Alumni Genomic Scholars

Stefanie Brizuela
Spring 2017- Spring 2018

BME – Bioengineering
Phenotypic analysis of mutant mouse mammary glands (Prickle2 gene: knock- out, heterozygote, and wild- type tissue)
Faculty mentor: Angela Brooks

Adrian Salguero
Fall 2017 – Spring 2018

Computer Science
Development of a parallel workflow to find structural variations and the phasing of these variants from a large cohort of human whole genome sequences
Faculty mentor: Benedict Paten

Thao O, 
Summer 2015 – Spring 2016

Molecular, Cell, and Developmental Biology

Worked on pre-RNA splicing and human disease.
Faculty mentor: Jeremy Sanford

Selam Gebremedhin
Summer 2017- Spring 2018

MCD Bio
Identifying functional links between transcription and splicing of mRNAs
Faculty mentor: Grant Hartzog

Yulia Zybina
Fall 2017 – Spring 2018

Chemistry/Biology (Neuroscience)Characterizing NOTCH2NL CRISPR mutants/determining CNV of NOTCH2NL paralogs in autism patients
Faculty mentor: David Haussler

 

Melawit Tekeste
Winter 2017 – Spring 2017

Molecular, Cell, and Developmental Biology
Phenotypic analysis of mutant mouse mammary glands (Prickle2 gene: knock- out, heterozygote, and wild- type tissue)
Faculty Mentors: Lindsay Hinck & Prestina Smith

Kevyn Hart
Summer 2016

Molecular, Cell, Developmental Biology
Assessment of spliced- alignment methods for nanopore sequencing reads.
Faculty mentor: Angela Brooks

Victoria Serrano
Summer 2017- Spring 2018

 Bio Chemistry
Meiotic recombination and the effects of inversions on chromosome pairing
Faculty mentor: Russ Corbett-Detig

Vanessa Veneer
2018
Chemistry/Biology,

Characterizing NOTCH2NL CRISPR mutants/determining CNV of NOTCH2NL paralogs in autism patients
Faculty mentor: Russ Corbett-Detig

 

Jacquelyn Roger
Fall 2017 – Spring 2018

Molecular, Cell, and Developmental Biology
Wolbachia Host-Switching
Faculty Mentor: Russ Corbett-Detig

Jessica Arozqueta

Chelsea Stewart
Fall 2016 – Spring 2017

MCD BIO (Neuroscience)
To be announced.
Faculty mentor: Bin Chen

Du Linh Lam
Summer 2015 – Spring 2016

Biomolecular Engineering
Worked on the project “Modeling Gliomas using human ES cells”
Faculty mentor: David HausslerOlena Morozova

 

Parisa Nejad 
Summer 2015

Molecular, Cell, and Developmental Biology
Worked on the analysis, visualization, and curation of stem cell genomics.
Faculty mentor: Jim Kent

Eric Curiel Lares
2013 – 2014

Ecology & Evolutionary Biology

The evolution and diversification of innate immunity genes in sea urchins. Read Eric’s undergraduate researcher profile

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He uses the UCSC Genome Browser to compare the complete genomes of nine sea urchins and search for patterns of duplication (paralogs) in innate immunity genes. Lares found that the majority of innate immunity genes contained paralogs in all species, suggesting a rapid rate of new gene formation. He then used a phylogenetic analysis by maximum likelihood (PAML) program to test for signs of positive natural selection in single-copy innate immunity genes. Tests for positive selection were significant at roughly a third of the genes examined. Lares’s results are consistent with those of earlier studies in drosophila where innate immunity genes demonstrated rapid diversification and evolution through antagonistic host-parasite co-evolutionary interactions.
Natalia Herrera
Fall 2014 – Spring 2015

Biochemistry & Molecular Biology with a minor in Bioinformatics.
Faculty mentor: Victoria Auerbuch Stone

Layla Cervantes
Fall 2013 – Fall 2015
Molecular, Cell, and Developmental Biology – Department of Microbiology and Environmental Toxicology (METOX)
Worked on “System for Continuous Mutagenesis of a Target Gene” and studied TEM-1 Beta-lactamase evolution in E.coli.
Faculty mentor: Manel Camps

