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Summer
Research Students 2007
Jaie Woodard ’11 (Double degree) Jackson,
MI
Advisor: Manish Mehta
Research Project: Computational
Studies of Peptide-Solvent Interactions
Small biological molecules, such as di- and tripeptides,
lend themselves well to quantitative computational
analysis, as well as experimental investigation.
The small tripeptides we are studying are chains
of three alanine and/or glycine amino acids.
I am using a combination of computational techniques
to investigate the secondary structure of these
molecules in their solvated state. Molecular
dynamics simulations use calculated forces and
Newtonian laws of motion to map the trajectories
of systems of atoms over periods of nanoseconds
or picoseconds. Ab initio and semiempirical calculations
numerically solve the Schrödinger equation,
using quantum mechanical principles to calculate
various molecular properties. Oberlin’s
70-node supercomputer makes it possible to carry
out such highly complex calculations in a reasonable
amount of time. Computational results complement
experimental data collected by other members
of the Mehta lab, using Nuclear Magnetic Resonance
(NMR) Spectroscopy. Discoveries we make in studying
these small peptides can be applied and expanded
to provide insight into important aspects of
larger peptides and proteins, including the process
of protein folding.
Other Interests: horn playing,
music composition, Wagner operas, Mahler symphonies,
physics, math, Bach cello suites, history/philosophy
of science, competitive walking, Schubert Lieder,
Beethoven piano concerti, movies, women’s
gymnastics.
~~~~
 Isaac
Nelson-King ‘08
Woodinville, WA
Advisor: Jason Belitsky
Research Project: Synthetic
Eumelanin for Environmental Remediation
Eumelanin is the black to brown pigment in
humans and our primary photoprotective agent.
It is
an unusual nano-structured biomaterial, with
many fascinating chemical properties that both
influence its biology and role in skin cancer,
and could also be exploited for non-biological
applications, including environmental remediation.
Natural and synthetic eumelanins are known
to bind a range of metals and organic compounds,
and could be applied to the sequestration and
potential photodegradation of environmental
toxins.
We are investigating melanin derived from human
hair, as well as synthetic melanin obtained
through biomimetic enzymatic polymerization,
metal-templated
oxidation, and step-by-step organic synthesis.
The resulting materials are being investigated
as binding agents for pollutants such as lead,
organic dyes, and PCBs.
Other interests: linguistics,
history, guitar, and cartooning.
back to the top
 Emily
Minerath ‘09 Ann Arbor, MI
Advisor: Matthew Elrod
Research Project: Kinetics Studies
of Acid-Catalyzed Reactions in Atmospheric Sulfuric
Acid Aerosols
Atmospheric aerosols (particles
small enough to remain airborne) have an important
effect
on air quality and climate through their ability
to scatter and absorb radiation and to serve
as nuclei for cloud formation. It is now well
known that these aerosols have significant
organic content, despite the fact that most organic
compounds
in the atmosphere are expected to be too volatile
to readily form condensed phase compounds.
The conversion of smaller more volatile organic
compounds
into larger less volatile compounds via acid-catalyzed
reactions has been proposed to explain this
seeming contradiction. In particular, carbonyl-containing
organic compounds are known to undergo aldol
condensation reactions in acidic media. Since
sulfuric acid aerosols are ubiquitous in the
atmosphere, it has been proposed that these
types
of reactions are responsible for the build
up of organic materials on aerosols. In order
to
address whether such reactions can take place
on atmospheric aerosols, we have undertaken
kinetics studies of reactions of organic compounds
in
sulfuric acid solutions that are representative
of atmospheric sulfuric acid aerosols.
Other Interests: Reading,
baking, cooking, knitting, ballet and modern
dance, aikido,
web comics, climbing trees, good food.
