...Updated Apr 6, 2021. If you’re doing high throughput work, it’s likely that you come into the lab wishing...transformation One protocol that has been automated is high throughput transformation. With our ever growing...the deck of the Biomek. The FXP id also able to do high throughput DNA preps and other molecular work if... through this process. With enough agar and the right program, the liquid handler can fill 400 vials in...hand. How can you start automating your lab? You might not be doing enough transformations, minipreps, ...

...expression and degradation. These workshops not only highlighted new tools but also included time for questions...presented at the C. elegans meeting. Here I’ll highlight a few toolkits that we have available at Addgene..., and Erik M. Jorgensen. "SapTrap, a toolkit for high-throughput CRISPR/Cas9 gene modification in Caenorhabditis...

...possible by the use of our high-throughput DNA isolation process that yields high-quality isolated DNA samples... on our ability to provide requesting scientists high quality data! Addgene's new in-house NGS process...be familiar with our efforts to ensure access to high quality, ready-to-use viral preps and pooled libraries...Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F (2017) Genome-scale CRISPR-Cas9...

...of the ABE8s ranged from 1.5x higher for positions A5-A7 to 3.2x higher for positions A3-A4 and A8-A10...synthetic library of TadA sequences to create the eighth generation of adenine base editors, called ABE8... in variants named “ABE8.x”: “8” stands for the eighth round of ABE evolution and the “x” is the placeholder...editing frequencies. For applications that require high DNA editing specificity, for example for potential...

...installment of the Early Career Researcher Toolbox will highlight four tools for finding journal articles related...summary of the topic and a chronological list of highly cited papers that contain your search term. When...of the page, as well as the number of citations highly influenced by this paper. Influence is measured...number of publications that heavily cite, or are highly influenced by the author. You can also see who ...

...of unionization continues to be a polarizing one. High-profile universities remain outspoken in their opposition...FLSA changes, including finding money in already tight lab budgets and even simply being able to categorize...salary perspective, while this is a move in the right direction, the increase notably still does not meet...Workshop 2016 At past symposia, FoR worked to highlight some of the problems facing postdocs and graduate...

...quality. To make sure our AAV vectors are of the highest quality, we undertake a rigorous quality control...vectors, and helper plasmids (Chadeuf et al., 2005, Wright et al., 2011). In fact, the majority of hits come...samples from 0.1-20% and discovered that, with a high enough sequencing depth, we could detect contamination...with exquisite detail (Lecomte et al., 2015). This higher level of quality control is recommended but not...Acids 4:e260 . https://doi.org/10.1038/mtna.2015.32 Wright JF, Zelenaia O (2011) Vector Characterization Methods...

...Addgene we've set out to fill this gap by both highlighting that researchers do learn MANY transferable ...the lab and by offering advice on areas where you might need some help. Today in our transferable skills...you will have a much better chance of creating a high-performing team - which is every manager’s dream... a weekly basis! The silence and maybe even the slight awkwardness can spur people to speak up. Once aware...

..., and so on and so forth. This also serves as a light technical control - an RQ value of 1.5 means you...quencher to quantify specific amplicons.  Sybr has high background noise, due to the large amount of dsDNA...DNA and the length of the amplicon and it has a higher rate of false positives (Colborn, 2008; Harridan...number of factors will determine which approach is right for your experiment. You’ll have to consider:  ...analysis of copy number variants based on real-time LightCycler PCR. Curr Protoc Hum Genet. 2014;80:7.21.1-7.21...

...chains and two small light chains that stick out to form the “arms” holding the highly variable regions that...membrane proteins that may unfold due to camelid high body temperature (37.2 - 39.2°C). The Seeger lab...References Geertsma ER (2013) FX Cloning: A Versatile High-Throughput Cloning System for Characterization of...resources on the Addgene blog Opto-Nanobodies: Using Light to Manipulate Cell Signaling and Protein Purification...

... vivo CRISPR screens. AAV vectors can be made at high titers equal to those achieved with lentivirus but...less involved setup when working with mice and slightly less red tape for approval processes. Additionally... means you can customize your CRISPR screen to a high degree. This is particularly helpful when investigating...Breakefield, X. O., Maguire, C. A., & György, B. (2019). High levels of AAV vector integration into CRISPR-induced...screening by AAV episome-sequencing (CrAAVe-seq) is a highly scalable cell type-specificin vivoscreening platform...

