... has been critical to the Broad’s success over the last 11 years and was certainly critical to drawing...background in history and specifically the history of RNAi left him a bit skeptical of the technology at the...cancer biology in Ed Harlow’s group at Harvard Medical School and then applied to work at the Broad Institute...towards the Broad. In order to ask interesting biological questions, you need a tremendous amount of technology... in true collaboration with scientists asking biological questions. Doench loves that he still gets to...terms of determining what genes are involved in biological process X, you can do with CRISPR technology....with Addgene - he says he’s “known of Addgene basically since the beginning and [has] been using Addgene...

... Clinical applications Viruses in vaccines helped pave the way for their use in other clinical applications...vector from basic science research all the way to clinical gene therapy. But how can you use these amazing...and delivering a genetic payload. This cargo is typically their own genome, but this step can be engineered...’ve decided on an application, our Viruses as Biological Tools blog can help you learn about the different... express proteins. Viral expression cassettes typically contain a promoter (inducible or constitutive)...delivery Screening libraries, large collections of biological independent variables, are becoming increasingly...development well over a hundred years ago. Since then, medical technology has changed a lot, but viruses have ...

...Rather than inhibiting protein function, these so-called “small molecule degraders” recruit the proteasome...degraders provide distinct advantages over pharmacological inhibitors including rapidly depleting a protein-of-interest...resistance to inhibitors, and inducing prolonged biological effects. While targeted degradation of endogenous...selective degradation of protein targets in time scales that are not possible with traditional genetic ...here. The Methods section of Nabet et al., Nature Chemical Biology additionally provides detailed information...FKBP12F36V binding ligand (ortho-AP1867) via various chemical linkers. Our current lead dTAG molecule is dTAG...FKBP12F36V-tagged LACZ) with dTAG molecules in your biological assay of choice to ensure that there are no toxicities...

...pathway (Raf1, EGRF), the KTR localized to the cytoplasm. This all-optical psMEK1 + ERK KTR-mRuby2 system...since other signaling networks can also be non-specifically activated and, like the game of telephone, often...must be transmitted by intermediate messengers. Optical control of kinase activity can provide greater ...greater spatiotemporal resolution than pharmacological or genetic approaches, but only a few such methods exist...Problem:  There is no common method for creating optically controlled kinases. The Solution: In Zhou et al...constitutively active MEK1. This photoswitchable MEK1 is called psMEK1. When exposed to 500 nm violet light, the...phosphorylation, much like endogenous ERK, and its localization serves as an indicator of MEK1 activity. When...

... 2016; Constantini et al, 2012). The localization and biological properties of new fusions can be compared...previous two posts in this series described a practical approach to selecting a bright fluorescent protein...ultracentrifugation. Sedimentation equilibrium analytical ultracentrifugation yields an affinity and has...efforts tested whether FP fusions to connexin localized correctly to gap junctions (Shaner et al, 2008... with native interactions, preventing proper localization in these assays. However, these strategies will...most likely in an antiparallel configuration), typical structures known as Organized Smooth Endoplasmic...the performance of fluorescent proteins in your biological system with the microscope that you will be using...

...networks underlying your favorite biological phenotype in a scalable way. This blog post will introduce...by guest blogger Alan Wong. The complexity of biological systems can hinder our attempts to study and ... guide RNAs (gRNAs) for genome editing in large-scale has led to the rapid generation of genome-wide gRNA...genetic perturbations in single cells. Methods to scale up multiplexed CRISPR systems for high-throughput... genetics that underlie complex regulation in biological systems. The CombiGEM platform provides a means...currently an Assistant Professor at the School of Biomedical Sciences of the University of Hong Kong. He is...technologies to interrogate and understand complex biological systems. He can be contacted at [email protected]. ...

...Organization has declared a global health emergency and called for the fast-tracked development of diagnostics...was a new class of programmable riboregulators, called toehold switches, which allow for the rational ...outbreak was reported, and we felt that, given the critical need for low-cost, field-based diagnostics, our...Our motivation was underscored by the potential scale of the emerging outbreak, as many as 2.2 billion...timeline to develop our paper-based platform into clinically relevant diagnostics for the Zika virus was daunting...ability to complete the project on such a short timescale. Our article ultimately reported the development...that has transformed the assay’s capabilities. Specifically this includes primer directed isothermal RNA...

