Welcome to Crocoduck

The Laboratory Webpage of David Ray

at Mississippi State University

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Welcome and thank you for visiting our lab website. Research in the laboratory revolves around the central theme of modern biology - evolution. Specifically, work in our lab involves the use of computational and experimental tools to explore and manipulate genomic DNA in various taxa ranging from flies to bats. We attempt to address questions related to how evolution works at the molecular level, how organisms are related to one another, how we can use information from the genome to investigate population dynamics, and how we can use information from DNA for forensic identification. Most of our projects involve the characterization and utilization of genetic markers known as transposable elements (TEs), which are DNA sequences that are able to make new copies of themselves and insert those copies elsewhere in the genome. Different types of transposable elements include the retrotranspsosons (SINEs, LINEs, etc.) and DNA transposons (P-elements, MITEs, etc.). Current projects include:

1. Sequencing and assembling the genomes of three crocodilians. More detailed information on this project can be found at www.crocgenomes.org.

2. Investigating small RNAs and their impact on TE and genome evolution in mammals.

3. Investigating the impact of transposable elements on genome evolution and diversification in a variety of taxa.


Current members of the laboratory: Top row (l-r) -Jungyeon Kim, Jeremy Smith, Meganathan Ramakodi, Neal Platt. Bottom row (l-r) - David Ray, Christine Lavoie, Amanda Chong (visiting from the University of Sydney). Heidi Pagan is not pictured.


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Funding

National Science Foundation (MCB-1052500) - "Completing the Crocodilian Triumvirate: A Genome Draft for the Indian Gharial", 2011-2012.

National Science Foundation (MCB-0841821) - "Genome Structure and Evolution in Crocodylia", 2010-2012.

National Science Foundation (DEB-1020865) - "Collaborative Research: A Novel Phylogenomic Approach to Bat Phylogenetics and Morphological Evolution", 2010 - 2012.

Mississippi Agricultural and Forestry Experiment Station - "Repetitive DNA Impacts on Agriculturally and Forensically Important Flies ", 2011.

3/29/12 - More bat TE data
The second chapter of Heidi Pagan's dissertation has been accepted at Genome Biology and Evolution. Expect "Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among bats" to be published in the near future. Great job, Heidi.

3/9/12 - A non-LTR extinction in squirrels
Congratulations to PhD student, Neal Platt, on his first first-author publication. The paper, "A non-LTR retroelement extinction in Spermophilus tridecemlineatus" will appear in the journal Gene sometime in the next month or so.

2/1/12 - Crocodilian genomes in print
Genome Biology has published our plan to sequence and assemble the genomes of the three crocodilians discussed below. Currently, the publication is the #1 Editors Pick at the journal. http://genomebiology.com/2012/13/1/415.

1/26/12 - CrocGenomes.org
The website for the International Crocodilian Genomes Working Group is up and running. There you can find information on our efforts to sequence and assemble the genomes of three crocodilians - the American alligator, the saltwater crocodile, and the Indian gharial. Enjoy! http://www.crocgenomes.org/

8/16/11 - NSF funding for the gharial genome!
NSF has just approved funding of our work to add a third genome to our list of sequenced crocodilians. As per MCB-1052500, "Completing the Crocodilian Triumvirate: A Genome Draft for the Indian Gharial", we will immediately begin working to sequence and assemble the genome of Gavialis gangeticus.

8/9/11 - Mobile DNA in Mammalian Genomes
Neal Platt and Dr. Ray attended the FASEB sponsored Mobile DNA in Mammalian Genomes meeting during the second week of August. Dr. Ray presented some of Heidi Pagan's recent dissertation work and Neal presented his recently submitted analyses of the Spermophilus tridecemlineatus genome. Both the talk and poster were well-received and multiple collaborative projects were initiated.

