Student Profiles Archive - MSD Scholars 2011-2012
Here you will find information about past and present students funded through scholarships administered by the Undergraduate Research Center - Sciences. We are proud of the achievements of our research scholars.
Please click on the program year to get information about the supported students, their mentors and their research projects.
| Ms. Nancy Wu
Mentor: Dr. Shimon Weiss
Title: Quantum Dots for Biological Probing
Ms. Wu is currently pursuing a Ph.D. in Chemical Biology at the University of Michigan.
| Mr. Joe Udeochu
Mentor: Dr. Patricia Phelps
Major: Physiological Science
Title: Effects Of Reeler and Dab1 Mutations On The Lateral Cervical Nucleus
Mr. Udeochu is currently pursuing a Ph.D. in Biomedical Sciences/Neuroscience at the University of California, San Francisco.
| Ms. Nancy Tu
Mentor: Dr. Richard Zimmer
Major: Environmental Science
Title: Chemosensory Basis for Keystone Predation
In predator-prey relationships, physiologically requisite biochemical compounds of prey may be exploited and used as honest signals by predators. The extrapallial (EP) fluid excreted by the mantle of the California mussel, Mytilus californianus, contains proteins involved in biomineralization; as these proteins are required for the production of shell, they may serve as the chemosensory signals guiding the primary predators of mussels, seastars, to their preferred prey. Seastar bioassays, comprised of placing the seastar in a tank with prey mimics and tracking its feeding choices, have shown that seastars are as responsive to the extracted and purified EP fluid as a live mussel, indicating that an active recognition cue is found within. After extracting the EP fluid and isolating its components through SDS-PAGE, four component proteins were identified using tandem mass spectrometry; KEYSTONin, paramyosin, heat-shocked protein 70, and an unidentified protein B3. Seastar bioassays have shown a strong feeding preference on KEY-filled faux prey when tested against the control-filled faux prey, thus pointing towards KEYSTONin as being the active cue by which a seastar identifies Mytilus californianus. Seastars are keystone predators and the signals they use can be considered as keystone molecules. Their effects resonate through the intertidal community as seastars reduce competition for space for other sessile organisms by consuming mussels, thereby increasing biodiversity on the rocky wave-swept shores.
Ms. Tu is currently pursuing a M.S. degree in Civil and Environmental Engineering at Stanford University.
| Mr. Chanrith Siv
Mentor: Dr. William Gelbart
Title: The Proximity of the 5’ and 3’ Ends of Single-Stranded Polynucleotides
Effective circulation of the RNA molecule is important for the genome replication of many RNA viruses, as well as for recruiting cellular cofactors to initiate translation of messenger RNAs. The proximity of the two ends of single-stranded (ss) nucleic acids has recently been argued to be a direct consequence of their large degree of self-complementarity, independent of nucleotide sequence and length. We test the hypothesis that the ends of RNA molecules are effectively circularized, and therefor enecessarily close to each other, by measuring the distance between the ends of linear molecules in electron microscopy (EM). Due to the limitation in EM resolutions that doesn’t allow actual RNA structures to be seen, we bind 5nm gold nanoparticles (AuNP) to the ends of a 500 nt RNA, as well a 3200 nt RNA, and measure the distance from the center of one AuNP to the next. The average end-to-end distance that we obtain is 7 nm for 500 nt and 10 nm for 3200 nt, suggesting that the ends are close but may be larger than those instrinsic to RNA because of denaturation and stretching by EM staining and interaction with the grid.
Mr. Chanrith is currently pursuing a Ph.D. in Biophysics at the University of Michigan.
| Mr. Brian Shevitski
Mentor: Dr. Chris Regan
Title: Characteriziation of Graphene and Bilayer Graphite Using Select Area Electron Diffraction
Dark field transmission electron microscopy coupled with select area electron diffraction (SAED) is used to image the spatial distribution of distinct crystallographic domains within regions of grapheme growth by chemical vapor disposition. This method also clearly distinguishes regions of different thicknesses in real space. Finally, the SAED pattern of grapheme is quantitatively compared to that of bilayer graphite and compared to a theoretical model.
Mr. Shevitski is currently pursuing a Ph.D. in Physics at the University of California, Berkeley.
| Ms. Audrey Salinas
Mentor: Dr. Victoria Sork
Title: Impact and Limitations of Introduced Pollinator, Apis mellifera, on Local Pollinator Communities in the Mojave National Preserve
Ms. Salinas is currently pursuing a M.S. in Biology at San Francisco State University.
| Mr. Esteban Ruiz
Mentor: Dr. Reggie Edgerton
Title: Development of Novel Polymer Insole for Knee Damage Prevention
The cartilage in the human knee is unable to regenerate after it has been worn down either through years of use as in the aged or excessive activity as in athletes. A new polymer shoe insole is explored which aims to reduce the force experienced by the knee during heel strike stepping. The insole will serve to absorb the ground reaction force on the foot during walking and running by increasing the impact time over which the force is applied. A finite element model of the posterior inferior portion of the human foot was created using Abaqus software to simulate heel strike stepping and to serve as a design aid in conjunction with experimental results taken from treadmill testing with human subjects. The anatomy of the foot has been greatly simplified in order to reduce the complexity of the computer model and reduce runtime for simulations. During treadmill testing, subjects were asked to run at four different speeds, and the forces on the knee were estimated using data from accelerometers affixed to the subjects’ tibias. By comparing the forces on the knee from various configurations of insole thickness and geometry, optimal insole configurations are determined. The finite element model of the hell was used to verify the findings and validate the experimental results.
