Archive for the 'Biotechnology' Category

Attention Whole Foods Shoppers

Published on 6/6/2010 in Africa and Biotechnology . Closed Tags: .

Organic farming is less econ-friendly than you think, and conventional farming is more so.

Robert Paarlberg, author of Starved for Science: How Biotechnology Is Being Kept Out of Africa and The Politics of Precaution, has a “don’t miss” essay Attention Whole Foods Shoppers in the June 2010 Foreign Affairs. The following reviews of Starved for Science give the gist of the FP article (which could be very crudely abbreviated to “Greenpeace succeeds in keeping Africa poor and hungry”):

Condoning the cultivation of genetically modified crops for food is not, Robert Paarlberg concedes, likely to win him friends in academic circles…But in this timely book, Paarlberg, a political scientist, makes a strong argument: Europeans, who have so much food they do not need the help of science to make more, are pushing their prejudices on Africa, which still relies on foreign aid to feed its people. He calls on global policymakers to renew investment in agricultural science and to stop imposing visions of “organic food purity” on a continent that has never had a green revolution. As governments look for ways of tackling what is now commonly called a “global food crisis” with unprecedented price increases in basic foodstuffs, this book offers welcome food for thought.

–Jenny Wiggins (Financial Times 20080627)

Except for South Africa, no African state has legalized the planting of GMOs for production and consumption. While citizens of rich countries have the luxury of deciding what kinds of foods–organic, nonorganic, GMO, non-GMO–to eat, droughts and insect infestations continue to wipe out crops, and rural African children die because they have no choices. Bringing another perspective to the GMO debate [is] Paarlberg’s provocative argument.

–Joshua Lambert (Library Journal 20080501)

[An] illuminating book on the state of science and agriculture in Africa…[It] has much of merit.

–Jules Pretty (Times Higher Education Supplement )

[This] book ends with an alternative perspective on globalization that will inspire open-minded skeptics to rethink the matter…[Paarlberg is] a pragmatic believer in separating babies from bathwater. The fact that current applications of GM technology primarily benefit a handful of corporations does not deter Paarlberg from envisioning a scenario in which nonprofits and private African corporations might employ GM technology to serve the increasingly dire needs of African farmers…An insightful book that deftly balances the benefits and drawbacks of globalization, all within parameters conforming to the real world, the one in which we live…A clarion call for corporations and NGOs alike to revisit issues that have been ideologically polarized rather than rationally examined.

–James E. McWilliams (Texas Observer )

From the FP essay:

(…) In Europe and the United States, a new line of thinking has emerged in elite circles that opposes bringing improved seeds and fertilizers to traditional farmers and opposes linking those farmers more closely to international markets. Influential food writers, advocates, and celebrity restaurant owners are repeating the mantra that “sustainable food” in the future must be organic, local, and slow. But guess what: Rural Africa already has such a system, and it doesn’t work. Few smallholder farmers in Africa use any synthetic chemicals, so their food is de facto organic. High transportation costs force them to purchase and sell almost all of their food locally. And food preparation is painfully slow. The result is nothing to celebrate: average income levels of only $1 a day and a one-in-three chance of being malnourished.

If we are going to get serious about solving global hunger, we need to de-romanticize our view of preindustrial food and farming. And that means learning to appreciate the modern, science-intensive, and highly capitalized agricultural system we’ve developed in the West. Without it, our food would be more expensive and less safe. In other words, a lot like the hunger-plagued rest of the world.

Craig Venter unveils “synthetic life”

Published on 5/25/2010 in Biology and Biotechnology . 1 Comment

“We can now begin working on our ultimate objective of synthesizing a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work.” – Dan Gibson

We’ve been following the efforts of the Venter Institute to develop a synthetic bacterial cell. The goal of this research has been to achieve the capability to “understand by building” as applied to the cell.

Last night we noted that TED.com was hosting a Craig Venter press conference where on May 20th he announced their success. The talk is a bit dry compared to the typical TED Talk, but we think you will find it exciting. Venter describes several of the unexpected roadblocks encountered in the project, commenting to the effect that “over 99% of our experiments were failures”.

