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02/12/2013

3-D Cell Viability Assay Kit
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The Perfecta3D Cell Viability Kit, from 3D Biomatrix and Cayman Chemical, is a new assay kit for measuring the viability of 3-D spheroids and one of the first viability assays optimized for 3-D cell culture. The kit includes 3D Biomatrix’s Perfecta3D Hanging Drop Plates, which facilitate the consistent and controllable growth of small spherical 3-D clusters called spheroids in a well-plate format. The kit provides an easy-to-use format for studying cell proliferation in spheroids formed in the Hanging Drop Plates. The assay, based on the enzymatic cleavage of the tertrazolium salt WST-1 to formazan by cellular mitochondrial dehydrogenases in viable cells, will allow investigators to screen drug candidates involved in cell cycle regulation in a 3-D format.
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30/11/2013

Google-backed company selling DNA analysis kits ordered to halt sales
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Health officials have ordered a start-up headed by the ex-wife of a Google co-founder to halt a service of DNA testing to determine health risks.

The US Food and Drug Administration said in a warning letter to the company, 23andMe, and made public on Monday in the US that its "saliva collection kit and personal genome service" needs to get regulatory approval.

The company was co-founded by Anne Wojcicki, who recently split with Sergey Brin, one of the co-founders of Google. The internet giant had been an investor in the firm.

The company provides a saliva analysis kit aimed at helping customers determine their genetic risks for diseases such as diabetes, coronary heart disease, and breast cancer.
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Kits similar to 23andMe are available in Australia online, through several companies, starting at about $300. The boom in business and interest in genomes and genetics has led to controversy about the commercial use of one of the most crucial medical breakthroughs of recent years.

The FDA letter said that most of the uses for the kit make it a "medical device" which requires regulatory approval.

The letter said some uses of the kit "are particularly concerning", because of "potential health consequences" of false positive or false negative results for some conditions such as

genetic predisposition for breast cancer.

"For instance, if the [genetic] risk assessment for breast or ovarian cancer reports a false positive, it could lead a patient to undergo prophylactic surgery, chemoprevention, intensive screening, or other morbidity-inducing actions, while a false negative could result in a failure to recognize an actual risk that may exist," the letter said.

The letter noted that "even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the [kit] for its intended uses".

As a result, "23andMe must immediately discontinue marketing the [kit] until such time as it receives FDA marketing authorisation for the device".

Fairfax Media has previously reported that the growth in online DNA testing raised a host of serious legal, ethical and medical concerns.

In January 2011, Associate Professor Kristine Barlow-Stewart, director of the Centre for Genetics Education at Royal North Shore Hospital, said then that it was no surprise when, in a commercial sting, US investigators sent the same DNA samples to four of the top companies - 23andMe, Navigenics, deCODEme and Pathway Genomics - and got back different predictions of disease risks.

"The science behind many of the results is still in its infancy. Interpretations should be taken with a very large grain of salt," she said at the time.

23andMe describes itself as "the leading personal genetics company dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools".

It has received financial backing from Google Ventures, Johnson & Johnson Development Corporation, The Roche Venture Fund and others.

Kendra Cassillo, a spokeswoman for 23andMe, said the company had received the warning letter.

"We recognise that we have not met the FDA's expectations regarding timeline and communication regarding our submission," she said in an email.

"Our relationship with the FDA is extremely important to us and we are committed to fully engaging with them to address their concerns."

