... encode which amino acids (see example to the right). With such simple rules, you might think it’s easy...codons unaccounted for. The result is redundancy; multiple codons encode single amino acids. Evolutionary...varied codon preferences among organisms aren’t completely understood, but some possible reasons include...resources for the entire translation process. For example, during high growth rate conditions, E. coli preferentially...encoded by highly abundant, charged tRNAs. For example Tuller et al. found that translation efficiency...translated regions a chance to fold properly. For example Pechmann and Frydman found that tracts of non-optimal...producing and charging specific tRNA pools. For example, tRNAs used in genes encoding amino acid biosynthetic...

...fully summarized in a short blog post, but some examples I’m personally interested in include: intracranial... is an approximation of reward or the sense of pleasure that the animal perceives through taking a drug... also models reinforcement but is considerably simpler than ICSS. The test chamber is divided into two...expression of the early response gene c-fos. For example, using Chr2 stimulation should result in robust...c-fos expression to get the evidence you need. For example, as shown in this study [3], hippocampal neurons...mouse is placed in a novel context. As a proof-of-principle test, the authors were able to show that HR blocked...involved in regulating the behavioral output. For example, if you are interested in studying a brain region...

...on living as a scientist in Beijing, talking to people about taking beautiful photographs of their studies...Story Telling at work Don’t believe me? Here’s an example of storytelling to answer an informational interview...it worked out for all of us.” This is a classic example of the STAR (Situation, Task, Action, Result) interview...than I’m able to produce. But it’s also a great example of storytelling – you get context, time, cause,... and wide, keep your website up to date, invite people to ask questions, be approachable. Engage with ...technique you have in your arsenal to make sure people pay attention. Highlight your lowest points and...into a scientific story, but it will ensure that people pay attention. Practice Nobody gets good overnight...

...will not affect single-plexed experiments, it needs to be addressed when multiplexing. It is imperative that...cannot be indirectly probed simultaneously on the sample. What to do?  If you’ve ever found yourself facing...the constant regions from an alternative isotype (purple, mouse). Depending on the cloning process, all ...conversion, gives users the flexibility needed for multiplexing. In the case above, you can’t costain with your...visualize both targets in parallel (Fig. 2). For example, if both of your antibodies are rat IgG1, then ...antibodies with the same isotype can not be used for multiplexed indirect staining methods since the secondary...the new Fc region. In addition to increasing multiplexing capabilities this process is frequently used...

.... HDR is crucial for certain applications, for example, correcting the allele that causes sickle cell ...decision. Our conclusions reinforce a key scientific principle: that understanding a biological process in detail...manipulate that process. We began our research with a simple question: how do Cas9 and sgRNA interact with and...tightly to three of the four strands of the cleaved duplex, while the fourth strand (the released strand in... in Figure 1 below) was free to anneal to complementary ssDNA molecules in vitro. Figure 1: Cas9...Cas9 binding to the cleaved DNA duplex. Image from Richardson et al., 2016. We next wondered if we ...discovered that single stranded donor DNA: Complementary to the released strand, 127bp in length, With...

...that need people who are data oriented, scientifically minded, and able to communicate complex information...research and potential solutions During the first couple of sessions of the symposium it was clear that,...postdocs. Unfortunately, even when universities have simple postdoc numbers sorted out there can be gaps in...Postdoc: An Institutional Perspective. This lack of complete information does not, however, prevent us from...these positions are available and that many of the people who work in them are incredibly happy with their...need to be able to network and interact more with people who have taken a variety of career paths and should...collaborators, others you know in the field, and even people who aren’t in the field. One PI on the panel even...

...remedy this, throughout the year we rolled out multiple changes to our website, including the recent homepage... new website search. Tackling findability from multiple angles    We assembled a cross-team team, with...interface.   The team approached the issue from multiple angles: the overall user experience of our website...website navigation paths, the organization and completeness of our information, and the accuracy and relevance...relevant to a specific query and category. For example, a search scoped to plasmids shows filters for ...appear in our data into a single filter value. For example, there is only one viral prep filter for promoter..., human synapsin, hSynap. Matching We capture multiple variations of the same information in our search...