You can read a summary in a Venter/Gibson WSJ op-ed which begins:

In 1995, we reported the DNA sequences for the first two cellular genomes. Nowadays genome sequences, which contain the genetic instructions for an organism, are routinely obtained and deposited in computer databases.

Last week, we reported that this process can be reversed. The digitized DNA information of Mycoplasma mycoides, a simple bacterium, can now be brought to life.

To make this happen, our group of 25 researchers had to decipher this bacterium’s set of instructions, synthesize them, and then express them in a recipient cell. Many technical hurdles had to be overcome. But 15 years and $40 million worth of research later, we are able to combine all of these steps and produce synthetic cells in the laboratory.

So what is new and unique about what we did? The process of synthesizing a cell began at a computer. We started with the more than one million letters of genetic instructions for Mycoplasma mycoides, and then made slight modifications to its DNA sequence. First, we deleted 4,000 letters, which removed the function of two genes. We then replaced 10 genes with four “watermark” sequences. These watermark sequences are each over 1,000 letters in length and can be decoded to reveal the names of people, famous quotations and a website address. The entire sequence of DNA letters was then partitioned into 1,100 pieces, and each was synthesized using four different bottles of chemicals that make up DNA. These DNA fragments were designed such that adjacent pieces contained an 80-letter overlap, which facilitated the assembly process by providing unique regions where the synthetic pieces could join.

For the in-depth results you can access at Science Express: Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome [full text available here as PDF]. And the Venter Institute press release.

What does this accomplishment mean? First, the pace of synthetic biology has been much slower than we hoped (and slower than advocates like Stanford’s Drew Endy forecast). Second, the technical feat of assembling a 1 million letter DNA sequence is still staggering. E.g., just consider the error-detection/correction challenge — this is the debugging method developed to isolate a synthesis error in the final stages:

The initial synthesis of the synthetic genome did not result in any viable cells so the JCVI team developed an error correction method to test that each cassette they constructed was biologically functional. They did this by using a combination of 100 kb natural and synthetic segments of DNA to produce semi-synthetic genomes. This approach allowed for the testing of each synthetic segment in combination with 10 natural segments for their capacity to be transplanted and form new cells. Ten out of 11 synthetic fragments resulted in viable cells; therefore the team narrowed the issue down to a single 100 kb cassette. DNA sequencing revealed that a single base pair deletion in an essential gene was responsible for the unsuccessful transplants. Once this one base pair error was corrected, the first viable synthetic cell was produced.

I feel confident in predicting that Venter will not be building a pilot plant for his synthetic biofuel next year. But I would definitely not bet against important breakthroughs in the next five or so years. At least I hope the promise is not always “just five years ahead”. Here’s Venter/Gibson from the WSJ op-ed on one of our priority wishes, that of rapid-response vaccine development:

(…) We are currently working on the design of new cells that can much more efficiently capture carbon dioxide and “fix” (or incorporate) the carbon into new fuel molecules, new food oils, and new biologically derived sources of plastic and chemicals. We already have funding from the National Institutes of Health to use our synthetic DNA tools to build synthetic segments of every known flu virus so that we can rapidly build new vaccine candidates in less than 24 hours. We are also being funded to see if we can take sets of genes out of bacteria to design new synthetic pathways to make antibiotic compounds that are currently too complex for chemists to make.

One (of many) things we don’t yet grasp is “why did Venter switch from the original goal of synthesizing the minimal organism?” Please comment if you know. Meanwhile, we have this from the useful FAQ:

Q: What are the next steps for this research at JCVI?

A: The work to create the first self-replicating, synthetic bacterial cell was an important proof of concept. The team at JCVI has learned a lot from the nearly 15 years it has taken to get to this successful stage. From this proof of concept experiment the team is now ready to build more complex organisms with useful properties. For example, many, including scientists at SGI, are already using available sequencing information to engineer cells that can produce energy, pharmaceuticals, and industrial compounds, and sequester carbon dioxide. The team at JCVI is already working on their ultimate objective, which has been to synthesize a minimal cell that has only the machinery necessary for independent life. Now that a cell can be synthesized from a synthetic genome in a simple near-minimal bacterial cell, it becomes possible for the team to test for the functionality of a genome. They can whittle away non-essential DNA regions from the synthetic genome and repeat transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal bacteria cell will enable a greater understanding of the function of every gene in a cell and a new vision of cells as understandable machines comprised of biological parts of known function.

