RNA Psuedoknots and the Universcale


I am in a hurry today, so this is going to be brief.

I was checking out the latest over at DIGG, and came across this cool flash applet make by Nikon Japan called Universcale that takes you from picometers to billion of light years in scale, showing objects (albeit, I expected a little bit more quality here) from neutrons to the edge of the universe.

Also, I’m reporting on a new discovery in the realm of viral research. Researchers at the Niels Bohr institute used optical tweezers to grab the ends of an RNA molecule produced by a bird flu virus. They found that the viral-encoded RNA has psuedoknots that cause human RNA polymerase to create the wrong protein (for human), but right for the virus! Check out more at the Science Daily article.

Biofuels Outlook Update


Invest in biofuels today. At least, 2 people think you should — Vinod Khosla of Khosla Ventures, and Dr. Jens Riese of McKinsey & Co. who gave keynote speeches at the World Congress on Industrial Biotechnology and Bioprocessing.

An article from TheAutoChannel discussed this in further detail, but I want to highlight some important points from the post:

In a speech titled “The Role of Venture Capital in Developing Cellulosic Ethanol,” Khosla outlined the range of technologies currently being commercialized to convert cellulosic biomass to transportation fuels. Khosla said that the U.S. Department of Energy’s recent grants to cooperatively fund biorefineries that produce ethanol from cellulose is an acknowledgment that the technology is moving faster than expected. He said that a 100 percent replacement of petroleum transportation fuels with biofuels is achievable, and predicted that ethanol from cellulose technology will be cost competitive with current ethanol production by 2009.

Dr. Jens Riese of McKinsey & Co. also addressed the World Congress plenary session with a speech titled “Beyond the Hype: Global Growth in the Biofuels Industry.” Riese predicted that global annual biofuel capacity would double to 25 billion gallons over the next five years and could reach 80 billion gallons – meeting 10 percent of world transportation fuel demand, enough to replace the annual oil production for fuel of Saudi Arabia – by 2020. According to McKinsey & Company’s model, biofuels can economically replace 25 percent of transportation fuel with crude oil above $50 per barrel. He concluded that the race is on to build a biofuels industry and that companies should invest now.

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World Innovation Forum


I’m planning a trip to California to do some business development and go to the World Innovation Forum amongst other things. The conference is from April 17-18, so if you want to join me, fire me an email because I would love a wingman on this mission! Seriously. (Oh, and there’s an unwritten student rate if you ask nicely …)

I ripped off a bit of content here from the HSM website for the World Innovation Forum, but I want to show you some of the people that are going to be speaking at this event:

CLAYTON CHRISTENSEN Disruptive Innovation

Author of The Innovator’s Dilemma, the business bestseller that outlines Christensen’s revolutionary theory of disruptive innovation

RENÉE MAUBORGNE Blue Ocean Strategy

“Blue Ocean Strategy challenges everything you thought you knew about strategy” (Business Strategy Review)

RAY KURZWEIL A Look into the Future

“The restless genius” (Wall Street Journal), “the ultimate thinking machine” (Forbes), “the rightful heir to Thomas Edison” (Inc. Magazine), and one of 16 “revolutionaries who made America” (PBS)

LYN HEWARD Creativity & Innovation at Cirque du Soleil

Lyn Heward is the creative fire behind Cirque du Soleil–one of the most innovative and creative companies in the world today–helping it grow to distinct 13 troupes that perform on a global stage

VINTON G. CERF Internet: An Engine of Innovation

Google’s Chief Internet Evangelist and widely considered to be the “Father of the Internet”

MICHAEL THIENEMAN A Model of Innovation: Whirlpool

Thieneman’s global position ensures innovative products and features across all of Whirlpool’s brands, reflected in an annual sales total of more than $19 billion

RICK RASHID Microsoft: Research, Product Development, and Future Technologies

As Senior Vice President, Research, Rick Rashid oversees Microsoft Research’s worldwide operations.

In November 2006 I attended the World Science Forum, which is another conference put on by HSM in New York. It was a great conference, where I had the opportunity to meet Francis Collins, Marvin Minsky, and listen to presentations made by some of the worlds greatest minds. I highly suggest getting the chance to get out to at least one of there.

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Genotyping Becomes More Affordable


A new machine called OpenArray(TM) from BioTrove, Inc. now allows genomic research to conduct genotyping (SNP) analysis across much larger patient groups.

