Standing Room Only-The Effects of Protein Crowding

 :: Posted by avi_wener on 01-12-2011

One of the biggest challenges for any scientist is to ensure that their experimental model of choice actually mimics natural biological circumstances. While it is one thing to conduct research in a test tube or cell culture dish it is quite another to translate those results into human biology. It is therefore imperative for scientists to choose a research model that most closely resembles its scaled up reality.

Over the past decade, the field of proteomics has experienced exponential growth. With the rise of technologies such as protein crystallography, protein arrays and surface plasmon resonance more information can be gathered on a proteomic-wide scale than ever before. Nonetheless, most proteomic experiments are conducted in-vitro often after protein extraction and clean-up techniques in an environment that is far removed from their cellular milieu. Under such circumstances, one must wonder how biologically relevant results techniques such as protein-protein interaction actually are. In fact, in a recent story published in Chemical and Engineering News (C&EN), staff writer Celia Arnaud describes the often overlooked effect of protein crowding on proteins function and stability.

According to the article, when proteins are packed into a cell (as is often the case under natural biological conditions), excluded-volume effects occur, which means that many things happen simply because molecules occupy space. This circumstance is often compensated on the bench with the addition of chemical agents such as Ficoll, however this is not an ideal way to replicate protein crowding and will not necessarily replicate biochemical conditions found in the cell.

According to Martin Gruebele, a chemist at the University of Illinois, Urbana-Champaign, “Eventually, people will expect that a complete protein data set includes in-cell or crowded studies of various kinds, in addition to the current aqueous buffer data. This is clearly where things will shift in the next five to 10 years.”

For more on the importance of protein crowding see Close Quarters

Boosting Biotech in Upstate New York

 :: Posted by avi_wener on 01-11-2011

SYRACUSE, N.Y.—January 11, 2011—During stops in Buffalo,
Rochester and Syracuse yesterday, U.S. Senator Kirsten Gillibrand
announced a new proposal to make the Research and Development Tax
Credit permanent—a move that would greatly boost jobs and business
growth for Upstate New York bioscience and medical technology
companies. According to Sen. Gillibrand, making the tax credit
permanent would increase private investments and provide stability
and certainty to innovative businesses and institutions. “This is
the kind of idea that can move us forward in creating a stronger
economy and creating the jobs that are so desperately needed,”
Gillibrand said. The senator’s proposal would: > Expand the
current credit by changing the formula to provide greater incentive
for companies to increase investment > Simplify the current
credit, which is highly complicated and confusing. > Make the
new credit permanent, which would provide private companies with
the confidence they need to make significant future investments in
R&D. “R&D is vital for the Bio/Med industry in Upstate New
York,” said Heather Erikson, president of MedTech and co-chair of
the State Medical Technology Alliance. “Supporting more competitive
incentives and investments in these areas, on both a state and
national level, will contribute to our industry’s ability to
develop major scientific and medical breakthroughs that fuel
business growth, create new employment opportunities, and promote
economic vitality.” The bioscience and medical technology industry
relies heavily on higher-paying, knowledge-based jobs. It is one of
the most stable industries in New York State paying employees an
average salary of $70,200 compared to the state’s overall average
wage of $60,400, according to the most recent data from the Empire
State Development Corporation. There are more than 200 Bio/Med
companies located in Upstate New York, 70% of which are
headquartered here. For more information about the Upstate Bio/Med
industry, visit ABOUT MEDTECH MedTech is an active
association of pharmaceutical, biotech, and medical technology
companies, their suppliers and service providers, and research
universities. We boost the growth and prosperity of our members by
connecting them for collaboration, offering educational programs,
sharing news and information, and advocating for the industry with
government and leaders. Our mission is to develop the
relationships, tools and programs that enable Upstate New York
companies to bring tomorrow’s medical solutions to the healthcare
marketplace. For more information, visit

Discovering Your Genome with the Click of a Mouse

 :: Posted by avi_wener on 01-11-2011

The world of personal genomics is becoming more accessible to the masses and the amount of information available to the general public is truly stunning. Today 5AM Solutions, a life science software engineering firm, announced the release of SNPTips, a Firefox browser plug-in that connects a user’s 23andMe personal genetic information to web content with a single mouse click.

Personal genetic testing services such as 23andMe provide genetic testing for individuals outside of a physician’s office. These services typically probe a person’s genome for thousands of single nucleotide polymorphisms (SNPs) that represent potentially important or interesting genomics differences between one person and another. 23andMe provides tools and reports for interpreting this information. For a user interested in connecting his or her genetic information with the treasury of literature and information on the World Wide Web, there’s no clear way to make the link. Which is why 5AM created SNPTips.

“SNPTips links your 23andMe raw data to SNP IDs that are mentioned in across a sea of web content. With the click of a mouse, you can view your personal genotype at any SNP mentioned the web – such as a genetics blog or journal article. SNPTips also includes smart links to other web resources, like SNPedia, Google Scholar, and NHGRI’s dbSNP – so you can delve deeper with a single click,” said Will FitzHugh, 5AM’s Chief Science Officer. “We started with 23andMe because it’s the market leader in personal genetics. We anticipate expanding SNPTips in the future to support other personal genetics services and browsers.”

