Faculty

The Genetics Graduate Group faculty members have a wide-range of research interests.

An alphabetical list of all faculty members affiliated with the Genetics Graduate Group is found on this page.

Chair of Genetics: Janine LaSalle

Click on a faculty member's name to view his or her full profile.

dlbannasch@ucdavis.edu Vet Med - Population Health and Reproduction

Our current and future research plans are directed towards elucidating the molecular basis of inherited diseases in companion animals. We are interested in developing tests to help breeders eliminate inherited diseases in dogs and horses. A large number of the diseases seen in veterinary practice that affect purebred animals have a heritable basis. Characterizing inherited diseases in dogs has the added benefit of providing an animal model for human diseases. Presently we have projects in both the horse and the dog.
dmbeckles@ucdavis.edu Plant Science
Lab

Regulation of carbon allocation in plants and how this changes in response to environmental stress; Starch granule biosynthesis and molecular structure; Postharvest quality of tomato fruit.
djbegun@ucdavis.edu Evolution and Ecology
Lab
Population genetics and molecular evolution
 Population genetics and molecular evolution. Drosophila evolutionary genetics.
abbennett@ucdavis.edu Plant Science
Lab
lfbisson@ucdavis.edu Viticulture & Enology
Lab
jlbowman@ucdavis.edu Plant Biology

Molecular genetic analysis of plant development and evolution
simeon.boyd@ucdmc.ucdavis.edu Pediatrics - Medicine
Lab
sbrady@ucdavis.edu Plant Biology
Lab
Genomics, Developmental Biology, Plant Biology, Systems Biology, Transcriptional Networks
abbritt@ucdavis.edu Plant Biology

Genetics of DNA repair and mutagenesis in the higher plant Arabidopsis. How plants repair and/or tolerate DNA damage generated by chemicals, UV light, and gamma radiation. Processes of genetic recombination, in meiotic and mitotic cells. Transcriptional regulation of damage response.
nlbrown@ucdavis.edu Cell Biol & Human Anatomy
Mammalian Developmental Genetics
 My research group aims to understand the molecular mechanisms regulating the formation of the mammalian lens and retina. We are investigating the genetic pathways underlying lens and retinal tissue formation during embryogenesis. This research will contribute to a better understanding of congenital eye diseases and ultimately inform therapies that can correct vision loss. Currently we are focused on understanding: 1) how lens progenitor cells stop dividing and turn into fiber cells, and 2) how retinal progenitor cells choose to become one type of neuron, although multiple fates are available to them.
smburgess@ucdavis.edu Molecular & Cellular Biology
Lab
Meiotic chromosome dynamics
 Work in my laboratory explores the dynamic chromosome events that occur during the process of meiosis and how these processes are integrated to achieve accurate chromosome segregation. Chromosome missegregation is one of the leading causes of birth defects in humans. We combine the use of a wide array of tools, including genetics, molecular biology, biochemistry and live-cell imaging using budding yeast Saccharomyces cerevisiae as a model system.
kcburtis@ucdavis.edu
DNA repair in Drosophila; specifically, the molecular basis of interstrand crosslink repair.
jcallis@ucdavis.edu Molecular & Cellular Biology
Lab

