Friday, May 22, 2015

Weekly Links May 22th ,2015



“MUST READ”
    •      At his firm, Andreessen Horowitz, the venture capitalist routinely lays out “what will happen in the next ten, twenty, thirty years.”
DISRUPTION, REVOLUTION
Now, however, lots of people are talking about CRISPR — particularly after a group of researchers in China recently used the technique to edit nonviable human embryos. Though the embryos would never turn into humans, this was the first time anyone had ever tried to edit the genetic material of homo sapiens, and the April 18 publication of the results sparked a massive outcry.
TOOLS/TECHNIQUES
    • The federal government opened the door to a new era of genetic medicine on Thursday by introducing a standard way to ensure the accuracy of DNA tests used to tailor treatments for individual patients.
  • Behind the Bench: Sanger Sequencing by CE 4: Bi...
    • Part four of a six-part series, here’s an overview of how data is converted by a capillary sequencing instrument from an analog signal to a digital one, assigned a base call (or fragment length) with a quality metric, and lastly variant reporting.
Sanger data-analysis-software.gif
HEALTH/MEDECINE
    • Arcturus BioCloud is a biotechnology startup on the outskirts of San Francisco that hopes to give science hobbyists the ability to gene splice their way to super bacteria with a few clicks on their laptop.
“You don’t need a lab,” co-founder Jaime Sotomayor said of the Arcturus platform. That’s because his team has created a lab in the cloud that will do the work for you with a combination of robotics, artificially intelligent software, and synthetic biology.
COMPANIES
SOMETHING DIFFERENT
    • We all want to work smarter—that’s why productivity is such a hot topic—but are we getting ahead or just spinning our wheels? Tracey Foulkes, CEO of Get Organised South Africa, says too many of us are in the "busy business of busyness." 
"We’re always rushing from meeting to meeting and drowning in work," she says. "It’s not about doing more; it’s about making wiser choices."
    • People think they’re adding value, but if they aren’t doing what they need to do, in reality they’re not. You’re only valuable to your organization when you are doing what you’re hired to do."
  • The Last Day of Her Life - NYTimes.com
    • Sandy Bem, a Cornell psychology professor one month shy of her 65th birthday, was alone in her bedroom one night in May 2009, watching an HBO documentary called “The Alzheimer’s Project.” For two years, she had been experiencing what she called “cognitive oddities”: forgetting the names of things or confusing words that sounded similar. She once complained about a “blizzard” on her foot, when she meant a blister; she brought home a bag of plums and, standing in her kitchen, pulled one out and said to a friend: “Is this a plum? I can’t quite seem to fully know.”

Monday, May 18, 2015

Weekly Links May 18th ,2015



“MUST READ”
    • Now Wartman is participating in an effort that could make DNA sequencing accessible to many more cancer patients. The Genome Institute at Wash. U. is one of 14 big-name cancer centers partnering with IBM IBM +0.83% to use the computing giant’s Watson artificial intelligence system to compare patients’ genetic data with databases of cancer genes and every scientific paper published about cancer genetics. What takes a team of experts hours or days can be accomplished in minutes. (Read a blog post Wartman wrote about the project here.)
TOOLS/TECHNIQUES
    • n the cell culture practice, heat inactivation of serum products has always been accepted and is one of the basic protocols passed on to new cell culturists. There is no strict standard protocol for heat inactivation, some say incubate at 56 °C for 30 minutes, while some say it can be efficiently performed using temperatures ranging from 45-62 °C and incubation times of 15-60 minutes
What ever way it is done, many people believe strongly that it is a necessary step to keep your cells happy. However, these protocols originated before the 1970’s when there were still technical flaws in the collection, processing, and understanding of serum
More recent practices suggest that heat inactivation of serum may not be all that necessary.
    • Every step of an experiment, from set-up to collecting, processing, and running assays, requires dozens of steps, all of which are potential sources of variation. In thinking about at an experiment holistically, consistency is key to minimizing variation. When you repeat an experiment, doing everything exactly the same as the first time is crucial.

HEALTH/MEDECINE
    • Linking a human DNA sample to a database of human DNA 'fingerprints' is the basis for forensic genetics, which is now a decades-old field. We've shown that the same sort of linking is possible using DNA sequences from microbes inhabiting the human body—no human DNA required,” said Eric Franzosa, Ph.D., a research fellow in the Department of Biostatistics at Harvard Chan. “This opens the door to connecting human microbiome samples between databases, which has the potential to expose sensitive subject information—for example, a sexually-transmitted infection, detectable from the microbiome sample itself."

