Frederick County Biotech Community

Everything Biotech in Frederick County, Maryland

Archive for the ‘Biochemistry’ Category

News, News Site announcement, Next Biobeers

Posted by Jim H on November 30, 2010

Some of you may know that I have been busy doing contract work at MedImmune for the past 14 months or so at the Frederick facility.  Well that contract came to a close, but I was picked up by another contractor, Raland Technologies,  to work on a different project for MedImmune at their Philadelphia facilities. So, sadly, I won’t be in Frederick as much as I’d like to, but you’ll still hear from me. I am the first official Biotech Ambassador for the Frederick Chamber of Commerce, after all.  And even though Raland runs their Maryland operations out of Montgomery County, they also have a major presence in my home town Rochester, NY.    Raland made a major announcement just a couple of weeks ago when Raland announced they were awarded  grant through the Qualifying Therapeutic Discovery Program (QTDP) for their extraordinary development efforts with RxFusion™ , a medical device offering an easier and safer home infusion treatment.  I am glad to be a part of their team.

Speaking of major news from Frederick County Biotech, I noted an article in Nature titled “Complex synthesis yields breast-cancer therapy” on my RSS feed yesterday.  This is cool in a number of respects.  First, coincident with the synthesis of this compound, researchers in Frederick at NCI discovered the compound inhibits a protein component of

The drug eribulin was inspired by a compound from the sea sponge Halichondria okadai. Nature: Yasunori Saito

the cytoskeleton, called tubulin, that is needed to support the rapid growth of cancer cells and is the target of several other cancer chemotherapies, including Taxol (paclitaxel).  Second, I spent two weeks in Seattle at the University of Washington round about 1991 working in the lab of future Nobel Laureate Eddy Krebs isolating Okadaic acid (a prolific and potent protein phosphorylator) from this very same species of sea sponge.  And what a stinking *effen* mess it was.  Let me tell you, if you drag a few kilos of fresh halichondria from deep off the floor of the Pacific, mix it with 20 L or so of Chloroform in a jumbo Warning blender, then extract with 20 L Methanol (all of this in 1991 was done in buckets, on the floor, without any special lab gear like safety glasses or lab coats or Kevlar) while trying not to contaminate my lab partner Joel’s  working on this new product he called “Lipofectamine” (which was indeed a multi million dollar product and I think continues to be to this day) because this was going to be the first million dollar product for the newly formed Cell Biology group of Life Technologies.  Those were the days.

But I digress in my fond recollections of past glory.  What I really, really want to do is to let you know the next Biobeers is almost certainly happening Friday December 17th at Lab Recyclers warehouse on Metropolitan Court (right next to FITCI).  And I really, really need everyone to switch over to the new MeetUp site and register.  Go here now:

MeetUp costs me about $10 per month, but it’s much better as compared to LinkedIn (which I will continue to maintain, just not set up events and calendar items through that site) for posting news and information and events.  I’m trying this as a platform to try to connect us more better than we are today.  I’ve started populating the site with the various and sundry seminars happening at Ft Detrick which are freaking free and open to the public!!  I’m still working on getting the MeetUp site to link to Ft Detrick web site, but it’s all good.

I’ll have the BioBeers posted on both LinkedIn and MeetUp for the next couple of events, but will force y’all over to MeetUp eventually.  Besides, my text file mailing list is getting way too long.

Posted in Awards and recognition, BioBeer, Biochemistry, Business, Funding Available, Government Funded research, Jobs, News, Public/Private Companies, Rants | Leave a Comment »

BioBeers Was Great, More Funding Available

Posted by Jim H on March 22, 2010

A great time was had by all at BioBeers Friday at ImQuest.  In my haste, I left home without a camera, so no pictures this time.  I think things went very well, aside form running out of beer after barely an hour and a half.  You BioGeeks are terrible at RSVP’ing.  A special thanks again to David Kaye and the other Sheer Partners for the sponsorship.

And thank you to all of the recruiters who showed up offering up jobs.  Please let me know if anyone lands a job out of this, as I know of one or two from past events.  Need to start trending this.

Next time we won’t run out of beer.  I already have plans to hold the next event outdoors at FITCI, a mere mile south of where we were on Friday.  Stay tuned.