The ubiquitin pathway is a protein modification pathway, whereby the protein ubiquitin is covalently attached to other proteins. This alters the longevity, activity or localization of the ubiquitinated protein. We are interested in understanding the specificity and regulation of the ubiquitin pathway. We try to understand how proteins are recruited to the ubiquitinating enzymes. There are are large number of ubiquitinating enzymes whose functions are not known. We are taking a reverse genetics approach to understand the function of RING E3 ligases which interact with substrate proteins and catalyze ubiquitin transfer. We also study a ubiquitin-like protein, RUB, for Related to ubiquitin, and are trying to identify RUB-modified proteins in plants. We use a variety of techniques- biochemistry, molecular biology and genetics.
lgcarvajal@ucdavis.edu Biochemistry and Molecular Medicine
Lab
Human and cancer genetics, Human Genomics
 We identify loci associated with increased risk of common cancers in humans. We have interests in functional genomics, genetic epidemiology and on how cancer somatic pathways vary across ethnic groups. We have a particular interest in the genetics and epidemiology of cancer in minority populations and have ongoing studies in several patient cohorts from Latin America. We apply a number of methods to identify cancer genes including genome-wide association studies, admixture mapping, linkage analysis and candidate gene approaches. We are increasingly using next generation sequencing in our studies and are shifting our focus from common to rare variant studies in families and population isolates
flchedin@ucdavis.edu Molecular & Cellular Biology
Lab
Mammalian epigenetics
 I am interested in elucidating the molecular mechanisms that are responsible for setting up cytosine DNA methylation patterns in the human genome. How these mechanisms go awry in disease conditions, in particular in auto-immune disorders and cancer, is also of direct relevance to my work. To investigate these question, my group makes use of (epi)genomics tools, mammalian cell culture assays and biochemistry.
hwzchen@ucdavis.edu Biochemistry and Molecular Medicine
Chromatin/epigenetic regulators in hormone signaling and in cancer
 Our research includes identification and elucidation of key epigenetic regulators that function in cancer and in hormone signaling. Steroid hormone signaling plays crucial roles in control of cell growth and differentiation through the nuclear hormone receptors such as estrogen receptors and androgen receptor and their associated coregulators. We focus on understanding how some of the coregulators (e.g. ANCCA, histone methylases and demethylases) mediate gene expression control and hormone-dependent growth and differentiation via chromatin histone modifications and remodeling and how their aberrant functions contribute to tumorigenesis. Our objectives are to identify the key chromatin regulators that play important functions in the nuclear receptor-dependent hormone signaling in prostate and mammary gland, to identify the important epigenetic regulators in the initiation and/or progression of breast cancer and prostate cancer, to elucidate the molecular mechanisms of the epigenetic regulators, and to demonstrate the potential of the epigenetic regulators as biomarkers and therapeutic targets.We employ a number of molecular and cell biology approaches, including gene expression microarray, chromatin immunoprecipitation (ChIP) or ChIP-seq, for analysis of chromatin modification and remodeling, coregulator assembly and gene expression, as well as genetic approach (e.g. mouse ko models) for determining the physiological and pathological functions of the chromatin regulators.
trchetelat@ucdavis.edu Plant Science
Interspecific Reproductive Barriers
 My lab studies prezygotic interspecific reproductive barriers, using cultivated tomato and related Solanum species as a model. Our focus is on the pollen factors that are important in unilateral interspecific incompatibility, and their genetic/biochemical role in self-incompatibility. We recently isolated the ui6.1 gene, which encodes a Cullin1 protein that interacts with a factor encoded by the S-locus. Our goal is to understand how these two genes function in inter- and intraspecific pollen rejection, and to isolate the other pollen factors that are important in these processes.
Recombination in Wide Crosses
 We also study meiotic recombination in wide crosses and the role of genes in the DNA mismatch repair system. Cultivated tomato and its wild relatives -- 17 species, many of which are intercrossable -- provide an excellent system in which to study recombination between homeologous (partially homologous) genomes.
 Genetic Resources
 We are transferring the genome of Solanum sitiens, a species native to the Atacama Desert of Chile, into the genetic background of cultivated tomato. The goal is to synthesize a complete library of introgression lines, each containing single recombinant chromosome segments that together represent the entire genome. These are expected to be useful for studies of drought and salinity tolerance, fruit ripening, etc.
glcoaker@ucdavis.edu Plant Pathology
Lab
plant microbe interactions
 Research in my laboratory includes studies on the mechanisms controlling pathogen evolution and virulence as well as plant resistance signaling cascades. A common thread to the research that is conducted in the laboratory is the use of the Gram-negative bacterium, Pseudomonas syringae, for understanding how disease is caused on susceptible genotypes whereas defense signaling is elicited on resistant plant genotypes.
lcomai@ucdavis.edu UC Davis Genome Center
Lab
drcook@ucdavis.edu Plant Pathology
Lab
gcortopassi@ucdavis.edu VM Molecular Biosciences
Lab
amdandekar@ucdavis.edu Plant Science
Molecular, biochemical and genomic dissection of tree fruit traits
 I am particularly fascinated by the biochemical/physiological manifestation of phenotypic traits. My lab is interested in understanding the relationship between specific traits and genes and is also interested in defining the system by understanding the functional relationships between traits in a genomics and whole plant context. We are also interested in developing technology and tools to enable trait specific diagnostics and to improve protein and/or gene based therapies.
sdandekar@ucdavis.edu Microbiology - Medicine

Molecular pathogenesis of HIV and SIV, Mucosal immunology of host-pathogen interactions and epigenetic regulation of mucosal immune defense in HIV and SIV infections and co-infections


