Oscar Azucena
Electrical Engineering Ph.D. Graduate Student

Lab Group: Joel Kubby

Research: My current research focus is on using ink-jet printer technology to fabricate Micro-electro-mechanical systems. An ink-jet printer is used to deposit layers of different materials to fabricate three dimensional devices. Conductive solvents, containing metallic nano-particles, are deposited and sintered at different temperatures to engineer the electrical and mechanical properties of each layer. Organic polymers are also used as sacrificial layers that can later be removed to develop mechanical subcomponents.

Publications:

Kevin Baker, Eddy Stappaerts, Don Gavel, Scott Wilks, Jack Tucker, Dennis Silva, Jeff Olsen, Scot Olivier, Peter Young, Mike Kartz, Laurence Flath, Peter Kruelivitch, Jackie Crawford, Oscar Azucena. High-speed horizontal-path atmospheric turbulence correction using a large actuator-number MEMS spatial light modulator in an interferometric phase conjugation engine. Optics Letters, 2004.

Yvette Alva
Ecology and Evolutionary Biology Ph. D. Graduate Student

Lab Group: Bernardi Lab

Research: The Tropical Eastern Pacific (TEP), the Pacific Ocean coastline from the Mexico to Peru, is unique because it has undergone radical transformations that are well documented; making the TEP a perfect platform to study evolutionary and ecological processes that may have influenced present day distributions of marine organisms. For my project, I will use phylogeographic tools to study the genetic structure of various reef fish species to determine levels of population migration and fragmentation, and perform a comparison among species by grouping species according to larval duration and habitat to determine if these factors influence their distribution. Because of historical and ongoing processes that have occurred in the TEP, I expect to find high population structure suggesting restricted gene flow among reef fish.

Publications:

Alva, Yvette R., Susan Masta, Eric J. Routman. In Prep. Population structure and history of Rana blairi, the plains leopard frog, . Molecular Ecology.2002.

Alva, Yvette R. and Jesus Maldonado. In Prep. Species identification marker for canid species. Molecular Ecology Notes.2002.

Internships/Presentations/Awards:

America Fisheries Symposium 2007 oral presentation; San Francisco, CAHistorical Biogeography of Reef fish that reside in the Tropical Eastern Pacific

Marine Evolutionary & Ecological Genomics workshop participant Summer 2007, Roscoff, France

1st Annual Graduate Student Symposium 2006 poster presentation; UCSCPhylogeography of Tropical Eastern Pacific reef fish.

Society for Evolution Symposium 2002 Oral Presentation; Urbana, ILPopulation structure and history of the plains leopard frog Rana blairi.

Evolution and Ecology Seminar- Oral Thesis Presentation May 2002; SFSUPopulation structure and history of Rana blairi, the plains leopard frog, via the nested cladistic analysis.

Society for Conservation Biology Symposium 2001 Poster Presentation; Hilo, HIPopulation structure of Rana blairi, the plains leopard frog.

Mary Ann Dassah
Molecular Cell & Developmental Biology Ph.D. Graduate Student

Lab Group: Zahler Lab

Research: I am interested in mutations to the intronic +1G nucleotide of 5‚ splice signals. These are common features sited in many human genetic disease alleles. Genetic suppression of intronic +1G mutations by mutant U1 snRNAs containing compensatory base-pairing substitutions has been discovered in our lab. My research focuses on finding genetic suppressors of 5‚ splice site mutations.

Internships/Presentations/Awards:

University of California Santa Cruz RNA Club. Santa Cruz, California, January 2008. TALES FROM THE CRYPTIC SPLICE JUNCTIONS: ACTS FROM SUPPRESSION TO SPLICE FIDELITY. MaryAnn Dassah, Dr. Alan Zahler.Oral Presentation.

A.M. Eukaryotic mRNA Processing, ColdSpring Harbor Laboratory. Cold Spring Harbor, New York. August 2007. IDENTIFYING AND CHARACTERIZING SUPPRESSORS OF CRYPTIC 5, Splice Sites. Mary Ann Dassah, Dr. Alan Zahler.Poster Presentation.

RNA Society Conference, Seattle, Washington. 2006. TALES FROM THE CRYPTIC SPLICE JUNCTIONS: SUPPRESSING MUTATIONS AT 5, SPLICE SITES. Dassah, M.A., V. Hunt, S. Patzek, A.M. Zahler. Poster Presentation.

