The DNA Laboratory

The DNA laboratory provides research and teaching space for faculty and students at Weber State University. The laboratory comprises 1800 sq. ft. of space distributed among four rooms. Major equipment includes:

      -      Bio-Rad digital imaging system
-       Eppendorf Mastercycler ep RealPlex RT thermocycler
-       Waters HPLC system
-       Perkin-Elmer liquid scintillation counter
-       Agfa X-ray film developer
-       networked Macintosh and PC computers
-       software for DNA sequence analysis and phylogenetic inference
-       equipment for nucleic acid and protein gel electrophoresis
-       high-speed and preparative centrifuges
-       visible-ultraviolet spectrophotometer
-       UV-crosslinker and hybridization oven
-       laminar-flow sterile hood
-       incubators, refrigerators, and freezers

Techniques Employed

Much of the work in the DNA Laboratory is based on the polymerase chain reaction (PCR). PCR mimics the normal process of DNA replication and, when used in the laboratory, results in the amplification of DNA associated with a gene of interest. This provides a sensitive technique for studying a variety of problems in molecular genetics. Other techniques employed in the lab include DNA cloning, polytene chromosome in situ hybridization, DNA sequencing, protein electrophoresis and western blotting.

Current Projects
Research in the DNA Laboratory is primarily concerned with the analysis of genetic variation in natural populations of animals. The primary research subject is the model genetic organism, the fruit fly, Drosophila. A focus of the laboratory is the study of transposable elements (TEs), genes that are capable of moving from one location in the genome to another. Occasionally, TEs move from one organism to another, a process known as horizontal transfer. Far from curiosities, TEs are a component of all eukaryotic genomes and in some species account for a significant portion of the DNA found in the nucleus. Research in the DNA laboratory is investigating their role in shaping the structure of eukaryotic genomes, and the mechanisms by which TEs are maintained in the genome over evolutionary time.

The research projects in the DNA Laboratory involve undergraduate students from Weber State University and collaborations with a number of faculty at Weber State and elsewhere. The following summarizes recent and current research efforts.

1. The Structure of Chromosome Ends in Drosophila.
Collaborator: Dr. Rosa de Frutos, University of Valencia, Spain

The ends of eukaryotic chromosomes, known as telomeres, perform two vital functions in the cell. First, they maintain the integrity of the ends of linear chromosomes, which tend to shorten each cellular generation. Second, they distinguish normal chromosomes from those that have broken ends as a result of mutation. In most eukaryotes, including humans, telomeres consist of a simple nucleotide sequence that is repeated hundreds or thousands of times. In Drosophila, telomeres are formed by a transposable element known as HeT-A. Using PCR, in situ hybridization and DNA sequencing, we are investigating the distribution and origin of this novel telomere structure. (Ostler, 2001; Freidekind, 2002; Bentley, 2002; Bentley et al., 2002; Lindley et al. 2005; Clark 2007; Llorens et al. in review)

2. Genetic Diversification of Brine Flies of the Great Salt Lake.
Brine flies (family Ephydridae) are among the most conspicuous components of the Great Salt Lake ecosystem. The flies are essential to the ecology of the lake, removing organic matter and providing food for millions of birds. Historically, two species of brine flies have been identified in the lake. Using a highly variable DNA marker, we have identified at least three additional species. We are interested in the distribution of these flies and their relative abundance in various regions of the lake. It is also possible that additional species, as yet unidentified, also exist in the Great Salt Lake ecosystem. (Gabrielsen and Clark, 2005a; 2005b; Suurmeyer and Clark, 2005; Oney, 2007; Oney and Clark 2007)

3. The Evolutionary History of P Elements in Drosophila.
Collaborators: Dr. Joana Silva, The Institute for Genomic Research (TIGR), Rockville, MD

The P element in Drosophila is among the best-studied eukaryotic transposable elements. We are continuing an on-going project that examines the evolutionary history of this TE in the genus Drosophila. DNA sequences of P elements from a number of different species are used to construct a phylogeny of the TEs. We have identified several major transition events in P element evolution, including instances in which the P element has been transferred horizontally between different species. This analysis is currently being extended to flies in other drosophilid genera. (Clark et al., 2002; Silva et al., 2004)

4. DNA Bar Coding and Molecular Species Identification.
Both drosophilids and brine flies are characterized by tremendous diversification over a relatively short time span, resulting in individual species that are morphologically similar. Differences among species can be revealed with carefully-chosen genetic assays, known as DNA bar codes. We use the highly-variable region know and ITS-1 to provide a simple, inexpensive diagnostic test that is able to unambiguously distinguish closely-related species of Drosophila. (Colton and Clark, 2001; Anderson and Clark, 2003; Anderson and Clark, 2004). We are extending this analysis to brine flies by including mitochondrial DNA sequences.