medelany@ucdavis.edu Animal Science
Lab
My laboratory research focuses on avian telomere biology, with chicken being the primary organism under study. Our studies concentrate on the organization, inheritance, regulation and stability of telomere array organization in normal, immortalized and transformed cell systems, both in vitro and in vivo. Telomere stability is one of the most significant genetic mechanisms controlling overall genome stability and influencing cellular proliferation, senescence and transformation. Current projects include analysis of the regulation and function of the telomere-telomerase pathway during oncogenesis induced by Marek’s disease virus (MDV), a DNA herpes virus which induces T-cell lymphomas and results in a high level of mortality. This particular disease is a problem of enormous significance for the poultry industry. MDV infection and disease in chickens also serves as a model system for human herpes virus infection and disease conditions (e.g., Burkitt’s lymphoma caused by Epstein Barr virus). Students studying in the lab (M.S. and Ph.D.) are trained in the disciplines of genetics, cytogenetics, and genomics with an emphasis on avian systems as well as comparative vertebrate biology. Research and technology levels range from molecular and cellular to the organismal. Other interests and areas of research include gene mapping and chromosome organization, congenital and inherited developmental mutations, and conservation of poultry and avian genetic resources.
bwdraper@ucdavis.edu Molecular & Cellular Biology
Lab
Germline stem cells
 We study mechanisms that regulate the development and function of germline stem cell in zebrafish, with a main focus on female germline stem cells. We study factors that function within the stem cells, as well as those that are required for the development of the somatic gonad, the germ cell niche.
 Sex determination and maitenance of the adult sexual phenotype
 While zebrafish do not switch sex as adults, our lab has recently discovered that maintenance of the adult female sexual phenotype is an active process that requires continuous input from germ cells, as reduction of germ cell numbers in an adult female results in female-to-male sex reversal. Our current research is focused on determining what signal is produced by the germ cells and how it influences the developmental state of the somatic gonad.
jdubcovsky@ucdavis.edu Plant Science
Lab
My research is focused on wheat geneticas and wheat improvement
jdvorak@ucdavis.edu Plant Science
jengebrecht@ucdavis.edu Molecular & Cellular Biology
Lab
Meiosis and checkpoint function in the C. elegans germ line
 Germ cells are specialized cells that undergo mitotic proliferation followed by meiosis and cellular differentiation to generate haploid gametes for sexual reproduction. We are investigating several aspects of germ line biology using the nematode, Caenorhabditis elegans, as a model. The C. elegans germ line is particularly amenable to these studies due to its unique structural organization, the molecular genetics of the system, and the high degree of conservation with genes and pathways in humans. We are currently investigating 1) how checkpoint pathways are differentially regulated in the female and male germ line; 2) how unpaired sex chromosomes of the heterogametic sex repair double strand breaks and are hidden from the checkpoint machinery; and 3) how different checkpoint pathways interact to ensure the faithful transmission of the genome.
hbernest@ucdavis.edu Vet Med - Population Health and Reproduction
Lab
Wildlife Genetics and Genomics
 Population genetics at landscape level; wildlife disease ecology, wildlife genomics. Dr. Ernest is a wildlife geneticist and research veterinarian with interests in the application of genomic tools for animal ecology, wildlife health; directs the Wildlife Ecology Unit of the UC Davis Veterinary Genetics Laboratory.
Species of interest
 California wild mammals and birds. Current projects involve mountain lions, black bears, sea otters, river otters, bighorn sheep, wild pigs, hummingbirds, yellow-billed magpies. One domestic species: domestic (pet) ferret population genetics in relationship to cancer incidence.
trfamula@ucdavis.edu Animal Science
nafangue@ucdavis.edu Wildlife&Fish Conservation Bio
Lab
csgasser@ucdavis.edu Molecular & Cellular Biology
Molecular basis of plant development and evolution of development.
plgepts@ucdavis.edu Plant Science
Crop bioidversity and bean breeding
 Since the beginning of agriculture, some 10,000 years ago, humans have molded the diversity of crop plants around them to suit their diverse needs for food and beverage, feed, clothing and other numerous uses. Starting with the process of domestication, crop biodiversity results from the fascinating interactions among humans, plants, and their environment. My research and teaching program is focused on elucidating the evolutionary processes that have shaped evolution of crop plants under cultivation. I focus particularly on Phaseolus beans because they are such an important part of the human diet, especially in developing countries, and provide many health benefits. Other crops of interest in my lab are additional crops from the Americas such as peppers (Capsicum), wild maize (teosinte), amaranth, and agaves. These provide a comparative dimension to studies of crop evolution because they encompass a wide range of reproductive systems, life histories, and human uses. On the more applied level, I look at the consequences of our findings for plant breeding. One of my main activities is a participation in the ABC-KT project (i.e., African Bean Consortium, funded by the Kirkhouse Trust), which seeks to develop a marker-assisted selection capability in East African bean breeding programs. I have recently taken over the grain legume breeding program at UC Davis, which focuses on the development of new varieties of lima and common bean and garbanzos for the state of California.
paghosh@ucdavis.edu Biochemistry and Molecular Medicine
Lab
Signal Transduction Pathways in Prostate Cancer
 The pathways we study include the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, the Ras/Raf/MEK/MAPK pathway and other signaling pathways both upstream and downstream of these. This includes the mammalian target of rapamycin (mTOR) pathway, and signaling by the epidermal growth factor receptor (EGFR), related receptor tyrosine kinases ErbB2 and ErbB3.
rlgilbertson@ucdavis.edu Plant Pathology
dggilchrist@ucdavis.edu Plant Pathology
tmglaser@ucdavis.edu Cell Biol & Human Anatomy
Genetic basis of mammalian eye development and congenital eye malformations

 We study genetic mechanisms of vertebrate eye development, evolutionary conservation of gene networks, and transcriptional regulation. Our major interests include early patterning of the optic primordia and retinal cell fate specification. We use mutant and transgenic mice, human pedigrees segregating congenital eye malformations, and a variety of genomic, molecular and cell-based techniques. Current lab projects focus on ganglion cells – the first-born retinal neurons whose axons form the optic nerves and relay all visual information from the eye to the brain, fate symmetry, bHLH transcription factors, Notch signaling, the retinoid pathway, and molecular identification of new eye disease loci.
tmgradziel@ucdavis.edu Plant Science
Lab
pjhagerman@ucdavis.edu Biochemistry and Molecular Medicine
Lab
nhagiwara@ucdavis.edu Cardiology (Internal Med)

Development and disease of skeletal muscle and the heart
jjharada@ucdavis.edu Plant Biology
Molecular, genetic, biochemical, and genomic dissection of embryogenesis and seed development in plants.
slharmer@ucdavis.edu Plant Biology
Lab
Understanding the molecular basis of circadian rhythms in plants and how these daily rhythms affect plant physiology.
dennis.hartigan-oconnor@ucdmc.ucdavis.edu
wdheyer@ucdavis.edu Microbiology and Molecular Genetics
Lab
Mechanism and regulation of recombinational DNA repair
 Double-stranded DNA breaks (DSBs) are among the most genotoxic lesions and can be generated by ionizing radiation, drugs, or cellular processes. In eukaryotes, several pathways compete for the repair of such lesions. Homologous recombination is the critical DSB repair pathway in yeasts and an important DSB repair pathway in all eukaryotes studied. We are using primarily Saccharomyces cerevisiae as a model system and employ genetical, molecular, and biochemical methods to elucidate the molecular mechanism of homologous recombination and recombinational DNA repair and its regulation by the DNA damage checkpoints.
jekhildreth@ucdavis.edu Molecular & Cellular Biology

My laboratory research is focused on understanding mechanisms by which HIV subverts host pathways and molecules during its replication cycle. We are particularly interested in the role of cholesterol and cholesterol homeostatic pathways in virus entry, virus release and viral gene transcription. The involvement of cholesterol-rich lipid rafts, late endosomes and exosomes is also the subject of investigations in our laboratory. Another major area of interest is the impact of viral co-infections on HIV’s tropism and replication. Many viruses are known to modulate cholesterol regulatory pathways and cellular cholesterol content and thereby can profoundly affect HIV replication. We are interested in this and other mechanisms of enhancement or suppression of HIV transmission and replication by co-infecting viruses.
rchovey@ucdavis.edu Animal Science
Lab

