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Eventful Days of April

Author: 
Theral Timpson

April Fools Day

There were some big discoveries in the life sciences on April Fools Day (did you hear about a 24th chromosome being found?). So many, in fact, that we were busy all day doing research. After coming across the following announcement of "The Theome Project" around mid-afternoon, we just decided to head out for a drink and call it a day. We so enjoyed this post over at Genotopia, we’ve invited blogger Nathaniel Comfort to join us here at mendelspod.com:

Human Theome Project Sets Sights on 2012

DNA Day - April 15

Perhaps we were a bit envious of the classy, and not too taxing way Daniel MacArthur, genetic testing blogger (@dgmacarthur), celebrated DNA Day. He and the team at genomesunzipped.org reveled in some nostalgia at The Eagle pub of Watson and Crick fame in Cambridge, UK. I often find myself wondering what it was like for Watson and Crick, or Nirenberg and Matthae (they discovered that the poly-uracil RNA sequence coded for the amino acid phenylalanine) the night before they told the world. Knowledge that would change everything, and they were the only ones who knew.

I celebrated DNA day by spitting mine into a vial. Earlier in the week 23andMe ran a sale for what they call their Personal Genome Service. Though the kit arrived on DNA Day, I have to wait six to eight weeks for the results, according to the site. I’ll be blogging about my experience as it happens.

This is the first year I’ve celebrated DNA Day (we went to a pub, too). I picked this up from a congressional website:

“Resolved by the Senate (the House of Representatives concurring), That the Congress--

(1) designates April 2003 as `Human Genome Month' in order to recognize and celebrate the 50th anniversary of the outstanding accomplishment of describing the structure of DNA, the essential completion of the sequence of the human genome, and the development of a plan for the future of genomics;

(2) designates April 25, 2003, as `DNA Day' in celebration of the 50th anniversary of the publication of the description of the structure of DNA on April 25, 1953; and

(3) recommends that schools, museums, cultural organizations, and other educational institutions across the nation recognize Human Genome Month and DNA Day and carry out appropriate activities centered on human genomics, using information and materials provided through the National Human Genome Research Institute and through other entities.” S. Con. Res. 10

The congressional resolution only intends for a one time celebration. We have the NHGRI--they set the day each year--to thank for the ongoing tradition. This year the NHGRI posted a video on YouTube demonstrating the isolation of strawberry DNA using household means. We gave it a try. It's a great way to impress friends at a dinner party. It's a piece of cake.

Happy DNA Day!

Theral

Attending Spring BioConference Live 2011

Author: 
Theral Timpson

This week I “attended” the Spring BioConference Live 2011, a virtual conference devoted to the life sciences put on by the folks at Lab Roots. In the new online age, the concept of “attending” continues to be redefined. Promotion and registration proceed like with any conference. I first heard of the online conference back in 2009, and though my curiosity was pricked, I declined the free registration. This year’s Spring Show boasted sessions covering topics ranging from genetics, genomics, proteomics, neurobiology, lab automation, social media & life sciences, autism, alzheimer's disease, and more. The Keynote address, “Biotech 2011 Life Sciences: Looking Back to See Ahead” featured Steven Burrill, writer of the Burrill Report. Steve gave a summary of his recently published book that looks back over the Biotech industry for the last 25 years. Other presentations included “Amyloid-beta: from Physiology to Pathology” with Ottavio Arancio, M.D., Ph.D., an Associate Professor at the Taub Institute of Columbia University. A complete list of the speakers and session topics is available at http://www.BioConferenceLive.com. Registration was free.

Promotion and Registration

This year an email arrived in early February promoting the Spring Conference and I immediately signed up. In late Feb another email came with highlights from the lectures for the conference. Each lecture listed was followed by a link to add the lecture to an electronic calendar. The email also contained an invitation to join a Linked-In discussion group which I did. Thereafter I was notified regularly of ongoing discussions. Reminder emails came in each week up to the day before the conference. When one is not traveling live to a show, these reminders are valuable. Indeed, the show snuck up on me, and I had do some last minute juggling to be able to tune in.

