Biology

Bailey Baumann

Hillary Cleveland

Rica Dela Cruz

Eileen Downs

Elizabeth Hamilton

Emma Hedman

Nelly Khaselev

Emily Lovejoy

Sara Marlow

Sahitya Penumetcha

Brielle Stark

Chemistry

Elena Brunner

Anna Giarratana

Ariana Hall

June Mbae

Sharan Mehta

Kim Mullane

Alison Panosian

Yuan Qiao

Mithila Rajagopal

Ashton Shaffer

Allison Shatz

Stephanie Vrakas

2009

Summer Science Research Program
and Student Abstracts

Undergraduate research initiatives are central to the College's approach to science education. All science majors are encouraged to conduct mentored research projects during the summer and/or academic year, and each year over 50% of all science majors do so. Students receive stipends for summer research and academic credit for research performed in the junior and senior years. Since 1989, each summer the College has provided 35+ students with ten-week research stipends to conduct independent research under the guidance of Bryn Mawr faculty members in the sciences and mathematics. The summer program is enriched by professional development workshops and a poster session at which students present their research to the college community.

The College gratefully acknowledges the financial support for undergraduate research provided by:

Ann Lutes Johnson Fund

Carlos Nathaniel Vicens and Maria Teresa Joglar de Vicens Fund
GlaxoSmithKline
Helen Louise Robinson '66 Fund for the Biological Sciences
Howard Hughes Medical Institute
Merck
National Institutes of Health
National Science Foundation
Office of the Undergraduate Dean
Robert Conner Undergraduate Biology Fellowship Fund

Biology 2009

Summer Science Research Abstract

The Role of Synaptotagmin in Early Neurite Development

Bailey Baumann

Mentor: Dr. Karen Greif

Neuronal communication is dependent on established connections between nerve cells within the nervous system. Nerve cells are connected through ‘processes’ that radiate from the cell body and terminate at chemical synapses. At the synapse, chemical signals called neurotransmitters are packaged in synaptic vesicles and released into the synaptic cleft through exocytosis and bound by receptors on the post-synaptic neuron. This process, known as neurotransmission, is mediated by the release of Ca2+. Synaptotagmin, a prominent synaptic protein, directs the exocytosis of neurotransmitters through its function in calcium regulation.

Although the role of synaptotagmin (syt) in neuronal communication has been well studied, little is known about the role of synaptotamin in early neuronal development. Syt is believed to play a role in neurite outgrowth because of its early presence in nerve cells. Syt is found in nerve cells days before synaptogenesis, the formation of synapes, occurs. Researchers have also found that increasing levels of synaptotagmin in developing neurons increases the growth and branching of neuron processes. The exact role that synaptotagmin plays in neurite outgrowth is still undetermined, but observations, such as a Ca2+ requirement for process growth, may implicate synaptotagmin in process outgrowth and branching.

In order to determine what role synaptotagmin plays in neurite outgrowth; we will be investigating how changes in intracellular concentrations of synaptotagmin affect the development of neuron processes in stagte-8 chicken embryos. I will be concentrating specifically on how a decrease in synaptotagmin expression affects development. To achieve synaptotagmin knockdown, I will be utilizing RNA interference, a technique that silences syt gene expression through siRNA. Another secondary goal of the present study is to develop a reliable and efficient mode of siRNA delivery. This summer, I will be using liposome methodologies to knockdown syt.

This research is supported by grants from NIH and the Pennsylvania Health Research Formula Fund.

 

Hillary Cleveland
Mentor: Dr. Greg Davis

With the recent completion of the sequencing of the Aphid (aphis pisum) genome many new areas are now open for research and exploration. One thing that has been discovered is that there are multiple versions of “one gene”. This is interesting because of the sexual polyphenism exhibited in the aphid. While it is the summer aphid populations are entirely female and reproduce asexually. They also produce young viviparously (live birth). Then when the nights start to get longer the aphids do something quite amazing. The asexual females produce viviparously sexual females and males. These sexual females and males mate producing eggs that can survive winter. In the spring these eggs hatch into asexual females and the whole cycle starts over again.

This summer we will be looking at the expression of genes in the embryos of asexual females and the ovarioles of sexual females. The genes we will be looking at are Torso-like 1, 2, and possibly 3 and Tailless 1 and 2. The Torso-like signalling pathway is important to the development of the posterior of the aphid. To do this we are replicating the DNA with primers that we designed ourselves. We will then clone the products to make our own probes for in-situ hybridization. We will also be looking at the protein expression in the two types of embryos of a protein, capicua, that is farther down in the pathway using anti-body staining.

This research is important because it will help us understand the differences between the two types of embryos. From preliminary work done we know that there is a difference in the expression levels of the torso-like gene, but that was only for torso-like 1. We are now going to look for the expression of the other versions of the gene. If one type of the gene is expressed in one type of embryo and another is expressed in the other this would then explain the earlier absence. We want to understand more about aphids because they are a good new model organism for polyphenisms in organisms.

