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...commonly, DSBs are repaired by the nonhomologous end-joining (NHEJ) pathway, leading to nonspecific nucleotide...Furthermore (3), we have developed a framework that, by combining these two strategies allows you to specifically...find the 0.2-0.5% correctly edited alleles, when screening reasonable amounts of single cell clones. Furthermore...Furthermore, CRISPR/Cas9 editing is often bi-allelic, meaning that even if one allele is accurately edited, the... few hundred. From these two steps, you’ll be screening a total of a few hundred clones - Still better...longer feasible to incorporate mutations without screening thousands of clones to find a positive one. So... single cell. We calculated the likelihood of obtaining homo- and heterozygous mutations by multiplying...

...alleviate those differences, they had a hard time maintaining their friendships. I put “neutral” in quotations...learn how to sell them. Types of Conflict Before explaining my approach to conflict resolution, it’s important... into a gap between teams that nobody is really owning. Conflict in this latter scenario usually manifests...disagreeable, you recognize their feelings as valid. Listening: In one of my favorite books, Michael Ende’s Momo... nearby village (and to the reader) by simply listening. Chances are, you know someone like this, even...conflicts.  Institutional Knowledge: Of the tools I’m mentioning here, this may be the most controversial, so ...also aggravate long-term personal conflicts.  Transitioning a conflict into a collaboration may not be the...

...will introduce you to a few useful labeling and staining techniques beyond standard surface labeling. Pro... Pro tip! Many people use 'labeling' and 'staining' interchangeably to refer to any technique that combines...Addgene uses 'labeling' to refer to antibodies and 'staining' to refer to small molecule dyes. Indirect labeling...labeling must be performed only after viability staining and surface labeling are already done. Intracellular... viability. Unlike intracellular labeling, dye staining can be done on live cells. For cellular proliferation...cell, the ester group is cleaved off by enzymes, turning the resulting molecule fluorescent and membrane-impermeant... for specific downstream applications, while maintaining a clean cell surface, dump gating is a useful...

...Agrobacterium-compatible, Cas9 containing vectors ready for Golden Gate mediated cloning of your gRNA of interest...researchers to insert targeting oligos with minimal cloning required. As with other model systems, multiple...promoters (Belhaj et al., 2013). Addgene carries Cas9-containing plasmids for knockout, activation and repression...on the helper plasmid and used to insert the intervening region into the plant genome. Created with BioRender.com...deaminase-mediated base editing (cytosine base editor or adenine base editor) and reverse transcriptase-mediated... et al., 2019). Both cytosine base editors and adenine base editors have been developed for plants and...Demirer GS, Zhang H, Ye T, Goh NS, Aditham AJ, Cunningham FJ, Fan C, Landry MP (2019) DNA nanostructures...

...that there was no cross-reactivity, opening the door for immunostaining analysis. To achieve even cell labeling..., but can be detected via immunostaining. This feature facilitates screening of Cre-negative Brainbow ...systems. Pre-Brainbow techniques, such as Golgi staining, injection of diffusible labels, or electron microscopy...segment, eliminating two color possibilities. The remaining cassette can invert as long as Cre remains expressed...Second, the system did not permit analysis by immunostaining. Although the fluorophores used are fluorescently... Cai et al. also created an Autobow construct containing both Cre and XFPs. Cre production drives recombination...

...demonstrates that transitioning from academia doesn’t have to mean abandoning it or running away screaming...weren’t some pretty hefty bumps during my graduate training. I particularly think that too many young scientists...talking to people about science and that I love explaining things to people. When I started my graduate ...keeps me on top of a variety of fields thereby broadening my knowledge. In addition, this position allows...careers outside of academia during my graduate training. PhDs have many roles to play inside, on the outskirts...

