs to 

construct a proper integrated system from smaller systems that function in many 

different tasks needed in the cooling process. We need lasers for cooling the dilute 

gas. We need a proper optical system to manipulate the laser beams. We need a 

vacuum chamber to keep the gas dilute in low temperature. We need a pump system 

to create and maintain the proper low-pressure environment within the chamber. 

We need a magnetic-field system to confine the cold atoms in a finite space. For our 

experiment all these component systems need to work well together in one complex 

system of cooling, like many pieces of a jig-saw puzzle are required for a complete 

picture. In the beginning of summer we already had most of the equipment, 

however we only had one laser and some part of optical system that had been set 

up and ready to use. My tasks are setting up two extra lasers, vacuum chamber and 

ion pump, and also helping in optical alignment. Now we already have a proper 

arrangement of the vacuum chamber and ion pump system that can maintain the 

pressure at 1.0x10 -10 Torr. We can also manipulate the three pairs of laser beams to 

cross each other in the middle of the chamber in the simple Cartesian configuration. 

Page 13

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16 

Nera Nesic ‘13 

Major: CSCI 

NSF Grant IIS-0917109 

(Scharstein) 

Xi Wang ‘14 

Major: CSCI, ECON 

NSF Grant IIS-0917109 

(Scharstein) 

Daniel Scharstein 

Professor of Computer Science 


3D Capture of Complex Real-World Scenes 

Nera Nesic, Xi Wang, and Daniel Scharstein 

Department of Computer Science, Middlebury College, Middlebury VT 05753 

The goal of this project is to create new datasets and benchmarks for 3D 

reconstruction methods. Middlebury hosts an internationally-known benchmark 

for stereo algorithms, which compute 3D depth maps from multiple input images. 

Existing test datasets, however, do not exhibit real-world challenges such as 

complex occlusion, large depth ranges, and specular objects. Building on work 

done in previous summers, we used a mobile stereo rig with four cameras and 

structured lighting from two video projectors to capture images and accurate 3D 

scene structure. We acquired 7 new datasets of different scenes, each under multiple 

lighting conditions and exposures. Our new datasets include a reconstruction of the 

famous Tsukuba “head and lamp” scene as well as a motorcycle scene in which we 

applied matte white paint to glossy surfaces in order to enable 3D measurements. We 

also improved both hardware and software of our system for increased robustness, 

accuracy, and usability. Finally, we created scripts for automatic generation of 

extensive webpages organizing and visualizing our results.

17 

Lucia Perez ‘14 

Major: Astrophysics at 

Wellesley 


(Winkler) 

Teddy Smyth ‘15 

Major: Undeclared 


(Winkler) 

Frank Winkler 

Professor of Physics 


An Atlas of Stars Past: Supernova Remnants in 

the Optical Spectrum 

Lucia Perez, Teddy Smyth and Frank Winkler 


Supernova remnants are the luminous shells of gas produced by the explosive 

deaths of large stars. They reveal the composition of stars and contribute to our 

understanding of star life cycles, the evolution of galaxies, and the formation 

of planets. In our work, we processed multiple narrow-band image datasets of 

supernova remnants (SNRs) taken by Prof. Frank Winkler at the 0.9m CTIO 

Schmidt Telescope at the Observatorio Interamericano de Cerro Tololo in Chile 

and the 0.9m Schmidt telescope at Kitt Peak National Observatory in Arizona. 

These optical images of thirteen SNRs were taken through filters revealing 

hydrogen-alpha, [sulfur II], and [oxygen III] emission lines and the red and green 

continuums. Using IRAF, we converted the raw data into images ready for analysis 

and presentation. First, we corrected many systematic imperfections in the raw 

images caused by effects of the charged-coupled device (CCD). We then set each 

image’s world coordinate system, combined multiple exposures into a single frame, 

and subtracted a color continuum frame to reveal the discrete gas emissions of the 

SNRs. Frames in each wavelength were corrected to standardize flux, allowing for 

direct comparison of the gas emissions through measurements of the integrated flux. 

