My 100th Post: Marligen Makes a Deal

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 businesswire.com:

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 Genisphere’s 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 Marligen’s 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 Genisphere’s 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 Marligen’s 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 Frames, 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%.

Updates from Ft Detrick

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.

Genome Projector

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?

Mammalian Protein Localization Database

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.

SuperArray Makes a Splash

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:

Yahoo!Finance

GenomeWeb Daily

Genetic Engineering News

PharmaLive

IP Today

Atlantic Biomass

Another nice write up in the FNP today about Atlantic Biomass

I hope, in the future, I can stop lifting stories off the FNP and come up somethings on my own, just our own Biodiesel testing business is starting to take off and I have been busy playing in the lab.

On a different topic, I added a couple new Biotech blogs to the blogroll via The Regeneration Station. I found this one through PIMM.  I like it because it is industry focused with a bend towards regenerative medicine and stem cell stuff. I copied a few other links off his blogroll, a couple sites I hadn’t seen before. Please check it out.

BioTechniques Techniques

I have been meaning to add some links for Protocols, Methods and SOPS. One useful web resource I encountered is to the BioTechniques Molecular Biology Techniques forum. There is just a ton of information, protocols and the like. I haven’t had a chance to play around with it too much, but this looks like a good resource to book mark.

For example:

Welcome to the BioTechniques® Molecular Biology Forums, a science-based bulletin board for techniques, tips, and questions concerning molecular biology, cell biology, microscopy, and bioinformatics.

BioTechniques® Molecular Biology Techniques Forums
Reasons for or against putting a hist tag at both ends?

Post new topic Reply to topic BioTechniques® Molecular Biology Techniques Forums Index -> Protein

PostPosted: Nov 16 2007 7:37 am Post subject: Reasons for or against putting a hist tag at both ends? Reply with quote
I ordered a custom made NusA fusion vector from Addgene recently and originally thought that the vector had only a C-terminal histidine tag. Upon closer inspection I noticed that there is also a N-terminal histidige tag. The C-tag is naturally optional so that by including a stop codon in your insert you can choose not to have it. My question is that is there especially something for or against using both tags? We can assume that the tag sequence does not affect the specifity of my assay and doesn’t need to be removed. The tag(s) are there for purification.

Question 2: Do you know if there is an actual difference in leakage between using TAA versus TGA as the stop codon in bacterial expression?
PostPosted: Nov 16 2007 10:42 am Post subject: Reply with quote
There is no reason to use both tags. I think the vector is designed that way, so someone can have a choice of putting the tag at the N-terminus or the C-terminus, depending on the protein being expressed. There may be restriction enzyme site upstream of the N-terminus His-tag to let you delete the tag sequence, if you so chose.

It is better to avoid TGA stop codon when you express protein in E. coli to avoid read through. Here is an example.

http://www.biochemj.org/bj/309/0411/3090411.pdf

Just like human, they go through STOP sign. Laughing

Research Tool Sites for Molecular Biology

I’ve added a new link to the Web Links page which contains a large number of links to other useful Molecular Biology web sites.  I would suggest you bookmark it for future reference

Research Tool Sites for the Molecular Biology

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[ What's New | Home | My Favorite | Yeast | Web | LINKS | Database | Protocol | Journal | Others | Software | General ]

My Favorite Sites

• Essential Research Tools
  • Tools for the Molecular Biology - Quick Access Table
  • EMBOSS - a graphical user interface to the EMBOSS suite of bioinformatics tools. : EMBOSS (European Molecular Biology Open Software Suite) is a suite of free software tools for nucleotide and protein sequence analysis
  • All-IN-ONE SEQ-ANALYZER - by Naohiro Inohara
  • The CMS Molecular Biology Resource - by Christopher M. Smith at SDSC
  • DNA & Protein Analysis Toolkit - Computing Services at The Rockefeller University (USA)
  • JaMBW - Java based Molecular Biologist’s Workbench
    • List of Java-based Molecular Biology Work Bench sites
  • ExPASy Proteomics tools - at Swiss Institute of Bioinformatics (SIB)
  • Research Tools: [FRAME] - by Jun Ishikawa at National Institute of Health (Japan) : You can select [NONFRAME]: [JAPANESE-NONFRAME]
• DataBases
  • GenomeNET: Institute for Chemical Research, Kyoto University Human Genome Center: Kyoto, Institute of Medical Science, University of Tokyo: Tokyo (Japan)
  • Restriction Enzyme Database - New England Biolabs, Inc.
• Table
  • Amino Acid Information
  • Codon_usage
  • Periodic table
• Reference Sites
  • Entrez - NCBI Entrez Browser (USA)
  • The Molecular Biologist’s Desk Reference: at NIH: National Institutes of Health (USA)
  • NCBI PubMed - A search tool for accessing literature citations and linking to their full-text versions at publishers’ Web sites - An experimental service of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)
  • PaperChase - PaperChase provides 9,337,834 references - MEDLINE | HealthSTAR | AIDSLINE | CANCERLIT
  • ingenta - Reference search and document delivery service
  • Chemfinder - Chemical Searching and Information Integration
• Others
  • Frontiers in Bioscience: [ THE VIRTUAL LIBRARY ] [ THE JOURNAL ] - The most informative Web-space
  • Schizosaccharomyces pombe & Yeast Sites