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30/11/2013

New tool developed for profiling critical regulatory structures of RNA molecules
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UNIVERSITY PARK, Pa. -- A molecular technique that will help the scientific community to analyze -- on a scale previously impossible -- molecules that play a critical role in regulating gene expression has been developed by a research team led by a chemist and a plant biologist at Penn State. The scientists developed a method that enables a more accurate prediction of how ribonucleic acid molecules (RNAs) fold within living cells, thus shedding new light on how plants -- as well as other living organisms -- respond to environmental conditions. Potential implications of the methodology for human health include, for example, learning how an infection-induced fever could affect the RNA structures of both humans and pathogens. A paper by the research team -- led by Sarah M. Assmann, Waller Professor of Biology, and Philip Bevilacqua, professor of chemistry -- was scheduled for early online publication in the journal Nature on Nov. 24

"Scientists have studied a few individual RNA molecules, but now we have data on almost all the RNA molecules in a cell -- more than 10,000 different RNAs," Assmann said. "We are the first to determine, on a genome-wide basis, the structures of the RNA molecules in a plant or in any living organism."

Temperature and drought are among the environmental stress factors that affect the structure of RNA molecules, thereby influencing how genes are "expressed" -- how their functions are turned on or turned off. "Climate change is predicted to cause increasingly extreme and unpredictable heat waves and droughts, which would impact our food crops, in part by affecting the structures of their RNA molecules and so influencing their translation into proteins," Bevilacqua said. "The more we understand about how environmental factors affect RNA structure and thereby influence gene expression, the more we may be able to breed -- or develop with biotechnological methods -- crops that are more resistant to those stresses. Such crops, which could perform better under more-marginal conditions, could help feed the world's growing population."

The scientific achievement of the Penn State research team-postdoctoral scholar Yiliang Ding, graduate students Yin Tang and Chun Kit Kwok, and professor of statistics Yu Zhang, along with Assmann and Bevilacqua -- involved determining the structures of the varieties of RNA molecules in a plant named Arabidopsis thaliana. This plant is used worldwide as a model species for scientific research.

Arabidopsis thaliana, commonly known as mouse-ear cress, is an ideal organism for RNA studies, the researchers say, because it is the first plant species to have its full genome sequenced and has the greatest number of genetic tools available.

RNA is the intermediate molecule between DNA and proteins in all living things. It is a critical component in the pathway of gene expression, which controls an organism's function. Unlike the double-stranded DNA molecule, which is compressed into cells by twisting and wrapping around proteins, RNA is single stranded and folds back on itself. The researchers set out to answer the question, "How exactly does RNA fold in a cell and how does that folding regulate gene function?"

"We needed a tool to answer that question," said Bevilacqua. "That tool involves introducing a chemical into the plant that can modify some segments of the RNA but not others, which then gives a readout of the structure of the RNA. Using this technique we can figure out which classes of genes are associated with certain RNA structural traits. And we can try to understand how these RNA structural changes relate to certain biological functions."

"Previously, researchers would query the structures of individual RNAs in a cell one by one, and it was a tedious process," said Assmann. "You can't abstract rules or generalities about how RNAs are behaving just from knowing the structures of one or a few RNAs -- you can't get a pattern. Now that we have genome-wide information for a particular organism, we can start to abstract patterns of how RNA structure influences gene expression and ultimately plant function. Other scientists can query their organisms of interest and ask what rules they can abstract. Are there universal rules that will be true for all organisms for how RNA structure influences gene expression?"

Bevilacqua added, "Because RNA is so central in its role in gene regulation, the tools we've developed can be transferred to scientists who are working with essentially any biological system." Long-term potential implications of the methodology include human health -- for example, how an infection-induced fever could affect the RNA structures of both humans and pathogens.

The research was funded by the Human Frontiers Science Program (HFSP), Penn State Eberly College of Science, and a Penn State Huck Institutes Huck Innovative & Transformational Seed Fund grant.

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26/11/2013

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26/11/2013

Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Most DNA molecules are double-stranded helices, consisting of two long biopolymers made of simpler units called nucleotides—each nucleotide is composed of a nucleobase (guanine, adenine, thymine, and cytosine), recorded using the letters G, A, T, and C, as well as a backbone made of alternating sugars (deoxyribose) and phosphate groups (related to phosphoric acid), with the nucleobases (G, A, T, C) attached to the sugars.
DNA is well-suited for biological information storage. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information. Biological information is replicated as the two strands are separated.
The two strands of DNA run in opposite directions to each other and are therefore anti-parallel, one backbone being 3′ (three prime) and the other 5′ (five prime). This refers to the direction the 3rd and 5th carbon on the sugar molecule is facing. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes biological information. Under the genetic code, RNA strands are translated to specify the sequence of amino acids within proteins. These RNA strands are initially created using DNA strands as a template in a process called transcription.

