... the materials in our catalog are very well-characterized. During this time, we’ve also created a variety...this, throughout the year we rolled out multiple changes to our website, including the recent homepage and... a look at the least visible part behind these changes: the backend technology that powers the new website...granularly customize the search engine, and a scoping mechanism that allows category-specific, narrow searches...among others. We also created a normalization mechanism to “collapse” variations and synonyms of the same...

...designed by the Toettcher Lab, OptoNBs are photoswitchable engineered nanobodies whose binding of their...small (~15 kDa), single monomeric variable heavy chain antibody domain.  How do these components interact... Sons of Sevenless (SOS), a guanine nucleotide exchange factor that activates Ras. They expressed this...message reaches the nucleus where gene expression changes lead to cell proliferation and differentiation....Optogenetic control of protein binding using light-switchable nanobodies." BioRxiv (2019): 739201.  Additional...

...results. GBEs seemed to follow the same initial mechanism as in mammalian cells — by excising the freshly... A's, producing C → A edits. Figure 3: Mechanism of cytosine transversion editors. Red arrows indicate...agreed on the first part of the likely editing mechanism: cytidine deaminase converts C to U, and UNG excises... Base Editing terms   Base transition Base changes between purines (A ↔ G) or between pyrimidines ...pyrimidines (C ↔ T).   Base transversion  Base changes from purine (A or G) to pyrimidine (C or T) or vice-versa...Glycosylase base editors enable C-to-A and C-to-G base changes. Nature Biotechnology, 39(1), 35–40. https://doi.org...

...viruses yield dsRNA through a slightly different mechanism thought to be associated with bidirectional transcription...knew about all the diverse in vitro production mechanisms. siRNA, also known as RNAi, are short, dsRNA ...and dysfunction, it is unclear what the precise mechanism behind the production of these dsRNAs is. A major...response. However, if dsRNA sensors are mutated or mechanisms which suppress endogenous dsRNA formation are...levels, possibly due to dysregulation of removal mechanisms, an array of diseases can result (Fanconi Anemia...

...from a camelid antibody lacking a light chain, called a heavy chain antibody (Muyldermans S., 2013). They...antibody: An ~150kD protein with both light and heavy chains made by immune systems. But here, we're not interested... or less immunogenic version is needed.  Single-chain fragment variables (scFvs) are ~27kD engineered ...They are comprised of the variable heavy and light chain regions, connected by a short linker peptide. The...

...matter of applying that framework to the myriad challenges we encounter. As you spend time in a lab learning...protocol modifications, and ultimately decided on the changes to implement. As with any skill, there will always...yourself if you missed any important details. Or challenge yourself to think of more creative solutions. ... know-how and more about how you approach new challenges.     Know your strengths! Research experience...employer that you are well equipped to work through challenges from day one in your new position. Of course,...

... in D.C. for a few years, Susan was ready for a change of scenery. She moved to Seattle and continued ...to articles for the Fred Hutch website, social channels and Hutch magazine. Getting pulled in all of these...finding that uninterrupted time to be creative is challenging,” says Susan.  Another difficulty is that some... scientist or someone who’s affected by climate change or affected by a superbug. I think we solve these...you enjoyed this series, subscribe to the Career Channel of the blog so you don’t miss out on future career...

...go ahead with raises. What will these further changes mean? The abrupt reversal in salary raises at institutions...Continuing efforts to gather information and expedite change We are continuing to update our FLSA and Postdocs..., under “How institutional plans have/have not changed since the injunction”. Postdocs around the country...enterprise and promote their voices in driving changes in science. Follow him on Twitter @BiophysicalFrog...the Addgene Blog Read Gary's Previous Article: Changing Labor Laws Bring Increased Postdoc Wages Read ...

...Sauermann, Henry, and Michael Roach. "Science PhD career preferences: levels, changes, and advisor encouragement...would be the effects, positive and negative, of changing the workforce structure? Helping to answer some... the following panel members: Jonathan Dinman, Chair of the Cell Biology and Molecular Genetics Department...collects data on the careers of science PhDs. Michael Teitelbaum is a Senior Research Associate at the...

...person in the group for your needs. Beth Schachter of Beth Schachter Consulting is part of that group and ...are for the coaching relationship. Do you want to change jobs? Grow your professional presence? Learn a ...and make direct suggestions for improvement and change. Work with the coach to define how you will know... Polk of From PhD to Life. She runs great tweet chats, has an outstanding blog and, while her PhD is in...

