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TypeBlog Post...The second Boston Symposium on the Future of Research will be held from 22-24 October. This blog has ... successful and sustainable biomedical research sector at our first Future of Research symposium. The ...the overall structure of the biomedical research sector, and what a tenable workforce structure may look...ideal and productive workforce look like for the sector – how many jobs are there for STEM graduates and...interested in communicating science and in the intersection between science and public policy. Follow David...
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CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics
TypeBlog Post...how the notation works? The + operator denotes intersection and the – operator denotes set difference. That...math. Figure 1: Genome math illustrated. Intersect (left) and set minus (right). Enhancers are...mono_methylation + acetylation) - tri_methylation In the next section we’ll apply the above formula to a real-world experiment...about clinical applications of CRISPR in the next section. In order to denote the NANOG enhancers from step...proteins called histones. Chromatin folds into secondary structures (loops) and tertiary structures (globules... -
28 Hot Plasmid Technologies from 2015
TypeBlog Post...Synchronization of secretory protein traffic in mammalian cells The journey of secretory proteins, from their...Cell Structure Plasmids: ER mCherry-Sec61 beta BFP-Sec61 beta BFP-KDEL Rtn4a-GFP (tubular ER) Microtubules...potentially perturbing, its function. In order to dissect protein traffic in different systems, Franck Perez...reporters which can then be tracked along the secretory pathway (Figure B). The RUSH system has already...Golgi and plasma membrane reporters as well as secretory proteins or proteins targeted to membrane sub-...reporter proteins that can be used to test diverse secretory routes in various conditions. The plasmids and... of both the luciferase mRNA (3’UTR AUUUA [5 consecutive]) and protein (C-terminal CL1 & PEST). These ... -
Antibodies 101: Beyond Surface Labeling
TypeBlog Post...example, rabbit or mouse. In a second step, a fluorophore-conjugated secondary antibody is added that binds... one primary antibody can be bound by several secondary antibodies, increasing the fluorescence signal...other antibodies in your panel. Otherwise, your secondary antibody will bind to multiple primary antibodies...cytosolic proteins, as well as proteins of the secretory pathway. Those can include cytokines and chemokines... -
Tips for Getting a Faculty Position
TypeBlog Post...expansions on the chalk talks and Zoom interviews sections, along with new thoughts on research statements...critiques of your postdoctoral research, etc. The second question is whether there is chalk. Sometimes. ...much easier to focus on the questions when you’re secure in the knowledge that you have given everyone a...Identify the key points you want to convey for each section or aim. Make sure those get priority. The fine ... His interests include the quality control of secretory proteins in the Endoplasmic Reticulum, optimization... -
Antibodies 101: The Basics of Western Blotting
TypeBlog Post...species-specific secondary antibody is used to visualize the proteins. In this set-up, multiple secondary antibody...denaturing. In a native western, the protein’s secondary and tertiary structures remain intact and the ..., consider reviewing the materials and methods sections of those publications. Finally, always verify...Visualizing your protein of interest with the help of secondary antibodies In order to visualize proteins on the... -
Finding Your Perfect Job After University
TypeBlog Post...and the pro’s and con’s of working in different sectors. Luckily, I have worked for a variety of different...another major factor held me back; I do not have a second language. During the recession there were many ...many qualified scientists with experience and a second language in Spanish or French, and so they were ideal...courses were interesting and luckily genetics is a sector which has been rapidly growing. These factors left...allowed me to try out working in many different sectors and to discover for myself what potential job opportunities... -
The Addgene Antibody Data Hub
TypeBlog Post...down the page to the materials and methods section. This section will vary slightly depending on the application...Figure 4: A screenshot of the materials and methods section for the data report shown in Figure 3. At the...the end of the report, you’ll find a results section, which will tell you if the antibody worked under ... -
Troubleshooting and Optimizing a Western Blot
TypeBlog Post...dilution range from 1:1,000–1:100,000. Secondary antibodies For secondary antibodies, the recommended dilution...recommendations, and if needed, optimize your secondary antibody concentration by running a protein gradient...issues, try running a reagent gradient with your secondary antibody to see if lower concentrations reduce...antibody* Run a reagent gradient with the secondary antibody* Inefficient blocking Check antibody...primary antibody* Run a reagent gradient for secondary antibody* Antibody not completely binding ... -