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Layla Cervantes studied how the beta-lactamase protein evolves in E. coli cells under antibiotic (cefotaxmine) selection. She identified how starting mutations condition subsequent mutational trajectories and more generally how individual mutations interact with each other phenotypically. She then subjects the bacteria to cefotaxmine to cause another mutation that increases resistance to this antibiotic. This will allow her to obtain combinations of mutations contributing positively to cefotaxmine resistance. Cervantes also studied how modulating the fidelity of replication affects beta-lactamase’s ability to evolve cefotaxmine-resistant mutants. She will be comparing side-by-side libraries generated by polymerases having different mutation frequency and spectrum, and she will compare the frequency and type of cefotaxmine-resistant mutants after parallel selection of the two libraries. Her work will elucidate how new biochemical activities evolve and provide the tools to anticipate the outcome of complex mutations. December 8, 2014: CONGRATULATIONS Layla who has received a $1500 Undergraduate Research Award from the Sciences Awards Division of UCSC. Layla plans to use the award to present her work at the 2015 Emerging Researchers National (ERN) Conference in STEM in Washington, D.C.

Jordan Hughey
Summer 2014
Bioinformatics

Site directed mutagenesis and pore formation testing of nanopores (graduated with BS in summer 2014)
Faculty mentor: Mark Akeson

Sandrine Kyane
Winter 2014 – Fall 2015
Biochemistry –

Worked on the “Introduction of NOTCH2NL Mutations into Human Cells”.
Faculty mentor: David Haussler, Sofie Salama, and Olena Morozova

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Gliomas are the most common malignant brain tumors diagnosed in the United States, and they are often incurable using available treatment options. While grade 2 and grade 3 gliomas are known to be associated with mutations in genes IDH1 and ATRX, the exact tumorigenic mechanisms of these mutations are unknown. Sandrine’s project will involve using the recently described CRISPR-Cas9 system to introduce IDH1 and ATRX mutations into human embryonic stem cells. In particular, she will work on constructing and testing special guide RNAs that will ensure the mutations are introduced at the sites of interest. Successful generation of embryonic stem cell lines carrying glioma mutations would provide an invaluable model system to study glioma development in the laboratory and develop new therapies for the disease.
Gerardo Perez
2013 – 2014

Biomolecular Engineering
The goal of HIV research is to produce a vaccine that offers complete protection from the virus.

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To date, no vaccine has shown this. Broadly neutralizing antibodies are antibodies capable of blocking infection from a wide variety of clinical isolates. PG9 is a broadly neutralizing antibody that targets the V1/V2 region of the HIV gp120. Gerardo’s project involves Structure-focused vaccine design of the V1/V2 region of gp120. The goal is to engineer a scaffold to fold like the native structure in the gp120 and stabilizing the β -hairpin leading to Mannose 5 at N160. This involves making mutations to V1/V2 scaffolds in variety of clades to optimize PG9 binding. Ultimately, these scaffolds could possibly be used in immunizations.

Elvira Contreras
2012 – 2013
MCD Biology
Analysis of a family of genes predicted to encode calcium/proton transporter
Faculty Mentor: Barry Bowman

Geoffrey Slaughter
2012 – 2013
MCD Biology
Regulation of lifespan by the MES complex in c.elegans. Read Geoff’s award-wining senior thesis, based on his research in the Strome lab. Faculty Mentor: Susan Strome

Rocio Ramos
Winter-Spring 2012

Molecular, Cell, and Developmental Biology
Investigating the relationship between VANGL2 and cilia in the mammary gland.
Faculty mentor: Lindsay Hinck

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Rocio’s project that examined the role of a planar cell polarity protein during mammary gland development. As a core planar cell polarity (PCP) protein, Vangl2 functions in uniformly orienting cells in a sheet of epithelium. One way PCP proteins such as Vangl2 accomplish this regulation is by aligning each cell’s cilia.  Rocio will evaluate whether Vangl2 functions in this manner in the breast. In order to investigate this question, Rocio is working to improve the staining of the primary marker for cilia, acetylated tubulin, by testing different dilutions of the antibody. Once this is completed, she will stain 5 week wild type (WT) tissue with Vangl2 and acetylated tubulin and look for co-localization. She will also compare cilia positioning in WT and Vangl2 knockout (KO) tissue.

