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:

Giacomo Bernardi, Yvette R. Alva-Campbell, Joao L. Gasparini, Sergio R. Floeter. 2008. Molecular ecology, speciation, and evolution of the reef fish genus Anisotremus. Molecular Phylogenetics and Evolution 48: 929-935.

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.

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.

Internship/Presentations/Awards:

PROGRESS TOWARD THE TOTAL SYNTHESIS OF (4/S/, 7/S/, 11/S/, 14/S/)-CYCLOCINAMIDE A. _Garcia, J.M._; Curzon, S.S.; Konopelski, J.P.SACNAS National Conference. Salt Lake City, UT, October 2008. Poster presentation.

Margarita Gonzales
Chemistry Ph. D. Graduate Student

Lab Group:

Genevieve Halpenny
Chemistry Ph. D. Graduate Student

Lab Group: Pradip Mascharak

Research: In the body, nitric oxide (NO) plays various roles in physiological processes such as neurotransmission, blood pressure regulation, and the immune response. Research in the Mascharak Lab focuses on the design and application of light-activated NO donors. Utilizing our ruthenium nitrosyls, we have prepared an NO-releasing, polymeric gydrogel. This material was used to deliver NO to myoglobin in solution. Our most recent investigation explored the antibiotic properties of NO photo-relearsed from similar polymer hydrogel containing a manganese nitrosyl.

Internship/Presentations/Awards:

Halpenny, Genevieve M.; Steinhardt, Rachel C.; Okialda, Krystle A.,; Mascharak, Pradip K. Characterization of pHEMA-based Hydrogels that Exhibit Light-induced Bactericidal effects via Release of NO (Submited)

Halpenny, Genevieve M.; Mascharak, Pradip K. Accelerated Photorelease of NO from {Ru-NO}6 Nitrosyls Containing Carboxamido-N and Carboxylato-O Donors: Synthesis, Structures, and Photochemistry Inorganic Chemistry 2009, 48(4), 1490-1497.

Halpenny, Genevieve M.; Olmstead, Marilyn M.; Mascharak, Pradip K. Incorporation of a Designed Ruthenium Nitrosyl in PolyHEMA Hydrogel and Light-Activated Delivery of NO to Myoglobin Inorganic Chemistry 2007, 46(16), 6601-6606.

Halpenny, Genevieve M.; Mascharak, Pradip K. Designed Ruthenium Nitrosyls with Carboxamido-N and Carboxylato-O Donors 237th ACS National Meeting and Exposition March 22-26, 2009

Halpenny, Genevieve M.; Olmstead, Marilyn M.; Mascharak, Pradip K.; Photo-induced Nitric Oxide Release from a Designed Ruthenium Hydrogel, UC Systemwide Bioengineering Symposium June 15-16, 2007

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:

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:

An intramolecular wolff rearrangement toward B-lactams. Yvette M. Vaske, Joseph Konopelski.SACNAS National Conference. Salt Lake City, UT, October 2008. Poster presentation.

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:

Reductive

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.

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