Mr. Ruiz is currently pursuing a Ph.D. in Rehabilitation Technology and Science at the University of Pittsburgh.
| Ms. Laura Mullens
Mentor: Dr. Dino Di Carlo
Title: Haptic Feedback for Rehabilitation with Prosthetics and Sensory Neuropathies
Ms. Mullens is currently pursuing a Ph.D. in Biokinesiology at the University of Southern California.
| Mr. Mioy Huynh
Mentor: Dr. Anstassia Alexandrova
Title: Late Onset of Metallic Bonding and Extraordinary Resilience of Covalent Bonding in the Boron-Aluminum Cluster Ions
The character of chemical bonding being covalent or metallic has profound effects on the structure and properties of solids. Undoubtedly, similar effects must be prominent at the small cluster scale. The interplay between covalent and metallic bonding in the series of mixed boron-aluminum cluster ions, doubly anionic BnAI6-n (where n ranges from 0-6), and their lithium salts was investigated. The global minimum structures of considered clusters were identified using our ab initio genetic algorithm method. State-of-the-art electronic structure calculations and analysis were performed on the found lowest energy isomers. Whenever possible in these clusters, boron atoms form covalent B-B bonds as assisted by strong 2s-2p hybridization of atomic orbitals on B, eradicate the AI-AI bonding, and sometimes even enforce less favorable 3s-3p hybridization on AI. The boron-induced covalent bonding in the studied clusters is surprisingly persistent and dominates over the metallic character, down to the smallest concentrations of boron atoms in the cluster. This in turn affects the ionization potential and the HOMO-LUMO gap in the clusters. These findings may be of importance to modern doped-cluster based technology.
Mr. Huynh is currently pursuing a Ph.D. in Chemistry at the University of Illinois at Urbana-Champaign.
| Mr. Charles Hernandez
Mentor: Dr. Julian Martinez-Agosto
Major: Microbiology, Immunology & Molecular Genetics
Title: Endocytosis regulates the growth and development of hematopoietic cells in Drosophila melanogaster
Hematopoiesis is a process by which undifferentiated stem cells give rise to specialized blood cells through specific signals received from a stem cell niche. The lymph gland of Drosophila melanogaster has three components: cortical zone (CZ), medullary zone (MZ), and a posterior signaling center (PSC). These compartments function together to derive all blood cells in the fruit fly from progenitor cells into differentiated cells. Our goal was to investigate if endocytosis affects hematopoiesis by overexpressing and downregulating components of the endosomal fusion machinery. Manipulation of endocytic fusion proteins in differentiating hemocytes causes loss of MZ progenitors. This suggests a role for secreted signals originating from the CZ that maintain the progenitor population. We identified a differential role for lysosomes in the PSC and MZ, where they are active, versus the CZ, where their activity is reduced. Interestingly, the expression of the transmembrane domain along with its cytoplasmic tail of human Lamp1 in both the PSC and MZ leads to a loss of progenitor cells and a fully differentiated lymph gland. This suggests a novel role for lysosomal function in maintenance signaling between niche and progenitor cells. In addition, Rabex5 and Gilgamesh appear to regulate the proliferation of MZ progenitors. This study demonstrates novel roles for the endocytic machinery in hematopoiesis.
Mr. Hernandez is currently pursuing a Ph.D. in Molecular Cell Biology, Genetics and Development at Yale University.
| Mr. Michael Gomez
Mentor: Dr. Imke Schroeder
Major: Microbiology, Immunology & Molecular Genetics
Title: Regulation of Burkholderia pseudomallei Virulence Gene Expression: Role of PhoBR System
Burkholderia pseudomallei is the causative agent of meliodosis, a potentially lethal, tropical disease characterized by abscess formation in human internal organs. Little is known about the regulation of virulence gene expression in this bacterium. The goal of this study is to characterize the role of the PhoBR phosphate-responsive regulatory system in virulence gene regulation and its global regulatory functions. Deletion and overexpression of phoB mutant strains were constructed in B. pseudomallei via an allelic exchange procedure. B. pseudomallei has the ability to infect macrophages and form plaques on a macrophage monolayer; however, PhoBR is not involved in this aspect of B. pseudomallei pathogenicity as the phoB deletion and overexpression strains were wild type in plaque forming efficiency. Burkholderia thailandensis was used as a surrogate for B. pseudomallei to determine phosphate-limiting growth conditions to be below 200 μM. While final cell densities correlated with phosphate limitations, the generation time was not affected. DNA microarray analysis is underway to identify PhoBR-regulated genes under phosphate-limiting and nonlimiting conditions. Study of the relationship between PhoBR and virulence may contribute to an increased understanding of B. pseudomallei pathogenesis which may be exploited for antimicrobial and vaccine development.