[ What's New | Home | My Favorite | Yeast | Web | LINKS | Database | Protocol | Journal | Others | Software | General ]

World-Wide-Web Sites

• All the Virology - by the Garry Laboratory in the Department of Microbiology and Immunology in the School of Medicine at Tulane University (USA)
• The Biotechnology Information Center - One of ten information centers at the National Agricultural Library of the US Department of Agriculture: ARS
• Computional Biology and Informatics Laboratory - at Pennsylvenia University
• Computational Molecular Biology: by the Computational Molecular Biology Section (CMBS) at NIH (USA)
• DNA Information and Stock Center: DISC - National Institute of Agrobiological Resources (Japan)
• EMBnet: The European Molecular biology network: [ http://ben.vub.ac.be/ | ftp://dbmdec5.ulb.ac.be/ | ]
• European Bioinformation Institute (UK)
• The ExPASy Molecular Biology Server - by Amos Bairoch at the Geneva University Hospital and the University of Geneva (Switzerland)
• GenomeNET: Institute for Chemical Research, Kyoto University Human Genome Center: Kyoto, Institute of Medical Science, University of Tokyo: Tokyo (Japan)
• Health Sciences Topics - Molecular Biology: Medical Center at Vanderbilt University (USA)
• Human Genome Center: Institute of Medical Science at The University of Tokyo (Japan)
• Image Library of Biological Macromolecules - featured as website of the day on February 19, 1997 by the ‘webzine’ HMS Beagle.
• MRC - Human Genetics Unit - WWW Server(UK)
• National Institute for Basic Biology: NIBB (Japan)
• Sheffield ChemDex - at University of Sheffield (UK)
• Theoretical Biophysics Group - NIH Resource for Concurrent Biological Computing at Beckman Institute for Advanced Science and Technology
• UK MRC HGMP Resource Centre - Human Genome Mapping Project Resource Centre (UK)
• Weizmann Institute Genome and Bioinformatics: (Israel)

[ What's New | Home | My Favorite | Yeast | Web | LINKS | Database | Protocol | Journal | Others | Software | General ]

Useful Database Sites

• ATCC - American Type Culture Collection
• Databases for Molecular Biology - NIH (USA)
• DNA Data Bank of Japan: DDBJ - Center for Information Biology of Genetics - SAKURA On-Line Gene Submission (Japan)
• DSHB: Developmental Studies Hybridoma Bank under the auspices of the National Institute of Child Health & Human Development (USA)
• EMBL DataBase
• Escherichia coli Databank - at The Graduate School of Biological Sciences: NAIST (Japan)
• E.coli Genetic Stock Center: CGSC - E. coli Stock Center Database at Yale University (USA)
• E. coli Genome Project: The purpose of this server is to provide a front-end graphical interface to our FTP site - at University of Wisconsin-Madison (USA)
• GenBank Database
• A Gene Map of the Human Genome - The Gene Map web site is hosted by the National Center for Biotechnology Information: NCBI (USA)
• GenLink - at Washington University (USA)
• Online Research Resources - The National Center for Human Genome Research: Genome and Genetic Data at The National Center for Human Genome Research (NCHGR): The Human Genome Project for the National Institutes of Health (NIH)
• MPDB: The Molecular Probe Data Base - The Molecular Probe Data Base (MPDB) contains information on ca. 4000 synthetic oligonucleotides with a sequence of up to 100 nucleotides - at The Interlab Project (Italy)
• National Collection of Yeast Cultures - at Genetics and Microbiology Department, Institute of Food (UK)
• NDB: Nucleic Acid Database - The goal of the Nucleic Acid Database Project is to assemble and distribute structural information about nucleic acids at The State University of New Jersey (USA)
• REBASE: Restriction Enzyme Database - by Richard J. Roberts
• Restriction Enzyme Information Resources - by Mary Hoenecke and Carolyn Stock at Promega Corporation (USA)
• SEQNET - The U.K. academic communitiesSEQuence NETwork computer for molecular biologists at Daresbury Laboratory (UK)
• TIGR Database- TDB: a collection of molecular biology databases (USA)
• TIGR Human Genome Sequencing Projects - at The Institute for Genomic Research: TIGR (USA)

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• Protein Database and Resources
  • ENTREZ: Protein and nucleotide database (NCBI)
  • ENZYME: Enzyme nomenclature database
  • Molecules R US: Web interface for accessing molecular structure data in PDB
  • ProDom: The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the SWISS-PROT database - The ProDom team in Toulouse (France)
  • PRO-SITE: Dictionary of protein sites and patterns
  • Protein Data Bank: Brookhaven National Laboratory
  • PROLYSIS: A protease and protease inhibitor Web server by Thierry MOREAU (France)
  • SCOP: Structural Classification of Proteins. Release 1.32. 4432 PDB Entries (all through May 96). 8330 Domains. 169 Literature References. - at MRC Laboratory (UK)
  • SWISS-PROT: Annotated protein sequence database

