Ian Holmes › Likes

Summary of foldit results in the 2008 Protein Structure Prediction competition (CASP8): "foldit players are on par, but not better than protein folding experts at trying to solve the same problem with all tools available to them. It also appears that foldit outperformed all fully automated server submissions. Hopefully over time foldit can do even better, but being able to produce solutions of same quality as experts means that the top science research can now also be done outside of labs by game players, significantly speeding up the process of scientific advancement! " - Michael Nielsen

sweet! - Ian Holmes from BuddyFeed

The role of naturally occurring D in living organisms has been examined by using deuterium-depleted water (30-40 ppm D) instead of water containing the natural abundance of D (150 ppm). The deuterium-depleted water significantly decreased the growth rate of the L929 fibroblast cell line, and also inhibited the tumor growth in xenotransplanted mice. Eighty days after transplantation in 10 (59%) out of 17 tumorous mice the tumor, after having grown, regressed and then disappeared. We suggest that the naturally occurring D has a central role in signal transduction involved in cell cycle regulation. - Steve Koch

Hey Jean-Claude, Interesting smell reference in a review I'm reading: "2.5.1. Olfaction in fish. Hara [40] investigated the ability of the whitefish, Coregonus clupeaformis, to distinguish between the odor of glycine (Gly) and fully deuterated glycine (Gly-ds). Over the concentration range of 10^-8 to 10^-4 M, these fish avoided solutions of Gly-ds and preferred solutions of Gly." From:... more... - Steve Koch

if only it involved real archaea, it might rival the Scandinavian LARPs for weirdness - Ian Holmes from BuddyFeed

Can't it be both? - Alex Scrivener

OMG! Glad you made it in safe! - Rachel Lea Fox

grrrr, ;) - chaz2b

There's MEME http://meme.sdsc.edu/ but I'm unaware of an AMI or a MR implementation. You can build it with MPI support though. - Adam Kraut

we did something a bit like this with xrate.. lots of EM algorithms mapreduce well. - Ian Holmes from BuddyFeed

And if anyone makes an AMI or a MapReduce implementation please let me know - Deepak Singh

Very nice work! - Ruchira S. Datta

The rapid shift of the microbial population back to the anaerobic state following ileostomy closing is interesting in itself, but it's the clinical relevance that can't be ignored. Great science and study. - Mark Strom

BMC Genomics, Vol. 10, No. 1. (2009), 431. BACKGROUND:MicroRNAs (miRNAs) are endogenous small RNA molecules that modulate the gene expression at the post-transcription levels in many eukaryotic cells. Their widespread and important role in animals is gauged by estimates that ~25% of all genes are miRNA targets. RESULTS:We perform a systematic investigation of the relationship between miRNA regulation and their targets' evolution in two mammals: human and mouse. We find genes with longer 3' UTRs are regulated by more distinct types of miRNAs. These genes correspondingly tend to have slower evolutionary rates at the protein level. Housekeeping genes are another class of genes that evolve slowly. However, they have a distinctly different type of regulation, with shorter 3'UTRs to avoid miRNA targeting. CONCLUSIONS:Our analysis suggests a two-way evolutionary mechanism for miRNA targets on the basis of their cellular roles and the length of their 3' UTRs. Functionally critical genes that... - Neil Saunders

Nature, Vol. 461, No. 7261. (26 August 2009), pp. 258-262. Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans1, 2, 3. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins4, 5, 6, 7. Here we show evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition8 as well as from viral biomes9. The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. The existence of this PSI cluster was confirmed with overlapping and long polymerase chain reaction on... - Neil Saunders

who wants to look for magnetotactic cassettes? - Ian Holmes from BuddyFeed

I know some gene cassette metagenomics people in Sydney who'd be interested. - Neil Saunders

So many coders hate writing documentation, I wonder if this makes them lousy teachers too? - Duncan Hull

Bingo. - Paulo Nuin

Nature, Vol. 461, No. 7260. (3 September 2009), pp. 114-119. TRAF6 is a ubiquitin ligase that is essential for the activation of NF-ºB and MAP kinases in several signalling pathways, including those emanating from the interleukin 1 and Toll-like receptors. TRAF6 functions together with a ubiquitin-conjugating enzyme complex consisting of UBC13 (also known as UBE2N) and UEV1A (UBE2V1) to catalyse Lys 63-linked polyubiquitination, which activates the TAK1 (also known as MAP3K7) kinase complex. TAK1 in turn phosphorylates and activates IºB kinase (IKK), leading to the activation of NF-ºB. Although several proteins are known to be polyubiquitinated in the IL1R and Toll-like receptor pathways, it is not clear whether ubiquitination of any of these proteins is important for TAK1 or IKK activation. By reconstituting TAK1 activation in vitro using purified proteins, here we show that free Lys 63 polyubiquitin chains, which are not conjugated to any target protein, directly activate TAK1 by... - Neil Saunders

Oh great. Ubiquitination network gets even more complex. Just what my poor brain needs. :-) - Bill Hooker

Quote: One small gripe: this article uses “low homology” and “high homology”. Argh indeed. - Neil Saunders

Happy anniversary/birthday/100th post/whatever-you-call-it... - Mickey Kosloff

I'm glad I upgraded a few weeks ago. - Khürt Williams

The mrFAST algorithm has three major goals: first, to map large amounts of next-generation (short-read) sequence data to the reference genome; second, to determine the depth of reads across the genome; and finally, to identifying single nucleotide polymorphisms (SNPs) across the genome, including duplicated regions. - Abhishek Tiwari from Bookmarklet

Completely unrelated, but I sometimes wonder how much software/protein/protocol names are motivated by "wouldn't it be cool if our algorithm was called Mr. Fast!?" - Benjamin Tseng

Benjamin that true although in this case mrFAST stands for “micro-read Fast Alignment Search Tool” - Abhishek Tiwari

Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. Ubiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class-balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase... - Neil Saunders

thanks - Pedro Beltrao