June 2010 marks the 10th anniversary of the sequencing of the human genome. As Francis Collins has pointed out, “we invariably overestimate the short-term impacts of new technologies and underestimate their longer-term effects.” As a member of the community for 14 years, I can tell you that this is true for San Diego, as the expectations in 2000 were likely too high, but the last ten years have brought unexpected progress in many areas.

San Diego has a great ecosystem to take advantage of these exciting longer-term benefits, ranging from our expertise in creating cutting edge research tools, to ground breaking drug discoveries, to new classes of diagnostics, to the exciting new field of synthetic genomics. Of course, Craig Venter has given us a big vote of confidence by relocating here. Let’s bring together experts in an interactive environment August 18th to discuss how we can take advantage of these exciting opportunities. Register here.

Panelists:

Michael Cooke, Ph.D., Director of Immunology Discovery, Genomics Institute of the Novartis Foundation (GNF)
Kelly Frazer, Ph.D., Chief of the Division of Genome Information Sciences for the UCSD Department of Pediatrics
Tom Novak, Ph.D.,, SVP of Research, of Fate Therapeutics
Aristides A. N. Patrinos, Ph.D., President, Synthetic Genomics
Emily Winn-Deen, Ph.D.,, Vice President, Diagnostics Development at Illumina (Bio)

Here are some seed questions for the discussion, and as always feel free to submit your questions as comments below:

• How will the direct to consumer genomics market impact our economy?
• How is genomics being used in drug discovery, and what therapeutic areas have the most promise for San Diego?
• Will the continuing affordability of sequencing affect the landscape of companies?
• What are the best adaptations we can make to take better advantage of the opportunities?

Sponsor

Sponsorship opportunities are still available, please contact us for more information.

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology August Event: The Human Genome 10 Years Later: What Does it Mean for San Diego Biotech?
When: Wednesday, August 18th, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $25/$20 Academic
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/august

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

Mary Canady BarcampSD 7 ‘Crowdsourcing Cat Herding’ from Mary Canady on Vimeo.

I presented at a local ‘unconference’ called Barcamp recently in San Diego. The event is great because it is unscripted and interdisciplinary, and we’d like to extend the model to biotech and life science, with the goal of having a ‘BiotechCamp’ in San Diego soon. Check out the presentation, and if you have any ideas, please feel free to add them to the wiki we’ve set up at http://biotechcamp.org. We have a team of about ten now who will be planning this event. As always, tell us what you think and stay tuned!

Our January Speed Networking event went so well that we promised we’d do it again so that you can meet as many local biotech professionals as possible in one night. How does it work? Check out our report of the last speed networking event for more details, and basically show up with plenty of business cards, something to take notes with, and craft a thirty second ‘elevator speech’ which describes who you are and what you’re looking for professionally. We always have a nice mix of professionals at our events, so it’s a great place if you’re looking for a job, for business partners, or just want to make a lot of new connections.

Our friends at Life Technologies are sponsoring the event, and we’re very excited because you’ve told us you want to learn more about them (2010 Poll). They’ll bring information on the business and open positions. With so much exciting news always coming from them, it will surely be an interesting night!

Sponsor

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology Speed Networking Event July 21st Sponsored by Life Technologies
When: Wednesday, July 21st, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $20/$15 Academic, +$5 at the door (cash/check only)
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/july

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

To share this post easily, cut and paste: SDBN July 21st Speed Networking Event Sponsored by Life Technologies http://sdbn.org/july

Rat hippocampal neurons and astrocytes: See photo credits below

The California Institute for Regenerative Medicine (CIRM) granted a local interdisciplinary research team from UCSD, Salk, and Life Technologies $11.5 million for research aimed at finding a cure for amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease. On June 23rd, CIRM hosted a public research update which I attended. The project is an excellent example of local research organizations and companies working together towards translating research into real cures, funded by California citizens who realize the promise of stem cell technologies.

The ALS team is led by Lawrence Goldstein, Ph.D., and Don Cleveland, Ph.D., from UCSD, and Samuel Pfaff from The Salk Institute. Drs. Goldstein and Cleveland spoke at the event, along with Life Technologies’ Mark Bonyhadi, Ph.D., UCSD’s Martin Marsala, MD, and Lucie Bruijn, Ph.D, from the ALS Association. Goldstein and Cleveland gave a great introduction to the project and explained that ALS is caused by the death of motor neurons, and that the cells’ environment is very important to their survival. Astrocyte cells have a very intimate relationship with motor neurons, and disease progression is predicted to be slowed if healthy precursors are introduced. As Goldstein and Cleveland explained, the ‘neighborhood’ of motor neurons is very important in determining their well being, and healthy astrocytes are the equivalent of neighbors who don’t have parties and mow your lawn for you. The team plans to create and transplant human astrocyte precursors (hAPs) from human embryonic stem cells (hESCs) into human spines. Begining with rodent models, they predict that the first clinical trials could take place in 2014.