Antibodies 101: Introduction to Antibodies
TypeBlog Post...which recognizes your protein of interest, and a secondary antibody, which recognizes the primary antibody... protein on the membrane. Then, addition of a secondary antibody allows the protein to be detected by ...takes place in a 96-well plate, where primary and secondary antibodies are used to capture the protein of ...conjugated to a fluorophore, to avoid the use of secondary antibodies in this experiment - are incubated ...then visualized using a fluorophore-conjugated secondary antibody or Fab. Image from Harden et al., 2014... -
Tips for Improving Your Next Manuscript
TypeBlog Post... the class, the moderator discussed individual sections of a paper, the abstract, figures, introduction...assignments, which consisted of reading that class’s section of a manuscript and critiquing it, were not too... manuscripts and discuss changes to particular sections. The focus groups allowed us to try out techniques...produce the figure, its legend, and write a results section for that figure. Writing a scientific manuscript... -
Scientific Peer-review: Providing Critical and Kind Feedback and Advocating for Open Science
TypeBlog Post...During this second read, I pay more attention to details and use a checklist for individual sections of the...Detailed assessment After this initial assessment, the second read of the paper is much more detailed. I prefer...the paper (see figures). After finishing my section-specific comments, I re-read what I wrote about the... -
Unique and persistent IDs for improved reproducibility: Addgene now supports RRIDs and compact identifiers for all plasmids
TypeBlog Post...plasmid through the “Articles Citing this Plasmid” section. Having IDs linked to these metadata and publications... Addgene plasmid in your materials and methods section have been updated to include the option of citing... will find that the “How to cite this plasmid” section now lists the multiple PIDs separated by semi-colons...cite using the PIDs in the material and methods section of your publication. You should carefully read ... -
How Dry Ice Affects Viral Vector Sample pH & How to Avoid It
TypeBlog Post...incubating the tubes in an upright position for 30 seconds, and then recapping the tubes prior to thaw. We...to dry ice. Does venting help? We found that 30 seconds of venting attenuated the pH change caused by storage... storage on dry ice (Fig. 3). However, 30 seconds was not sufficient to prevent any pH change, as we still...recommend both venting the tube for at least 30 seconds prior to thaw, and also using the thawed virus ... -
Antibodies 101: Isotypes
TypeBlog Post...during a secondary immune response, which is when the immune system encounters an antigen for a second or ...s the second most common antibody after IgG; but it's the most prevalent antibody in secretions (e.g. ... -
Writing Scientific Manuscripts: Literature Searching, Reading, & Organizing
TypeBlog Post... figures in the results section. As you’re sorting through the results section, this is where the authors...trying to replicate an experiment, the methods section probably won’t get much attention reading through...appropriate controls? Refer back to the methods section for finer points of the protocols. Are there any... -
Savvy Advocates Needed to Navigate a Scientific Enterprise in Flux
TypeBlog Post..., these issues which will continue to shape the sector throughout their careers (McDowell et al, F1000Research... by many institutions to set postdoc wages. The second event of note is a ruling in August by the National...funding and funding mechanisms require an engaged sector with effective advocacy skills. Advocating for ...interested in communicating science and in the intersection between science and public policy. Follow David... -
xCas9: Engineering a CRISPR Variant with PAM Flexibility
TypeBlog Post...phage-assisted evolution, generating xCas9 2.0-2.6. This second round of evolution included continuous outflow ...GAT, and CAA PAMs, while xCas9 3.6 displayed the second best PAM range. Characterizing xCas9 in mammalian...efficiency fits the previous observation that NGA is a secondary PAM for SpCas9. Hu et al. performed GUIDE-seq ...know how xCas9 is working for you in the comments section! References Hu, Johnny H., et al. "Evolved Cas9... -
Hot Plasmids and Viral Preps - May 2021
TypeBlog Post...preps from the Deisseroth Lab INTRSECT project. We now have over 40 INTRSECT 2.0 project vectors available...light to deactivate photocleavable gRNAs within seconds. A CRISPR-based lineage tracing tool captures rare... labeling. Now available in serotype AAV1! New INTRSECT viral preps available! We are expanding our inventory... -
Quick Guide to Working with Drosophila Part 1: Getting Started with Flies
TypeBlog Post...how to get started on fly work in this post. The second post will detail a major tool used by Drosophila...genome. They have four chromosomes: the X (and Y), second, third, and fourth chromosomes. Also, the fourth...generally do not manipulate them. Essentially, the X, second, and third chromosomes are the ones you’ll work...dominant phenotypes visible on the flies. For example, second chromosome balancers often have the curly O (CyO...