INQUIRY

INQUIRY • Volume 19, 2015
systems. The dielectric properties of an ionic, and proton
conducting liquids helps explain the charge screening,
charge stabilization and ion (proton) conduction that occurs.
To calculate the dielectric properties, the total molecular
dipole moment must first be determined. Currently, it is
impossible to determine the total molecular dipole moment
using experimental methods, and highly non-trivial using
computational methods. A proposed computational method
that has shown some success utilizes Maximally Localized
Wannier Functions analysis, partitioning the periodic electron
density, and applies it to a trajectory generated using ab
initio molecular dynamics. Using both ab initio molecular
dynamics and classical molecular dynamics to calculate the
dielectric properties it was determined that the average total
molecular dipole moment was in very excellent agreement
even though there was a difference between the calculated
dielectric constant value from ab initio molecular dynamics
and classical molecular dynamics.
Self-Assembly of a Three-Turn Tensegrity Square
Lakpa Lama, Chemistry
Isabelle Levin, Individualized Major
Victoria Zlotnikova, Neural Science
Sponsor: Professor Nadrian Seeman, Chemistry
Structural DNA nanotechnology facilitates the construction
of various nanostructures in 1-, 2- and 3-dimensions.
Previous work has shown the affective self-assembly of the
tensegrity triangle into a 3D lattice (Liu, Wang et al., 2004;
Zheng, Birktoft et al., 2009). Further work has been done to
expand the notion of the tensegrity triangle to a tensegrity
square motif. It has previously been reported that a two-turn
DNA tensegrity square containing either 5, 6 and 7 nucleotide
pairs between junctions was able to successfully self-assemble
into a 3D lattice (Chen, Mohsen et al., 2013; Wady, Mohsen
et al., 2013; Chen, Jurgensen et al., 2014). Potential applications
of such motifs require the design of larger motifs that
could accommodate protein hosts for X-diffraction studies.
The current research designed a symmetric 3-turn tensegrity
square. Gel studies have shown the successful formation
of the motif while optical images have demonstrated the
self-assembly of the motif into 3D crystals. X-ray diffraction
analysis will reveal the actual arrangement of the motif.
Furthermore, this study proposes that employing a similar
approach will lead to the successful self-assembly of RNA
lattices that can bind proteins. The use of RNA tensegrity
squares will be very amenable to the formation of 3D RNA
crystals since the corners of RNA squares tend to adopt 90
degree-angles. RNA-binding proteins such as zinc-fingers
play significant control over numerous cellular functions such
as transcription. Due to their importance in the biological
field, several discoveries regarding RNA-binding proteins
potentials continue to be unveiled.
Using a Novel, Combinatorial Profiling Technique to
Decode the Fragile X Proteome in Mouse Hippocampi
Joseph Lebowitz, Psychology
Sponsors: Professor Eric Klann, Neural Science; Dr. Aditi
Bhattacharya, Neural Science
Fragile X mental retardation protein (FMRP) regulates
protein synthesis, particularly in neurons. In individuals with
Fragile X Syndrome (FXS), transcriptional silencing of the
Fmr1 gene leads to loss of FMRP and, in turn, changes in
neuronal protein expression and function. In FXS, there is
also increased activity of mammalian target of rapamycin
complex 1 (mTORC1), extracellular-regulated kinase 1/2
(ERK 1/2) and p70 ribosomal s6 kinase 1 (S6K1), all of
which promote protein synthesis and help regulate synaptic
structure, plasticity and signal transmission. BONLAC, a
novel, combinatorial proteomic profiling technique, was
used to examine the altered protein expression in FXS and
WT mouse hippocampi. Western blot analysis was then
used to validate candidate hits from the proteomic screen.
As FXS is the leading monogenetic cause of autism spectrum
disorders (ASD), identifying differences in protein
expression between FXS and WT conditions will add to the
currently incomplete understanding of the underlying causes
of ASDs. This may lead to the establishment of an effective
biomarker for early detection in affected humans, provide
a basis for the development of a diagnostic test or provide
a direct target for therapeutic intervention.
Exploring the Role of a Transmembrane Protein in the
Drosophila Color Vision Circuit
Gina Lee, Biochemistry
Sponsor: Professor Jessica Treisman, Cell Biology, NYU
School of Medicine
Neural circuits, the basis of sensory perception in the
central nervous system, are established through synaptic
connections that require growing axons to locate appropriate
target cells. Within the visual system of Drosophila melanogaster,
networks of synaptic connections are arranged in
a stereotypical manner in distinct layers of the brain. The
photoreceptors that mediate color vision, R7 and R8, terminate
in two distinct layers within the medulla, R7 in M6 and
R8 in M3. R7 and R8 detect specific wavelengths of light:
R7 is UV-light sensitive, and R8 is blue or green-sensitive.
An RNAi screen in the lab to identify cell-surface molecules
that provide targeting information to the axons of these color
photoreceptors yielded a novel candidate, CG8909 (homolog
of Low density lipoprotein receptor-related protein, Lrp4), a
transmembrane protein with LDLR, EGF and beta-propeller
domains. Preliminary findings reveal that knocking down
this candidate in photoreceptors and lamina neurons causes
defects in targeting of R8 axons to the appropriate M3 layer.
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