...and has provided clues to their previously uncharacterized cellular roles. In the current phase of NURSA... expression and reporter plasmids and the free exchange of these vectors between laboratories. The development...example, was a key development in the functional characterization of NRs and coregulators, and although the ...Bert O’Malley, M.D., is Tom Thompson Professor and Chair of the Department of Molecular and Cellular Biology...Nuclear Receptor Signaling.   Further Reading: Chawla, A., Repa, J. J., Evans, R. M.and Mangelsdorf, ...

...base-to-base conversion in principle, but some changes require multiple steps and enzymes. Prime editing...can encode any of the 12 possible base-to-base changes in a single edit. Prime editing is also more precise...breaks has been widely used to generate precise changes. However, the efficiency of Cas9 cleavage is relatively....2021.09.018 Choi, J., Chen, W., Suiter, C. C., Lee, C., Chardon, F. M., Yang, W., Leith, A., Daza, R. M., Martin...J., Pierce, S. E., Tolar, J., Meissner, T. B., Chaikof, E. L., Osborn, M. J., & Liu, D. R. (2024). Efficient... L., Schmidt, R., Solley, S. C., Gilbert, L. A., Chan, M. M., Bauer, D. E., Marson, A., Parsons, L. R....

...insertion, inversion, translocation or cassette exchange. By utilizing recombinases to manipulate genomes...Optogenetic tools use light to induce conformational changes in a protein.    Cells expressing an RFP...crRNA-guided DNA cutting, unlike other well-characterized Cas enzymes, which rely on multiple active sites...AAV-flex-taCasp3-TEVp here The red-shifted channelrhodopsin (C1V1) targeting parvalbumin cortical interneurons...use viral prep in serotype AAV5.  Get the channelrhodopsin here Astrocyte specific tight affinity glutamate...

...work,” she said. “School will always be there.” Changing your path! It’s okay! Our blog writer, Beth Kenkel...research and technical assistant, when her life changed––she had a daughter. Needing a career switch because...thought, ‘Let me pursue this, let me make a slight change so I can have flexibility and be up to date with...Bioinformatics it is.’” Though she misses the bench, the change gave her the balance she needed. It is incredibly...incredibly helpful to me to know that you can make big changes in your career path and still find comfort and ...

...conformational change that placesTagRFP-T and Dronpa in close proximity. By monitoring changes in TagRFP-T... to blue light, CRY2 undergoes a conformational change that permits it to bind to the CIB1 (cryptochrome-interacting...optogenetic system (OptoSTIM1), caused two-fold faster changes in intracellular Ca2+ levels than the original ...techniques for live-cell imaging of the dynamic changes in biochemical activity within the cell. Their ...

...with characterized behaviors are available from Addgene and other sources; second, characterizing a part...strangers to cloning. If you’re reading this, then chances are you have been in the cloning trenches yourself...specific functions. Most individual parts have characterized activities with predictable behaviors. While...part in different contexts and plug different characterized parts into a TU! What is modular cloning useful...

...synaptic connections and physiology is particularly challenging as they are great in number, generally very small...’s native locus, but introducing large genetic changes in C. elegans with CRISPR can be difficult since...her colleagues at Yale University fused a color-changing fluorescent timer (FT) protein to the histone ...synthesis and, after a few hours, a conformational change causes the protein to fluoresce red. H2B-FT-red...a Cre-dependent, soma-targeting inhibitory channelrhodopsin. It’s now available as AAV5. Find the AAV...

...Although FPs have enabled discovery of many cellular mechanisms, there are some limitations to working with FPs...the tag for each insertion. Also, it remains challenging to screen for the genetically modified strains...SpyTag). The Foerstemann lab developed a polymerase chain reaction (PCR)-based system that allows users to...can be modified to assay additional protein characteristics. For example, Masato Kanemaki's lab has developed...base-specific gene tagging using a ligase-4-dependent mechanism.” Nat Commun. 7 (2016):12338. PubMed PMID: 27465542...

...again to science.   Acknowledgements Chan Zuckerberg Initiative Chan Zuckerberg Biohub Manuel Leonetti Ryan...contributed by Greg Dingle, a software engineer with the Chan Zuckerberg Initiative. We hereby announce the general... us your questions or comments to gdingle@chanzuckerberg.com. We're eager to hear your thoughts. Many...Dingle! Greg Dingle is a software engineer with the Chan Zuckerberg Initiative, working on assignment at ...

