The Imumorin lab has adapted genotyping-by-sequencing (GBS) used in plants for genotyping a number of cattle breeds in the US and Africa.  Their success with this method could potentially significantly cut down the cost of genotyping livestock populations for GWAS studies.  More details can be found in their paper in PLOS ONE.

3CPG Scholar Applications are next due July 1, 2013 and Jan 1, 2014
Travel award review dates are Sept 15, 2013 and Apr 15, 2014

3CPG Priming/Infrastructure grants are next due Oct 15, 2013 and May 15, 2014.
 

See 3CPG Member Funding Opportunities page for more information on each type of grant including detailed information on applying..

Cornell's Bioinformatics Facility (aka, "Computational Biology Service Unit", or CBSU) is happy to announce their newest workshop:

Perl for Biologists, March 6-June 12, 2013

The aim of this workshop is to teach practical Perl programming skills in the context of biology and bioinformatics. The workshop will span 15 hour-and-half long sessions (March 6 - June 12, 2013). It will start from the very basics, no previous programming experience necessary. After completing the

Erin Kelleher and Dan Barbash found that Drosophila hybrids have increased transposon activity due to the rapid evolution of proteins in the piRNA pathway. piRNAs act to repress transposons, and while piRNA transcripts are still made in the interspecific hybrids, they are not processed to their mature, functional forms. More details can be found in their PLOS Biology paper here.

Funding opportunities and deadlines for 2012-2012 for 3CPG members have been announced. They include Priming & Infrastructure Grants (10/15/12 & 5/15/12), 3CPG Fellowships (9/15/12 & 1/1/13), and Travel Grants (9/15/12 and 1/1/13). For details, criteria and application information, please see the 3CPG Funding Opportunities web page.

Over three hundred proteins get phosphorylated during egg activation, an event necessary for D. melanogaster reproduction, report the Wolfner group in a recent Developmental Biology paper. These findings provide a new list of genes necessary for fertility in flies, including mrityu, which had no known function before.

The Lazarro group found that female flies are less able to fight off bacterial infection after mating, likely because the fly needs to channel her energy towards reproduction instead of her own health.

More details can be found in their Journal of Insect Physiology paper here.

The Jannink group used a genome-wide association study on oat crops to find genes that control the levels of soluble fiber are controlled. Fiber levels in human diets are linked to lower blood pressure and cholesterol levels.

Their paper in Theoretical and Applied Genetics can be found here.

The Stanhope group used comparative genomics to understand how Streptococcus pyogenes gained the ability to infect humans but not other mammals. They found that genes gained from phages and other Streptococcus species were able to adapt current and create new virulence pathways.

For more details, the PLoS One paper can be found here.

Ruth Ley and colleagues report in the August 2nd issue of "Cell" that pregnancy drives dramatic changes in the gut microbiota, which can then induce metabolic changes that are healthy for pregnancy.  See the report in the Cornell Chronicle.

Alon Keinan and Andrew Clark report in the May 12th issue of "Science" evidence of the genetic signature of the dramatic recent expansion of human populations, clarifying the impact on efforts to link genetic variation with disease.

Link to Cornell Chronicle Article

The Brooks lab found that 3% of Arabian horses carry a mutation in the MYO5A gene that causes the deadly Lavender foal syndrome, and they warn that horse inbreeding can lead to higher incidences of disease.

More details can be found in the Animal Genetics paper here.

The Lovette lab found that small gaps between habitats correlate strongly with genetic isolation for Florida scrub jays.  Effective species conservation will require new landscaping practices in order to prevent impenetrable gaps between habitats that prevent mating between populations.

For more details, the Biology Letters paper can be found here.

Check out the new Profiles of current graduate students and postdocs in 3CPG member labs as a way to illustrate the type of work they are doing, and their often very interdisciplinary backgrounds, approaches, as well as to highlight some of the really neat science they are doing!  (links also available from "index" on left side of web page, and from the "For prospective grad and postdocs" page). Thanks to Erin Wissink, graduate student in Andrew Grimson's lab, for her

Different species of crickets use different mating songs, leading to the question of how genes for male mating songs are able to evolve with genes for female receptivity to these songs.  The Shaw lab has found that the the male and female genes are physically linked, thus explaining how these two distinct traits can co-evolve in the two different sexes.

