linkstream2 microblog

http://michorlab.dfci.harvard.edu/publications/Evolutionary%20Theory%20of%20Cancer,%20NYAS2009.pdf

.@drbachinsky Basically, SNP w. prostate #cancer risk + mechanistic insight …allele at 6q22 increases RFX6 expr…
http://go.nature.com/HEpOHG

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2862.html

http://genome.cshlp.org/content/early/2013/01/02/gr.144600.112.abstract

Nature. 2013 Aug 29;500(7464):593-7. doi: 10.1038/nature12364. Epub 2013 Jul 28.

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu JY, Horvath S, Fan G.

QT:{{”
…We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing…. By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks.
“}}

A paper on C. elegans that’s very informative:
http://www.nature.com/ng/journal/v44/n3/full/ng.1050.html
Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

Most notable of their findings is evidence of recent selective sweeps on chromosomes I, IV, V and (sort of) X. These sweeps have the potential to fix pseudogenes that might have been present at the time.

Long-span PET mapping reveals characteristic patterns of #SVs in… cancer [v norm] genomes, but no MEIs or small events
http://genome.cshlp.org/content/early/2011/04/05/gr.113555.110.abstract

The described study used long paired-end-tags (PET) to analyze and compare SVs in cancer and normal genomes. It determined the prevalence of different types of SVs in normal and cancer sample. Overall, the results are interesting and convincing on a qualitative level; however, for the reasons outlined below, more precise and quantitative delineation of the observed effects is highly desirable.

1) Small sample size of normal genomes (only 2 normal genomes)

2) Validation rate was low (< 77%) for everything except deletions, and for singletons it was even lower. .

3) Long PET is not good for finding smaller events (few kbps). Thus, this analysis missed smaller scale SVs and cancer rearrangements.

4) While there is a discussion about breakpoints and associated repeats, it is not very informative as breakpoint locations were not determined to basepair resolution.

5) No MEI were considered — particularly, no cancer MEI were considered in the analysis, while recently it was found that somatic retrotransposition occurs in cancer (Lee et al., PMID: 22745252)..

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes –

Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.

Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.

100 Years of #Atomic Theory: explains why deriving the #Rydberg const. from more fundamental ones was so important
http://www.sciencemag.org/content/341/6143/244.summary

http://bioinformatics.oxfordjournals.org/content/early/2013/12/12/bioinformatics.btt719.short

Best Season to Get #Pregnant: not May. Unfortunately, winter babies will suffer more #healthproblems!
http://news.sciencemag.org/2013/07/best-season-get-pregnant

QT:{{”
We’ve known for a long
time that summer babies are healthier than winter babies but not the why. …
Right. And these are babies that are born in the summer versus those that are born in the
winter. There’s been this correlation that’s been around for a long time. Scientists have
seen that children that are born in the winter tend to have more health problems later in
life. They tend to be slower growers, have higher incidences of mental illness, and even
early death.
“}}

Around 12 July interesting discussion of correlation between the months of ones birth and later
health problems. Winter born children are more susceptible to health problems. The theory
proposed is that this has to due with flu and the shortening and premature birth.

Battle for the Americas: between N & S American #fauna coming together after the Isthmus of Panama was formed 3 Mya
http://www.sciencemag.org/content/341/6143/230.summary

QT:{{”
Alfred Russel Wallace, the father of biogeography, recognized the faunal melting pot created when the tip of Central America collided with South America and forged the Isthmus of Panama, and in 1876 he postulated what is now called the Great American Biotic Interchange. The story has a dark ending: South American fauna compete poorly at home and away, and many species go extinct.
“}}

Interesting discussion of the Isthmus of Panama. The Isthmus was formed about three million years ago from volcanic action and divided the two oceans. It allowed two very different groups of fauna, that from North America and that from South America to come together. Most of the South American fauna expired as predicted by Wallace.