...inputs, such as the file name. We started small with a print statement and tested that the desired data...associated publications, but our quality control (QC) standards have evolved over the years to keep up with the...     Fig. 1: QC'ing data at Addgene is like standing under a Niagara Falls sized rainbow   Over...problems was deciding on the right system for us to start using. Prior experimenting with open source assembly...perform:      Fig. 2: Quick-stepping to a FASTA file   With our outline of individual steps ...Creating a bioinformatics workflow in Nextflow Establishing a complete pipeline however, required more than...libraries such as Pandas, Numpy, and Biopython.  We started at the usual recommended place: documentation. ...

...regulatory elements or use a non-canonical code (Gustafsson et al., 2004), such as Hoogsten base pairs and...could affect protein conformation, folding and stability, change post-translational modification sites ...actually be necessary for proper protein folding (Stadler and Fire, 2011). Therefore, codon optimization ...translation initiation (Dresios et al., 2006) and mRNA stability (Hausser et al., 2013) to name a few. This could... you may want to codon optimize before you get started. There are a ton of online resources available ...Biol 13:30–34 . https://doi.org/10.1038/nsmb1031 Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias...tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Research 28:292...

.... I started watching the questions and preparing answers early in the day. Although I didn’t start answering...people or discussing science, it is a great way to establish yourself as a thought leader and have real conversations...Software for Biology) on Reddit and got some substantial traffic that we thought it would be a good idea...definitely glad we did - you can see some of the stats from the AMA to the right - the Reddit community...description of our AMA and Joanne’s preferred time to start answering questions. r/Science has pretty strict...was posted at 8:00 am and Joanne didn’t have to start answering until 5 pm). The ability to see the questions...Fortunately, Reddit Science is heavily moderated. I started watching the questions and comments go up early...

...experiments and understand their data. Likewise, we want to contribute to helping others understand ours. Improving.... The PLOS policy on data access is a formal statement that is already practiced or required by many ... errors in assumptions, use of inappropriate statistical methods, omission of some data, etc.  The firestorm...published, this data is usually condensed into a statistically evaluated set of values.  However, to evaluate...sharable form is indeed a significant effort. Our standards of data recording are highly variable and usually... images are said to be representative or the statistical variation is calculated and placed in the legend...are used to publications presenting a polished, standard and usually limited view of data. In addition ...

...with physical map distances of 75 and 2 Mbp, with the calculated fluorescent distances correlating with...organization of the nucleus in space and time, and to understanding how nuclear organization varies across the life..., or how organization may be altered in disease states. dCas9 gets a colorful makeover Even without its...with the previously established physical map. In comparing pairs of targets ~2 Mbp apart, they noticed that...degree of chromatin compaction even for this small distance! To the authors’ knowledge, this work represents...applications Ma et al. developed this technique using standard fluorescence microscopy, and are thus limited ...priority, as researchers work to increase our understanding of chromatin organization. This fluorescent ...

...various stages in their careers to get advice on choosing a lab, picking your research topic, starting a lab... hard work, collaboration, and staying honest with personal goals. Stay tuned for the follow up blogs ... lab, and more. Before we start, we'd like to extend a special thank you to Dr. Tom Ellis (Imperial College...with full force. George Church 1. “Initial and sustained motivation is a huge component of success.” 2... "Choosing Your Research Project," “Advice for Starting Your Lab,” “Fun in the Lab!" and more.   Acknowledgments...Choosing a Research Project Advice for Scientists Starting a Lab ...

... on the variable domain and not so much on the constant, or Fc, domain. Sure, we all know that the Fc ... immune system's classical complement pathway, starting a cascade of events that results in the pores ...phagocytosis (ADCP) So far, our antibodies have induced “stabbing” and “poisoning,” but let’s be honest, the elimination... functions and all that antibodies can do! For instance, some Fc receptors, once bound to an antibody,...Fc receptors are intriguing from a therapeutic standpoint. Engineered monoclonal antibodies that can drive... and resources References Clynes RA, Towers TL, Presta LG, Ravetch JV. Inhibitory Fc receptors modulate... Greenspan, N. S., & Casadevall, A. (2016). Ig Constant Region Effects on Variable Region Structure and...