Using our images, we began creating an online atlas to serve as a resource for the 

greater astronomy community. Astronomers will be able to access scientific-grade 

narrow-band optical images 

primed for significant 

research use. Also included 

in our atlas are images of 

the SNRs from the WISE 

and 2MASS all-sky infrared 

surveys and Chandra X-ray 

observations, allowing 

for side-by-side emission 

comparison. We will 

continue making images 

from more SNRs available, 

expanding the atlas to 

encompass as many SNRs 

as possible. 

Combined false-color image of the supernova remnant IC 443 (Jellyfish Nebula) 

with stars subtracted away. 

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18 

Lauren Pincus ‘14 

Major: CHEM, GEOL 

Gretchen Augat Reilly ‘60 

Environmental Studies Fund 

Peter Ryan 


19 

Nathan Rudd ‘13 

Major: CHEM 


(Larrabee) 

Jim Larrabee 

William R. Kenan Jr. Professor 

of Chemistry 


Phosphorus Abundance and Reactivity in 

Champlain Valley Sediments: Implications for 

Nutrient Transport to Lake Champlain 

Lauren Pincus and Peter Ryan 


Phosphorus is the main limiting nutrient responsible for eutrophication and toxic 

algal blooms in Lake Champlain, and in order to model P transport from the 

basin to the lake, a better understanding of P concentrations across the basin is 

necessary. Research and modeling efforts thus far have mainly focused on the 

release of phosphorus from point sources such as sewage treatment plants and from 

agricultural non-point sources; however, data is needed on P release from natural 

sources, especially eroding stream beds and lake shore deposits in order to accurately 

model the transport of P to Lake Champlain. This project seeks to collect data on 

P abundance in non-point sources such as river floodplains, eroding cut banks, and 

forest soils. Soil, sand, and clay samples have been collected at sites along multiple 

tributaries to the southern and central parts of Lake Champlain. X-ray diffraction 

was used to understand the mineralogical composition of collected samples. Relative 

amounts of the minerals were measured with particular importance placed on 

minerals with the potential to adsorb P such as smectite and iron hydroxides. This 

data provides insight into which minerals are present in clays, sands, and soils to 

release phosphorus or hold it in an insoluble form. Comparisons between weathered 

and unweathered samples can also potentially indicate which minerals may be 

preferentially weathering to release phosphorus. Research will continue with 

measurements of total P using LiBO 2 fusion and ICP-AES analysis of the samples. 

Additionally available P will be extracted and measured using sodium bicarbonate or 

another extractant. 

Characterization of 4- and 5-coordinate 

Co(II) Model Complexes by Magnetic Circular 

Dichroism Spectroscopy 

Nathan Rudd and Jim Larrabee 

Department of Chemistry & Biochemistry, Middlebury College, Middlebury VT 05753 

The determination of zero-field splitting (ZFS) parameters provides valuable 

insight into the geometric and electronic structure of metalloenzyme active sites. 

Variable-temperature, variable-field magnetic circular dichroism (VTVH MCD) 

sheds light on the phenomenon of ground-state zero-field splitting, as well as a basis 

for investigating paramagnetic metal-containing enzyme active sites to see how 

structure correlates with mechanisms. VTVH MCD spectroscopy has been applied

20 

Juliet Ryan-Davis ‘13 

Major: GEOL 

John M. White ‘52 Memorial 

Fund and Northeastern GSA 

Undergraduate Research Grant 

Ray Coish 

Robert R. Churchill Professor of 

Geosciences 

Will Amidon 

Assistant Professor of Geology 


to eight mononuclear, high spin (S=3/2) Co(II) model complexes with coordination 

numbers of four or five. These complexes vary with skeletal structure and bound 

ligands. VTVH MCD has been used to investigate the ground state electronic 

structure of each species. The MCD spectra for the four-coordinate complexes 

have positive and negative transition bands between 500-750 nm, while the fivecoordinate 

Co(Et 4 dien)Cl 2 complex spectrum has bands between the larger range 

of 200–900 nm. Axial (D) and rhombic (E) zero-field splitting values—as well as 

spin Hamiltonian parameters—are determined computationally through a Fortranbased 

fitting program. Analysis of only the complex Co(L1)N 3 [L1: HB(3-tertbutylpyrazole) 

3 ] is finished to date (average D and E values of 8.6188 and 0.1872 cm -1 , 

respectively). Future work will include fitting for the additional model complexes, 

as well as elucidating connections between computational parameters and enzyme 

active site structure and function. 

