Genetics and Genomics
Tahmer Ahmed, MD, PhD
Department of Population Health & Reproduction
I am a geneticist/bioinformatician focused on making use of the immensely growing Next Generation Sequencing data to understand, diagnose and treat biological disorders. I have contributed to multiple genomic resources including the chicken genome and a tissue-specific equine transcriptome. Also, I participated in large-scale sequencing efforts for gene discovery, using multiple animal models, including the dog, horse and cow. In addition, I collaborated in the development of software algorithms and platforms to detect sequencing errors, visualize structural variants, detect gene fusions, and identify novel transcriptomic structures. I am eager to collaborate with one of our STAR students on using new bioinformatic approaches a creative analysis of publicly available. In this project, he/she should 1) Learn how to search for publicly available RNAseq data for a phenotype of interest. 2) Benchmark classical RNAseq expression analysis techniques against the new alignment free approaches. 3) identify possible novel transcriptomic structures associated with our phenotype.
Please email me at tahmed@ucdavis.edu.
Website: https://scholar.google.ca/citations?user=xo-4__IAAAAJ&hl=en
Monica Aleman
Department of Medicine & Epidemiology; VMTH: Large Animal Clinic (see also: Internal Medicine, Neurology)
Dr. Monica Aleman obtained her veterinary degree at the University UNAM-Mexico. She completed residencies in large animal internal medicine (equine emphasis) and neurology and neurosurgery at UC Davis; and achieved board certification for both specialties by the American College of Veterinary Internal Medicine. She completed a PhD in comparative pathology of neuromuscular diseases at UC Davis. Her research and clinical interest has focused in neurology, neuromuscular and muscle disorders in all species with equine emphasis. Currently, she is a faculty member of the equine internal medicine and neurology services, and Director of the Neuromuscular Disease Laboratory at UC Davis. Dr. Aleman is one of the founding members of the Comparative Neurology Research Group, and is affiliated with the Clinical Neurophysiology Laboratory at UC Davis. Dr. Aleman is author of over 90 peer reviewed medical publications, over 100 proceedings and abstracts, and over 25 book chapters; and is a regular speaker in national and international meetings. Currently, she works in the investigation of neuromuscular disorders in multiple species including humans.
For more information, please contact Dr. Aleman at mraleman@ucdavis.edu or visit her faculty profile page.
Danika Bannasch
Canine and Equine Genetics
Department of Population Health and Reproduction
The Bannasch laboratory focuses on understanding the molecular mechanism of inherited naturally occurring diseases in companion animals. Prior to genome assemblies, my group successfully positionally cloned the gene for hyperuricosuria in dogs, and HERDA in horses. We subsequently successfully utilized genome wide association as a technique to determine the chromosomal location of many Mendelian and non-Mendelian disorders. Positional candidate genes were interrogated to define causal variants (Addison’s disease, Alaskan Husky encephalopathy, hoof wall separation syndrome, spinal dysraphism, Saluki encephalopathy, cleft palate and cleft lip, palate and syndactyly). We more recently have utilized whole genome sequencing approaches to define disease causing variants following GWAS (DCM and sudden death, an animal model of Robinow syndrome and coat color variants). We have also identified an unusual structural variant, an FGF4 retrogene, underlying canine chondrodystrophy and intervertebral disc disease. We followed this research with a molecular and bioinformatic investigation of retrogenes in animals. We identified and cataloged over 2000 canine retrogenes which are much more common than human or equine retrogenes. We continue to pursue this research through investigation into canine transposable elements (LINE-1) that mediate retrogene formation.
I really enjoy having summer research students. Depending on the project, students will gain experience in both wet lab molecular genetics techniques and running genetic analysis programs.
Please contact Dr. Bannasch via email at dlbannasch@ucdavis.edu.
Rebecca Bellone
Equine genetics and genomics
Department of Population Health and Reproduction
Veterinary Genetics Laboratory
Dr. Bellone is a molecular geneticist whose research interests include elucidating the genetics of economically and medically important traits in the horse as well as traits that serve as models for other species. Current projects in horses involve investigating the genetic and molecular basis of several ocular disorders and in some cases associated pigmentation phenotypes. Recently her laboratory discovered the genetic risk factor for the second most common tumor of horses, ocular squamous cell carcinoma. Other findings include identifying the genetic mechanisms for congenital stationary night blindness in multiple horse breeds, as well as distichiasis in Friesian horses. Currently her collaborative research team is trying to identify the genetic risk factor for equine recurrent uveitis, the leading cause of blindness in horses, among other projects. The primary research goal is to develop DNA diagnostic tests that assist animal breeders in making informed mating decisions and work towards better clinical management practices, by understanding the biological mechanisms behind complex heritable traits. Dr. Bellone is passionate about training and working closely with students in her laboratory to assist them in making significant contributions to these projects.
