...Pubmed PMID: 24463574. Pubmed Central PMCID: PMC3988262. 4. Hart, Traver, et al. "Measuring error rates...flaws of RNAi screens are well characterized and strategies exist to control for these faults. However, it...to patterns seen in single-guide studies? Many strategies exist for reducing Cas9 off-target effects, but...DNase hypersensitivity, or are in an enhancer, transcription factor binding site, or a coding region. Targeting...on- and off-target effects, but also presents a strategy to control for these effects. By testing thousands...generalizable conclusions about off-target activity, demonstrate safe-targeting guides as a potential control,...8 (2017): 15178. Pubmed PMID: 28474669. Pubmed Central PMCID: PMC5424143. 2. Tsai, Shengdar Q., et al....

...plasmids, investigating different viral production strategies or developing novel methods for data analysis...inhibitor sucrose. Previous work by Stoneham et al. demonstrated that the entry of AAV2 into target cells is ...formulation buffers, this sugar may be a more attractive choice for labs looking to improve their AAV ...wanted to be certain that this supplementation strategy would have no effect on the purity or infectivity...preparation. Through sugar detection assays, in vitro transduction, and silver stain approaches we show that there...effect on our overall yield, we were unable to demonstrate that these results were, in fact, due to impaired...test the endocytosis of a fluorescent dye and transduction of GFP-expressing AAV particles we did not observe...

...from the OD and concentration of the known samples is used to calculate the concentration of protein in ...cells. They bind to proteins on the surface of extracellular pathogens such as parasites or microbes, or ... methods. Each type of antibody and production strategy has advantages and disadvantages compared to each...from the animal is drawn and the antibodies are extracted. These antibodies recognize a variety of epitopes...Hybridomas are formed by fusing B cells that have been extracted from animals injected with protein antigen to ...molecular weight by SDS-PAGE, and are subsequently transferred to a membrane. A primary antibody recognizing...appropriate controls for normalizing the protein concentration. To get even more details, check out our article...

...antibody stability, half-life, tumor penetration, inadequate concentration, mutation of cell surface targets...infections, or other strenuous biological changes. In contrast to the acute immune responses that eliminate early...associated with the onset of colorectal cancer. Strategic immune evasion mechanisms - The tumor microenvironment...relapse. Chemical and radiation therapies cause a transient shutdown of the immune system, hampering its ability...of even these conventional antitumor treatment strategies can be enhanced. Types of immunotherapeutics ...being injected back into the body in 3 doses intravenously. B cells and T cells activated ex vivo are also...susceptible to elimination by T cells. Immunotherapy strategies that synergize with these positive impacts on...

... beliefs. I asked participants to read short abstracts comparing the mortality rates between two controversial...peer-reviewed study. The second group read the same abstract but with the names reversed, meaning that the ...reversed. The third group read a version of the abstract where the real medical conditions had been swapped...asked to evaluate the quality of the study those abstracts represented. The point of this study was to see...see if their evaluations of the abstracts were driven by the quality of the study design or by their preconceived... significantly more favourable ratings to the abstracts that affirmed their personal beliefs even though...identical. Likewise, when participants read an abstract for a study with findings that challenged their...

...RNaseP. Although the Gao Lab demonstrated efficient MBE with such a strategy, the need for lengthy promoters..., lengthy genetic payloads and insufficient transcription on the array have limited the scalability and...multiplex gene editing. Moreover, existing multiplex strategies have been facing difficulties in pairing with...both efficiency and multiplexity, with these constraints? The Gao lab first thought to enable MBE by ...efficient base editing. They then worked to develop a strategy that would independently generate multiple gRNAs...kinds of CRISPR tools, without compromising their strategic advantages in gene editing, while keeping the ... Led by PhD student Qichen Yuan, the Gao Lab demonstrated that the tRNA-gRNA array can drive the expression...

...antibodies from an Andean mammal called alpaca could neutralize the SARS-CoV-2 virus. But while the early results...facility needed to perform the experiments to demonstrate that this approach was useful in humans. Then...preprint repository BioRxiv. This example clearly illustrates the power of collaboration, which despite the...help researchers working on COVID-19. Its origins trace back to March 2020, when the first coronavirus lockdown.... None of us works directly with viruses or transmissible diseases, so we were left with no choice but...simpler and the volunteers helped with things like translations, bibliographic searches, etc.     Expanding...we call “asymmetric collaborations.” These are transient partnerships where a researcher makes a small ...