~~~~
 Alex
Nichols ‘08 Concord, MA
Advisor: Manish Mehta
Research Project: Hydration
studies of a series of alanyl- and glycyl-containing
tripeptides using solid-state NMR
By virtue of their size and relatively
simple structure, small peptides (short strings
of amino
acids) often assume a wide range of low-energy
conformations in solution. As such, they are
exciting and challenging model system for understanding
subtle elements of solvation and their effects
on backbone torsion angles. Using a combination
of liquid NMR, solid-state NMR, X-Ray and neutron
diffraction, and quantum mechanical calculations,
we seek to understand how the solvation state
and associated chemical properties of glycine-
and alanine-containing dipeptides and tripeptides
change as the molecule transitions from the liquid
state to the solid state.
Once branch of our work involves the study of
a series of 8 glycine- and alanine-containing
tripeptides. Collecting a complete set of chemical
shift data requires knowledge of each peptide’s
crystal structure as well as high quality crystals.
I have therefore divided my efforts this summer
between performing liquids experiments to make
chemical shift assignments, crystal growth, and
performing solids experiments on crystalline
samples of known polymorphs.
Other Interests: Guitar, Running,
Cycling, Rock Climbing, Russian Kettlebell, Vintage
Audio Equipment, Valve Amplifiers, Electronics,
Reading, Eating and Drinking Well.
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Erika Rohrs ‘09 Kalamazoo,
MI
Advisor: Matthew Elrod
Research Project: Mechanistic
Studies of the Atmospheric Oxidation of Aromatics
Aromatic compounds make up roughly
one quarter of the atmosphere’s organic inventory.
It is well known that the oxidation of aromatic
compounds leads to the formation of both ground
level ozone and visibility-impairing aerosols
(smog). However, the specific oxidation mechanisms
are not well known. We have undertaken studies
of mechanism of the oxidation of several atmospherically
abundant aromatic compounds. We are carrying
out product identification and kinetics experiments
that are performed using the Turbulent Flow Chemical
Ionization Mass Spectrometric (TF-CIMS) kinetics
technique.
Other Interests: electronica,
sudoku, pineapple, modern dance, cooking, The
Big Swap, medieval siege weapons, reptiles.
~~~~
 Craig
Packard '09 Wolcott, NY
Advisor: Michael Nee
Research Project: Cucurbiturils
as Nanocontainer Catalysts for Aza-Cope Rearrangements
Cucurbiturils are pumpkin-shaped
macrocyclic molecules with
cavities large enough to bind other molecules
inside the cavity. We are
interested in using cucurbiturils as nanocontainers
for the catalysis of
reactions. The aza-Cope rearrangement of different
vinyl allyl aminium ions has been found to
be catalyzed by binding inside a cucurbituril.
The
shape selectivity of the different sizes of
cucurbiturils is being investigated by NMR
kinetics studies
of this rearrangement reaction.
Interests: Volleyball, musicals/vocal
music, armchair philosophy, that feeling in
the air just before a thunderstorm, bad puns,
alternate
histories, chocolate-covered pretzels.
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 Katie
Mauck ‘09 Worthington, OH
Advisor: Catherine Oertel
Research Project: The Role of Sodium
Chloride in Corrosion of Lead-Tin Alloys: Applications
to Conservation of Organ Pipes
Around the world, pipes in historic
organs are suffering from damaging corrosion
that eventually
causes formation of cracks and holes, robbing
valuable instruments of their ability to produce
sound. Degradation of the pipes, which are made
from lead-tin alloys, occurs primarily through
attack by acetic acid vapor that is emitted from
the wood of organ cases. Surface deposits, such
as sodium chloride, that come from an organ’s
environment can also influence the corrosion
process. While sodium chloride generally increases
corrosion of metals, a preliminary set of experiments
showed decreased corrosion on samples treated
with salt. We are examining in detail the role
of sodium chloride on corrosion of lead-tin alloys
containing between 1 and 10% Sn.
We are using laboratory exposure experiments
in which metal coupons of specific compositions
are exposed to low, controlled concentrations
of acetic acid vapor. A coating of sodium chloride
is applied to sample surfaces using a spraying
technique. The extent of corrosion is monitored
on treated and untreated samples through gravimetric
analysis, and corrosion products are characterized
using powder X-ray diffraction and scanning electron
microscopy.