For more details, the Proceedings of the Royal Society paper can be found here.

An updated full listing of courses offered Spring 2012 (and tentative Fall 2012)  is now posted under "Courses" heading on the "For Current Grad Student & Postdoc" page (as well as for Prospective Grads and Postdocs, and For Undergrads pages).  Revision dated 1-15-2012

Adam Siepel's group has published a paper in Nature Genetics on new statistical methods for making inferences about ancient human demography from whole-genome sequences.  Their analysis reveals that the San, an indigenous group of hunter gatherers from southern Africa, diverged from other human populations earlier than previously thought -- about 130,000 years ago. In comparison, they also estimate that the ancestors of modern Eurasian populations migrated from Africa only about 50,000

Congratulations to Alon Keinan, Assistant Professor, Department of Biological Statistics and Computational Biology, and a 3CPG faculty member, who has been named a 2011 Sloan Foundation Research Fellow.

The Alfred P. Sloan Foundation has awarded six Cornell faculty members Sloan Research Fellowhips for 2011. The awards recognize early-career scientists and scholars for their achievements and their potential to contribute substantially to their fields.  Alon Keinan, assistant

Adam Siepel's group (Andre Martins and former members Carolin Kosiol, Tomas Vinar, and Vikas Taliwa) contributed to sequencing and comparative analysis of orangutan genomes.  Former 3CPG member Carlos Bustamante's group also contributed while at Cornell.

Research Article in Nature

Andrew Clark (MBG/EEB) and Alon Keinan (BSCB), both 3CPG faculty members, lead parts of international effort to sequence and analyze more than 2,500 human genomes from 27 populations worldwide as part of the “1,000 Genomes Project”. Clark is a co-PI for the major international research project and member of the steering committee, and his group has developed and contributed new sophisticated statistical analysis methods to quantify and characterize the DNA sequence diversity. Keinan

TA needed for Spring 2010 for BioMG1250-003  "Personal Genomics and Medicine: Why you should care about what's in your genes?"
Taught by Chip Aquadro (MBG) together with Spencer Wells (National Geographic and Frank H.T. Rhodes Class of '56 Professor at Cornell)

A great opportunity to both participate in a seminar-type course for freshman & sophomores spring semester but to also help develop this 1credit course into one of several new "university" courses as

Ruth Ley (Micro/3CPG) and members of her lab from Cornell (Omry Koren and Ayme Spor) and collaborators from the University of Gothenburg, Sweden have shown that the same types of bacteria found in arterial plaque, which causes atherosclerosis, are also found in the mouth and gut. The research, which is first general survey of all bacteria found in plaques from the mouth, gut and blood, and published online ahead of print Oct 11, 2010 in the Proceedings of the National Academy of Sciences, may

Sophie Cardinal and Bryan Danforth (3CPG member) recently published a paper in PNAS that provides the first, robust estimate of phylogeny in the largest bee family, Apidae. The family Apidae is an important bee group because it includes the honey bee, the most important managed pollinator. Over 30% of apid species and over 50% of apid tribes are cleptoparasites that do not build nests or collect pollen. Instead, females enter the nests of other bees and lay their eggs, much in the same way that

Ruth Ley's lab has contributed to a recent Science paper showing that mice that lack Toll-like receptor 5 exhibit pronounced metabolic changes that are correlated with changes in the composition of gut microbiota.

The first round of competition for 3CPG Fellowships was held in May 2009. Three individuals were named 3CPG Center Postdoctoral Fellows and were provided postdoctoral support starting 7/1/09.  The 2009-2010 Fellows are:

• Dr. Roman Arguello (working with Andy Clark):  Population and quantitiative genetics of olfactory neuron functional variation in Drosophila
• Dr. Erin Kelleher (working with Dan Barbash): Evolution of piRNAs and germline transposon control in Drosophila

Several 3CPG members received funding from the National Institutes of Health under the American Recovery and Reinvestment Act (ARRA).  See Cornell Chronicle articles on major grants awarded to Brian Lazzaro and Chip Aquadro.