26/11/2013

New method generates unlimited, high-quality antibodies for genetics research
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Modern genomic studies rely on precise and sophisticated technology, but the antibodies used to identify proteins that control gene expression can be unreliable as a research tool, placing time, money and study results at risk. Now, scientists from the University of Chicago have devised a novel method for creating high-quality, specific and reproducible antibodies that eliminate an "antibody bottleneck" that has plagued genomics research.

While the sequence of DNA serves as the blueprint for life, the regulation of that genetic code relies on a variety of critical mechanisms, collectively called epigenetics. Among the most important are histones, proteins that act as spools around which DNA winds. Subtle chemical modifications to histones play an essential role in turning genes on or off and are an important target for genetic research. Antibodies, short segments of protein that bind to these modifications, are the primary tool used by scientists to identify the effect of histones on gene regulation.

However, as antibodies are generated from animals, the variations in quality and efficacy between batches can be great. Considerable time and effort have to be spent on testing new antibody lots, and unpredictable differences can make it hard to compare results between groups and, over time, prevent progress in the field.

To address this "antibody bottleneck," Shohei Koide, PhD, professor of biochemistry and molecular biophysics at the University of Chicago, and his team harnessed the power of directed evolution, a method that mimics natural selection and protein design. They first created a large catalog of bacteria that were programmed with artificially synthesized, recombinant DNA to produce different antibodies. After isolating a single antibody that appeared promising in recognizing histone modification, the team analyzed its structure in detail to look for possible improvements. Based on this analysis, they created another set of recombinant DNA, programmed bacteria with it and looked for a new, improved antibody.

They repeated this iterative process of analysis and improvement until they created a sequence of recombinant DNA that produced a highly reliable, reproducible and specific antibody suitable for histone modification research.

"For the first time, we've demonstrated that high-quality histone modification antibodies can be generated through recombinant techniques. We can produce the same antibody over and over again, in large quantities, with no change in quality," Koide said. "We believe our antibodies will replace conventional antibodies in standard research applications and enable new methods."

The team is applying this method toward generating antibodies that can be used to recognize other regulatory proteins and transcription factors important to genetic research. They also are exploring the utility of their antibodies in clinical applications. Koide and his collaborators are developing tests to identify genetic abnormalities in diseases and recently received funding from the Facioscapulohumeral Muscular Dystrophy Society to pursue research in this area.

"Variation of antibody quality was a fundamental roadblock for establishing clinical tests that look at abnormalities in chromatin modifications. Clearly, in order for such a test to be reliable, antibody properties must remain constant. We will be able to make fundamental contributions to realizing such methods," Koide said.
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23/11/2013

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23/11/2013

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21/11/2013

Zyppy Plasmid Miniprep Kit- Transfection Quality Plasmid DNA Directly from E. Coli Cultures!

21/11/2013

Zyppy Plasmid Miniprep Kit- Transfection Quality Plasmid DNA Directly from E. Coli Cultures!
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Scientists at Zymo Research take you through the fastest and easiest method available to separate plasmid DNA from E. Coli efficiently with the Zyppy™ Plasmi...

21/11/2013

Recombinant Antibodies The generation of recombinant monoclonal antibodies includes advances, alluded to as collection cloning or phage display/yeast display. Recombinant antibody acting age...

21/11/2013

DNA sequencing DNA sequencing is the procedure of confirming the exact request of nucleotides inside a DNA molecule. It incorporates any methods or technology that is utilized to determine the re...