Scientists routinely use techniques to alter gene expression or to label specific cells, but there are too few resources to teach students how to perform these experiments in the beginning. In most classrooms, the laboratory experience is focused on classical embryology techniques such as basic observation and dissections. Students don’t usually perform more modern techniques used in genetics or molecular biology because the experiments are either not accessible or too challenging for amateur scientists. Planarians, wormy creatures commonly found in freshwater ponds, provide a good potential solution to this problem. Planarians are easy to buy, cultivate, and have interesting phenotypes to study. In addition, the Sánchez lab has made it easier to perform advanced developmental biology experiments in planarians with their recent plasmid deposit.

This post was contributed by guest blogger Clare O'Connor an Associate Professor at Boston College.

National reports stress the importance of providing authentic research experiences to undergraduate students (1, 2), but educators face significant challenges in designing suitable projects. In the O'Connor lab, we recognized that genome sequencing projects were generating huge amounts of data that could provide the basis for student projects in introductory labs. Genome projects use computational methods to identify genes by their similarities to genes in other species, but these studies generally leave questions about gene function wide open. What if two seemingly similar proteins have acquired divergent functions due to mutations accumulated over time? Undergraduates can help to answer this question!

Last Wednesday we worked with the Harvard GSAS Science Policy Group to organize a Minisymposium on Reproducibility. The minisymposium focused on solutions to reproducibility issues in the biological sciences and featured speakers from academia, industry, nonprofits, and publishing. The livestream video from the event can be found below along with a description of the program beneath it. You can jump to the different time stamps in the description to watch any sections you’re particularly interested in, but I’d recommend watching the whole livestream for a more holistic understand of reproducibility issues and their potential solutions.

Prior to this event, I gave my own talk on reproducibility at Addgene and here I summarize what I learned both in preparation for my talk and at the minisymposium. You can find a variety of additional resources and information about organizations promoting reproducibility in this booklet (which was also handed out at the event).

This post was contributed by guest blogger Talley Lambert, a Research Associate at Harvard Medical School.

The need for a community fluorescent protein database

As recognized by the 2008 Nobel Prize, fluorescent proteins (FPs) have become one of the most indispensable tools in modern biological research.  Any microscopist will tell you that selection of a fluorescent probe (be it an organic dye or FP) is one of the most important steps in the design of an imaging experiment.  The choice is non-trivial, however, as FPs are tremendously complicated entities with a large range of characteristics (color, brightness, photostability, maturation, oligomerization), many of which are dramatically affected by environmental conditions (such as temperature, pH, fusion protein, etc...).  There are many online guides – including an excellent series of posts by Joachim Goedhart on the Addgene blog – outlining various important considerations when choosing a FP, but much of the primary data one might require when making such a decision remains spread across literature in publications that introduce these tools.

Every few months we highlight a subset of the new plasmids in the repository through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and we hope they'll make it easier for you to find and use the plasmids you need. If you'd ever like to write about a recent plasmid deposit please sign up here.

Expanding the Optogenetics Toolbox with CRY2clust

Article contributed by Brook Pyhtila

The Won Do Heo lab at the Korea Advanced Institute of Science and Technology (KAIST) and Institute for Basic Science (IBS) has developed another useful optogenetic tool that enables robust and efficient oligomerization of target proteins in response to blue light. This tool, CRY2clust, was created by adding a 9-residue peptide to the C-terminus of human codon-optimized  cryptochrome 2 (CRY2) from Arabidopsis thaliana. When exposed to blue light, CRY2 undergoes a conformational change that permits it to bind to the CIB1 (cryptochrome-interacting basic-helix-loop-helix) protein. After fusing the CRY2 and CIB1 domains to separate proteins of interest, a researcher can cause them to interact by stimulation with blue light.  Similarly, light can also be used to control homo-oligomerization of a protein fused to CRY2, although some studies have shown that this clustering only happens under certain conditions.