Posts Tagged ‘quote’

Jackson Lab: Jackson Lab Opens To Big Hopes For Bioscience Growth – Hartford Courant

October 11, 2014

http://www.courant.com/health/hc-jackson-laboratory-20141002-story.html

QT:{{”

The facility is funded in part by $291 million from the state through a legislative act passed three years ago, largely along party lines. In general, Democrats backed the plan by Gov. Dannel P. Malloy’s administration, and Republicans said it was too much money in exchange for 300 jobs over the course of a decade.


About 150 people work at the Farmington location, most of them hired in the past 16 to 18 months,said Charles Lee, director of the Jackson Laboratory for Genomic Medicine.

Last week, as Lee arrived by plane in Seoul, Korea, to check on a collaborative research project there, he was greeted at the airport by media reporting on a recent announcement that Lee is a 2014 Thomson Reuters Citation Laureate, meaning that he is a strong contender this year for a Nobel Prize in physiology or medicine. Nobel winners will be announced Oct. 6.

The lab is headquartered in Bar Harbor, Maine, and it has another location in Sacramento, Calif. All told, the laboratory has an annual budget of $262.4 million for fiscal year 2014 and employs more than 1,500 people, mostly in Maine.

Much of its revenue — $165.3 million — comes from the JAX Mice & Clinical Research Services through its sale of mice to other researchers. Jackson Laboratory in Bar Harbor ships more than 3 million mice annually to researchers around the globe, Lee said.

The lab also received $69.6 million in public support, including grants and contracts in fiscal year 2014. The rest of its budget is funded by contributions and other sources.

In 10 years or so, the Farmington facility could become a $70 million-to-$75 million operation, said Mike Hyde, a spokesman for The Jackson Laboratory.

Jackson is partnering with various Connecticut hospitals and universities, too. Lee has reached out to researchers at Quinnipiac, Wesleyan and Yale.

“I already have a collaboration that’s funded by the NIH with Mark Gerstein, a full professor at Yale University,” Lee said. “I’m developing ties with Rick Lifton, who is the head of genetics at Yale.”

Perhaps the closest academic relationship, in proximity and in collaboration, is between Jackson and both the UConn Health Center and UConn School of Medicine.

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Signaling hypergraphs: Trends in Biotechnology

October 9, 2014

Signaling #hypergraphs
http://www.cell.com/trends/biotechnology/abstract/S0167-7799(14)00071-7 Edges from interactions of 2 sets of nodes. Better representation of assemblies & #complexes.

QT:{{”
each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs)……The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies).
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Signaling hypergraphs. Ritz et al. (2014) TIB

This opinion paper advocates the use of hypergraphs to complement graph-based signaling network and pathway analyses, where each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs). They argue that
hypergraphs is a set-based method that acts like a more general version of a graph. The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies). They propose that hypergraphs can be very useful in situations where the effects of individual proteins might be neglected in graphs but will have a noticeable effect when these proteins are included in protein complexes as hypernodes. They use 3 applications as examples: pathway enrichment, pathway reconstruction, and pathway crosstalk.

Here, Ansel! Sit, Avedon!

September 14, 2014

Here, Ansel! Sit, Avedon!
http://www.nytimes.com/2014/09/04/garden/here-ansel-sit-avedon.html (Also, cowcam.ch) #Gopro #Lifelogging for cats. Next: fitbit & calorie-counting for dogs?

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Last week, GoPro, a camera company made famous by surfers and other athletes who clip on its waterproof miniature Heros to record their adventures, introduced its own version: Fetch, a harness and camera mount designed for dogs. For years, pet owners had been rigging Heros to attach to their pets; perhaps you’ve seen the YouTube video of that surfing pig? …. As programmable digital cameras get smaller and cheaper, the universe of pet, uh, journalism — or is it fine art? — has exploded. Scientists on both sides of the Atlantic have been using these technologies to learn more about the habits of all manner of animals, including house cats. The work of Leo, a cat from
Yellowknife, Northwest Territories, has been made into a poster…. A collaborative (what else to call them?) of Swiss cows posts their oeuvre at cowcam.ch.

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The Debate on Salty Foods, Continued

September 10, 2014

The Debate on Salty Foods, Continued
http://www.nytimes.com/2014/08/24/opinion/sunday/the-debate-on-salty-foods-continued.html Americans consume 3400 mg Na/day; should it go to 2300 (~1 teaspoon of #salt)

QT:{{”
The current average sodium consumption in the United States is about 3,400 milligrams per day. This is mostly ingested in processed foods and is equivalent to the amount of sodium in about 1 1/2 teaspoons of salt. Dietary guidelines endorsed by the federal government and leading medical groups recommend reducing the average to 2,300 milligrams for the general population and 1,500 for groups deemed at greater risk, like adults older than 50, African-Americans, people with high blood pressure and diabetics, among others.
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The Year at Yale 2013-2014

September 6, 2014

President @Yale’s highlights from last year
https://messages.yale.edu/messages/University/univmsgs/detail/109439 “Honored to join several colleagues at Yale’s 1st 6th-grade
graduation.”

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Even as we are gearing up for a new academic year, I had the opportunity to look back on my first year as president of this extraordinary and inspiring institution. I am grateful for what we have achieved and enthusiastic about the future….

