Great post about a Mol Ecol paper

Noah Reid over at Nothing in Biology has written a wide ranging and very interesting post about a recent Mol Ecol paper on inbreeding depression in bighorn sheep. I particularly liked this part:

“I found this paper fascinating in that it is the first I’ve read that tries to examine the genomic architecture of this important phenomenon. As the authors note, similar analyses have been conducted in the past, but they are often directed at specifically trying to find loci that cause incompatibility between populations in the context of speciation, rather than examining this complex phenomenon.”

The whole post is here. There’s also an excellent perspective piece by Zach Gompert that accompanies the Miller et al. paper, and both will very likely appear in issue 21.6 (mid March).

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Do famous researchers have biased perceptions of peer review?

I thought some of you would be interested in this:

http://scholarlykitchen.sspnet.org/2012/02/01/the-famous-grouse-do-prominent-scientists-have-biased-perceptions-of-peer-review/

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A penny for your method: AMPure Substitute

This week may stand as the most exciting week of the year for decreasing the cost of PCR cleanup, DNA cleanup, and library prep. Why, you ask? Because a great paper was published over in Genome Research by Nadin Rohland and David Reich entitled “Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture”.

Among several great nuggets within this paper is what the authors describe as a “[replacement for] a commonly used commercial kit (AMPure XP kit) for SPRI-clean-up steps with a home-made mix”, and in the supplementary information (available to everyone), they provide the components of this home-made mix.

Below, I’ve added a gel image illustrating differences between this home-brew mix and commercial AMPure XP – I refer to the home-brew mix by the name of the beads in solution (SeraMag Speed Beads). The numbers above each lane show the ratio of AMPure or SeraMag Speed Beads used to product being cleaned – in this case, the product being “cleaned” is the same ladder on the far left of each image.

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Winter break

Since all the bloggers are heading back to their homes and log fires for the Christmas break, we’re going to put the blog on hold until early in 2012… we hope to see you then!

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Lego my regex

Regular expressions are something that pretty much everyone working with more than a handful of data should take the time to learn (a handful being around 500 lines). They can easily improve your life, particularly if you’ve ever had to make multiple, mind-numbing changes over more than about 50 lines of an excel file, for instance. They can also be terribly frustrating to learn and often are similar in appearance to Sumerian for the uninitiated. All that’s changing – Zed Shaw’s excellent series of books now delves into regular expression territory (the tutorials for other languages are also very, very good), and it’s a learning exercise that’s worth looking into (keep in mind that this is an early “alpha” version that is evolving):

http://regex.learncodethehardway.org/

Decent knowledge of regular expressions combined with a very good text editor and perhaps a data manipulation tool can fundamentally change the way you work, increase repeatability, and improve your science.

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A penny for your method: Nutator

This one requires a little ingenuity on your part (and perhaps some craft, duct tape, construction, and/or welding skills).

A nutator (AKA nutating mixer or rotating mixer) is a gently rocking/rotating platform useful for continuously and gently mixing samples. They are particularly useful if you’re doing bead-binding sorts of operations – like binding biotinylated oligos to streptavidin-coated beads. This is a pretty common workflow for lots of tasks including one that is increasingly useful… target enrichment (AKA sequence capture or solution hybridization).

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Ottawa, July 6th 2012

Unlike most of the big journals in the field, Mol Ecol isn’t affiliated with an academic society, and one consequence is that there’s never been a ‘molecular ecology’ get together along the lines of the Evolution meetings or ESEB. Seeing as 2012 is the 20th year of the journal and it coincides with the big SSE/ESEB/CSEE/ASN/SSB conference in Ottawa, we’ve organised a ‘Molecular Ecology’ symposium for the 6th July, the opening day of the main conference (i.e. the one with registration and the evening reception).

The overall goal is to showcase some of the best research in each of the fields covered by the journal (adaptation, speciation, phylogeography etc.) and then map out future research priorities with panel discussions. We may even give out t-shirts. I’ve put the current speaker line-up here.

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Dr. Prepper

Library preparation for next-gen sequencing has become a fact of life in many labs working with model and non-model organisms. The problems with library preparation are that (1) library prep is slow and (2) library prep is expensive. Generally speaking, you can improve #1 OR you can improve #2, but you can’t do both simultaneously.

Most of us can justify time in the lab as long as we can reduce per-sample costs, so I wanted to quickly present a few options for library preparation along with their per-sample (list price/units) cost. In the following, I’m going to focus on the exact “kits” that you would use to prepare DNA libraries for Illumina sequencing using the TruSeq (Tm) adapter/reagent system:

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Stretching in new directions – Part II: Interview with Jane Lubchenco

On May 7, NOAA Administrator Jane Lubchenco received an aerial tour of coastal Louisiana with Nancy Sutley, chair of the White House Counsel on Environmental Quality. NOAA Corps CAPT Michele Finn coordinated the flight. Here, Lubchenco and Finn discuss the situation after the survey. Credit: NOAA.

So how does one become a successful academic and then turn around and create an equally successful career as a scientific leader and advisor to the, ahem, President of the United States? One important factor, that arose not with just Jane Lubchenco but with all the women I interviewed, was explicit mentorship.   Each one of these women described a mentor(s), who championed them as scientists and encouraged them to step beyond what they might imagine for themselves.  In Part II of our interview, Dr. Lubchenco summed it up nicely when she said, “Each of my mentors told me in their own way to believe in myself and to stretch in new directions.”  What else contributed to her astounding success?  Read on.

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Science in our society – Part I. An interview with Dr. Jane Lubchenco

In early July, Dr. Lubchenco was kind enough to spend some time with me over the telephone talking a little bit about her life as the under secretary of commerce for oceans and atmosphere and administrator of NOAA.

NOAA Administrator Dr. Jane Lubchenco, NOAA Fisheries Assistant Administrator Dr. Eric Schwaab, and Council on Environmental Quality Chair Nancy Sutley assess how the sample is processed aboard the Research Vessel Caretta and chain of custody protocol used when handling specimens associated with the oil spill. Credit: NOAA.

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