linkstream2 microblog

Iron production electrified. New tech for extraction of Fe directly from its oxide w/o C via high-T #electrolysis.
http://www.nature.com/nature/journal/v497/n7449/full/nature12102.html

This piece contains an interesting discussion of new blast furnace technology, which enables one to extract the oxygen directly from iron oxide without the need for carbon or the creation of carbon dioxide as it uses electrolysis. The key idea is being able to do this at very high temperatures.

QT:”
Kerri Smith: Extracting iron from its naturally found form, iron oxide is a hot and heavy business. You throw your iron oxide and some carbon into a blastfurnace and then heat it to 1600 degrees Celsius, out comes iron, worldwide about a billion tons of it a year, but also outcomes carbon dioxide- bad news for the environment. Scientists would like to use other friendlier methods to make iron. This week a team from MIT reports a way to convert iron oxide to iron using electricity. It’s not a new idea. It’s basically a form of
electrolysis which extracts the oxygen leaving pure iron behind. But they’ve gotten over the biggest problem, finding material that can withstand the temperatures of molten metal oxides. Metallurgist Derek Fray at the University of Cambridge in the UK has written a News and Views article about the research. He started by telling me how much CO2, iron production is responsible for. Nature (2013); Nature(2013) ”

http://www.nature.com/nature/journal/v497/n7449/full/nature12102.html

Anatomy of successful #compbio software: Right place at right time, Packages, Clean design, Insight.. go.nature.com/aUCA5y MT @BetaScience The anatomy of successful computational biology software
http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

Content Disputes in #Wikipedia Reflect Geopolitical Instability: bio #network ideas applied to social context
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020902

Content Disputes in Wikipedia Reflect Geopolitical Instability http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020902

(guilt-by-association)

http://database.oxfordjournals.org/content/2013/bat069.abstract.html

http://www.ncbi.nlm.nih.gov/pubmed/23925245

Contains a personal-genome like construction for HeLa
with 100X shotgun and then paired ends used for variant discovery and sequencing of pools of fosmid clones for haplotype resolution. Finally, low-freq. somatic and passage variants layered onto this.

Haplotype-resolved genome… of #HeLa: Has mapping of #ENCODE RNA- & chIP-seq against a personal genome
http://dx.doi.org/10.1038/nature12213 via @aemonten

Cell, Volume 155, Issue 1, 70-80, 26 September 2013
10.1016/j.cell.2013.08.030
David R. Blair,Christopher S. Lyttle,Jonathan M. Mortensen,Charles F. Bearden,Anders Boeck Jensen,Hossein Khiabanian,Rachel Melamed,Raul Rabadan,Elmer V. Bernstam,Søren Brunak,Lars Juhl Jensen,Dan
Nicolae,Nigam H. Shah,Robert L. Grossman,Nancy J. Cox,Kevin P. White,Andrey Rzhetsky

http://www.cell.com/retrieve/pii/S0092867413010246

Variants in #Mendelian Loci Contribute to Complex Disease Risk: connecting rare & common diseases
http://www.cell.com/retrieve/pii/S0092867413010246 via @neilfws

http://www.citeulike.org/user/neils/article/12718324?utm_source=twitterfeed&utm_medium=twitter

Genome Biol. 2012 Dec 13;13(12):R115.

Whole-genome reconstruction and mutational signatures in gastric cancer. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y.

http://www.ncbi.nlm.nih.gov/pubmed/23237666

Some thoughts, much from WC:

Looks like the data is freely available via GEO ID : GSE30833 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30833

The article by Nagarajan et al. highlights the authors efforts to utilize de novo genome assembly of gastric cancer genomes to detect not only single nucleotide variants (SNV’s) and short
insertions/deletions (indels), but also larger scale genomic structural variation (SV) that could be signatures of cancer genomes. It is to be applauded that this is a whole genome analysis.

The authors present several interesting findings such as enrichment for C->A and T->A mutations in both cancer genomes, enrichment for C->A and C->T mutations in the H. pylori infected cancer genome (evidence of cytosine specific transcription mediated DNA repair due to deamination), and amplification and deletion of regions on chromosome 12 in the non-H. pylori infected genome.

Although copy number variants (CNV) could potentially be detected by exome sequencing alone, whole genome sequence enables the precise localization of such events, as well as the detection of variation in non-coding regions.

Their methodology relies on combining high-throughput short-read sequencing with longer DNA-PET (paired end tags) in order to construct higher confidence de novo assemblies with longer contiguous regions.

QT:”One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.” http://www.ncbi.nlm.nih.gov/pubmed/21962505

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2768.html Replicative mechanisms for #CNV formation are error prone: CNVs associated with SNVs in 67 cases http://dx.doi.org/10.1038/ng.2768 MT @LeucineRichBio
Lupski paper