Our lab seeks to define the processes underlying how the mammary glands - either during their growth, for milk synthesis, or in the case of breast cancer - respond to hormonal signals. We use a variety of methods, animal models and systems to study this regulation ranging from the molecular to the whole organism. In particular we are interested in how hormones such as estrogen, progesterone and prolactin affect tissue function and how factors such as diet and lifestyle also can have positive or negative effects.
liping.huang@ars.usda.gov Nutrition

Dr. Huang has primarily focused on mammalian zinc transporter proteins and their roles in maintaining body zinc homeostasis, regulating body adiposity, and modifying insulin expression. She is also interested in the molecular mechanisms by which zinc and lunasin reduce the risk of prostate cancer. Her work involves cell lines and mice to investigate the roles of zinc in reduction of prostate cancer risk and in regulation of body weight, body fat, and insulin resistance.
nhunter@ucdavis.edu Microbiology and Molecular Genetics
Lab
Homologous Recombination.
 The mechanism and regulation of chromosome repair by homologous recombination and its role in chromosome transmission and genome stability.
 Post-Translational Protein Modification in Meiosis.
 The nature and function of post-translational modifications of proteins involved in homologous recombination during meiosis.
kinoue@ucdavis.edu Plant Science
Lab
Gene Duplications
 What is their biological significance? We address this question by comparing properties and functions of two sets of prokaryote-derived homologous proteins in chloroplasts (protein translocation channel Toc75 and its paralog OEP80/Toc75-V; three type I signal peptidases, Plsp1, Plsp2A, Plsp2B).
 Organelle Biogenesis - Protein evolution
 How did the protein import channel in the organelle envelope evolve from a protein in the outer membrane of an ancestral cyanobacterium? We elucidate the functions and sorting/assembly mechanisms of Toc75 and OEP80/Toc75-V, which are homologous to a family of proteins essential for the viability of Gram-negative bacteria.
 Organelle Biogenesis - Development of Membrane System
 How do the intraorganellar membrane systems develop? We take three strategies. Strategy 1 is to define the molecular bases underlying thylakoid disruption due to the lack of signal peptide processing. In strategy 2, we elucidate the mechanism by which Plsp1 is sorted to the envelope and thylakoid within a chloroplast. In strategy 3, we attempt to address how citrus fruit peel changes its color from green to orange, then back to green. (dis-assembly and re-assembly of thylakoids).
mjasien@ucdavis.edu Plant Science
Lab
Population genetics and evolution of agricultural weeds and invasive plants
 The Jasieniuk lab studies the population genetics, molecular ecology, and evolution of agricultural weeds and invasive plants. Our research focuses on elucidating the genetic, demographic, and evolutionary processes underlying the introduction, establishment, and spread of weeds and invasive plants, and their adaptation to changing environments, including management practices.
skanthaswamy(at)ucdavis(dot)edu Environmental Toxicology

My research focuses on primate genetics and forensic DNA analysis. My primate research uses genetic markers to define the population structures of captive and wild populations of non-human primates. I use comparative genomic methods to understand human and non-human primate biology. My forensic science research is based on the analyses of traces of human and animal blood, saliva and hair collected at crime scenes or from civil cases for DNA-typing. My research also focuses on establishing species-specific DNA markers for accurate and precise genetic identification and to enhance our population genetics database for each species. My research activities provide excellent educational opportunities for students. I serve on the Editorial Board of Animal Genetics and I provide expert witness testimony on animal/veterinary forensic DNA analysis and casework review.
Plant Science
Lab
Quantitative Systems Biology
 We focus on two major questions using plant natural chemistry as our model system. Plant natural chemistry generates compounds that provide the taste, flavor, color and medicinal activities that people associate with specific plants. However, their primary role appears to be helping the plant cope with its environment by attracting pollinators, repelling attackers and protecting the plant from sunlight. These aspects make these compounds easy to measure and key tools in understanding modern systems biology and genomics. The first question that we use these chemicals for is to understand how thousands of genes coordinate within a system to control the proper functioning of the system. This involved modern quantitative genomics and tools such as genome wide association mapping and QTL analysis. We are at the forefront of developing network analysis approaches and theory to help with the modern synthesis of the gene-to-phenotype linkage. The second question we focus on is why plants make these chemicals. They have broad activities and plants make an amazing diversity of chemicals, each potentially with its own function and evolutionary history. We are primarily using the model plant, Arabidopsis thaliana, to study how its secondary metabolites control interactions with both insects and fungi. As a part of this we are using a mixture of functional genetics, quantitative genetics, plant biology, evolutionary biology and metabolite profiling to develop as in depth and broad a picture as possible. To broaden this picture, we are expanding into rice, tomato, Lycopersicon, and grapes, Vitis. An additional avenue that we are pursuing is the fact that fungi also make secondary metabolites. For instance, Botrytis cinerea produces a suite of secondary metabolites whose main role appears to be killing plant cells. Thus by studying how Arabidopsis and Botrytis interact, we hope to analyze how organisms can combat each other through metabolism. We are expanding our quantitative systems approaches to study genetic variation in both the host and pathogen of this system simultaneously.
knoepfler@ucdavis.edu Cell Biology & Human Anatomy
Lab