And speaking of funding, I would be remiss if I didn’t pass on the great news earlier Friday of the “Tilt-up Party” held by Matan at NCI-Riverside Park.

According to the Press Release:

Matan Companies and Morgan-Keller, Inc. hosted a tilt up party celebrating  the construction progress for  The National Cancer Institute’s  332,000 square foot Advanced Technology Research Facility at Riverside Research Park in Frederick, Maryland.  The goal of this state of the art laboratory facility slated for delivery in early 2012, is to enable scientists to more rapidly develop a new generation of highly targeted treatments for cancer patients.

And on this historic day of absurd government spending, I have a lead on some ARRA funded research going on at SAIC-Frederick.

Making lyophilized IL15 for clinical trials.  Not sure how many people out there may be interested, but here’s the link:

And the Summary:

IL-15 is a 14 – 15 kDa member of the 4 α-helix bundle family of cytokines. It shares a number of biological activities with IL-2, including stimulation of the proliferation of activated CD4+, CD8+ and gamma-delta subsets of T cells. Recombinant human IL-15 (rhIL-15) expressed in E. coli was manufactured by the BDP under cGMP to yield active rhIL-15 for cancer therapy adjuvant vaccines in human clinical trials. The purpose of this document is to describe the requirements for the development of a cGMP lyophilized product for future clinical studies.

I hope someone local takes this before the out of towners do.

Posted in BioBeer, Biochemistry, Events, Funding Available, News | 2 Comments »

Opportunities Abound

Posted by Jim H on February 4, 2010

As you may already be aware, one of the primary reasons the National Cancer Institute is building the new Riverside Research Park is to provide space for “synergistic partners” from academia and Industry to work together to cure cancer.  I was just alerted to several new opportunities by my friends at FITCI

A new collaboration opportunity, “Gene Expression Signature Predictive of Response to Chemotherapy” has been added to the NCI Technology Transfer Center web site. Please go to:

A new collaboration opportunity, “Antibody and Immunotoxin Treatments for Mesothelin-Expressing Cancers” has been added to the NCI Technology Transfer Center web site. Please go to:

A new collaboration opportunity, “Knockdown and Enhanced Expression of P53 Isoforms to Treat Age-Related Disorders and Cancer” has been added to the NCI Technology Transfer Center web site. Please go to:

A new collaboration opportunity, “Engineered Biological Pacemakers” has been added to the NCI Technology Transfer Center web site. Please go to:

A new collaboration opportunity, “Novel Kinase Inhibitors Targeting the PH Domain of AKT for Preventing and Treating Cancer” has been added to the NCI Technology Transfer Center web site. Please go to:

Posted in Biochemistry, Funding Available, Government Funded research, Molecular Biology | 1 Comment »

More Positive ImQuest Results

Posted by Jim H on February 21, 2009

In a PR Newswire release, ImQuest is coming forth with more data on their original anti-HIV microbicide and a new topical cream.  The data on their lead candidate, IQP-0410, lead to the safe daily dosing of the compound.  From the release:

The highly attractive safety profile, ability of the compound to positively interact in combination with other HIV drugs, and the high intrinsic genetic barrier to resistance of the clinical candidate, was emphasized in these presentations. ImQuest, in collaboration with their drug development partner Samjin Pharmaceutical Co. Ltd of Seoul, Korea, have recently engaged in an effort to develop more active pyrimidinediones possessing this higher genetic barrier to resistance. It is believed that these compounds will prolong the therapeutic utility of the pyrimidinediones by preventing HIV from easily evading the action of the drug and will allow ImQuest to develop even more potent HIV inhibitors following the entry of IQP-0410 to Phase 1 human clinical trials in early 2009.


General 2, 4 (1H,3H)-Pyrimidinedione Structure

Interestingly, the mechanism of action of these compounds seems to be both an inhibition of viral reverse transcriptase and inhibition of viral attachment by binding some cell surface “conformational marker”, as shown in THIS POSTER (warning PDF).

This is also the first time I recall reading about their topical cream, IQP-0528.  This is a vaginally applied topical used “as both a gel and an intravaginal ring product in combination with other highly active microbicide products” to block transmission of HIV.