A.M. Eukaryotic mRNA Processing ColdSpring Harbor Laboratory. Cold Spring Harbor, New York August 24-August 28, 2005. TALES FROM THE CRYPTIC SPLICE JUNCTIONS--SUPPRESSING +1 MUTATIONS AT 5' SPLICE SITES . Dassah, M.A., Zahler.Poster Presentation.

Meeting on Eukaryotic mRNA Processing, Cold Spring Harbor Laboratory, New York, 2003.

ABRCMS October 31- November 3, 2001. ANALYZING THE SPLICING FUNCTION OF SR PROTEINS AND THE RNPS1 HOMOLOGUE BY GENE KNOCKOUTS IN CAENORHABDITIS ELEGANS. MaryAnn Dassah, Alan Zahler. Poster Presentation.

Jacqueline Epps
Chemtistry Ph.D. Graduate Student

Lab Group: Kliger Lab

Research: My current research deals with trying to deduce the oligomeric state of rhodopsin. Rhodopsin is the photopigment that is responsible for human scotopic (dark-adapted) vision. It has been considered to be a monomer for some 30 years. However, recently a paper was published that suggests that rhodopsin exists as a dimer (or even a higher order oligomer) in its native membrane environment. Members of the rhodopsin community are rather divided in their beliefs of the hypothesis. In order to address this question I am using time-resolved linear dichroism measurements which uses linearly polarized light to measure the rotational diffusion of rhodopsin in the disk membrane. By using the Einstein-Debye equation I can tell by the rate of rotational diffusion whether rhodopsin is a monomer, dimer or higher order oligomer. The rotational diffusion time for a rhodopsin monomer is known to be on the order of 20 microseconds. If rhodopsin exists in as a higher order oligomer then the rotational diffusion constant will increase according to the oligomeric state.

My current experiments suggest that rhodopsin does exist as a monomer in the disk membrane. I am in the process of exploring this further by altering the disk membrane environment using various detergents and repeating the linear dichroism measurements.

Rhodopsin is important because of its critical role in the correct function of the human eye. Further, rhodopsin is a G-protein coupled receptor (GPCR). GPCR's are make up over 50% of the membrane receptors in the body. Therefore, studies on rhodopsin will also contribute to that body of work which furthers drug discoveries.

Publications:

Elsa C. Y. Yan, Jacqueline Epps, James W. Lewis, Istvan Szundi, Aditi Bhagat, Thomas P. Sakmar and David S. Kliger. “Photointermediates of the Rhodopsin S186A Mutant as a Probe of the Hydrogen-Bond Network in the Chromophore Pocket and the Mechanism of Counterion Switch.” Journal of Physical Chemistry C (2007) Vol 112 Issue 25 pp. 8843-8848.

Istvan Szundi, Jonathan J. Reprecht, Jacqueline Epps, Claudio Villa, Trevor E. Swartz, James W. Lewis, Gebhard F. X. Schertler, and David S. Kliger. Rhodopsin Photointermediates in Two-DImensional Crystals. Physiological Temperature Biochemistry 45(15):4974-4982 April 2006.

Jacqueline Epps, James W. Lewis, Istvan Szundi and David S. Kliger. Lumi I --> Lumi II: the Last Detergent Independent Process in Rhodopsin Photoexcitation. Photochemistry and Photobiology 82(6): 1436-1441 November 2006.

Internships/Presentations/Awards:

Biophysical Society Meeting, Long Beach, California, February 2008. INFLUENCE OF LIPID MEMBRANE COMPOSITION ON THE KINETICS OF RHODOPSIN ACTIVATION BY TIME-RESOLVED UV-VISIBLE SPECTROSCOPY. Jacqueline Epps, Dr. David S. Kliger, James W. Lewis, Karina Martinez-Mayorga, Istvan Szundi, Victor U. Constantino, Michael F. Brown.Poster Presentation

Conference on Retinal Proteins. Chiemsee, Germany. June 2004. DETERMINATION OF THE OLIGOMERIC STATE OF RHODOPSIN IN MEMBRANE. Jacqueline Epps, James Lewis and David Kliger.

Aura Alegra Eroy-Reveles
Chemistry Ph.D. Graduate Student

Lab Group: Pradip Mascharak

Research: Nitric oxide (NO) plays important roles in a wide variety of physiological processes, including neurotransmission, immune response, blood pressure control, and inhibition of tumor growth. Thus, compounds that deliver NO under controlled conditions are of great interest. For example, metal nitrosyl complexes that release NO upon illumination of light could be used as antitumor agents in photodynamic therapy. I am working on a project that looks into the design and synthesis of manganese nitrosyl complexes that release NO under mild conditions (low-intensity visible light). These complexes will enable us to identify factors responsible for the controlled release of NO.