...using a high-speed ultracentrifuge. During the spin, the virions will form a band due to their high density...nationwide where you can obtain excellent quality, high titer rAAV (including Addgene!), but you can also...terminal repeats (ITR). You should always have a high-quality plasmid standard and rAAV reference material...Zen, Z., Espinoza, Y., Bleu, T., Sommer, J. M., & Wright, J. F. (2004). Infectious titer assay for adeno-associated...

... backbone might be more prone to recombination, while a library with a large backbone might be more difficult...to ensure the highest possible transformation efficiency. Using Stbl4 or other ultra-high efficiency cells...specifically calculated based on the size of and weight of your library plasmids. As long as you achieve...

...cells to grow and divide only at the right times and in the right places. Checks and balances: protecting...proteins naturally lack areas that are accessible, high-affinity binding targets for potential therapeutic...therapeutic agents. Nevertheless, a glimmer of light remains for this elusive target. Recent improvements in ...results and customize the small molecules for a higher affinity fit. Kevan Shokat’s group at the University...

...now, 2 decades later, is it finally back in the limelight. On December 19, 2017 the FDA approved Luxturna... brought all these key elements together at the right time and place. But it is the hard work and persistence...immunogenicity is critical when systemic delivery of high doses of vectors are needed. Additionally, AAVs ...ultra-rare ocular diseases are being benched due to the high cost of clinical development. As a result, Luk Vandenberghe...8. Trapani I and Auricchio A., 2018. Seeing the Light after 25 Years of Retinal Gene Therapy. Trends Mol...

...project she needs one of you to lead. At first you might think, “I’m not a leader,” because you don’t see...you. How is this new opportunity much different? Might you already have leadership skills that are just...and develop your nascent leadership skills. You might just find that you’re more of a leader than you ...External collaborators For further advice on highlighting your transferable skills in that big job interview...

...ancestry groups rather than self-reported race, it highlights the myriad issues researchers need to reflect...associated dependencies across ancestry groups (right).    Seeking an explanation  First, they looked...guides from being designed that target regions with high genomic variability.   Moving forward It took a ...Stephanie M. Fullerton et al. Getting genetic ancestry right for science and society." Science 376, (2022): 250...

...excluding Starbucks. Taking a nerdy perspective, you might denote your search as follows: (my_house + coffee...math illustrated. Intersect (left) and set minus (right). Enhancers are regions of DNA that demonstrate...enhancers, check out the Appendix. Conclusion: Shedding light on dark matter Precise knowledge of which stretches... courtesy of beyondthedish (left) and biobabel (right). People commonly think of DNA as a linear polymer...meters long. You twist and roll the string into a tight ball. Now the two ends of the string, instead of...

... may be just the method needed to jumpstart the fight against antibiotic resistance. Advantages of CRISPR... despite this resistance gene being encoded by a high-copy plasmid. In the case of the genomically encoded...distinct beta-lactam resistance genes, again with very high specificity. This double phage system both favors...bacteria. In mixed populations, their phages were highly specific for certain bacteria, just like the CRISPR...new strategy can help us win back ground in the fight against bacterial superbugs. References 1. Citorik...

... species, Zetsche et al. hypothesized that Cpf1 might represent a functional CRISPR nuclease that could... cleaves relatively far away from the PAM, NHEJ might retain the PAM site. Therefore, if HDR does not ...possibly mediate HDR. This “second chance” mechanism might improve the frequency of desired HDR edits, but ...editing efficiency for the Cpf1 orthologs was only slightly lower than that of the widely used SpCas9 and ...that AsCpf1’s off-target rate is similar to that of high fidelity Cas9s eSpCas9 and SpCas9-HF1. Both AsCpf1...

...has drastically increased, it would have been a tight squeeze for all of us to fit in Joanne’s back yard...discovered my hidden talent in Ladder Ball... there might be a possibility it was just beginner’s luck, but... (only if it’s cool with your legal department) right in your breakroom. 5. Throw some physical activity...you have a very intricate itinerary, there is a higher likelihood that something will go awry. Don’t plan... My grandma used the old adage “many hands make light work” all the time. She was a wise lady for many...

