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Archive for July, 2007

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Robert Shapiro recounts in scientific American many criticisms of many popular models for the chemical origin in life. First he talks about the various theories of why many scientists reject DNA as the first genetic material and turn to believe RNA as the first form of life. and goes on to explain and criticises the various RNA world theory. Finally proposes to define life as a thermodynamic state , as an energy driven network of chemicals which can reduce entropy in a system, and most importantly, can grow, reproduce, and evolve under natural selection.

I hope the various arguments that highlights many problems with chemical origin of life scenarios and the Golf scenario analogy does not mislead to belive the watch maker theory.

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Today I read a paper from Genome Research 17:746-759, 2007. The authors have tried to annotate transcript products(RNA) from 399 annotated protein-coding loci which represent 1% of the human genome. Just as a reminder, from a single gene locus a large number of diverse transcripts can be produced, this is majorly through alternative splicing. This process generates on an average more than 5.4 transcript variants per locus. In addition we also have mammalian genes regulated by alternative promoters also producing transcript variants.

The authors in this paper show that for 82% of the gene locus tested had transcript variants with new perviously unknown internal exons or 5′ distal exons. More than half of the new transcript variants also span large segments of genome sequences and overlap with the upstream unannotated genes. Also they have shown that 20% of the transcripts have open reading frames fusing with that of adjacent genes. this they describe as chimeric transcript, where the fused ORFs produce a new protein.

But most of novel exons of the new transcripts did not show significant evolutionary conservation, which makes doubt the biological significance of the novel exons, as by definition conservation is a measure of some kind of biological function. Which leaves open that these novel exons could represent transcriptional noise as explained in Kevin struhl’s commentary on the infidelity of RNA Pol II.

Finally the authors have shown that the novel 5′ distal exons to be associated with hallmarks of transcription start site. But both functional RNA and transcriptional noise are produced by the same machinery and will obviously share many characteristics. Hence I believe such regulatory properties are inadequate criteria to distinguish biological significance from transcriptional noise.

I am not sure if these transcripts have been discovered due to increased sensitivity of experimental procedures or if they really are functional biological products. As Kevin struhl has pointed it would be “useful to have an experimental measurement of transcriptional noise that is not cofounded by the possibilty that the observed RNAs are biologically significant”.

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Today I went to a wonderful seminar by Sebastian J Maerkl. He gave a talk on the a high-throughput microfludic platform that measures the binding affinity of transcription factors.

Transcription factors are protein molecules that bind to the DNA molecule and help to copy the information(genes) in the DNA to RNA and proteins. These transcription factors interact with very specific DNA base sequences generally present upstream of genes. The transcription factors bind to these sequences very strongly and the affinity between a DNA sequence and a protein molecule is due to the chemical complimentarity between them. This affinity is measured in terms of a constant called association constant or the reverse of it called the dissociation constant.

Special techniques have been described to measure this affinity at very low concentrations. Some techniques are filter binding assay, gel shift assay, surface plasmon resonance etc. These techniques are all low throughput techniques. The protein binding microarrays is a high throughput method that was used to measure the affinity, but actually the PBMs measure only the off-rate of the DNA-protein interaction because of the strigent wash that is involved in the protocol. The wash also causes loss of weakly bound DNA-protein complexes.

The method described by Maerkl et al, measures the binding affinities of a large number DNA molecules in high throughput manner by trapping the bound DNA-protein complexes mechanically and allows one to measure the the equilibrium concentrations of the molecular interactions. The experiments have shown a very high reproducibilty in measuring the affinty values(only 20% error on the golbal measurement).

It has been published in Science 12 January 2007: Vol. 315. no. 5809, pp. 233 – 237. Although yeilding a lot of useful information, a major limitation of this approach is that it requires knowledge of the likely consensus site to be used as the starting sequence, a requirement that is not inherent in PBM or SELEX-SAGE techniques. But the another major advantage of this method is it allows for the designing oligonucloetides with more than one single base substitutions(which is has been traditionally done) and hence allows us to examine the inter nucleotide dependence.

It would be great to have such microfludic platforms to study long promoter sequences which will enable us to study the binding specificities and affinities for all transcription factors in several model organisms, including yeast, Drosophila and mouse, which span a range of genome sizes and modes of transcriptional regulation.

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Michael Barton has a wonderful article published on six different alternatives to pubmed. My favourite is the hubmed.

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I came across several biolinks that are very interesting to a researcher.

Bioscreencast  -is a database of video tutorials for sevaral bio tools.

DNAtube –  contains several videos and animations on various topics in Biology.

Jove –  Journal of Visualized Experiments, that describes itself as “an online research journal employing visualization to increase reproducibility and transparency in biological sciences”.

scitalks.com  – a searchable repository of video recordings of science lectures from all over the world.

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