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Data Freedom: The Expansion of Data Sharing in Research Publications

Posted by Guest Blogger on Aug 5, 2014 2:51:13 PM

This post was contributed by Jim Woodgett.

Public Library of Science (PLOS) created a stir earlier this year when it announced its data access and sharing policy. Since early March, the open access publisher has required authors to include a note as to where readers may locate data supporting the research reported in PLOS publications. The policy was not an overnight revelation, rather it was the result of consultations between researchers and publishers. Nonetheless, the initial release caused a storm as the organization left open the question of how much data was necessary and reasonable. PLOS has since clarified their data sharing policy and recently announced that of the 16,000 manuscripts that had been processed since the declaration, only a small fraction (<1%) of authors have asked for advice about the scope of the policy. End of story? Not quite.

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Topics: Scientific Sharing

The Michael Davidson Collection: One-Stop Shop for Fluorescent Proteins

Posted by Kendall Morgan on Jul 29, 2014 2:16:00 PM

In the world of fluorescent proteins and their use for imaging cell biology, Michael Davidson’s lab at Florida State University has been the go-to place. In 2012, his National High Magnetic Field Lab worked with an impressive 1,350 scientists from more than 275 institutions all over the world. In the course of all those collaborations over the years, he and his colleagues built a Molecular Expressions collection including some 3,300 plasmids along with image galleries and educational resources to go with them. This collection of plasmids is available in an easily searchable format on Addgene’s Michael Davidson Fluorescent Protein Collection webpage. (Check back regularly as new plasmids are being added to the webpage every week.)

Over 300 Backbones in a Rainbow of Colors

“It’s a great collection with over 300 backbones alone,” said Addgene’s Lianna Swanson, who has been working with members of the Davidson lab to coordinate the impressively big deposit. “He has every fluorescent protein under the sun, from the standard oldies but goodies (e.g., EGFP and YFP) to the new and improved fruit colors (e.g., apple, papaya, and tomato) and the photoactivatable fluors (e.g. Phamret and Dendra). It’s just such a great collection with such variety.”

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Topics: Hot Plasmids, Fluorescent Proteins

3 Challenges in Plant Synthetic Biology

Posted by Guest Blogger on Jul 22, 2014 1:46:10 PM

This post was contributed by Nikolai Braun and Keira Havens, co-founders of Revolution Bioengineering. Read their previous blog post about how they started their company here.

The first transgenic plant was engineered over 30 years ago, but plant synthetic biology is still in its infancy. A long timeline from transformation to testing and a lack of well-characterized genetic tools make it challenging to engineer a specific function in these multicellular organisms. However, the rewards are great if you take the plunge – plants are the foundation of life on earth, and opportunities abound to build better fuels, feeds, foods, and fibers. And because working with plants can be challenging, there are a lot of unexplored areas in plant biotechnology that are ripe with opportunity. We’ve decided to jump into one of those unexplored areas with our color-changing flower, but to do that we’ve had to navigate the challenges involved in plant synthetic biology.

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Topics: Synthetic Biology, Plant Biology, Plasmid Kits

Plasmids 101: Viral Vector Elements

Posted by Marcy Patrick on Jul 17, 2014 3:09:00 PM

The use of viral vectors in research is beneficial for a number of reasons, including but not limited to: helping to get difficult-to-deliver DNA into mammalian cells, increasing the efficiency of gene transduction, allowing for control over which cells are infected through viral pseudotyping, and ease of vector cloning and modification. At the most basic level, viral vectors consist of a viral genome that has been adapted into a plasmid-based technology and modified for safety through the removal of many essential genes and the separation of the viral components. Read on for a brief description of the viruses used to make these vectors as well as a table defining the major elements found within the plasmids comprising the viral vector systems.

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Topics: Plasmid Elements, Plasmids 101, Viral Vectors

Working with Nuclear Receptors

Posted by Guest Blogger on Jul 15, 2014 12:03:00 PM

This post was contributed by Neil J. McKenna and Bert W. O’Malley.

Survival of all organisms depends on efficient energy maintenance - through acquisition, storage, and utilization - and on self-propagation by reproduction. Both physiological processes are controlled by deliberate and compulsory actions instigated by the central nervous system signaling to peripheral effector organs, which then return information such as nutritional status. Within the animal kingdom, this information is relayed through factors (both of endocrine and dietary origin) that are diffused or actively transported from cells, traverse the body through the bloodstream, and eventually elicit their actions on other tissues. At the Nuclear Receptor Signaling Atlas (NURSA), one of our primary goals is to promote an understanding of how these processes are regulated at the cellular, tissue and organ level by nuclear receptors (NRs), their coregulators, and their physiological endocrine ligands.

Nuclear Receptors and their Ligands

NRs represent the largest family of transcription factors found in metazoans. The superfamily is comprised of 48 human and 49 murine members. NRs permit the integration and communication of such signals between central and peripheral organs because of their established roles as molecular sensors and governors of endocrine-hormone signaling.

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Topics: Hot Plasmids

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