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Using phylogenetics to reconstruct a 59 million year old drug

Good news: Press Release 2011-10-03 The Nobel Assembly at Karolinska Institutet has today decided that The Nobel Prize in Physiology or Medicine 2011 shall be divided, with one half jointly to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity and the other half to Ralph M. Steinman […]

Shavuot is a microbial holiday

  Tonight is Shavuot. That wonderful holiday which includes midnight studies, water-bombing and dairy products. Mmmmm…. cheese. A food product heavily embedded in the science of microbiology. Cheese is the founding product of the biotech industry (along with beer and bread). So here’s to Lactobacilli and Lactococci which are at the center of the production […]

Reverse Translation Discovered?

  We will never look at life at quite the same way again.   Until now, information flow in biology looked like this:   DNA gets transcribed to RNA, wheich in turn is translated to protein. While reverse transcription does take place with retroviruses using reverse transcriptase, the central dogma of molecular biology held that […]

A non-post about Craig Venter’s new bug

In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The […]

Combrex: Computational Bridge to Experiments

Combrex is an exciting new project at Boston University to bridge computational and experimental techniques to functionally annotate proteins. They are hiring, see below: JOB POST We are seeking to hire a creative computational scientist for a transformative project: COMBREX: A Computational Bridge to Experiments. The work will involve building a novel resource that combines […]

Colbert on Gene Patents

Recently, a judge in Federal District Court in Manhattan ruled that Myriad’s patents on BRCA1 and BRCA2 genes were invalid, being a “products of the law nature” and could be patented no more than, say, mount Everest. These two genes are associated with breast and ovarian cancer, and are used in testing for susceptibility to […]

“Codon” is now a four letter word

As part of the process of manufacturing  a new car,  the designers will take the blueprints to the factory floor. There they will set up an experimental assembly line, tinkering with the manufacturing process of the prototype until it is ready for mass-production. Can we do the same with the machinery of life — the assembly […]

The polypharmacome

Pharmaceutical companies are always on the lookout for secondary drug targets. After all, if you invest billions developing a single drug, you would be more than happy to sell it as a treatment for two, three, or more different ailments. Sildenafil citrate was developed to treat angina and hypertension, but during phase I clinical trials, […]

Videos on sequencing

A few cool vids on sequencing. Company infomercials, but still entertaining and informative. Thanks to my student, David Ream, for finding these. Pyrosequencing: Helicos: SOLiD: BASETM nanopore sequencing:

Weekly Poll: will you have your own genome sequenced?

CLARIFICATION: the events described here have not happened. Yet. We are a few years into the future. Whole human genomes can be sequenced relatively cheaply and accurately. Direct to Consumer Genomics companies offer true genomic analyses now, not just marker analyses. They BLAST* your sequence against known genotype & disease databases, looking for known genotypic […]

The new natural history

Before the 20th century biology was, to a large extent, “Natural History”. It was an observational rather than the experimental science it is considered to be today. At that time, the typical biologist, a natural historian, was going about the (European colonized) world, collecting specimens of new and fossilized species, classifying and recording them for […]

Light for Cellular Communication?

Don’t you know We’re all light Yeah, I read that someplace –XTC This is interesting: an article in PLoS ONE that claims that Paramecia can communicate using light. The author, Daniel Fels from the Swiss Tropical Institute in Basel, separated two Paramecia populations using quartz or glass vials, grew them in the dark, and checked […]

Multitasking Antibody

We learned in high school and/or undergrad biology that one antibody would bind to one antigen. This is what makes our immune system so effective: antibodies bind with high affinity to foreign proteins or other molecules. Not only that, but those antibodies are specific: they would bind only to a specific site on the foreign […]

Challenges with Data Quality, Sharing, and Versioning in Next-Generation Sequencing

An fine talk by David Dooling highlighting  some of the false impressions about second generation sequencing. A partial list: Why sequencing quality trump base pair output Why genomes are really probabilities rather than strings Why centralized repositories break down when it comes to second generation sequencing data. Collaborative Software development and versioning has been moving […]

Post-apres-next generation sequencing

<RANT> OK, I don’t like the term “next generation sequencing”. It is a relative term, points at a changing target, and therefore inexact. What is the “this-generation sequencing”? Sanger? 454 used to be “next generation”, but now 454 sequencing went from 100bp to 600bp per read, making it qualitatively different.. so “post-next generation sequencing”? If […]