The research in the Knoepfler lab focuses on the epigenetic and transcriptional control mechanisms that direct cell fate. We are particularly interested in the relationship between tumorigenicity and pluripotency. Our model systems including both mouse and human ESC, induced pluripotent stem (iPS) cells, and cancer stem cells.
akopp@ucdavis.edu Evolution and Ecology
Lab
Our lab combines developmental and evolutionary genetics to understand the origin of new phenotypes and ecological adaptations. Our interests include the evolution of developmental pathways, the origin of sex-specific morphological traits, evolution of insect behavior and host plant preferences, and molecular mechanisms and ecological impact of insect-bacterial symbiosis. We address these questions by integrating molecular-genetic, genomic, quantitative-genetic and phylogenetic approaches in a variety of Drosophila species.
ifkorf@ucdavis.edu Molecular & Cellular Biology
Lab
Genomics & Bioinformatics
 High-throughput technologies are transforming biology, medicine, agriculture, and related fields. Biology is now incredibly data-rich and requires computers to organize and analyze the data. My research program mixes -omic technologies and information technology to make new discoveries in genome structure and function. My lab is highly collaborative, and we always welcome potential research partners. My students can all do lab work and program, and many are co-mentored. Current interests include gene prediction, genome assembly, sequence alignment, DNA-protein interactions, intron function, and epigenetics.
sckowalczykowski@ucdavis.edu Microbiology and Molecular Genetics
Lab

Biochemical mechanism of genetic recombination and DNA repair; DNA helicases and motor proteins; Physical and structural aspects of protein-nucleic acid interactions; Single-molecule biophysics; Nanotechnology; Cancer biology.
dkueltz@ucdavis.edu Animal Science
Lab

Proteomics and physiological genomics of environmental stress adaptation in fishes; Evolution of environmental stress tolerance and phenotypic plasticity; Osmosensory stress signaling in animal cells.
hkung@ucdavis.edu Biochemistry and Molecular Medicine
kit.lam@ucdmc.ucdavis.edu Hematology-Oncology (Int Med)
chlangley@ucdavis.edu Evolution and Ecology
Population genetics and molecular evolution.
jmlasalle@ucdavis.edu Microbiology - Medicine
Lab
Epigenetics of autism-spectrum disorders
 Our laboratory is interested in the role of epigenetics in human autism-spectrum disorders. Epigenetics is the study of heritable changes in chromosomes that are not encoded in the DNA sequence, including DNA methylation and chromatin organization. The clinical applications of our research include understanding the pathogenesis of the neurodevelopmental disorders autism, Rett syndrome, Prader-Willi syndrome, Dup15q syndrome, and Angelman syndrome. We take a “Rosetta’s stone” approach to decoding the elusive etiology of autism by looking for clues in the epigenetic pathways disrupted in rare genetic disorders on the autism spectrum. Our laboratory focuses on understanding the neuronal methylome and a protein that binds to methylated DNA, methyl CpG binding protein 2 (MeCP2). The gene for MECP2 is on the X chromosome and is mutated in Rett syndrome and other neurodevelopmental disorders. In addition, we are interested in the functions of noncoding RNA at the heart of the Prader-Willi locus that are expressed in postnatal neurons. We also are investigating the impact common organic pollutants on DNA methylation and chromatin organization in 15q11-13 duplication syndrome. We have several ongoing collaborations that seek to integrate genetics with fields of Neuroscience, Nutrition, Toxicology, and Epidemiology.
tledig@ucdavis.edu Plant Science
slin@ucdavis.edu Microbiology and Molecular Genetics

Molecular mechanisms of Calorie Restriction and Aging

Regulation of NAD+ metabolism
selott@ucdavis.edu Evolution and Ecology
Lab

Our research focuses on how genetic variation in translated through the developmental process into phenotypes, and how these phenotypes evolve. The importance of sequence changes that affect development to morphological evolution has been well established. But the phenotypic consequences of mutations that alter developmental regulators are often muted by the systems that buffer development against variation encountered in ontogeny. By studying the relationship between mutation and developmental phenotype, we gain insight into both the molecular forces that drive and constrain phenotypic evolution and the systems that keep development robust. To pursue these questions, we use a combination of genetic, genomic, computational, and imaging techniques, primarily in the model system of Drosophila.
wjlucas@ucdavis.edu Plant Biology
Lab

Our lab is interested in the evolution and function of plasmodesmata, the intercellular organelle of the plant kingdom that mediates in both nutrient delivery and cell-to-cell signaling of information macromolecules, including transcription factors and RNA-protein complexes. We are also working on cellular and molecular aspects of virus infection involving transport of infectious RNA/DNA through plasmodesmata, during local infection, and long-distance movement of virus through the phloem for systemic infection within the plant. A major current focus of our lab is the isolation and characterization of the proteins that constitute the supramolecular structure of plasmodesmata.These studies are providing insights into the mechanisms involved in the selective trafficking of proteins/RNA that contribute to supracellular control over plant growth and development. A second emphasis in the lab involves studies on the role of the plant vascular system, and the phloem in particular, as an information superhighway for the delivery of proteins and ribonucleoprotein complexes involved in regulating developmental events in distantly located tissues and organs.
sluckhart@ucdavis.edu Microbiology - Medicine
lalyons@ucdavis.edu Vet Med - Population Health and Reproduction
Lab
pcmack@ucdavis.edu Hematology-Oncology (Int Med)

