Nature blogs

It’s funny, but I was searching Nature for my blog last week.  A few months ago, I noticed that I was in the “most popular blogs” section.  A couple days ago, I couldn’t find my blog anywhere on Nature.  I thought maybe it was some link through SciFoo association, since Nature is a sponsor of SciFoo.

Then today, there is a write up about the meme that I posted a couple days ago in Nature.

I guess we’re back in favor.  You can read it HERE, but will cut & paste below:

Why do we blog and other important questions, answered by 34 science bloggers

Date:  Sunday, 30 Nov ember 2008 – 22:05 UTC

What started out as a few questions to science bloggers in the Nature Network Bloggers Forum, has turned into a collection of more than 30 blog posts not limited to Nature Network (big thanks to Bora and others for spreading the word). The following science bloggers answered a set of 10 questions about their blogging (roughly in chronological order):

Henry Gee
Eva Amsen
Steffi Suhr
Stephen Curry
Maxine Clarke
Martin Fenner
Bora Zivkovic
Clare Dudman
T. Ryan Gregory
Massimo Pinto (and another post in Italian)
Mike Haubrich
Larry Moran
John Wilkins
Kristi Vogel
Paolo Nuin
Heather Etchevers
Lee Turnpenny
Ricardo Vidal
Bob O’Hara
Deepak Singh
Frank Norman
Jim Hardy
Andrew Perry
Pedro Beltrao
Shirley Wu
Angelos Markos
Thomas Soderqvist
Sandy Gautam
Duncan Hull
John Dupuis
Mike Fowler
Viktor Poór
Richard Grant
Ed Yong
GrrlScientist

Please contact me if I missed a blog post.

Reading these blog posts is not only interesting and entertaining, but probably also a very good introduction to the current state of science blogging. Below is a personal summary of some of the answers. Oh, the best title was probably from Frank Norman: La meme chose.

1. What is your blog about?
Most bloggers seem to write about many different science-related topics. And only a minority about the actual science they are doing. Some bloggers gave more specific answers:

• My blog is about science, in particular evolution and genomes. (T. Ryan Gregory)
• It’s a sort of a window of transparency over a weird scientific environment, the Italian science jobs and funding market. (Massimo Pinto)
• Basically the philosophical implications of science. (John Wilkins)
• Anything releted to Biotechnology in Frederick County, MD. (Jim Hardy)
• The general theme is how we can bring the worlds of information technology and the life sciences together. (Deepak Singh)
• I am trying to put the people behind the science into the spotlight: the technicians, operational support, science management and others. (Steffi Suhr)
• We write about making sense of medicine and medical science in museums. (Thomas Soderqvist)
• Ostensibly about theoretical population biology. (Mike Fowler)
• I am interested in how the internet is changing the way we publish and communicate science. (me)

2. What will you never write about?
Several people mentioned that they would not give out personal information about other people, or comment directly on what’s going on in their institution/company. Most people also avoid to talk religious beliefs or politics. Confidential information, including unreleased papers, was mentioned several times. The release of calcium from intracellular stores is another topic that several people would never blog about. Also:

• Only write about things I actually understand. (Ed Yong)
• I will never ask anyone to give me money via this blog. (Maxine Clarke)
• I hope that I will not have to write blog posts that are evaluated, measured and put on a resumé. (me)

3. Have you ever considered leaving science?
Several people said something similar to Bora Zivkovic: Leaving research – yes, I already did that. Leaving science – never.

4. What would you do instead?
Some interesting answers. And a science background would be helpful in most of the jobs:

• Zookeeper, or an animal trainer in a circus (Bora Zivkovic)
• Jazz trumpeteer (Massimo Pinto)
• Own a used book store (John Dupuis)
• I’d try my best to get a job in video game development (Andrew Perry)
• Tend olive trees in Greece (Duncan Hull)
• Graphic designer (Ricardo Vidal)
• Write very bad science fiction (John Wilkins)

5. What do you think will science blogging be like in 5 years?
This was a difficult question that some didn’t answer. Larry Moran said: pretty much the same as it is now. T. Ryan Gregory thinks that more professional researchers will join the blogosphere as this becomes socially acceptable. Andrew Perry thinks that research groups will be tied together more and more by their blogs. Eva Amsen thinks that there will be so many science blogs that we have to specialize. And I wrote that some science bloggers will be able to make enough money to earn a living from it.