Origin of the Moretown Formation, Vermont: 

A Detrital Zircon Study 

Juliet Ryan-Davis, Ray Coish, and Will Amidon 


Vermont’s geology reveals a series of collisional and rifting events, evidence for 

which is preserved in the various geologic belts. Detailed studies of these belts 

provide insight into the complex history of the northeastern Appalachian Mountains. 

U-Pb age analysis of detrital zircons from the Moretown Formation, part of the 

Rowe-Hawley belt, Vermont, will be used to determine the age of deposition of the 

formation and constrain its sedimentary provenance. The formation, mainly quartzrich 

granofels, phyllite and quartzite, with minor volcanogenic material as well as 

regions of greenstone and other metamorphosed mafic rocks, is currently interpreted 

to have been deposited in an arc-trench gap, likely a forearc basin, between the 

> 900 Ma Laurentian continental rocks and the approaching Shelburne Falls Arc, 

active between ~485 and 460 Ma. That arc is preserved in the highly deformed 

Barnard Volcanic unit in Vermont, which extends southward into the Hawley 

Formation in Massachusetts. In constraining the age of the sedimentary source of the 

Moretown Formation, we will determine whether it was formed by erosion of the 

young Shelburne Falls volcanic arc, or from older Laurentian continental material. 

Seven samples, 25 or more kilograms each, were collected from the Montpelier 

quadrangle, three quartzites and two phyllites from the Dumpling Hill belt, and two 

quartzites from the Wrightsville belt. Zircons were extracted from those samples 

using standard mineral separation procedures. Roughly 20 kilograms of rock was 

crushed using a large jaw crusher, and sifted into several size components, of which 

the finest grain size, less than 208 nm, was used. Samples were rinsed and panned 

in a standard gold pan to separate rock powder and fine sheet minerals from the 

sample. The sample was run through a Frantz magnetic separator up to 1.2 amps to 

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21 

Wisath Sae-Lee (Momo) ‘13 

Major: BIOCHEM 


(Larrabee) 

Jim Larrabee 


of Chemistry 


separate magnetic minerals. The remaining non-magnetic fraction was run through 

heavy liquid separation, using Methylene Iodide which has a density of 3.3 g/cm 3 

to collect minerals that were higher in density—zircon has a density of ~4.6 g/cm 3 . 

Pyrite also has a higher density, close to 5 g/cm 3 , and so some samples were reacted 

in strong hydrofluoric acid baths to dissolve minerals other than zircons. Collected 

zircons were then mounted in epoxy and polished for use in the scanning electron 

microscope (SEM) and, later in the summer, the electron microprobe (EMP) at RPI 

in Troy, NY for cathodoluminescence (CL) imaging. The laser ablation inductively 

coupled plasma mass spectrometer (LA-ICP-MS) at RPI will be used to date a 

random selection of ~80 detrital grains from each sample, by comparing the ratios 

of uranium and lead isotopes to a standard. Geochemical and petrographic data for 

each sample will be found using the ICAP spectrometer at Middlebury and by thin 

section analysis. Further sampling and analysis farther north in the Craftsbury area 

may provide insight into variability along the length of the formation. 

Comparative MCD study of DapE-Encoded 

N-Succinyl-l,l-Diaminopimelic Acid 

Desuccinylase (DapE) from Haemophilus influenza 

and Neisseria meningitides 

Wisath Sae-Lee (Momo) and Jim Larrabee 

Department of Chemistry and Biochemistry, Middlebury College, Middlebury VT 05753 

DapE-Encoded N-Succinyl-l,l-Diaminopimelic Acid Desuccinylase (DapE) plays 

an integral role in the biosynthesis of lysine (Lys) and meso-diaminopimelic acid 

(mDAP). These biosynthetic processes provide essential components for both 

protein synthesis and the construction of peptidoglycan in the bacterial cell wall. 