[ What's New | Home | My Favorite | Yeast | Web | LINKS | Database | Protocol | Journal | Others | Software | General ]

Research Protocol & Tool Sites

• To Get More Software: TRY This Page !!
• BioPD - at Interdepartmental Biological Building - University of Padova (Italy) 05.5.21
• BOXSHADE 3.21 - Pretty Printing and Shading of Multiple-Alignment files - by the Bioinformatics Group at the ISREC (Swiss Institute for Experimental Cancer Research) in Epalinges s/Lausanne
• Computational Biochemistry Research - at ETH: Eidgenossische Technische Hochschule Zurich
• FramePlot.pl: v.0.5 - coding region prediction of high G+C-content bacteria by Jun Ishikawa at National Institute of Health (Japan)
• Genome Information Research Center: Home Page in Japanese - at Osaka University (Japan)
• A Guide to Structure Prediction (version 2)
• IDEAS - Integrated Database and Extended Analysis System for Nucleic Acids and Proteins - at GenomeNET (Japan)
• Molecular Biology Club - Biology Courses|Protocoles|Data Analysis|Software for Science|Other Sotware…
• Molecular Phylogenetic Tree - Making Molecular Phylogenetic Tree at Kyoto University (Japan)
• Multiple Alignment Resource - VSNS BioComputing Division (Germany)
• NIH Image Home Page - The most powerful “Image” soft
• PCR Methods
  • Long PCR Protocol
  • PCR Jump Station - The ultimate Web page for information and links on all aspects of the Polymerase Chain Reaction (PCR)
  • Primer3: Pick PCR primers from nucleotide sequence by Steve Rozen and Helen J. Skaletsky at Whitehead Institute for Biomedical Research (USA)
• Molecular Biology Protocols
• Search the Genentech Web Site - Genentech, Inc.
• SOSUI - Secondary Structure Prediction of Membrane Proteins at GenomeNET (Japan)

NCI-Frederick November events

I lifted this table off NCI-Frederick’s web site and included it as a new link on the Calendar page:

Tuesday, November 06, 2007
8:30:00 AM	Michael Dean, PhD	Bldg 549 Conf. Rm B
	Cancer, Inflammation, and Stem Cells	Details Series
Wednesday, November 07, 2007
12:00:00 PM	Sina Bavari	Bldg 549 Auditorium
	Innate Immune Responses to Highly Pathogenic Microbes	Details Series
Friday, November 09, 2007
12:00:00 PM	Dr. Hal Broxmeyer	Bldg 549 Auditorium
	Regulation of Hematopoietic and Embryonic Stem Cells	Details Series
Tuesday, November 13, 2007
8:30:00 AM	Jacques Banchereau, PhD	Bldg 549 Conf. Rm B
	Harnessing Dendritic Cells to Build Cancer Vaccines	Details Series
Wednesday, November 14, 2007
12:00:00 PM	James Kelley	Bldg 549 Auditorium
	Getting a Charge Out of Chemistry: Making and Using Ions for Bioanalysis	Details Series
Friday, November 16, 2007
11:00:00 AM	Dr. Joseph Lakowicz, Director	Bldg 549 Auditorium
	Plasmon-Controlled Fluorescence: A New Paradigm in Biological Fluorescence	Details Series
12:00:00 PM	Dr. Licia Selleri	Bldg 426 Conf. Rm
	A First Step Towards a Genetic and Transcriptional Control of Spleen Development	Details Series
Tuesday, November 20, 2007
8:30:00 AM	Ian F. Tannock, MD, PhD,FRCPC	Bldg 549 Conf. Rm B
	Limited Drug Distribution and Repopulation as Important and Neglected Causes of Drug Resistance in Solid Tumors	Details Series
Tuesday, November 27, 2007
8:30:00 AM	Catherine M. Handy, PhD, RN, AOCN	Bldg 549 Conf. Rm B
	The Future is Bright Yet so Small: Nanotechnology and Cancer Therapy	Details Series
Wednesday, November 28, 2007
12:00:00 PM	Steven Hou	Bldg 549 Auditorium
	Molecular Genetic Study of Stem Cell Regulation in Drosophila and Mice	Details Series
Thursday, November 29, 2007
9:00:00 AM	Various Speakers	Bldg 10 Lipsett
	The IL-10 Cytokine Family: IL-10, IL-19, IL-20, IL-24 and IL-28/IL-29	Details
Friday, November 30, 2007
12:00:00 PM	Dr. William Paul	Bldg 549 Auditorium
	The2 Cells: Differentiation and Repertoire-dependent Immunopathology	Details Series

I think that these would be open to the public, but am awaiting verification from someone at NCI. This is the type of information I’ve been looking for that would benefit everyone in the Frederick County Biotech community. I was delighted and surprised to see Dr Harold Broxmeyer speaking 11/9. He is a giant in the field of hematopoeitic stem cell research and transplantation.

APE Bio Featured in Gazette

FITCI Tenant, Advanced Product Enterprises featured in 10/18 Gazette Article.

Get the complete article here!