... many biological research situations, the relevant volume is that of the cell. For the physical behaviors...major applications of FPs is to visualize the localization, dynamics, and behavior of a POI. As an investigator...monomeric FPs are not actually monomeric, at least in practical terms. The propensity of a particular type of ...fusion protein, as in a FRET biosensor, then the local concentration of FPs around that fusion protein ...consequences can be dramatic. For a membrane POI localized to the endoplasmic reticulum, the normally spiderweb-like...structures are large (microns), bright, non-physiological, and difficult to ignore [1, 2]. 2. Fusion to...fusion proteins that form as a result will often localize incorrectly and may function improperly. 3. Incorporation...

... the brain. A more locally defined set of neurons can then be targeted with optical stimuli. The restricted...viral vectors (AAV), neuroscientists can combine classical genetic tools with the manipulation of specific...of these discussions as a publicly accessible practical guide which was recently published in Frontiers...of molecular tools and sensors Combinations of classical genetic tools, for example Cre/loxP or Flp/FRT...transgene expression by restricting expression to genetically defined cell types. Specific transgene expression...result in opsin expression in their cell bodies. Optical stimulation in a different brain area can then ... more versatile. To complement the wealth of genetically encoded tools available, researchers are also...

... In vitro, ligases (notably T4 DNA ligase) are critical reagents for many molecular biology protocols,... smaller pyrimidine:pyrimidine mismatches are typically worse ligation substrates than pyrimidine:purine...design and reaction condition optimization, will be critical for success. Online tools are available to help... the Thermostable Ligase Reaction Temperature Calculator can be used to estimate an appropriate incubation... structure, reaction mechanism, and function." Chemical reviews 106.2 (2006): 687-699. PubMed PMID: 16464020... ligases: progress and prospects." Journal of Biological Chemistry 284.26 (2009): 17365-17369. PubMed ...reaction-capillary electrophoresis assay." Journal of clinical microbiology 45.6 (2007): 1927-1935. PubMed PMID...

...interaction with limited biological materials. Problems with Chip-seq ChIP-seq typically requires a large amount...activity of a Protein A fused micrococcal nuclease (MNase) to specifically isolate DNA that is bound by...material for a ChIP-seq experiment can be a major technical hurdle.   ChIP-seq requires  cross-linking during...development using the Drosophila wing as a model. A typical ChIP-Seq experiment requires around 1,000 wings...addition of Protein A MNase. Once MNase has been localized to target sites, the nuclease is briefly activated...targeted digestion is controlled by the addition of calcium, which MNase requires for its nuclease activity...and simplification of the original technique, specifically in terms of initial steps of cell or tissue ...

...screened for toxicity against local insect pests. By developing biological agents such as insecticidal ...get tested for their potential agricultural and medical use. Find More Optogenetic Tools Like pDawn  Making... improving expression of nutritionally and therapeutically significant proteins. In this project she aims...insecticidal proteins, the use of chemical pesticides may be avoided or decreased. Biosensors for herbicide detection...one of the reaction’s metabolites. One useful genetically encoded H2O2 probe is pQE-30-HyPer3 (2) which...working in a wide range of research fields and geographical locations. We are excited to see how all of ...et al. “Endophytes as sources of antibiotic” Biochemical Pharmacology 2017 Jun 15;134:1-17. PubMed PMID...

... well as neural development. Specifically, SHH is a morphogen, a chemical signal that diffuses down a ...exhibit abnormal segmentation during embryogenesis. Typically, regularly spaced denticles (bristles) outline...on the spindle of a spinning wheel but also a biological transposon system. Sleeping Beauty is a synthetic... cellular contraction You may think that a gene called "spaghetti squash" originated from the squash itself...contract depending on the context. Contraction is critical for processes such as cell movement/motility, ...or dead cells (Jiang and White-Cooper, 2003). Why call a gene required for spermatogenesis after a Sesame...mesoderm, is necessary to activate bagpipe which is localized to segmental clusters of the mesoderm. This subdivision...