Publications

Eroy-Reveles, A. A.; Leung, Y.; Beavers, C. M.; Olmstead, M. M.; Mascharak, P. K. “Near-Infrared Light Activated Release of Nitric Oxide from Designed Photoactive Manganese Nitrosyls: Strategy, Design, and Potential as NO Donors.” J. Am. Chem. Soc. 2008. Accepted for Publicatio.

Eroy-Reveles, A. A.; Hoffman-Luca, C. G.; Mascharak, P. K. “Formation of a Triply Bridged μ-oxo Diiron(III) Core Stabilized by Two Deprotonated Carboxamido Groups upon Photorelease of NO from a {Fe-NO}6 Iron Nitrosyl.” Dalton Trans. 2007, 5268-5274.

Eroy-Reveles, Aura A.; Leung, Yvonne; Mascharak, Pradip K. Release of Nitric Oxide from a Sol-Gel Hybrid Material Containing a Photoactive Manganese Nitrosyl upon Illumination with Visible Light. J. Am. Chem. Soc. 2006, 128, 7166-7167.

Afshar, R. K.; Eroy-Reveles, A. A.; Mascharak, P. K. Stoichiometric and Catalytic Secondary O-Atom Transfer by Fe(III)-NO2 Complexes Derived from a Planar Tetradentate Non-Heme Ligand: Reminiscence of Heme Chemistry. Inorg. Chem. 2006, 45, 10347-10354.

Madhani, M.; Patra, A. K.; Miller, T. W.; Eroy-Reveles, A. A.; Hobbs, A.; Fukuto, J. M.; Mascharak, P. K. Biological Activity of Designed Photolabile Nitrosyls: Light-Dependent Activation of Soluble Guanylate Cyclase and Vasorelaxant Properties in Rat Aorta. J Med. Chem. 2006, 49, 7325-7330.

Szundi, I.; Rose, M. J.; Sen, I.; Eroy-Reveles, A. A.; Mascharak, P. K.; Einarsdottir, O. A New Approach for Studying Fast Biological Reactions Involving Nitric Oxide: Generation of NO using Photolabile Ruthenium and Manganese Donors. Photochem. Photobiol. 2006, 82, 1377-1384.

Ghosh, Kaushik; Eroy-Reveles, Aura A.; Olmstead, Marilyn M.; Mascharak, Pradip K. Reductive Nitrosylation and Proton-Assisted Bridge Splitting of a (μ-Oxo)dimanganese(III) Complex Derived from a Polypyridine Ligand with One Carboxamide Group. Inorg. Chem. 2005, 44, 8469-8475.

Ghosh, K.; Eroy-Reveles, A. A.; Avila, B.; Holman, T. R.; Olmstead, M. M.; Mascharak, P.K. Reactions of NO with Mn(II) and Mn(III) Centers Coordinated to Carboxamido Nitrogen: Synthesis of a Manganese Nitrosyl with Photolabile NO. Inorg. Chem. 2004, 43, 2988-2997.

Internship/Presentations/Awards:

234th American Chemical Society National Meeting, Boston, MA, August 19-23, 2007. Alegra Eroy-Reveles, Dr. Paradip Masharak, Yvonne Leung. PHOTOACTIVE MANGANESE NITROSYLS: SYNTHESIS OF A NITROSYL THAT RELEASES NITRIC OXIDE UPON EXPOSURE TO NEAR-IR LIGHT.Poster Presentation.

231th ACS National Meeting, San Francisco, CA, United States, March 13-17, 2005. RELEASE OF NITRIC OXIDE FROM A SOL-GEL HYBRID MATERIAL CONTAINING A PHOTOACTIVE MANGANESE NITROSYL UPON ILLUMINATION WITH VISIBLE LIGHT. Eroy-Reveles, Aura A.; Leung, Yvonne; Mascharak, Pradip K.Poster Presentation.

2nd SACNAS National Conference. Denver, CO, Sept. 29-Oct 2, 2005. Reactivity of Nitric Oxide with Mn (II) and Mn (III) centers coordinate to a Tetradenate Dicarboxamiden Na ligand. Eroy-Reveles, A.A; Olmstead, M.m.; Mascharak, P.K. Oral Presentation.