Other Interests: art, playing
soccer, baking things, making things, art, playing
Euchre, Set, and other card games, reading, being
amongst greenery, singing.
~~~~
 Lee
Moore ‘08 Durham, NC
Advisor: Rebecca Whelan
Research Project: Synthesis
of a peptide mimic of the ovarian cancer biomarker
CA125
The ovarian tumor marker CA125 contains a highly
conserved repeat domain that defines the site
of recognition for all known classes of CA125
antibodies. The goal of this project is to synthesize
a peptide with the same amino acid sequence as
the antibody-binding region of the repeat domain.
It is hoped that the antibodies that have affinity
for CA125 will also bind the peptide and that
analytical assays designed to detect the peptide
will also be useful in detecting CA125 in the
form found in blood. Compared to the intact protein,
the peptide is expected to be more stable, more
amenable to crystallization for structural characterization
by x-ray diffraction methods, and substantially
less costly.
Other interests: bike rides
and mechanics, emergency medicine, music.
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the top
 Serena
Hsin ‘09 Phoenix, AZ
Advisor: Matthew Elrod
Research Project: Kinetics Studies
of the Atmospheric Oxidation of Alkenes by Nitrate
Radical
The nitrate radical (NO3) is the
dominant oxidant in the nighttime atmosphere.
Because both ground
level ozone and aerosols are primarily photochemically
produced during daytime hours, nighttime oxidation
chemistry has less received less study. We
have undertaken studies of the kinetics of the
nitrate
radical-initiated oxidation of several atmospherically
abundant alkene compounds. We are carrying
out product identification and kinetics experiments
that are performed using the Turbulent Flow
Chemical
Ionization Mass Spectrometric (TF-CIMS) kinetics
technique.
Other Interests: Modern/ contemporary
dance, dance techniques, Feve brunch, Black
River coffee, biking, white peaches, blueberry
picking,
dresses, healthy-active lifestyle, reading
short stories.
~~~~
 Deacon
Nemchick ’09 North
Huntingdon, PA
Advisor: Norman Craig (supported by a grant from
the Dreyfus Foundation)
Research Project: Synthesis
of Isotopomers of 1,4-Difluorobutadiene for Use
in High-Resolution Infrared
Spectroscopy and
Equilibium Structures of the cis and trans Isomers
Methods are being applied to synthesize specific
deuterium and carbon-13 isotopomers of 1,4-difluorobutadiene.
This chemistry depends on preparing isotopomers
of fluoroethylene and fluoroiodoethylene, joining
these two substances by a photochemical reaction
into a difluoroiodobutene, and removing hydrogen
iodide with base to make 1,4-difluorobutadiene.
High-resolution (0.0013 cm-1) infrared spectra
will be recorded of isotopomers of the cis,cis
and trans,trans isotopomers by cooperating scientists
at the Pacific Northwest National Laboratory.
From the rotational constants obtained from analyzing
the rotational structure in the high-resolution
spectra and from quantum chemical calculations
of vibration-rotation constants, an equilibrium
structure good to 0.001 Å will be found.
The goal is to assess the structural consequences
of substituting hydrogen atoms with fluorine
atoms in butadiene.
Other Interests: Jack Bauer
and Nina Meyers, skiing, ping pong, the Pittsburgh
Penguins, digg.com, citrus fruits, bikes, goodies
and treats, golfing, Beck, action movies, snow,
coffee, Little Debbie Oatmeal Cream Pies, Rubik’s
Cubes, and DeCafe sandwiches…that’s
it.
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 Robin
Holmes ‘09 Homewood, IL
Advisor: Norman Craig (supported by a grant from
the Dreyfus Foundation)
Research Project: Synthesis
of Isotopomers of 1,3,5-Hexatriene for Use in
High-Resolution Infrared Spectroscopy and Equilibium
Structures of the cis and trans Isomers
Chemistry is being explored for
preparing deuterium and carbon-13 isotopomers
of 1,3,5-hexatriene.