...degradation with dTAG-13. Example experiments See our recent papers noted below for examples of dose-responses... pharmacological inhibitors including rapidly depleting a protein-of-interest, increasing target selectivity...FKBP12F36V-tagged proteins. The dTAG molecule induces ternary complex formation between the FKBP12F36V-fusion and the...happy to share aliquots of dTAG-13 in the meantime, please address your requests for dTAG molecules and any...parental cells (or cells expressing a control -- for example, an FKBP12F36V-tagged LACZ) with dTAG molecules...5 in Nabet et al., Nature Chemical Biology for examples). Monitor neo-substrates Small molecule degraders...neo-substrates varies in different contexts (for example, IZKF1 and IZKF3 are cell-type specific transcription...

...resources of a cell. The objective is to give people the complete toolbox for taking on very large genetic ... do as genetic circuits become larger and more complex? Voigt: If you look at all the products of biology... on genes at different times. It requires more complex synthetic networks. Addgene: What hurdles did you...overcome and what hurdles remain? Voigt: There are a couple of hurdles we haven’t yet overcome. For this particular...CRISPR chemistry for a NOR gate. But there are a couple of problems. You couldn’t do it without repeating...first one worked in each case. Sometimes in CRISPR people talk about off-target interactions. That’s relevant.... There haven’t been enough genetic parts for complexity. We have characterized almost 600 terminators...

...reducing editing from ~30% in control samples to 0-10% in Acr samples. Acr proteins can also be used to prevent...assembly of the crRNA-Cas complex (Zhu et al., 2019). Inhibiting DNA cleavage Example: AcrIIC1 binds to the...protein while others can inhibit CRISPR enzymes from multiple species of bacteria.  A note on anti-CRISPR nomenclature... of discovery (Bondy-Denomy et al., 2018). For example, AcrIIA4 mentioned above indicates that it’s the...activity one of three ways: Inhibit DNA binding Example:  AcrIIA4 blocks Cas9’s interaction with the PAM...site (Harrington et al., 2017). Inhibit crRNA loadingExample: AcrIIC2 interactions with Cas9 interferes ...and spatial control of CRISPR-Cas activity. For example, fusing AcrA4II to the photo-sensitive LOV2 domain...

...Plasmid Kit Multiple Lentiviral Expression System Kit (Kit #1000000060) The MuLE (Multiple Lentiviral ...several different viral vectors to choose from, for example gamma-retrovirus, lentivirus, Adenovirus, and Adeno-associated...and lentiviral envelope plasmids are listed here. Please note that both lentiviruses and gamma-retroviruses...combined with high-throughput sequencing to perform multiplexed analysis of cells pre-treated with a compound...Transfer Vectors    Expressing your gene of interest pLenti-puro (Plasmid #39481) You can clone your gene ...We are constantly improving our CRISPR reagents. Please check www.genome-engineering.org for the most up-to-date...system facilitates the simultaneous introduction of multiple genetic alterations into mammalian cells. The ...

...predecessors. Changes were implemented and I had to adapt accordingly. For example, the quarterly and annual...annual NPA meeting to learn more. Having met many people at that conference, I later became involved with...volunteered for various tasks as things came up. For example, I updated some sections of the NPA’s website. ...volunteering, you can gain experience working with other people mostly online and on monthly phone calls. This ...distance communication and learning to work with people despite the distance improved my verbal and written...understand how to work with many different types of people both above and below you. During my time at the...NPA. You must accommodate many different types of people in order to harness their strengths and work effectively...

...are often thought of as simple organisms , they have many levels of complexity, especially when trying...about it, the more I realized that it cuts across multiple disciplines, which really epitomizes what the ...learning how to grow and care for the worms. As an example of one of the problems we work collaboratively ...We attempt to deconstruct and understand this complexity using existing C. elegans mutants. For instance...data is freely available, and the collection of samples and sequencing is being organized and funded by...allows the project to be open to a wider group of people. This is a perfect starter project for our computer...Kittybiome project gives them access to rich and complex microbiome data for analysis. And, well, cats.....

