CBSE Research Mentoring Institute Student Projects

Sponsored by the CBSE Research Mentoring Institute
with funding from the National Human Genome Research Institute (NGHRI)

CBSE RMI Fellowships and Awards in Genomic Science

The CBSE Research Mentoring Institute (RMI) is an academic research training  and professional development program for UCSC students who are interested in genomic science, the application of genomic knowledge, and it’s implications for today’s world. RMI awards support undergraduate scholars and graduate fellows  who are pursuing careers in genomic sciences and related fields. In addition to supporting scientific research, RMI awards support projects addressing the ethical, legal, and social implications of genome research.

• Read about the graduate fellowship recipients' projects
• Read about the undergraduate diversity award recipients' projects
• Application information

Projects by CBSE Diversity Fellows (Graduate Students)

Martha Arciniega, Ocean Sciences-Genetic diversity of the toxin mediating aryl hydrocarbon (AhR) genes in resident Oncorhyncus mykiss
2010-2011
Martha is working with John Carlos Garza, studying sea otters, Enhydra lutris ssp, known as a “keystone species” because they have a strong influence on diversity of near-shore marine communities. Unfortunately, sea otters were hunted almost to extinction and population sizes have dramatically decreased in the past 50 years. Information about the amount and distribution of genetic variation is vital for implementing effective conservation efforts. Martha’s project involves adding variable markers to the microsatellites already in use for sea otters. Microsatellites--DNA sequences that include tandem-repeated base pairs--are used to determine the relatedness between individuals and among populations. Microsatellites can provide information about population history, genetic drift, mate choice and migration. This project will provide enough statistical power to reconstruct pedigrees and investigate levels of differentiation between otter populations in California, Alaska and Russia. The pedigrees will show the lineages of sea otters that are closely related or part of the same family. A more complete knowledge regarding otter pedigrees will help marine scientists understand patterns of dispersal as well as past historical demography.

Rigo Dicochea, Computer Engineering-Enhancing Performance of Genome Sequencing Processors
2010-2011
Working with Jose Renau and Mark Diekhans, Rigo is examining how architectural modifications to a general purpose processor design can increase the computational performance of current genome sequencing algorithms. Scientific applications, like those necessary in the Genomic Sciences, are heavily data parallel. Thus, the issues addressed in the design of a CPU for scientific applications must take into account additional parameters above what is specified for a general purpose processor. Rigo's research project seeks to explore those parameters. His goal is the design and fabrication of a microprocessor architecture aimed at providing very high computational performance on very large genomic data sets. He also hopes to introduce a new suite of benchmarks to the computer architecture community that will enable researchers to quantify the performance of genomic applications on their processor designs.

Carolina Reyes, Microbiology & Environmental Toxicology-Microbial genetics underlying iron geochemistry in anaerobic microorganisms 2010-2011 The way in which bacteria metabolize a solid mineral externally is of interest to microbiologists and geologists. Carolina is currently a researcher in the Saltikov Lab, where she is investigating how bacteria metabolize iron minerals using the model bacterium Shewanella sp. strain ANA-3. The precise steps involved in bacterial metabolism of the iron mineral are not known, however, several hypotheses have been proposed. One hypothesis is that the bacterium metabolizes the iron using proteins inside the cell and sitting on the cell surface. These cytochrome proteins are thought to pass electrons from inside the cell to the iron mineral outside the cell. All organisms possess cytochrome proteins, and animals and plants use them in oxygen metabolism. In certain bacteria, these cytochrome proteins are composed of multiple residues that allow for the passage of electrons, a feature not common in animals and plants. The goal of Carolina's project is to determine why these bacterial cytochromes require multiple residues to pass electrons from inside the cell to iron minerals outside the cell. By altering the genetic material of ANA-3, Carolina has eliminated specific regions of a cytochrome involved in iron metabolism in hopes of discovering which components enable this protein to pass electrons to the mineral outside the cell.

Margarita Gonzales, Chemistry and Biochemistry—Investigations on DNA Sequence Vulnerability to
NO-mediated DNA Damage—Mentor: Pradip K. Mascharak
RMI Support 2009-10, 2011-12
Working in Pradip Mascharak’s lab, Margarita utilizes photoactive metal complexes that deliver nitric oxide (NO) to DNA bases and eventually to selected oligonucleotides. Because DNA damage is a hallmark of programmed cell death or apoptosis, their group is interested in the interaction between NO and other reactive nitrogen species with specific nucleobases. She uses HPLC techniques and UV-Vis spectroscopy in characterizing the initial products of NO-mediated DNA damage.

