- University of Utah
- Department of Human Genetics
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- Bioscience PhD Program Profile
The Feschotte Lab
Eccles Institute of Human Genetics
15 North 2030 East
Salt Lake City, UT 84112
Office: Rm. 6150
Office: (801) 585-6061
Tommy Carter, PhD student, is our newest addition to the lab!
Tommy Carter graduated Summa Cum Laude from CU Boulder where he worked in Brad Olwin's lab developing a hydrogel culture system to promote satellite cell selfrenewal in vitro. During his undergrad project, Tommy also developed a techinique for isolating primary Sdc4+ satellite cells using magnetic dynabeads. His undergraduate honors thesis can be found here.
Currently, Tommy is investigating the impact of transposable elements in the birth and evolution of lncRNAs.
In his free time, Tommy enjoys scuba diving crossfit, playing fetch with his cat, growing his beard out for the winter.
Opening Pandora's Box (and unleashing Submariner)
This is a typical mariner DNA transposon family that has spread to 30 copies in the viral genome and is similar to a mariner transposon from the alleged Pandoravirus host, Acanthamoeba - suggesting Pandoravirus acquired it from a eukaryotic host. As often, my contribution to the actual work was minimal, largely limited to the branding of the element as 'submariner'.
This discovery continues to blur the division between viral and cellular genomes and highlights the remarkable promiscuity of mariner transposons.
The paper, published in BMC Biology, is here.
Greetings to Alesia McKeown, a new postdoctoral associate jointly working with Nels Elde.
Alesia obtained her PhD from the University of Oregon where she worked with Joe Thornton (now at Chicago). Her research elegantly combined biochemistry, biophysics phylogenetics, and ancestral protein reconstruction to delineate the molecular evolution of DNA binding specificity in the steroid receptor family of transcription factors (read her fantastic Cell paper).
In her current project Alesia is studying the evolution and function of novel antiviral proteins.
As an outdoor enthusiast, Alesia is fully enjoying Utah's natural playground as the pic above can attest!
Fight Fire with Fire: ERV Envelope genes as antivirals
In this 'Gem' article in the Journal of Virology, Ray and I discuss the mechanism by which some envelope genes derived from endogenous retroviruses offer host cells protection against exogenous retroviral infection. We argue that many more envelope-derived restriction factors await discovery in vertebrate genomes, including the human genome.
The paper is available here in Open Access.
Transposons catalyzed the evolution of pregnancy
Ed talks at CSHL meeting in Puerto Rico
Ed has promised to stay away from Pina Colada until he delivers his talk 'Endogenous retroviruses facilitate the evolution of gene regulatory networks encoding immune defenses' [collaborative work with Nels Elde].
Danger danger! Volatile evolution of lncRNAs!
Ray awarded F32-NRSA NRNIH postdoc fellowship
Congrats to Ray for being awarded a prestigious F32/NRSA grant from NIH/NIAID to work on cellular genes born from endogenous retroviruses.
[True that bottle of TBE looks yum but let's go for champagne this time]
Cedric is now on Twitter...
Also be warned: views expressed here are solely my own.
piRNAs, lncRNAs and mobile DNA
We collaborated with Jin Xing and Kevin Chen at Rutgers to shed light on the intricate relationship between human piRNAs, lncRNAs, and mobile elements.
Paper is here.
Image: human testis uncensored [credits]
Ed becomes HHMI fellow of Jane Coffin Childs Fund!
Congratulations Ed for landing a 3-year postdoctoral fellowship from the prestigious Jane Coffin Childs Memorial Fund for Medical Research.
To top the cake off, Ed was designated as one of eight HHMI Fellow of this year's JCC Memorial Fund.
Ed's project on ERVs in innate immunity is co-sponsored by Feschotte and Elde.
Secrets of Snakes - Python and Cobra Genomes
Analyses of the first two snake genome sequences published in PNAS. Feschotte lab contributed to transposon analysis of the Burmese python genome, as part of a consortium led by Todd Castoe.
Python genome paper is here.
New Pritham-Feschotte group picture!
We closed 2013 with this group picture taken right here in the mighty Wasatch foothills. Click to enlarge. From left to right: Ellen Pritham, Ed Chuong, Jainy Thomas, Mauro Ortiz, Julia Carleton (roton), John McCormick, Ray Malfavon-Borja, Clay Carey (roton), Aurelie Kapusta, Xiaoyu Zhuo, Peng Wei (roton), CF.
Mauro Ortiz visits us from Brazil
We are very pleased to host Mauro de Freitas Ortiz, a visiting graduate student from the Federal University of Rio Grande do Sul in Brazil. Mauro is carrying his dissertation under the mentorship of Dr. Elgion Loreto, who has been studying the evolutionary genetics of Drosophila transposable elements for more than two decades with a strong focus on horizontal transfer. Mauro was awarded a fellowship from the Brazilian government to train for nine months in the lab. He is carrying a systematic assessment of the rate of horizontal transposon transfer in various mammal lineages.
Julia and Clay rotate in the lab
This month we welcome two new MB rotation students in the lab:
Julia Carleton, who grew up and studied in Portland, Oregon. Julia's rotation project is to annotate DNA transposons in Biomphalaria glabrata, a freshwater snail that is an intermediate host for Schistosoma parasitic trematodes. Almost nothing is known about mobile elements in molluscs so we are curious to see what lurks in this genome. This work is part of a large collaborative effort led by Pat Minx at The Genome Institute of Wash U.
Clay Carey comes from Humboldt, California. During this rotation, Clay will contribute to another transposon annotation project: that of the micronuclear (germline) genome of the model ciliate Tetrahymena thermophila. This genome project is led by Bob Coyne at the J. Craig Venter Institute. A unique feat of ciliates is that their single cell harbor two nuclei: a micronucleus (MIC) which is a transcriptionally silenced "sexual" germline genome, and a macronucleus (MAC) which is a derived, simplified, and edited version of the MIC that serves all somatic cellular functions. All transposon sequences are thought to be removed from the MIC during its transition to MAC. However only the MIC genome has been analyzed thus far, so we don't actually know much about the amount and type of transposons hiding in the MIC. Surely Clay's work will tell us a lot more soon!
Clay is also a talented nature photographer, make sure to take a peek at his amazing photos here.
Keystone symposium 'Mobile Genetic Elements and Genome Evolution'
Together with Nancy Craig and Henry Levin, I am co-organizing a Keystone Symposium on Mobile Genetic Elements and Genome Evolution in Santa Fe, New Mexico, March 9-14, 2014.
This international meeting will draw speakers and participants studying a wide range of organisms, systems, and questions.
The list of invited speakers can be found here. There will also be many short talks selected upon abstract, two special workshops (themes to be determined based on abstracts) and of course poster sessions.
Deadline for Abstract submission is Dec 9, 2013.
Deadline for Discounted Registration is Jan 8, 2014.
Congrats Xiaoyu on the paper and cover in JVI !
Xiaoyu Zhuo's paper on bat endogenous retroviruses is now published in the Journal of Virology.