6. What is the most extraordinary thing that happened to you because of blogging?
Thomas Soderqvist said that there is no the most extraordinary thing. But I hadn’t expected to get so many interesting contacts with colleagues around the world. Many people (including myself) had similar answers. Going to SciFoo is certainly an extraordinary thing an SciFoo invitation was mentioned by Pedro Beltrao, Jim Hardy, Duncan Hull and Deepak Singh. Some other answers:

• The Editor-in-Chief of Nature once told David Attenborough that he should read my blog. (Ed Yong)
• Getting a job with PLoS in the comments of one of my posts. (Bora Zivkovic)
• Co-founded a network of science bloggers (The DNA Network) and been invited (and accepted!) to work at MIT. (Ricardo Vidal)
• Getting interviewed by Jon Udell. (Deepak Singh)
• I loaned a power cable to a Nature editor. (Bob O’Hara)

7. Did you write a blog post or comment you later regretted?
For most people that was not a big issue. Ed Yong regrets to have written nice things about studies that later turned out to be rubbish not so good.

8. When did you first learn about science blogging?
Many different answers. Nodalpoint was mentioned by several bloggers, including Duncan Hull, Paolo Nuin and Pedro Beltrao. T. Ryan Gregory was introduced to science blogging by his graduate student. The most hilarious answer is from Henry Gee and involves a garage, an old washing-machine motor and heavier-than-air flight.

9. What do your colleagues at work say about your blogging?
The standard answer seems to be that most of them don’t know or don’t care. I would hope that in the future we will have more answers like the one from Bora Zivkovic: That’s what they are paying me for and I hope they are happy.

10. How the heck do you have time to blog and do research at the same time?
Most people blog in their spare time. I hope to see more daytime bloggers that blog as part of their science job in 5 years (this relates to questions #5, #8 and #9).

11. Extra credit: are you able to write an entry to your blog that takes the form of a poem about your research?

Not all bloggers answered that question, but you can find poetry by Heather Etchevers (who suggested that question), Stephen Curry (who inspired it), Henry Gee, Eva Amsen, Bora Zivkovic, Maxine Clarke (a play), Massimo Pinto (science fiction), Shirley Wu (karaoke), Mike Fowler, Bob O’Hara (art), Viktor Poór (a dance) and myself. Paolo Nuin needs a few more encouraging comments before he will write a poem.

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Last updated: Sunday, 30 Nov 2008 – 22:05 UTC

Nature Methods a la Frederick

At the last BioBeers, I didn’t have a lot of time to talk to Jim Hartley.  He’s now with SAIC/NCI-Frederick working in the Protein Expression group with Deb Chatterjee.  It did give me great pleasure, though, as I was scrambling to get my laptop to communicate with the PC projector, to eavesdrop on a conversation Jim was having with Mike Smith about this new cell-free system they’ve come up with for screening genome wide protein expression.  An “all DNA” protein microarray, of sorts.  This was described in a September PLoS publication:

Protein Microarray On-Demand: A Novel Protein Microarray System

Deb K. Chatterjee^1,3*, Kalavathy Sitaraman^1,3#, Cassio Baptista^2,3#, James Hartley^1,3, Thomas M. Hill⁴, David J. Munroe³

1 Protein Expression Laboratory, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America, 2 Laboratory of Molecular Technology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America, 3 Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America, 4 Department of Microbiology and Immunology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America

Abstract

We describe a novel, simple and low-cost protein microarray strategy wherein the microarrays are generated by printing expression ready plasmid DNAs onto slides that can be converted into protein arrays on-demand. The printed expression plasmids serve dual purposes as they not only direct the synthesis of the protein of interest; they also serve to capture the newly synthesized proteins through a high affinity DNA-protein interaction. To accomplish this we have exploited the high-affinity binding (~3-7×10 ^-13 M) of E. coli Tus protein to Ter, a 20 bp DNA sequence involved in the regulation of E. coli DNA replication. In our system, each protein of interest is synthesized as a Tus fusion protein and each expression construct directing the protein synthesis contains embedded Ter DNA sequence. The embedded Ter sequence functions as a capture reagent for the newly synthesized Tus fusion protein. This “all DNA” microarray can be converted to a protein microarray on-demand without need for any additional capture reagent..