Engineering Biology: A Talk with Drew Endy

Published on 2/22/2010 in Biotechnology . Closed

At Edge, John Brockman interviews Stanford prof. Drew Endy on the question “how to make biology easy to engineer?”

(…) The underlying goal of synthetic biology is to make biology easy to engineer. What does that mean? It means that when I want to go build some new biotechnology, whether it makes a food that I can eat or a bio-fuel that I can use in my vehicle, or I have some disease I want to try and cure, I don’t want that project to be a research project. I want it to be an engineering project. In the science of biology, the people you’re talking to are scientists, they’re not engineers, and—not to be arrogant, just to be an observationalist—the question is, if you’re an engineer looking at biotechnology, what do you need to do in order to make it easy to engineer? That’s what synthetic biology is about.

The interview concludes with this

(…) When we organized the First Synthetic Biology Conference at MIT in 2004, we were expecting about 150 people, so we booked a room for 297. And 500 people wanted to come given six weeks of notice. Now it’s going on four years later, the fourth meeting will be at the Hong Kong University of Science and Technology, which I think will blow doors off of most places in the world 20 years from now. The University is in Clearwater Bay in Kowloon, Hong Kong. I got off a flight there to meet with the local organizers, and the fellow who’s championing our organizational visit is a retired banker, who was responsible for helping take Apple public all the way up to building up capital markets in China recently. He looks at what’s going on and he says, explaining to a real estate tycoon in Hong Kong, ‘I remember the personal computer and I remember recombinant DNA, and what’s happening here is both. And this is important, and Hong Kong needs to support this.’ And he looks at me, and asks, ‘Did I get that right?’ This is the first time I’ve ever met this fellow. ‘Yeah, that’s pretty much right.’ He is a very impressive fellow and a very, very good person.

There are some people who understand what’s going on, and who are in a position, or who have comfort acting on time scales that are relevant. It is interesting for me to learn how difficult it is for folks to appreciate what an exponential technology really implies. The fact that sequencing goes from approximately zero to human genomes in ten years. The same thing is happening with construction of genomes. And with the parts collection—the standard biological parts doubling every year. And the same thing is happening with the number of teenagers who would like to do genetic engineering; it’s doubling every year. How do you actually live in a world where you’re surfing that exponential in a way that’s constructive and responsible? Very few people get that.

(…) How do you recognize this exponential and serve it and bring more people to participate in it? The rewards of doing this are greater than any one group’s project. For instance, the team from Melbourne, Australia showed up with a 6,000 base pair fragment of DNA that they found, which somehow, I don’t know how this actually works, folds up … the proteins get made and the proteins self-assemble into a 50 nanometer, very tiny, sphere that is filled up with gas. The protein shell is somehow gas-impermeable, and these little balloons, these protein balloons, get booted up inside the cytoplasm, the insides of cells, and you can control how many different balloons there are. Depending on the number of balloons, the cells will either float or sink or be neutral.

Who knew? I didn’t know anything about this biology, and they showed up, they made this standard biological part, such that we can now snap it together with the 2,000 other parts that we’ve got in our collection so far, which is a free collection. We shipped over a hundred thousand parts around the world last year, for free, and the collection’s doubling in size every year.

Very highly recommended. Dr. Endy is the founder of the MIT IGEM competition (International Genetically Engineered Machines), and a co-founder of BIOFAB. See BIOFAB and BioBricks: synthetic biology is taking off. More here.