...shielded from quenching by aqueous solvent. This tightly-packed structure explains the importance of the...permutations within each color also exist with only slight variations separating them.  Please note that many... Improves folding at 37C, reduces aggregation at high concentrations T203Y Red-shifts the wavelength...biosensors here. Optogenetics: Scientists can use light to detect, measure, and control molecular signals... blog, you should! He's got great articles and insight on the newest tools and techniques in fluorescent...

... This powerful negative selection system ensures high editing efficiency; the only non-edited cells to...The simpler system of pCRISPomyces-2 displays a higher editing efficiency, perhaps due to its condensed...Streptococcus thermophilus, Cas9sth1 as a robust and highly active enzyme for transcriptional silencing Mycobacterium...efficiency of knockdown and developed new, more tightly controlled, Tet responsive promoters to avoid leaky...dCas9 variant as well. Furthermore, they provide a high-fidelity (HF) variant of the BE3 that further improves.../10.1038/nbt.3011 Cobb RE, Wang Y, Zhao H (2014) High-Efficiency Multiplex Genome Editing of Streptomyces...

...technology has become very popular as a rapid and highly efficient way to move DNA sequences into multiple...two new recombination sites (attL-left- and attR-right-, Figure 1). Under certain conditions, the attL ...’ll walk through an example experiment where we might use Gateway cloning to generate our desired constructs...another, the inserted DNA fragment stays in frame. High efficiency The positive (antibiotic) and negative...M. (1992). A Genetic Switch: Phage (Lambda) and Higher Organisms (Cambridge, MA: Cell Press). Additional...

...three scenarios, but a short treatment regiment might wipe out bacteria that are completely susceptible...concentrations of a drug, but will be killed by a higher concentration, or sometimes more exposure time ... corresponds to the level of susceptibility you might expect if a certain antibiotic were chosen for treatment...survive for millennia. What we can do, however, is fight smarter, not harder. We can utilize tactics like...antimicrobials to learn how scientists are using CRISPR to fight bacteria. From a societal standpoint, we can all...

...Department of Labor’s general guide to the effect on higher education, you can see that those in teaching roles...lot of us, frankly quite surprising. Consortia of higher education institutions submitted letters to the...exemption. Discussions about the drastic effects on higher ed had been seized upon by opponents of the ruling...convincing as the recommendations for postdocs to be on higher salaries (which have been made by multiple organizations...recommendations that postdoc salaries be raised to $50,000 - higher than the level they will be raised to on Dec 1st...

...you can see some of the stats from the AMA to the right - the Reddit community is active, engaged, and has...resources at her disposal, she was writing all day and straight on through her designated two hours for answering... to other scientists who will find it useful, I highly recommend doing an AMA! Before I turn it over to... Kudos to the moderators for keeping the quality high and thus enabling a productive discourse. They even...to resources. I’ve said this before, but I also highly recommend taking every opportunity you get to speak...

...found that the accuracy of ICE analysis results was highly comparable (within r2=0.96) to that of NGS data...coefficient (r) is also computed and reported.  The higher the R2 value, the more confident you can be in ...the Download Analysis Data button on the bottom right of the analysis screen. ICE analysis details Contributions...genomes that contain the indel. The discordance plot (right panel) shows the level of disagreement between the...that continues after the cut site, representing a high level of sequence difference. Traces The Traces...

...SDS-PAGE...Electron microscopy… Any guesses? That's right... ways to titer AAV! The point is there are many...linear region of the standard curve. In addition, high and low-concentration samples can also behave differently... reference sample of known titer, which is at a higher titer than the AAV RSM. By using these samples ...) AAV titers are approximations and they depend highly on the experimental conditions used, titer values...PMID: 10455443. 3. Hindson, Benjamin J., et al. "High-throughput droplet digital PCR system for absolute...

... procedure (Mortensen et al., 2019). Our method might provide some useful guidelines for the development...transformation was successful at all. Once we were on the right track, we switched to luciferases to more easily...simple and easy technique to implement. Success might vary between experimenters. Vacuum infiltration ...especially problematic with reporter genes as you might observe expression from Agrobacterium, but not the...leaf transformations, but we hope that these tips might help to get you started. Once you have established...