Britney Martinez 
2012 – 2013

MCD Biology
Genomics of the RNA binding splicing factor Mer1
Faculty Mentor: Manny Ares

Cynthia Smith 
2012-2013
Microbiology and Environmental Toxicology
Role of antiretroviral-selected mutations in HIV-reverse transcriptase in shaping the HIV genome.
Faculty Mentor: Manel Camps
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Drug resistance limits use of antiretroviral drug treatment for patients infected with HIV, primarily drugs that inhibit reverse transcriptase (RT). Cynthia’s project focused on the mechanisms by which RT functions in HIV to understand how replication fidelity impacts viral fitness and determine the frequency of selected mutations generated by HIV wild-type and variant polymerases. She used an E. coli in vivo model and direct sequencing to generate a distinct replication and mutation footprint for each polymerase. Determining distinct replication mechanisms and patterns will help predict the risk for developing resistance to additional drugs and understand how these mutations increase persistence.

Alex Salazar  
Winter 2012 – Spring 2013

Biomolecular Engineering
Semi automated MagArray chip fictionalization
Faculty mentor: Alan Zahler

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Alex is currently designing and engineering a device that will simplify the immobilization of specific receptor molecules on a magnetic chip. The magnetic chip’s system is based on GMR (Giant Magnetic Sensor), and with the help of paramagnetic nanobeads, one can detect the presence of a specific protein/molecule. Ideally, we would test and detect multiplex proteins on a single chip by transferring a solution to a specific region on the sensor array. However, the current method is rather challenging and inefficient. With the help of this device, researchers will be able to detect multiplex proteins more efficiently and accurately. Read about Alex’s project at the Harvard-MIT Broad Institute Summer Research Program in Genomics. View Alex’s ISMB 2014 Poster presentation Investigating large sequence variants in drug resistant Mycobacterium tuberculosis

Laci Hampton
Summer 2010 – Spring 2011

Biomolecular Engineering
Improving next-generation sequencing flow
Faculty mentor: Nader Pourmand

Santiago Salazar
Winter – Spring 2011
Microbiology & Environmental Toxicology)—The role of SLIT signals in the regulation of  breast stem cell growth and cancer initiation
Faculty mentor: Lindsay Hinck
Update: As of September 2013, Santiago entered the graduate program in Biology and Biomedical Science at Yale University. Congratulations, Santiago!
Rene Moreno
Spring 2011

Microbiology & Environmental Toxicology
Green fluorescence protein based biosensor for arsenic contamination detection
Faculty mentor: Chad Saltikov

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Rene worked on two projects. The first focused on creating a bio-sensor for arsenic 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. Moreno graduated in June 2011 and is currently working as a program coodinator at the SACNAS main office, in Santa Cruz, CA, and applying to graduate programs.

Katrina Luna
Winter – Spring 2010
Ecology & Evolutionary Biology
Genetic diversity arising from bacteria-bacteriophage interactions driven by different genetic mechanisms
Faculty mentor: Samantha Forde

Christopher Robles
Fall 2008-Spring 2009

Biomolecular Engineering
Faculty mentor: Nader Pourmand

Regina Chavez
Fall 2008 – Winter 2009
Community Studies
Obesity and genetic research: What are we really learning?
Faculty mentor: Claudia Chaufan

Jose Loza
Winter – Spring 2010

Computer Engineering
Analyzing the effectiveness of the IZON resizable nanopore device.
Faculty mentor: William Dunbar

Christine Sinclair

Winter – Spring 2009

Molecular, Cell, and Developmental Biology
Molecular paternity analysis of the side-blotched lizard, Uta stansburiana
Faculty mentor: Barry Sinervo

Nicole Milner
Fall 2009

Ecology & Evolutionary Biology Determining the presence of T3 and Lambda in communities of coevolving bacteria and bacteriophage
Faculty mentor: Samamtha Forde

 

Claudia Mariella
Lavarreda-Pearce

Winter  – Spring 2010

Microbiology & Environmental Toxicology—Transposon mutanogenesis of Shewanella sp. ANA-3
Faculty mentor: Chad Saltikov

Nicole Coppage
Fall 2009
Microbiology & Environmental Toxicology
Creation and phenotypic characterization of a cheZHP mutant
Faculty mentor: Karen Ottemann

Tiffany Lopes 
Fall 2008
Molecular, Cell, and Developmental Biology—Can stalling of RNA polymerase influence alternative splicing?
Faculty mentor: Manny Ares, Jr.

