...communication graduates are often well-equipped. Many institutions are sincerely interested in connecting with ...the experimental aspect of my thesis: a survey instrument designed to measure how individuals respond to...science. Understanding just how the public utilizes insights gleaned from scientific research is, after all... this power and the tools to deploy its wisdom remains a challenge. Departments like ours reflect a growing...

...have recently received a grant from the National Institutes of Health that will address this problem.The ...produce a subset of this collection as ready-to-use-proteins to facilitate use. Dr. Trimmer’s lab will ensure... represent the official views of the National Institutes of Health.     References and Resources References...10.1038/520295b Bradbury ARM, Trinklein ND, Thie H, Wilkinson IC, Tandon AK, Anderson S, Bladen CL, Jones B,...

...locus or more commonly via cloning of recombinant proteins. Why use a tag? If you are fortunate enough to...may not need to read this - but for many other proteins, quality antibodies do not exist, or they don’...benefits – as discussed above – but there are a few instances when they should be used with caution or not at...protein may disrupt the biological function of some proteins. Protein folding issues, steric hindrances, and...

... use similar processes to add overhangs to your insert of interest for Gibson assembly. The steps following...to choose enzymes that: Do not cut within your insert Are in the desired location in your recipient...our cDNA into the recipient plasmid. Remember to insert your DNA in the correct orientation in the recipient...cloning Run the PCR reaction Run PCR to amplify your insert DNA. It is important to use a high fidelity polymerase...

...secondary structure that can bind specific proteins via aptamer domains. Combined with dCas9, this new scaffold... sites. With hundreds of characterized aptamer domains available, an unprecedented level of flexible tunability... Designing and using RNA scaffolds to assemble proteins in vivo. Nature protocols. 7(10) 1797-1807 (2012...

...As MIT's Ed Boyden explains it, his goal is "to understand the brain at a level of abstraction that enables...opsin from algae that is sensitive to red light instead of blue, which will allow researchers to independently...cells within them work together or perhaps compete against each other. Getting two-color stimulation has been...maybe we could treat patients suffering from Parkinson's, chronic pain, deafness, or other conditions....

... hands-on, it will be “brains-on”! I know that even lectures should be “brains-on”, but as much as I try...received a whole set of cards (Promoters, Inserts, Tags, Origins of Replication, Resistance gene and Selection...

...organisms. However, lengthy genetic payloads and insufficient transcription on the array have limited the ...editing. How do you then set up an MBE system that contains a double-win for both efficiency and multiplexity...lentivirus, demonstrating simultaneous editing of genes against multiple genetic diseases, such as muscular dystrophies...CRISPR-based gene editors, for correcting mutations or installing functional genes to study and potentially treat...

...and are not used for general plasmid selection. Instead, reporter genes are often employed to easily monitor...of picking up positive traits (i.e. the plasmid contains a cassette that will make cells resistant to a...picking up of a negative trait (i.e. the plasmid contains a cassette that will make cells sensitive to a... should not be used for mammalian expression – instead use G418. This can be confusing since the neo/kan...

...immune system to fight progressing cancers. It was inspiring to participate in the 2017 Cell Symposium on Cancer...presentation by Professor Guido Kroemer from the Institut Gustave Roussy. Professor Kroemer discussed the...Professor Caetano Reis e Sousa from the Francis Crick Institute concluded “Aspirin promotes autophagy, inhibits...session I got a chance to talk with Dr. Friedmann-Morvinski about tools used to analyse the tumor microenvironment...

...resistance genes, selectable markers, promoters, origins, tags, and certain ORFs. Their sophisticated detection...only a few nucleotides, such as the fluorescent proteins EGFP and mEGFP. Many of these features, such as...Map” and “Sequence” tabs. Primers This tab contains a table listing commonly used primers detected...Additionally, align a custom nucleotide sequence against a given sequence using BLAST2. See this blog post...

...looking to study the level of protein expression, instead of its presence or absence, the plots can look ...These smears tend to occur when you are looking at proteins that are expressed regularly in cells and might...Created with biorender.com.   In such cases, instead of trying to quantify based on percentage positive...with normal gates, just based on a histogram plot instead of a dot plot. However, the histogram plots look...

