linkstream2 microblog

mis-sense change (G84E) in HOXB13 was found overall in 1.4% of prostate cancer cases and in 0.1% of unaffected controls

http://www.ncbi.nlm.nih.gov/pubmed/22236224

http://www.pnas.org/content/early/2013/12/13/1310750111.abstract

Worried baby will develop asthma/allergies? Get a dog: alter gut microbiome–> protection vs both (at least in mice)
@sxbegle will this work for cats too?! goldfish?

http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3655.html

on the various sources of errors in NGS and the role of replicates in reducing errors:

came across this paper: http://genomebiology.com/content/11/2/R14, which uses GO for RNA-seq data analysis
looks interesting – GoSeq !

QT:{{”
We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.
“}}

http://www.sciencemag.org/content/342/6164/1325.summary
http://www.sciencemag.org/content/342/6164/1367.abstract

QT:{{”
So this is a therapy that goes by a somewhat unwieldy name of CAR T cell therapy….
So it’s sort of combining a few different types of
therapy; it’s the gene therapy, although the genetic modifications happen outside of the
person’s body, that’s one piece. It’s what’s called an immunotherapy, which means it’s
trying to kind of harness the immune system to fight cancer. And it’s also highly
personalized because every patient’s therapy is their own; you can’t just create T cells
and give them to everybody, it’s sort of a unique batch for each patient. “}}

Dizzying Journey to a New #Cancer Arsenal: CAR Tcell therapy combines gene therapy, immunotherapy & personalization into an effective treatment for ~$50K
http://www.sciencemag.org/content/340/6140/1514.summary

How Long Can the US Stay on Top? Universities are increasingly tied to #philanthropy vs federal & state #funding
http://www.sciencemag.org/content/340/6139/1394.summary

Robber Baron University: Stanford, JHU, Rockefeller, CMU, Vanderbilt, Rice, Drexel

http://www.sciencemag.org/content/340/6139/1394.summary

Genome-Wide Comparison of Medieval & Modern M. #leprae, reveals ~1600 #pseudogenes, w/ slightly more in modern strain
http://www.sciencemag.org/content/341/6142/179.abstract

QT:{{”
Most bacteria will have some pseudogenes in their genome, maybe, you know, in Mycobacterium tuberculosis, for instance a close relative, there are 4,000 genes
present and perhaps 20 pseudogenes. In Mycobacterium leprae, there are 1,600 real
genes and as many pseudogenes. For me, this has always been puzzling, because bacteria
generally tend to, once a function has been lost, the corresponding genes are usually
eliminated and we see the genome shrinking. This hasn’t happened in Mycobacterium
leprae, because there’s still such a huge number of pseudogenes present. And that makes
me think that maybe Mycobacterium leprae emerged in this form only very recently and
that there hasn’t therefore been sufficient time for these pseudogenes to be lost.
However, this is clearly speculation, and it needs to be tested by further experiment. For
instance, looking at older samples might be helpful because the analysis described in the
recent Science paper shows that there are more, a few more pseudogenes present in
modern strains of Mycobacterium leprae than there were in medieval European strains.
So if we could go back a few thousand years more, we might find that actually there were
a couple more functional genes at that particular point.
….
Now is there any evidence that the successive number of pseudogenes contributes to
either its slow growth or its resistance to growing in the lab or its just kind of long
standing plague on humanity?
….
Yes, I think while there’s no experimental evidence to prove that the pseudogenes are
responsible for the slow growth, I think it’s highly likely that they do contribute because
lots of very essential functions have been lost, and this means that M. leprae, for instance,
has difficulty in acquiring iron because it’s lost the genes required for iron uptake.
“}}

http://en.wikipedia.org/wiki/Graphene

High-Strength Chemical-Vapor–Deposited #Graphene and Grain Boundaries. Sheets of this are the strongest material yet!
http://www.sciencemag.org/content/340/6136/1073.abstract

Science for All. Interesting factoids on #India: more cellphones than toilets & plans for national #biometric numbers
http://www.sciencemag.org/content/340/6136/1032.abs

QT:{{”
Nationwide connectivity is transforming India in other ways as well. Today, the country has 900 million cell phones. “Only about 35% of Indian homes have toilets. About 60% have mobile phones,” says Jairam Ramesh, who as India’s minister for rural development is searching for innovative solutions for poverty alleviation (see p.1034).
…
Prime Minister Singh threw his weight behind the venture, and in July 2009 the Unique Identification Authority of India (UIDAI) was formed. Its ambitions have since grown: UIDAI is now striving to assign a random 12-digit “Aadhaar” ID number to every resident of India, based on photos, iris scans, and a full set of 10 fingerprints. Some critics blast the program as far too ambitious to succeed. Others say it feels like Big Brother; they point out that security agents will have access to the database. Nevertheless, 300 million people have received Aadhaar numbers since the authority’s enrollment centers, scattered across the country, opened in September 2010.
“}}