...bluntly with WT Cas9 and one gRNA, you can create a staggered cut using a Cas9 nickase and two gRNAs.  For ...test nickase preferences using HEK293 cells. They started by comparing D10A and H840A total editing efficiency...PAM-in and PAM-out configurations with varied nick distances (40 - 130 nt). From these results, it’s clear ...than that of H840A, especially with smaller nick distances. Using D10A, they subsequently showed that editing...low when the gRNAs are too close (7-23 nt nick distance). Both D10A and H840A are potent editors, but ...obtain high HDR efficiency. Nickases create a staggered cut - could this system mediate repair throughout...the target site rather than the optimal <10 nt distance. Employing two gRNA sites that are further away...

...named NeuroStack was used (Orguc et al., 2020). Using a programmable microcontroller, NeuroStack coordinates...admittedly for self-serving reasons – I want to understand my obsession with the combination of chocolate...connection to study on a molecular level. The brain is constantly influenced by signals it receives from the entire...digestion of food, while brain tissue is relatively static). To operate both types of implanted fibers simultaneously...stimulation in target tissues of a live animal. They started by delivering an AAV construct expressing channelrhodopsin...tissue. They performed optical stimulation using NeuroStack and the fibers as previously described, then ...implantation of fibers, indicating the system was indeed stable for continuous monitoring. On the gut side of things...

... are a few out-of-the-box ideas that might jump start your learning. 1. Create a peer mentoring group ... career and life goals. For tips on how to get started see Form Your Own Peer Mentoring Group: A How-To...for the live audiences in your future.     3. Start something In almost every career talk I present,...charge before others do”. Candidates who have “started something” which they can share on their resumes... of things: led a grad or postdoc association, started a speaker series or biotech club, managed their...ukelele...perhaps you get the idea. What will you start? 4. Do informational interviews (on a schedule) ...you can’t wait until you imminently need a job. Start now. Informational interviews are 1:1 discussions...

... MIT's Ed Boyden explains it, his goal is "to understand the brain at a level of abstraction that enables...Once scientists can do that, they will not only understand how the brain works, but also how to fix it when...then alongside blue they actually have a lot of crosstalk. So we developed a red molecule. We also had to... use dim blue light and red light together. Understanding the brain through optogenetics research Addgene...areas of benefit: First, there is fundamental understanding of the brain, which has humanistic and philosophical...region, the animals became aggressive. If we can understand the neural basis of violence or aggression, it... neuroscience has so many different goals: to understand how a mouse changes emotions, to see how a monkey...

...This system ablates tumors just as effectively as standard CAR-T cells, but it reduces the off-target effects...expression (or the eGFP proxy for CAR) is elevated at stable levels for 6 days - after just 15 minutes of FUS...PMCID: PMC6377228. Hyperfolder YFP- a chemically stable tool for microscopy by: Susanna Stroik Microscopy...these applications have lagged. Fixation, chemical staining, and light exposure can negatively affect FPs ...hfYFP is not only brilliantly bright, but it also withstands denaturing conditions, high temperatures, and...fluorescence resilience to these preparations. After crystalizing the hfYFP structure, the group rationally designed...similar capabilities. If you’re looking for a super stable FP for your next microscopy experiment, consider...

...easily started and easily credited. And nothing stops these one-time favors from becoming starting points... rewarding way of making science.   How we started Crowdfight-COVID19 Crowdfight was born as a collaborative... all over the world had signed up, and soon we started receiving dozens of requests every day.    ...suitability and availability; 3) Make the contact to start a direct collaboration between researcher and expert...are undergraduates or PhD students who are just starting their journey into science. Others are experienced...Crowdfight is also open to other topics.  In this new stage of the project we are focusing on what we call “...-and-error. A recommendation for the correct statistical test can save a retraction. Today, collaborations...