...promising therapeutic tools. The two unique characteristics that define stem cells are: Their ability...disadvantages. Here is a table listing some of them: Characteristic ESC ASC Self-renewal High Low once isolated...Embryos are destroyed during ESC isolation. Low Chances of post-transplantation rejection when used therapeutically...patient’s adult cells when used therapeutically, the chances of post-transplantation rejection are low. Further...Central PMCID: PMC2752493. 4. Bongso, A. and M. Richards, History and perspective of stem cell research...

... plasmid via sequencing or restriction digest. Chances are, you’ll even have DNA left over for other applications... the culture medium. Improve the culture media Changing to a richer media or adding supplements can improve... low copy plasmids or slower growing strains, a change in media may be advantageous. Reduce the antibiotic...oxygen for optimal growth, as insufficient gas exchange will prevent your cultures from reaching the desired...shaker speed is fast enough for sufficient gas exchange in the overnight culture. Generally, large cultures...

...conformational change to bring two FPs on a single protein closer together or further apart. Changes in distance...dimers can form in the absence of environmental changes that the biosensor is designed to detect resulting...reporters for your studies and greatly lower your chances of finding artifactual results. Many thanks to...14581454. PubMed Central PMCID: PMC2173526. 2. Zacharias, D.A., et al., Partitioning of lipid-modified ...

...enable plant science in general. We are funded by a charity and since we are making all the tools for plant...fluorescent proteins. Visualizing fluorescence can be challenging in plants because of the auto-fluorescence of...U.K. organization called Athena SWAN that is a charter for advancing women in science. Universities sign... been a lot of engagement with the Athena SWAN Charter and it has really strengthened the network of female...tell them to work in plant science. I think their chances of doing something amazing will be equally high...

...you select? In this blog, we’ll break down the mechanism of action of the most common antibiotic resistance...presence of an antibiotic resistance gene is a mechanism to culture only bacteria which have retained a...carb and amp, due to their common degradation mechanism. How to choose between the two? Carb is generally... colonies are an issue. Pros: Very stable, interchangeable with Amp, timesaving for transformations. Con...similar relationship as amp and carb (they are interchangeable). Like carb, spectinomycin is the more stable...

...that you will contribute openness, clarity, approachability, and professionalism to team meetings and projects...yourself  standing in front of a crowd and using your charisma to give people hope for some shiny vision on the... you’re more of a leader than you thought! When change happens at your organization, when your boss needs...presents itself even outside of work, consider challenging yourself, take the opportunity, and discover ...to manage these responsibilities. If you are in charge of completing many meticulous protocols or tasks...

...plants produce lots of seeds. More seeds mean more chances to recover a transformant. Use young plants: If...flowers to Agrobacterium. More seeds mean more chances to recover a transformant. Use lots of plants: ...per construct I transform. More seeds mean more chances to recover a transformant. Remove mature siliques...Agrobacterium all over your gloves, so be sure to change gloves between constructs if you are transforming...This won’t hurt them, and it will increase the chances of tDNA integration. Selecting Arabidopsis transformants...

...may provide a method for doing just that. While challenges remain in the delivery of these agents, CRISPR...resistance using multiple approaches. Major restaurant chains including Chipotle and Panera Bread have pledged...remain to help recolonize the niche, reducing the chance of an opportunistic infection like for organisms...quinolone resistance, mediated by a single base pair change in DNA gyrase, CRISPR phagemids were cytotoxic .... PubMed Central: PMCID: PMC4317352. 3. Beisel, Chase L., Ahmed A. Gomaa, and Rodolphe Barrangou. “A CRISPR...

...coordinating the annual Math & Science Night, a chance for parents and other members of the community ...district that has a lot of parents in STEM careers, chances are they’re wondering how they could contribute...etc. Though I talked about CRISPR’s molecular mechanism, I was careful to keep it relatively simple. I... key concepts (Fig. 2). One thing I will likely change for next time is giving fewer examples and think...much in the making. One of the exciting, and challenging, aspects of talking to 8th graders was the broad...

...developing novel technologies to analyze molecular mechanisms of genome functions such as epigenetic regulation...epigenetic regulation. To elucidate molecular mechanisms of regulation of genome functions, we need to...will markedly accelerate research of regulation mechanisms of genome functions in the hope of developing... which is very disappointing. I hope I can help change the situation in the future. Addgene: What advice... they may be able to achieve something that may change the rules of the game. In this regard, I believe...