Previous gene knock-out studies showed that the deletion of DapE gene induced 

lethality even in lysine-supplemented media, suggesting that lysine cannot be 

imported by other pathways. Since the lysine biosynthetic pathway is distinctive 

to most gram-negative and some gram-positive bacteria, inhibitors of DapE could 

provide selective bacterial toxicity. In this work, DapEs from Haemophilus influenza 

(HiDapE) and Neisseria meningitides (NmDapE) were studied with various equivalents 

of Co(II) with and without two different inhibitors—Caprtopril and Dithiothreitol 

(DTT)—using magnetic circular dichroism (MCD). The result from the study of 

the DapEs with Co(II) showed the electronic geometry of the two binding sites to 

be 4- and 6-coordinate which have not been found in any other metalloenzymes. 

The affinities of both sites in NmDapE appeared to be the same while the affinity of 

the 4-coordinate site was higher than the 6-coordinate site for HiDapE. The MCD 

spectra showed both inhibitors to be antiferromagnetically couple with the two 

metals through a sulfide bridge.

22 

Garron Sanchez ‘13 

Major: MBB 

National Institutes of Health 

(Spatafora) 





Constructing mutant variants of the S. mutans 

SloR metalloregulatory protein: A crystal 

structure on the horizon 

Garron Sanchez and Grace Spatafora 


Streptococcus mutans, the primary causative agent of dental caries in humans, regulates 

multiple virulence genes with its 25kD SloR metalloregulatory protein. The present 

study sets out to elucidate the interaction of SloR with its SloR Recognition DNA 

Binding Element (SRE) via a site-directed mutagenesis approach. We recently 

obtained plasmid pAG from Dr. Arthur Glasfeld at Reed College that harbors 

the 654bp sloR coding sequence immediately downstream of a T7 promoter, a 

poly-histidine tag and a small ubiquitin-related modifier (SUMO). We will use 

this plasmid and the QuikChange II Site directed mutagenesis kit (Stratagene) to 

generate site-specific mutations in the N-terminal DNA binding domain, the central 

dimerization domain, and the C-terminal FeoA domain of the SloR protein. The 

mutations will be confirmed by nucleotide sequencing and the pAG-derivative 

constructs used to transform 

E. coli BL21 for subsequent 

IPTG induction and protein 

expression. The resulting SloR 

mutant variants will be purified 

from E. coli cell lysates and 

culture supernatants by cobalt 

column chromatography. 

The fusion proteins will 

be cleaved with a SUMOspecific 

protease (Ulp1) to 

generate sufficient quantities 

of native SloR for subsequent 

X-ray crystallography. In 

collaboration with Dr. 

Glasfeld we will crystallize 

the SloR variants under a 

variety of different conditions, 

including in the presence of 

the 22bp SRE and in various 

concentrations of manganese. 

In this way we will be able to identify the impact that specific amino acids have on 

SloR-SRE binding, metal ion coordination, and protein dimerization, all of which 

are likely paramount for SloR-mediated virulence gene expression. This work is 

especially significant because it can reveal amino acid residues for targeting with a 

mimetic and so foster rational drug design aimed at alleviating caries. 

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23 

Avery Shawler ‘13 

Major: ENVS, BIOL 

Bob Churchill Fund 

Bill Hegman 

GIS Specialist 

24 

Annika Silverman ‘13 

Major: ENVS, GEOL 

Gretchen Augat Reilly ‘60 

Environmental Studies Fund 

Peter Ryan 



Mapping Natural Communities for the Nature 

Conservancy/ Vermont Natural Heritage 

Program 

Avery Shawler and Bill Hegman 

Department of Geography, Middlebury College, Middlebury VT 05753 

This summer I’m mapping natural communities for the Vermont Natural Heritage 

Program. A natural community is an interacting assemblage of organisms, their 

physical environment, and the natural processes that affect them. Identifying 

natural communities helps ecologists understand how species interact with each 

other and their physical environment. Classifying natural communities is important 

for conservation, land management and land use planning. The Vermont Natural 

Heritage Program has been working on mapping natural communities owned by 

The Nature Conservancy. I’ve just finished mapping the High Pond Preserve in 

Brandon, VT. Using a preliminary map created by Eric Sorenson, his field notes and 

aerial photography I’ve been creating a final map. I’ve worked in the field identifying 

species and natural communities and also in the GIS lab mapping out the natural 

communities. The next site that I’m mapping is the LaPlatte River delta. 