Mr. Gomez is currently pursuing a Ph.D. in Plant & Microbial Biology at the University of California, Berkeley.
| Ms. Karina Chavarria
Mentor: Dr. Jennifer Jay
Major: Civil & Environmental Engineering
Title: Mercury Methylation by the Acetyl-CoAPathway in Biofilm and Planktonic Cultures of Desulfovibrio desulfuricans
Widespread mercury contamination in the environment poses serious health risks to humans and wildlife alike. Mercury often enters aquatic bodies via atmospheric deposition and undergoes methylation to form methylmercury by sulfate-reducing bacteria (SRB) that dwell amongst periphyton and aquatic sediments. Methylmercury [CH3Hg] is a potent neurotoxin that may inflict deleterious effects on the immune and nervous systems, alter genetic and enzyme systems, and damage developing embryos. Since methylmercury bioaccumulates throughout the food chain, it is an especially harmful and problematic contaminant. This study focuses on one particular strain of SRB, Desulfovibrio desulfuricans ND132, and the acetyl-coA pathway of methylation that has been commonly associated with it. Using a microbiological assay to compare mercury methylation by SRB in different modes of growth, particularly biofilm and platonic cultures, this study aims to confirm past research that has shown biofilms to be the primary mode of methylation. Using RT-qPCR on RNA extracted from biofilm and planktonic cells, results of mRNA copies per cell suggest that biofilms use this pathway orders of magnitude more than planktonic cultures do to methylate mercury. These results have future implications on the ability to counteract mercury contamination by proposing that environments conducive to biofilm formation are of particular importance. Knowing targeted locations of mercury methylation allows for better development of remediation measures in the future.
Ms. Chavarria is currently pursuing a joint M.S./Ph.D. degree in Environmental Engineering at the University of California, Berkeley.
| Ms. Josefa Baker
Mentor: Dr. Michael Jura
Title: Spectral Lines of the Circumstellar Gas of Ophiuchi 51
Ophiuchi 51 contains a circumstellar, or star-orbiting, disk of dust and gas that will eventually condense into one or more rocky planets like those found nearest our sun. Such protoplanetary disks are relatively common; what makes Ophiuchi 51 exceptional is the fact that some of the material is accumulating onto the star itself and can be observed in the spectra of its atmosphere. By studying the absorption lines of this pre-main sequence star, the elemental components of the dust can be determined since each line corresponds to a unique atomic energy transition. Knowing what elements are present and in what distributions reveals the likelihood of that gas producing a possibly life-bearing planet. Using the software collection Image Reduction and Analysis Facility (IRAF), the spectra are graphed on a plot of wavelength versus intensity. This makes it easier to recognize and analyze absorption lines, which appear as sharp downward spikes. The center of each of these spikes is recorded and compared to a list of known lines in order to identify which transitions are present. The Doppler shift resulting from the circular motion of the dust around the star is also identified. Next, each line’s equivalent width, or the area above the spike, is measured. The equivalent width is proportional to the column density, a gauge of the abundance of a particular transition. Together, these quantities help establish if planets that form from the dust and debris surrounding Ophiuchi 51 could engender life, as well as offer further understanding on late-stage planet formation.
| Mr. James Allen
Mentor: Dr. Gil Travish
Title: Design Optimization of a Gamma-Ray Target for Replacement of Radionucleotides in Industrial Applications
The development of a gamma ray source, the gamma ray non-proliferating irradiator technology (GRANIT), is under way at the University of California, Los Angeles to replace 137Cs, a dangerous radioactive material, in oil well logging and other industrial processes. This presentation focuses on the design of the gamma ray converter target within GRANIT. The target takes accelerated electrons and converts them into high-energy photons through a process called bremsstrahlung. G4Beamline, a simulation toolkit based on the Geant4 framework), a Monte Carlo particle transport code, is used to simulate the gamma ray production process. The target thickness and materials are optimized by analyzing different characteristics such as the energetic efficiency, average gamma ray energy, and the overall gamma ray energy spectrum. The main material for the target will be tungsten due to its high radiative yield. Using a 1.5 MeV electron beam, the optimum thickness of a single-material tungsten target is approximately 0.18 mm. The results of these parametric studies are presented along with future plans to simulate and fabricate a multi-material target.
Mr. Allen is currently pursuing a Ph.D. in Physics at Stanford University.