Show Days

Monday morning I went through the list of talks and added those of interest to my calendar. I was interested naturally in several talks/panel discussions on social media and the life sciences. The first of these entitled “Social Media in Science Marketing: Fad or Function? Dispelling Four Myths and Capitalizing on Three Opportunities was given by Hamid Ghanadan, President of the Linus Group. Editor of the Linus Report, Hamid has devoted his career to understanding the psychology of scientists as consumers. It was no mystery which side Mr. Ghanadan would embrace, fad or function. Beginning by pointing out that though science has lagged behind other industries in embracing social media, there is a natural synergy between science and social media. “The peer review process could be considered an early form of social media,” he asserted. Hamid continued by dispelling common misperceptions such as that social media is only for young people. In fact the majority of content consumers on the most popular scientific sites and social media sites are over 35. Another myth: Facebook and Twitter represent social media. In fact Hamid visited over 300 sites that could be qualified as social media sites. Of those 128 sites are gaining steam. The crux of Hamid’s talk used a quadrant graph for charting scientific consumers in the following ways: from objective to subjective, from skepticism to creativity. Hamid urged marketers to engage customers early on with content that would spark creativity in a subjective way, for example, being provocative and taking a stand on present scientific conflicts. If one immediately presents ‘features and benefits’ to the consumer, they are likely to go into filtering mode and move on to something else. From creativity, Hamid argues, a marketer must take the potential scientific customer to the place where he forms a hypothesis. Only then is the customer ready for the final phase which is objective validation.

Each talk was followed by a question/answer session. Conveniently located under the YouTube like video of the presenter was a box for entering questions. The box was open throughout the talk. One final question for Hamid went “Are you finding a large number of science vendors embracing social media.” The answer, “chances are high that they (vendors Hamid is engaged with) are spending most of their marketing money on social media.”

What was the presentation like? Dry and straightforward with heavy use of slides. Just like a live presentation at scientific conferences. Hamid did a good job of looking directly at the camera to engage his listeners. So how was the presentation different than a live presentation? I found it easier to become disengaged with the speaker. The online conference is perhaps too convenient. I took several phone calls while listening. Of course this is up to the viewer, but it’s certainly easier to allow distractions than in a quiet room filled with serious folks. Any advantages? This biggest plus to this online gig, is that Hamid’s talk is still posted online and one can run through it like a YouTube video. And it will stay online until the next conference in the summer.

At the end of Hamid’s talk he mentioned another presenter, Kristy Meyers, who handles social media for Sigma Aldrich. Her talk came the next day. I missed it. So I listened to the archive file. And it proceeded as though I had been there at the right time with the added benefit that I could go forward or backward with the video. I couldn’t, however, ask any questions. Ms Meyers gave an account of Sigma’s engagement with social media and offered a list of helpful sites for the online marketer. She mentioned the new Beta feature at Linked-In where one can search for others by scientific techniques or skills. Other sites referred included www.benchfly.com, www.bitesizebio.com, and www.jove.com. She also mentioned several important blogs to the life science community including www.scientopia.com, www.researchblogging.com, and www.centralscience.com. Blogs and sites that take off, she pointed out, are ones that show the life of or poke fun at scientists. A Facebook site she recommended is titled, “We look so sexy in our lab coats, we need safety goggles.”

Ms. Myers show had a constant irritating background noise and while I watched the picture froze up several times. This of course could have been my own issue, but the technological glitches from time to time do tend to disengage one from the speaker. Again, it was a nice feature to be able to move the cursor on this talk back and forth.

I did catch a couple ‘scientific’ talks, including one by the Special Advisor to the Director for Genomic Medicine at NHGRI, Dr. Greg Feero. This talk had a very catchy title, “From base pairs to the bedside: charting a course for the next decade of genomics research.” Mr. Feero gave a straight forward overview of genomics to date and went over the NHGRI’s plan for the future. I couldn’t read Greg’s slides in the small screen, so I went to the “Resource Center” and downloaded them into my own Power Point file.