 

Israel Murguria
Spring 2007

Politics/Community Studies
Combating health disparities
Faculty mentor: Mike Rotkin
Murguia researched 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

 

Sonia Arevalo
Spring 2006

Environmental Toxicology — Rho-independent termination in Helicobacter pylori
Faculty mentor: Karen Ottemann

 

Matt Riese 
Spring 2005
Philosophy
The biological meaning of “race”.
Read the paper

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Riese outlined 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 described a range of issues related to understanding race from both ethno-cultural and scientific vantage points. He laid 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.

Lucy Silva
2004

Computer Science
The possibility of a DNA database society (1 quarter)
Silva examined the practices of genetic profiling by police and collecting DNA samples from prisoners in California and the related legal and social implications.
Read the paper.

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She also explored the issues of DNA ownership and genetic privacy. In the age of computers, she looked at legislative solutions to the question “do we want the government to have our genome?”

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

 

Emily Berry
Winter – Summer 2006

Molecular, Cell, and Developmental Biology—Role of the Caenorhabditis elegans extracellular matrix protein F-spondin/SPON-1 in neural development
Faculty mentor: Andrew Chisholm

Read the paper

 

Alexander John Yambao 
Spring 2006

Molecular, Cell, Developmental Biology — Using immunoliposomes in combination with the immune system to treat cancer. The project was conducted in Doug Kellogg’s laboratory.
Faculty mentor: Melissa Jurica

Daphne Ochoa
2004 – 2005

Molecular, Cell, and Developmental Biology
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.
Faculty mentor: John Tamkun

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Ochoa worked 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.

Emilia Lopez
2004

Philosophy and Education
Genetic modification (1 quarter), Cloning (1 quarter)

Read the genetic modification and egalitarianism paper

Read the cloning and regulation paper

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In her first paper, “Genetic modification and  egalitarianism: distinguish and distribute,” Lopez illustrated the difference between “preventative” gene therapy and “enhancement” gene therapy. She described 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 defined and evaluated DNA cloning, reproductive cloning, and therapeutic cloning. She referred to current legislation in the US and examines the results of the California Advisory Committee of Human Cloning.

Shewit Tekeste
Fall 2007 – Spring 2008

Molecular, Cell, and Developmental Biology
Splicosome structural analysis

Faculty mentor: Melissa Jurica

Read about Shewit and her research

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Tekeste worked 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.

Edward Cabral
Spring 2006
Environmental Toxicology
Quantitative real time PCR detection of Helicobacter pylori
Faculty mentor: Karen Ottemann

Oscar Hernandez
2005

Molecular, Cell, Developmental Biology – Gene expression. Hernandez worked on a project that involved solving the structures of 150 proteins that make up the spliceosome, a critical macromolecular complex in gene expression.
Faculty mentor: Melissa Jurica

Marcia Soriano
2004

Biomolecular Engineering
Protein structure prediction
Soriano worked on developing a program to evaluate the output of various computer algorithms for predicting local protein structure.
Faculty mentor: Kevin Karplus

Alexis Rojas
2003-2004

Philosophy and Biology
Moral issues of genetic engineering (2 quarters), Somatic cell gene therapy (1 quarter)
Read the germline engineering paper
Read the somatic cell gene therapy paper

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In his first paper, “Future consequences for potential persons and our parental obligations regarding human germline engineering,” Rojas argued 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 compared somatic cell gene therapy with traditional medicine in order to dispel fears and examine the present values and definitions of “healthy.”