...causes instability: CoIE1 encodes a determinant essential for plasmid monomerization and stability. Cell...Multimeric plasmids are also considered to be less stable and more prone to being lost in bacterial cells... of multimer present in your sample. In these instances, please note that the supercoiled dimer band can...1981). E. coli strains such as DH5α, HB101, NEB Stable, Stbl3, etc., are recA- mutant strains, and therefore...the transformed bacterial culture into the late stationary phase. Growing the culture at a lower temperature...R, Walther W, Michel ML, Schmeer M. Long-term stability study and topology analysis of plasmid DNA by ...direction are the secrets of multicopy plasmid stability. Mol Microbiol. 1998 Sep;29(5):1137-45. doi: 10.1046...

... “You seriously didn’t add 3 microliters of 5 mM star anise?” This is something I was expecting when I...chicory root, but considering this is a needle in a haystack type of objective, it was surprisingly easy. It...particular experiments, we generated A549 cells stably expressing Cas9 via transduction with Cas9 lentiviral...with too many Cas9 integrations per cell, and my stable cell pool had wildly variable Cas9 expression (...59702-LV) was used to assay Cas9 activity in my stable A549 cell pools. Using this virus, it’s expected...introduce the gRNA, but I just randomly chose one of my stable pools. Viruses containing BRAF gRNA (BRDN0000561167...(80034-LV) were individually used to transduced stable pools of Cas9-A549 cells at an MOI of 0.3, as recommended...

... beneath it. You can jump to the different time stamps in the description to watch any sections you’re...watching the whole livestream for a more holistic understand of reproducibility issues and their potential...limits of knowledge as they develop new ways of understanding how the body works, generating new therapeutics...have intricacies that aren’t always mentioned in static written protocols. It is therefore a bit ridiculous...reproducibility is making sure that others can understand your analyses and repeat them. Companies like...initial hypothesis through validation are easier to understand. The need for great stories has, however, made...experiments with too few replicates leading to suspect statistical significance (you can read more about this problem...

...lab members stay around? Is it too long or do they leave prematurely? Do lab alumni stay in the same ...why not? It may not be a bad thing if the lab has stayed that size on purpose, but it could also be a sign...is workplace bullying? Threats to professional status – including belittling opinions, public professional...discipline or competence procedures Threats to personal standing – including undermining personal integrity, destructive...impossible deadlines, unnecessary disruptions Destabilization – including failure to acknowledge good work... observe grant writing? Get equipment quotes? Understand administrative responsibilities? Is the work ...on more than one project at a time or over their stay in the lab? Do all lab members attend scientific...

... our scientific support staff receives – in fact, the blog originally started as a way to easily store...Thus, we are constantly updating our content to reflect the newest breakthroughs and standards. It’s always... be surprised to learn that Addgene’s mission statement extends beyond plasmids, AAVs, and antibodies ...in the spring of 2022. The first step was to understand information our guide needed to have. Through...someone new to antibodies might need to successfully start using them at the bench, along with questions we...Making content is an iterative process. We are constantly reviewing the resources we currently offer to...

...repeating your work or making similar mistakes in the future. Stay organized Set up a table of contents...computer at the command line, and so was really starting from the beginning. Luckily, a fellow graduate...that it is helpful to those of you just getting started. The practices suggested here may seem tedious ... the analyses: Goal: Before you begin, briefly state the goal of the analysis, including background on... you to perform this analysis. Having a clearly stated, specific goal for each analysis will help you ...computer and is just another name for a folder. For instance, your Desktop directory contains the folders and...code does are very useful for those that are just starting out, and helps clarify the role of the code. ...

... microorganisms, yeast have both a stable haploid and diploid state which is useful for genetic analysis...will catch you up on the core replication and resistance features of yeast vectors and explain how they...the yeast chromosome; however, they tend to be unstable and may be lost during budding. Yeast Centromere...single copy. Unlike the ARS vectors, CEN vectors are stable without integration. Yeast Episomal plasmids (YEp...natural yeast plasmid) allows for 50+ copies to stably propogate per cell. The copy number of these vectors..., due to high rates of spontaneously occuring resistant mutants and the insensitivity of yeast strains...auxotrophic markers. The MX series of antibiotic resistance cassettes is most commonly employed, with the...