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Genes Protect Themselves Against Being Silenced

 :: Posted by American Biotechnologist on 10-10-2013

Harvard Stem Cell Institute (HSCI) researchers have settled a century-old debate over whether occurrence of DNA methylation acts to silence gene expression, or if genes are turned off by other means before they are methylated.

As explicated today in the journal Nature, methylation in fact enforces gene silencing, and it is levels of a newly identified form of RNA produced by individual genes that determines whether they are turned off by the addition of a methyl (CH3) group by the enzyme DNA methylase 1 (DNMT1).

The study, led by HSCI Principal Faculty member Daniel Tenen, MD, found that during transcription of DNA to RNA, a gene produces a small amount of what the investigators named “extracoding RNA,” which stays in the nucleus and binds to DNMT1, blocking its ability to methylate, or silence the gene. The discovery of RNA’s new function has therapeutic potential as an on-off switch for gene expression.

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Fast new, 1-step genetic engineering technology

 :: Posted by American Biotechnologist on 05-22-2013

A new, streamlined approach to genetic engineering drastically reduces the time and effort needed to insert new genes into bacteria, the workhorses of biotechnology, scientists are reporting. Published in the journal ACS Synthetic Biology, the method paves the way for more rapid development of designer microbes for drug development, environmental cleanup and other activities.

Keith Shearwin and colleagues explain that placing, or integrating, a piece of the genetic material DNA into a bacterium’s genome is critical for making designer bacteria. That DNA can give microbes the ability to churn out ingredients for medication, for instance, or substances that break down oil after a big spill. But current genetic engineering methods are time-consuming and involve many steps. The approaches have other limitations as well. To address those drawbacks, the researchers sought to develop a new, one-step genetic engineering technology, which they named “clonetegration,” a reference to clones or copies of genes or DNA fragments.

They describe development and successful laboratory tests of clonetegration in E. coli and Salmonella typhimurium bacteria, which are used in biotechnology. The method is quick, efficient and easy to do and can integrate multiple genes at the same time. They predict that clonetegration “will become a valuable technique facilitating genetic engineering with difficult-to-clone sequences and rapid construction of synthetic biological systems.”

Thanks to the American Chemical Society for contributing this story.

Candy Consumption Vindicated

 :: Posted by American Biotechnologist on 05-20-2013

Check out the following story:

At a time when the spotlight is focused on obesity more than ever, new research suggests that frequency of candy consumption is not associated with weight or certain adverse health risks. According to a recent data analysis published in the April 30th issue of Nutrition Journal, adults who consume candy at least every other day are no more likely to be overweight nor have greater risk factors for cardiovascular disease (CVD) than moderate consumers (about once a week) or even less frequent candy eaters (less than 3 times per month).

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Feel like eating candy?

What if I told you that it was publicized by the National Confectioners Association? Would that change your opinion of the veracity of the findings?

The Ugly Side of the Journal Impact Factor

 :: Posted by American Biotechnologist on 05-16-2013

Are you obsessed with publishing in high ranking journals such as Cell or Science? Do you gloss over your works that have been published in low ranked journals when talking with colleagues or attending a job interview? If the answer is yes, you are not alone.

Since its invention approximately 60 years ago, the Journal Impact Factor (JIF) has been used to assess the quality of academic literature and the influence of scientific papers on the scientific community. The JIF was proposed by Eugene Garfield in the early 1950s and originally published by his Institute for Scientific Information (ISI) as a subscription buying tool for academic and medical librarians. The JIF assigns a score to scientific journals based on the average number of citations received in a year per paper published in the journal during the two preceding years. It has since become the authority on which journals are considered top tier publications are therefore premiere space for scientists wishing to best publicize their work and gain notoriety.

Unfortunately, the JIF has also become a tool used to ascertain a scientist’s worth and can often be a determining factor in the levels of funding they are to receive. This is an unfortunate turn of events since the JIF contains many deficiencies such as glossing over differences between fields, and lumping primary research articles in with much more easily cited review articles. As such, researchers that publish quality work in lower ranked journals are often at a disadvantage compared to those publishing secondary research in higher ranking journals.

In order to “protest” and counter this phenomenon, a group of publishers from both high impact and low impact journals have formed the Declaration on Research Assessment (DORA) which aims to lower the influence of the JIF on assessing scientific merit.

Dora has released 18 principles which are geared towards accomplishing these goals. Some of the recommendations that stand out the most include:

  • JIF should not be used to measure quality of individual articles or to asses an individual scientist’s contributions, or in hiring, promotion or funding decisions
  • Funding agencies should place more weight on the scientific content of a paper than its JIF
  • Scientific content of a paper should be considered a more important hiring decision than the JIF
  • A call for organizations to be open and transparent by providing data and methods used to calculate all metrics
  • Researchers should challenge research assessment practices that rely inappropriately on JIF

To download the full list of recommendations visit http://am.ascb.org/dora/files/SFDeclarationFINAL.pdf.

Another Lucky Science Student Wins $100,000

 :: Posted by American Biotechnologist on 03-13-2013

For the past 14 years, Intel has been distributing hundreds of thousands of dollars in prizes to winners of their annual Science Talent Search competiton. With over 1,700 applicants, chances of securing the grand $100,000 prize is very tough. However,Sara Volz, a high-school senior from Colorado Springs, won the top award for her research of algae biofuels. Jonah Kallenbach of Pennsylvania came in a close second for his bioinformatics study on protein binding for drug therapy and Adam Bowman, of Brentwood, Tennesee came in third for pulsed plasma device design.

Altogether, $630,000 was awarded to ten high-school seniors from across the United states. The truth is that the talent search actually streches back more than 70 years to 1942 when it was sponsored by Westinghouse. One of the most interesting things about this type of contest is understanding how useful it is for encouraging young adults to pursue a career in science and discovering whether or not it has helped launch the careers of those fortunate enough to win. With 2,500 contest finalists since its inception, figuring out where the winners are today is a mighty tall task. Thankfully, Scientific American has taken upon itself this mission and has uploaded a webpage that asks the question “Where are they now?

Among the winners are Nobel prize receipients Ben Roy Mottelson, Roald Hoffmann, Walter Gilbert and Sheldon Lee Glashow.

In the video below, this year’s prize recepient, Sara Volz, explains her research on Algae Biofuels.