Associate Professor, Department of Nutritional Science and Toxicology, University of California, Berkeley
Associate Professor and Associate Toxicologist in the Agricultural Experiment Station
Office : 317 Morgan Hall
Tel : (510) 642-1834
Fax : (510) 642-0535
Email : vulpe(at)berkeley(dot)edu
NST Faculty Profile
Ph.D. 1994, Genetics, M.D. 1996, University of California, San Francisco
Current research projects are: 1) Use of fish cell lines in ecotoxicology as an alternative to animal toxicity testing; 2) Using Ecotoxicogenomic approaches to produce a biological monitoring tool for regional water quality assessments using the Horneyhead turbot (Pleuronichthys verticals); and 3) Validation of genomic data with chemical exposure profiles from PAHs and pesticides using Daphnia magna.
B.S Biology (concentration in Cell Biology), 1993, Hood College, Frederick, MD
M.S Coastal Zone Studies, Natural Resource Law, and Ecotoxicology, 1997, University of West Florida, Pensacola,FL
Oak Ridge Fellowship, 2002-2008, US Environmental Protection Agency, Cincinnati, Ohio
Disturbances of iron homeostasis can have significant clinical consequences. Iron deficiency is the world’s most prominent nutritional deficiency and anemia of chronic disease (ACD) from decreased intestinal iron absorption and impaired iron release from macrophages is common in hospitalized patients. The overall goal of this study is to help us understand the genetic basis of variation in iron metabolism between people. Inbred mice show significant variation in multiple traits including iron metabolism. We aim to identify loci underlying strain specific differences in iron metabolism through a combination of "in silico" SNP association and gene expression profiling.We will also assess candidate genes for a role in human iron metabolism through population based studies.
B.Sc. University of Newcastle Upon Tyne, UK (2006)
Ph.D. University of Manchester, UK (2011)
Data Analysis Specialist
Projects involved with: Toxicant Susceptibility, Ecotoxicogenomics
(Microarray Bioinformatics / Data Analysis / Statistical Programming / Biostatistics)
Applying statistical, computational and programming tools to evaluation and validation of algorithms for gene expression data analysis based on microarray experiments (mostly in metal toxicology and plant physiology):
- Developed new robust single-slide and multiple-slide/chip algorithms for exploratory and confirmatory differential gene expression analysis using simultaneous tolerance/prediction intervals, regression smoothers (super smoother, lowess, loess), and outlier identification procedures (quantile-quantile normal plots with simulation envelopes, box plots for residuals etc.).
- Developed, debugged and maintained S-plus and HTML code to present results of single- and multiple-slide gene expression analysis as html-documents.
- Developed robust algorithms for exploratory and confirmatory differential yeast strain sensitivity analysis based on Affymetrix® purpose-built oligonucleotide microarrays for parallel deletion analysis.
- Applied methods for statistical inferences based on qPCR data sets.
- Applied statistical and programming methods to quantify dose-response relationships for toxicants at the whole genome level.
- Acted as a resource on microarray data analysis to staff scientists, research associates, and students with biological background.
- Applying statistical and computational methods to various experimental results based on “experiment vs. control” design.
Vanessa De La Rosa
I am a 4th year graduate student in Molecular Toxicology. I am interested in using a functional genomics approach in model systems such as yeast and the DT40 avian cell line to identify mechanisms of toxicity for various environmental contaminants (TCE, benzene, etc). In addition, I am interested in using functional genomics in C. elegans to investigate neurotoxicity of contaminants and next generation sequencing to look at DNA damage.
IMSD Graduate Fellow
B.S Chemistry, 2008, University of Texas at El Paso
I am a graduate student in the Metabolic Biology program, and my research interests lie in understanding how iron is absorbed and trafficked by the body. I have generated several knockout mouse models to study the role of multicopper ferroxidases in mammalian intestinal iron absorption. Currently I am abroad doing collaborative studies in the Iron Metabolism Laboratory of Professor Greg Anderson at the Queensland Institute of Medical Research in Brisbane, Australia.
NSF Graduate Research Fellow
Berkeley Graduate Fellow
B.S. Biochemistry, 2003, The University of Texas at Austin
Projects involved with: Toxicant susceptibility
I am a fifth year graduate student in Molecular Toxicology. Using a yeast model, I am identifying potential cellular mechanisms of toxicity as well as human biomarkers of susceptibility for various emerging (flame retardants) and legacy (organochlorinated pesticides) contaminants. Additionally, I am interested in applying the concept of toxicity pathways- the cellular signaling pathways that are induced or perturbed in response to a toxicant- to our model system.
Email : bgaytan(at)berkeley(dot)edu
NSF Graduate Research Fellow
Berkeley Graduate Fellow
M.A. 2008, Biology, Clark University, Worcester MA
B.A. 2007, Molecular Biology and Computer Science, Clark University, Worcester MA
Projects involved with: Ecotoxicogenomics
I am a graduate student in Molecular Toxicology analyzing Daphnia magna's genomic response to flame-retardants. I hope to 1) determine modes of toxicity and 2) develop a method for detecting flame-retardants in water, using D. magna. I also sequenced the D. magna expressed genome (mRNA) and am looking for novel genes and EST gene fragments..
Email : lds(at)berkeley(dot)edu
B.S 2007, Molecular Toxicology, University of California, Berkeley
Undergraduate Research Assistants
Carrie (San Heen) Park