The Effect of Metamorphic Grade on Arsenic in 

Bedrock and Groundwater: An Analysis of Shales, 

Slates, Phyllites and Schists from the Champlain 

Valley Sequence in Quebec and Vermont 

Annika Silverman and Peter Ryan 


Recent research in Vermont (e.g. Ali Thompson thesis of 2011, Diego Russell thesis 

of 2012) and previous work in the Himalayas (Hattori et al 2005) and California 

(Bebout et al 1999) suggests that the concentration of arsenic (As) in shales 

decreases as they are heated and compressed by metamorphism into slates, phyllites 

and eventually schists. This clearly has potential implications for predicting the 

occurrence of arsenic in groundwater. In the Taconic region of Vermont, low-grade 

slates contain an average of 44 mg/kg As and 33% of bedrock water wells contain 

>10 mg/L (ppb) As, the EPA maximum contaminant level for drinking water. 

By comparison, higher-grade phyllites and schists from other areas of Vermont 

contain an average of 3.5 ppm As and only 4% of wells contain >10 ppb As. Thus, it 

appears that the rocks of Vermont contain evidence for the control of metamorphic 

grade on arsenic in groundwater—the higher the grade of metamorphism, the less 

naturally-occurring As in rock and in well water. In order to minimize variability

25 

Meghan Stang ‘13 

Major: MBBC 

NIH Summer Research Fellow 





in initial rock composition, sedimentary and metamorphic rocks the Connecticut 

Valley Sequence (CVS) were sampled. The CVS rocks are of similar age (Siluro- 

Devonian) and were deposited in a basin off the astern margin of North America. 

In Vermont, the CVS is highly metamorphosed (to zones that range from biotite 

grade to garnet and staurolite), and the incidence of elevated As in wells in this part 

of Vermont is very low (only one well out of 41 contains > 10 ppb As); conversely, 

in the Lac Megantic region of Quebec, the CVS is effectively still sedimentary rock 

(at most, it is metamorphosed to chlorite zone), and the Quebec Ministry of Health 

reports numerous wells that exceed 10 ppb As. Given that the CVS was deposited 

in the same Siluro-Devonian basin off the eastern margin of North America, 

this project provides the chance to examine the effect of metamorphic grade on 

As within a single rock sequence. Thus, this phase of the study seeks to test the 

hypothesis that high-grade rocks in Vermont will contain very low concentrations 

of As (preliminary analysis indicates that they contain an average of 3.5 mg/kg) 

relative to stratigraphically-equivalent unmetamorphosed shales from Quebec, 

which are expected to contain > 20 ppm As on average. Field work was conducted 

in late June in southeastern Quebec with Denis Lavoie of the Geological Survey 

of Canada and Jonathan Kim of the Vermont Geological Survey to examine the 

Quebec rocks of the CVS. Samples were obtained from several formations that 

outcropped near the town of Saint-George—most notably the Compton Formation, 

which is the lithological equivalent of the Gile Mountain Formation in Vermont. 

Samples are currently undergoing analysis by inductively coupled plasma-atomic 

emission spectrometry (ICP-AES) in the Geology Department as well as by ICPmass 

spectrometry (ICP-MS) at an independent lab (for As, in particular). Emerging 

geochemical data from this sequence of shales, slates, phyllites and schists from 

the CVS is expected to help further constrain the role of metamorphism on the 

concentration and speciation of arsenic and other trace elements in sedimentary and 

metasedimentary rocks. 

