Tuesday, December 30, 2014

Weekly Links January 13,2015

 “MUST READ”
o    The fight is over CRISPR/Cas9, a potential Nobel-winning biotech discovery, and shorthand for a new way to edit and otherwise modify genomes. As a biologist’s research tool, it’s already invaluable. As a medicine, it could fulfill the promise of gene therapy, snipping out faulty genes that cause disease, perhaps replacing them with new, improved ones.
Who invented it and when is the subject of the fight which, like battles over other once-in-a-generation biotechnologies such as RNA interference, monoclonal antibodies, and polymerase chain reaction

DISRUPTION, REVOLUTION
o    The BioFabricate summit in New York rearranged my thinking. BioFabricate was about the intersection of manufacturing and biology: not just “we can make cool new microbes,” but using biology to manufacture products for the real world. Biological products have always seemed far off. But they’re not: the revolution in biology is clearly here now, just unevenly distributed.
TOOLS/TECHNIQUES
o    Luckily, sequencing choices abound, but choosing the right platform can be tricky. Here, we offer a brief guide to your next gen sequencing choices.
HEALTH/MEDECINE
o    It is all in service of researchers who work for the Broad Institute, a gleaming, lavishly endowed genetics center a few blocks away. The sequencing center has worked on human DNA from an international effort, the 1,000 Genomes Project, that looks at the genes of thousands of people from around the world. It has gotten sequences of microbes, like dengue fever, malaria and West Nile virus
COMPANIES


SOMETHING DIFFERENT
o    how about taking a short tea break with a quick science read? Here are a few of my favourite tea-break sites:
o    mazon is a global superstore, like Walmart. It’s also a hardware manufacturer, like Apple, and a utility, like Con Edison, and a video distributor, like Netflix, and a book publisher, like Random House, and a production studio, like Paramount, and a literary magazine, like The Paris Review, and a grocery deliverer, like FreshDirect, and someday it might be a package service, like U.P.S.
o    Scientists at Philip Morris International are experimenting with ways to deliver nicotine — Big Tobacco’s addictive lifeblood — that are less hazardous than cigarettes but still pack the drug’s punch and smoking’s other pleasures. The smoking carousels, stuffed with burning cigarettes or glowing electronic devices, are among dozens of high-tech instruments being used.
The rush by Philip Morris and other tobacco companies to develop new ways of selling nicotine is occurring as more consumers are trying e-cigarettes, devices that heat a nicotine-containing fluid to create a vapor that users inhale.


Monday, December 29, 2014

Weekly Links 2 January 2015

“MUST READ”
    • They found that for every billion dollars spent on research and development since 1950, the number of new drugs approved has fallen by half roughly every nine years, meaning a total decline by a factor of 80. They called this Eroom’s Law, because it resembled an inversion of Moore’s Law (the observation, first made by the Intel co-founder Gorden E. Moore in 1965, that the number of transistors in an integrated circuit doubles approximately about every two years).
  • Learning How Little We Know About the Brain - NYTimes.com
    • Research on the brain is surging. The United States and the European Union have launched new programs to better understand the brain. Scientists are mapping parts of mouse, fly and human brains at different levels of magnification. Technology for recording brain activity has been improving at a revolutionary pace.
TOOLS/TECHNIQUES
    • Total Cost 
The figures above get me to a 2014 cost of about $3500 for a 30x Human genome, and nearly all of that is still sequencing. However that ignores the actual costs of sample handling and downstream biological analysis.
    • Lastly, although the $1000 genome is not available to most of us we should not lose sight of the fact that in 10 years we’ve come from a $300M genome to one that’s realistically available at around $3000. That’s a 100,000 fold drop!