Great work, guys!

Posted in Biochemistry, Business, News, presentations, Vaccines | Leave a Comment »

Nature Methods a la Frederick

Posted by Jim H on November 25, 2008

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. Chatterjee1,3*, Kalavathy Sitaraman1,3#, Cassio Baptista2,3#, James Hartley1,3, 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


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.

Posted in Awards and recognition, BioBeer, Biochemistry, Government Funded research, Molecular Biology, News, Rants | Leave a Comment »

My 100th Post: Marligen Makes a Deal

Posted by Jim H on April 11, 2008

It’s been a while since I’ve heard anything about Marligen, the only Biotech company in my home town of Ijamsville. And even though they are less than a mile from the Montgomery County line, they’re still a FredCoBio member. That’s like having a semi-sterile cell culture flask, I guess. Here’s the news clip, via

Marligen Exclusively Licenses Genisphere Labeling Technology for the Detection of microRNAs on the xMAP® Platform

Marligen Launches Vantage Line for the Purification, Labeling and Detection of microRNAs

IJAMSVILLE, Md.–(BUSINESS WIRE)–Marligen Biosciences, Inc., a supplier of innovative products for the life sciences research market, will become the exclusive provider of Genispheres biotinylated labeling kits for detection of microRNAs on the xMAP® multiplex platform. The microRNA labeling kits using Genisphere Inc.’s 3DNA dendrimer signal amplification technology will be an integral product to Marligens new offering supporting researchers studying microRNAs. The Vantage product line includes reagent kits for purifying, labeling and detecting microRNA species.

Genisphere’s unique 3DNA dendrimer technology is based on highly branched DNA structures serving as scaffolds for multiple biotins. The use of Genispheres signal amplification technology in combination with the Vantage microRNA detection panels offers researchers a fast and cost-effective system to directly profile multiple microRNAs in a single sample. The complete system offers exceptional sensitivity and throughput capabilities of greater than 100 samples in a single day and is compatible with total RNA or enriched RNA including degraded RNA from archived tissues. The initial Vantage microRNA Detection Panels are designed for profiling the relative abundance of different microRNA species known to be relevant in oncology. The Vantage Products will be launched at the upcoming annual meeting of the American Association of Cancer Research.

High throughput profiling of MicroRNAs presents a challenge when combining rapid, effective labeling with improved detection sensitivity, said Dr. Robert Getts, Director of R&D at Genisphere. The complete Vantage package, having integrated our rapid 3DNA dendrimer microRNA labeling method with Marligens carefully designed detection panels, provides an optimized solution with consistent performance and much needed sensitivity on the xMAP® high-throughput detection platform.

“Because microRNA play such an important role in tumor development and progression, it is vital we offer researchers innovative tools that allow them to profile these biological markers in archived samples. Our collaboration with Genisphere allows us to provide one of the most rapid and sensitive methods to screen directly from such samples,” said James Lazar, Chief Scientific Officer of Marligen Biosciences. This will not only advance basic research but should expedite the application of microRNA detection in the diagnosis of cancer.

It’s strange, because this article couldn’t be more timely. The Founder & CEO, Sherry Challberg, was the one who hired me in April 1988 to move South to Maryland. It’s hard to believe that it has been 20 years ago to this day.

I was working in a lab at the University of Rochester doing papilloma virus research (which supported research leading to a Nobel prize for Micheal Bishop in 1989 and in support of research into Open Reading Baltimore Sun Business 12/21/88Frames, which lead to the 1993 Nobel Prize for Sharp & Roberts and also 1989 Nobel prize in Chemistry for Thomas Cech’s discovery of Ribozymes) and steroid hormone modulation of gene expression (in support of research into Protein Phosphorylation as a regulatory mechanism of proteins leading to the 1992 Nobel prize for Edmund Fisher and Edwin Krebs and leading to the discovery of COX-2 enzyme and COX-2 inhibitors in 1991 which was subsequently “borrowed” by Pfizer and made into the blockbuster drug Celebrex, reaffirming Dr Young’s assertion that I was leaving academia to go work in the “Evil Empire” that is Industrial research).

But enough name dropping, lest you think this blog is just about shameless self-promotion.