...scientists achieve a high titer (reviewed in Joglekar and Sandoval, 2017). This high titer is one of the...your virus, there are many other reasons when you might pseudotype your virus:  Lowering cytotoxicity. ...reaching the target cells. VSV-G is also toxic at high concentrations as described above and is inactivated...vector to be transported retrograde and also has higher neuronal transduction efficiency and a better safety...

... develop and optimize the method termed Specific High Sensitivity Enzymatic Reporter UnLOCKING (SHERLOCK... the promiscuous cleavage and degradation of neighboring ssRNA and ssDNA by Cas13 and Cas12a, respectively... of CRISPR-based diagnostics. SHERLOCK- Specific High Sensitivity Enzymatic Reporter UnLOCKING Cas13 (...SHERLOCKv2 provides a method to detect nucleic acids with high sensitivity and specificity without compromising...the ability to rapidly detect nucleic acids with high selectivity and sensitivity from patient samples...

...change and screen a few hundred clones to find the right one Step 2 – Edit the cells a second time using ...corrects the blocking mutation and again identify the right clone from a few hundred. From these two steps, ... few hundred clones - Still better than 10.000, right? (Kwart, Paquet, et al  2017). Find Additional CRISPR...increasing mutation incorporation efficiency, we might exploit this relationship to direct the zygosity...Additional Resources on the Addgene Blog Learn about High Fidelity Cas9 Variants How to Design Your gRNA Delivering...

...created vectors for Lambda Red that contained one of eight bacterial toxin genes isolated from E. coli or Psuedomonas...both rhamnose- and arabinose-inducible promoters. Tight control of toxin expression is absolutely necessary...induction system is well-characterized and quite tight (Giacalone et al., 2006). The Chen lab demonstrated... selected the three toxins so that at least one might be useful in a broad array of pathogenic Proteobacteria...expression in Escherichia coli using a rhamnose-based tightly regulated and tunable promoter system." Biotechniques...

... a great plan to start consistently knocking out high-quality videos for you all. The next day...we got...Everything we had set up involved multiple people in tight locations. Conference rooms for on-screen presenters...raised on an ironing board, giving it the perfect height (Fig. 2). We recorded video using a simple, external...comfortable on camera while thinking about things like lighting, camera angle, and shot composition.  So back ...could transmit a signal between a wall. There was a SLIGHT delay, but I could work with that.  Focus: Next...

...cells. However, for some applications, integration might be considered a double-edged sword with unintended... lentiviral vectors, how they work, and why you might choose them over integrating lentiviral vectors....lentiviral vectors? There are several reasons why you might choose an IDLV over a lentiviral vector: 1. No risk...mind is that titering these IDLVs may require a slightly different protocol than regular lentiviral vectors...Reyon, D., Joung, J. K., & Sander, J. D. (2013). High-frequency off-target mutagenesis induced by CRISPR-Cas...

... cell mixes, like bulk lympho-/splenocytes, you might only be interested in one of the various cell populations...markers of all cell types except CD8+ T cells. We might choose the markers CD4, CD19, and CD11c, which would...rest can be excluded, or “dumped”. From left to right: B cell, CD4+ T cell, dendritic cell, CD8+ T cell...host species reactivity. When sorting cells with a high resolution for specific downstream applications,...immunity. When he's not in the lab, Paul enjoys weight lifting, sailing, and reading.   More resources...

... together on a tight budget. To help popularize our kit resources,  we’re highlighting just a few of ...covering a wide range of fields from Addgene. What you might not know is that Addgene distributes curated collections...Morgan’s blog post on the PUF Assembly Kit for some insights on its potential from its creators. We hope you...

...amount of high-quality DNA, real-time PCR has several advantages including easier automation, higher throughput...method called pyrosequencing. The drive for faster, higher throughput and less expensive sequencing fuels ...commercially available although they are reported to have high error rates (10). It is projected that nanopore-...and research progress. These will bring faster, higher throughput, and potentially more accurate techniques...