In the spring of 2011 she published a paper on an additional research project that investigated the physiological roles of carbon monoxide (CO) in neurotransmission,vasorelaxation, and cytoprotective activities.
Inorganic Chemistry 2011, 50(7), 3127-3134. Link: http://pubs.acs.org/doi/pdfplus/10.1021/ic2000848

Hector Macias, Molecular, Cell, & Developmental Biology—Uncovering the mechanism behind SLIT2/ROBO 1 mediated mammary gland branch inhibition—Mentor: Lindsay Hinck 2009-10 Hector’s research in the Hinck laboratory focuses on developing therapeutic strategies for diagnosing and treating breast cancer. Read the paper Dr. Hector Macias received his PhD in 2010, and is a post doctoral researcher in the Hinck Lab, UC Santa Cruz. His breast cancer research focuses on mechanisms related to SLIT2/RPBO1 mediated mammary gland branch inhibition.

Gabriel Roybal, Molecular, Cell & Developmental Biology—Capture and chacterization of catalytic complex spliceosomes: understanding how genomes are used, maintained, and regulated. Faculty Mentor: Melissa Jurica RMI Support 2006–2007, 2009-10 Gabriel's project in Melissa Jurica's lab focuses on investigating how our cells process genetic information.  Gabriel uses small molecule inhibitors of pre-mRNA splicing as tools to isolate and study the human spliceosome.  In particular, Gabriel has worked with the small molecule known as Spliceostatin A to investigate the role of SF3b protein during the later stages of spliceosome assembly.  This work will be crucial to understand the mechanism and structure of the spliceosome. Dr. Gabriel Roybal received his PhD in 2010, and is currentlly a post doctoral researcher UC San Francisco in the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research Center. His research focuses on studying the mechanisms that regulate the epigenetic landscape of adult neural stem cells.

Daniel Garalde, Computer Engineering—Electrical, structural, and biological refinement of a nanopore sensor for sequencing DNA and RNA
RMI Support 2007–2009
Daniel worked with William  Dunbar, Associate Professor, Department of Computer Engineering,   and chemist David Deamer, Research Professor, Department of Biomolecular Engineering.  Through  his unique, interdisciplinary research,  Daniel developed new nanopore-based technology for sequencing DNA and RNA. He focused on addressing weaknesses in current alpha-hemolysin-based sensor technology developed at UCSC to improve its effectiveness. You can read about Daniel's research in a 2011 paper that he co-authored with other members of his research team:  "Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection".

Dr. Daniel Garalde received his PhD in 2011, and now works as a research scientist at Oxford Nanopore Technologies in Oxford, UK.

Janine Ilagan, Molecular, Cell & Developmental Biology—Structural changes in spliceosomes created by pre-mRNA trimming as visualized by electron microscopy. Faculty Mentor: Melissa Jurica
2007–2009
This project in Melissa Jurca's lab aims to better characterize the structure of the human spliceosome, an important catalyst for gene expression.

Sachiko Reed, Sociology—Considering implications of mixed race identity and genomics. Faculty Mentor: Jenny Reardon
2007–2008
Sachiko combines qualitative research methods with surveys of physicians, geneticists, and researchers at UCSF and Stanford University to examine the implications of how race, especially for people of mixed race, is included and accounted for in genomic research. Her advisor is sociologist Jenny Reardon.

Daniel Sam, Biomolecular Engineering—Computational approaches for predicting gene function. Faculty Mentor: Josh Stuart 2007–2009, Fall 2010-Winter 2011 Working in Josh Stuart's lab, Daniel develops computational tools to predict and elucidate functional relationships between biological data collected from a variety of sources.

Josue Samayoa, Biomolecular Engineering—Protein structure prediction
2004–2006, 2008
Samayoa worked with Carol Rohl to expand and improve modeling methods for predicting 3-dimensional protein structure. The project is called, "Homology-based modeling with Rosetta and NMR data."
Samayoa then participated in two related interdisciplinary projects with advisors Kevin Karplus and Fitnat Yildiz. The project is called, "A bioinformatic analysis of simple repeats and small proteins in Vibrio cholerae El Tor."