Eroy-Reveles, Aura A.; Ghosh, Kaushik; Olmstead, Marilyn M.; Mascharak, Pradip K. Reactions of various proton sources and NO with a m-oxo Mn(III,III) dimeric complex of a pentadentate ligand containing a carboxamido N. Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005. (Poster Presentation)

Eroy-Reveles, A. A.; Ghosh, K.; Olmstead, M. M.; Mascharak, P. K. Reactions of NO with Mn(II) and Mn(III) Centers Coordinated to Carboxamido Nitrogen. 227th ACS National Meeting, Anaheim, CA, March 28-April 1, 2004. (Poster presentation)

Eroy-Reveles, A. A.; Ghosh, K.; Olmstead, M. M.; Mascharak, P. K. Stability of Mn(II) and Mn(III) Centers Coordinated to Carboxamido Nitrogen. 30th SACNAS National Conference, Albuquerque, NM, October, 2003. (Oral presentation)

Jessica Garcia
Chemistry Ph.D. Graduate Student

Lab Group: Joe Konopelski

Research: I am currently working on the total synthesis of the cytotoxic marine natural product Cyclocinamide A. The absolute stereochemistry of this unique halogenated pseudo-hexapeptide has yet to be assigned. The first synthetic target is 4(/S/),7(/S/),11(/S/),14(/S/)-cyclocinamide A. With this isomer, the absolute stereochemistry of the natural product can be confirmed or deduced. In addition, we plan to efficiently synthesize a stereoisomer library of cyclocinamide A - via fluorous chemistry - for extensive biological testing.

Monica Lares
Chemistry Ph.D. Graduate Student

Lab Group: Bill Scott

Research: HAR1 is a RNA gene discovered during a scan of regions over 100 base pairs long and that are highly conserved in mammalian evolution but show extensive change in the human lineage since the common ancestor of human and chimpanzee. There is a segment of DNA at the 5’ end of HAR1 that is 118 bases long and contains 17 substitutions in the human lineage, when only 0.27 substitutions are expected. The transcript of this region is what will be examined with x-ray crystallography. HAR1 is strongly expressed in the subpial granular layer (specific to humans) and the cortical plate during early cortical development. Since HAR1 contains the most altered segment of DNA in the human genome and is also part of a brain development process that has changed during human evolution it is expected that HAR1 played a significant role in human evolution, yet its function remains unknown. The goal of this research project is to determine the structure of this transcript in order to deduce what its function may be.

Internship/Presentations/Awards:

Lares, Monica Rae Jung; Mendoza, Joseph; Scott, William. Towards the structure and function of a novel RNA gene. Abstracts of Papers, 232nd ACS National Meeting, San Francisco, CA, United States, Sept. 10-14, 2006.

Mendoza, Joseph Ramon; Lares, Monica Rae Jung; Scott, William. Towards the structure of RERTY using X-ray crystallography. Abstracts of Papers, 231st ACS National Meeting, Atlanta, GA, United States, March 26-30, 2006.

Gengenbach, Alan J.; Sieu, Anthony O.; Lares, Monica; Shachter, Amy M. Metalloporphyrin systems inspired by nitrophorins. Abstracts of Papers, 222nd ACS National Meeting, Chicago, IL, United States, August 26-30, 2001.

Hector Macias
Molecular Cell & Developmental Biology Ph. D. Graduate Student

Lab Group: Lindsay Hinck

Research: Proper cell to cell and cell to extracellular environment communication is seminal in the creation and maintenance of tissue morphology. The breakdown of this communication between cells and tissues is a hallmark in the development of solid malignant tumors. Abnormal tissue morphology is a consequence of the errant signaling taking place in these malignant tumors. In order to identify and target these errant communication pathways, we must first elucidate the normal roles played by the major signaling factors that govern tissue morphology. My thesis work involves deciphering the adhesion systems utilized during mammary gland ductal morphogenesis. I will specifically target the adhesion system induced by SLIT/ROBO signaling. Insight into these adhesion systems will aid in the classification, and targeting of mammary gland ductal carcinomas.

Publications:

McKenna WL, Wong-Staal C, Kim GC, Macias H, Hinck L, Bartoe JL. “Netrin-1-independent adenosine A2b receptor activation regulates the response of axons to netrin-1 by controlling cell surface levels of UNC5A receptors.” J Neurochem. 2007 Nov 8; PMID: 17995930.

Royou A, Macias H, Sullivan W.The Drosophila Grp/Chk1 DNA damage checkpoint controls entry into anaphase.Curr Biol. 2005 Feb 22;15(4):334-9.