8/3/11 - Dr. Heidi Pagan
The Ray laboratory welcomes its first PhD. Dr. Heidi Pagan successfully defended her dissertation, "A STUDY OF MOBILE DNA CONTENT AND ACTIVITY IN NON-MODEL MAMMALIAN ORGANISMS". Heidi will be moving on to a postdoctoral research position at Florida Atlantic University to study the impact of environmental stress on marine mammals. Congratulations to her!

8/2/11 - First meeting of the International Crocodilian Genome Working Group
MSU welcomed researchers from three countries and multiple US universities to participate in a meeting to organize efforts to sequence and assemble the genomes of Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). The meeting was a resounding success with plans to complete the sequencing and assembly by mid-Fall and to submit a high-profile genome assembly and analysis manuscript (as well as multiple satellite papers) by mid-Spring).

1/3/11 - Papers, additional funding, and a new graduate student
Over the last several months, we have had several publications submitted and accepted. Postdoctoral researcher Meganathan has published two manuscripts from his doctoral research in India (see pubs 40 and 44). Well, one is published and the other is under revision. Dr. Ray has had a commentary on recent developements in transposable element assays in humans accepted at Genome Research (see pub 42). Finally, all of Jeremy's hard work in analyzing the Anolis carolinensis genome is coming to fruition (see pubs 37 and 41). In addition to our publication successes, we received our second consecutive year of funding from the Mississippi Agricultural and Forestry Experiment Station to continue our examination of TEs in agriculturally and forensically important flies. Last but not least, we welcome Christine Lavoie into the laboratory as a new MS student. She will take over work on the fly TE research. Welcome Christine.

6/1/10 - NSF Funding for bat phylogenetics
NSF has recommended funding for our collaboration with Dr. Richard Stevens at Louisiana State University entitled, "Collaborative Research: A Novel Phylogenomic Approach to Bat Phylogenetics and Morphological Evolution". This project will involve the development of a novel method for inferring phylogenies using genome-wide analysis of SINEs. The resulting phylogenetic hypotheses will allow us to answer questions about the evolution of morphological characters in these unique mammals.

5/14/10 - Lemur transposons and the Biology of Genomes meeting.
Our research detailing DNA transposon activity and horizontal transfer of piggyBac elements in the mouse lemur, Microcebus murinus, was published online at Genome Biology and Evolution. Congratulations to Heidi on her first first-author publication! The laboratory also travelled to Cold Spring Harbor in New York to attend the Biology of Genomes meeting. We presented four posters detailing our work on squirrels, bats, lizards, and primates.

2/21/10 - MCBIOS awards.
The laboratory attended the MidSouth Computational Biology and Bioinformatics Society conference in Jonesboro, AR. As a group, we presented three posters and one oral presentation. Heidi Pagan won the title of best oral presentation for her talk on lemur TEs and Neal Platt was awarded first prize for his poster on TE discovery in Spermophilus tridecemlineatus.

1/6/10 - Postdoctoral research opportunity.
NSF funding (see below) has provided us. with funding to hire a postdoctoral researcher for 2.5 years to perform research on crocodilian genome evolution. The official announcement remains to be approved by MSU but will be posted here in the near future. Apply to join our research team. Application information.

12/15/09 - Strategic Research Initiative Funding.
Our proposal to the Mississippi Agricultural and Forestry Experiment Station (MAFES) was funded and will allow us to continue our research into the TE content of oestroid flies (see pub #35 by Thompson et al.)

12/7/09 - Two new publications.
We have recently published two new papers. The first is in collaboration with Dr. Mark Batzer at LSU and is a review of a recent analysis of TEs in the genome of the extinct mammoth. The second is the result of collaborative efforts with the laboratory of Stephane Boissinot and explores the TE dynamics of the Anolis carolinensis genome.

6/29/09 - NSF funding.
In July 2009, the Ray lab was awarded National Science Foundation funding to study crocodilian genomics via a proposal titled Genome Evolution and Mobile Element Dynamics in Crocodylia. Using these funds, we will investigate aspects of genome structure, function and diversity in representatives from all three crocodilian families (gharials, alligators and caimans, and true crocodiles). Exciting work is ahead!