Genevieve Halpenny, Chemistry—DNA damage via light-activited nitric oxide release. Faculty Mentor: Pradip Mascharak
2006–2007
Working in Pradip Mascharak's lab, Genevieve delivers nitric oxide (NO) to living cells such as E. coli and ultimately cancer cells and then uses microscopy to observe NO-induced DNA damage.

Mark Rivero, Computer Engineering—Data visualization of genomic information
2006
Working in Pat Mantey's Lab, Mark is looking for ways to improve the UCSC Genome Browser by allowing 3-dimensional visualization of any given data.

Monica Lares, Chemistry and Biochemistry—Structure and function of a novel RNA gene
2005–2007
Working in William Scott's laboratory, Monica studies a novel RNA gene occurring in a segment of the human genome that has evolved with surprising rapidity between the chimpanzee and the human genomes. She uses x-ray crystallography to investigate the structure and possible function of this RNA gene. Monica's project is called, "Towards the structure and function of a novel RNA gene/determining the structure and fragile X syndrome of CGG RNA repeats."

MaryAnn Dassah, Molecular, Cellular, and Developmental Biology—Splicing and mutation suppression of pre-mRNA
2004–2006
Dassah works in Al Zahler's laboratory on the mechanism for pre-mRNA splicing. Almost all higher eukaryotic mRNA molecules give correct genetic information only after the introns (non-coding regions) are spliced out of the RNA and the exons (protein-coding regions) are joined in the cell nucleus. Many heredetary diseases are caused by disorders in the splicing process. Dassah's project is called, "Refining the rules of 5' splice site selection and suppression of +1G mutations of pre-MRNA."

Veronica De Guzman, Chemistry—Nanopore devices
2003–2005
In her work with the UCSC Nanopore Project, De Guzman studies a nanopore device, which is an artificial membrane that has a single ion channel through it. The ion channel is used to capture and examine one molecule of DNA at a time. The interaction of double-stranded DNA or single-stranded DNA with the channel can readily be observed via changes in an electrical current through the channel. De Guzman observes and studies double-stranded-DNA ends fraying and reforming in a channel—an important step in biological processes. In HIV infection, for example, DNA fraying is necessary for HIV DNA to be spliced into human host DNA.

• MORE... the Nanopore Project at UCSC

Edward Olano, Chemistry—Developing assays for prostate-specific antigen and early detection of ovarian cancer
2004–2005
Working in Jin Zhang's laboratory, Olano is developing an immunoassay for prostate-specific antigen and also designing a biomarker using quantum dots for detecting ovarian cancer. Both assays will employ a spectrophotometric technique called surface-enhanced Raman scattering (SERS).

Blake Riggs, Molecular, Cellular, and Developmental Biology—The process of cell division in animals
2004–2005
Riggs works in Bill Sullivan's laboratory to better understand what happens during the last phase of cell division in animals, using Drosophila melanogaster (the fruit fly) as a model. He is looking at the phase where the plasma membrane constricts to form two daughter cells. The project is called, "The centrosome-associated protein, nuclear fallout, and its role in metaphase furrow formation."

Marc Hanson, Computer Engineering—Visualizing database queries
2003–2004
Hansen studies information visualization interfaces that allow biologists to look at and easily query visual representations of biological information. The interfaces are used for information such as phylogeny charts, chromosomes, genes, and sequence alignments. For example, a user could start with a phylogeny chart, then click on "fly" to get a sub-chart that lists different species of flies. The user could then click on "Drosophila melanogaster " to get a picture of fruit fly chromosomes. Clicking on a chromosome of interest would bring up a zoomed-in view showing which genes have been mapped. The user might also be able to click on notes to see the full text of annotations researchers may have attached.