As described on Traditional Medicine:

Unlike other technologies, which can genotype hundreds of thousands of SNPs in a few patient samples, OpenArray allows researchers to analyze SNPs across tens of thousands of patient samples – dramatically expanding study size and data significance. OpenArray SNP genotyping is also more efficient than previous technology because of its flexible design. A single OpenArray plate holds as few as 16 or as many as 3072 separate assays, which can be run against 48-144 samples per plate. Since the OpenArray NT Imager can process three OpenArray plates at once, it can generate more than 9000 data points in less than 10 minutes, ultimately generating over 100,000 data points per day with a single employee.

This is a huge step forward in genetics research, but we are still awaiting the $1 genomic sequence. Right now we are bordering on the $1000 dollar genome, which was talked about by Michael J. Heller, Ph.D., Departments of Bioengineering/Electrical and Computer Engineering, University of California, San Diego – yesterday at the Cambridge Healthtech Institute’s “Next Generation Sequencing Applications and Cast Studies” conference in San Diego, CA.

If you’re wondering just how competitive this space is, there is a $10 million X-Prize for Genomics that was issued by Craig Venter, for the first team to successfully sequence 100 human genomes in 10 days. Details of the prize are as follows:

The $10 million X PRIZE for Genomics prize purse will be awarded to the first
Team that can build a device and use it to sequence 100 human genomes within 10
days or less, with an accuracy of no more than one error in every 100,000 bases
sequenced, with sequences accurately covering at least 98% of the genome, and at
a recurring cost of no more than $10,000 per genome.

As it seems, the race is on!

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Chicken McNuggets


Okay, this may not have to do with biotech, but since there was mention of mutations, mutagens and tumorigenic additives, I figured it “could fit”. In any case, I loved McD’s Chicken McNuggets (notice the past tense there…) until I read this article, that got its founding from the book called The Omnivore’s Dilemma by Michael Pollan.

Apparently McDonald’s Chicken McNuggets are composed of 38 ingredients, and are 56% corn! The book goes into each in detail, but I want to concentrate on the genetics aspect of this. Here is a list of chemical additives that are harmful to your DNA:

dimethylpolysiloxene: suspected carcinogen, established mutagen, tumorigen, and reproductive effector. It is also flammable.

tertiary butylhydroquinone (TBHQ): antioxidant derived from petroleum. TBHQ is a form of butane (lighter fluid). FDA limits addition of TBHQ to less than 0.02% percent of the oil per nugget [Suggestion: choose hotdogs over chicken mcnuggets in a spur of the moment eating contest.]

So, what are you eating next time you go out to McDonald’s?

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New Video 2.0 Website to come from NBC and News Corp


I’m not sure who would really want to go head to head with Google, but apparently the answer to that question is NBC and News Corp. who are launching a competitor to YouTube.com in Summer 2007.

The company, which has “yet to be given a name, or a managment team” already has distribution deals with AOL, MSN, Yahoo!, and MySpace and are planning on featuring TV shows and full-length films. Hmm … pretty good job considering there is no management team! More details on the venture can be seen in this NY Times article.

The unnamed company plans to generate revenue by making the video feeds free to watch, but subjecting the users to advertisements. How will they structure these ads?

My Thoughts
I’m not sure how the company plans to work advertising into the streaming video, if its alongside the video, or if there are interruptions within the streaming videos themselves. I can say right now that people are NOT going to like interruptions in their programs being streamed from this website; so, if that’s the plan, many people will surely be disappointed.

I wonder how long it will take before some 15-year old tech-geek programs a method of “PVR-ing” the streaming video, and either (1) cuts out the commercials and saves the video commercial-free on the computer for later playback when its convenient for them; or (2) saves the video allowing for playback with a fast-forwarding option.

I guess we’ll see what happens … either way, it could be an interesting service to check out.

Pharma and Biotech Update


Pharma seeking patents on old drugs, and a 40x increase venture capital spent on biofuel-related companies:

An article from CNN talks about big pharmaceuticals looking to acquire new patents on old drugs to fend off generic competition. They are using the creative minds of their in-house, legal teams to try to “work the system” to their advantage… see Big Pharma teaches old drugs new tricks for the full story.

On the biotech side, there was a report today that discussed a 4000% year-over-year increase in the amount of venture capital spent on biofuel companies from 2005 to 2006. The majority of the funds were geared toward genetically engineering enzymes in the production of bioethanol.

Biofuel Investment Jumps 4000%


Dramatic increases in Venture Capital in the area of Biofuels was realized in 2006. I just caught wind of an article from the Associated Press, Biotechnology that highlights one of the largest one-year increases in venture-backed funding I have ever seen.