BioConference Live certainly appears to have a future. Technically the show is very well organized and the “lobby” even conveys a sense that you are at the show with a flash picture of a conference lobby with people walking around and doors into the Exhibit. One almost felt like you were entering the realm of 2nd Life (www.secondlife.com) and perhaps this will be the future. Someday we will create an avatar to go into the Exhibit hall and chat with other avatars. The current Exhibit Hall was merely a collection of booths with links to the vendors’ websites. Many vendors did have videos created, it appeared, specifically for such a show. Other links, or ‘rooms in the lobby’ included a Resource Center, where I found the slideshow from Mr. Feero’s talk, and the ‘Networking Lounge,’ a chat room. No one was hanging around in there.

Lab Automation 2011 - All things nano

Author: 
Theral Timpson

The Lab Automation conference offers an exhibition of all the major players in the industry and a great opportunity for education in all things automation with over 100 sessions and over 150 poster presentations. The conference begins with a weekend of short courses ranging in the expected topics from basic Introduction to Laboratory Automation, Liquid Handling Boot Camps to Bar Code Technology. Again this year, the nano world dominated the topics. One well attended poster presentation covered “Nanocrystal Clusters for Bioseparation” proposing a strategy for the production of novel porous nanoparticles for separating biomolecules such as proteins and peptides. Nanoparticles cannot be conveniently separated from a mixture by centrifugation because they are so small. Another problem comes from the fact that nanoparticles are normally dispersed in nonpolar solvents. On the surface, they are typically coated with a layer of protecting ligands that prevents them from trapping biomolecules. The authors of the poster from UC Riverside, Zenda Lu and Yadong Yin, come up with the process for synthesizing some novel particles which can be used as a powerful absorbent for the enrichment of peptides and proteins in solution. These new nanoparticles can then be easily separated from solution by an external magnetic field, thereby further enhancing peptide separation.

Another poster by Debkishore Mitra, Hinesh Patel and Luke Lee from UC Berkeley proposed a new theranostic platform for breast cancer. Present biomarker analysis systems are limited by the small volumes available. The Berkeley team is developing a portable, robust microfluidic-based integrated molecular diagnostic system (iMDs) that would only require small samples and could do multiplexed analysis of a panel of biomarkers. This system works through cell trapping and cell lysis. The cell trapping pre-concentrates the cellular biomarkers of interest. Once the cells are trapped, they are lysed so that intracellular and surface proteins can be probed.

The longer educational sessions were kicked off on Monday by a keynote address to an overflowing ballroom (over 4000 participants at the conference), again on nanotechnology. Chad Mirkin, Director of the International Institute for Nanotechnology at Northwestern University presented a new ployvalent oligonucleotide nanoparticle conjugate. His team has been working with gold particles that are loaded with 20-80 mer oligos. These particles have proved “highly resistant to nuclease digestion, have high tailorable binding constants for large mRNA, and exhibit high entry efficiency into multiple cell types. In an experiment with mice, the team was able to knock down cancer tumor growth by injecting mouse tumors with siRNA nanoparticles. The particles have proven effective deep into organs and are good for local environments as well as for use in the circulatory system. The biggest concern for this novel particle is toxicity. Mirkin said toxicity has not been perceived as a problem so far, though the group has done no long term studies. He went on to claim the team has developed a carrier free particle. In this case, once the particles are fabricated, the gold could then be removed. “With the introduction of these very special new constructs much of what people do with siRNA will become obsolete. We can now get into cells the way other delivery methods cannot.”

Most of the sessions continued the subject of nanotherapeutics and nanoparticles. Other sessions over the next three days were devoted to bioinformatics and cloud computing and evolving applications for automation with renewable bioenergy and bioproducts.

The conference is billed with the slogan, “bringing science, technology and industry together.” Perhaps this was best done at a two hour session on Monday evening called Late Night with LRIG, a rapid-fire session. Fifteen companies with innovative technologies were chosen to give 10 minute presentations. New products included a novel data management software by the German company BSSN Software and deep UV LED’s made by the Japanese company, DOWA.