For more information please visit Dr. Bellone’s website at https://vgl.ucdavis.edu/research/bellone
Please email Dr. Rebecca Bellone (rbellone@ucdavis.edu) for more information.
Elva Diaz, PhD
Med: Pharmacology (see also: biochemistry, neuroscience and pharmacology/toxicology)
Dr. Diaz is trained in molecular and cellular biochemistry and functional genomic approaches to understanding nervous system development. The two main areas of interest are neural proliferation and synaptic differentiation in rodent model systems. The Diaz lab uses genomic approaches such as DNA microarrays to identify genes differentially regulated in nervous system development. Individual candidates genes are studied with molecular and cellular techniques including primary neuronal culture, immunocytochemistry, electrophysiology, and transgenic mouse models. Potential projects include: 1) understanding the role of transcription factors during neural proliferation in the cerebellum and potential implications for diseases such as brain tumors; 2) dissecting the role of a novel family of transmembrane proteins in synapse development and potential implications for neurological diseases such as mental retardation and schizophrenia.
Please visit Dr. Diaz's website for more information. Email at ediaz@ucdavis.edu.
Kristin Grimsrud, DVM, PhD
Assistant Clinical Professor, Dept of Pathology, School of Medicine
Associate Director of Vivaria and Veterinary Care, Mouse Biology Program (MBP)
(See also: Anesthesia/Pain Management, Pharmacology/Toxicology, Translational Research)
Dr. Grimsrud is a laboratory animal veterinarian and her research focuses on translational medicine and animal model optimization and development. Her current major research efforts are in collaboration with the Knockout Mouse Project, Metabolic Mouse Phenotyping Center and Mutant Mouse Resource and Research Center. Additionally, she is involved in a variety of microbiota bariatric surgery research projects that utilize mouse models. Lastly, Dr. Grimsrud has a strong interest in translational clinical pharmacology where she investigates variation in pharmacokinetics and pharmacodynamics in special populations (e.g. burn patients, pediatrics) and assess the influences of polymorphisms on drug efficacy.
Research projects that students could be involved with relate to studies to optimize anesthesia and analgesia protocols, optimizing superovulation techniques in rodents and a variety of other projects related to the genetically engineered rodent models and microbiota/gnotobiotic research.
Contact Information:
Email: kngrimsrud@ucdavis.edu
Office Phone: 530-757-3220
Carrie Finno, DVM, PhD, Diplomate ACVIM (Large Animal Internal Medicine)
Equine Genetics
(see also: Neurology/Neurobiology)
Dr. Finno investigates the molecular basis for genetic diseases in the horse and other companion animals. One of the strong translational focuses of Dr. Finno's laboratory is to investigate the role of vitamin E in neurodegeneration using a well-established mouse model and a naturally-occurring model of equine neuroaxonal dystrophy (eNAD) in the horse. The laboratory also focuses on the inherited bases of many genetic diseases in the horse including juvenile idiopathic epilepsy (in conjunction with Dr. Monica Aleman) and occipitoatlantoaxial malformation, among other diseases. Dr. Finno's research is funded by the NIH, Grayson Jockey Club Foundation and the Center for Equine Health at UC Davis. Her laboratory incorporates clinical research in the field with molecular tools in the laboratory. Website: https://www.vetmed.ucdavis.edu/labs/finno-laboratory
Please contact Dr. Finno for more information: cjfinno@ucdavis.edu
Cecilia Giulivi
VM: Molecular Biosciences (see also: biochemistry and neuroscience)
Bioenergetics: changes in intermediary metabolism with diets deficient of essential amino acids. Role of mitochondria dysfunction in Huntington's disease. Fragile X, ataxia and tremor syndrome. Autism Neurodegeneration in Alaskan huskies Type 2 diabetes. Role of mitochondria in different organs during prediabetes and diabetes. Citrullinemia: changes in nitric oxide pathways in cerebellum. Aging and protein nitration, oxidative and nitrative stress pathways.
