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David Carlini

Associate Professor
Department of Biology

  • I am broadly interested in molecular evolution and empirical population genetics. The main research focus of my lab is on the functional significance of genetic variation in protein-coding genes. We are particularly interested in synonymous variation, as it may impact translational accuracy and/or efficiency, as well as mRNA splicing and stability. The main ongoing projects in my lab include: 1) experimental manipulation of codon bias in bacteria, 2) analysis of codon usage in hemimetabolous and holometabolous insect genomes, 3) synonymous mutation rates in proto-oncogenes and tumor suppressor genes, and 4) transcriptome profiling of cave and surface populations of the freshwater amphipod Gammarus minus, with an aim toward identifying genes undergoing divergent modes of natural selection in the two habitats.
  • Degrees

    PhD, College of William and Mary
    MS, Florida Institute of Technology
    BA, University of California, Santa Barbara
  • OFFICE

  • CAS - Biology
  • Hurst - 112B
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Teaching

Scholarly, Creative & Professional Activities

Research Interests

       
  • Molecular evolution, population genetics, & molecular systematics.

Honors, Awards, and Fellowships

       
  • Cave Conservancy of the Virginias. Evolutionary genetics of opsin visual pigment genes in cave and surface populations of the freshwater amphipod Gammarus minus. (2011-2012)
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  • National Science Foundation. Functional analysis of the codon bias in Adh gene of Drosophila melanogaster.(2003-2008)
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  • LI-COR Genomics Education Program (2005)
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  • NOAA Sea Grant.Phylogenetic Systematics and Cepalopod Biodiversity (1998-1999)
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  • National Science Foundation Doctoral Dissertation Enhancement Award (1996-1999)

 

 

Work In Progress

       
  • Experimental evolution of codon bias in Escherichia coli.
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  • Comparative molecular evolution of genes in cave and surface spring populations of the freshwater amphipod Gammarus minus.
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  • Computational analysis of codon bias and gene ontology in the genomes of holometabolous and heterometabolous insects.

 

Selected Publications

  • Carlini DB, Satish S, and Fong DW. In press. Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda). BMC Evol Biol.
  • Aspiras AR, Prasad R, Fong DW, Carlini DB, and Angelini D. 2012. Parallel reduction in expression of the eye development gene hedgehog in separately derived populations of the amphipod Gammarus minus. J Evol Biol 25:995-1001.
  • Hense W, Anderson N, Hutter S, Stephan W, Parsch J, and Carlini DB. 2010. Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity. Genetics 184:547-555.
  • Hutchins B, Fong DW, and Carlini DB. 2010. Genetic population structure of the Madison Cave isopod, Antrolana lira (Flabellifera; Cirolanidae) in the Shenandoah Valley of the eastern United States. J Crust Biol 30:312-322.
  • Carlini DB, Manning J, Sullivan PG, and Fong DW. 2009. Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus. Mol Ecol 18:1932-1945.