Exhibition

Highlights from this year’s exhibit floor were centered around small steps toward automation. The new pipettor company, ViaFlow, and lab supply house, Phenix Scientific, displayed two different versions of a manual 96 well pipetting station. These hybrids--not really a machine, but much more than a multichannel pipettor- offer a lab an inexpensive and simple way to move toward high throughput processing. The bigger automated liquid handling manufacturers including Hamilton, Teacan, Thermo all presented smaller footprint machines designed as first step automated systems for labs. They were priced between $20,000 to $30,000. A couple new systems at the other end of the scale, very large footprint stations that integrated storage with sample handling were introduced by Hamilton and BioNex Solutions.

Personalized Medicine World Conference 2011

Author: 
Theral Timpson

This week I attended the 3rd annual World Conference for Personalized Medicine held at Microsoft’s Computer Science Museum in Mountain View, California. A museum for the history of computing seemed appropriate for a new industry which has been dramatically impacted by the accelerating pace of technological innovation. The most oft quoted theme in the conference: that the price of sequencing an entire genome has dropped at breathtaking speed over the last few years. Just four years ago, the price for a genome sequence hovered in the tens of millions of dollars. Now the price is below $10,000 and still dropping. This is hardly news. But how is this affecting the industry? It was ventured by Randy Scott, CEO of Genomic Health, that the price would go to zero dollars in time and that we as patients would all be part of a network and subscribe to a service, that of having one’s genome carefully scrutinized for genes that mean something of significance for our personal well being. This was quickly countered by Clifford Reid who held on to the idea that the price for the genome sequence would continue to drop but would end up more in the neighborhood of a few hundred dollars. Reid’s company, Complete Genomics, is a leading provider of complete genome sequences, having sequenced thousands of genomes for the NIH, academic hospitals, and private requests. Whether the price will be zero or the price of a cell phone, clearly the age of personalized medicine is upon us. What does this mean? How will this vast increase in technology affect medicine as we know it? How will this vast potential for such personalized data change the patient/doctor relationship? Will regulation keep pace or slow things down? These are some of the questions the conference, filled with speeches and presentations by the industry’s leaders--scientists, entrepreneurs, investors, IP lawyers, and government representatives--sought to address.

Day 1

Lasting two very full days, the conference was split into four major categories: Targeting Cancer, New Business Models, Regulation, and Personal Wellness.

Cancer

Speaking at the outset, Randy Scott contrasted the model of the healthcare world we’ve been living in with what it will be. For the past 30 years, he said, medicine has been “drug centric, where the patient has been fit to the drug.” Now we embark on an era away from the drug centric toward a diagnostic centered world. His example was breast cancer. $20 billion dollars has been spent in breast cancer drugs. Yet these drugs work only 50% of the time or less. Mr. Soctt and others after him affirmed that these numbers are not good enough with the availability of a person’s genomic data. There are certain things we know about breast cancer. With the patient’s genetic information we can give a score for low vs. high recurrence. We can target the therapy to the patient. “We are redefining the molecular biology of breast cancer,” claimed Scott whose company, Genomic Health, offers the OncoTypeDX, a diagnostic test for breast cancer patients to aid in treatment. The test can help indicate how likely it is that a woman’s cancer may return in the future (distant recurrence). Scott was the first to bring up the idea of targeted clinical trials, that is trials for a group of individuals with a homogenous genotype. According to Scott, such a targeted approach would bring the success rate up for clinical trials and shorten the length of the approval cycle.

Clifford Reid sought to dispel the myth that cancer grows fast. Instead, according to Reid, it takes 10 years from the original mutations to parental cancer cells. Mr. Reid talked about a cancer signature. With a few cells from a lung cancer tumor, his company has mapped the genome of the tumor, finding 50,000 mutations. He believes we will find signature genotypes for the lung cancer so that we can identify it in the body long before the tumor grows. Finding the cancer during the stage from mutation to the first parental cancer cells--and by beginning treatment at this stage, we can halt the cancer early. Reid also talked about a new subject which floated on the tongues of many in the audience during the breaks--that of circulating tumor cells. Many times patients hear that they are cancer free after surgery or other treatment only to find later that the cancer has come back. Tumor cells that are circulating free in the blood may be responsible. Potentially we will be able to insert “killer genes” in the cells and stop the cancer before another metastisis.