...Immunoprecipitation Overview An immunoprecipitation reaction is typically carried out in one of two ways. Both methods utilize.... 2) An antibody immobilized on a bead binds specifically to the blue triangle protein but not the other... to the process of anchoring an antibody, often called the capture antibody, to agarose or magnetic beads... or magnetic beads with commercially available chemical agents. Directly conjugating the primary antibody...interactions To prepare for an IP, samples are typically lysed in a non-denaturing buffer containing non-ionic...sample to remove any proteins that may interact nonspecifically with the capture antibody or Protein A/G. To...interaction and/or the downstream application. Typically, if the target protein will be detected in a Western...

...order in which specific chemical inputs are received by a cell. These so-called recombinase-based state...light and chemicals respectively. Didem Goz Aytruk from Connie Cepko’s Lab at Harvard Medical School describes...although fluorescent proteins are incredibly useful, chemical fluorophores can still be used in a wide variety...variety of experiments. Read more to find chemical fluorophores for your next experiment. Nucleic acid based...report upon and/or engineer “temporally ordered biochemical events” such as those that occur during development...to pH changes without the need for ATP or other chemical fuel sources.” In her work, Dr. Polka made R-body...repression of different genes in a single cell, and localization of a fluorescent signal to your target gene....

...Different antibodies bind different protein sequences called epitopes and scientists can use these to tag their...lab used an alternative strategy to develop a genetically encoded antibody based probe that detects the... epitope in diverse cellular environments. They called this probe the HA frankenbody (Zhao et al., 2019...targets, the scientists fused them to sequences called complementarity determining regions (CDRs, or loops...concept experiment the Stasevich lab observed colocalization of GFP tagged HA frankenbody with an mCherry...meaning that scientists can track the movement and localization of single HA-tagged molecules over time.  The... Inbar, D., Hochman, J., & Givol, D. (1972). Localization of antibody-combining sites within the variable...

...by fluorescence photoactivation localization microscopy." Biophysical journal 91.11 (2006): 4258-4272....Berlin, Shai, et al. "Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging...tag cellular proteins and investigate protein localization, interaction, and expression. However, one caveat...oligomerize, disrupting cellular function and localization, or leading to protein aggregation. Another ...important applications for PA-FPs involve enhancing optical live imaging of proteins, organelles, and cells...proteins, scientists can track single protein localization, turnover, and trafficking, as well as organelle...new imaging methods, including photoactivation-localization microscopy (PALM, also FPALM) (11). For PALM...

...run it? And, most importantly, what are the methodological and experimental limitations and considerations...numerous scientists at NIDA and some of the practicalities and considerations you may not find in the ...stimulate 2) Fabrication and implantation of the optical fiber into the region of interest 3) Behavioral...region and cell type of interest is obviously of critical importance to any optogenetic experiment. There...pioneered the development of optogenetics, has genetically manipulated a number of the opsin genes to alter...your opsin  The standard opsin delivery method is local injection of an adeno-associated viral (AAV) construct... or more mice and the injections must be near identical for all of these surgeries. Identify coordinates...

...MSDS for a lab chemical of choice. Now, I can’t guarantee every reagent in your chemical closet is in this...tried to find an app that could help me with calculations. This is how I came across the Gibco Cell Culture...culture and include a counter, lab timer, dilution calculator, and a couple of other nice features. This app...sequence for your enzyme of interest. Lastly, the Tm calculator helps you set up an optimal PCR depending on ...enzyme sequence resource is universally useful. 4. Chemical Safety Data Sheets by ThatsMyStapler Safety always...experiments. Hence, I’m including this MSDS app. The Chemical Safety Data Sheets app has a search function that... if you get quizzed randomly about a hazardous chemical and can’t find your lab’s MSDS book, this is a...

...general (1). Science and politics? Science is an apolitical process for seeking knowledge. The process begins... again. No part of this process is inherently political so why is there a march in Washington, D.C., the...States government? Politics and science are intrinsically linked: governments exist in reality and science...as evidence of climate change, the safety of genetically modified organisms (GMOs), the absence of a link... it.  3) Linking scientists to one particular political party while alienating the other While scientists... yet research shows that thoughts on some non-political issues are split along party lines (18). Feeling...alternative. Inclusion of data informing policy specifically related to the following subjects: Climate ...