One method involves making methyl ethers of trans,trans-2,4-hexadien-1-ol
and 1,5-hexadien-3-ol and subjecting these ethers
to hydrogen-deuterium exchange in sodium deuteroxide
at 120°C. Another method consists of reducing
the ester of 2,4-pentadienoic acid to the aldehyde
with dibutyl aluminum hydride and then forming
hexatriene with methyl triphenylphosphonium iodide,
as the carbon-13 or deuterium isotopomer. The
goal is to obtain equilibrium structures of the
cis and trans isomers of hexatriene, which should
show larger structural consequences of pi-electron
delocalization than butadiene, the first member
of the polyene series. The spectroscopic and
calculational methods described in Deacon Nemchick's
project will be applied.
Other Interests: Food, backpacking,
horsebackriding, food, sleep, food, Dr. Pepper.
~~~~
 Nathan
Gorham’07 Philadelphia, PA
Advisor: Jason Belitsky
Research Project: Synthetic
Eumelanin for Environmental Remediation
Eumelanin
is the black to brown pigment in humans and
our primary photoprotective agent. It is
an unusual nano-structured biomaterial, with
many fascinating chemical properties that both
influence its biology and role in skin cancer,
and could also be exploited for non-biological
applications, including environmental remediation.
Natural and synthetic eumelanins are known
to bind a range of metals and organic compounds,
and could be applied to the sequestration and
potential photodegradation of environmental
toxins.
We are investigating melanin derived from human
hair, as well as synthetic melanin obtained
through biomimetic enzymatic polymerization,
metal-templated
oxidation, and step-by-step organic synthesis.
The resulting materials are being investigated
as binding agents for pollutants such as lead,
organic dyes, and PCBs.
Other Interests: weight-lifting,
chess, brazilian jiu-jitsu, backpacking and
traveling, golf, any one-on-one sport, attempting
to learn
French.
back to the top
 Karin
Sono ‘08 Kyoto, Japan
Advisor: Jason
Belitsky
Research Project: Synthetic
Eumelanin for Environmental Remediation
Eumelanin
is the black to brown pigment in humans and
our primary photoprotective agent. It is
an unusual nano-structured biomaterial, with
many fascinating chemical properties that both
influence its biology and role in skin cancer,
and could also be exploited for non-biological
applications, including environmental remediation.
Natural and synthetic eumelanins are known
to bind a range of metals and organic compounds,
and could be applied to the sequestration and
potential photodegradation of environmental
toxins.
We are investigating melanin derived from human
hair, as well as synthetic melanin obtained
through biomimetic enzymatic polymerization,
metal-templated
oxidation, and step-by-step organic synthesis.
The resulting materials are being investigated
as binding agents for pollutants such as lead,
organic dyes, and PCBs.
Other Interests: opera, piano,
Spanish, religions, and geography.
~~~~
 Matt
Thayer ’08 Livonia, MI
Advisor: Rebecca Whelan
Research Project: Development
of an SPR immunoassay for CA125
Surface plasmon resonance (SPR) sensing enables
the sensitive detection of protein molecules
in real time, and without the need for labels.
The goal of this project is the development of
an immunoassay for the glycoprotein CA125, the
most important biomarker of ovarian cancer. Detection
is accomplished on a gold surface that is functionalized
in serial fashion, first by deposition of a self-assembled
monolayer containing reactive head groups, next
by covalent coupling of recombinant Protein G,
then by affinity capture of an antibody with
affinity for CA125, and finally by binding of
CA125 itself. The SPR signal changes with each
step in the deposition, enabling the development
of a calibration curve when solutions of known
CA125 concentration are captured. Preliminary
results indicate that our method can reliably
detect CA125 at levels three-fold below the clinically
relevant threshold with a linear dynamic range
of three orders of magnitude.
