...small errors that significantly impacts your experiments. What do you do when you’re in the lab and you're... steps like “check drawers for light-sensitive reagents” or “re-sterilize now.” Have a physical copy of...Have a physical copy on hand as you run your experiments. Try drawing out a protocol as you read it, or...an investment in accuracy.  Bench setup Small adjustments in the physical organization of your workspace...you track samples as you add them. Moving your reagents from your left side to your right as you use them...are endless.    Fig. 2: Blugene moves reagents from left to right as they use them.    Prevent...focus, which was extremely effective. Others ran experiments at odd hours, used more secluded workspaces, ...

...of DNA Elements Project (ENCODE), an NIH-funded effort to define all of the functional elements in the...similar. There may be other variants of this that are better for some experiments than those we’ve put up....Eric Mendenhall of the University of Alabama in Huntsville explains it, a major goal in his laboratory is...groups got together to adapt CRISPR for tagging experiments and it’s already looking like it’s making a big... system is really quite simple but it offers improvements in efficiency and throughput. In adapting the...developed their own system or who use and adapt our reagents to think about adding them to Addgene’s special...

... just that as part of their CRISPR work in rice plants. Yang was intrigued by the tRNA processing machinery... in eukaryotes (E in bacteria), and only a few elements of tRNAs are necessary for recognition and cleavage...addition, tRNAs contain internal transcriptional elements that enhance pol III transcription, potentially...also examined editing efficiency in intact rice plants, comparing traditional gRNA constructs with PTGs... five gRNAs were tested, they found that 50% of plants had biallelic mutations at all five loci. This ...Although Xie et. al characterized the system in plants, PTGs will likely work well in many different biological... regions, such as noncoding RNAs or regulatory elements, to examine their function. Bacteria and viruses...

...Mentoring Group all participants act as both mentors and mentees. Because the participants are at a similar...make mentoring less mysterious and train the participants in skills useful for future mentoring relationships...at the same time Broadens the network of the participants Can be a lot of fun! Form your own peer mentoring...mentoring group In my travels speaking to grad students and postdocs I have started to talk to trainees....g. all women, all men, all postdocs, all grad students) or mixed for one or both of these criteria. If...you can, include people from different labs, departments or organizations as it brings a diversity of ...perhaps a 3 hour breakfast once a month. All participants must commit to making the meetings a scheduling...

...We are excited to announce the recipients of this year’s Michael Davidson and Roger Tsien Commemorative...researchers, in addition to postdocs and graduate students as we have done in the past. Below, read about...Filip Tomaska and Tim Hanson, are characterizing variants of iGluSnFR3 in vivo and have used it to detect...post-transfection, excited at 505 nm (right). Scalebar represents 100 µm. Image from Abhi Aggarwal.   Brandán...providing insight into new methods for treating patients in recovery from opioid use disorder,” says Hubbard...line engineered to be electrically excitable. The mutants are co-expressed with a photoconvertible fluorescent...photoconverted, sorted, and sequenced to identify the mutants for further enrichment. Tian notes that this platform...

...that stability of the RNA used in CRISPR-Cas9 experiments – the “gRNA” – suffers from the same issues as...nuclease-resistant, resulting in less off-target events. While both have similar advantages, bridged nucleic... Editing). This is particularly important in experiments in which viability is being compromised by introduction...CRISPR-Cas9 system can initiate targeted editing events. Both technologies utilize chemical modifications...gRNAs? Dye labeling the RNA in your targeting experiments allows you to visualize transfection efficiency...efficiency and even track localization in cellular experiments. There are many suitable dyes to choose from ...-703 (2020). https://pubs.acs.org/doi/10.1021/acscentsci.9b01093 More resources on addgene.org  View ...

... from their native regulatory elements. Controls for RaPID experiments RaPID negative controls include...interest. See figure 1 below for details on the key components of RaPID. Ramanathan et al. also tweaked BirA... the role played by RNA-protein interactions in events that occur on a short timescale, such as during... BirA*-based affinity purification mass spec experiments. These background proteins were then subtracted...correlated with poor survival in breast cancer patients. By digging into the literature and analyzing ...disease. RaPID can also be used to test how RNA variants associated with human disease affect protein binding... with increased serum iron levels seen in HHCS patients. These are just three examples of how RaPID can...