Do-It-Yourself Genetic Engineering

Published on 2/11/2010 in Biotechnology . Closed


(…) Or consider the case of the Slovenian iGEM team, the most intimidating squad coming into last fall’s jamboree and also the hardest to miss, having forgone mere team T-shirts for severe, blue athletic jerseys that made the dozen young Slovenians seem capable of sprinting 200 meters or throwing a discus at a moment’s notice. “I think the last two years, we have 100 percent, beyond doubt, the best shirts,” the team’s adviser, Roman Jerala, told me.

Slovenia had won the BioBrick trophy in two of the past three iGEMs, including the previous fall, when it produced a possible vaccine for a virus that causes stomach ulcers, presenting promising data in mice. The team is covered consistently by the Slovenian media, and Jerala had recently lectured about synthetic biology to the Slovenian National Assembly. A television network named him one of Slovenia’s seven most influential people.

I first wrote about (then) MIT’s Drew Endy, synthetic biology, BioBricks and the iGEM competition three years ago. And then an update on the opening BIOFAB, founded by prof. Endy and other leaders in the field. Now the NYT Magazine has done a nice survey of synthetic biology and the latest iGEM competition. Here’s a sample:

(…) The story of iGEM and, to some degree, the vision of synthetic biology that it champions, begins not with biologists but with engineers. From the beginning, the approach was rooted less in the biologist’s methods of patient observation than in the engineer’s childlike love of building cool stuff and hyperrational expectations about the way things ought to work.

Drew Endy came to M.I.T. as a bioengineering fellow in 2002 at the age of 32. He now teaches at Stanford and is probably the field’s most voluble and charismatic spokesman. “I sort of Facebook-stalk him,” I overheard a student say at the jamboree. (Last month, the National Science Foundation financed the creation of a full-scale BioBrick part factory in the Bay Area, called the Biofab; Endy is a founding director.) At M.I.T., Endy found a group of colleagues — like him, all originally engineers by training — who were disappointed with how unmethodical a field that was termed “genetic engineering” appeared to still be: its major successes were more like imaginative, one-off works of art than systematic engineering projects. As Endy told me, “I grew up in a world where you can go into a hardware store and buy nuts and bolts, put them together and they work.” Just as you tell a computer to add 2 and 2 and know you’ll get 4, Endy said, you should be able to give a cell simple commands and have it reliably execute them — and explaining this, he still managed to sound honestly flummoxed that something so absolutely logical wasn’t actually true; his approach to the living world is astonishingly Spock-like. “Biology is the most interesting and powerful technology platform anyone’s ever seen,” he said. “It’s already taken over the world with reproducing machines. You can kind of imagine that you should be able to program it with DNA.”

Arguably this has been an implicit dream of genetic engineering all along. But starting in the mid-’90s, synthetic biologists concluded that we had amassed enough knowledge about how genomes work and developed enough tools for manipulating them that it was time to actively pursue it. In 2003, Endy formed a partnership with three other like-minded engineers at M.I.T., Gerald Sussman, Randy Rettberg and Tom Knight. Rettberg, who now directs iGEM, had absolutely no background in biology until, after retiring as a chief technology officer at Sun Microsystems in 2001, he started reading textbooks and hanging around Knight’s lab; the two friends worked early in their careers on designing computers. Knight had already developed the concept of BioBrick parts and a method for connecting them.

The four men decided that rather than spend decades figuring out how to turn life into the predictable machinery they wanted it to be and then teaching that to their students, they would enlist the students to help. They taught a monthlong course challenging teams of students to design E. coli that “blinked” — that is, generated fluorescent light at regular intervals. That first experimental class rapidly evolved, by 2006, into an iGEM Jamboree involving 35 schools. And from there, Endy told me, “this thing goes international fast.”

(…) Most students I met at iGEM said they were attracted to synthetic biology because of the immense good it might accomplish and had spent their summers engineering very altruistic microbes: ones that generate cheap alternative energy, attack tumors or deliver pharmaceuticals within the body, detect fertilizer runoff in drinking water, reveal the location of land mines or, in the case of Stanford’s team, wipe out irritable-bowel syndrome. iGEM has begun to require students to consider any ethical or safety questions their projects raise, and Endy seems particularly intent on making sure that these issues, as they pertain to the field in general, are discussed publicly.