...their goal of PhD training when selecting a research topic. The end point of training is not to become ...After joining a lab, the focus shifts to choosing an unexplored and impactful research topic that aligns...consider when choosing a research project After joining a lab, the next important decision to make is “...what approach will I take and what can I learn, learning the difference between good and bad data, and ... dreams. He also highlights the importance of combining “new discoveries or technologies increase chances...Advice for Choosing a Research Project Finding and Joining Your Dream Lab Advice for Choosing a Research Project...

...scientist-in-training will spend 10 or more years with a small number of formal advisors learning how to be...priorities will help in determining a good fit. Here are just a few suggestions for determining whether an advisor... will be ones that help them succeed after the training period. While there are many aspects to choosing...time hanging out with members of the lab. It is a warning sign if the PI does not welcome you to visit and...Precision and Plasticity in Mentoring" Don’t ignore warning signs If lab members, neighbors or alumni give ...

... add the CACC and AAAC cloning overhang. Q3: When designing oligos for cloning my target sequence into...CRISPR forum's most popular questions and answers. Designing your CRISPR genome editing experiment Q1: Should...Should I add the PAM sequence to the oligo when cloning my target spacers into the PX330 vector backbone... A7: A few notes below are considerations for designing HR donor. Generally if off-target (non-specific... lab bench Q12: How can I quickly check if the cloning of my oligo into a backbone like PX330 worked? ...Why does the PX260 plasmid use 30 nt oligos for cloning but PX330 only uses 20 nt? A16: The reason for ...the construct is from our 'Chimeric RNA' design (meaning the mature processed form of crRNA is fused chimerically...

...for staining. To address this, the membranes are incubated before staining in a buffer containing nonfat...in the presence of a reducing agent, typically containing thiols, to cleave disulfide bonds. Load the samples...variety of tissues to demonstrate that the protein staining matches the expected expression patterns across...level of validation ensures that the antibody is staining the intended target.  Once you have chosen an ...used by the vendor for validation could contain unintended cross-reactive proteins. Similarly, if you vary...with a good overview of the western blot. When planning a western, take care to include the proper positive...

...mutated methionine was not enough to prevent alternative initiation, so they mutated the methionines at position... You can use DNA sequencing or other molecular cloning techniques to determine CRISPR/sgRNA efficiency...homology directed repair (HDR) and non-homologous end joining (NHEJ). In these reporters, editing typically results...H2B-GFP. This visual read out allows for easy screening of different gRNAs by simply changing the gRNA...transfected cells will express RFP while cells containing the reporter gene that was cleaved by Cas9 and...start site initiation, the lab removed the native methionine start site. This first iteration was named GEmCherry1...

...and cloning sites for inserting the guide sequence (pSpCas9(BB)). The 2A-GFP allows for screening of transfected.....From moving office locations three times, to opening our UK office in 2014, to starting our viral vector...virus, making it ideal for CRISPR pooled library screening experiments. Find lentiCRISPR v2.(If you’ve peeked...  Find the scrambled shRNA vector. pLKO.1 - TRC cloning vector - This vector from the David Root lab is...3rd generation lentiviral transfer plasmid for cloning and expressing new shRNA sequences. For more information...slowly than standard plasmids. Find pLKO.1 - TRC cloning vector. Tet-pLKO-puro - Tet-pLKO-puro contains ...

...the next step in high-throughput, genome-wide screening,” Konermann said. “If you want to activate all...her colleagues demonstrated the new system by screening for genes that, when turned on, make melanoma ...CRISPR library enabling genome-scale, knockout screening). As the Zhang lab's Nature paper reports, “Here... can facilitate genome-scale gain-of-function screening when combined with a compact pooled sgRNA library...validation of the top 10 hits.” Two-way CRISPR screening In October, Jonathan Weissman’s lab introduced...developing sgRNAs that will enable even more fine-tuning of gene expression levels and on software for analyzing...Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman...

