We narrowed to 1,104 results for: Ide

...with the guide RNA.   Non-target strand The DNA strand that does not base pair with the guide RNA. Despite...hypoxanthine (shown) is the nucleobase component of the nucleoside inosine. Created with BioRender.com. Although...ABEs are base transition editors. They adjust the side groups of DNA bases and leave the core ring structure...some cases, the same repair pathways that were considered problematic in the development of CBEs and ABEs...structure. In order to bind DNA, Cas9 requires (1) a guide RNA, (2) a complementary DNA sequence, and (3) a...strands called an R-loop (Figure 2). This allows the guide RNA to base pair with the DNA target strand, leaving...non-target strand unpaired and accessible on the outside of the enzyme. Figure 2: CRISPR R-loop. ...

...industry, nonprofits, and publishing. The livestream video from the event can be found below along with a description...reproducibility “crisis” on our hands and instead provide a brief conceptual framework for the causes of ...protocols and use one another’s reagents with the confidence that they aren’t simply doing an experiment wrong...Luckily, many organizations have been working to provide tools that make it easier to share in-depth information...working with a plasmid from Addgene, you can be confident that you’re using the actual tool that you ordered...research needs. Other companies like NEB and ATCC can provide you with additional validated reagents, and, with...Protocols.io, JoVe, and Bio-protocol all work to provide more descriptive and interactive protocols that...

...knockdown, or other factors, consider using one of the alternative, albeit less ideal, verification approaches...the results across runs. If the results vary considerably, then the high degree of variability in the ...replicates are distinct samples that are treated identically, used to assess naturally occurring random biological...assays have their own unique controls that must be considered (Burry 2011). Perhaps the most critical are those...wild-type and knockout samples are treated with the identical protocols that the experimental samples undergo...with its antigen or a small epitope-containing peptide to block the antigen-binding site. The sample is...detectable, it is likely due to binding interactions outside of the antigen-binding site.      Secondary antibody...

...designed small RNA, or guide RNA (gRNA). The gRNA conventionally contains a 20-nucleotide sequence that is ...Activators: A Practical Guide Additional Resources on Addgene.org Check Out Our CRISPR Guide Pages Find Empty...nuclease-null—in order to effect different perturbations. Consider, for instance, the challenge of attempting to ...interacts with a distinct gRNA that allows users to decide which Cas9 protein is directed to which target ... truncated such that it exhibits 15 or fewer nucleotides of complementarity to a target site, Cas9’s DNA...truncated gRNAs Importantly, the use of truncated guides has largely been demonstrated to result in decreased.... An additional benefit of the use of truncated guides is that they can be delivered into systems that...

... about my interests and my ideas all the time. Once, I had this crazy idea that I needed help with: wouldn... you make the most of the opportunities you’re provided throughout your PhD program.   Find people who.... They didn’t always know the best direction to guide me because they had no experience with my career... open mind and open ears. Everyone I talked to provided new data. Every new experience taught me something...troubleshooting.” Trying out new experiments and new ideas is nothing new to a scientist. Framing my efforts...efforts in these comfortable terms helped guide me through the process. As I mentioned, my graduate office...disappointed in the lack of participation, but I decided to focus on what the experience taught me. The ...

...as well as highlight some considerations for their use. Then, we’ll provide information about commonly...decision tree can help guide your choice on which systemic capsid to use. Factors to consider include the delivery...goes beyond such restrictions, you may want to consider a systemic capsid for your AAV.   Systemic capsids... definition of systemic capsids. After some consideration, we offer this definition: A systemic capsid... after intravenous administration, distributing widely throughout the organism to target large or diffuse...commonly used and emerging capsids to help you decide which ones may be suitable for your experiment. Like all...and/or its intermediate engineered precursor. Considering systemic capsids for your research? While systemic...

...disciplines. Cast your net wider, explore tangential subjects, and let curiosity guide your intellectual journey...thus feel grateful) and identify areas in need of improvement. These unrelated ideas might hold the key to...simple steps to welcome these unforeseen moments. Widening your search The first step towards inviting serendipity...ultimately enhancing your project's potential. Widening your search creates fertile ground for serendipitous...encounters that could spark unforeseen connections and ideas. Maintaining openness and looseness of spirit The... exploration of tangents or seemingly unrelated ideas. It's beneficial to carry a notebook at all times...confines of a predefined path, opening doors to novel ideas and approaches. Moreover, the ability to embrace...