(…) In fact, the students from City College heard this from people, spontaneously, throughout the weekend: as one man who approached Colby Sandate put it, they embodied the audacity and the grit that iGEM is supposed to be about. The competition, after all, is itself a machine, engineered to absorb enthusiastic young people and produce synthetic biologists. “I was like, ‘Really?’ ” Sandate told me. “Nobody’s ever complimented us that much before.” He had chosen to genuinely embrace Team City College’s status as the Bad News Bears of synthetic biology. Like the head of a small start-up, he was already lining up equipment, lab space and seed money for the next year.

BIOFAB and BioBricks: synthetic biology is taking off

Published on 2/5/2010 in Biotechnology . Closed

The research laboratory hopes to create thousands of standardized DNA parts to help synthetic biologists create new drugs and chemicals.

At least that is my hopeful take. The press release shows an impressive list of founders, from Drew Endy (ex MIT, now at Stanford), Jay Keasling (Lawrence Berkeley National Laboratory), and Adam Arkin, also of LBNL.

BIOFAB: International Open Facility Advancing Biotechnology announced on Jan. 18 that it has begun efforts to standardize the control elements used in the creation of microbes. The organization will provide synthetic biologists with a toolbox for engineering new drugs and chemicals. BIOFAB is supported by a two-year grant from the National Science Foundation (NSF), Lawrence Berkeley National Laboratory (LBNL), and the BioBricks Foundation, a standardized registry for existing biological parts. Bioengineers from the University of California, Berkeley (UC Berkeley) and Stanford University will manage the project.

Co-Director of BIOFAB, Drew Endy. Source: NIGMS.

“Synthetic biology has the potential to make the engineering of biology much easier and more affordable,” Drew Endy, founding director of BIOFAB, assistant professor of bioengineering at Stanford, and president of the BioBricks Foundation, said in a press release. “Via the BIOFAB, we will help ensure that the public’s investments and interests in the next generation of biotechnology return the greatest benefits.”

Currently, researchers spend a significant amount of time and money to create a microbe since each part, including promoters and transcription factors, must be individually identified, characterized, and modified. A recent project by Jay Keasling, UC Berkeley professor of chemical engineering and bioengineering—which created microbes that produce the anti-malaria drug artemisinin—took 10 years and $25 million to complete. The researchers at BIOFAB intend to shorten development timeframes and reduce costs by producing thousands of standardized DNA parts that will be available to researchers for free.

Chair of the BIOFAB executive committee, Jay Keasling. Source: Lawrence Berkeley National Laboratory.

“The professionally staffed BIOFAB production facility will provide an essential resource that will allow many academic researchers and others to rapidly prototype, test, and translate their foundational discoveries and ideas into practice,” Keasling, who is also acting deputy director of LBNL and chair of the BIOFAB executive committee, said in a press release. “By enabling everyone to better work together, the BIOFAB will make the engineering of biology easier and more predictable.”

Though BIOFAB is an acronym, the name’s significance comes from the idea of fabrication service laboratories, or fablabs, established in the semiconductor industry to facilitate the creation and manufacture of custom chips. Endy co-directs BIOFAB with Adam Arkin, UC Berkeley professor of bioengineering and head of synthetic biology for LBNL’s physical biosciences division. Endy and Arkin proposed the idea of a fablab for biological parts 10 years ago.

“Besides Tom Knight [of the Massachusetts Institute of Technology], very few people were talking about standard biological parts 10 years ago,” said Endy. “We now need to move beyond Lego metaphors and genetic toys to professional technologies.”

While standard biological parts are not yet readily available, they are important in current research. Such parts are used by college students as part of the annual International Genetically Engineered Machine (iGEM) competition and are used daily in synthetic biology labs. Endy quantified the problem by stating that of the estimated 3500 critical control elements in Escherichia coli; fewer than 100 have been seriously studied. Of the 500-plus promoters listed in the current registry, fewer than 50 have been measured.

Co-Director of BIOFAB, Adam Arkin. Source: Lawrence Berkeley National Laboratory.