Martin LeBlanc of Caprion took the conference into the field of proteomics, or protein based biomarkers. There are many instances where tumor cells cannot be reached, such as lung cancer. In this case LeBlanc’s company has had success with tests that target certain proteins in the blood. They are collaborating with pharma companies on new drug target discoveries relating to prostate cancer, lung cancer, and TB, among others. LeBlanc was enthusiastic about his company’s approach, saying they had been profitable since 2006.

With such exciting discoveries and new tests, what is holding the industry back? Mara Aspinall is the Vice Chairman for the Personalized Medicine Coalition and CEO of On-Q-ity, a company focused on circulating tumor cell diagnostics. Mara spoke of a “battle to be waged. The question for her was whether big pharma and the insurers will play. She called for strong action and for the need for clarity with regulation and reimbursement reform. She is requesting that a new center at the FDA be dedicated to diagnostics. She proposed a pretty revolutionary drug reimbursement system based on performance. That if there was no response by a patient to a drug, that the patient shouldn’t pay. This would be an incentive for both big pharma and insurers to come to the diagnostics table.

The cancer session could best be summed up in the words of Alexis Borisy of Foundation Medicine who sat with several of his peers on a panel for questions. “Personalized medicine is no longer stories about the future, but about now.” Mr. Borisy spoke also to the need for a universal, comprehensive diagnostic test, one which includes perhaps hundreds of biomarkers.

After this first session, there was certainly a palpable excitement in the large ballroom. The show was designed with several long breaks for networking. In the audience, which overflowed out the front doors and into the entryway, many standing without a chair, one noticed employees from Genentech, investors, scientists from Stanford, doctors, all taking notes, emailing colleagues on the spot, or tweeting about the latest discoveries. Perhaps the only word of caution during the entire morning came from one of Mr. Borisy’s colleagues in the panel discussion, Hartmut Juhl of Invidumed in Germany. He spoke to the fact that although looking at genetic mutation is certainly a robust science, there are many other variables in the tumor cell which regulate its action. We typically study a tumor cell in the lab. Yet the same tissue analyzed in the lab can be very different than when it is in the body. When Hartmut said he was tired of hearing about new break throughs which didn’t take into account these variables he received an immediate applause from the audience.

New Business Models

The afternoon session afforded its highlights as well beginning with Kathy Hudson from NIH. She announced the creation of a new center within the NIH to be called NCATS or the National Center for Advanced Translational Sciences. Kathy was speaking to the vanguard in this field, she knew it, and she reached out and connected. (Unlike the FDA who made a presentation the next day.) She made sure she showed a slide with a picture of the new NIH website which the crowd acknowledged with applause. Later Kathy joined a panel with some industry heavy hitters: George Church, well known scientist from Harvard, Ralph Snyderman, Chancellor from Duke University, Lee Hood, who developed the five instruments which are the foundation for modern molecular biology, and Brook Byers, VC investor who has worked closely with and funded over fifty new companies.

More than anything, these experienced veterans in their field all sought to design new mental models for how the future will look. Church, who was involved in the first genome sequencing project and the first commercial sequencing, talked about the day when genetic information will be shared over a social network such as Facebook. He brought up Wikipedia as an example of users being involved, putting it out there that people are willing to take healthcare into their own hands. Church, honorary keynote speaker the next day, began the Personal Genome Project which recruits volunteers willing to share their genomic data with the research community and general public. Ralph Snyderman from Duke talked about a program he set up within the Duke Medical System that gets individuals more involved in their health, saying the results were dramatic. In this system, patients (employees of the University) are given a Health Risk Assessment that includes their genetic information. An individual is then given a healthcare coach and then sets their own health goals. Snyderman said that costs had gone down, emergency visits had declined and there was a conformity of care. When the panel was asked to predict what personalized medicine would look like in 2020, Hudson said she saw everyone being a participant in research. All of them talked of patients going outside the current system. Byers said it will be all about networks--on the social level and on the molecular level. The work now was to educate patients and physicians.