Research: My laboratory focuses at understanding the mechanisms of mitochondrial dysfunction in a variety of phisiopathologies such as triplet nucleotide diseases (Huntington's disease. Fragile X, ataxia and tremor syndrome), autism, and metabolic diseases (diabetes, essential amino acid deficiency, thiamine deficiency). We use a variety of techniques ranging from biophysics and biochemistry to molecular biology including in silico modeling.
Please visit Dr. Giulivi's website at: http://faculty.vetmed.ucdavis.edu/faculty/cgiulivi/
Hong Ji, PhD
California National Primate Research Center
(See also: Pulmonary Medicine)
The main interest of Dr. Ji’s research group is to elucidate the epigenetic basis of chronic diseases and examine the impact of environmental exposures. We utilize an integrative approach combining methylome, chromatin, gene expression and gene network analysis to identify genes and pathways that may contribute to disease pathogenesis. We perform our research in animal models (rodent and rhesus monkey), cell culture, and human biological specimen. Our current research focuses on understanding the epigenetic regulation of heterogeneous asthma phenotypes and how the epigenome mediate the impact of environmental exposures on disease risk.
Email: hgji@ucdavis.edu
Sree Kanthaswamy, Ph.D.
California National Primate Research Center
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.
Please contact Dr. Kanthaswamy at skanthaswamy@ucdavis.edu for further information.
Sina Marsilio, Dr. med. vet., PhD, DACVIM (SAIM), DECVIM-CA
VM: Medicine and Epidemiology
(see also: GI Physiology/Gastroenterology, Microbiology/Parasitology)
I am a small animal internist with a special clinical and research focus in small animal gastrointestinal diseases. My current research focuses on the intestinal microbiome and its disruption during acute and chronic intestinal diseases. In addition, I am currently launching several projects on the use of fecal microbiota transplantation as a therapeutic tool for intestinal disease. I am also actively involved in translational research using stem cells in animals with gastrointestinal disease. I am looking forward to mentor students with an active interest in small animal gastrointestinal and translational research and who would like to be involved in clinical research projects.
Please email Dr. Marsilio for more information: smarsilio@ucdavis.edu
Mike Mienaltowski, DVM, Ph.D.
Tendon repair, stem/progenitor cell biology
College of Agriculture and Environmental Sciences (See also: Orthopaedics/Biomechanical Engineering, Biochemistry/Cellular Biology, and Translational Research)
My primary research interests include:
(1) the development, maturation, and repair of musculoskeletal connective tissues like tendon and ligament
(2) cellular mechanisms behind broiler muscle pathology
(3) the roles of the microbiome in proper gut transition in foals from birth to weaning.
In my musculoskeletal research projects, I am particularly interested in how differences in niche affect cells within the environment in growth and repair. Moreover, I am interested in the physiology of usage and elite performance as well as pathophysiology from over-usage, acute and chronic injury for all musculoskeletal tissues on all species as they might be related to use, environment, or genetics, and as they might be related to the manipulation of niche and collagen regulation genes. Furthermore, because the proper development of the musculoskeletal system depends greatly upon proper foal growth and foal growth subsequently depends upon appropriate nutrition, I am interested in understanding how gut microbes facilitate healthy gut transitions in the foal.More information can be found at: http://animalscience.ucdavis.edu/faculty/mienaltowski/index.html
Contact information for Dr. Mienaltowski: e-mail: mjmienaltowski@ucdavis.edu
Emmanuel Okello, BVM, MSc, PhD
VMTRC
(see also: Microbiology/Parasitology, Epidemiology)
Dr. Emmanuel Okello is an Assistant CE Specialist in Antimicrobial Stewardship at UC Davis, School of Veterinary Medicine. The goal of his research and extension program is to develop antimicrobial stewardship guidelines and best management practices that reduce antimicrobial resistance while maintaining the health and welfare of the herds and flocks. Okello’s specific areas of interest include the use of alternatives to antibiotics to control infectious diseases in livestock, development and evaluation of vaccines and rapid diagnostics tests, and improved management practices for disease prevention.