Rica Dela Cruz
Mentor: Dr. Monica Chander

SoxR is a redox-sensitive transcriptional dual regulator and activator protein. Homologs of this protein, in addition to the specific DNA sequences it binds, exist in various bacterial species. Traditionally, SoxR has been known to be an oxidative stress-defense protein, such as in the enteric bacterium, E. coli. In the presence of oxidative stress agents, SoxR’s characteristic iron-sulfur clusters become oxidized inducing a conformational change. This allows the protein to bind to a specific DNA promoter site to activate the expression of certain genes, which in turn produce various antioxidant proteins. Unlike E. coli, however, studies in other bacterial species have suggested that SoxR may play a role in the transport and/or modification of small molecules within the cell. For example, it has recently been found that SoxR regulates the efflux of the redox-active antibiotic, pyocynin, produced by the bacteria, Pseudomonas aeruginosa.

Analogous to P. aeruginosa, the soil bacterium, Streptomyces coelicolor, also seems to show a possible link between SoxR and one of the redox-active antibiotic it produces, actinorhodin. Though, this has only been shown phenotypically. DNA sequences homologous to the consensus sequence of the SoxR binding site have been found in promoter regions of S. coelicolor genes, SCO2478 and SCO4266. It is hypothesized that SoxR may either be activating or inhibiting the expression of SCO2478 and SCO4266 in the presence of endogenous actinorhodin. Gel shift assays do show that SoxR can bind to these regions in vitro. However, how SoxR binds and its downstream mechanisms are still unknown.

Other consensus sequences of the SoxR binding site have also been found in regions upstream of the ecaA, ecaB, and ecaC genes of S. coelicolor. One goal is to find out whether SoxR does bind to these regions. This will be answered by the analysis of gel shift assays. Another goal is to find out whether SoxR functions to activate or inhibit the expression of these genes: SCO2478, SCO4266, and possibly the eca genes. Thus, quantitative RT-PCR and microarrays using both wild type and mutant SoxR strains of S. coelicolor will be analyzed. 

Eileen Downs
Mentor: Dr. Gregory Davis

Because of their unique life and reproductive cycle, aphids are an ideal model organism for studying epigenetics. At present, however, there is no way to study the effects of knocking out or knocking down a gene in this organism. Anti sense molecules such as iRNA have no quantifiable effect. As such, it is impossible to truly ascertain the effects of any given gene or protein on the organism. Vivo morpholinos are unique molecules that can travel between cells and can be administered to an adult organism to knock down a gene. We believe that since adult female asexuals contain offspring of many different levels of development, that the vivo morpholinos will be successful in knocking out genes in some of the offspring. In out experiment we will be attempting to inhibit the translation of the “eyeless” gene which is believed to be a Pax-6 homolog. Adult asexual female aphids will be injected with the vivo morpholinos in hope of affecting the eye development to the point that the eyes do not develop at all or are significantly reduced. Studies done with juvenile hormone (JH) demonstrate the after a certain point in development, the presence JH had no effect. We believe it is possible that only the newest of the developing offspring will be affected by the introduction of these molecules. This technological development would open the door to a number of possibilities within aphid research. For example, researchers would be able to knock out the genes that result in the production of JH, leading to a more comprehensive understanding of the effects of this hormone.

Turning Off Leech Swimming

Elizabeth Hamilton

Mentor: Dr. Peter Brodfuehrer

Movement in a leech is controlled by a series of ganglia, small clusters of nerve cells, distributed along the length of the body. Each ganglion controls muscles in its own segment of the body but shares information with adjacent ganglia by means of connective fibers that run all along the animal. The nervous system is capable of producing a specific pattern of movements, swimming, which can be stimulated at any point along the body, but which is maintained by coordinated activity in the entire nervous system.

According to a current model leech swimming is maintained by a network of cells with mutually excitatory connections both within and between the segmental ganglia. If this is the case, one would expect that activity during a swim bout could be observed along the connective fibers between ganglia and that this activity along the connectives would change at the end of a swim bout as the reciprocal excitation was somehow disrupted. The Brodfuehrer lab is examining how activity along the connectives correlates with the end of swimming in the reciprocal network.

Emma Hedman

Mentor: Dr. Greg Davis

Recently, Aphids are becoming more and more important as model organisms ind evelopmental biology due to a wide range of polyphenisms, including the so-called reproductive polyphenism. During the summer aphids exist as exclusively female, asexual clonal populations. Female aphids which give rise to more asexual females are known as virginoparae. During the fall, when aphids are exposed to long nights, they will asexually produce a new generation of females known as sexuparae. Sexuparae reproduce asexually, but give rise to females which must reproduce sexually. The details of this process are foggy, and understanding it could be a major step in developmental biology by giving insight into what sorts of molecular responses are responsible for polyphenisms in nature. We do know is that an active signal exists that promotes the production of asexual females, though the nature of the signal is unknown.