Projects by CBSE Diversity Award Recipients (Undergraduates)

Rocio Ramos (Molecular, Cell, and Developmental Biology), Hinck Lab
Project Title: TBD
Winter 2012, Spring 2012

Alex Salazar (Biomolecular Engineering), Pourmand Lab
Project Title: TBD
Winter 2012, Spring 2012

Santiago Salazar (Microbiology & Environmental Toxicology), Hinck Lab
Project Title: The role of SLIT signals in the regulation of  breast stem cell growth and cancer initiation
Winter and Spring 2011

Santiago is now a MARC Scholar, and is continutuing his research in the Hinck Lab

Rene Moreno (Microbiology & Environmental Toxicology), Saltikov Lab
Spring 2011
Project Title: Green Fluorescence Protein based biosensor for arsenic contamination detection

Rene worked on two separate projects in the Saltikov Lab. The first project focused on creating a bio-sensor for arsenic. This research was done in collaboration with UCSC adjunct professor Dr. Dominik Rabus (Electrical Engineering and Computer Science). The bio-sensor will serve as a microbial sensor in which arsenic in found in-front of a green fluorescence protein, which can be used to detect arsenic more efficiently using fluorescence.

Rene’s contribution to the  project was to help determine how robust the bio-sensor strain is at detecting different arsenic concentrations and how accurately it can be read by fluorescence and optical density.

The second project consisted of engineering a more proficient strain that contains the arsenic genome, by inserting a green fluorescent protein element into a region of the genome that regulates arsenic. The approach was to develop a molecular approach such as polymerase chain reaction and genome sequencing to determine where the green fluorescence protein is inserted. Once the arsenic bio-sensor is successful, the Saltikov Lab plans to develop bio-sensors for other metals.
Rene graduated in June 2011. He is currently working as a program coodinator at the SACNAS main office, in Santa Cruz, CA, and applying to graduate programs.

Laci Hampton (Biomolecular Engineering) Pourmand Lab
Project Title: Improving Next Generation Sequencing Flow
Summer 2010-Spring 2011
Laci worked with Nader Pourmand

Jose Loza, Computer Engineering-Analyzing the effectiveness of the IZON resizable nanopore device Winter 2010-Spring 2010 Jose worked with William Dunbar

Katrina Luna, Ecology & Evolutionary Biology-Genetic diversity arising from bacteria-bacteriophage interactions driven by different genetic mechanisms Winter 2010-Spring 2010 Katrina worked with Samamtha Forde

Claudia Mariella Lavarreda-Pearce, Microbiology & Environmental Toxicology-Transposon mutanogenesis of Shewanella s.p. ANA-3
Winter 2010-Spring 2010
Claudia worked with Chad Saltikov

Nicole Milner, Ecology & Evolutionary Biology-Determining the presence of T3 and Lambda in communities of coevolving bacteria and bacteriophage
Fall 2009
Nicole worked with Samamtha Forde

Nicole Coppage, Microbiology & Environmental Toxicology-Creation and Phenotypic Characterization of a cheZHP Mutant Fall 2009 Nicole worked with Karen Ottemann

Christine Sinclair, Molecular, Cell, and Developmental Biology-Molecular paternity analysis of the side-blotched lizard, Uta stansburiana
Winter 2009-Spring 2009
Christine worked with Barry Sinervo

Regina Chavez, Community Studies-Obesity and Genetic Research: What are we really learning?
Fall 2008-Winter 2009
Regina worked with Claudia Chaufan

Christopher Robles, Biomolecular Engineering Fall 2008-Spring 2009 Christopher worked with Nader Pourmand

Tiffany Lopes, Molecular, Cell, and Developmental Biology—Can stalling of RNA polymerase influence alternative splicing? Fall 2008 Tiffany worked with Manny Ares, Jr. Read the paper

Busola Oluwole, Chemistry and Biochemistry—Biochemical mechanisms that control the cell cycle
Winter and Spring 2008
Busola worked with Seth Rubin to deepen understanding of the process involved in regulating retinoblastoma protein, which is implicated in a childhood cancer of the eye.

Shewit Tekeste, Molecular, Cell, and Developmental Biology—Splicosome structural analysis
Fall 2007, Winter and Spring 2008
Shewit worked with Melissa Jurica whose lab seeks to understand a critical step in the process where information in DNA is read and then used in cells. The step is called pre-mRNA splicing, and errors in this process are responsible for a large number of human genetic diseases. Shewit focused on the structural analysis of an early phase of the spliceosome, called E complex.

• Read about Shewit and her research

Israel Murguia, Politics/Community Studies—Combating health disparities
Spring 2007
Israel worked with Mike Rotkin to research minority access to healthcare, the disparities minorities face in receiving equitable medical care, and how genomic information may help to improve health outcomes.