Former Graduate RMI Scholars

An RMI Graduate fellowship for genomics scholars was offered in years past, but funding for the 2017-2018 academic year was discontinued*

Terrill Yazzie
Winter 2017

Ocean Sciences
The role of phytoplankton- associated bacteria in degrading polycyclic aromatic hydrocarbons via host lipids with concomitant transcriptomics
Faculty mentor: Marilou Sison-Mangus

Jessica Morgan
Fall 2016 – Spring 2017

Microbiology and Environmental Toxicology (METOX) — Identifying molecular targets of the Yersinia pseudo tuberculosis type three secretion system inhibitor piercidin A1.
Faculty mentor: Victoria Auebuch-Stone

Martha Arciniega
2010 – 2011; Fall 2015 – Winter 2016

Ocean Sciences
Genetic diversity of the toxin mediating aryl hydrocarbon (AhR) genes in resident Oncorhyncus mykiss.
Faculty Mentor: John Carlos Garza

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Arciniega studied 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. 

In Fall 2015 and Winter 2016, she worked on a project, “Parallel  evolution & adaptive genomics of the steelhead summer ‘ecotype’ in multiple populations in Oregon and California.

Javier Morales
Fall 2014

Biomolecular Engineering—Engineering V1/V2 scaffolds to bind the broadly neutralizing antibody PG9 produced in normal cell lines.
Faculty mentor: Phillip Berman

Rigo Dicochea
2010 – 2012,
Spring 2013

Computer Engineering
Enhancing performance of genome sequencing processors.
Faculty Mentors: Jose Renau and Mark Diekhans

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Dicochea examined how architectural modifications to a general purpose processor design can increase the computational performance of current genome sequencing algorithms. Scientific applications such as 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.

Pamela Ruth Tilus Watson
2012 – 2013

Microbiology and Environmental Toxicology
Molecular mechanism for arsenic reduction.
Faculty mentor: Chad Saltikov

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Pamela studies a key component of the molecular mechanism whereby arsenic, a naturally occurring toxic metal, leaches into drinking water aquifers. Arsenic contaminated drinking water is tasteless and odorless, and therefore hard to detect. Arsenic gets into the natural water system because in natural sediments low in oxygen and rich in arsenic and carbon, microbes generate energy by reducing arsenic instead of oxygen during cellular respiration. The reduced form of arsenic is water soluble, and thus can seep into drinking water aquifers. Pamela’s research aims at understanding exactly which aspects of microbial respiration impact the mobilization of this toxin.

Walter Adams
2010 – 2012

Microbiology and Environmental Toxicology
The role of the central region of YopD in Yersinia pseudotuberculosis virulence.
Faculty Mentor: Victoria Auerbuch Stone

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All three human pathogenic Yersinia species, Y. pseudotuberculosis, Y. enterocolitica, and Y. pestis utilize a needle-like apparatus called a type three secretion system (T3SS) that is required for virulence. The T3SS forms a pore in the membrane of host cells and injects Yersinia effector proteins into the host cell cytoplasm. Once inside the host cell, these effector proteins disrupt the host immune response to Yersinia infection. YopD is a T3SS translocator protein involved in the post-transcriptional regulation of yop synthesis and pore formation in host cell membranes, both of which are directly linked to the effective translocation of effector proteins into the host cell cytosol. Groups have identified and described several discrete functional domains on YopD that are involved in chaperone binding, membrane interactions, and the translocation of Yersinia effector proteins. Despite these efforts, the central region of YopD between amino acids 150-227 (YopD150-227) remains largely uncharacterized. Walter’s research aims to identify the role that YopD150-227 plays in Yersinia pseudotuberculosis infection. Understanding the function of this domain will generate a more comprehensive picture of YopD in the context of Yersinia virulence and host-pathogen interactions.

Janine Llagan
2007 – 2009

Molecular, Cell & Developmental Biology
Structural changes in spliceosomes created by pre-mRNA trimming as visualized by electron microscopy.
Faculty mentor: Melissa Jurica

Iligan aimed to better characterize the structure of the human spliceosome, an important catalyst for gene expression.

Daniel Garalde
2007 – 2009

Computer Engineering
Electrical, structural, and biological refinement of a nanopore sensor for sequencing DNA and RNA.
Faculty mentors: William Dunbar and David Deamer

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Through his unique, interdisciplinary research, Geralde 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 his 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”. Garalde received his Ph.D. in 2011 and now works as a research scientist at Oxford Nanopore Technologies in Oxford, UK.

Monica Lares
2005 – 2007
Chemistry and Biochemistry
Towards the structure and function of a novel RNA gene/determining the structure and fragile X syndrome of CGG RNA repeats. 
Faculty mentor: William Scott
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Lares studied 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 used x-ray crystallography to investigate the structure and possible function of this RNA gene.