Dr. Mark Bonyhadi from Life Technologies then explained how they will help create and analyze the hAPs and develop the processes to prepare them for FDA submission. Life Tech’s long history with high quality cell media and wide-ranging protein and cell analysis tools makes them a perfect partner. Dr. Martin Marsala described the preclinical animal studies that will be performed, and indicated that they have worked with a company called Neuralstem previously to show that spinal cell transplantations can be successful.

Dr. Lucie Bruijn from the ALS Association talked about the fact that there is only one drug available for the disease, and that other stem cell efforts are underway which will help develop the transplantation methods in parallel (Side note: normally drug discovery research is highly secretive, but do publicly funded efforts benefit from removing this veil?). ALS clinical trials are tracked on their website.

The research presented was inspiring, but the clear highlight of the event for me was to hear from ALS patient Dan Desmond. As a veteran, he is unfortunately part of a group that has a higher prevalence to contract the disease, the cause of which is only 10% genetic in nature. From his wheelchair, Dan told us about the progression of the disease, his carpe diem attitude, and he thanked the researchers for their work. Dan received a well-deserved standing ovation at the end of his courageous speech.

Hearing directly from patients is perhaps an unexpected benefit of moving basic research towards a more translational model, where curing disease is viewed as a near-term goal. As described by Dr. Goldstein, CIRM has challenged researchers to rethink assumptions and timelines to come up with solutions to fast-track therapeutics. CIRM is clearly ’stepping up to the plate’ (pun intended) to make Prop 71’s goals of making California a leader in stem cell therapies come to light. This exciting project pairing our local institutions is a fantastic example of the synergies. Have you thought about who you could work with locally? (Hint: come to our events for ideas…)
Photo by GEHealthcare on Flickr under a Creative Comments License

There’s a cool local event we think would be a great opportunity to explore new ways to communicate science. A group of us are going to BarCamp San Diego, a two day ‘Unconference’ which is described below. Check it out (use link above and more info/register here) and contact us if you’d like to give a presentation, if your company would like to sponsor (very affordable, great for tech-friendly life science companies), or if you’re just interested in learning more.

What is BarCamp?

BarCamp is an international network of “unconferences” where geeks, hackers, makers, and others passionate about Internet culture and technology come together to share ideas and learn from one another. It’s an unconference because there is no theme or pre-set list of speakers – the agenda is built onsite of and by the attendees. Every attendee is expected to be a presenter (but they’re pretty lenient on first timers).

The crowd is largely composed of those from technical fields, but topics can range from handmade books to the biochemistry of beer. All you need is a desire to learn and demonstrate cool stuff to fellow geeks. Admission is free, too! Barcamp is what you make it, so leave the slidedecks at home and get ready to “show and tell”.

Here’s some exemplary pics from previous years:
http://www.flickr.com/photos/n8foo/4283743276/in/set-72157623222288102/
http://www.flickr.com/photos/kevlar/4286598334/in/set-72157623113989159/
http://www.flickr.com/photos/kevlar/4285856393/in/set-72157623113989159/
http://www.flickr.com/photos/n8foo/4283677534/in/set-72157623222288102/

The SDBN’s eventual plan is to have an unconference completely devoted to life science and biotechnology. To learn more join us at BarcampSD July 10/11!

To share this post easily, cut and paste: Join Us at BarCamp in San Diego July 10/11 http://bit.ly/c12rkD

You may know that the San Diego Biotechnology Network, and its partner company, Comprendia, are dedicated to improving communication between life scientists and the companies that serve them. As part of this objective, we like to pass on resources for both groups to help, check out our video resources for life science and the list of life science companies using social media. Life scientists can use the wiki list below as a reference and to learn and contribute, and companies should realize the potential that resources such as these present for helping their customers put the complex science behind their products in context.

What is a wiki? Many use the term loosely these days, to refer to any web resource. To us, a wiki is a community-driven, content rich website in which many of the pages are interconnected. There are many free software programs to generate wikis, and even a resource which lists wikis and helps you choose which one will best meet your needs.

We’ve been looking into life science wikis, and with help from the Life Scientists group on Friendfeed, came up with the list below. There are a few schools of thought on wikis. Some believe that all content should reside on Wikipedia (only two Wikipedia-based wikis are listed below). Others feel as though wikis specific for life science, outside of wikipedia, offer a more targeted approach. Also, some feel as though they must remain ‘pure’ and have no advertising. However, these wikis require a lot of work, I see no problem with this as long as the companies are transparent with their association with the resource, and are careful to not turn it into solely self-serving.