...develop their career skills for positions both inside and outside academia. Inspiring future scientists At ... ever heard of a Freshers Fair? If you’re from outside of Europe, the answer is probably no, but these...be used as welcome events for new students that provide ways for students to network, find groups with ...come. Some Freshers Fairs can include fairground rides and other fun activities and even invite members...thought we’d take some time to introduce you to the idea of the Freshers Fair and some of the great biological...students so that they can help support each other and provide advice. The society organizes numerous recreational... high schools to promote chemistry degrees and provide advice to students who want to study chemistry....

...mentoring for instructors, and provides opportunities for students to exchange ideas and results with peers and...al., 2020). Many have interpreted this trend as evidence that the best teachers and mentors pass on more... Biochemistry at the University of San Diego), decided to take a different approach. His own most impactful...experiences happened in the lab, and he wanted to provide the same kinds of opportunities for his students...but one that left him overwhelmed. Therefore, he decided to adopt a more focused format, where all students...analysis, structural prediction, and bench work to identify regions of MDH that interact with citrate synthase...Meeting. Some of my students published their work identifying new genes required for stem and progenitor cell...

...individual molecules. Poor photon budgets are a widespread issue with fluorescent proteins—even the thriftiest... “ligand” that binds to the tag. Like most good ideas in biological imaging, the initial breakthrough ...breakthrough for in-cell labeling techniques was provided by Roger Tsien, who showed that the selective interaction...short genetically encoded tetracysteine (Cys4) peptide tag could be used to label proteins in cells (Figure...tags (e.g., SNAP-tag, HaloTag, TMP-tag) – These widely used systems consist of a genetically encoded enzyme...covalent attachment of a fluorophore ligand to a peptide tag (Figure 1c). Click chemistry (e.g., transcyclooctene–tetrazine...fluorophores were designed as antibody and oligonucleotide labels for fixed-cell imaging, not for live-cell...

...the cell might consider junk protein. Though there are a number of chemical and peptide-based proteosome... Protein tags are usually smallish peptides incorporated into a translated protein. As depicted in the...these challenges, researchers have amassed a considerable molecular tool box of tags and fusion proteins...proteins, such as Thioredoxin A (TrxA) that improve disulfide bond formation in order to help keep your protein...bacterially derived in-vivo biotinylation signaling peptide (Bio), flanked by hexahistidine motifs (6xHis) ... a combo tag comprised of a calmodulin binding peptide (CBP), a TEV cleavage site (more on that in a moment...The efficiency of this cleavage depends on the identity of X. A number of other proteases are available...

...and dampness of any kind should be avoided. Distilled water provided to maintain the humidity should be...contamination (Uphoff, 2002). Mycoplasmas are considered to be one of the simplest and smallest bacteria...Drexler, 2011). Culturing on agar plates/broth is considered the ‘gold standard’ for detecting mycoplasmas...steps start from you. If you are careful enough to provide a sterile environment for work, it will soon become... coughing in the lab. The human mouth contains a wide variety of mycoplasmas and these can enter the cell...you keep all the required equipment and reagents inside the laminar airflow before and while you are working...regularly as mycoplasma, bacteria, and fungus can reside in these containers. Clean up any media or culture...

...so good with video calls, how about trying your hand at a video presentation? Most video platforms make...months past a worldwide shift to work-from-home and just now realizing that we can’t bide our time and ...are moving forward. Here are a few out-of-the-box ideas that might jump start your learning. 1. Create a...and most of us could use more mentors to listen, guide and support us during training and throughout our...see Form Your Own Peer Mentoring Group: A How-To Guide for Scientists.   Once in-person, peer-mentoring...others and get their input as well. Giving a great video presentation is going to be a useful skill for the...learned to play the ukelele...perhaps you get the idea. What will you start? 4. Do informational interviews...