MaryAnn Dassah 
2004 – 2006
Molecular, Cellular, and Developmental Biology
Refining the rules of 5′ splice site selection and suppression of +1G mutations of pre-MRNA.
Faculty Mentor: Al Zahler

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Dassah worked 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.

Gabirel Roybal
2006 – 2007,
2009 – 2010
Molecular, Cell & Developmental Biology
Capture and chacterization of catalytic complex spliceosomes: understanding how genomes are used, maintained, and regulated.
Faculty mentor: Melissa Jurica

 

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Gabriel’s project focused on investigating how our cells process genetic information. He used small molecule inhibitors of pre-mRNA splicing as tools to isolate and study the human spliceosome.  In particular, he 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.

Update: Gabe 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. Congratulations, Dr. Roybal!

Brandon Saint-John 
Fall 2017 – Spring 2018

BME Determining the effects of SMARCA4 mutation on alternative splicing in lung adenocarcinoma.
Faculty mentor: Angela Brooks

Prestina Smith
2012 – Winter 2017

Molecular, Cell & Developmental Biology
Vangl2 and planar cell polarity genes in mammary gland morphogenesis.
Faculty mentor: Lindsay Hinck

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Tissues are distinctly engineered to carry out a given function. The breast (or murine mammary gland) is an example of this, forming a network of bi-layered ducts that terminate in alveoli formed during pregnancy. These specialized structures have an outer layer of myoepithelial cells that will contract during lactation to squeeze milk from an inner layer of polarized epithelial cells. In order to generate this system of ducts, the mammary gland undergoes growth by branching; therefore, mechanisms involved in branch formation define mammary architecture. Diseases, such as breast cancer, often result in highly unorganized tissues; therefore, understanding the genes that regulate the overall architecture of the mammary gland could aid in understanding breast cancer pathology and identify potential therapeutic targets. Recent studies have identified genes involved in establishing proximal-distal (planar) polarity in epithelial cells as regulators of branching morphogenesis, however the mechanism of their action is currently unknown. Prestina’s project aims to understand how the core planar cell polarity (PCP) gene Vangl2 regulates branching in the mammary gland by investigating changes in mammary morphology in Vangl2 mutant mice, identifying regulators of Vangl2 and determining how VANGL2 cooperates with other PCP proteins to promote mammary development. Smith’s studies will provide insight into the mechanisms that function to establish the architecture of the mammary gland and elucidate a novel role for planar cell polarity in tissue morphogenesis.

Richard Cathey
2012 – 2014

Microbiology and Environmental Toxicology
How early life manganese exposure disrupts dopamine function and leads to attention deficits.
Faculty mentor: Donald Smith

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Soriano worked on developing a program to evaluate the output of various computer algorithms for predicting local protein structure.

Richard’s research focuses on how early life manganese exposure disrupts DNA methylation patterns in dopamine receptor genes, which alters prefrontal cortex dopamine function and ultimately leads to deficits in attention. He aims to determine the mechanistic basis for how oxidative stress may alter a gene’s DNA methylation “blueprint” to cause altered protein expression. These DNA changes can be heritable, and this mechanism can span a wide range of fields such as environmental toxicology, nature, and nutrition.

Joseph Parks
2012 – 2013

Biochemistry
Understanding telomerase activity through single-molecule methods.
Faculty mentor: Michael Stone

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In the fall of 2012 Joe received the prestigious NSF Graduate Research Fellowship Award. Congratulations, Joe!
Telomerase is an essential eukaryotic enzyme that extends the ends of chromosomes. This enzyme is of particularly interest to the cancer field as telomerase hyperactivity is associated with over 90% of all cancers. Similarly, telomerase over-expression in normal cells has been shown to increase the lifespan of yeast and rats by up to 20% without an increase in cancer occurrence. Although many researchers have studied telomerase at a biochemical level, the detailed telomerase mechanism and structural features of the enzyme remains unclear due to the lack of a complete crystal structure. In order to dissect the structure and function of telomerase components, Joe will study individual molecules and their structural dynamics using single molecule FRET. Through real-time observation of telomerase internal dynamics, he hopes to gain direct insight into the function of telomerase sub-domains.