“Our company works to make the web the place for life science collaboration,” said 5AM’s President & CEO, Brent Gendleman. “SNPTips brings that ability directly to consumers of personal genomic information. People can translate their genetic information into what they want to know, right through the browser. It can’t get more convenient than that.”

“The very existence of 23andMe allowed us to innovate and meet a need that leveraged what they do, extending it in a simple way through a common mechanism – the browser. SNPTips represents a way to extend their work, furthering people’s ability to tackle the complexity of genomics in a way that is straightforward and consumable by a wide audience,” said Gendleman.

SNPTips makes use of a person’s complete 23andMe SNP raw data profile, and requires that a user safeguard the use of that information by employing it only on a machine under his or her control. SNPTips does not move any personal information across the Internet.

SNPTips is available for free at and requires a Firefox 3.6+ browser.

About 5AM Solutions
5AM Solutions develops innovative software solutions for academic, government, commercial, and non-profit life sciences organizations. The company helps evolve the way biomedical researchers work and collaborate by using software to reveal new insights hidden in vast amounts of data, facilitate translational research, and solve workflow challenges. The company’s solutions can overcome IT-based roadblocks to discovery and accelerate progress toward the ultimate goal of better health and improved patient outcomes.

About SNPTips
For information on SNPTips, visit To install on a Firefix 3.6+ browser, simply click the Install Now button, and follow the directions on the website to configure. SNPTips is free, and is released under the Creative Commons Attribution-ShareAlike 3.0 Unported license.

About 23andMe
SNPTips is not affiliated with 23andMe. SNPTips is a product and a trademark of 5AM Solutions, Inc. 5AM Solutions makes no claims regarding, and is not responsible for, 23andMe’s content, products, or services. Visit for information on 23andMe.

source:PRWeb press release

A Video Tutorial for High Resolution Melt Analysis

 :: Posted by avi_wener on 01-10-2011

High resolution melt (HRM) analysis is a relatively new technique used in detecting small variations in DNA sequences between varying populations. Important applications of HRM include SNP analysis, genotyping and methylation analysis.

In the following 20 minute tutorial presented by Sean Taylor, Field Application Specialist, Bio-Rad Laboratories, you will learn the basics of high resolution melt analysis and how to practically use it in your research. The video contains information on:

  • what is high resolution melt analysis, how does it work and why it is useful
  • various applications for high resolution melt analysis including single nucleotide polymorphism (SNP) analysis and DNA methylation analysis
  • the difference between a standard melt curved performed in routine QPCR and HRM
  • the difference between non-saturation dyes such as SYBR green and saturation dyes such as evagreen
  • the definition of the four class types of SNPS
  • critical factors for good experimental design
  • what technique you should be using for your SNP analysis (it is not one size fits all…think HRM VS Sequenome VS multiplex array
  • and more!!!

For more information on HRM see A Practical Guide to High Resolution Melt Analysis Genotyping

America’s Doctoral Dilemma

 :: Posted by avi_wener on 01-06-2011

Over the past few weeks we have discussed the merits of America’s PhD programs and the darkness at the end of the tunnel facing many newly minted doctoral graduates. See PhD: A Tale of Immigration, Slave Labor and Joblessness and Are Scientists Over-Educated?

This past week, Norman Johnson, an evolutionary geneticist, science writer and adjunct professor at the University of Massachusetts added his two cents based on a recent report on the state of doctoral graduates by the National Science Foundation . According to the report, 2009 marked the largest single-year increase in the proportion of doctorate recipients taking postdoc positions during the 2004–09 period against a backdrop of decreasing employment opportunities for recent doctoral graduates.

Dr. Johnson’s reaction to this news is mixed. He writes:

If we expect most biology graduate students to go on to research faculty or even teaching faculty positions, then 8,000 biology doctorates a year is clearly too many. There just aren’t enough jobs. If, however, biology researchers and teachers at institutions that award doctorates seriously consider jobs in non-academic positions as being worthy of the doctoral students, then 8,000 a year may not be enough.

I am not sure whether or not the private sector can absorb that many PhD graduates but in order to move in that direction, there needs to be an increased effort to educate recent graduates on their employment options and government programs encouraging them to emigrate from their comfortable academic cocoon into the rough and tumble world of industry.

Science graduates have poured oodles of time and money into their education and they deserve recognition and fair compensation for their efforts. Let’s give them the vocational support and respect they’ve earned. I believe that society will benefit from it in the long run.

BetterBio for More Meaningful Science Journalism

 :: Posted by avi_wener on 01-05-2011

If you are interested in meaningful, accessible news about biotechnology and its impact on our lives without all the hype that is usually associated with tabloid journalism be sure to watch the video below and show your support for BetterBio. According to BetterBio founder Khadijah Britton, the reality of every day science does not usually involve earth-shattering breakthroughs or setbacks as is often reported in the popular media, but it does involve a more complicated set of circumstances with small steps forward and (hopefully) few steps back.