One candidate is Juvenile Hormone (JH), as application of JH has been shown to turn sexuparae back into virginoparae. Since previous research continues to show that JH is sufficient to cause the switch from producing sexuals to asexuals, my goal is to prove that it is also necessary. I plan to do this by conducting experiments opposite to the current research, and trying to induce production of sexual offspring in mothers which would typically give rise to asexual offspring by targeting JH production as exclusively as possible. Since JH is suspected of being the asexual signal, it would follow that blocking the production of JH in asexual mothers would make them incapable of continuing the production of asexual offspring in favor of sexuals. We will first try to accomplish this using the new technology of in vivo morpholinos. These are unique molecules which can move between cells and block translation. I will investigate the expression of the gene Juvenile Hormone Acid Methyl Transferase (JHAMT) using the morpholino, and hope to see a drop in JH production in the offspring of the mother injected. I also hope to use RNA interference to block the mRNA produced by JHAMT, preventing the production of the protein which is thought to be the rate-determining step in the biosynthesis of JH. By using these two methods, I hope to either credit or discredit JH as a major contributor in the sexual polyphenism. If this research was successful, it would be a major contribution to understanding the underlying role of hormones on phenotypic expression and development.

Summer Institute 2009: Exploring Science and Education with K-12 Teachers

Emily Lovejoy, Brielle Stark

Mentors: Drs. Paul Grobstein, Wil Franklin

I will be exploring the relationships among mental health, science education, and the brain by pursuing long standing interests of my own in the mental health area and connecting them to contemporary thinking about the brain and about education. As part of my research I will be helping to prepare and teach materials on science education and the brain to K12 teachers. I expect these interactions will in turn help me to develop new ways to think about the intersections of research on the brain, education, and mental health.

Chemistry 2009

Summer Science Research Abstract

Analysis of the different mobilities of K-turn RNA and Base-paired RNA

Elena Brunner
Mentor: Dr. Susan White

 

Ribonucleic acid (RNA) allows for the production of proteins, which aid in the cellular growth and regulation, through the utilization of the genetic coding present in DNA during transcription and the processing and editing of the RNA structure during splicing. The double stranded structure of the RNA customarily consists of the Watson-Crick base-pairing of the purine and pyrimidine nucleotides—hydrogen bonds between adenine-uracil, and guanine- cytosine. However, the nucleotides may not pair traditionally; one example among many is helix-internal loop-helix motif (the kink-turn motif). The internal loop consists of a strand of unpaired nucleotides, which follows a Watson-Crick base-paired stem and precedes a non-Watson Crick base-paired stem. Advances in the understanding of the structure and binding affinities of the K-turn in comparison to those of the Watson-Crick representative RNA (base-paired RNA) enhance the understanding of the RNA-protein interactions.

To test mobility of the kink-turn and base-paired RNA, we will utilize Analytical Ultracentrifugation and Gel Filtration Chromatography. Using Analytical Ultracentrifugation, sedimentation experiments can extract the rate of migration and possibly be used in the determination of shape as the RNA settles in solution. The rate of sedimentation is dependent on the shape and density of the molecule, as each differently sized molecules settle at different minimal centrifugal forces—dense, spherical molecules sediment at a more rapid rate, while elongated molecules at a slower rate. Our hope is to determine whether kink-turn and base-paired RNAs sediment differently in the presence of Mg2+. We will test the Analytical Ultracentrifugation with Mg2+ in solution with the kink-turn and base-paired RNA to determine any difference in mobility of the two forms of RNA. When binding to Mg2+, kink-turn RNA is assumed to be bent and “folded over,” suggesting a more rapid sedimentation than the base-paired RNA, which is more elongated. The gel filtration chromatography allows for analysis of mobility in the two RNA forms through chromatography columns. Greater mobility depends on the more condensed shape of the molecule traveling through the column. Our hope is to determine whether the kink-turn and base-paired RNAs have different mobilities through the columns. If there is a difference, is magnesium and heat required to maintain that difference? Testing this approach with both forms of RNA with and without the presence of magnesium at two main temperatures, we predict that the K-turn RNA, having a “folded over structure” will have a greater mobility than the base-paired RNA. Both the analytical centrifugation and the gel filtration chromatography help to determine the size relationship between the two forms of the RNA, and indirectly aid in the determination of structure and binding capabilities.

Anna Giatarrana

Mentor: Dr. Bill Malachowski

 

Cancer is a disease that affects millions of people worldwide, and is the 2nd leading cause of deaths in the United States. It is thought that indolamine deoxyhydrogenase oxide (IDO) plays a role in immunosuppression, allowing tumors to grow in the body undetected. It has been shown that IDO inhibitors are able to slow the progress the cancer in conjunction with chemotherapy. By using computer modeling, molecules that may be more potent inhibitors than those that currently exist have been proposed. The purpose of thus study is to find synthetic methods to create these molecules in fewer steps and greater yield.

Implementing the Birch-Cope Sequence and Rearrangement for the Synthesis of Natural Therapies

Sharan Kaur Mehta

Mentor: Dr. Malachowski

 

Within the scope of organic synthesis, the goal of attaining biologically active compounds has proven its extensive value as well as its array of strategic challenges, specifically in the creation of enantiomerically pure carbocyclic quaternary stereocenters. However, the implementation of the three-stage Birch-Cope sequence, comprising of the Birch reduction-allylation, enol ether hydrolysis, and Cope rearrangement has become a proven method of effectively generating such chiral stereocenters, which are crucial synthetic intermediates. Expanding on the procedure’s prior successes, its discovery has stimulated a wealth of synthetic opportunity in the ultimate hopes of developing innovative therapies in the way of antibiotics, which the Malachowski research team currently seeks to explore. Within the scheme of the project, my role this summer specifically involves the production of the o-anisic acid derivative starting material possessing a chiral auxiliary, which is derived from a reaction with L-prolinol. Longer range goals include conducting the Birch-Cope sequence and contributing to the exploration of the product after the Cope rearrangement.