HEALTH/MEDECINE
    • Taken together, findings suggest that some viruses may be working to keep us healthy. “They did a very good job of starting to crack that nut,” said Julie K. Pfeiffer, a virologist at University of Texas Southwestern Medical Center who was not involved in the new study.
David T. Pride, a microbiologist at the University of California, San Diego, said that the new study would spur other researchers to see if they can find similar results in humans.
COMPANIES
    • The global PCR market by technique is segmented into standard PCR, real-time quantitative PCR, reverse transcriptase PCR, digital PCR, assembly PCR, multiplex PCR, hot-start PCR, and others. Real-time quantitative PCR accounted for the largest revenue in 2013 and is poised to reach $5.65 billion by 2020. Further, digital PCR market segment is expected to grow at the highest double-digit CAGR of 12.2% during the forecast period. Among PCR products, reagents and consumables commanded the largest market in 2013 with services segment poised for highest growth rate.
  • Data Companies Carve Out Niche In DNA Test Interpretation | Xconomy
    • For more than a decade researchers have been unleashing a deluge of information about the role of genes in disease, based on automated sequencing of DNA. Genetic tests on individual patients are slowly becoming more common, more detailed, and less costly. 
But patients won’t benefit if their doctors don’t know what to make of those test results. They need interpreters, and that’s the role being staked out by small companies like San Francisco-based CollabRx (NASDAQ: CLRX) and Lexington, MA-based N-of-One, which help doctors wade through the flood of genetic information and choose the best treat
SOMETHING DIFFERENT
    • “How Google Works” is a breezily written and occasionally insightful guidebook for running companies in an age of rapid technological change. It is not, as that exceedingly lame footnote shows, an especially revealing look into the influential juggernaut that has changed the way we learn about one another and the world.
  • Dan Dennett: The illusion of consciousness | Talk Video | TED.com
    • Philosopher Dan Dennett makes a compelling argument that not only don't we understand our own consciousness, but that half the time our brains are actively fooling us.
  • How to Give a Killer Presentation - HBR
    • On the basis of this experience, I’m convinced that giving a good talk is highly coachable. In a matter of hours, a speaker’s content and delivery can be transformed from muddled to mesmerizing. And while my team’s experience has focused on TED’s 18-minutes-or-shorter format, the lessons we’ve learned are surely useful to other presenters—whether it’s a CEO doing an IPO road show, a brand manager unveiling a new product, or a start-up pitching to VCs.

Weekly Links 27 December 2014


“MUST READ”
o    Langer came to believe that one way to enhance well-being was to use all sorts of placebos. Placebos aren’t just sugar pills disguised as medicine, though that’s the literal definition; they are any intervention, benign but believed by the recipient to be potent, that produces measurable physiological changes.
DISRUPTION, REVOLUTION
tags: sequencing
o    Last week, US tech giants Google made a splash in the media, announcing plans to develop new ‘disease-detecting magnetic nanoparticles’.
o    But when we tried to dig deeper into the detail behind the story, things remained pretty light on actual context and detail. So we spoke to Professor Duncan Graham – a UK-based nanoscientist from University of Strathclyde and expert advisor to Cancer Research UK – to get his take on the announcement.
TOOLS/TECHNIQUES
o    Herein, we tested four cDNA synthesis and Illumina library preparation protocols on  a simplified mixture of total RNA extracted from four bacterial species. In parallel,  RNA from each microbe was tested individually. cDNA synthesis was performed on rRNA  depleted samples using the TruSeq Stranded Total RNA Library Preparation, the SMARTer  Stranded RNA-Seq, or the Ovation RNA-Seq V2 System.
o    When targeting genes, drug developers may opt for knockdown via CRISPR or silencing via RNAi. These weapons, however, may fit different battle plans.
o    Recent progress in probing gene function via the RNAi and CRISPR methods were a strong theme of the Discovery On Target conference, which took place last month in Boston. Both methods enable researchers to impair the function of a targeted gene.
HEALTH/MEDECINE
o    Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.
As these correlations have unfurled, so has the hope that we might fix these ailments by shunting our bugs toward healthier states. The gigantic probiotics industry certainly wants you to think that, although there is little evidence that swallowing a few billion yogurt-borne bacteria has more than a small impact on the trillions in our guts.
COMPANIES
o    Cell-free protein expression, as is called the method Invenra and Sutro use, still requires all the “goo” —the protein-making machinery—from inside cells as the growing medium. But it doesn’t require the cells themselves. Once the right mix is in place, the next key ingredient to add is the DNA of the desired protein.
Much faster than conventional cell-based methods, cell-free expression has been available to researchers for years, but Sutro is likely the first biotech to scale it up into what could be a major therapeutic platform
o    When we last left Jonathan Rothberg, the entrepreneur who first throttled DNA sequencing onto its Moore’s Law-beating path, he was leaving behind his genetics work in the tangle of Thermo Fisher’s $14 billion purchase of Life Technologies Life Technologies, which had previously bought his startup, Ion Torrent.
 
Rothberg, one of the most colorful entrepreneurs in biotech, went strangely quiet for eighteen months. Now he’s back with a new incubator (called 4Combinator) and a new startup, Butterfly Network, into which he has put $20 million of his own money and $80 million more from investors to develop a device that sounds like it’s right out of Star Trek: an ultrasound scanner that can give vivid images quickly and cheaply, and that will eventually be able to use beams of concentrated sound to perform some types of surgical procedures.
SOMETHING DIFFERENT