Other Interests: Microbiology,
Middle Eastern Politics & History, Cooking,
Hiking, and Electronica.
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 Fall
Tian ’10 Wuhan, Hubei, China
Advisor: Catherine Oertel
Research Project: Synthesis
and Characterization of Ternary Sulfide Nanoparticles
Synthesis of nanoparticles is
currently a very active area of chemical research,
largely because
of the interesting properties exhibited by these
nanometer-scale crystals. The high surface-to-volume
ratio of nanoparticles makes them useful in catalysis.
Hydrodesulfurization of fuels, particularly diesel,
is a process that is frequently catalyzed by
molybdenum sulfide activated by nickel and/or
cobalt. That is, the active site of the catalyst
contains Mo, S, and Co/Ni atoms. The goal of
our research is to synthesize nanoparticles of
MMoS4 (M = Ni, Cu, Co…) compounds, combining
hydrodesulfurization activity with the high surface
area offered by nanosize particles.
Both room temperature and solvothermal reaction
conditions are being used to prepare these ternary
sulfide nanoparticles. In order to control particle
size and prevent particle agglomeration, we are
using reverse micelle reaction media as well
as solvents such as ethylenediamine and ethylene
glycol that are capable of capping particle surfaces.
Reaction products are characterized using powder
X-ray diffraction, scanning electron microscopy,
and thermogravimetric analysis.
Other interest: reading and
sleeping.
~~~~
 Ryan
Felix ‘08 Willoughby, OH
Advisor: Albert Matlin
Research Project: Intramolecular
Photocycloaddition Reactions of 4-oxa-1,5-hexadienes
A series of 2-acyl-4-oxa-1,5-hexadienes
are being synthesized with the enone system incorporated
in a six-membered ring. These compounds are then
irradiated with ultraviolet light (? = 350 nm)
to give intramolecular [2+2] photocycloadditon
products in high yield. Initial results suggest
that the 4-oxa substitution does not signficantly
change the regiochemistry of the photoreaction
from that observed with the deoxy compounds.
Other Interests: Defeating never-do-wells
at every step of their evil schemes; taking long
walks on the beach while reading to orphans;
good books; keeping in shape, because fighting
crime just isn’t enough to stay the development
of those pesky love-handles; Concerns: developing
workaholism.
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 Michaela
Hull ‘10 Saint Paul, MN
Advisor: Catherine Oertel
Research Project: Synthesis
of Low-Symmetry Inorganic-Organic Network Materials
In recent years, there has been
increased interest in synthesis of hybrid inorganic-organic
network
compounds, in which single metal atoms or metal
clusters are linked by organic ligands. Of particular
interest are structures that lack centers of
symmetry. These low-symmetry materials have useful
applications because they can interact selectively
with chiral guest molecules or behave as non-linear
optic (NLO) or piezoelectric materials. The choices
of both metal and ligand can be important in
promoting formation of low-symmetry products.
Chiral ligands can lead to non-centrosymmetric
solids, as can asymmetrically coordinated metals
that contain stereochemically active lone pairs.
We are using room temperature and hydrothermal
methods to grow inorganic-organic network compounds
with the potential for non-centrosymmetric structures.
In particular, we are using the amino acids cysteine,
aspartic acid, and glutamic acid – naturally
occurring chiral ligands – and Pb2+ as
building blocks to promote low symmetry. We are
using powder X-ray diffraction as a primary means
of product characterization, with the goal of
using single-crystal X-ray diffraction to determine
structures of new non-centrosymmetric networks.
Other Interests: Art, horseback
riding, tae kwon do, dance (all kinds), sewing,
travel…
~~~~
 Matthew
Aaron Leyden ‘08
Trumbull, CT
Advisor: Albert Matlin
Research Project: 5-Hexenyl
Radical Cyclizations: A Computational Study
5-Hexenyl radicals cyclize to form either cyclopentyl
or cyclohexyl systems.