Synthesis of o-anisic acid derivative with chiral auxiliary:

 

Birch-Cope Sequence and Rearrangement:

 

The Synthesis of a Solubilized [11]Phenacene Derivative

Kim Mullane

Mentor: Dr. Frank Mallory

 

[n]Phenacenes are molecules containing n aromatic rings joined together in a zigzag pattern. Since they can be thought of as graphene ribbons, which have conductive properties, they should have the potential to be used as molecular wires. The solubility of unsubstituted [n]phenacenes decreases dramatically with increasing n; [7]phenacene was found by the Mallory group to have negligible solubility. Currently the longest known [n]phenacene is an [11]phenacene derivative that was synthesized by the Mallory group with tert-butyl substituents acting as solubilizing groups, but it was found to have only modest solubility. The goal of my research is the synthesis of the [11]phenacene derivative shown below. The purpose is to test whether the long-chain alkyl groups R can provide the necessary solubility to allow the synthesis of even larger [n]phenacenes with n = 15 and n = 19.

The planned 15-step route for the synthesis of this compound involves a sequence of different types of chemical reactions, including Grignard, Friedel-Crafts, bromination, Arbuzov, Horner-Wadsworth-Emmons, and photocyclization reactions.

Modeling the Molybdenum Cofactor: An Exercise in Synthesis

Alison Panosian

Mentor: Dr. Sharon Burgmayer

 

Molybdenum is a metallic trace element and is necessary for the functioning of most living organisms. Molybdenum is found naturally in lima beans, spinach, grains, and peas. In humans, a deficiency of molybdenum can lead to health problems, since molybdenum enzymes catalyze many important processes. For example, the enzyme sulfite oxidase utilizes the molybdenum cofactor (Moco) when it transforms sulfite to sulfate via a redox reaction. Allowing the body to metabolize sulfur containing amino-acids, the failure of this reaction can cause neurological disorders. Moco is found in almost all of the molybdenum enzymes in humans is critical to biological reactions. The cofactor consists of a dithiolene organic complex coupled with a molybdenum. The chemistry of the molybdenum cofactor is unknown, and synthesizing model Moco compounds will help one understand the bioinorganic chemistry of molybdenum enzymes.

To create Moco requires the convergence of two synthetic pathways. The first is a seven-step process creating the pterinyl alkynes. The pterin is a heterocyclic compound composed of a pyrazine ring and a pyrimidine ring, containing a carbonyl oxygen and an amino group. Once the pterin is synthesized, a series of anaerobic reactions are performed to add the alkyne. The other pathway creates the tetrasulfide molybdenum complex through three steps resulting in the oxidation of molybdenum by adding sulfur ligands. The pterinyl alkyne reacts with tetrasulfide molybdenum complex resulting in the synthesis of a molybdeunum pterinyl-dithiolene complex to mimic these cofactors. These products will be characterized by FT-IR, NMR and mass spectroscopy. The goal of this research is to follow both synthetic pathways, developed by the Burgmayer laboratory, in an effort to develop the model molybdenum cofactor.

Synthesis of functionalized cis-fused bicarbocyclic structures via olefin cross metathesis and tandem conjugate/Michael addition

Yuan Qiao
Mentor: Dr. Bill Malachowski

Syntheses of cis-fused bicarbocyclic systems are of great interest for constructing complex organic architectures. We report a new synthetic method to functionalized bicarbocyclic structures using the final product from the Birch-Cope sequence that has been developed by the Malachowski group. The two-step method (Scheme 1) includes an olefin cross metathesis and a tandem conjugate/Michael addition.

A wide range of olefin cross metathesis alkenes and a variety of conjugate addition nucleophiles are explored to illustrate the versatility of this synthetic strategy. The alkenes (Table 1) chosen are commercially available and all have precedent for their use in olefin metathesis. It has been shown that 2.5mol% of second generation Hoveyda-Grubb’s catalyst afforded excellent yields with the listed alkenes. The nucleophiles (Table 1) for tandem conjugate/Michael addition come in several forms: non-stabilized carbon nucleophiles, stabilized carbon nucelophiles, heteroatom nucleophiles and carbon radicals. Our work demonstrates the accessibility of constructing functionalized cis-fused bicarbocyclic structures using this tool.

Visualization of the Kink-Turn Structure of RNA

Mithila Rajagopal
Mentor: Dr. Susan White

X-ray and NMR Refined structure of Yeast L-30e-mRNA Complex. (Chao, 2004) 1

RNA, like proteins, folds into 3D structures, consisting of motifs such as hairpins, pseudoknots, and internal loops. This research project focuses on visualizing one such motif, which is called the kink-turn. The kink-turn region consists of Watson-Crick base pairs on either end of a short asymmetric bulge that consists of non-base paired nucleotides, which results in a sharp bend in the phosphodiester backbone. This region is of particular interest because it has been found that proteins bind to RNA selectively at this region. The figure above shows the yeast L30e protein binding to the kink-turn region of its m-RNA. The biophysical structure characterization of the kink-turn of RNA would thus give information about the nature of this motif and its importance in protein-RNA interactions. Such research will aid in studying potentially useful protein-RNA interactions as well as construction of RNA molecular units capable of self-assembling into RNA nanostructures. The goal of this research is to use Atomic Force Microscopy (AFM) to visualize and characterize RNA molecules that have a kink-turn.