...a repressible binary system for transgene expression, lineage tracing, and mosaic analysis., Cell 141,...more detailed level, the Gal4/UAS system is a transcription activation system co-opted from yeast (1). It...workhorse to turn genes on or off. Gal4 is a transcriptional activator that binds to UAS enhancer sequences...sequences found in DNA. It then recruits transcription machinery to the site to induce gene expression. Thus... my next post, I’ll explain the relatively straightforward process of generating your own fly lines. In...Kagan, Environmental Stress Causes Lethal Neuro-Trauma during Asymptomatic Viral Infections, Cell Host...9, 47–55 (2012). PubMed PMID: 22205518. PubMed Central PMCID: PMC3574576. 7. S.-L. Lai, T. Lee, Genetic...

...the hACE2 transgenic mouse strain, for example, is sustained by the availability of this strain from The..., they remain accessible during these times. Centralized reagent repositories, also known as biobanks,... Biological repositories that distribute mouse strains, plasmids, cell lines, and much more have been ...19 plasmids and resources! Case study 3: Mouse strains Reagents developed during the SARS-CoV pandemic...University of Iowa (McCray et al., 2006), the hACE2 transgenic mice were designed after it was discovered that...appearing with regards to SARS-CoV-2, this mouse strain is regaining popularity. The Jackson Laboratory...institution, has been able to rapidly propagate this strain, making it available to scientists around the world...

...Library amplification seems straightforward: E. coli bacteria are transformed with the library DNA, they... Each Addgene library has its own depositor transformation and amplification protocol, but the overall...Maintain representation of the library during transformation First, use enough DNA and competent bacteria...and we use electroporation to ensure a good transformation efficiency. For a typical library, Addgene ...growing the cells on solid plates, where each transformant forms its own colony, uninfluenced by the growth...concern, but Addgene still recommends plating the transformation mixture on solid media. The colonies are then...then scraped off the plates and pelleted for DNA extraction. Prepare library product for next-generation ...

...that green fluorescent protein through transcription and translation. Unfortunately, having live cells in...being able to actually hold all those seemingly abstract biological reactions that I learned about from... like gel electrophoresis to separate DNA or transforming cells with green fluorescent protein, these ... Making proteins outside of a cell - cell free extracts Typically, if you want to make a protein – say... into a host cell (through a process called transformation), essentially giving the cell all the instructions...perhaps consider using some elements of BioBits to transition your undergraduate students from the classroom...give your undergrads hands-on experience with the central dogma while also giving them practice with practical...

...dDetermined as effective NIR fluorescence in transiently transfected live HeLa cells with no supply of exogenous...2015). The effective brightness reflects the concentration of BV-containing molecules in a cell and depends...and xenon lamps are the best for working in this spectral range. You can also check that no filters and/...multiscaling NIR-shifted spectrum is perfect for use in spectral multiplexing (Shcherbakova et al., 2018). NIR ...low autofluorescence, low scattering, and deep penetration of red-shifted light. The same NIR FPs and biosensors...in your applications.  There is a whole set of spectrally distinct (e)miRFPs available. The numbers in ...names correspond to the maxima of their emission spectra. These probes can be combined in two-color and ...

...Washington Post: Trump administration tells EPA to freeze all grants, contracts The Guardian: Trump to...Formally, a government can be defined as a social contract citizens enter into in order to protect their ...science: “humility in the face of evidence” (4). Frustration among scientists has been rising as evidence ...general public agrees (5, 6). Many of the new administration’s actions, including taking down the climate...lab and march. Unintended consequences While frustration and anxiety have inspired people to rally for... marchers or supporters be scientists – on the contrary, anyone and everyone is welcome. Why? There are...following subjects: Climate change Vaccines GMOs Transgender issues Reproductive health Immigration Pollution...