There is an enormous potential for life science companies to leverage wikis. Why not a signal transduction wiki sponsored by the companies who sell products in that area (in fact, there is a defunct cell signaling portal on Wikipedia which could be rescued)? Enzyme classes, areas of study (e.g. stem cells), disease areas…the possibilities are limitless! See German distributor Biomol’s wiki–they’ve created a wiki-based product listing supplemented with supporting biological information (p.s. search engines love wikis, perhaps for this reason). We see some life science companies creating fancy flash animations to highlight their products…guess what, search engines cannot see the content in flash! In addition, scientists are accustomed to wikis, there is no need to reinvent the wheel with a fancy new application, something we’ve discussed on the Comprendia blog.

If you represent a life science company who would like to learn how to leverage wikis, attend Comprendia’s Social Media for Life Science and Biotechnology Workshop in San Diego June 22nd, where we’ll cover the Basics, Benefits, Best Practices, and Biotech Examples. Don’t live in San Diego? Contact Comprendia to learn about virtual workshops or visits to your area.

Life Science Wikis

What are your opinions about these ‘free standing’ wikis, outside of wikipedia? Is the redundance found on the wikis troubling, are these private efforts confusing and contrary to the objectives of NCBI, RCSB, etc.? Also, how would you feel if life science companies started to sponsor more wikis? Leave a comment below, and let the discussion begin!

To share easily, cut and paste: The Wonderful World of Wikis for Life Scientists http://bit.ly/apZTOs

Advanced BioHealing (ABH) is a great local company that has turned their product for diabetic foot ulcers, Dermagraft, into a success story for regenerative medicine. I met them at the BIO convention in May and wrote a blog post about their work. They really impressed me, and we thought SDBN members would be interested in hearing their story. ABH doesn’t fit neatly into a single category (perhaps somewhere between medical devices and stem cells, according to the ‘buckets’ we used in our 2010 poll), but perhaps that is part of their success. As we’ve discussed, San Diego Biotech has seen its share of companies who have difficulties traversing the ‘valley of death’ leading to product commercialization, so we think this story is of great interest.

Kathy McGee, Advanced BioHealing’s Vice President and General Manager, will give a short presentation (Bio/Abstract), and representatives from ABH will be on hand to network with throughout the event. ABH is HIRING so this will be a great opportunity for you if you are interested. Sponsorships for the event are also available, contact us for more information. The event will take place June 23rd at 5:30 p.m., and you can register here.

Sponsors

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology Network Event June 23rd featuring Advanced BioHealing
When: Wednesday, June 23rd, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $20/$15 Academic, +$5 at the door (cash/check only)
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/june

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

I recently attended the 2010 American Society for Microbiology General Meeting with my colleague Mary Canady. I’ll be covered the scientific sessions and shared interesting developments in genetics, microbiology, and technology. See also the #ASMGM hashtag on twitter for conference tweets.

Jonathan Eisen spoke Tuesday on the Genomic Encyclopedia of Bacteria and Archaea, an ambitious project to sample across the breadth of microbial diversity and get a sense of just how much genetic diversity is represented across all bacteria. This project was undertaken to get a more balanced picture of genetic diversity, which is currently skewed in modern sequencing projects by under-representation of some groups. Genome sequence data has diverse uses including development of new antibiotics and drugs, as well as for the identification of new species, but without a big picture overview of the “Tree of Life“, scientists are very much like tourists in a strange city without a map, only finding the interesting stuff if they happen to stumble upon it.

Using a method based on an outline of this tree of life, Dr. Eisen was able to sequence species that covered the entire range of genetic diversity. They were then able to more easily analyze sequence data from environmental samples where the species in the sample are not known by essentially filling in the gaps in the branches. Once they had a means to estimate how genetically different one organism was from another, they could more easily discover novel proteins by intelligently selecting genetically distinct organisms and looking at the places where the sequences differed between the organisms.

Another area of research helped by the above framework is in sequencing of samples taken from nature in which novel organisms may be found. Often, many of the microbial species found in a sample don’t survive under the laboratory conditions necessary to grow enough of the bacteria for a sequencing project. These species then go undetected in the sample, unless you can predict something about the number and relationships of species in the initial mixed sample, so that you can tell that a certain genetic puzzle piece doesn’t fit with the known species in the sample. Dr. Eisen’s method aids this identification process by giving a framework for aligning gene sequences recoved from the sample against the known gene sequences of microorganisms, making the guesses about which genes belong to which organisms a little more certain.

Slides from Dr. Eisen’s talk are available at Slideshare.

[Disclosures: Dr. Gunn is a San Diego-based scientific consultant and academic community liaison for Mendeley. Former clients include a private single molecule sequencing startup.]