For this purpose, previous work done in the lab involved the construction of a relatively large molecule of double stranded RNA with a kink-turn. Two different sequences of 9 and 6 nucleotides respectively were inserted into commercially provided plasmid using site-directed mutagenesis. Linearization of DNA containing these sequences and subsequent transcription with T7 RNA polymerase resulted in the production of RNA that was approximately 900 nucleotides in length. The region of insertion, because it contained non-complementary sequences, resulted in a kink-turn in the RNA molecule. This molecule is large enough to be visualized with the AFM and to study the degree of bending caused by the kink-turn accurately.

Currently, we are focusing on exploring the technique of atomic force microscopy and using it to visualize DNA samples in order to arrive at a method of sample preparation that is suitable for our goals. The most common way of preparing samples is to use functionalized mica surfaces on which the molecules of interest have been immobilized. This general method has to be made specific to our RNA molecules. Further experiments will involve the visualization of kink-turn and non kink-turn RNA molecules in dry as well as liquid environments, and studying the effect of protein (L30e-Maltose Binding Protein) and metal-ions (Mg2+) on the degree of bending of the kink-turn. It is expected that the protein will bind to the kink-turn region and that this will be visible in the AFM images. It is also anticipated that this will change the degree of bending of the kink-turn and we hope to be able to make accurate measurements of the angle of bending.

1 Chao, J A, Williamson, J R. Joint X-Ray and NMR Refinement of Yeast L-30e-mRNA Complex. Structure. (2004). 12(7): 1165-1176

 

Allison Shatz

Mentor: Dr. Sharon Burgmayer

Heterocyclic Ruthenium complexes have been shown to be DNA intercalators. These planar compounds contain carbon-nitrogen aromatic rings that insert between AT and GC base pairs of DNA. The Ruthenium compounds used are tri-chelated Ru (II) compounds. The basic structure includes two 2,2-bipyridine and a varying third ligand, phen-alloxazine, phen-aminopteridine, phen-dimethylalloxazine, phen-diaminopteridine, and phen-pterin. Upon exposure to UV light, many of the Ruthenium compounds have been shown to cleave DNA. Results of varying concentration and UV exposure time is explored through gel electrophoresis to determine optimal conditions, observe quenching and to elucidate ligand effects. Cleavage mechanism is largely unclear, though reactive oxygen species (ROS) are suspected. Investigating the effects of different ROS inhibitors, such as dimethylsulfoxide, superoxide dismutase, and sodium azide, will hopefully provide insight into the mechanism. DNA intercalation is confirmed using viscosity experiments. A parallel investigation is also being conducted with Copper and Cobalt complexes. Initial investigation into toxicity is also being conducted on cancer cell lines. Because of their ability to be selectively activated upon ultraviolet exposure, these complexes have potential future applications in cancer therapy.

Stephanie Vrakas
Dr. Sharon Burgmayer

 

Metals are crucial for many biological reactions due to the fact that they are functionally versatile. Transition metals can be employed as biological catalysts, used as a means to transport molecules or ions, and function as the structural backbone of a compound. In order to better understand the complexity of transition metals and their complexes, model compounds are often used. Molybdenum is a transition metal that is present in many biological enzymes. Although there are many different molybdenum containing enzymes that function to control the redox activity of a variety of substrates, all molybdenum enzymes contain a molybdenum cofactor (Moco). The Burgmayer group has developed an innovative model for the Moco, which incorporates many of the vital structural elements that are present in all Mo enzymes. The Moco model is a molybdenum dithiolene complex is synthesized via the convergence of two synthetic pathways with the reaction of a molybdenum polysulfido compound with a pterinyl alkyne. The goal of this particular research was the synthesis of the molybdenum polysulfido compound and the alkyne reagents. The molybdenum polysulfido compound is also known as ‘tetrasulfide’. Tetrasulfide was synthesized effectively in two steps, in which Mo0 was oxidized to MoIV through the addition of sulfur to produce a tetrasulfide ligand. The pterinyl alkyne was synthesized effectively in seven steps. The first six steps created the pyrimidine and pyrazine rings that together are the pterin framework. In the seventh step an alkyne was combined with the pterin framework via a Sonogashira cross coupling reaction. Spectroscopic techniques such as H1 NMR, infrared spectroscopy and mass spectroscopy were all used to confirm the identities of the various compounds. The ability to effectively synthesize the compounds precedes the next step of constructing the Moco model. Through these reactions the Burgmayer group will be able to continue studying the reactivity and chemical nature of molybdenum enzymes, which hopefully will lead to a greater understanding about how the Moco enzyme functions within biological systems.