To take it back a step further, I saw Jim in a professional capacity at LTI frequently primarily because our names are nearly homophones (Hardy vs Hartley).  Seems like we were always swapping mail or phone messages (back in the days before e-mail).  And just to let you know, back in thise days Jim was working in R&D “cloning” the native restriction enzymes everyone uses today (which some bone-headed marketing guy dcided he’d share with NEB, but that’s a whole other story), working on recombinant TdT (a real popular enzyme back in the day we were making from frozen calf thyroids we bought from a meat packing plant.  Talk about variable yield..).  He may be best know for working on the team that discovered/commercialized the Gateway Cloning system.  he is also the inspiration for me starting BioBeers, and this is the first one he’s made it to.

Mike Smith worked on creating all the Competent Cells at LTI. Things like DH5 alpha, Electromax, LE cells. When IVGN laid us all off (yet another example of wasting talent, but don’t get me going again), he started GeneChoice (now a shell of its former self after being peddled around like rubbish by another bunch of marketing geniuses), making better comp cells than the one’s he created 10 years earlier.

Anyway, back to my original story.  Just reading the abstract in Nature Methods this week (you have to subscribe to Nature our buy the article on-line, despite this research being funded by our tax dollars on a Federally owned land).  The abstract is pretty sparse, but here it is (proper citation: Nature Methods 5, 1001 – 1002 (2008) doi:10.1038/nmeth1208-1001):

Comprehensive sets of clones and improved high-throughput methods for production of functional proteins now allow proteome-scale in vitro experiments on nearly 15,000 human genes

And lastly comes this article I just found from BioTechniques in September:
Biotechniques. 2008 Sep;45(3):307-15.

Identification of highly expressed, soluble proteins using an improved, high-throughput pooled ORF expression technology.

Waybright T, Gillette W, Esposito D, Stephens R, Lucas D, Hartley J, Veenstra T.Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
This article describes an improved pooled open reading frame (ORF) expression technology (POET) that uses recombinational cloning and solution-based tandem mass spectrometry (MS/MS) to identify ORFs that yield high levels of soluble, purified protein when expressed in Escherichia coli. Using this method, three identical pools of 512 human ORFs were subcloned, purified, and transfected into three separate E. coli cultures. After bulk expression and purification, the proteins from the three separate pools were digested into tryptic peptides. Each of these samples was subsequently analyzed in triplicate using reversed-phase high-performance liquid chromatography (LC) coupled directly online with MS/MS. The abundance of each protein was determined by calculating the average exponentially modified protein abundance index (emPAI) of each protein across the three protein pools. Human proteins that consistently gave high emPAI values were subjected to small-scale expression and purification. These clones showed high levels of expression of soluble protein. Conversely, proteins that were not observed by LC-MS/MS did not show any detectable soluble expression in small-scale validation studies. Using this improved POET method allows the expression characteristics of hundreds of proteins to be quickly determined in a single experiment.

The New, New Life Technologies

Since I have received two emails from former Life Technologies (i.e. pre-IVGN) colleagues, I guess I need to post this update.

The merger between Applied Biosystems and Invitrogen is now finalized, creating a global leader in biotechnology reagents and systems. Our new company will be called Life Technologies, a name that symbolizes our commitment to promoting discoveries that improve the human condition. I am confident that the combined company will create tremendous value through meaningful innovation targeted to your needs, and greater expertise to help answer your most complex challenges. Our new company will leverage expanded capabilities in sales, customer service and technical support, to ensure that you are afforded choices for products that best suit your research needs. We will also increase our R&D efforts, and collaborate strategically with our customers and partners, to increase the pace of innovation. We look forward to providing you with cutting edge solutions for today’s research, while looking to accelerate your work toward tomorrow’s breakthroughs. As we combine, let me emphasize that continuing to serve your needs at the high standard you have come to expect from us remains our top priority. To maintain that standard, there will be no change at this time to the way you conduct business with us. To ensure continuity and minimize any disruptions to your operations, we will maintain separate ordering and shipping processes. Please continue to communicate directly with your respective contacts through the existing channels for Applied Biosystems and Invitrogen products and services. We will share any changes and developments with you promptly. Moving forward, we will maintain Invitrogen and Applied Biosystems as separate brands. Through the Invitrogen brand, we will continue to provide you with the reagents and service offerings that have consistently made us a partner of choice regardless of the platform of your choice. Soon, many of Applied Biosystems’ reagents, such as Ambion products, will also be available for sale through Invitrogen channels. Similarly, we recognize the value you place in the Applied Biosystems brand for pre-eminent instrument solutions. Therefore, Applied Biosystems will remain the channel through which those systems, such as SOLiD™, RT-PCR and mass spectrometry, will be sold. Through Applied Biosystems, you will continue to receive not only the best instrumentation available, but also certified reagents that best optimize those systems. Thank you for continuing to be a valued customer and for your support and trust in us. For any additional information on this merger, or if you have any questions, please visit:

www.appliedbiosystems.com/tellmemore or www.invitrogen.com/tellmemore

Sincerely, Greg Lucier Chairman & CEO

Can anyone on the insdie at 7335 Executive Way give a summary of today’s renaming festivities?  Just curious….

(EDIT 11/25:  Ooops, left a bunch of code in there, which I clened out)

BioBeers Five recap

We all had a great time yesterday at BioBeers.  As usual, the folks at Flying Dog were most generous.  When we got there, their LN2 supply was being refilled, so no beer on tap.  Instead, they opened their cooler and we got a couple of bottled beers before the taps were put on-line at about 5 PM.

The attendance was just over 60 people, so interest continues to grow.  A lot of new faces in the crowd, which I appreciate.

I think my spit in a shot glass demo went OK, but the shampoo made the shot taste horrible. Especially after drinking all the good beer. So I wussed out and didn’t toss the shot. Makes for a pretty picture, though.

My thanks again to all those in attendance. Especially Jon for giving his presentation on Lonza and Bob Buckheit for talking about ImQuest and bringing his people to mingle. Thanks also to Howard for recruiting a number of people from Ft Detrick. Too many new people to mention, but I think everyone had a good time. I am also getting pushed to make this a monthly event, and the participation/interest seems to be there.

I may try to get my buddy, Brian Malow (Science Comedian) to come while he’s in town. Perhaps we can have a venue at the Bentz Street Sports Bar in December?

Frederick News Post

I have been chatting with report Ike Wilson at the Frederick News post on and off again over the past week about Stem Cell research as it relates to the Obama administration and potentially lifting restrictions on ES research.

The article ran today.  I wish the FNP would include hyperlinks, but they don’t so I added some.  They also didn’t include my bloody placenta picture, so I added that for additional impact.

Rescinding Bush’s stem cell limits creates biotech glee

Originally published November 21, 2008

By Ike Wilson
News-Post Staff

	IF YOU GO Join BioBeers — a networking event for local biogeeks from MedImmune, Lonza, SAIC, NCI and a group of small biotechs 4:30 p.m. today at the Flying Dog Brewery. The limit is 120 people so RSVP to hardy@gahaga.com or call 301-639-6718.ON THE WEBJim Hardy’s blog fredcobio.wordpress.comIF YOU GO The first Maryland Stem Cell Research Symposium will be held from 8 a.m. to 6 p.m. Dec. 3, at the The Johns Hopkins University Applied Physics Laboratory, Kossiakoff Conference Center, 11100 Johns Hopkins Road, Laurel. Keynote speakers include Gov. Martin O’Malley; Rudolf Jaenisch, Massachusetts Institute of Technology; Jeremy Sugarman, Johns Hopkins University. Registration ends Nov. 28. For information on the Symposium or the Maryland Stem Cell Research Fund, visit http://www.mscrf.org or e-mail registration and event coordinator Mark Glazer at mglazer@techcouncilmd.com.

President-elect Barack Obama should rescind President Bush’s limits on stem cell research, said Jim Hardy, president and CEO of Gahaga Biosciences Inc. in Frederick.

Bush’s decision not to fund stem cell research is keeping the U.S. behind other countries like Southeast Asia, India, Japan and most parts of Europe, said Hardy, who writes a blog on the Frederick County Biotech Community.

“These countries will likely own most of the patent discoveries and make most of the money off products or therapeutics in the future,” Hardy said.

Obama’s transition chief John Podesta has said the new president could end the ban.