Back to the story. We moved down here in 1988 to work in the Molecular Diagnostics Division of Life Technologies. This was sold in 1990 or ’91 to become Digene. To the left you see the 25 year old version of yours truly, pretending I am doing lab work. This is from the front page of the Baltimore Sun’s Business section on Dec. 21, 1988. The story was about our pending FDA approval for (one of?) the first clinically approved DNA test on the market. You may notice that the paper has a tinge of orange from age, and if you look closely, you’ll see my beard was still orange, too. By the way, the Dow closed at a mere 2,166 that day, a 1-year CD would yield 9.00 % and the Prime was 10.5%.

Posted in Academia, Awards and recognition, Biochemistry, Business, Genetics, Government Funded research, Molecular Biology, News, Public/Private Companies, Rants, Rumors | 2 Comments »

Updates from Ft Detrick

Posted by Jim H on March 30, 2008

It’s Sunday morning, watching Meet the Press, so I guess it is a good time to update a few things going on at the Fort.

First, I will make a disclosure that much of my information is coming through my affiliation with the Frederick Chapter of AFCEA International. I have blogged this before, but wanted you to take a look at the updated and improved web site. Of particular note is the AFCEA Golf Outing at Whiskey Creek May 13th. Since we all like to golf and MdBio is no longer sponsoring their tournament in Frederick (which was always one of the best BioTech social events of the year IMHO), we’re going to try ad carry on the tradition. There are still sponsorships available and you can bet I’ll be harassing my friends at MedImmune, Lonza and other big Bio’s to get involved.

The presentation last month was by David W. Williams, US Army Medical Research & Material Command. You can get a copy of his presentation HERE. The USAMRMC and Mr Williams command a huge purchasing budget for all things related to Medical Materials and Medical-directed Research. The emphasis of this presentation were updates regarding the construction of the consolidated Logistics facility, the Defense Medical Logistics Center.

Also at the Fort this month, I wanted to highlight the excellent Seminar series, which is open to the public. I put the whole schedule on the Calendar page. A couple of highlights (for me) are
Dr. Valeri Vasioukhin, PhD, Cell Polarity in Self-Renewal and Differentiation of Stem/Progenitor Cells on April 7th and on April 18th Stem Cells and Early Lineage Development given by Janet Rossant, PhD. from the Hospital for Sick Children of Toronto.

There is also a very interesting looking retreat to Gettysburg on April 10th & 11th called the Cancer And Inflammation Program Workshop. Looks like a very comprehensive and interesting agenda, but not sure if I’ll be able to sneak out for two days.

Posted in Academia, Biochemistry, Events, Government Funded research, News, presentations, Stem Cells | Leave a Comment »

Genome Projector

Posted by Jim H on March 15, 2008

I ran across this neat little tool called the Genome Projector via My BioTech Life. It’s a Google Maps based graphics program which contains 320 bacterial genomes and gives you a zoomable view of circular DNA sequences, pathways and a DNA walk. It’s pretty cool and I’ll link it in the Gene Jockey section later. Why don’t you give it a try?

Posted in Biochemistry, Genetics, Molecular Biology, prokaryotic | Leave a Comment »

Mammalian Protein Localization Database

Posted by Jim H on February 21, 2008

I found a write up in this week’s Genetic Engineering News about a web site from Australia that provides an interactive guide to the subcellular location of proteins.  I think it’s a pretty neat tool and will be add this to the Gene Jockey section momentarily.

Posted in Biochemistry, Molecular Biology | Leave a Comment »

SuperArray Makes a Splash

Posted by Jim H on December 4, 2007

And I almost missed it. The story broke on Friday, but didn’t make a splash locally.

They have licensed a technology through Carnegie Institute which allows SuperArray to theoretically silence every gene in human, mouse and rat genome. Pretty damn powerful if it works as billed.

Kudos to Paul Nisson (former Life Technologies and University of Rochester colleague) and everyone at SuperArray (Fred. County Incubator Company of the year in 2006)!

Here are a few of the links:


GenomeWeb Daily

Genetic Engineering News


IP Today

Posted in Biochemistry, Business, Expansion, Jobs, Molecular Biology, News, Public/Private Companies | 1 Comment »


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