Internship/Presentations/Awards:

Eric Mejia
Chemistry Ph.D. Graduate Student

Lab Group: Phil Crews

Research: Fungi harvested from marine habitats are known to produce organic compounds, commonly referred to as ‘secondary metabolites’, with intriguing structural, biological and pharmacological properties. One aim of Dr. Phil Crews’ research is to probe the chemistry of marine-derived fungi for chemotherapeutic drug leads that target major human solid tumor cancers. Fungi are collected by members of the Crews group during ocean expeditions and subsequently isolated and cultured. Our process of ‘fishing out’ drug leads continually utilizes bioactivity data to guide the extractive and chromatographic isolation of pure compounds. Samples are submitted to collaborative researchers to assess activity in cell and biochemical-based tests for selective cytotoxicity and inhibitory modes of action. As activity is confirmed the crude extracts are fractionated via chromatography, and samples re-submitted to test for sustained activity. The identities of pure compounds are established using spectroscopic and spectrometric methods (i.e. nuclear magnetic resonance and mass spectrometry) to provide insights into molecular structures/sub-structures and molecular formulas. The novelty of all pure compounds is assessed through extensive literature searches using the analytical data in search queries. This work supplements the growing body of knowledge concerning the chemistry of marine-derived fungi and their pharmacological application.

Internship/Presentations/Awards:

Mejia, Eric. Carl Storm Underrepresented Minority (URM) Fellowship. Recipient February, 2007.

Yvette Vaske (Mimieux)
Organic Chemistry Ph.D. Graduate Student

Lab Group: Joe Konopelski

Research: My research involves exploring a novel intramolecular Wolff type rearrangement discovered in our lab. The intramolecular rearrangement affords enantiomerically pure azetidin-2-ones (b-lactams), as verified by an X-ray crystal structure. Since b-lactams are important in their application as broad spectrum antibiotics, improved methodologies to affect the synthesis of existing b-lactam targets is desirable. Furthermore, bacterial resistance continuously necessitates the development of new b-lactam analogues. The aim of my present project is three-fold: 1) to survey and optimize the catalytic system, 2) to explore the functionalization tolerated in the b-lactam precursor, and 3) to explore derivatization of the b-lactam product. Our methodology for obtaining b-lactams will be applied in the enantioselective synthesis of the biologically active and industrially important b-lactam thienamycin. Thienamycin is active against gram-positive and gram-negative bacteria. It is also resistant to bacterial b-lactamase, the enzyme that confers bacterial resistance to b-lactam antibiotics.

Publications:

Gerstenberger BS, Lin J, Mimieux YS, Brown LE, Oliver AG, Konopelski JP. “Structural Characterization of an Enantiomerically Pure Amino Acid Imidazolide and Direct Formation of the beta-Lactam Nucleus from an alpha-Amino Acid.” Org Lett. 2008 Feb 7;10 (3):369-72 (In Press). Epub 2008 Jan 9.

Maiti, A.; Gerken, J. B.; Masjedizadeh, M. R.; Mimieux, Y. S.; Little R. D. From Dimerization, to Cycloaddition, to Atom Transfer Cyclization: The Further Chemistry of TMM Diradicals. J. Org. Chem.; 2004; 69(25), 8574 – 8582.

Internship/Presentations/Awards:

Mimieux, Yvette. Sebatical Fellowship. Recipient, 2007.

Carolina Reyes
Environmental Toxicology Ph.D. Graduate Student

Lab Group: Chad Saltikov

Research: Iron(III) and arsenate respiring prokaryotes contribute to contamination of arsenic in water, specifically in places such as Bangladesh. In the presence of oxygen arsenate predominates and is often adsorbed onto mineral surfaces such as iron(III) oxide. However, in the absence of oxygen prokaryotes can metabolize arsenate by reducing it to arsenite, which becomes the predominant form of arsenic. Microbial release of arsenic from sediment to water most likely involves a combination of metabolic pathways specific to iron and arsenate respiration. These metabolisms are encoded on gene clusters encoding a number of c-type cytochrome proteins important for iron and arsenate respiration. We are currently investigating the role of c-type cytochromes encoded by the mtr/omc gene cluster with respect to iron reduction in Shewanella ANA-3, an iron and arsenate reducing bacterium. Single gene deletions in the mtr/omc gene cluster had little affect on iron reduction. However, strains carrying multiple gene deletions were greatly impaired in iron reducing abilities. An ANA-3 strain carrying a complete deletion in the mtr/omc gene cluster could still reduce iron(III) oxide. These results suggest additional pathways or other cytochromes are involved in iron reduction. Work is currently underway to identify addition genes essential to iron reduction. Future work will be to generate combinations of iron and arsenate reducing mutants in order to investigate the contribution of iron and arsenate reduction to arsenic mobilization. This work addresses the importance of metal reducing prokaryotes as a major risk factor for human exposure to arsenic in contaminated drinking water.