Most current research and therapeutic applications use adult stem cells, not embryonic stem cells, Hardy said.

“Although the Bush legislation only affects embryonic stem cell research, it is having an impact on all stem cell research,” he said.

Hardy said Frederick County has some of the largest suppliers of stem cells in the world, including Lonza, International Stem Cells, Invitrogen and NCI-Frederick.

“So this suppression of stem cell research hits really hard right here at home,” Hardy said.

Gahaga Biosciences was established in 2006 to commercialize a method to isolate stem cells from placental and umbilical tissues for use in basic research. The company provides the scientific community with a variety of products derived from proprietary stem cell purification technologies.

The Bush legislation specifically restricts embryonic stem cell research by institutions using National Institution of Health funds, Hardy said.

Every person has a different DNA and different genes, and science is moving rapidly towards a personalized approach to medicine through genomics research, Hardy said. It will be necessary to look at large populations of cells to understand how differences among individuals are a result of differences in the genetic make-up, or genotype. This relates to disease potential and treatment for medical conditions, he said.

“The more we are learning about genomics, the more we’re convinced that genomics will give answers to many questions regarding human health and wellness,” Hardy said.

Embryonic stem cell research is important for cancer research, Hardy said.

“We think that cancer behaves in some ways like embryonic stem cells. A single cancer cell may generate a whole tumor mass containing many different types of cells in a manner similar to how a single-celled embryo changes into heart, lung, blood, skin and brain cells in the first two weeks after fertilization,” Hardy said.

Biotechnology provides hope for millions of people suffering from debilitating diseases like cancer, HIV and AIDS, Parkinson’s and diabetes, and by reducing the incidence of disease, the industry can dramatically reduce health care costs and help spur economic growth, Biotechnology Industry Organization’s president and CEO Jim Greenwood said in a recent press release.

Busy week in FredCo

It’s been a busy week in FredCoBio, so I haven’t been posting as much as I’d like.

I am off to the FITCI lecture for lunch, drop in on Victor at Veracity Biosystems this afternoon and check out the labs at Hood. 

But BioBeers tomorrow is a GO!  We’re going to have a big crowd, probably close to 70 people.  There will be a large contingent from Ft Detrick, shepherded in by Howard with Meso-Scale, The Gazette will be covering the event (note to self, groom nose hair so no more embarrassing shots like the one on the right), people from the City, County, Holiday Inn, FITCI, Lonza, Invitrogen and a couple of speakers.

For fun, I will be doing a demo promoting one of my other follies, the DIYbio community.  I will demonstrate how to isolate DNA from spit in 5 minutes. If I have enough beer in me, I may even deomonstrate using other bodily fluids.

We have two featured, brief speakers.  Jon Rowley, formerly founder of the Regeneration Station blog and now R&D Director with Lonza Cell Therapy group (I think), will be giving us a little information about the R&D activities at Lonza. Bob Buckheit of ImQuest is bring a bunch of people over (I bet a couple former LTI in the mix) and will be giving us a presentation on how they are going to spend the all of their SBIR money.

And my thanks go out again to Aerotek for picking up the “admission fee” so we can all enjoy the many, many beers Flying Dog has on tap.

And a quick shout out to all of the award recipients at last nights 2008 Annual Business reception.  It was a full house, standing room only.  And in special recognition, SABiosciences was named the Frederick County Life Science Company of the Year, continuing their award winning tradition.  They also announced the made the Inc Magazine list of Fastest Growing companies, but I can’t find a press release anywhere on that.  Maybe they should put one on their web site?

BioBeers will kick off tomorrow, Fri 11/21, promptly at 4:30 and will be over around 7 PM.  I hope to see you all there!

Scientistist & Their Desks

I’ve been spending quite a bit of time on the web, following Twitter messages and FriendFeed and reading blogs all over the world. Mostly science based, most of them from associations made in August at SciFoo or BioBar Camp in California.  Eva posted this video, which I think you would find if you went into just about any academic lab setting here in FredCoBio

Portrait Of A Scientist – Scientist and Their Desks from Imagine Science Films on Vimeo.

And I got this Science Blog meme from Blind.Scientist.  My answers follow

The Science Blog Meme

It started here and I got it from here. Here are my responses:

1. What is your blog about?

Anything releted to Biotechnology in Frederick County, MD (and occasionally else where).