Publications:
Nucleic Acids Res. 2013 Feb 1;41(4):2746-55. doi: 10.1093/nar/gks1341. Epub 2013 Jan 8.
Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy. Long X, Parks JW, Bagshaw CR, Stone MD.
PMID: 23303789 Free PMC Article
2. Plast Reconstr Surg. 2012 Oct;130(4):739-46. PMID: 23018685
Human acellular dermis versus no acellular dermis in tissue expansion breast reconstruction.
Parks JW, Hammond SE, Walsh WA, Adams RL, Chandler RG, Luce EA.

Margarita Gonzalez 
2009 – 2012

Chemistry and Biochemistry
Investigations on DNA sequence vulnerability to NO-mediated DNA damage.
Faculty mentor: Pradip Mascharak

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Margarita utilized 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

Update: In August of 2013, Margaria completed all the requirements of her graduate research training and filed her dissertation. Congratulations, Dr. Gonzales!

Hector Macias
2009 – 2010

Molecular, Cell & Developmental Biology
Uncovering the mechanism behind SLIT2/ROBO 1 mediated mammary gland branch inhibition.
Read the paper
Faculty mentor: Lindsay Hinck

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Hector’s research focused on developing therapeutic strategies for diagnosing and treating breast cancer.

Update: Hector received his Ph.D. in 2010 and is currently a post doctoral researcher in the Michael German lab at the University of California, San Francisco. The German lab is interested in identifying genetic factors that influence diabetes by identifyingthe genes that regulate the transition of stem cells to mature pancreatic beta-cells. Pancreatic beta-cells are the body’s sole provider of insulin. By understanding the role of these factors inbeta-cell production the German research team is developing novel strategies for curing diabetes. Congratulations, Dr. Macias! We look forward to your future contributions to biomedical science.

Josue Samayoa
2004 – 2006,
2008

Biomolecular Engineering
Protein structure prediction.
Faculty mentors: Carol Rohl, Kevin Karplus, and Fitnat Yildiz

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With Carol Rohl, Samayoa worked to expand and improve modeling methods for predicting 3-dimensional protein structure. The project is called, “Homology-based modeling with Rosetta and NMR data.” He then participated in an interdisciplinary projects with advisors Kevin Karplus and Fitnat Yildiz: “A bioinformatic analysis of simple repeats and small proteins in Vibrio cholerae El Tor.”

Mark Rivero
2006

Computer Engineering
Data visualization of genomic information.
Faculty mentor: Pat Mantey

Rivero looked for ways to improve the UCSC Genome Browser by allowing 3-dimensional visualization of any given data.

Edward Olano 
2004 – 2005

Chemistry
Developing assays for prostate-specific antigen and early detection of ovarian cancer.
Faculty mentor: Jin Zhang

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Olano worked on developing an immunoassay for prostate-specific antigen and also designing a biomarker using quantum dots for detecting ovarian cancer. Both assays employed a spectrophotometric technique called surface-enhanced Raman scattering (SERS).

Veronica De Guzman
2003 – 2005
Chemistry
Nanopore devices.
De Guzman studied a nanopore device, which is an artificial membrane that has a single ion channel through it. 
Faculty mentor: Mark Akeson, UCSC Nanopore Project.

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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.

LEARN MORE about the Nanopore Project at UC Santa Cruz

David Balderas
Fall 2017
METX
Regulon of the Iron-sulfur cluster transcription factor IscR in Yersinia
Faculty mentor: Victoria Auerbuch-Stone

 

Jamie Hernandez
Fall 2015 – Spring 2016

Microbiology and Environmental Toxicology (METOX)
System biology of anoxygenic photosynthetic arsenite oxidation in Ectothiorhodospira  BSL-9.
Faculty mentor: Chad Saltikov

Angel Resendez 
Spring 2015

Chemistry
Chemistry — Development of a chemical tool for measuring gut permeability.
Faculty mentor: Bakthan Singaram

Tara deBoer
Fall 2014, Winter 2015
Chemistry and Biochemistry—Investigation into the potential epigenetic nature of peroxynitrite.
Faculty Mentor: Pradip Mascharak
 