jnmaloof@ucdavis.edu Plant Biology
Lab

Light is essential for plant growth. Perhaps as a consequence, plants have an intricate set of photoreceptors and responses that they use to optimize their development and physiology to suit their light environment. We study the ways in which plants have evolved differences in their light perception and responses that allow them to thrive in different environments. We are interested in both the genetic and molecular basis of variation in light response as well as the adaptive consequences. A combination of molecular and quantitative genetics is used in Arabidopsis, Tomato, and Brassica
bpmay@ucdavis.edu Animal Science
Lab
jfmedrano@ucdavis.edu Animal Science
Lab
fjmeyers@ucdavis.edu Internal Medicine - Medicine
rwmichelmore@ucdavis.edu UC Davis Genome Center
Genetics and genomics of disease resistance in plants
 Please see website for details
micmiller@ucdavis.edu Animal Science
Genetics and Genomics
 Animal genetics and genomics; conservation and ecological genetics and genomics; genomics and bioinformatics technology development; salmonid fishes.
mmudryj@ucdavis.edu Microbiology - Medicine
Prostate cancer, Retinoblastoma (RB) E2F transcription factors, Androgen Receptor
 Prostate carcinoma is the most commonly diagnosed cancer in men, and the second leading cause of death due to cancer in Western civilization. Androgen ablation therapy is effective in treating androgen-dependent tumors, but eventually, androgen-independent tumors recur and are refractory to conventional chemotherapies. Tumor recurrence is often due to reactivation of androgen receptor (AR) signaling but is also accompanied by deregulation of cell cycle and proliferative controls. The mechanism by which AR promotes proliferation has not been established. The RB/E2F pathways has been shown to be deregulated in prostate tumors, but recent studies indicate that E2F3 overexpression is predictive of a poor clinical outcome. However it is currently unknown how E2F3 contributes to tumorigenesis. My lab is dedicated to defining the molecular mechanisms that govern tumor progression. We currently have three main projects in the lab: 1. Regulation of AR dependent gene expression and cellular proliferation in prostate cancer 2. The interplay between E2F3 overexpression, RB deregulation and the AR in prostate tumorigenesis 3. The role of E2F3B isoform in prostate tumorigenesis
jdmurray@ucdavis.edu Animal Science

My research program is divided between to areas: genetic engineering of mammals and horse genomics. Within the work centered on transgenic animal biology we work on a number of gene systems designed either as research models (ovine growth hormone transgenic mice) or to livestock for use in agriculture. Within the latter area we are focused on manipulating the mammary gland to improve the properties of milk for human consumption. We also carry out work to improve the technology associated with genetically engineering large animals. Mammary gland directed transgenes: The expectation for this work is that the expression of specific transgenes in the mammary epithelium will lead to altered processing properties, changed lipid composition, increased anti-microbial properties, or result in other health-related or economically valuable alterations in the milk. My laboratory’s work principally has been centered on the development and characterization of transgenic mice, then goats, as models for the eventual genetic manipulation of dairy cattle. We have worked on the expression and characterization of transgenic animals expressing human lysozyme, bovine kappa-casein, and the rat stearyol-CoA desaturase. The most advanced work, in collaboration with Dr Elizabeth Maga, concerns the consequences of expressing human lysozyme in the milk of dairy animals. We have an established a herd of human lysozyme transgenic dairy goats and are currently studying the properties of this milk. We are also studying the potential effects of carrying and expressing this transgene on the health and welfare of the animals and the safety of the dairy products for human consumption. In this regard, recent publications report on the effects on the health of the GI tract in young pigs consuming goats’ milk that contains human lysozyme. Bacterial plates showing growth after 48 hours at room temperature in un-pastuerized human lysozyme-containing milk (left) and control milk (right). Improving the efficiency of gene transfer: The laboratory has conducted a number of studies with the goal of developing promoter systems, improved technology, or methods to increase the efficiency of genetic engineering in livestock. Work initially focused on using the bacterial Rec A protein to coat DNA constructs and has since shifted to the application of RNAi to manipulate endogenous protein levels in an attempt to influence the mechanisms responsible for the integration of exogenous DNA. Mapping the Horse Genome: With a colleague in the School of Veterinary Medicine, Dr Cecilia Penedo my laboratory is involved in an international effort to develop genomic tools for use in horse research. We have contributed to international efforts to develop physical and genetic maps of the horse genome and the application of these tools to the identification of loci responsible for traits of interest in the horse. In addition to developing genomic tools we are currently working to determine the genetic basis for the Dun dilution in the horse.
jenatzle@ucdavis.edu Molecular & Cellular Biology
Gene regulation, especially steroid hormone regulation of gene expression in Drosophila. Molecular mechanisms of morphogenesis and differentiation of epithelia during embryogenesis and imaginal disc development at metamorphosis. Drosophila developmental biology and developmental genetics. Identification and characterization of steroid biosynthesis pathways in insects.
dbneale@ucdavis.edu Plant Science
Lab

Genomics, Population Genetics, Landscape Genetic, Complex traits
jan.nolta@ucdmc.ucdavis.edu
amoberbauer@ucdavis.edu Animal Science

Molecular and cellular regulation of bone growth; genetic disorders in the dog
deparfitt@ucdavis.edu Plant Science
ncpedersen@ucdavis.edu Veterinary Medicine
Infectious and immunologic diseases of dogs and cats. Animal models for human AIDS (feline and simian immunodeficiency virus infections).

