Comment: Putting evolutionary theory into practice – opinion – 06 May 2008 – New Scientist

May 7, 2008 at 8:03 am (evolution, journal, review) (, , )

fascinating thoughts and a new journal! Didn’t know there can be a field called applied evolution. although I have to disagree that it has only surfaced recently on how fast evolution can be.

One of the earliest research I have read about genetics and applied evol pressure is done on guppies size variation in Trinidad due to predator pressure.

how ‘fast’ evolution proceeds is in most parts due to the lifespan and reproductive patterns of the organism in question.


— Nesse says that progress is being hampered by the fact that many medics still think of the body as a machine designed by an engineer, when in fact it is a “bundle of compromises … designed to maximise reproduction, not health”. There is no question about the importance of applied evolution. The trouble is, if biologists themselves are only just waking up to how relevant and crucial evolution can be, what hope is there of educating the leaders and policy makers who need to understand and act upon this research? Not much, I fear.

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De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

March 17, 2008 at 6:51 am (genome, journal, sequencing, software) (, , )

 Chanced upon this interesting paper!

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Geneva University Hospitals;

Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing datasets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5 – 3.0 kb fragments. We also provide indications that the broad coverage achieved by high throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.

PMID: 18332092 [PubMed – as supplied by publisher]

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