An interview at Associated Press with Ron Pernick, who co-founded Clean Edge (a company tracking venture capital investment), said that “Venture capital investment in biofuels has increased from less than $1 million in 2004 to $20.5 million in 2005 to $813 million last year [in 2006]. Much of that investment is flowing to biotechnology companies that genetically engineer microbes that produce enzymes needed to break down crops into alcohol.” If we’re cracking out the calculator, that’s about a 4000%, or 40x increase year-over-year! Now, it is extremely helpful to the venture investors, and the companies, that the US Department of Energy (DoE) has awarded $385 million over the last four years (to six companies, albeit) to develop ethanol.

Please see Biofuels Spark Biotech Rally for the full article.

Some other relevant links include: Biotechnology Industry Organization, and US DoE.

Are you investing an a Biofuel company yet? Maybe you should jump on that wagon before it leaves town…

New Pre-Cancer Biomarker Found


MIT scientists just discovered the function of 14-3-3 sigma protein, and also, what happens if it isn’t present in cells. This is a HUGE discovery toward preventative measures in cancer screening technology. It won’t be long before there are a new set of diagnostics out that screeen for a wide range of cancer precursor biomarkers that increase risk of cancer to a give tissue.

So, what do scientists propose that 14-3-3 sigma does? It plays a role in cell division. Specifically, it helps cells finish cytokinesis and separate into two distinct cells, right at the end of cell division. Michael Yaffe, an associate professor of biology and biological engineering and leader of the research team said “The cells try to divide and try to divide, and they just give up. They can’t finish cytokinesis.” This results in a single cell with two nuclei.

Key information not to be missed from the article:

  • Fused, or binucleate, cells have recently been shown to be precursors to cancer cells. They are often found in so-called “dysplastic” tissue, which consists of cells that are not fully normal but are not cancerous. Comparing tumors to weeds, Yaffe explained that those tissues act as fertile “soil” for tumor development. “Tumors grow in epithelial tissues that are already deranged for some reason, and something about that soil makes it better able to grow weeds.”
  • Loss of 14-3-3 sigma in dysplastic tissue could serve as a marker to help doctors predict whether tumors will develop. “Our hope is that it will be possible to monitor 14-3-3 expression in these ‘benign’ conditions, a subset of which may not be so benign,” said Yaffe.
  • The researchers were initially intrigued by the fact that 14-3-3 sigma is missing in normal tissue that surrounds tumors, which suggested that its function is lost very early in tumor development. Once the researchers started investigating the protein, they eventually unraveled a complex signaling pathway whose disruption leads to the failure of cell division.
  • They discovered that 14-3-3 sigma is most active during mitosis, when it helps control production of proteins necessary for division.
  • 14-3-3 sigma interacts with a translation factor known as eIF4B, whichforms part of an enzyme that allows mRNA to unwind so the ribosome can read its sequence.
  • When 14-3-3 sigma is knocked out, eIF4B is not produced, and mRNA for the protein p58 cannot be translated. p58 plays a critical role in the final splitting of one cell into two during mitosis, so when it is missing, the cells cannot fully divide.
  • When p58 function is restored, the cells resume normal division.

    The story was orginally issued by MIT, and covered by ScienceDaily under the title: MIT Identifies Role Of Key Protein In Tumor Growth

Scientists Rejoice as Google Solves Data Management Crisis


Okay … so maybe “rejoice” is going a little too far, but scientists in the astronomy world are quite happy with Google’s innovative solution to managing their massive amounts of data received from imaging done in space, whether its infrared, gamma-ray, x-ray, etc…

The processes has been coined “FedExNet” by scientists who have already adopted and are using the new service. So what is this new service? I have highlighted some of the main points from the originating Wired article below:

  • Google acts as both a repository and courier for large data sets
  • Google ships both the PC and array to teams of scientists at various research institutions, which then connect their local servers to the array via an eSATA connection. Once the data transfer is complete, the drives get sent straight back to Mountain View, where the data is copied to Google’s servers for archival purposes. The idea then is that if other scientists around the world needed access to such a large quantity of data, Google would simply reverse the process.
  • Chris DiBona, the open-source program manager at Google, says “We make a copy of [the data], and then we can use the hard drives for something else. They’ll get banged around a little bit too much (to store the data directly on the drives). They’re not intended to be a long-term storage medium — they’re like envelopes to us.”
  • With a set of Google drives, Gorelick (who came up with the FedExNet moniker) can copy his team’s data in about 24 hours or less, something that can make a big difference when the time comes to collaborate with other research groups.

    See full article at Wired: Google’s Next-Gen of Sneakernet

Think of all the separate databases out there that manage genetic information. There are many independently operated bioinformatic databases and if they can all be centralized and indexed in a way that only Google can do, think of the potential implications for the scientific community working to progress the knowledge of DNA, RNA and protein interactions. This might be an essential step working towards the completion of the proteome and transcriptome …