This reaction has been
the subject of numerous mechanistic studies and
has found wide application in the synthesis of
complex organic molecules. Previous work in the
Matlin lab investigated the effect of 4-oxa substition
on the regiochemistry and rate of the cyclization.
This summer we are carrying out a comprehensive
computational study of the cyclization as a function
of alkyl substitution at C3 and C5 and oxa substitution
for C4. The geometries and energies of several
competing transitions states are being calculated
inorder to understand the factors affecting the
mode (exo vs. endo) of cyclization.
Other Interests: Music: The
Fray, Counting Crows, Goo Goo Dolls, and anything
Korean. Academic: ethics, Korean language, math,
micro-biology Recreational: socializing, hiking,
dancing, dismantling computers… systematically
of course.
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 Melissa
Tai, 08 South Kingstown, RI
Advisor: Rebecca Whelan
Research Project: Optimization
of tools for aptamer selection
The selective detection of biomolecules in serum
is an important tool for basic research and clinical
applications. Traditionally, such assays have
relied on antibody molecules as the basis of
detection. A long-term goal of research in the
Whelan lab is to explore a relatively new class
of affinity molecules—aptamers—and
to develop analytical assays that exploit their
advantages. Aptamers are single-stranded nucleic
acid molecules with recognition ability comparable
to antibodies. The process of aptamer selection
begins with a large pool of oligonucleotides.
The oligos are allowed to interact with the target
protein of interest, and those that bind well
to the target are separated from those that do
not. Good binders are amplified by polymerase
chain reaction, and the cycle of selection and
amplification continues until the pool converges
on a small number of excellent binders. This
summer, we will optimize the processes by which
candidate oligos are amplified and made single-stranded
in pursuit of our goal to select a DNA aptamer
that recognizes CA 125, a protein that is widely
used as an ovarian cancer biomarker.
Other Interests: Viola, Classical
Music, cooking, drawing, science fiction and
fantasy books, Buffy the Vampire Slayer!!, movies,
making jewelry.
~~~~
 Robert
Hartley ‘08 Seattle, WA
Advisor: Manish Mehta
Research Project: Research Project:
Computational Studies of Peptide-Solvent Interactions.
As the available computing power
continues to increase, computer models of chemical
systems
are becoming more and more important and informative.
I am performing molecular dynamics simulations
(which use pre-calculated atom, bond and angle
properties to simulate molecular motion) and
quantum chemical calculations (which numerically
solve the Schrödinger equation) to study
the effects of solvation on simple di and tripeptides.
We are performing these simulations using desktop
machines and Oberlin’s 70-node supercomputer.
Our computational studies complement experimental
NMR measurements, made locally by other members
of the research group, and provide a more detailed
view of the structure and dynamics of model proteins
in various solvent environments. Our ultimate
goal is to apply what we learn about these small
peptides to larger ones and to the secondary
structure of biologically significant proteins.
Other Interests: Coming of Age
Movies from the ‘80s, Novel Computing,
EMS, Ice Cream, Diet Pepsi, Wandering Aimlessly.
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 Sydney
Williams ‘09 Chico, CA
Advisor: Rebecca Whelan
Research Project: Selection
of an aptamer that recognizes CA125 via capillary
electrophoresis
Aptamers are single stranded oligonucleotides—DNA
or RNA—that are selected out of a large,
random pool on the basis of a particular function.
Often aptamers function as high-affinity binders
to biological molecules. The process of selecting
aptamers relies on repeated cycles of selection
and amplification until a small number of oligos
with the desired binding property dominate the
pool. Selection can occur in one of two formats,
on a stationary phase or in free solution. My
contribution to this project is the development
and optimization of a selection process based
on the microscale separations method of capillary
electrophoresis that will identify candidate
oligos that bind to the ovarian cancer biomarker
CA125. It is hoped that such aptamers may form
the basis of new detection methods for ovarian
cancer.
Other Interests: drawing, graphic
novels, listening to music.