“What exists today is not a professional parts catalog,” said Arkin. “But the parts we have, while not perfect, are better than nothing, and they are helping researchers all over the world.”

The BIOFAB will operate in partnership with the UC Berkeley–led Synthetic Biology Engineering Research Center (SynBerc) which is also supported by the NSF. BIOFAB intends to hire 29 full-time staff in the near future to standardize the genetic control elements in E. coli. The research will aid parts collection for other microbes and be used to assemble synthetic biological systems.

“Even though we will be building parts and making systems, we are still in the foundational research stage,” said Arkin. “But in starting BIOFAB, we will accumulate the specialized know-how and the community of researchers necessary to become a resource for production and training in synthetic biology.”

Will genomics help prevent the next pandemic?

Published on 11/4/2009 in Biotechnology and Healthcare . Closed

I think that the Infectious Disease Genomics Project could turn out to be VERY important. This is Larry Brilliant’s INSTEDD on steroids (as you no doubt know, Larry was the first head of Google.org).

(…)

Genomics is rapidly changing both the way diseases are diagnosed and the way medications and vaccines are developed – but will it give us the tools to prevent the next pandemic?

  • What if countries where emerging infections originate, from Cameroon to Cambodia, could rapidly sequence suspect samples and discover new pathogens when only a few people have become sick?
  • What if all such sequence data were immediately shared in a single global open access database?
  • What if you could search for a string of sequence data and all associated data, annotations or publications as easily and effectively as a Google search?
  • What if markers discovered for a new disease would quickly be incorporated into affordable hand held multi-pathogen diagnostic tests widely available at the point of care?
  • What if the results of those tests were uploaded to a database where surveillance tools like Google Flu Trends could discover outbreaks?

Today the Public Library of Science, a mission driven, non-profit and open access publisher, presents “The Genomics of Infectious Disease” a collection of essays, perspectives and reviews that explores how genomics—with all its associated tools and techniques—can provide insights into our understanding of emerging infectious disease. This collection was produced with financial support from Google.org with the editorial independence and rigor of PLoS and the expert opinion of leading researchers.

(…)

You can read more in this blog from PLoS and listen to a fascinating audio interview debate with with Jonathan Eisen, Siv Andersson, and Raj Gupta, led by Kirsten Sanford.

See also “Outbreaks Near Me” for your iPhone.

Forgotten Benefactor of Humanity – Norman Borlaug.

Published on 9/13/2009 in Biotechnology . Closed

Read the speech Borlaug gave on The Green Revolution and its implications for humanity when he accepted the Nobel Peace Prize.

I’ve been writing about the father of the Green Revolution, Norman Borlaug for a good while. I certainly could not have written this wonderful essay by Gregg Easterbook for The Atlantic. Excerpt:

Borlaug is an eighty-two-year-old plant breeder who for most of the past five decades has lived in developing nations, teaching the techniques of high-yield agriculture. He received the Nobel in 1970, primarily for his work in reversing the food shortages that haunted India and Pakistan in the 1960s. Perhaps more than anyone else, Borlaug is responsible for the fact that throughout the postwar era, except in sub-Saharan Africa, global food production has expanded faster than the human population, averting the mass starvations that were widely predicted — for example, in the 1967 best seller Famine — 1975! The form of agriculture that Borlaug preaches may have prevented a billion deaths.

Yet although he has led one of the century’s most accomplished lives, and done so in a meritorious cause, Borlaug has never received much public recognition in the United States, where it is often said that the young lack heroes to look up to. One reason is that Borlaug’s deeds are done in nations remote from the media spotlight: the Western press covers tragedy and strife in poor countries, but has little to say about progress there. Another reason is that Borlaug’s mission — to cause the environment to produce significantly more food — has come to be seen, at least by some securely affluent commentators, as perhaps better left undone. More food sustains human population growth, which they see as antithetical to the natural world.

