Author Archives: bgaertner

The Individual in the Genomic Era

The grad students in this department (CEEB) are organizing a public seminar series this spring about how genomic technology is developed and applied to issues in human health.
The series is targeted towards undergraduates and the rest of the Eugene & surrounding community.  Bill Cresko will open the series on April 5 and give a brief tutorial on how we acquire genomic information) and will then go on to explore how this information has changed the way we view our world, the history of hominid evolution, and how we think about medical care.

Lee Silver, from Princeton University, will talk on May 3 specifically about Personal Genomics, personalized medicine and genetic testing.

Carlos Bustamante, from Stanford University, will close the series on May 23 by speaking about how genome variation data has been used to identify the evolution of different traits in domesticated animals (specifically dogs) and how we can use that same type of technology to map migration of humans over the past several millennia as well as explore the genetic basis to physical differences among humans.

We realize most of our readers won’t be able to attend, but we are planning on podcasting & videotaping the lecutres to post on the seminar website.  We’ll note on here when we update so keep your eyes peeled!

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We’ve noticed an astounding increase in pageviews the past few days, all thanks to PZ’s blog entry. Please let us know what you think about the blog’s organization and content. This is a work in progress but our goal is to have a good set of interpretable paper summaries on a pertinent topic each quarter.

The wonders of statistics in gene expression experiments

Post by Bryn Gaertner

Paper:

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

RK Bradley, XY Li, C Trapnell, S Davidson, L Pachter, HC Chu, LA Tonkin, MD Biggin, MB Eisen

PLoS Biology 8(3) 2010

Flies in the Drosophila genus all look about the same, and the early-development transcription factors that we all know and love (Hunchback, kruppel, bicoid, giant, knirps, etc.) are expressed in roughly the same patterns. However, there is about one SNP per 10 bp between these species, which strongly suggests that the TF binding targets are no longer conserved. How do the TFs still know where to go?

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Identifying the function of a locus of adaptation in high-altitude deer mice

Posted by: Bryn Gaertner

Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin.

Storz JF, Runck AM, Sabatino SJ, Kelly JK, Ferrand N, Moriyama H, Weber RE, Fago A.  Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14450-5. Epub 2009 Aug 10. PubMed PMID: 19667207; PubMed Central PMCID: PMC2732835

This paper performed both evolutionary and functional analysis of duplicated genes adapted to altitudinal zones.

They found parallel functional differentiation at multiple unlinked duplicates, the two alpha-globin genes on chromosome 8 and the two beta-globin genes on chromosome 1.  In this paper, they found that there is a change in beta-chain binding affinity: The difference is in 2,3-DPG affinity, which is an allosteric cofactor that stabilizes the de-oxy conformation of the heme molecule.  This difference encourages O2 binding in high altitude environments, which would enhance pulmonary loading under hypoxia.  However, our discussion lead us to wonder whether this is actually a *low* altitude adaptation

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Putting morpho-phylogenetics in an Evo-Devo context

Posted by: Bryn Gaertner

Today we had a seminar speaker who talked about ways to map morphological data (the technique is a way to quantify shape, called Geometric Morphometrics) onto existing phylogenetic trees, and then inferring when vital morphological transitions happened (and specifically whether big shape transitions happened, or whether it’s gradual).  Brian Sidlauskas gave three specific examples of these strategies. Conceptually, his MO is to synthesize the fields of phylogenetics and morphometrics.  His argument is that each of them on their own are modestly informative, but in the words of G.G. Simpson, “we’re learning more and more about less and less.”  By synthesizing the two fields, we’re able to learn more about both than by studying either of them separately.

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