References

Anderson, A. and J.B. Clark. 2003. Distinguishing closely-related species of Drosophila using DNA fingerprinting. Undergraduate Research Conference, Weber State University, Sept. 26, 2003.

Anderson, A. and J.B. Clark. 2004. Distinguishing closely-related species of Drosophila using DNA fingerprinting. Annual Undergraduate Research Symposium, Weber State University, March 29, 2004.

Bentley, M.J. 2002. Molecular phylogeny of the Het-A transposable element in the melanogaster species subgroup of Drosophila. Senior Thesis, Department of Zoology, Weber State University. (J.B. Clark, faculty advisor)

Bentley, M.J., J.W. Wilson, and J.B. Clark. 2002. Molecular phylogeny of the HeT-A transposable element in the melanogaster species subgroup of Drosophila. Molecular evolution: A meeting on evolution, genomics, and bioinformatics (Organized by Society for Molecular Biology and Evolution). Sorrento, Italy. June 13-16, 2002.

Clark, J.B. 2007. Extreme sequence divergence of the telomere-associated transposable element, HeT-A, in Drosophila. Annual meeting of the Society for Molecular Biology and Evolution, Halifax, NS. June 23-28, 2007.

Clark, J.B., J.S. Silva, and M.G. Kidwell. 2002. Evidence for horizontal transfer of P transposable elements. In: Horizontal Gene Transfer, second edition. M. Syvanen and C. Kado, eds. pp. 161-171. Academic Press, London.

Colton, L. and J.B. Clark. 2001. Comparison of DNA isolation methods and storage conditions for successful amplification of Drosophila genes using PCR. Dros. Info. Service 84:180-182.

Freidekind, Olga. 2002. Practical training protocol: In situ hybridization to polytene chromosomes in Drosophila. Diplomate thesis, University of Heidelberg, Germany. (J.B. Clark, faculty advisor)

Gabrielsen, E.J. and J.B. Clark. 2005a. Genetic identification of brine flies of the Great Salt Lake. Annual Undergraduate Research Symposium, Weber State University, March 28, 2005.

Gabrielsen, E.J. and J.B. Clark. 2005b. Initial genetic characterization of brine flies of the Great Salt Lake. Council on Undergraduate Research, “Posters on the Hill”, Washington, DC, April 19, 2005.

Lindley, K., J. Bambrick, and J.B. Clark. 2005. Molecular phylogeny of the telomere-associated transposable element, HeT-A, in Drosophila. Society of Systematic Biologists, Annual Meeting, Fairbainks, AK, June 11-14, 2005.

Llorens, J.V., I. Martínez-Garay, J.B. Clark, R. de Frutos and M.J. Martínez-Sebastián. The gypsy endogenous retrovirus maintains potential infectivity in several species of  Drosophilids. J. Molec. Evol. In review.

Oney, B.J. 2007. The utility of the ITS-1 region in assessing genetic variability in the brine fly, Ephydra gracilis. Senior Thesis, Department of Zoology, Weber Sttae University. (J.B. Clark, faculty advisor).

Oney, B.J. and J.B. Clark. 2007. Genetic variation in natural populations of the Great Salt Lake brine fly, Ehydra gracilis. Nacional Conference on Undergraduate Research, Dominican University. April 12-14, 2007.

Ostler, C. 2001. Identification of a HeT-A transposable element in Drosophila teissieri. Senior Thesis, Department of Zoology, Weber State University. (J.B. Clark, faculty advisor)

Silva, J.S., E. L. Loreto, and J.B. Clark, 2004. Factors that affect the horizontal transfer of transposable elements. Current Issues Mol. Biol. 6:57-72  Suurmeyer, E. and J.B. Clark. 2005. Genetic studies of brine fly diversification in the Great Salt Lake. Sigma Xi, Annual Meeting and Student Research Conference, Seattle, WA, November 3-6, 2005.