2. What will you never write about?

Biotech in Montgomery County (unless it is a company that moved from FredCo to MoCo or has ties in MoCo)

3. Have you ever considered leaving science?

Yes.  After college, I was in Sales at Xerox and selling Windows in Upstate NY.  After a couple of years I realized that I would never be happy selling office equipment, so I got a lab job.  The rest is history.

4. What would you do instead?

I’d live on a beach somewhere, just fishing all day

5. What do you think science blogging will be like in 5 years?

More interactive and more people involved.

6. What is the most extraordinary thing that happened to you because of blogging?

Getting invited to SciFoo camp and meeting all of these famous people at Google.  Mind boggling.

7. Did you write a blog post or comment you later regretted?

Yes, one time I left a comment on PIMM when I was half in the bag late one night which I retracted.  I had to pull down a blog post last week, at the request of MATAN, inviting everyone to the Ground breaking at Riverside.  I was asked to post it by a former colleague, but apparently it was a “private” invitation.

8. When did you first learn about science blogging?

I owe it all to Attila at PIMM.  I was googling about making stem cells from afterbirth and found his famous post. We already had a home blog and this inspired me to start a work blog (and since my wife doesn’t let me post on the home blog any more.)

9. What do your colleagues at work say about your blogging?

“What is a blog?”

10. Extra credit: are you able to write an entry to your blog that takes the form of a poem about your research?

Never considered it, but maybe I’ll give it a try some time.  I don’t really do research, though.  I am an operations guy who makes stuff.

One more thing I found interesting this morning, again from PIMM.  A new Science based Search engine called VALDO.  Check out the PROTOCOLS page (search term Stem Cells added by me, but you can change to whatever interests you).  It’s really good and will be added to my Protocols & SOPS page momentarily.

Digits Sprouting, BioElectronics bubble and other news…

I have been busy planning for BioBeer V next week, but I also wanted to post a few news-worthy articles I have read recently.

Major General Weightman

The first one actually came from Major General Weightman‘s talk at the Ft Detrick Alliance Annual Meeting I attended at the Ceresville Mansion on Wednesday.  MG Weightman was the Keynote speaker and gave a very interesting talk on the different activities he commands.  The topic I found most interesting was the research going on in regenerative medicine.  Specifically, he talked about a Mandated project (I believe it was one of the congressionally mandated projects, but may be wrong) to develop technology to regenerate a human digit (finger or toe) in the next 5 years.  This is the stuff of scienc fiction, but it is within our grasp.  I will send you off to read on your own, from the sensationalized Fox News post (a nude mouse growing a human ear?),  from a

From Fox news. The Caption is "a Marines ear grows from a mouse". Fantastic.

recent article on the Army’s web site, growing fingers from “pixie dust, or a more factual article from The Tartan, Carnegie-Mellon’s student newspaper (much of the research is going on in Pittsburgh).

In another story I read in the Wall Street Journal’s Market Watch section, NCI’s Nanotechnology Lab (NCL) is partnering with a Cincinnati company to develop nanotechnology directed against HPV:

PDS Biotechnology Corporation Progresses Development of Nanotechnology Cancer Therapies

Last update: 3:00 p.m. EST Nov. 6, 2008
CINCINNATI, Nov 06, 2008 /PRNewswire via COMTEX/ — PDS Biotechnology Corporation today announced that the company has been selected as a collaborator of the US National Cancer Institute’s Nanotechnology Characterization Lab (NCL) to complete preclinical development of Versamune(TM)-HPV prior to filing of the Investigational New Drug Application. The NCL will perform selected physical, chemical and biological studies on behalf of the company at its facilities at the National Cancer Institute (NCI) in Frederick, Maryland. Dr. Frank Bedu-Addo, President of the Corporation stated that, “PDS Biotechnology Corporation’s partnership with the NCL provides significant value to the company. The invaluable expertise of the NCL’s scientists will provide the company with additional expert resources and technologies, and will facilitate rapid development of the product.”
Versamune(TM)-HPV is an immunotherapy drug which has demonstrated significant promise in curing HPV infection and HPV-related cancer in preclinical animal and human model studies. Cancers caused by infection with the human papilloma virus (HPV) include cervical, head and neck and anal cancers. No cures exist for these cancers. Based on promising in vivo and in vitro efficacy data, PDS Biotechnology Corporation was awarded in August 2008, a phase I SBIR grant by the US National Institutes of Health/National Cancer Institute to develop Versamune(TM)-Melanoma to treat melanoma, which is the most aggressive form of skin cancer.

