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Hot Plasmids June 2018 - Reverse transcriptase, nanobody, and protein-DNA interaction tools

Posted by Various Addgenies on Jun 27, 2018 9:16:28 AM

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.

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Topics: Hot Plasmids

dTAG - You're it!

Posted by Guest Blogger on Jun 21, 2018 10:06:52 AM

This post was contributed by guest blogger Behnam Nabet, a postdoctoral fellow at Dana-Farber Cancer Institute.

Targeted Protein Degradation

In the Bradner and Gray labs, we synthesize compounds that enable selective removal of proteins-of-interest from the proteome. Rather than inhibiting protein function, these so-called “small molecule degraders” recruit the proteasome to destroy targeted proteins. We previously developed small molecule degraders that achieve selective degradation of endogenous proteins (notably, BRD2/3/4, CDK9, TRIM24, FLT3, BTK, and ALK) by linking small molecules that bind these target proteins to other small molecules that bind an E3 ligase. These bifunctional degraders co-opt E3 ligases such as cereblon (CRBN) or von Hippel-Lindau (VHL) to bring the endogenous degradation machinery into close proximity with the target protein, leading to polyubiquitination of the target protein and proteasomal degradation. Remarkably, small molecule degraders provide distinct advantages over pharmacological inhibitors including rapidly depleting a protein-of-interest, increasing target selectivity, overcoming resistance to inhibitors, and inducing prolonged biological effects.

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Topics: Hot Plasmids, Techniques

Using ultrasound to image bacteria in vivo: acoustic reporter genes

Posted by Beth Kenkel on Jun 19, 2018 9:38:21 AM

Knowing where bacteria are located within their host is often key to understanding their role in both health and disease. To observe bacteria in action, researchers have developed in vivo bacterial reporters that use fluorophores and luciferases to track bacteria in real time, but each of these reporters has its drawbacks. Acoustic reporter genes (ARGs) overcome these limitations by using gas vesicle reporters that are detectable by an inexpensive and widely available imaging platform: ultrasound.

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Topics: Hot Plasmids, Imaging, Microbiology

Pathways Over Time Plasmids Engage Students in Functional Genomics Research

Posted by Guest Blogger on May 22, 2018 9:38:25 AM

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!

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Topics: Hot Plasmids, Education

Hot Plasmids May 2018 - Optogenetics, Decaffeination, Biosensors, and Fluorescent Protein Tools

Posted by Various Addgenies on May 15, 2018 8:43:38 AM

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.

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Expanding the Optogenetics Toolbox with CRY2clust

Article contributed by Brook Pyhtila

 Listen to the CRY2clust podcast segment

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.

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Topics: Hot Plasmids

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