I’m blogging this week from the 2010 American Society for Microbiology General Meeting with my colleague Mary Canady. I’ll be covering the scientific sessions and sharing interesting developments in genetics, microbiology, and technology. You can also follow the #ASMGM hashtag on twitter for updates.

Sunday night kicked off the conference with a presentation from Stanford bioengineering professor Dr. Stephen Quake, founder of Helicos Biosciences. Dr. Quake attained a mild amount of fame for being the first person to sequence his own genome, as opposed to the multi-center effort that went into the Human Genome Project.

Dr. Quake’s company Helicos has dramatically reduced the time and cost for sequencing projects, broadly expanding the application reach of sequencing. Faster, cheaper sequencing puts genomes within the grasp of smaller research groups, so it’s no surprise that microbiologists have begun to use it to sequence their favorite subjects.

Because the Helicos instrument is so sensitive, it can actually get a sequence from as little as a single cell, so biologists have begun to sample the “sequence space” of interesting microbiological habitats. One such habitat is the termite gut. Termites have the unique ability to digest wood due to microorganisms resident in their gut, but what Dr. Quake’s collaborators found is that it’s not just one species, but as many as 13 species are present, based on sequences recovered from gut samples. Knowledge of the different species living in this habitat can be used to develop new termite-resistant building materials, but just the fact that 13 different species are found in the gut of this tiny little creature was enough to impress the crowd here. Even more interestingly, it seems that the functions of the microbes are non-overlapping, so it’s no accident all these species are there, rather they serve as a form of evolutionary insurance for the termite. Even though one species would have been enough, having multiple species allows the termite to survive habitat changes that might have been less compatible with the resident bacteria.

As with the sequencing of his own genome, the technical details behind this effort are likewise fascinating (if you ask me, the engineering details nearly put those next to me to sleep). The key advance to make the sequencing work is the applicability of the technique to very small samples, such as you might be forced to work with if you wanted to study a bacteria found in nature that no one has yet learned how to cultivate in the lab. To work with samples in the nanoliter range, they developed an ingenious tiny valve controlled by overlapping expandable microchannels. Inflating one set of tubes would expand the wall into the adjacent tube, shutting of the flow of the adjacent channel. Printing complex patterns via lithography allowed them to sample, mix, and separate volumes small enough to contain a single bacterium. Next, they had to solve the problem of off rates, which are a fundamental limitation to how miniaturized an assay can be. They solved this by using a clear polymer to trap the solution over the assay surface, vastly reducing the volume into which the dye could diffuse.

Speaking before Dr. Quake was Yoshi Kawaoka, describing the synthesis of 1918 flu in the lab, technical advancement that aids the study of modern pandemic flu by comparison with this older, more deadly strain. Further work by Dr. Kawaoka led to the development of a novel neuraminidase inhibitor with activity against pandemic H1N1.

[Disclosures: Dr. Gunn is a San Diego-based scientific consultant and academic community liaison for Mendeley. Former clients include a private single molecule sequencing startup.]

Wednesday I attended a regenerative medicine-focused breakfast at the BIO convention and learned about San Diego company Advanced BioHealing (ABH), who took a ‘fallen’ asset, Dermagraft, and not only turned it into an $85M/year product, but is also looking for new indications. Dermagraft was sold by Advanced Tissue Sciences, who had invested hundreds of millions into developing it, and even got FDA approval for the product to treat diabetic foot ulcers.
I spoke with Advanced BioHealing’s Senior VP Dean Tozer, and he describes their methodology as ‘reverse biotech,’ meaning that they first focused on commercializing products, and just recently hired their CSO Charles Hart. Hart will be spearheading the efforts to find soft tissue indications for Dermagraft. This is counter to how most biotechs in San Diego form, and it appears to be working for ABH as they are predicting 30-50% growth over the next few years.
This growth translates to jobs in San Diego, with 15 listed on the ABH careers page currently. ABH has locations in Westport, Connecticut and Nashville, Tennessee as well, and plans to continue manufacturing products in their 70,000 square foot La Jolla site near the Burnham Institute, and has recently acquired 20,000 square feet of office space nearby in an old Pfizer site. I asked Tozer whether the jobs will continue to be created in San Diego, and he said yes, because the talent pool here is so valuable to them.
What can other San Diego biotechs learn from this example? At BIO this year, I have seen successful repurposing of assets and information. It may simply be the product of a down economy, but I wonder what we can learn, and what could be gained by investigating failed assets that exist from local companies who have not survived? Tozer also believes strongly that the right people make the difference, and they were lucky to bring together a team which understands biotech commercialization. Surely, attracting or training more commercially focused professionals in the area would be a great start.