Internship/Presentations/Awards:

University of California, Santa Cruz. Third Annual Graduate Research Symposium June, 2007."MICROBIAL PATHWAYS FOR ARSENATE REDUCTION." Carolina Reyes, Roseanna Due–as, and Chad Saltikov.Physical & Bological Sciences Poster Award.

University of California, Santa Cruz. 2nd Annual Graduate Research Symposium June, 2006. UNDERSTANDING THE ROLE OF OUTER MEMBRANE PROTEIN MTRB IN SHEWENELLA ANA-3. Carolina Reyes, Chad Saltikov.

American Geophysical Union Fall Conference 2006. Understanding the role of multiheme cytochromes in iron (III) reduction and arsenic mobilization by Shewanella sp. ANA-. Carolina Reyes, Roseanna Due–as, and Chad Saltikov.

European Geophysical Union April 13-18, Vienna, Austria.The role of multiheme c-type cytochromes in Shewanella sp. ANA-3 with respect to iron (III) reduction. Carolina Reyes, Roseanna Dueñas, and Chad Saltikov.

Reyes, Carolina. UC Toxic Fellowship. Recipient, 2007.

Reyes, Carolina. UCSC Graduate Mentorship Fellowship. Recipient, 2007.

Reyes, Carolina. Eugene Cota-Robles Fellow Fall 2005-June 2007

Reyes, Carolina. Costa Robles Fellowship. Recipient, 2005-2007.

Brent Rubio
Chemistry Ph. D. Graduate Student

Lab Group: Crews Lab

Research: A primary goal of Phillip Crews' marine natural products research is to understand the chemistry of tropical marine sponges that we personally
hand collect by SCUBA. Using bioassay-guided isolation assists us in the discovery of natural products potent against human diseases such as
cancer or viruses. Our search for novel active compounds incorporates elements of structure elucidation but there are other dimensions to this
research, including questions in the areas of chemical ecology, marine natural products biosynthesis and metagenomics, and the relationship
between secondary metabolite chemistry and taxonomy. Added to these interests are emerging projects which examine sponges as a source of new
cultured marine microorganisms. We are also interested in examining sponges that are rich with cyanobacterial symbionts.

Publications:

Rubio BK, Soest RW, Crews P. “Extending the record of meroditerpenes from Cacospongia marine sponges.” J Nat Prod. 2007 Apr;70(4):628-31. Epub 2007 Mar 9.

Internship/Presentations/Awards:

12th International Symposium on Marine Natural Products (MaNaProXII). Queenstown, New Zealand, February 2007. ANTIMICROBIAL MERODITERPENES FROM A CACOSPONGIA MARINE SPONGE. Brent Rubio, Dr. Phil Crews, Van Soest, R. W. M. Poster Presentation.

Josue Samayoa
Bioinformatics Ph. D. Graduate Student

Lab Group: Karplus Lab

Research: The role of simple repeats as a mechanism for genetic variation has been demonstrated in other organisms, specifically in the genus of bacterium Neisseria. In Neisseria meningitidus several genes involved in host interaction are thought to be regulated by simple repeats. For example, the expression of the pilin protein is partially regulated by an internal repeated sequence of guanine (G). Simple repeats cause changes in the expression of genes via slipped-strand mis-pairing. Slipped strand mis-pairing can occur during DNA replication and transcription. In all cases, the cause is a mis-pairing event between the template nucleic acid and the nascent complementary chain.

The aim of my current research is to identify simple repeats in the Vibrio cholerae El Tor genome that are over or under represented and to measure the conservation of those repeats across four different Vibrio genomes (V. vulnificus, V. parahaemolyticus, Vibrio cholerae and V. fischeri). Simple repeats are defined as those comprised of either single or double nucleotide repeats such as "AAAA" or "ATAT".

Internship/Presentations/Awards:

Utilizing Rosetta and NMR Data in a Homology-based Modeling Approach. Josue Samayoa, Carol Rohl. CASP 2006, December 2006.

Blanca Silva
Chemistry Ph. D. Graduate Student

Lab Group: Fink Lab