...Nature gives us even more to talk about, as it represents another step towards CRISPR germline editing ... the field will move forward from this work. Experiments & major findings Let’s start with the paper itself...forward with gRNA 1 to conduct microinjection experiments in S phase zygotes at 18 hr post fertilization...are needed for proper development. Ma et al.’s experiments showed a 3% mosaic rate, and this rate would ...to correct the hype when we see it. This paper represents a huge advancement in our understanding of how...perform in embryos but also shows that many more experiments are needed before we can consider clinical applications...applications for germline editing. Although this paper represents a large step forward in the CRISPR field, it’...

... about postdocs. Among other involvements, he helped to establish grants through the Sloan foundation ...biomedical workforce. Quotes taken directly from participants (summarized in 2) touched upon many problems...hired to produce results, not scientists”  These comments are well correlated with published data. For example...better solution would be to reduce the number of entrants into PhD programs to more closely reflect the ... market for PhDs Later this week, postdocs and students will again gather in Boston - this time with the...arguing against reducing the number of graduate students accepted in STEM fields (6). Melanie Sinche ...PMC4484856. 5. Bourne, Henry R. "A fair deal for PhD students and postdocs." Elife 2 (2013): e01139. Pubmed ...

...(electronic table of contents) alerts from journals you read often. The contents of each issue will be...explain some of the rationale behind the line of experiments, what data they collected and what it means. ... model or overall conclusion. In others, the experiments are geared towards eliminating possibilities ...deeper about the data they are showing. Are those experiments the best way of figuring out what’s going on?...controls? Refer back to the methods section for finer points of the protocols. Are there any red flags about... days of file cabinets filled to the brim with reprints and papers with scribbled notations in the margins...searching, reading and organization tips in the comments below. Additionally, read more of the Beginner...

...Many neuroscience experiments that require gene expression in a specific cell type rely on transgenic...of off-target expression and ways to optimize experiments to minimize it. Overview of DIO/FLEx vector design...problem of DIO/FLEx vectors, the cause of these events, until recently, was not known. A recent paper ... both the serotype and promoter with in vivo experiments to determine the optimal/minimal injection titer...interest. You should now be able to make smaller adjustments to a set of injections into your animal model...may be tempting to skip some steps and get to experiments. However, by optimizing all conditions first,...results.  Conclusion Using AAV vectors in your experiments requires a full understanding of vector performance...

...). If you are wondering which virus fits you experiments best have a look at this viral vector overview...and expression of these vectors when used in experiments. Retroviral vectors make up a large toolbox ...screening of thousands of genes in genome-wide experiments. Gamma-retroviral vs. lentiviral vector systems.... More detailed descriptions of the lentiviral elements and the 2nd and 3rd Generation Lentiviral Systems...and tips for using retroviral vectors in your experiments. Gamma-retroviral vectors Popular gamma-Retroviral...can be used to induce site-specific recombination events and is widely used in the field of mouse transgenics...Zhang lab: We are constantly improving our CRISPR reagents. Please check www.genome-engineering.org for the...

... viral components or the transgene itself are used to quantify the number of integration events. Another...common assays for physical titer are direct p24 measurements via ELISA and qPCR for viral RNA. Measuring ...quantified using qPCR primers targeting specific viral components such as LTRs, gag, WPRE, antibiotic resistance-genes...genome and a cell that has had multiple integration events. In addition, promoter choice can also impact transgene... approach can discriminate multiple integration events, reducing the possibility of underestimating the...titering as this will better represent future experiments. The aforementioned titering options all have...of infection (MOI) for predicting gene transfer events." Genetic vaccines and therapy 2.1 (2004): 1. PubMed...

..., safety requirements and expression limitations may be too constraining for some experiments, particularly...that often affect which is chosen for certain experiments. AAV can be safely handled at BSL-1, while lentivirus...vectors is how the cargo — in this case, the CRISPR components — are expressed. Unlike lentivirus, cargo delivered...AAV genome can integrate at double-stranded break points caused by CRISPR-Cas9 editing. The good news is...the amount of cloning, another option is to use variants of Cas9, like split Cas9, or a smaller Cas9 ortholog...tissue-specific diseases has grown exponentially, aided by advancements in in vivo CRISPR screens. AAV vectors have ...have played a large role in these advancements, due to their many benefits for in vivo models. Over the past...