Joe DeRisi: Computers + Biology = Virus Detector

Published on 4/1/2009 in Biotechnology . Closed

Some of the more exciting progress in biotech is the work of the group at DERISILAB at UC San Francisco. We were exposed to the general theme of their research by a recently released TED Talk: Hunting the next killer virus – by lab founder Joe DeRisi. Please do not miss this remarkable presentation.

Biochemist Joe DeRisi talks about amazing new ways to diagnose viruses (and treat the illnesses they cause) using DNA. His work may help us understand malaria, SARS, avian flu — and the 60 percent of everyday viral infections that go undiagnosed.(Recorded February 2006 in Monterey, California. Duration: 16:06.)

In October 2008 Claudia Dreifus at NYT wrote up a two hour interview with Dr. DeRisi — which provides a short overview of the DERISILAB work on virus detection/identification, particularly their ViroChip microarray. Excerpt:

Q. AND YOU DID BUILD IT. WHAT DOES YOUR VIROCHIP LOOK LIKE?

A. It’s a glass slide onto which we’ve printed little DNA fragments of every virus ever discovered ó about 22,000 different viral sequences. I designed the robot that made the chip. I then built that robot and wrote all the software to automate it. I’ve always been a serious computer nerd, as well as a biologist. Now is really the right moment for a scientist with that combination of interests. The way the chip works is this: If we are looking at a virus and trying to figure out what it is, we take some DNA and some RNA from a patient and we tag it with a fluorescent dye. Then we put that material onto the virus chip. Because matching genetic sequences stick to each other ó the double helix ó if there’s a match between what’s on the chip and our biological sample, a particular spot on the chip will glow. That tells us which virus the sample is. And, thanks to computers, we can do this with thousands of viruses at one time.

Q. CAN YOUR CHIP FIND UNDISCOVERED viruses?

A. It can. The ability to do it relies on evolution. It turns out that viruses evolve from each other, like everything else. So if you look at the evolutionary tree of viruses, you can find parts of their genome that haven’t changed over evolutionary time. You can recognize what may be a new virus by identifying this little piece of their genome that hasn’t changed and is represented on the chip.

Q. IS THAT WHAT YOU DID IN 2003 WITH SARS?

A. Yeah. We had just finished building the full version of our ViroChip, when we read about SARS in the newspapers. We literarily begged the C.D.C. to send us samples of the virus. Once we had it, we immediately put it onto a chip. In less than 24 hours we confirmed that this was a novel coronavirus. We confirmed the ViroChip’s finding by subsequently sequencing this virus’s genome. This had never in history happened before. It was unthinkable five years earlier.

From now on, I don’t think there is going to be any new viral epidemic that we will not be able to identify within a few days. It doesn’t mean you’ll find a cure right away. But you will be able to separate people who have it from those who don’t. You can stop it from spreading, if you have a diagnostic. That’s what got SARS under control.

Q. I UNDERSTAND THAT YOUR CHIP HAS BEEN HELPFUL IN DIAGNOSING SOME AVIAN VIRUSES. IS THAT TRUE?

A. After SARS, we got calls from veterinarians in Israel and Florida who told us that parrots, macaws and cockatiels were dying from this wastingdisease, which they suspected was viral. Once we got tissue samples, the ViroChip quickly picked up that this was a bornavirus, something seen in livestock, but that hadn’t been identified in birds before.

As with SARS, once we had a diagnostic tool, you could separate the sick birds from the healthy ones. You might not be able to save an infected bird, but you can certainly stop the epidemic from going any further.

Q. ARE YOU USING THE SAME TECHNOLOGY TO STUDY MALARIA?

A. Yes, we use DNA microarrays that are similar to the virus chips. Malaria is a one-cell parasite; it’s not a virus. We built a chip that represents that organism’s genome ó 6,000 genes. And we grew large amounts of the parasite in vats of human blood. We were then able to use the chip to understand what genetic program these parasites run at the moment they infect human blood cells. This is important because all the clinical symptoms of malaria occur when the parasite infects a person’s blood cells. This knowledge will assist drug and vaccine development.

Before we did this, it was anyone’s guess which of the 6,000 genes were important. Now this data has gone to every malaria lab in the world, and they are picking specific genes to work on, many times based on our data. That’s just amazing!

