Archive for the 'SciLit' Category

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

February 12, 2016

Reprogramming…#epigenome & transcriptome in…muscle after training http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622000/ Delta(Me) from #exercise in 1 leg v. other

QT:{{”
Exercise has long been known to have an effect on health, lowering the incidence of cardiovascular disease, obesity, and type 2 diabetes. Recently, it has been found that exercise can have a direct effect on DNA methylation and gene expression. A group of 23 subjects exercised one leg but not the other for 45 minutes four times a week for three months. At the end of this period, the methylation and gene expression patterns were different in the exercised leg relative to the one that did not exercise, indicating a direct effect of exercise on
epigenetics.
“}}

Quote from:

https://books.google.com/books?id=qotyCwAAQBAJ&pg=PA91&lpg=PA91&dq=Exercise+has+long+been+known+to+have+an+effect+on+health,+lowering+the+incidence+of+cardiovascular+disease,+obesity,+and+type+2+diabetes.+Recently,+it+has+been+found+that+exercise+can+have+a+direct+effect+on+DNA+methylation+and+gene+expression.+A+group+of+23+subjects+exercised+one+leg+but+not+the+other+for+45+minutes+four+times+a+week+for+three+months.+At+the+end+of+this+period,+the+methylation+and+gene+expression+patterns+were+different+in+the+exercised+leg+relative+to+the+one+that+did+not+exercise,+indicating+a+direct+effect+of+exercise+on+epigenetics.&source=bl&ots=paSuwD6wvw&sig=gwFDNYvSMRlkFouTcaoyf9q3c20&hl=en&sa=X&ved=0ahUKEwjZzv7imu3KAhXK5SYKHaP6DdEQ6AEIHjAA#v=onepage&q=Exercise%20has%20long%20been%20known%20to%20have%20an%20effect%20on%20health%2C%20lowering%20the%20incidence%20of%20cardiovascular%20disease%2C%20obesity%2C%20and%20type%202%20diabetes.%20Recently%2C%20it%20has%20been%20found%20that%20exercise%20can%20have%20a%20direct%20effect%20on%20DNA%20methylation%20and%20gene%20expression.%20A%20group%20of%2023%20subjects%20exercised%20one%20leg%20but%20not%20the%20other%20for%2045%20minutes%20four%20times%20a%20week%20for%20three%20months.%20At%20the%20end%20of%20this%20period%2C%20the%20methylation%20and%20gene%20expression%20patterns%20were%20different%20in%20the%20exercised%20leg%20relative%20to%20the%20one%20that%20did%20not%20exercise%2C%20indicating%20a%20direct%20effect%20of%20exercise%20on%20epigenetics.&f=false

The Aging Stress Response

February 12, 2016

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987618/

Aging Pathways: insulin-foxo, mTOR, AMPK, Sirtuin

mTOR is a key modulator of ageing and age-related disease

February 12, 2016

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3687363/

A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue

February 10, 2016

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694844/

Dietary modification of the microbiome affects risk for cardiovascular disease. – PubMed – NCBI

February 10, 2016

http://www.ncbi.nlm.nih.gov/pubmed/23656565

Age-related macular degeneration – Genetics Home Reference

February 10, 2016

A Variant of the HTRA1 Gene Increases Susceptibility to Age-Related Macular Degeneration

Zhenglin Yang1,2,3,*,
Nicola J. Camp4,*,
Hui Sun5,
Zongzhong Tong1,2,
Daniel Gibbs1,2,
D. Joshua Cameron1,2,
Haoyu Chen1,2,
Yu Zhao1,2,
Erik Pearson1,2,
Xi Li1,2,
Jeremy Chien6,
Andrew DeWan7,
Jennifer Harmon1,2,
Paul S. Bernstein1,
Viji Shridhar6,
Norman A. Zabriskie1,
Josephine Hoh7,
Kimberly Howes1,
Kang Zhang1,2,†

http://science.sciencemag.org/content/314/5801/992

QT:{{”
Age-related macular degeneration results in blindness, and one major locus (HTRAX) accounts for approximately one-half of genetic cases. “}}
Should be HTRA1

http://ghr.nlm.nih.gov/condition/age-related-macular-degeneration

Similarity network fusion for aggregating data types on a genomic scale : Nature Methods : Nature Publishing Group

February 9, 2016

Similarity #network fusion for aggregating data types
http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2810.html Combines mRNA, miRNA & gene fusions to classify cancer subtypes http://compbio.cs.toronto.edu/SNF/SNF

The European Bioinformatics Institute in 2016: Data growth and integration

February 9, 2016

.@emblEBI in ’16 via @ewanbirney
http://europepmc.org/articles/PMC4702932/ Seq DB growth stable w/ yearly doubling (post ~’08 spike) & EGA now faster than ENA

cite the data growth stats here:
http://europepmc.org/articles/PMC4702932/figure/F2/

Fig 2
– amt prvt data incr as for ncbi + arrays are falling now less than masspec – after a huge incr from ’07 to ’12 , now stab. at12-mo doubling

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations : Nature Communications : Nature Publishing Group

February 9, 2016

http://www.nature.com/ncomms/2015/150121/ncomms7033/full/ncomms7033.html

Julie Brind’Amour,
Sheng Liu,
Matthew Hudson,
Carol Chen,
Mohammad M. Karimi
& Matthew C. Lorincz

Nature Communications 6, Article number: 6033 doi:10.1038/ncomms7033

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex : Nature Neuroscience : Nature Publishing Group

February 9, 2016

http://www.nature.com/neuro/journal/v19/n1/abs/nn.4181.html

Andrew E Jaffe,
Yuan Gao,
Amy Deep-Soboslay,
Ran Tao,
Thomas M Hyde,
Daniel R Weinberger
& Joel E Kleinman

Nature Neuroscience 19, 40–47 (2016) doi:10.1038/nn.4181