COMPANIES
    • Seattle experts in computer science and immunology are rallying around a new spinoff company from the Fred Hutchinson Cancer Research Center.
Seattle-based Adaptive TCR has nailed down a $4.5 million round of angel investment to get up and running, Xconomy has learned. The basic concept is to provide scientists with a high-speed, high-resolution look into the vast diversity of T-cells of the adaptive immune system that we all produce to ward off infections, and which sometimes go awry and cause disease.
    • The idea of modifying genes is heralded by some as holding the potential for new therapies addressing rare, genetic diseases, or producing agricultural products with certain desirable characteristics. Precision BioSciences believes that its technology can beat out other emerging gene-editing technologies and it has closed on $25.6 million to prove it.
SOMETHING DIFFERENT
    • Manicurists are routinely underpaid and exploited, and endure ethnic bias and other abuse, The New York Times has found.

Friday, May 15, 2015

Weekly Links May 15th ,2015



“MUST READ”
    • The CRISPR-cas9 system makes gene editing in many organisms and cells — like our own egg, sperm or embryo — more efficient, accessible and simple than ever before. These groundbreaking capabilities have spawned discussions surrounding the ethics and applications of the new system, and have garnered significant attention around the world to ensure ethically correct usage.
TOOLS/TECHNIQUES
    • Since its first use as a forensic tool in the 1980s, DNA analysis has become   the gold standard of evidence in criminal justice. Early forensic scientists   used Restriction Fragment Length Polymorphism (RFLP) analysis to compare   profiles of likely suspects. More recently, improvements in nucleic acid   purification and amplification techniques made it much easier to obtain   reliable DNA profiles from minimal sample material. And next generation   sequencing (NGS) technologies are identifying new targets that will yield   markers more specific for individual suspects, as well as allow the   collection and sharing of these data through centralized databases.

HEALTH/MEDECINE
    • More than 200 scientists working on an ambitious federal project have begun to understand the complicated system of switches that regulates genes, turning some on and others off, making some glow brightly while others dim. They hope these discoveries, described in two dozen papers released on Wednesday, will eventually lead to a deeper understanding of diseases and new ways to treat or cure them.

COMPANIES
    • The big idea at Adaptive is in immune sequencing, and figuring out what to make of the ever-shifting DNA sequences in that make up the immune defense repertoire. Unlike other cell types, which operate on a fixed set of code from the human genome, immune system cells rearrange their DNA constantly in response to the environment, providing infinite possibilities for defense against an infinite number of threats. That phenomenon calls out for repeated sequencing to see how an individual’s immune response adapts over time. Sometimes things go haywire and the immune system starts attacking healthy tissues (autoimmune disease) or certain immune system cells start proliferating out of control (cancer).
  • Alexion to Buy Synageva BioPharma in $8.4 Billion Deal - NYTimes.com
    • Alexion Pharmaceuticals became one of the most valuable companies in the biotechnology industry on the strength of a single drug that treats two extremely rare diseases. Its secret: charging about $500,000 a year for the drug for each patient and scouring the planet for every potential patient. Now, the company hopes to repeat this process with a new drug.
Alexion said on Wednesday that it would pay about $8.4 billion to acquire Synageva BioPharma, another company specializing in rare diseases with one drug expected to come to market this year.
    • The Rales brothers, who work hard to avoid publicity and each own about 6% of Danaher, are capital allocation masters, building their fortunes through leveraged acquisitions and tax-efficient business restructurings. In addition to building Danaher, which has a market capitalization of $62 billion,
SOMETHING DIFFERENT
    • We all want to work smarter—that’s why productivity is such a hot topic—but are we getting ahead or just spinning our wheels? Tracey Foulkes, CEO of Get Organised South Africa, says too many of us are in the "busy business of busyness."
"We’re always rushing from meeting to meeting and drowning in work," she says. "It’s not about doing more; it’s about making wiser choices."
    • People think they’re adding value, but if they aren’t doing what they need to do, in reality they’re not. You’re only valuable to your organization when you are doing what you’re hired to do."