The Effect of SloR on Streptococcus mutans 

susceptibility to chlorhexidine digluconate 

Meghan Stang and Grace Spatafora 


Streptococcus mutans is a facultatively anaerobic gram-positive bacterium believed to 

be the main cause of dental caries. Because it can stick tenaciously to the dentition 

via bacterial surface glycoproteins and salivary proteins present in the tooth pellicle, 

S. mutans persists as a prevalent component of the dental plaque biofilm. The plaque 

biofilm is comprised of numerous different bacteria, including the commensal S. 

mutans microflora that forms microcolonies which, depending on environmental 

factors such as carbohydrate availability and pH, can develop to form a community 

of microorganisms on the enamel surface. If conditions in the oral cavity are such 

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26 

Matthew Thomas Stanley ‘15 

Major: Undeclared 


(Larrabee) 

Jim Larrabee 


of Chemistry 


that they facilitate the growth of S. mutans, then dietary carbohydrates will be 

continuously fermented by this oral cariogen, leading to the accumulation of lactic 

acid at the plaque-enamel interface. The end result is the deminerization of tooth 

enamel and the onset of dental decay. A 25kDa SloR metalloregulatory protein was 

described previously in the Spatafora laboratory as a modulator of various S. mutans 

virulence attributes, including plaque architecture. A SloR knockout mutant, called 

GMS584, as well as a SloR-overexpressing strain, called GMS541, were constructed 

in the Spatafora laboratory and shown to have altered biofilm architectures on 

scanning electron micrographs. As an obligate biofilm former, S. mutans is especially 

resistant to antibiotics and antimicrobial agents that are commonly used to reduce 

microbial load before dental manipulations and oral surgery. Chlorhexidine 

digluconate is an antimicrobial that is commonly used in the clinical setting. In 

this study, S. mutans UA159, GMS584, and GMS541 will be investigated in growth 

determination, crystal violet release, and chlorhexidine susceptibility assays to 

determine whether SloR has any impact on the access and susceptibility of S. mutans 

biofilms to chlorhexidine digluconate. This research is significant because it can 

reveal a novel role for SloR in antimicrobial susceptibility and to facilitate oral health 

and hygiene practices. 

Expression and purification of the enzyme 

methionine aminopeptidase for magnetic circular 

dichroism and equilibrium dialysis studies 

Matthew Thomas Stanley and Jim Larrabee 


The enzyme methionine aminopeptidase (MetAP) is a metallohydrolase that 

facilitates the removal of the N-terminal methionine on select polypeptides. Interest 

in this specific metallohydrolase stems from its significant role in angiogenesis 

and its anti-bacterial implications. Production and purification of MetAP on a 

large scale is a critical and time-consuming step, which provides the necessary 

enzyme for later spectroscopic and thermodynamic metal-binding studies. This 

work presents the specific procedure developed to express and purify MetAP using 

Escherichia coli bacteria mutated to over-express the six-histidine tagged MetAP, the 

protein was purified from the cells using a series of chromatographic methods. The 

chromatographic method utilizes the histidine tag located on the protein by using a 

nickel agarose gel to effectively separate the protein from other cell particulates. The 

His-tag was cleaved, and the protein was purified further by using a mass exclusion 

column. Successful isolation of MetAP was confirmed using an HPLC enzyme 

activity assay. This procedure is robust and allows for a large yield of protein, 

approximately 400 milligrams of protein from 25 grams of E. coli cells. Future 

applications for this enzyme will include magnetic circular dichroism spectroscopy 

and equilibrium dialysis studies of the cobalt-binding center to determine an 

enzymatic mechanism for MetAP.

27 

Karl Wetterhorn ‘13 


Ostro Family Molecular Biology 

and Biochemistry Research 

Fund 

Emily Martine ‘13 


Janet C. Curry Biological 

Sciences Research Award 

Roger Sandwick 


Chemistry & Biochemistry 


Glycation Inhibits Cytochrome c’s Ability to 

Induce Apoptosis 

Karl Wetterhorn, Emily Martine and Roger Sandwick 


Apoptosis is the highly regulated process of programmed cell death that occurs in 

response to cytotoxic stress, genomic damage, or developmental cues. The intrinsic 

apoptotic pathway is initiated when cytosolic cytochrome c binds to apoptotic 

protease-activating factor-1 (Apaf-1) causing subsequent conformational changes 

leading to the formation of a heptamer and binding to cytosine-dependant aspartatedirected 