... Protocol Exchange Website: http://www.nature.com/protocolexchange/ Nature Protocol Exchange (NPE) is ...your favorite protocols for future reference. The exchange currently boasts over 2,500 protocols covering...life science labs and offers the service free of charge to scientists by allowing companies to pay publish...

...buy that charming fixer-upper house you have always admired or volunteer to lead a charitable cause.  ... your work. Nobody wins, and you need to make a change. #2 Thou shalt sometimes put work ahead of life... spouse won’t be at every school performance, chaperone every field trip or cheer at every soccer game...your plan to live a good life may be the most challenging assay you will ever have the opportunity to develop...

...and Discovery As part of their quest to find, characterize, and develop new CRISPR systems and technologies...proteins that could cut RNA or DNA via a CRISPR mechanism. The weird black pellet's DNA yielded a new CRISPR...Prime editing — the ability to now make any small changes, including base edits, insertions, and deletions...right integrase for this new approach proved a challenge. The old standby of CRE/flp didn’t work – it turns...be independent of gene repair.) This lowers the chance of the insert being “dropped” in the wrong place...

...Addgene’s YouTube channel.   Figure 4: Global viewership of the Addgene YouTube channel, 2023. Views from...protocols. In 2013, we launched the Addgene YouTube channel to add a strong visual component to our educational...is achieved through interconnected incremental changes. It was only after creating a plasmid repository...learned about the importance of smaller, systemic changes, like using alt-text, captions, and inclusive design...

...When you think of Addgene, chances are software development is not one of the things that comes to mind...the flexibility to adapt and easily respond to changing needs of the teams at Addgene. Another advantage...to bake a cake. Instead, you go to a store and purchase flour. However, buying a bag of flour is not the...updated in several years) or they make significant changes that make it incompatible with our software. When...Python 2.7 to Python 3.5. There are significant changes to the language and it took us a total of two years...

...methods measure different characteristics of the solution. These characteristics give us information on ...temperature parameters. For example, we found that changing the annealing temperature of the PCR from 60° ...al. "Systemic errors in quantitative polymerase chain reaction titration of self-complementary adeno-associated...PMCID: PMC3216358. 4. Lock, Martin, et al. "Characterization of a recombinant adeno-associated virus type...

...better prepare for your career, and increase your chances of landing that next coveted job! Professional...development (or lack thereof) One of the biggest challenges facing students today is that many graduate and...your credentials to HR, greatly increasing your chances of getting a phone interview! If you don’t have...touch and reach back out when you are looking to change positions in the future. Anyone looking for work... Michael G. Lemieux...

...inverted vectors expressing light inducible ion channels (plasmid # 20298 for example) have revolutionized...FLEx vectors expressing the light activatable ion channel under the control of Cre recombinase are used in... M. Sternson. 2008. “A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-Range...Sadowski. 1985. “The FLP Recombinase of the Saccharomyces Cerevisiae 2 Micron Plasmid Attaches Covalently...PMC41617. 7. Metzger, D, J Clifford, H Chiba, and P Chambon. 1995. “Conditional Site-Specific Recombination...

...Enzymatic Domains Guide RNA Target PAM (PFS) Cleavage Mechanism Cas9 HNH, RuvC TracrRNA, crRNA DNA 5' NGG... Leptotrichia shahii (LshCas13a) to begin to characterize this new effector (Abudayyeh et al., 2016). ...and cleavage through a series of conformational changes in the Cas13a molecule. Like Cas9, Cas13a tolerates... plant cells (Abudayyeh et al., 2017). They characterized Cas13a from Leptotrichia wadei (LwaCas13a), ..., Sergey, et al. "Discovery and functional characterization of diverse class 2 CRISPR-Cas systems." Molecular...

...counter-intuitive, but I find office work more mentally challenging than lab work at times.” Sometimes a desk job...experience will be a little different. Some of these changes you may enjoy immediately and some of them may ... just take some getting used to. Just remember: change is good. You can experience a real onboarding...to non-scientists can be a fun and gratifying challenge. You’re also getting the opportunity to learn ...eventually. If you approach that transition dreading the change, the adjustment period will be that much longer...

...Resistance can be intrinsic, meaning a basic characteristic that naturally occurs in the bacterium, and...another bacterium died for instance). These three mechanisms of acquired drug resistance are referred to as...competition drives microbes to develop survival mechanisms. Some microbes even make their own antibiotic...killed), thus increasing the initial microbe’s chances of survival. This was the whole basis of how penicillin...targets (ones that are less likely to mutate or change in order for the bacterium to survive). Check out...