... It can be applied for identification of essential MYC binding sites in a wide range of human cells.  ...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ...disease-causing point mutations. They allow single-nucleotide modifications to edit DNA without requiring a...recently deposited a set of plasmids that helps identify base edited cell populations without end-point...reporter for editing enrichment”, or XMAS-TREE, to identify base edited cell populations without end-point...should have changed from “TGA” to “TGG.”  After identification of ABE activity, XMAS-TREE can also be used...difficult to modify in the past.   Figure 1: Identification and enrichment use of XMAS-TREE. a) Cells are...

...Salegio et al., 2013). Zingg et al. 2017 also provide evidence that AAV1 and AAV9 are capable of synaptic...particle is taken up on one side of the cell and released again at another side of the cell after intracellular...Conclusion An ideal comprehensive toolset for neuronal tracing and network identification requires both...single synaptic step, thus preventing further widespread expansion of RABV. This improvement resulted ...delivering neuronal tracers AAV vectors have been widely used by neuroscientists for some time due to their...proteins. For a brief overview see Addgene’s AAV guide. AAV particles are relatively small (20 nm) in size... transgene expression. Fluorescent proteins are widely used for tracing and their expression is often ...

...properly onboarded. Most work environments outside of academia provide a formal training regime and the right...transition. In this installment of the Addgene career guide, we’ll think about what causes this culture shock...enjoyable aspect of their chosen career. You can confidently call yourself a Scientist. You work in a lab....during the lab → office transition? I’ve already provided a few counterpoints to some of the causes of culture...colleagues, we’ve come up with a list of things to consider as you make this transition. Of course, a “desk...these--get started with our Transferable Skills Guide.     Over the last decade, my peers and I have... the first place. Finally, if you still find the idea of not holding a pipette again upsetting, there ...

...trying to decide which CRISPR tools are best for your experiment, check out our CRISPR guide or leave ...can be used to modify any desired genomic target provided that (1) the sequence is unique compared to the...Protospacer Adjacent Motif (PAM sequence). The 3-5 nucleotide PAM sequence serves as a binding signal for Cas9...For more details on the PAM site, check out this video from IGI!) Synthetic S. pyogenes Cas9s with novel...series of positive selection screens in bacteria to identify mutants of S. pyogenes Cas9 that were able to ...Kleinstiver et al. 2015). From these screens, they identified four novel SpCas9 variants with altered PAM binding...Sontheimer EJ (2018) NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol 19: . https...

...experimental work, but with this guide, we hope you feel more confident incorporating them into your research... We strongly recommend following the protocols provided by the depositing lab whenever available. Addgene...library sample, and any other information or scripts provided by the depositing lab for data analysis.  I'm ... If not, our protocol on Lentivirus Production provides a general approach for producing lentivirus in... the virus–the right amount of virus, that is. Ideally, each cell will be transduced by no more than one...from Addgene? Take a page from our book and put aside an aliquot for titering and optimizing before you... number of cells to transduce, you may want to consider spinfection. Spinfection is the process of transducing...

...as a newbie reprogrammer, to decide which method to use. This post provides a brief overview of reprogramming... them with peptides that help mediate their transduction, such as the polyarginine peptide described in...variation between iPSC clones. Retroviruses are not considered safe for clinical applications.     Lentiviral...Like retroviruses, lentiviral delivery is not considered safe for clinical applications. Excisable Cre-lox... site of excision, this approach is still not considered safe for therapeutic applications. piggyBac (...insertional mutagenesis, adenoviral vectors are considered a safer way to express reprogramming factors ... includes measles and mumps. Sendai transduces a wide range of cell types and replicates in the cytoplasm...

...through triglyceride/cholesterol does not provide a clear view of either of these metrics (Sniderman et al...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ...popular tools for genetic screens, enabling genome-wide interrogation of the genes required for cellular...processes. For a successful screen, it is necessary to identify the gRNAs that elicit the phenotype, and this ... the gRNAs responsible for a phenotype can be identified by next-generation sequencing of the genomic ...contributed by Leah Schwiesow A leading cause of death worldwide, cardiovascular disease is driven by atherogenic...ApoB-LPs) are indirectly measured through their triglyceride or cholesterol contents (what is commonly called...