Edwin Oh

We are a research group that thrives on collaboration. Through our interactions with collaborators, public health labs, and patients we have developed a research program that interrogates the following themes:

1) Wastewater genomics and COVID-19

Wastewater testing has been used for years to investigate viral infections, to study illicit drug use, and to understand the socioeconomic status of a community based on its food consumption. While tools are in place in many states to evaluate the presence of specific viral strains, the community has not needed previously to collaborate on a global scale to standardize procedures to detect and manage COVID-19 transmission. In response to this challenge, our laboratories in Arizona, Nevada, and Washington have developed collection techniques and genomic and bioinformatic approaches to harmonize and visualize the impact of SARS-CoV-2 infection and viral mutation rates in communities populated by local citizens and international tourists. Our findings will contribute to the development of best practices in sampling and processing of wastewater samples and genomic techniques to sequence viral strains, an area required for environmental surveillance of infectious diseases, and has the strong potential to improve the clinically predictive impact of the viral genotype on patient care and vaccine utility.

2) Rare neurological conditions

An association between the 16p13.2 copy number variation deletion and seizures has suggested that a) systematic suppression of each of genes in the loci might yield similar neurological phenotypes seen in the 16p13.2 deletion; and b) such genes might be strong candidates for harboring rare pathogenic point mutations. Through these studies, we discovered USP7 as a message capable of inducing abnormal neurological activity in brain organoids, cultured neurons, and loss-of-function mouse models. Together with collaborators at the Foundation for USP7-Related Diseases (www.usp7.org), our studies are centered on the mechanism by which USP7 gene dosage and rare variants can induce pathology. In addition, we have also identified other gene loci that mimic USP7-related disorders in human and animal models.

3) Ciliary biology and neurodevelopmental conditions

Large-scale studies have begun to map the genetic architecture of Schizophrenia. We now know that the genetic contribution to this condition arises from a variety of lesions that include a) rare copy number variants (CNVs) of strong effect; b) common non-coding alleles of mild effect; and c) rare coding alleles that cluster in biological modules. The challenge that has emerged from these studies is the requirement for large sample sizes to detect significant genetic signals. These findings intimate that SZ is genetically heterogeneous and manifesting potentially as a clinically heterogeneous group of phenotypes with discrete physiological drivers. To address this challenge and to complement the ongoing sequencing effort of cross-sectional SZ, we propose to sample individuals with extreme phenotypes (i.e., resistant to treatment: TRS) to potentially discover an enrichment of causal rare variants which would have otherwise not been observed or been difficult to detect in a large, random sampling of SZ. In addition, we will focus on the role of a specific biological module, the pericentriolar material (including the centrosome, basal body, and primary cilium) and how it relates to the development of the brain and behavior through the genomic and functional dissection of PCM1.

David Alvarez-Ponce

Assistant Professor, University of Nevada, Reno, 2014 – present

Juan de la Cierva Postdoctoral fellow, Consejo Superior de Investigaciones Cientificas, Spain, 2012-2014

Postdoctoral fellow, Trinity College Dublin, 2012

Postdoctoral researcher, National University of Ireland Maynooth, 2010-2012

See our lab webpage for research description: https://genomeevol.wordpress.com

Jeffery Shen

Dr. Shen’s research focuses on development of databases and bioinformatics tools for genome analyses and gene annotations, predictions of genes responsive to environmental/developmental cues, and predictions of gene functions (subcellular localization, and protein motifs). Another focus of my research is the molecular mechanism controlling plant responses to abiotic stresses, seed dormancy and germination. He is also interested in the mechanism underlying tissue-specific and developmentally-regulated gene expression.

The recent accomplishment in sequencing the genomes of thousands of organisms, including human being and important crops such as rice, is leading to a revolution in scientific research, medicine discovery, and improvement of the quality of our food. His lab is interested in developing (adopting, modifying, and inventing) bioinformatics tools for genome analyses and gene ontology studies. Gene ontology addresses: Biological Process (Why is this, such as cell enlargement, being done?), Molecular Function (What kind of molecule is this? Enzymes or transcription factors?), and Cellular Component (Where is this located? Nuclei or Mitochondria?).

Brian Hedlund

Dr. Brian Hedlund is a Professor in Life Sciences at the University of Nevada, Las Vegas.  Hedlund’s research focuses on the microbiology and biogeochemistry of geothermal ecosystems, the genomic exploration of “microbial dark matter”, and the role of the intestinal microbiome in prevention of Clostridium difficile infection. Dr. Hedlund is editor for Antonie van Leeuwenhoek journal, a member of Bergey’s Manual Trust, and editor for Bergey’s Manual of Systematics of Archaea and Bacteria, the authoritative reference manual for microbial taxonomy.