Like Khadijah, I too am disappointed with the way science is portrayed in the media and I would love to see meaningful, accessible news that presents the reality of biotechnological progress to a diverse public audience. I believe that most members of the scientific community share my sentiments and I encourage you to show your support.

Better Bio’s Promise from Better Bio on Vimeo.

Huge Boost for Personalized Medicine at Johns Hopkins

 :: Posted by avi_wener on 01-04-2011

Liberty Media Corp. chairman and Johns Hopkins alumnus John C. Malone has given the university’s Whiting School of Engineering $30 million for a building where researchers will collaborate with colleagues from other Johns Hopkins divisions to learn to tailor therapies for individual patients and devise systems-based approaches to some of society’s biggest problems.

The gift, the largest ever to the Whiting School, will fund construction of a 56,000-square-foot research building on the university’s Homewood campus.

Malone Hall will house two planned interdisciplinary research efforts in which the Whiting School will have a leadership role: It will be the home of the Systems Institute and the Homewood base for Johns Hopkins’ emerging initiative in individualized health.

The initiative in individualized health is expected to bring together engineers, life scientists and medical researchers from across Johns Hopkins. They will focus on bringing information science into the practice of medicine, with an initial emphasis on cancer, in a manner that will allow an unprecedented focus on treatment designed for the individual patient. The approach grows out of the recognition that genetic and epigenetic differences among patients explain, at least in part, why traditionally developed drugs help some people and not others.

For more information see the JHU Gazette

Real Time Quantitative PCR Software Tutorial

 :: Posted by avi_wener on 01-04-2011

If you are a user or potential users of Bio-Rad’s CFX or MiniOpticon systems be sure to see the message below and the accompanying real time quantitative PCR software tutorial from Bio-Rad’s Sean Taylor, Field Applications Specialist.

I am pleased to provide our recently upgraded version of CFX Manager. Version 2.0 has significant improvements and new tools from the last version 1.6 of the software. I recently did a little test drive and have recorded a 25-minute training video to help you navigate around the new features. Some key highlights include:

1. Scheduling module so that you can schedule your time on the instrument. A great tool for a multi-user instrument.
2. Master Mix Calculator…Just type in your primer concentrations and you get the volumes required for your experiment. No more thinking and more importantly…no more mistakes in volume conversions!
3. Copy and paste wells in the plate editor. I am personally very pleased with this feature.
4. Much easier access to the data you need and very nice and new data view and data export features.

The link to the video is here:
video link

The specifications for the software can be found here:
software specifications

To access the upgrade, you can go to:

Click on “Downloads” and you will find:

A. The CFX96 and CFX384 Real-Time PCR Detection Systems Firmware Update.

B. The upgrade patch for CFX Manager 2.0.

C. Precision Melt Analysis™ v1.1 Software Upgrade (This is only required for those who are using Version 1.0 of Precision Melt Analysis Software).

Important: The firmware update comes with detailed instructions that are easy to follow but do not hesitate to call tech support (1-800-4Bio-Rad) if you have any questions about the procedure.

I would like to take this opportunity to wish you and your families health and happiness in 2011!

Sean Taylor
Field Application Specialist
Bio-Rad Laboratories

Click here for other technical resources from Sean including his video entitled “A Practical Approach to MIQE for the Bench Scientist,” A Practical Guide to High Resolution Melt Analysis Genotyping, and the article A Simple Solution to Chromatography for High-Purity Protein Preparations: The Modular Approach

Inspirational Women Scientists

 :: Posted by avi_wener on 01-03-2011

What a great story!

According to the YouTube description: When Carla Shatz, PhD, professor of neurobiology, and Helen Blau, PhD, professor of microbiology and immunology, came to Stanford in 1978, they were two of he first women to be hired on the tenure tract for basic science faculty. Over the decades, as their professional and personal paths have diverged and converged, they have remained the closest of friends. In this video, they discuss the courses their paths have taken and reflect on the rewards and challenges of their lives as women scientists.

Hat tip to the PostDoc Forum for pointing out this video.

Blog updates

 :: Posted by avi_wener on 01-03-2011

Welcome to a new year! I hope that everyone enjoyed the holidays with family and friends and that you’re all geared up for a great 2011.

I’ve been receiving dozens of messages from wordpress (the publishing platform used to power the American Biotechnologist blog) that many of the plugins and themes used on the American Biotechnologist were out of date. As any good molecular biologist would have done, I listened to my gut which told me that if it aint broke, don’t fix it. (Isn’t that how molecular biology works? If you get your best transfection results Tuesday afternoons at five while wearing a pink labcoat and blue nitrile gloves, you wouldn’t dare transfect cells under any other conditions.) Nonetheless, the warning messages of vulnerabilities in the site and necessary “emergency fixes” started eating at me and so, this weekend I bit the bullet and gave the site a thorough upgrade. All of this happened behind the scenes and hopefully you won’t notice any difference to the look, feel and functionality of the site (I didn’t). However, if you do come across any abnormalities such as links not working or strange things appearing on your screen please email me or send me a message using the comment section.

As always, if you have ideas or suggestions for improving the blog or topics you would like us to cover (or if you are interested in doing a guest post) please let us know! I look forward to your comments!