~~~~
 Valentin
Rusu ‘08 Parma, OH
Advisor: Jason Belitsky
Research Project: Aminooxy Serine
Peptide Ligation
We are developing a new reaction
that will be useful for the synthesis and chemical
modification
and peptides and proteins. The proposed reaction
is member of a class of reactions known as chemoselective
ligations that allow specific sites on biomolecules
to be modified in aqueous solution without the
use of protecting groups. Such reactions are
contributing to advances in bio-imaging, proteomics,
and drug development. The new reaction, aminooxy
peptide ligation, will extend this chemistry
to the amino acids serine and threonine, and
feature peptide formation and site-specifically
labeling in the same pot. Research this summer
will focus on the synthesis of O-aminoserine,
the unnatural amino acid necessary for the reaction
with peptides, and on reaction development with
model systems.
Other Interests: I love learning
or practicing foreign languages and traveling
to places I haven’t yet been. I also like
listening to music, and, when I feel especially
creative, playing guitar or writing poems.
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 Tera
Levin ‘07 Champaign, IL Advisors: Rebecca Whelan and Mary Garvin (Biology)
Research Project: Detection of volatile
compounds in the uropygial gland secretions of
catbirds
The uropygial gland of birds,
also known as the preen gland or oil gland, produces
secretions
that are important in maintaining the health
and structural integrity of feathers. The gland
is located at the base of the tail where birds
may easily use their bill to squeeze the gland,
extract the secretions, and distribute them
over the feathers. These secretions are believed
to
play a number of functions including waterproofing
and conditioning the feathers, as well as protection
from insect pests, and even predators. Some
of the components of the gland secretions, including
waxes, lipids, and alcohols, have been described
over the past 50 years in several species of
birds. However, only in 2004 it was discovered
that preen gland secretions contain volatile
compounds. Such compounds are particularly
interesting
because of their potential importance in olfactory
communication both within and across species.
The goal of this project is the use of solid-phase
microextraction headspace sampling followed
by gas chromatography-mass spectrometry to detect
and identify volatiles in uropygial gland secretions
of catbirds.
Other Interests: biology,
movies, volleyball, and kittens.
~~~~
 Matt
Rumizen ‘09 Reading, MA
Advisor: Manish Mehta
Research Project: NMR analysis
of Alanine/Glycine “Capped” Dipeptides
Over the past 20 years, nuclear
magnetic resonance (NMR) spectroscopy has developed
into a powerful
technique for determining 3-dimensional protein
structures. Our research over the summer involves
NMR experimentation on modified dipeptides, which
consist of linked pairs of amino acids; as such,
they can be considered “smaller versions” of
biologically occurring proteins, which may contain
thousands of amino acids.
Since a traditional (1-dimensional) NMR spectrum
is a series of peaks along a single axis, 2D
correlation experiments must be done on each
compound to deduce which peak corresponds to
which atomic nucleus. After these assignments
are made, we can return to the 1D spectra and
match each atom with a specific chemical shift:
a number that corresponds to the horizontal position
of that atom’s peak on the spectrum.
Chemical shift values are extremely sensitive,
and are affected by virtually every aspect of
a nucleus’s local environment, including
bonding geometry, oxidation state, participation
in one or more hydrogen bonds, and proximity
to neighboring atoms. Using chemical shift data
from solution-state and solid-state NMR experimentation,
combined with ab initio calculations performed
by Jaie Woodard and Rob Hartley on Oberlin’s
supercomputer, we can gain insight into the preferred
spatial arrangement and solvation states of our
dipeptides. Our hope is to place this smaller-scale “close-up” work
in the context of general protein structure research.
Other Interests: learning about
people, learning out of books, running, planning
elaborate road trips, Calvin & Hobbes, outdoor
stuff like camping/hiking/sailing, record collecting,
biofuels, Elephant 6, Thai cooking, self-actualization,
having a porch, and playing/hearing/seeing music
of any kind.
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