Nursing was not the only school to take up residence on the West Campus this year. When Peck Place School, an elementary school in Orange, Connecticut, was forced to close in late December due to water damage from burst pipes and the subsequent discovery of asbestos, Yale provided alternative space for the entire school. The students will return to their school building nextyear, but in June, I was honored to join several of my colleagues at Yale’s first sixth-grade graduation.
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Next-Gen Sequencing Is A Numbers Game | August 18, 2014 Issue – Vol. 92 Issue 33 | Chemical & Engineering News

September 1, 2014

NextGen #Sequencing Is A Numbers Game http://cen.acs.org/articles/92/i33/Next-Gen-Sequencing-Numbers-Game.html Overview of contenders w/ snippets categorizing #chemistry, eg seq-by-synthesis

QT:{{"

So far, Illumina leads the race. In January, the San Diego-based firm

launched its HiSeq X Ten system with a price tag of $10 million.
Consisting of 10 ultra-high-throughput sequencers, each capable of
generating up to 1.8 terabases of data in less than three days

Illumina uses a sequencing-by-synthesis method. After DNA fragments

are amplified on a chip, sequencing occurs by synthesizing a DNA
strand complementary to the target strand by enzymatically attaching
fluorescently labeled nucleotides one at a time. When reactions occur,
the labels are optically imaged to identify what was attached, and the

cycle is repeated.

Thermo Fisher holds second place in the NGS market, with about 16% of
sales. ….ABI launched its first NGS system based on sequencing by
oligonucleotide ligation and detection, known as SOLiD.

Unlike highly accurate but less parallelizable Sanger methods, NGS

systems carry out massive numbers of reactions, or sequence reads, at
one time. Like Illumina’s approach, SOLiD uses sequencing by synthesis
of amplified DNA fragments on either a bead or chip. Instead of
nucleotides, it uses fluorescently labeled probes that are repeatedly

ligated to the growing strand, optically imaged, and cleaved off. How
long these processes can be kept going determines the “read length”
that can be sequenced in a run.

The first lower-cost, nonoptical system appeared in 2010 after Life

Technologies—now part of Thermo Fisher and formed from the 2008 merger
of ABI and Invitrogen—acquired Ion Torrent for $725 million. Its
systems use sequencing by synthesis, but with unlabeled nucleotides on
a semiconductor chip. The chip electrically senses the release of

hydrogen ions when bases attach. The full sequence is read by
sequentially adding bases and tracking reactions across millions of
microwells.

Pacific Biosciences’ single-molecule real-time sequencing is a
sequencing-by-synthesis approach that doesn’t use an amplified set of
DNA fragments and doesn’t require stopping and starting the reaction

to add reagents and image results. Reactions on individual DNA
molecules are tracked in real time across 150,000 nanoscale wells
where isolated polymerases read the DNA and incorporate fluorescently
tagged nucleotides. Because detection occurs only at the bottom of the

wells, the background noise from the other reactions is reduced.

Stability of the sequencing process depends in large part on the
polymerase. Pacific Biosciences has modified a simple bacteriophage
enzyme, slowing it down so that it incorporates about three bases per

second and its detector can keep up.

cleardot.gif

Most interest has been in the U.K.’s Oxford Nanopore Technologies as
it moves closer to launching a new sequencing device. Its MinION uses

protein nanopores held in a polymer membrane to sequence
single-stranded DNA in real time. Individual bases are identified
through changes in electrical current as a linear, single-stranded DNA
molecule moves through a nanopore.

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‘A Troublesome Inheritance’ and ‘Inheritance’

August 10, 2014

‘A Troublesome Inheritance’ and ‘Inheritance’
http://www.nytimes.com/2014/07/13/books/review/a-troublesome-inheritance-and-inheritance.html

http://www.amazon.com/Inheritance-Genes-Change-Lives—Lives/dp/1455549444

available via audible

QT:{{”
One can find more productive ways to think about genes. As a physician who researches and treats rare genetic disorders, Sharon Moalem, the author of “Inheritance,” sees firsthand how sharply DNA can constrain our lives. Yet “our genes aren’t as fixed and rigid as most of us have been led to believe,” he says, for while genetic defects often create havoc, variable gene expression (our genes’ capacity to respond to the environment with a flexibility only now being fully recognized) can give our bodies and minds surprising resilience. In his new book, Moalem describes riveting dramas emerging from both defective genes and reparative epigenetics.
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Oncotator

August 4, 2014

http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator

Useful listing of data sources, viz:

QT:{{”

Protein Annotations

Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.

Cancer Annotations

Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.

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Uses bamboo testing software
https://www.atlassian.com/software/bamboo

How the Paleolithic Diet Got Trendy

August 3, 2014

How the Paleolithic #Diet Got Trendy
http://www.newyorker.com/magazine/2014/07/28/stone-soup #Paleo may look faddish, yet you could argue the reverse: agriculture is a fad

QT:{{”
Paleo may look like a food fad, and yet you could argue that it’s really just the reverse. Anatomically modern humans have, after all, been around for about two hundred thousand years. The genus Homo goes back another two million years or so. On the timescale of evolutionary history, it’s agriculture that’s the fad.
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Annals of Alimentation JULY 28, 2014 ISSUE
Stone Soup

Myosin gene mutation correlates with anatomical changes in the human lineage : Abstract : Nature

July 23, 2014

From S Caroll, “Many approaches are being taken, and a few intriguing associations of candidate genes and the evolution of particular traits have been discovered, such as the…MYH16 muscle-specific myosin pseudogene and the evolutionary reduction of the masticatory apparatus.”

QT:{{”

Powerful masticatory muscles are found in most primates, including chimpanzees and gorillas…. In contrast, masticatory muscles are considerably smaller in both modern and fossil members of Homo. …Here, we show that the gene encoding the predominant myosin heavy chain (MYH) expressed in these muscles was inactivated by a
frameshifting mutation after the lineages leading to humans and chimpanzees diverged. Loss of this protein isoform is associated with marked size reductions in individual muscle fibres and entire masticatory muscles. Using the coding sequence for the myosin rod domains as a molecular clock, we estimate that this mutation appeared approximately 2.4 million years ago.

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http://www.nature.com/nature/journal/v428/n6981/abs/nature02358.html