...untreated individuals. Symptoms of AIDS include rapid weight loss and an increased risk of infection, including...models, and it’s difficult to tell if one approach might be more successful. “Shock and kill” has the advantage...expression of Cas9/gRNAs, which could result in higher rates of off-target cleavage. In both cases, translating...each of these gRNAs will need to be validated for high on-target binding and low off-target binding. It...stable expression of Cas9/gRNA. Viral production is higher in this model than in latent HIV-1 infection, which...

...the perfect empty backbone, made sure to add the right tags to your gene, and may have even put a fluorescent...are marketed for a specific purpose: fast growth, high-throughput cloning, routine cloning, cloning unstable...  Propagation of ccdB-containing plasmids Hte   High transformation efficiency deoR constitutive expression...synthesis Allows uptake of large plasmids hee   High electroporation efficiency supE44 (glnV44)   Suppression...+)  XL10 Gold Tetracycline and Chloramphenicol High competency cloning and propagation of large plasmids...

...This Depositor Week, we're highlighting eight amazing posts on research done in our depositor labs. Some... Andrew Willoughby introduced us to RUBY-red, a bright red pigment reporter for plants.  Cas7-11 and PASTE...

...community like Watertown to bulk purchase energy from a higher percentage of renewable sources. This program offers...sources and we have chosen to participate at the highest level offered. As a result, we will be drawing ... our electricity from renewable energy projects right here in New England- the majority of which are solar...temperatures, biosafety cabinet ventilation, and lab lighting/HVAC requires a significant energy expenditure...

...Sleigh bells, please! It's time to announce the winners of the 2022 #DeckTheLab contest!  and it's.....in our building. Unfortunately, snow is thawing right now, so today noone could see my (not so) little...                     A post shared by 草方 (@gracie_fang) That’s right, researchers of the world. Cap your Eppendorf tubes...Instagram! Happy decorating, all, and to all a good light!    🤩 our lab in Bayliss Building @SMS_UWA is getting...

...vector pAAV-CAG-RdLight1 AAV9 Biosensor Tian New viral vector pAAV-hSynapsin1-RdLight1 AAV9 Biosensor...lab. Also of interest is the Tian lab's pAAV_hSynapsin_psychLight2 (AAV9), which contains a biosensor that...Biosensor Tian New viral vector pAAV_hSynapsin_psychLight2 AAV9 Biosensor Tian New viral vector pAAV.hSynapsin.SF-iGluSnFR.A184S...

...that infectious wild-type viruses were produced in high-titer retroviral stocks generated by the transfer...In this kind of approach, a population of cells might express only the tTA or your transgene resulting...developed, but these vectors are quite large and you might get lower viral titer when using them.   Regarding.... If you are transducing non-adherent cells you might need to centrifuge your cells with the virus in ...Trouble Shooting Viral Transductions Learn Why You Might Want to Use AAV in Your Research Lentiviral Vector...

...unless the source of culture is irreplaceable or highly expensive). Detecting mycoplasma contamination ...induces a noticeable color change. This method has high sensitivity but low specificity (Degeling, 2012)...required in this process because result interpretation might be difficult. The low density of mycoplasmas, contamination...media as much as possible and the ones that are tightly packed with seals. Use disposable pipettes to avoid...exposure of the cell culture to air and make sure to tighten the flask cap before placing them in the incubators...

...decades of my life following a very straightforward conveyor belt from high school to college to graduate school...Veterans Health Administration, I could never get one straight answer about what science policy even is! In this... “little p” policy.  “Big P” policy is what you might typically think of. It occurs in a government setting... challenging if you are trying to apply for an outright job in a field where you have no specific scientific...

...and four chaperones from Denis-Yarmouth Regional High School visited our labs in Cambridge, MA to learn... Outreach Scientist Jessica Welch showed some highlights of his travels from 2015, including a great European...Website Learn more about Dennis-Yarmouth Regional High School Resources at Addgene  Read more Inside ...

...working with AAV or lentivirus in your research, you might want to use one of our virus backgrounds. Addgene...backgrounds for you as well! If you use FRET, you might be interested in our fluorescent protein background....           Did you get the joke? If not, you might want to check out Addgene’s Fluorescent Proteins...background.     We hope these science backgrounds will brighten up your virtual meetings!  ...