...consisted of two plasmids: the packaging plasmid containing all the structural genes necessary for the production...retrovirus into the packaging cell line PA12 (containing the psi deletion). A double crossover event between... LTRs, the ψ sequence, a part of the env gene containing the rev response element (RRE), an internal promoter...transfer vector plasmid), 2) the HIV-1 genome containing all viral genes with the exception of the env...distinct expression vectors to target cells - one containing the gene of interest (pTet-IRES-EGFP, pPRIME-...bottleneck for your experiment. Single vector systems containing both your transgene and tTA/rtTA (pINDUCER20,...your institution’s Biosafety Committee before beginning any work. Lentiviral production and transduction...

... the cellular DNA. Fluorescent DNA staining is another DNA staining alternative. This method uses DNA ...proper training and guidance to the people working in the lab facility. This can be done by training eligible...this task, you can use PCR based detection, DNA staining, fluorescent tagging, agar plating, etc. Be wise... is added to the liquid or semi-solid medium (containing nutrients essential for mycoplasma growth). Infected...facility periodically. The CO2 incubators, used for maintaining cell lines, must not be overcrowded (filled no...contamination. Be aware and cautious rather than learning it the hard way! Many thanks to guest blogger...

...channelrhodopsin-expressing neurons, the channelrhodopsins respond by opening and allowing an influx of ions into the neuron ...s lab and Viviana Gradinaru’s lab used machine learning to design new channelrhodopsins that are more ...channelrhodopsin that’s successful in vivo. Using machine-learning to overcome channelrhodopsin design challenges... Arnold and Gradinaru Labs developed a machine-learning model to help them construct “designer” channelrhodopsins...the library to 1,161 sequences. Thirty of these remaining sequences were selected for characterization with...mice that received ChR2(H134R) did not turn. Left-turning behavior in ChRger2-treated mice ceased when the...Mackey ED, Gradinaru V, Arnold FH (2019) Machine learning-guided channelrhodopsin engineering enables minimally...

...can also affect patterning and in some cases even override genetically encoded patterning. Based upon trends... Bioelectric states can alter cell types and patterning There is mounting evidence that signaling via... even be necessary and sufficient for certain patterning activities of entire tissue types or even organs...Since bioelectrical signals are controlled by the opening and closing of ion channel proteins, they are not...developmental biologists and cancer researchers are beginning to turn their attention to bioelectricity. One...Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis." Development 139.2 (2012):...

...found that many researchers feel they lack formal training in a variety of transferable skills. At Addgene...puzzling through your broader research questions and designing future experiments. Being able to work through...at work.   While I was in graduate school and beginning to research non-academic careers, I always felt...dozens of career advice articles, I settled on defining problem solving skills as: One’s ability to logically...the process, you might need to go back to the beginning, reassess the situation, and try a new strategy...scientific method is a core part of our academic training.  Developing strong problem solving skills is ...challenges we encounter. As you spend time in a lab learning techniques and taking on independent projects,...

... a plasmid? Or how much time you have to spend cloning before you can start your experiment? What about...order? Sometimes, it feels like an eternity of cloning, waiting, and repeating before you can finally ...course, these were all 2018 numbers, and the intervening five years, inflation has occurred. Here at Addgene...in science – the time spent by the scientists designing and performing the experiments. This cost varies...and money across the board. Consider alternative cloning strategies There are many strategies beyond the...well) plate! How much do repositories help?   Designing precise calculations for any of the numbers in...Addgene Blog 5 factors to help you choose the right cloning method Find blog posts about scientific sharing...

... the tides may be turning. In 2013, the NIH announced its first round of Broadening Experience in Scientific...achieved tenure-track positions within 5-7 years of earning their PhDs (3), showing that the ‘standard’ pathway...Scientific Training (BEST) awards, which are designed to support new approaches that address the need to... School. Graduate education programs are also beginning to address these issues independently; for example... may look like. The panel discussion on Friday morning will be dedicated to Academic data and the Labor...PMC3342243. 4. Mathur, Ambika, et al. "Transforming training to reflect the workforce." Science Translational...