...generations. Figure 1: Mobile-CRISPRi's modular components. Image from Peters et al., 2019 with permission...using the bacterial integrative and conjugative elements in Bacillus subtilis (ICEBs1) system. ICEBs1 carries... Top: A Tn7 transposon containing the CRISPRi components and a plasmid with the Tn7 transposition genes...lacking DAP select against donor bacteria and for recipients with an integrated copy of CRISPRi. Bottom: An... An ICE element containing the CRISPRi components is transferred to recipient bacteria by bi-parental ...suited for genome-wide CRISPRi library screening experiments where maintaining library diversity is important...rates are only suited for single-gene knockdown experiments. Mobile-CRISPRi applications Mobile-CRISPRi expands...

...contamination free environment for successful experiments: To clean air and beyond Turn on the hood for...wipes) before and after your work. Keep your contaminants away While it’s likely that you’re the main ...main source of contamination for your experiments, the bright side is that you also have the power to take...aerosols that may enter the hood. Planning your experiments thoroughly before entering the hood is another...microscope will help you identify bacterial and yeast contaminants. Set up a routine to split cells Don’t be lazy...rendering their continued use inadvisable for experiments requiring reproducible results. Most cell culture...should not be used for important transfection experiments right after they’ve been thawed. Additional passages...

...introduce their students to this otherwise invisible molecular world. For the students, the models force...hand-deliver the model, the following sequence of events plays itself out: The researcher breaks eye-contact...membrane of the endoplasmic reticulum. And graduate students, momentarily forgetting that the physical model...Subscribe to CRISPR Blog Posts How do educators and students use molecular models?   We created the Center ...instances of focused attention become magical teaching moments. The models function as thinking tools – eliciting... Team modeling program in which small teams of students work closely with local researchers to learn about... designed to make the molecular world real for students. Many thanks to our guest blogger Tim Herman!...

... mutually exclusive elements. Labs have successfully utilized 2A and IRES elements within the same multicistronic...for research purposes are described below. IRES Elements Translation in eukaryotes usually begins at the...translation initiation independent of the 5’ cap.  IRES elements are very useful and commonly found in bicistronic...however, they do have some disadvantages. These elements are quite large (500-600 bp) and may take up precious...express more than two genes at a time using IRES elements. Further, scientists have reported lower expression...features and spend more time developing the clever experiments and innovative solutions necessary for advancing...ITAMs ensures effective negative selection and prevents autoimmunity. Holst et al (Nat Immunol. 2008 Jun...

...colors and 10 points to keep in mind when choosing an FP (or two) for your upcoming experiments. Fluorescence...FPs just keeps getting larger with hundreds of variants available. Read on to familiarize yourself with...emission wavelenght range).  By mutating GFP, the variants blue FP (BFP), cyan FP (CFP), and yellow FP (YFP...YFP) were derived. For a breakdown of GFP, it's variants, and their relevant mutations, check out Marcy's...Bimolecular Fluorescence Complementation (BiFC). 8 points to keep in mind when choosing a fluorescent protein...you are planning to express the FP in acidic environments (e.g. yeast cytosol, which is slightly acidic...with very comprehensive data sheets on many FP variants Plasmids 101: Green Fluorescent Protein (GFP) ...

...in high pH environments and is less susceptible to degradation in agar plates. This prevents satellite ...less stable at high temperatures and in acidic environments.   Carbenicillin   Carbenicillin, colloquially...genomes. If you need a plasmid that can go between plants and bacteria, it’s a great option! Otherwise, since...eukaryotic cell culture, yeast, bacteria, and even plants! The zeocin resistance gene is present in bacteria...et al). Thus, it may not be a good choice for experiments in which off-target mutations are undesirable..."Check icon" %} Zeocin Excellent No Bacteria, plants, and eukaryotes Not Tn5-containing cells {% icon...temperature and pH on the stability of antimicrobial agents in MIC trays. Journal of Clinical Microbiology,...