Welcome to Mendelspod.com!

Author: 
Theral Timpson

Here’s how it works. We produce fascinating shows on highly relevant topics, and you come and listen. You, the researcher at the university lab, you, the researcher in the small biotech start-up or in the large pharma lab, you, the management for the growing diagnostics company or you, the doctor wishing to know what is new in genetic research. Log on and play the podcast at any time, anywhere in the world. Hear from someone in the show that you’d like to contact? Go to Guests and there you’ll find them listed with contact information. Follow my blog here.

First of all, I’d like to acknowledge Mitch Joel whose book gave me the idea for this site, “Six Pixels of Separation.” A friend of mine and now our executive producer, Ayanna Monteverdi, had recommended the book some time back. It went to my reading list. One day as I was searching for answers the book stared out at me from my list and I went immediately to Amazon. Joel is an expert for online social marketing and has done over 500 podcasts himself. I wasn’t but ten pages into the book when the idea for mendelspod.com came along with our mission: advancing life science research by connecting people and ideas. Within a month we were writing the business plan. “Why did you pick up the book just now,” Ayanna asked. Who knows.

Why mendelspod?

Gregor Mendel showed up as an intriguing figure as soon as we began working on this business. I had been reading a book by James Watson on the history of DNA science and heard again the story of this Austrian monk who was trained as a physicist. Monk-physicist-father of human genetics--huh? The journey to scientific discovery is not always the predicted one. It is fueled by a passion to ‘find out why,‘ by a love of what one does. And by fortuitous connections. I have read also--to move to another discipline--of the ‘scientist’ who discovered Uranus, Frederick William Herschel. Herschel was a musician in Bath, England with a love of astronomy. He started building his own telescopes and discovered Uranus while viewing the night sky in his own garden. (Gardens must be fertile places for scientific discovery. ) Herschel named the new planet the “Georgian Star” after King George III, but the French would have none of it. The name from Greek Mythology was adopted to match the names of the other planets. Still, the king was impressed and ordered Herschel to move to Windsor and bring along his telescopes for royal viewing. Herschel went on to discover the two major moons of Uranus as well as two moons of Saturn and infrared radiation. Of the twenty-four symphonies Herschel wrote, which have you heard?

It has been often said that Mendel’s training as a physicist--learning to keep lots of accurate data--was key to his work with the pea plants. Unlike Herschel, Mendel’s discoveries were not immediately hailed as such. Though he published his ideas in 1866 in the leading journals of the day, they went largely unnoticed until 1900, long after his death. No royal patronage. In fact, one leading scientist urged Mendel to give up his studies of the pea plant. In 1868, Mendel was appointed head abbot of his monastery. Burdened with the daily duties of maintaining the order, Mendel gave up his pea experiments, strolling out to the garden later in life only for the occasional cigar.

Power of the Podcast

What if Mendel had a computer and could blog about his own work? Though they lived simultaneously, it turns out that two great scientists, Charles Darwin and Mendel knew nothing of each other. In 1859 Darwin published “Origin of the Species,” three years after Mendel began his pea experiments. Though Darwin had clearly laid out the evidence for natural selection--the adaptation of life based on the environment--his theory about the hereditary factor which he called “pangenesis” was wrong. Darwin held that hereditary particles in our bodies were affected by the things we do during our lifetimes. These modified particles, he thought passed through the blood to the reproductive cells and could therefore be inherited by the next generation. If Darwin had known of Mendel’s work, he would have had clear evidence that his theory of pangenesis was wrong.

At mendelspod.com we will bring you interviews with the Darwins and the Mendels of today. And shows with the leaders of industry. As you see from our first show on the World Conference of Personalized Medicine, scientific research is advanced when not only scientists, but also businessmen and regulators get together and trade ideas and visions for the future.

Come back again soon!




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