PROJECTS BY CBSE DIVERSITY FELLOWS (Graduate Students)

Daniel Geralde, Computer Engineering—Electrical, structural, and biological refinement of a nanopore sensor for sequencing DNA and RNA
2007–2008
Working with computer engineer Bill Dunbar and chemist David Deamer, Daniel develops new nanopore-based technology for sequencing DNA and RNA. He is addressing weaknesses in current alpha-hemolysin-based sensor technology developed at UCSC to improve its effectiveness.

Janine Ilagan, Molecular, Cell & Developmental Biology—Structural changes in spliceosomes created by pre-mRNA trimming as visualized by electron microscopy
2007–2008
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
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—Identification of modular conserved biological networks across species
2007–2008
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.

Gabriel Roybal, Molecular, Cell & Developmental Biology—Capture and chacterization of catalytic complex spliceosomes: understanding how genomes are used, maintained, and regulated
2006–2007
Gabriel's project in Melissa Jurica's lab uses biochemical and structural approaches to improve our current understanding of how introns are spliced out of mRNA substrates to allow for the proper use of the genome.

Genevieve Halpenny, Chemistry—DNA damage via light-activited nitric oxide release
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."

Josue Samayoa, Biomolecular Engineering—Protein structure prediction
2004–2006
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."

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)

Shewit Tekeste, Molecular, Cell, and Developmental Biology—Splicosome structural analysis
Fall and Winter 2007, 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.
MORE... 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.
MORE... 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
MORE... 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.
MORE... 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."
MORE... read the germline engineering paper
MORE... 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.
MORE... read the genetic modification and egalitarianism paper
MORE... 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?"
MORE... read the DNA database society paper