...plasmids for use in CRISPR and Tol2 transposase induced transgenesis.  Xenopus Xenopus, or frogs, are one...organism in microbiology and biochemistry. Certain strains have been specifically developed to thrive in laboratory... laboratory settings. One of its most attractive features is its stability and easily obtainable growing... areas of microbial research like metabolism. Transport, biofilms, and much more. Because of it’s BSL-...ability to regenerate, the axolotl has several attractive characteristics that make them an ideal model...have created molecular biology tools to generate transgenic axolotls for an array of different studies. Elly...for human disease research. One of their most attractive features are their eggs. Frog eggs are large,...

... if not archived. Remove bias with preregistration Preregistration is the process of creating a time-stamped...and funders in the Transparency and Openness Promotion Guidelines; preregistration to increase clarity... sampling and inference-making. Even perfect transparent and rigorous studies will give false signals ...repository before conducting the experiment (note: registrations can be embargoed while the research is ongoing... tested with a specific statistical test.  Preregistration makes clear the distinction between hypothesis...author submits the research plan (similar to a preregistration, but usually with a fully fleshed out introduction...for Open Science in order to reward increased transparency and reduced bias in scientific research. These...

...complexes with LacZ𝜔 and forms an active LacZ tetramer.  This tetramer cleaves chlorophenol red-b-D-galactopyranoside...particular strain of norovirus, it can be tailored for the detection of other norovirus strains and even.... elegans. These dsRNAs target specific mRNA transcripts for degradation. Despite how easy these experiments...often completely ineffective or results in low penetrant phenotypes that are hard to study. To overcome...target gene between two inverted T7 promoters. Transcription from each promoter progresses past the specific...promiscuous labeling enzyme and a small-molecule substrate to map the spatiotemporal distribution and interaction...virus costs time and money, and viruses at low concentrations often escape detection. The Alexander Green...

...dam–/dcm– strain of E. coli such as JM110 and re-purifying it. These specialized E. coli strains have been...DNA. The other component of these systems, methyltransferases, methylate DNA at particular sequences to...restriction modification systems containing methyltransferases that add methyl groups to specific DNA sequences...effectively cleave DNA. Common lab E. coli K12 strains such as DH5alpha contain 3 methylases that recognize...plasmids with no methylation (there are no methyltransferases in the PCR reaction). The template plasmid...other hand, should be derived from a dam+ E. coli strain and will therefore have methylated adenines in ...site blocked by methylation), the figure below illustrates how sequence visualization software (we used ...

...-lab experiments using a “traditional” lab notebook; however, keeping track of computation work comes ...to keep track of why you are doing what you are doing. Another common challenge is to keep track of what...was run. This technique leaves a trail that further helps you keep track of your exact changes. Alternatively...was contributed by guest blogger Kate Palozola Traditional lab notebooks just won't cut it for bioinformatics...began, I realized that I needed a system to keep track of the files that I was continuously generating....comment in C++ and Java Command line history: Tracking command line history by recording all commands...Learn about Software You Can Use to Save Time and Track Your Experiments Try out the CRISPR Software Matchmaker...

... do just that! (To read about other screening strategies, check out our screening overview blog post.)...β-galactosidase enzyme can break down a dye-linked substrate called x-gal (5-bromo-4-chloro-3-indolyl-β-D-galacto-pyranoside...α-peptide) to a lacZΔM15-mutant bacterial cell in trans complements the mutation allowing for a functional...produces pigment from x-gal (included in the transformation plate medium), turning the bacterial colony...IPTG is also included in the medium to ensure transcription of the lac operon.   Tips for blue-white screening...screening Use a good control: Transform the backbone plasmid without insert. All colonies on this plate...restriction digest. Make sure you use a proper E. coli strain (i.e. contains the lacZΔM15 mutation): XL1-Blue...

...they have certifications? How can they demonstrate their track record? Look for a coach that specializes...help with transitioning out of academia (because so many scientists are making this transition). Another...have experience and knowledge to help scientists transition out of the academic sphere into a different meaningful...not always as effective in mentoring for this transition. Second, a coach will help you set goals and ...scientific backgrounds. For a stated purpose of transitioning a scientist from academia to industry, you might...in coaching for communication skills. Industry transition is also an area of specialty for Michelle Capes...it can be helpful having a coach that can offer extra support for issues of diversity in science.  A great...