[ Side note, my SIL is moving from Hopkins to Ohio State.  She happens to be a major player in the HPV world, as indicated in this Press release.  Her husband and my BIL works for NCI-Frederick, so presume everyone will be moving back to the Buckeye State some time soon]

Photo by Sam Yu, Frederick News-Post

In today’s FNP there is yet another article about BioElectronics.  Now it appears that they have signed a nice contract to use their patch on animals.  I have ranted about the benefits and my personal experience using the patch before.  It is a fine product and frankly I am surprised it is taking this long to gain popularity.  the thing practically sell itself.

I also read an interesting article in the “free” print version of Genome Technology I got in the mail yesterday.  Unfortunately, it’s in the ProteoMonitor section of the print edition, which requires a paid subscription to access on-line.  If you have your paper copy, it is on page 51 in the November 2008 edition.  The title is “New Method for Cheap, Stable Protein Arrays” and it talks about developments coming out of NCI-Frederick from my former LTI colleagues in Deb Chattergee’s lab, James Hartley (no releation, although he was the insipration for BioBeers and the blog) and Kala Sitaraman.  You can read the whole,article on PLoS One, so I don’t really understand why GT doesn’t make it available for “free”.  From the PLoS One Abstract: “We describe a novel, simple and low-cost protein microarray strategy wherein the microarrays are generated by printing expression ready plasmid DNAs onto slides that can be converted into protein arrays on-demand. The printed expression plasmids serve dual purposes as they not only direct the synthesis of the protein of interest; they also serve to capture the newly synthesized proteins through a high affinity DNA-protein interaction.”

From the BioInfoBank web site, looks like Kala & Deb have another very interesting article coming out in Methods Mol Biol. 2009 ;498 :229-44 “High-throughput Protein Expressin using Cell-free System”

That abstract states

“One of the main challenges in this post genomic era is the development and implementation of efficient methods of protein synthesis. A clear understanding of the role of genes in an organism is to comprehend the biological functions of all of its proteins. Acquiring this knowledge will depend in part on the success of rapid synthesis and purification of proteins. The future of structural genomics and functional proteomics depends on the availability of abundantly expressing, soluble proteins in a high-throughput manner. Conventional cell based methods of protein expression is rather laborious, time consuming and the ways to fail are numerous including solubility, toxicity to the host and instability (e.g. proteolysis). Cell-free or in vitro protein synthesis, on the other hand allows the expression and analysis of protein synthesis, may solve many of these problems. It is a simple open system which lends itself for manipulations and modifications to influence protein folding, disulfide bond formation, incorporation of unnatural amino acids, protein stability (by incorporating protease inhibitors in the system) and even the expression of toxic proteins. Cell-free synthesis can also be used as a reliable screening methodology for subsequent protein expression in vivo. Furthermore, this technology is readily amenable to automation. Here, we present a protocol for expressing recombinant proteins with high yield in a standard 96-well plate format using E. coli cell-free extract in a batch mode.”

Invitrogen just never got the point of what they were giving up by letting people like this go when they shut down Maryland operations and LTI R&D.  Oh well…

And finally FredCoBio’s rant on the breaking news the president elect Obama may overturn the “Bush Stem Cell Legislation”.  I was interviewed by Ike Wilson of the FNP on the topic, but haven’t seen a story printed.  So for the record, these are the reasons Obama should rescind the Bush Stem Cell legislation:

1.  Although the Bush legislation only affects Embryonic stem cell research, it is having an impact on all stem cell research. Most current research & therapeutic applications involve Adult (not embryonic, cells from human embryos) stem cells. Frederick County has some of the largest suppliers of stem cells in the world (Lonza, International Stem Cells and Invitrogen) and one of the largest research institutions (NCI-Frederick), so this suppression of stem cell research hit really hard right here at home in FredCOBio land.