Computer Science 2009

Summer Science Research Abstract

 

Human-robot interaction (HRI) is the study of interactions between robots and people. The underlying goal of HRI is to develop principles and algorithms to allow more natural and effective interaction and communication between humans and robots. HRI has been and will be applied to many fields including law enforcement, entertainment, scientific exploration, hospital care, search and rescue, and military battle. In many cases, a robot becomes more than a tool, instead serving as almost another member of the team. Thus, these robots must not only coordinate their behavior with the requirements and expectations of human team members, but must also be able to integrate their tasks with those of their human counterparts. Using HRI and computer vision, the science and technology of machines that see, I will develop a facial recognition algorithm that can be used to create “eye contact” between a robot and a human being. Facial recognition technology is applicable to a plethora of problems facing the world today. Specifically, it has contributed a great deal to the areas of surveillance and security. In researching HCI I want to gain insight into the weaknesses of current facial recognition systems and perhaps develop some theories for improving current research.

Helping Robots Learn Their Purpose

Meena Seralathan
Mentor: Dr. Doug Blank

Developmental robotics is a interdisciplinary field of study working towards understanding the human mind, and emulating such complex processes in mathematical computations done by a computer chip. In doing so developmental roboticists must give the robot's mind the ability to learn in real-time, on its own, and to develop its own goals and motivations in time based on what it has learned. Many existing artificial neural networks (ANN; mathematical representations of a human neural network) cannot handle real-time input, or have poor memory handling, causing the networks to forget what they have learned once the robot travels to a different environment, and to be unable to effectively process new input. Thus the purpose of this experiment is to explore the many different structures for ANNs, and to modify them to create a better learning system for robots. By improving the way the ANN retains memory, how it reacts to different stimuli, and how it makes generalizations and abstractions of its environment, we hope to work towards developing a network that can learn effectively as it explores its environment.

Geology 2009

Summer Science Research Abstract

Anne Bugnaski

Mentor: Dr. Pedro Marenco

 

The end Permian mass extinction (~252mya) was the largest mass extinction in Earth's history. Marine invertebrates were drastically affected with ~80% of genera going extinct. Biotic recovery did not take place in earnest until ~5my later at the beginning of the Middle-Triassic (Anisian). Combining paleontological data (biostratigraphy, fossil abundance, diversity, presence/absence)and chemostratigraphic data (stable isotopes of S, C, and O) from the Prida Formation at Fossil Hill, Nevada we can better understand recovery patterns in correlation with changes in environment. Much research has been conducted on conodont and ammanoid biostratigraphy at Fossil Hill but we will be examining the correlation between changes in ocean geochemistry and the biotic recovery. We predict that we will find a link between the return of favorable environmental conditions and increasing faunal diversity.

Julie Griffin
Mentor: Dr. Don Barber

 

Global sea level has been thought to be consistently rising for the past 20,000 years. Recently, new technology and research has indicated to scientists that sea level has fell approximately three times since the Last Glacial Maximum, and risen from each fall. I am researching this concept of sea level dropping by determining the formation of a series of ridges on Cedar Island, located in the Outer Banks in North Carolina. To study the history of these ridges, I am working with three sediment cores that my advisor, Don Barber, took in 2005 on a ridge in the middle of the 19 sequential ridge construction. Some of the experiments that I have run on the cores include making observations of all the samples from each part of the core, and diagramming my results. Also for each sample I am wet sieving for particle size analysis, and performing loss on ignition to determine the percentage of organic matter in each section of the core. For the deepest samples, I selected material that I thought could be radio carbon dated to determine approximate ages for the cores. These tests, and hopefully some field work taking more sediment cores, will aid me in constructing images of how each ridge was created, depositional environments, and overall how the ridges formed. By determining the order of formation of the sequential ridges, I will be able to see whether sea level was rising or falling during the time period of the creation of the ridges. Through this study, I will contribute research to other pieces of global data that attempts to determine the progression of sea level over the past 20,000 years.

Tanya Nelson
Mentor: Dr. Lynne Elkins

 

Mid-ocean ridge basalts (MORB) are extruded on the ocean floor at divergent tectonic plate boundaries, where they interact with seawater as they cool. This interaction can cause chemical changes to occur that weather and alter the rocks. Understanding the composition of the MORB and determining which samples have been altered helps us to determine primary melt chemistry and better understand the origins of those basalts. We also hope to better constrain the complexities of the seawater alteration process. We are specifically looking at a suite of variably altered MORB from the Kolbeinsey Ridge in the Artic. This ridge is particularly interesting because it is a shallow, slow spreading ridge that thus represents near-end member mid-ocean ridge conditions, and because it is adjacent to Iceland and thus may reflect dynamics of plume-ridge interaction. To explore the extent of alteration, we will examine the Cl concentrations and Cl/K ratios within the rocks. With increased chemical exchange with seawater, the rocks develop higher concentrations of Cl. However, the original rocks can have varying levels of Cl, while seawater alterations does not affect K levels, so Cl/K ratios are commonly used to indicate the degree of seawater alteration that has occurred. Increased exposure time to seawater will increase the Cl/K ratios. We will conduct analyses of major element concentrations and Cl/K ratios using electron probe microanalysis. If results show high levels of Cl concentrations, which would indicate that there has been a more chemical interaction with seawater, we will compare Cl abundance and Cl/K results to other measures of alteration and look for systematic variations. We hope to place new chemical constraints on the nature of the alteration of MORB.