Q. HAVE YOU PATENTED YOUR VIROCHIP?

A. My colleagues and I considered it. But in the end, we saw no value in doing that. We want people to use this technology. By disseminating the technology freely, more researchers can utilize it faster. And that can produce more rapid advances in human health. We put the specifications into the public domain.

Q. YOU’VE JUST WON THE HEINZ AWARD. WHAT DO YOU PLAN TO DO WITH THE $250,000 PRIZE MONEY?

A. I intend to use a percentage for special research projects on infectious disease, and I’ll give a percentage to field operations working against malaria. After that, I’ll pay my two young daughters’ day care bills and also set up college funds for them.

I did my undergraduate work at the University of California when it was still affordable. But tuition keeps on rising. We’d better start saving now.

If you would like to read some of the published work demonstrating the power of the ViroChip approach, try Genome-wide diversity and selective pressure in the human rhinovirus.

Aging: calorie-restriction benefits from a molecule (SRT1720)

Published on 11/7/2008 in Biotechnology . 1 Comment

A potential longevity-enhancing drug has passed its final animal testing challenge, pushing closer to reality the dream of all-purpose drugs against diseases of aging.

Mice given the new drug, called SRT1720, gorged on high-fat food for four months without gaining weight or developing diabetes, and ran twice as far on a treadmill as their control-group counterparts. Similar drugs are expected to follow down the pipeline.

While still early days, we now have another encouraging milestone in the search for molecules that mimic the longevity benefits of long-term starvation. So far, caloric restriction is the only therapy I know of that has solid anti-aging benefits for mice (and by inference, for humans).

Marc Pelletier, host of the Futures in Biotech podcast has interviewed some of the principal researchers in this field — but tonight I have failed to search up the specific interview with one of the founders of Sirtris — whose researchers contributed to this research just published in Cell Metabolism. Excerpts:

“If you look at all the things that have fundamentally changed medicine in the last 150 years, washing hands would be one, and antibiotics another. This could be the third,” said study co-author Philip Lambert, a pharmacologist at Sirtris Pharmaceuticals, the drug’s developer. “If you could keep your health for another 10 or 15 years, that would be amazing.”

SRT1720 activates one of several enzymes that regulate the function of mitochondria — cellular power generators that convert glucose into chemical energy. The wearing down of these generators has been linked to heart disease, Alzheimer’s disease, diabetes, cancer and other age-related afflictions.

That same enzyme is also targeted by resveratrol, a naturally occurring compound that reduces age-related diseases in lab animals and is already used by longevity enthusiasts. Researchers at Sirtris showed last year that synthetic drugs that activate the enzyme produced the same cell-level changes as resveratrol, but the tests only lasted for two weeks. The latest study lasted four months, suggesting that SRT1720 — and perhaps the class of enzyme activators expected to follow — are for real.

“This shows you can make drugs that work even better than resveratrol,” said David Sinclair, co-founder of Sirtris, who compared the finding to the synthesis of antibiotics inspired by early fungal components. “Now we’ve got human-designed synthetic molecules. We’re not talking about plant extracts anymore.”

Rafael de Cabo, a National Institute on Aging gerontologist who is researching SRT1720 but was not involved in the study, published today in Cell Metabolism, agreed with Sinclair’s assessment, though he cautioned against premature celebration.

“From rodents to humans is a long, long process,” he said. “We’ve demonstrated this in cells, and in mice. Now we need to move to the next level — primates or humans.”

A previous post on this topic.

Fungi Discovered in Patagonia Rainforest Could Be Used to Make Biodiesel

Published on 11/4/2008 in Biotechnology and Energy Policy . 3 Comments

G. Roseum can even be used to make myco-diesel directly from cellulose, meaning that, if the fungus were to be used for large scale biodiesel production, a complete step in the production process could be skipped. The experiments have completely astounded the team. Speaking about the outcome, Prof. Strobel said, “The results were totally unexpected and very exciting and almost every hair on my arms stood on end.”

I hope this still looks promising five years from now!

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