mlprivalsky@ucdavis.edu Microbiology and Molecular Genetics
Lab

Our research focuses on understanding how cells regulate their proliferation and differentiation and the aberrant events which lead to neoplasia. Our specific goal is a better understanding of the actions of the nuclear receptors (also known as nuclear hormone receptors) in normal cells and in disease. Nuclear receptors are a family of hormone-regulated transcription factors, and include the steroid, retinoid, and thyroid hormone receptors; collectively they play critical roles in vertebrate homeostasis, differentiation, and reproduction. Nuclear receptors bind to specific target genes and modulate gene expression in response to hormones of extracellular origin, Intriguingly, these receptors can either repress or activate transcription by recruiting partner proteins denoted corepressors and coactivators. An alpha-helical domain (helix 12) at the C-terminus of these receptors functions as a hormone-regulated “molecular toggle switch;” by altering its conformation, helix 12 determines whether a corepressor or a coactivator is recruited to the nuclear receptor. Notably, defects in the operation of the helix 12 toggle switch result in aberrant corepressor and coactivator acquisition and, as a result, human disease (including both endocrine and neoplastic disorders). Our research seeks to employ these aberrant receptors as tools to determine the molecular pathways that operate in human diseases and to elucidate the actions of the normal receptors in the normal cell. We are currently investigating the contributions of nuclear receptor function in normal adipose cell differentiation, in thyroid hormone resistance, in leukemia, and in renal clear cell and hepatocellular carcinomas.
brannala@ucdavis.edu Genome Center
Lab
Computational evolutionary and population genomics
 Research in the group focuses on mathematical aspects of population genetics, phylogenetic inference, and human genetics. Topics of interest include statistical methods for linkage disequilibrium gene mapping and Bayesian phylogenetic inference, as well as more general questions in theoretical population genetics. Topics of current research include the role of hypermutability and mutator phenotypes in cancer genetics, multipoint linkage disequilibrium mapping, and methods for detecting an association between genetic markers and disease in heterogeneous populations. A unifying theme of research in the group is the application of analytic theory and computer simulation to address questions of importance in evolutionary biology and human genetics.
pcronald@ucdavis.edu Plant Pathology
Lab
abrose@ucdavis.edu Molecular & Cellular Biology
The effect of introns on gene expression.
 Introns are often dismissed as junk DNA, but they can have huge effects on gene expression through mechanisms that are not yet understood. I am investigating this interesting phenomenon in plants using molecular genetics, and by testing bioinformatic insights generated by Dr. Ian Korf and his group.
lsrose@ucdavis.edu Molecular & Cellular Biology
Lab
Developmental and cell biology of C. elegans, with an emphasis on the control of cell division patterns and polarity.
pross@ucdavis.edu Animal Science
Reproductive biology, gamete and embryo development, epigenetics, somatic cell nuclear transfer, embryonic stem cells, induced pluripotency.
 Our long term research goal is to uncover the mechanisms of epigenetic remodeling orchestrated by the oocyte during early embryonic development and after somatic cell nuclear transfer. We use that knowledge to improve and develop methods of cellular reprogramming for the production of cloned animals for agricultural and biomedical uses, and to create autologous cells for transplantation therapies in animals and humans.
rossibarra@ucdavis.edu Plant Science
Lab