Nithya Vasudevan

Mentor: Dr. Don Barber

 

With the advent of Western medicine, scientists have started to question the validity of alternative and natural healing methods. More specifically, the ingestion of clays has been a disputed self-prescribed means to prevent morning sickness for pregnant women and treat digestive issues in parts of the United States, Central America, Africa, and Asia. While some argue that eating clay is a beneficial way to cleanse the digestive tract as well as to provide a good source of calcium, others fear that it actually leaches vital nutrients, like iron for instance, out of the digestive system. The goal of this research is to examine commonly ingested clays and study their interaction with digestive fluids. The samples will not only be found in mainstream American markets, but also in stores within various immigrant communities on the East Coast. The clays will undergo XRD analysis to determine their mineral content. Surface area, pH, and EH tests will be performed to understand the basic nature of the clays. Total digestions and bulk chemical analyses will also be conducted, along with gastric fluid extractions and dissolution kinetic experiments with simulated digestive fluids. Through this research, we hope to gain a better understanding of how these clays function in the digestive tract and to draw parallels and distinctions between the types of clays consumers are able to buy in the United States.

 

David Wicks

Mentor: Dr. Arlo Weil

The kinematic evolution of curved mountain belts can be examined by combining several different types of paleomagnetic analyses with detailed structural studies of finite strain. The combination of these methods provides a data set varied enough to produce quantifiable data that can be compared to general patterns of curvature in mountain belts. While many mountain belts have been assessed in this method, not much analysis has done on what occurs simultaneously farther into the foreland of the continent. We are now examining the expression of orogenies(mountain building events) in locations further away from the source of deformation, as well as seeing if the same analytical methods can still be used to create a rigorous model for the dynamics of the creation of a mountain chain.

Sophia Wolfenden

Mentor: Dr. Pedro Marenco

 

For my summer research, I chose to analyze the shells of bivalve and other mollusca genera from the Near Eastern archaeological site of Muweilah, UAE. In order to determine the provenience of the shells found at the site of Muweilah, and specifically those found within the interior spaces of the site, it was necessary to undertake a series of dating techniques including stratigraphic dating, carbon isotope analysis and shell classifications through direct study of geographically similar collections. From this research the age and potentially, the location of origin of these shells can be determined and classified. Such research regarding the geological availabilities on hand in the region during the late Bronze age is useful when determining the likelihood of ecological and resource management practices of the early settlers.

Math 2009

Summer Science Research Abstract

Mathematics and the environment: A compilation of useful information

Naomi Hamermesh

Mentor: Dr. Victor Donnay

 

Sustainability as it relates to the environment is the concept that we need to use our natural resources in such a way that future generations will still be able to live and be ‘sustained’ by our planet. This summer, I will be looking into ways that we can incorporate environmental sustainability concepts into mathematics education to better engage students in both math concepts and issues of sustainability. I will conduct research on the web to see what curriculums already exist on the subject and test the curriculums that I find by actually doing the problems associated with the various curriculums. I will also meet with Jim McGaffin, the Assistant Director for Energy and Project Management in the Facilities department at Bryn Mawr College to come up with a few topics on sustainability as it relates to Bryn Mawr for use in Professor Donnay’s spring semester Senior Conference as well as other future math courses taught at Bryn Mawr. This information could be used to incorporate sustainability concepts, as they relate specifically to our campus, into the math curriculum at Bryn Mawr. My hope is to compile a database of information including where information on sustainability curriculums can be found as well as answer keys to various curriculums and a few problem sets, which I will develop over the course of the summer about sustainability at Bryn Mawr. This database will be used as a resource for the Environmental Sustainability program for teachers that Professor Donnay is developing in conjunction with faculty from various Pennsylvania area colleges and universities spanning several different disciplines. It is my hope that in conducting this research, I will discover a potential topic of interest for me to look into in further detail in the form of a senior thesis.

On the Boundedness of Oscillatory Integral Operators in Harmonic Analysis

Manal Zaher

Mentor: Dr. Leslie Cheng

My summer research is in the area of harmonic analysis, the branch of mathematics which studies the representation of signals or functions as the superposition of basic waves. The basic waves are called "harmonics", hence the name "harmonic analysis”.

In this branch of mathematics, there is great concern about examining mathematical objects by decomposing them into many simpler building blocks and studying these simpler components. This would make the study of the original object easier and more comprehensible in most cases. For instance, to study a function (a musical sound, for example) we could break it down into a sum of the pure harmonics, sine and cosine, which will allow us to study these simple graphs, to better understand our original function's behavior. Harmonic analysis has become a vast subject with applications in areas as diverse as acoustics, optics, electrical engineering, quantum mechanics, and neuroscience.

My research will focus on some theoretical aspects of the field - in particular the boundedness of oscillatory integral operators. I have started studying previous work in the field as a background. I will try to extend some of the results obtained by BMC undergraduates in the past (Zoryanna Dopko '05, Kirsten Kemp '07, Sarah Khasawinah '09). Once I have finished learning the techniques used in their proofs, I will work on similar problems extending their results by modifying their techniques.