Please contact Dr. Okello for prospective STAR projects (eokello@ucdavis.edu). Website: https://www.vetmed.ucdavis.edu/faculty/emmanuel-okello
Richard Pereira, DVM, PhD
SVM: Population Health and Reproduction
(See also: Epidemiology, Food Animal Medicine/Food Safety, Microbiology/Parasitology)
Dr. Pereira research focuses on evidence based medicine on antimicrobial resistance in livestock and judicious use of antimicrobials through interventions that promote livestock health and well-being. Maintaining the effectiveness of antimicrobial drugs to treat infections is of relevance to the health of both animal and human populations. Recent project investigated enteric microbiota of calves using metagenomic sequencing approaches, and herd management impacts on prevalence of resistant enteric bacteria, including evaluation of drug use, feeding practices, and housing management of dairy calves and heifers.
Epidemiology is the foundation of his research which also employs statistics, microbiology, and molecular and genomic approaches. Using these tools, some current research projects include investigating and identifying risk factors for selection and spread of antimicrobial resistance in Salmonella from livestock, and investigating impacts on drug resistance and animal health from feeding pre-weaned calves waste milk (milk containing drug residues) with the aim of identifying interventions to reduce unwanted impacts from this practice.
Previous projects accomplished include:
Spatial-temporal trends in antimicrobial resistant Salmonella isolates recovered from Northern California dairy cattle at a veterinary microbiology laboratory between 2002 and 2017.
Potential 10 week projects for Summer 2018:
Antimicrobial resistance in bacteria causing metritis in dairy cows.
Evaluation of on-farm factors affecting antimicrobial drug on the dairy farms.
Contact information: rvpereira@ucdavis.edu
Please visit Dr. Pereira's website at: www.vetmed.ucdavis.edu/faculty/results.cfm?fid=22811
Benjamin Sacks, Ph.D.
Veterinary Genetics Laboratory, Canid Genetics & Population Health
(See also: Wildlife/Exotic Animal Medicine/Zoonoses)
The Canid Diversity and Conservation Laboratory specializes on ecology and conservation of wild canids and other carnivores, including the application of genetic techniques, disease surveillance, and field methods (see web site below). STAR students will initially learn necessary skills from students, technicians, and faculty, and will spend most of the summer collecting data for their project under faculty supervision.
Dr. Sacks can be reached via email at bnsacks@ucdavis.edu, or you can visit his website for more information.
David J. Segal, Ph.D.
Genome Center, Biochemistry and Molecular Medicine, Pharmacology, and MIND Institute
(See also: Neurology/Neurobiology, Translational Research, Biochemistry/Cellular Biology)
Research in the Segal Lab revolves around engineering zinc finger, TALE, and CRISPR/Cas nucleases and transcription factors. 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. We continue to develop new methodologies for genome editing. Our most recent efforts focus on creating epigenomic editing tools that can precisely manipulate epigenetic information at specific loci. Such tools can be used for the long-term control of gene expression for both research and therapeutic applications. Angelman syndrome is a rare neurogenetic disease that is the textbook example of an imprinting disorder. We are using artificial transcription factors to activate the epigenetically silenced gene in in the brains of mice and other animal models.
Please visit Dr. Segal's website at: http://www.ucdmc.ucdavis.edu/biochem/faculty/segal/index.html
Bart Weimer, PhD
(see also Microbiology)
Dr. Weimer is a microbiologist that combines genomics to study the intersection between the host and microbiome. This ranges from single organisms that are zoonotic to the complex microbiome communities of various tissues of animals and humans. He leads the 100K Pathogen Genome Project that is focused on population microbial genomics to understand genomic diversity of infectious microbes but also virulence, antimicrobial resistance, zoonotic transmission dynamics, clinical diagnostics, and global traceability. This project also provides a basis for reference genomes for metagenomic studies that integrate metabolism and host association that impact health and disease.
His group studies problems that range from single gene and single organism disease impacts on disease and diagnostics to community interactions that impart host changes via small molecules between the epithelium and distant tissues. His work with bacterial/stem cell interactions is one model for movement of bacteria between different sites in the body. His group ranges from bench experiments to population bioinformatics to metabolomics of microbial systems.
Some focus areas for his lab are: Salmonella diversity, Campylobacter zoonoses between wildlife, animals and humans, as well as infectious organisms from horses, ruminants, and feed. He is also interested in respiratory diseases, gut/brain interactions, epithelial microbiome, and the molecular methods that the microbiome uses to alter the host response. He uses food and infection to also understand how bacteria persist in chronic infections as well as the environment.
Dr. Weimer can be reached via email.