Evolutionary genomics of maize and its wild relatives
jrroth@ucdavis.edu Microbiology and Molecular Genetics
Lab
Origin of Mutations Under Selection
 While natural selection is simple to define, it is difficult to follow in natural settings since small-effect mutations often dictate the sequence of events. The high rate at which small-effect mutations arise seems to underlie a controversy that has continued about whether or not the stress of selective growth conditions induces an increase in mutation rate. We propose that growth limitation seems mutagenic because small-effect mutations are more common than generally appreciated and make an unexpectedly large contribution to selective adaptation. We are trying to dissect in detail one system that is often cited as evidence for stress-induced mutagenesis (adaptive mutation). We think we can convince you that it's all about growth under selection and has nothing to do with mutagenesis.
 A lifestyle that may define a bacterial species
 All Salmonellae dedicate 1% of their genome in synthesis of cobalamin (vitamin B12) and another 1% of their genome to use this cofactor in support of anaerobic growth on two non-fermentable carbon sources -- ethanolamine and propanediol. This constellation of functions must contribute heavily to Salmonella's fitness in a natural setting. Laboratory studies have had difficultly suggesting how these several functions might contribute to success of natural populations. Recently an solution has been suggested by our colleage Andreas Baumler at the UC Davis Medical School. Baumler's lab has shown that these functions contribute together to enhance Salmonella proliferation in an inflammed mouse gut. Salmonella induces gut inflammation and thereby causes the mouse to provide both of the two carbon sources and an repiratory electron acceptor. The inflammed host gut releases ethanolamine and propanediol and oxidizes hydrogen sulfide to tetrathionate which Salmonella can use as electron acceptor. This give Salmonella a source of nutrients that are not availbable to other gut inhabitants. The functions described above (B12 synthesis, ethanolamine and propanediol degradation, tetrathionate oxidation) have been used individually by taxonomists to identify Salmonella. Since essentially all Salmonella isolates show all of the properties, we suggest that these functions may be central to defining the lifestyle that characterizes Salmonellae and selective holds them together as a taxonomic group. Enzymes for catabolizing ethanolamine and propanediol are held within a protein cage or microcompartment that resembles the carboxysome of photosynthetic bacteria. We are trying to determine how this compartment works and how it benefits Salmonella in the wild. We think that understanding this compartment in Salmonella, may help us understand why similar compartments contain enzymes of CO2 fixation in bacteria that perform 30% of the global carbon fixation.
 Recombination as an Inside Job
 While DNA recombination is generally studied by perfoming genetic crosses in the laboratory, the process of recombination is used internally in bacteria, primarily for DNA repair and replication fork restarting. Sexual recombination is very rare in natural populations. We use chromosome rearrangments in Salmonella to learn about recombination mechanisms. Most recently we've found (to our surprise) that gene duplications arise at an extremely high rate and form by a mechanism that does not require recombination. This is despite the general belief that they form by unequal recombination. Many duplications are not simple tandem repeats but contain direct repeats that flank a central third copy positioned in inverse order (a tandem inversion duplication or TIDs). We're testing a model by which TIDs form by a series of events initiated by short palindromic sequences in the normal genome. These are then converted by remodeling deletions into the several types of duplications that are commonly studied.
bnsacks@ucdavis.edu
djsegal@ucdavis.edu UC Davis Genome Center
Lab
• Engineered DNA-binding proteins as therapeutics and molecular tools for genomics.
 Almost every disease has a genetic component. Often this information is used only to determine how condemned a person is to develop disease. We would like to use the genetic information to fix the disease. A guiding principle for our work has been to study how nature does what it does, then attempt to use that knowledge to make useful tools to improve public health, either through increased knowledge or therapeutic intervention. Specific research foci in the Segal Lab revolve around engineering custom zinc finger DNA-binding proteins for specific applications. We also continue to make methodological improvements, many of which have been widely adapted in the field. Specific research foci in the Segal Lab revolve around engineering custom DNA-binding proteins for the following applications: • Genetic variation and human diseases: SNP functions in Coronary Artery Disease • Gene therapy: epigenetic therapy for Angelman and Rett Syndromes • Gene therapy: permanent disruptors of the HIV genome • Zinc finger and TAL effector proteins: targeted nucleases, transposases, transcription factors. • Biology of human zinc finger transcription factors: role of genetic variation • Probes and diagnostic tools of genetic and epigenetic information
Structure/function of DNA-binding proteins and their application in functional genomics and gene therapy; protein engineering of sequence-specific therapeutics and molecular tools that can modify target genes in the human genome.
mfseldin@ucdavis.edu Biochemistry and Molecular Medicine
Lab
Genome based approaches towards defining the etiopathogenesis of disease. Approaches towards defining complex genetic disease in humans and mouse. Genetic mechanisms underlying predisposition
blshacklett@ucdavis.edu Microbiology - Medicine
Lab
frsharp@ucdavis.edu; frank.sharp@ucdmc.ucdavis.edu Neurology - Medicine
Lab
Professor of Neurology
dashaw@ucdavis.edu Plant Science
jbsiegel@ucdavis.edu
nrsinha@ucdavis.edu Plant Biology
Lab
Genetic and molecular analysis of compound leaf development in tomato. Genetic and molecular analysis of epidermal differentiation in corn. Evolution and expression of homeobox genes.
dastclair@ucdavis.edu Plant Science
dastarr@ucdavis.edu Molecular & Cellular Biology
Lab
There are many examples throughout development where nuclei or other organelles migrate to a new position in the cell. Once the nucleus has migrated to the correct location, there are mechanisms to anchor the nucleus there. Defects in nuclear positioning can lead to developmental defects and diseases such as Lisencephaly and Muscular Dystrophy. However, very little is known about the mechanisms of nuclear positioning. We are using the Nematode Caenorhabditis elegans as a model organism to study how nuclei and other organelles are positioned within a cell. We use genetic, biochemical and molecular approaches to study this basic problem in cell biology.
sundar@ucdavis.edu Plant Biology
Lab
For details please see the lab website at
Genetics and molecular biology of plant reproduction. Functional genomics in model plants- Arabidopsis and rice. Bioinformatics of small RNAs. Microbiomes and metagenomics.
msyvanen@ucdavis.edu Microbiology - Medicine
Lab
thtai@ucdavis.edu Plant Science
ftassone@ucdavis.edu Biochemistry and Molecular Medicine
lrteuber@ucdavis.edu Plant Science
Lab
mctorrespenedo@ucdavis.edu Veterinary Medicine
alvaneenennaam@ucdavis.edu Animal Science
Lab
Applied use of biotechnologies in animal agricultural systems
Integrating DNA information into beef cattle production systems to provide beef cattle producers with the background information and research-derived data they need to make informed decisions about the use of DNA-technologies in the context of commercial cow-calf operations. Research and education on the use of animal genomics and biotechnology in livestock production systems Applied use of biotechnologies in animal agricultural systems
awalker@ucdavis.edu Viticulture & Enology
Development of grape rootstocks with resistance to soil-borne pests and development of new disease resistant fruiting cultivars. Current research projects include: development of rapid screens for resistance; determining the inheritance of and mapping resistance to grape pests and pathogens; characterizing the genetic diversity of grape pests; studying the taxonomy and evolution of grape.
chwarden (at) ucdavis (dot) edu Neurobiology, Physiology and Behavior
Lab
My laboratory seeks to identify genes that promote accumulation of body fat. We study humans, mice, and C. elegans. We use a variety of techniques, including genetic mapping, mRNA expr
rwu@ucdavis.edu Internal Medicine - Medicine
Gene expression and regulation in airway epithelium
lfxu@ucdavis.edu Microbiology and Molecular Genetics
Telomeres are the protective nucleoprotein structures at the ends of linear eukaryotic chromosomes. Telomere dysfunction contributes to cancer progression and aging. Our laboratory employs molecular and cytological approaches to study telomere maintenance in human normal cells and cancer cells.
enyamoah@ucdavis.edu Otolaryngology - Medicine
jiyoder@ucdavis.edu Plant Science
Lab
Molecular genetics of plant-plant interactions
kzarbalis@ucdavis.edu Pathology - Medicine
mazern@ucdavis.edu Internal Medicine - Medicine
cjzhou (AT) ucdavis.edu Cell Biology & Human Anatomy
Lab

We are interested in morphogenetic signaling mechanisms of mammalian organogenesis, stem cells, birth defects/congenital diseases, and regeneration
 We study morphogenetic signaling regulation in mammalian development and regeneration. We are primarily interested in tissue/organ morphogenesis that is regulated by several inductive factors such as Wnts. Incorrect activity and timing of morphogenetic signaling during development frequently result in embryonic death or severe birth defects. Currently we are investigating the molecular and cellular mechanisms of several developmental disorders and their prevention strategies using Wnt signaling mutants as the research model. We are also investigating the role of Wnt signaling in tissue/organ-specific stem cells and related regeneration processes to enhance their therapeutic potential.
hzhou@ucdavis.edu Animal Science

Research in immunogenetics, molecular genetics, functional genomics, and bioinformatics. My group is focused on elucidating the molecular and cellular mechanisms of host-pathogen interaction including disease resistance, immune response, and pathogenesis of infection. The overall goals are to understand genetic regulation of host response and basic mechanisms of pathogen virulence in animals, to identify host and pathogen genes that are involved in the host-pathogen interplay. The pathogens of interest are food-borne bacteria such as Campylobacter and Salmonella and avian influenza virus.

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