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University of Colorado Department of Biochemistry and Molecular Genetics

Biochemistry and Molecular Genetics

Kenneth Jones, PhD

Assistant Professor

PhD, University of Illinois – Chicago, IL, 2003

Contact Information:

Phone: (303) 724-3235


Research Interests:

Throughout my career, I have focused on collaborative multi-investigator research where I have applied genetic techniques to solve specific issues. My current research focuses on the fields of Ecological and Environmental Genomics, where ecological aspects describe the direction and amplitude of phenotypic variation and genomic aspects seek to determine the genetic pathways that influenced those phenotypes. I have personally conducted work on a diverse array of taxa including bacteria, fungi, plants, vertebrates, and invertebrates, including some highly endangered taxa. I have recently been involved with the use of genomic techniques to facilitate ecological or genetic projects that would not be feasible without such approaches. I am currently involved in using massively parallel DNA sequencing techniques to assay bacterial and fungal diversity in various field projects, as well as using the same technology to map genomes and sequence transcriptomes. My unique skill set provides the ability to use existing molecular tools to develop molecular tools and approaches where none exist (e.g., high density genomic maps and transcription profiling for de novo species). Using a combination of high-throughput sequencing and traditional approaches, I am now poised to address fundamental ecological/evolutionary questions (e.g., hot/cold tolerance, hybrid variation in body morphology, genomic/genetic selection, etc.) on basically any species of interest.

In addition to my own research, a major component of my current position at the University of Colorado (and previously at UGA’s Georgia Genomics Facility) is to collaborate with other researchers, where I assist in the design, implementation, and analysis of next-generation sequencing data. In that capacity, I have been appointed as the Co-Director of the University of Colorado Cancer Center’s Biostatistics and Bioinformatics Shared Resource, where I lead the bioinformatics group.

Current Research:

Environmental and Ecological Genomics
Effects of low dose radiation on gene expression in Medakafish
Sensitivity to radiation varies significantly among different cell types and among families. To understand the variation in radiosensitivity among families, we established breeding pairs of medaka and collected offspring to observe pre-exposure mutation rates. The same pairs of fish were then exposed to varying levels of acute Cobalt-60 irradiation (0 – 5 Gy). Resulting offspring were then collected and assessed for mutation rates at microsatellite DNA loci. As expected, mutation rates of STRs increase with level of irradiation, but vary significantly among families. Based on these results, we are now investigating the genomic effects of exposure. We have produced EST libraries from exposed and non- exposed fish and are using a combination of 454 and Illumina sequencing to directly quantify the effects of radiation exposure on gene transcription (e.g., mRNA-seq). This study will provide data on the level of genomic effect across various exposure rates. We hypothesize DNA repair mechanisms are especially sensitive to irradiation, where the dysfunction in repair leads to an increased mutation rate.

Transcriptomic effects of living in a contaminated environment
Chronic exposure to environmental contaminants can cause effects at higher levels of biological organization such as populations and communities. However, due to inherent challenges in assessing these impacts most studies focus on individual survivorship under acute exposure. To assess the long- term effects of contaminant exposure it is critical to examine sub-lethal endpoints, and the potential for organisms to adapt to contaminated environments. We are investigating the relevance of sub-lethal endpoints in amphibians exposed to copper contamination. We are using RNASeq approaches to look at the transcriptional changes that may be related to sub-lethal effects and possible contributors to differences in survival and other life history endpoints. In our amphibian studies we are examining three species: Southern leopard frogs (Lithobates sphenocephalus), Southern toads (Anaxyrus terrestris), and Eastern narrowmouth toads (Gastrophryne carolinensis). We have found significantly different sensitivities to chronic copper exposure at the individual, population, and species levels. We are currently investigating the effects of copper exposure on the transcriptome of developing Southern toads from several individuals from two populations throughout egg, larval, and post-metamorphic development.

Population/Conservation Genetics
Empirical relatedness estimation based on microsatellite DNA genotypes
My Master’s work sought to refine genetic management of the endangered Whooping Crane population by developing comprehensive genetic pedigrees for the captive population. Improvements to the pedigree were accomplished by incorporation of founder similarity coefficients calculated from microsatellite DNA profiles. Incorporation of microsatellite “relatedness” coefficients provided information on background relatedness not previously realized and led to a view of the population structure that would be expected for a severely bottlenecked population. Similar approaches are currently being utilized for the Masked Bobwhite and Mississippi Sandhill Crane captive breeding programs. As an addendum to this, I have recently received funds to genotype the Whooping Crane population using Next-Gen sequencing and RAD-tag technology to discover SNP loci. From this information, thousands of SNP loci will be genotyped to determine fine-scale relatedness in this highly endangered species.

Current Lab Colleagues

 Results From Research : Selected site and subsites
PicturesLast NameFirst NameJob TitleEmailBio Page
FarrellDavidSenior Professional Research