...things started. Give a couple of audience members a chance to participate. For example, at a recent event ... Reddit AMA Perhaps we should start with some examples of a bad panel discussion? You know, the one where...interesting stories that will make for a fun discussion. People are much better at remembering these things on ... is tough for women in skirts, especially short people – which I am, so I hate stools). I like it when... with an unexpectedly great turnout). This gets people to sit close to the front so the interactions are...interesting discussion. The audience knows these people and bios were likely part of the publicity. Good...science or expertise by listing some and asking people to raise hands in response. I am always ready with...

...news is there’s a few simple ways to deal with this issue. One way is to grow multiple bacterial cultures...helps me figure out if I have enough plasmid to complete my experiment. AAV is usually the limiting reagent...concentrate the purified virus. This process can be completed in one long day, or the virus can be stored at...aliquots to use for qPCR titering. This helps avoid multiple freeze/thaws of your larger aliquots of virus....particles that are present in an AAV prep. AAV samples are first DNaseI digested to remove any residual...technology or a TaqMan primer/probe set can be used and samples are quantified by comparing to an AAV standard ... plasmid. This whole process takes ~3 hours to complete: 1 hours hands-on time and 2 hours for the qPCR...

...co-expression of multiple unique genes, you can start with a plasmid that has multiple cloning sites flanking...Co-expression of multiple genes is valuable in many experimental settings. To achieve this, scientists...co-transfection of two or more plasmids, the use of multiple or bidirectional promoters, or the creation of... are useful almost anytime you want to express multiple genes in the same cell. Although it is possible...to drive co-expression by using a plasmid with multiple, individual expression cassettes, having the genes...viruses to allow for the efficient translation of multiple genes from a single transcript. The two strategies...20 amino acids) and produce equimolar levels of mulitple genes from the same mRNA. The term "self-cleaving...

...in protein complex studies where tagging of multiple protein products is desired, as multiple selection...cerevisiae and S. pombe. The protocol is surprisingly simple, requiring only a PCR product containing the modifying...for easy capture and detection of proteins and complexes, without the artifacts sometimes associated with...Formosa, at the University of Utah, has built a complete collection of yeast tagging modules with each ... Dr. Formosa has deposited six plasmids with a multiple cloning site in place of the epitope tag for creation...ideal for tandem affinity purification of protein complexes. John Pringle and Jürg Bähler have deposited a... S. cerevisiae, with the additional benefit of multiple selection markers for combining modifications ...

... affected by gene activation rather than depletion. Multiple strategies have been developed to recruit... stranded DNA breaks that commonly result in a complete loss of function while nuclease-deactivated Cas9...and assessed the libraries performance via the depletion of a gold standard set of genes (1,580 essential...effective than other popular CRISPR libraries in the depletion of essential genes. In the subsampling analysis...have several limitations. CRISPRko results in a complete loss of function meaning that if an essential ...libraries utilize an engineered Cas9, which contains multiple point mutations in the nuclease domain. These ...domain such as VP16 to dCas9 or the recruitment of multiple copies of VP16 termed the “Sun Tag” method (Tanenbaum...

...many biological fields. In synthetic biology for example, high-throughput cloning can be used to combine...powerful imaging technologies, the combination of multiple fluorescent protein sequences to develop diverse...one such technique and has been used to produce complex fluorescent reporter constructs. These fluorescent... variety of other clever applications. In one example, modular constructs generated with MXS-chaining...Tubulin Repeatable, directional cloning   The principle behind MXS-chaining is repeatable, restriction-enzyme...individual plasmids and are each flanked by the same multiple cloning site (MCS). Modules are assembled one ...being directional, meaning that (in the previous example) one can control whether the third module is added...

...downregulate multiple genes at once. Read the paper in mBio Find the CRISPRi plasmids A multiplexed gRNA piggyBac...Base editing CRISPRi in Caulobacter crescentus Multiplexed gRNA for human pluripotent stem cells CRISPR-... Blue light renders the NLS accessible and the complex enters the nucleus where dCas9-Mxi1 can repress.... In the dark, the NLS is inaccessible and the complex remains in the cytoplasm. Read the paper in Cellular...differentiation, but it takes several weeks to delete or deplete individual genes. Michael Laub’s lab developed ... deliver uniform and sustained expression of multiplexed gRNAs in human pluripotent stem cells. Previously... construct and the fluorescently-labeled gRNA multiplex. Read the paper in Scientific Reports Find the...