2.   The Bush legislation specifically restricts access to Embryonic Stem research (but only to research institutions using NIH funds) to a few cell lines that were established by the NIH in the 90′s. There are issues in the research community with the quality of these cell lines, as well as the small fraction of the population these limited cell lines represent. As you know, every person has different DNA, different genes and we are moving rapidly towards a “personalized” approach to medicine through genomics research. In order to understand how differences among individuals are a result in differences in the DNA (the genetic make-up or genotype) as this relates to disease potential and treatment for medical conditions, it will be necessary to look at large populations of cells. The more we are learning about Genomics, the more we’re convinced that genomics will give answers to many questions regarding human health and wellness.

3.  The legislation only restricts research labs who are using NIH funding to using stem cell lines “approved” by the NIH. So, that means there is no law against anyone making embryonic stem cells, as long as they are not using NIH money. This means research institutions like the NIH, John Hopkins, NCI are restricted in their ability to do research, but big Pharma companies (who don’t use NIH grants) are free to conduct ES research because they do not get any NIH funding. Therefore, research in the US is falling behind other countries (like SE Asia, India, Japan and most parts of Europe)and these countries will likely own most of the patent discoveries and make most of the money off products/therapeutics in the future.

4.  Embryonic stem cell research is important is the case of Cancer research. We think that cancer behaves in some ways like embryonic stem cells. A single cancer cell may generate a whole tumor mass containing many different types of cells (like its own blood vessels to feed its growth) in a manner similar to how an single-celled embryo changes into heart, lung, blood, skin, and brain cells in the first two weeks after fertilization.

Rant accomplished.  A penny for your thoughts?

NCI Ground Breaking at Riverside

I was invited to attend the Ground Breaking Ceremonies yesterday at the new NCI facility near Monocacy Blvd and Gas House Pike.  I don’t know if people around town appreciate what a monumental occasion this is for FredCoBio.

The new facilities, situated on 117 scenic acres, will be comprised of a 330,000 sq. ft state-of-the-art Research and Development building (housing the Biopharm. Manufacturing and Advanced Technology Programs) and an additional 470,000 sq. ft for “synergistic partners.”  The campus will be complete with gardens and walkways, plenty of open green space for Scientific Contemplation.

The Biopharm Mfg group will be making material for clinical trials.  The ATP group will be conducting basic R&D.  The “Synergistic Partners” will be a melding of Acedemia & Industry in an Incubator-like Think Tank to create a “vibrant  new research facility” according to Dr John Niederhuber (Director of NCI).

This will, in effect, make Frederick the center for rapid discoveries that will impact human health and people around the world.  I don’t recall who specifically said this, but the facility, planned to open in early 2011, is expected to be testing new thereapies, diagnostics and cancer treatments within the next 5 years.  As Dr. Niederhuber stated “The efforts today will change the lives of millions”

One focus of the research will be in “Personalized Oncology”. Every cancer is essentially different and every person reacts differently to treatments and therapies.  This vision was elegently presented by Dr Niederhuber when one looks at the “miraculous, single case” scenerio.  Today we see that one individual among many who responds to a particular therapy and is “cured”, while the other 95% are deceased within a few months of diagnosis.  It appears that something specific, genetic, to this individual would be the cause for the favorable reaction to therapy. Understanding these mechanisms will be a focus of a genomic approach to cancer research.

And as recently re-elected Congressman Roscoe Bartlett put it, “Frederick will be known around the World” as the center of Cancer research, just as Bethesda was analogous to the NIH in the 70′s and 80′s.  He painted the picture of the “slow crawl” of biotech up the 270 corridor which is now “Blooming in Frederick.”

I had intended to scooop the Frederick-News Post on this story, but I got distracted and didn’t get my post up yesterday.  But I will scoop them on the golden shovel ceremoney by posting a video of the pinnacle of the event:

BioBeers East, Part V

It is offical.  The next BioBeers has been scheduled at the Flying Dog Brewery on Friday November 21st.

As in previous events, please RSVP as a comment to this post, by using the contact icon in the left hand column or just give me a call and left me know you are coming!  Anyone interesting in giving a brief presentation of their research or in sponsoring some snack, please let me know.  Aerotek has already volunteered to pick up the “tipping fee” again, so everyone will at least get a nice Flying Dog pint glass to take home in commemoration of the event.

More to follow….