Andrew Knutson
2012 – 2014
Molecular, Cell & Developmental Biology—The role of SUMOxylation in preventing expression of germline proteins in somatic cells of Caenorhabditis elegans.
Faculty Mentor: Susan Strome

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Andrew uses the nematode C. elegans as a model to study the role of the SUMOylation pathway in preventing somatic cells (e.g., muscle, neurons, intestine) from acquiring germ cell (eggs and sperm) characteristics. Germ cells and somatic cells are fundamentally different: while somatic cells are differentiated and mortal, germ cells retain the ability to develop into any cell type (called ‘totipotency’) and are immortal from generation to generation. Knutson found that removing the highly conserved SUMOylation pathway causes somatic cells to express germline proteins. The SUMOylation pathway modifies many nuclear proteins, thereby affecting their activity and function. Knutson employs genome-wide techniques, including microarray analysis and ChIP-seq technology, to assess how removing the SUMOylation pathway affects gene expression and to determine where SUMOylated proteins reside in the genome. His studies will elucidate mechanisms that control genome organization and development and how those mechanisms contribute to distinguishing germ and somatic identities.

Publication: Comparative effects of histone deacetylase inhibitors on p53 target gene expression, cell cycle and apoptosis in MCF-7 breast cancer cells.
Oncol Rep. 2012 Mar;27(3):849-53. doi: 10.3892/or.2011.1590. Epub 2011 Dec 12.
PMID: 22159450

Josh Parks
Fall 2015 – Spring 2016
Electrical Engineering — Single molecule detection on an optofluidic platform.
Faculty mentor: Holger Schmidt
Daniel Sam
2007 – 2009,
Fall 2010 – Winter 2011
Biomolecular Engineering—Computational approaches for predicting gene function.

Sam developed computational tools to predict and elucidate functional relationships between biological data collected from a variety of sources.
Faculty mentor: Josh Stuart

Carolina Reyes
2010 – 2011

Microbiology & Environmental Toxicology—Microbial genetics underlying iron geochemistry in anaerobic microorganisms.
Faculty mentor: Chad Saltikov

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How bacteria metabolize a solid mineral externally is of interest to microbiologists and geologists. Reyes investigated 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 her 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, she 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.

 Reyes received her doctorate in 2011 and is  curently a research fellow at the Hanse-Wissenschaftskolleg Institute for Advanced Study in Bremen, Germany. Her research is supported in part by a fellowship from the J. William Fulbright Foundation, and an International Research Fellowship from the National Science Foundation.

Sachiko Reed
2007 – 2008
Sociology—Considering implications of mixed race identity and genomics.

Faculty mentor: Jenny Reardon

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Reed combined 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.

Genevieve Halpenny
2004 – 2007
Chemistry—DNA damage via light-activited nitric oxide release.
Halpenny delivered nitric oxide (NO) to living cells such as E. coli and ultimately cancer cells and then used microscopy to observe NO-induced DNA damage.
Faculty mentor: Pradip Mascharak

Blake Riggs
2004 – 2005
Molecular, Cellular, and Developmental Biology—The centrosome-associated protein, nuclear fallout, and its role in metaphase furrow formation.
Faculty mentor: Bill Sullivan
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Riggs worked 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.

Loni Townsley-Montoya, 
2012 – 2013

Microbiology and Environmental Toxicology—Construction and characterization of regulatory networks controlling cold shock adaptation in Vibrio cholerae.
Faculty mentor: Fitnat Yildiz 

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Bacterial pathogens are a major cause of mortality worldwide, yet we know little about how these organisms adapt to habitats outside of the human host. Vibrio cholerae, the causative agent of the severe diarrheal disease cholera, is an excellent model system to study environmental adaptation because it must survive in aquatic habitats for prolonged periods between outbreaks. Temperature is a critical environmental signal governing the occurrence of V. cholerae, and cholera outbreaks are highly correlated with sea surface temperature.  However, it is unknown how V. cholerae senses and responds to temperature change or how this response impacts environmental survival and infectivity of this pathogen.  Loni’s research aims to identify the regulatory networks responsible for temperature adaptation in V. cholerae and determine their impact on the environmental survival of this pathogen.      

Marc Hanson
2003 – 2004

Computer Engineering—Visualizing database queries.

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Hansen studied 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.