• Read the paper

Alexander John Yambao, Molecular, Cell, and Developmental Biology—Using immunoliposomes in combination with the immune system to treat cancer
Spring 2006
Alexander works in Doug Kellog's laboratory; this research project was done under Melissa Jurica's mentorship

Sonia Arevalo, Environmental Toxicology—Rho-independent termination in Helicobacter pylori
Spring 2006
Sonia worked in Karen Ottemann's laboratory

Edward Cabral, Environmental Toxicology—Quantitative real time PCR detection of Helicobacter pylori
Spring 2006
Edward worked in Karen Ottemann's laboratory

Emily Berry, Molecular, Cell, and Developmental Biology—Role of the Caenorhabditis elegans extracellular matrix protein F-spondin/SPON-1 in neural development
Winter–Summer 2006
Berry worked in Andrew Chisholm's laboratory

• Read the paper

Matt Riese, Philosophy—The biological meaning of "race" (1 quarter)
Spring 2005
Riese outlines the debate now raging in academic circles as to whether race is a scientifically valid descriptor of humans or simply an arbitrary social label. He describes a range of issues related to understanding race from both ethno-cultural and scientific vantage points. He lays out the dangers of relying on race to categorize people for medical and social purposes and argues that while humans may fall into “races” that are at least somewhat biologically dissimilar, we must make sure this information is used only to benefit people.

• Read the paper

Oscar Hernandez, Molecular, Cell, and Developmental Biology—Gene expression
2005
Hernandez works in Melissa Jurica's laboratory on the project of solving the structures of 150 proteins that make up the spliceosome, a critical macromolecular complex in gene expression.

Dafne Ochoa, Molecular, Cell, and Developmental Biology—Research into mammary gland development
2004–2005
Ochoa worked in John Tamkun's laboratory on mammary gland development, with the aim of understanding the biology of breast cancer. One in 10 women develop breast cancer during their lifetime, making it one of the leading cancer-related deaths of women in the western world. Her research project is entitled, "Interactions between the 17-beta-estrodiol/estrogen receptor-alpha and the mitogen-activated proten kinase (MAPK) cascade in regulating mammary gland development; the effect of antiestrogen and MAPK inhibitor."

Marcia Soriano, Biomolecular Engineering—Protein structure prediction
2004
With Kevin Karplus, Soriano worked on developing a program to evaluate the output of various computer algorithms for predicting local protein structure.

Alexis Rojas, Philosophy and Biology—Moral issues of genetic engineering (2 quarters), Somatic cell gene therapy (1 quarter)
2003–2004
In his first paper, "Future Consequences for Potential Persons and Our Parental Obligations Regarding Human Germline Engineering," Rojas argues for the therapeutic use of genetic engineering while evaluating a broad range of possible applications and concerns. In this paper he examined parents' responsibilities to their children in an age of germline engineering. In his second paper, “Somatic Cell Gene Therapy: a Leap in Technology and Reassessment of Values,” Rojas compares somatic cell gene therapy with traditional medicine in order to dispel fears and examine the present values and definitions of "healthy."

• Read the germline engineering paper
• Read the somatic cell gene therapy paper

Emilia Lopez, Philosophy and Education—Genetic modification (1 quarter), Cloning (1 quarter)
2004
In her first paper, "Genetic Modification and Egalitarianism: Distinguish and Distribute," Lopez illustrates the difference between "preventative" gene therapy and "enhancement" gene therapy. She describes the threat genetic engineering poses in a society with an unequal distribution of health care. In her second paper, "Three Types of Cloning and the Necessity to Regulate," Lopez defines and evaluates DNA cloning, reproductive cloning, and therapeutic cloning. She refers to current legislation in the US and examines the results of the California Advisory Committee of Human Cloning.

• Read the genetic modification and egalitarianism paper
• Read the cloning and regulation paper

Lucy Silva, Computer Science—The possibility of a DNA database society (1 quarter)
2004
Silva examines the practices of genetic profiling by police and collecting DNA samples from prisoners in California and the related legal and social implications. She also she explores the issues of DNA ownership and genetic privacy. In the age of computers, she looks at legislative solutions to the question "do we want the government to have our genome?"

• Read the paper.