protease 9 (caspase 9). This large, death-signaling protein complex, aka, 

the apoptosome, activates executioner caspases which dismantle the cell into easily 

digested apoptotic bodies. We investigate the effects of the glycation of cytochrome 

c on its ability to induce apoptosis. Glycation, the non-enzymatic addition of 

reducing sugars to free amino groups of proteins, has been shown to modify 

key lysine residues of cytochrome c that could inhibit its binding to Apaf-1 and 

consequently its ability to initiate formation of the apoptosome. We have observed 

diminished activities of caspase 9 and caspase 3 for cytochrome c glycated with 

ribose 5-phosphate (R5P) in comparison to un-modified cytochrome c in cell lysate 

apoptosis assays. We have also noted the capacity of reactive sugars to reduce ferricytochrome 

c to ferro-cytochrome c, perhaps further limiting its ability to induce 

apoptosis. By a combination of microfiltration and western blot analysis, we hope to 

demonstrate directly whether glycation of cytochrome c affects its ability to bind to 

Apaf-1 and form the apoptosome. 

Page 23

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28 

Peter Hetzler ‘14 

Major: CHEM 

Dr. Brendan ’94 and Mrs. Tristan 

Phifer O’Leary ’95 

Mark Isbell ‘14 

Major: CHEM 

Dr. Brendan ’94 and Mrs. Tristan 

Phifer O’Leary ’95 

Rachel Fowler ‘14 

Major: NSCI 


(Byers) 

Jeff Byers 

Philip Battell & Sarah Stewart 

Professor of Chemistry and 

Biochemistry 


The Production of Molecular Wires through 

Acyclic Diene Metathesis (ADMET) and Ring 

Opening Metathesis Polymerization (ROMP) of 

Chromium Organometallic Arenes 

Peter Hetzler, Mark Isbell, Rachel Fowler and Jeff Byers 


To create an organic electrically conductive wire we chose chromium complexes 

as our study subject due to their ease of production and handling along with their 

interesting innate chemical properties. For example, the addition of the chromium 

to an organic backbone decreases the π-π* gap causing the normally colorless 

compound to turn yellow, a key indication of a successful reaction. This implies the 

effect of resonance is increased, effectively enhancing conjugation and conduction 

of the molecule as a whole. Through Grubb’s Catalyst-facilitated Acyclic Diene 

Metathesis (ADMET) and Ring Opening Metathesis Polymerization (ROMP), we 

attempted the polymerization of several chromium organometallic monomers. Each 

monomer was produced through a de-novo synthesis involving mainly benzene and 

indole derivatives as starting materials. We have successfully synthesized six different 

organometallic chromium compounds, and studies of their successful polymerization 

and isolation are still ongoing. We have, however, managed to dimerize a monomer 

with a tert-butyl styrene backbone, offering proof of principle that the Grubbs can 

successfully catalyze the polymerization of a chromium complex. The results of this 

research could show that ADMET polymerization of arene chromium complexes is 

feasible in relatively straightforward and cost-effective ways. This will open a route 

to a family of potentially useful and interesting polymers. If successful, we could, 

in theory, fine-tune a molecular wire to the exact specifications needed for distinct 

applications.

Monomers: 


Cr (CO)3 

P(Octyl)3 

Cr (CO)3 

O 

S O 

O 

N 

Cr (CO)3 

O 

N 

Cr (CO)3 

Cr (CO)2 

P(Octyl)3 

Example of De-novo Synthesis of a Monomer: 

O 

O 

1) Methyltriphenylphosphonium bromide 

2) Potassium carbonate 

3) Dioxane 

4) Water 

5) Heat 

1) Tris ( acetonitrile )tricarbonylchromium (0) 

O 

N 

Cr (CO)3 

S 

CF 3 

Cr (CO)3 

2)Dioxane 

3)Heat Cr (CO)3 

1) Phosphorous acid trioctyl ester 

2) Dioxane 

3) UV light Cr 

(CO)2 

Cr 

(CO)3 

P(Octyl)3 

O 

Page 25

2012 Summer Symposium Program - Middlebury College

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