Psychology 2009

Summer Science Research Abstract

Iconicity and Conventionality in Children’s Symbol Learning

Madeline Berkowitz
Mentor: Dr. Lauren Myers

The current study seeks to investigate the role of iconicity and conventionality in children’s gesture learning. Iconicity is the extent to which a symbol looks like its referent (the thing that it represents). Conventionality is the meaning that is assigned to an object with repeated use between social partners. Our culture has many conventional gestures. For instance, people may place their arms in an oval shape and rock them back and forth to represent a baby. Most people find this gesture easy to understand. Is this because the gesture is iconic (e.g., the action resembles that of rocking a baby) or because it is conventional (e.g., we have learned that people use this gesture to represent rocking a baby)?

Our research will experimentally manipulate the conventionality and iconicity of gesture symbols in order to examine which of these features is most important in 3-to 5-year-olds’ symbol learning. Each child will participate in two experimental sessions. In the first session, children will view eight novel toys. Each toy will be assigned an iconic gesture; that is a gesture that looks like the action we performed with the object. For example, the gesture for a hollow tube is placing the thumb and fingers in a circle and raising it to your eye. Pilot studies with adults have shown that the chosen gestures match the toys that they represent. For half of the objects, the gesture will be conventionalized during the experiment session and for the other four, the gesture will not be conventionalized. For the conventional toys, two experimenters will establish the iconic conventional gesture through a social interaction. The child will be asked to perform the gesture and choose the toy from among two other toys. The procedure for the unconventional toys is identical except that instead of seeing a gesture the child will see an action performed on the toy. In the second session, the child will see the experimenter perform a gesture. For the conventional toys, the gesture will be identical to the gesture that the child saw in the first session. For the unconventional toys, the gesture will be derived from the action the child saw in the first session. The child will then be asked to choose the object that matches the gesture from among four toys. One toy, the target object will closely resemble the toy the child saw in the first session. The other four toys appear very different from the toy the child saw in the first session, but have the same function. For instance, for the hollow tube mentioned above, the target is a similar hollow tube and the distracter objects are a plastic disk with holes, a bracelet and a ball with holes. Each of these objects could be brought to the face and looked through as the gesture suggests.

If children are more successful on the conventional trials than the non-conventional trials, it will indicate that conventionality is more important than iconicity. However, if children choose the target objects with equal success across conditions, it will indicate that iconicity is sufficient, and that conventional use of a gesture does not impact children’s understanding of gestures as symbols.

Symbols are everywhere in our world. At one time it was thought that the relationship between iconic symbols and what they represent was self-evident. However, developmental psychology research reveals that relationship between iconic symbols and their referents is not obvious to young children. We seek to learn more about what children do and do not understand about the nature of symbols. Our research also has implications for the development of communication symbols for non-verbal individuals. It is important to know what aspects of symbols are most understood when choosing symbols for these systems.

Monkey See, Monkey Do: Learning Symbols Through Conventionality

Megan Roberts
Mentor: Dr. Lauren Myers

 

Understanding how children learn gesture and word labels for objects provides insight into language acquisition and early cognitive development. To date, much research has focused on the importance of iconicity of gestures, or the resemblance of a gesture to its referential object. Previous literature on the subject indicates that children are able to understand iconic gestures much earlier than they understand arbitrary gestures, or gestures that do not necessarily resemble the referential object or action. However, this might have more to do with the conventionality of these gestures than their iconicity. Conventionality refers to the repetitive use of the symbol or gesture in a communicative manner during social interactions. To truly determine the roles of iconicity and conventionality, we have designed an experiment to assess children’s ability to differentiate iconic gestures used in a conventional context from those used in a non-conventional setting.

In this study, we will manipulate the conventionality of the gestures in the first experiment session by teaching the children conventional gesture labels for 4 sets of objects and word labels combined with actions for another 4 non-conventional sets of objects. After a period of 5-10 days, we will test children with a gesture label for each of the 8 novel object sets. Four of these gesture labels will be ones they have previously used as conventional symbols with the experimenter. The other four gesture labels will be extracted from the actions that children learned in the non-conventional condition. For instance, in session 1 the children learned that an egg-shaped novel object may be opened, and in session 2 the gesture extracted from that action is an opening gesture made with two hands. Although the gesture can be performed by all of the four objects in each set, the target object most closely resembles the demonstration object to which the children were introduced during session one. We will then analyze their ability to map gesture labels to target objects, as measured by the number of correct object selections in each condition.

If iconicity is more important than conventionality in children’s symbol learning, then during the second interaction with the children, there should be no difference found in the children’s recall of gesture-object matches between the conventional and non-conventional conditions On the other hand, if conventionality, rather than iconicity, is a more useful component of children’s understanding of symbols, then the participants should be able to better match the conventionalized gesture labels to their appropriate target objects during the second interaction of this two-part study.

The knowledge that iconicity or conventionality plays a more important part in symbol learning provides scientists with information about the developing lexicon and children’s understanding of symbols. In turn, knowing whether iconicity or conventionality increases children’s ability to retain information could influence teaching techniques for children in early development. The results of this study have implications into the development of cognitive processes involving language, symbolic understanding, and symbol-to-referent-mapping.