...) if NHEJ joins the distal ends together. Similarly, it may be possible to direct insertion of an exogenous...of breaks) by NHEJ-dependent repair (“pop-in” insertion) provided a template containing compatible overhangs...Renouf B, Renaud J-B, Sallmyr A, Ruis B, Oh S, Tomkinson AE, Hendrickson EA, Giovannangeli C, Jasin M, ...

...healthcare settings, etc. What project in the Collins lab inspired Sample6? The initial work focused on using..., and the team that packages its pitch the best, wins. He explained that entrepreneurs must clearly communicate...failure at all stages in the startup". To gain insight into "the random-walk" of a budding startup, I ...

...3-100 per cell, a stabilized promoter buffered against the effects of copy number on reporter gene expression...promoters drove maximal gene expression near genomic origins of replication, the stabilized promoters created...deoxychromoviridans requires three genes whose proteins are needed sequentially. When Segall-Shapiro et...optimization of gene dosage in E. coli using DIAL strains." Journal of biological engineering 5.1 (2011):...

...make sure that they’ll be compatible with your instruments, each other, and your target. I love FPbase’s...reaction, can be detected using specialized imaging instruments or X-ray film and lends itself well to assays...mechanisms. Most take advantage of chemical groups intrinsically present on antibodies, such as the primary amine...that make up the disulfide bonds between antibody chains. 3) Endogenous carbohydrates added to antibodies...

... the imbalance of electrical charge between the inside and the outside of the cell. This imbalance is ... Examples of some genes encoding gap junction proteins cx43 GJB1 GJB2 Bioelectric states can alter ... even between many cells (through gap junction proteins which connect the cytoplasm of two cells) can ...controlled by the opening and closing of ion channel proteins, they are not always easy to track at the transcriptional...

... to train our young scientists for futures both inside and outside of academic research (4). There are...industry, regulatory, or clinical environment. It remains contested, however, whether a better solution would...University, has recently published an article arguing against reducing the number of graduate students accepted...grassroots organisations that represent postdocs and institutes that employ them, the diversity of trainee backgrounds...

...though you may need to be on a network with an institutional subscription), archived on PubMed Central, or...Check out the hashtag #365papers on Twitter for inspiration and accountability. There are a few different...reprints and papers with scribbled notations in the margins. If you prefer, printing and hand-writing notes...guest blogger! Johnna Roose is a biochemistry instructor in the Department of Biological Sciences at Louisiana...

...number of important plasmid elements – promoters, origins of replication, protein tags, and antibiotic resistance... Cre acts independently of any other accessory proteins or co-factors, thus allowing for broad applications...no chance of it occurring randomly. Therefore, inserting loxP sites at deliberate locations in a DNA sequence... a parallel orientation, allowing the four Cre proteins to form a tetramer. A double-strand DNA break ...

...high titer virus for transfer plasmids with small inserts (such as CRISPR guides) while a single 72h harvest... This is due to inefficient packaging of large inserts; a study by Kumar et al. found that in some cases...titers can drop 10-fold for every 2kb increase in insert size. To overcome this, lentivirus can be concentrated...require an ultracentrifuge, PEG will precipitate all proteins in a solution, not just the lentivirus; consequently...

...that treat disease at the molecular level. For instance, if a disease is caused by a mutation in a single...deficiency, Cystic fibrosis, Muscular Dystrophy, Parkinson’s disease, and HIV. A notable landmark study showed...showed significant clinical efficacy against a form of blindness known as Leber’s congenital amurosis ...example, prevalence of neutralizing antibodies against some AAV types, AAV1, 2, 3 and 5 are thought to...

...in different fields that can provide different insight into an area - not just working within the established...of expertise, equipment, or excellence of the institution). Likewise, if you’re staying in the same lab... applying for smaller grants from within your institute or a private funding body. Success breeds success...collaborators can also help you get some critical insight into what you're doing wrong. All this helps to...

...unreliability: cross-reactivity (binds to non-target proteins), variability (separate batches can perform differently...mostly uses whole-mount IHC techniques on rodent brains and is expanding to more complex brain systems ...larger-volume antibodies for thicker tissues and whole brains, we chose monoclonal antibodies (mAbs) and their...negative control which does not have primary and only contains secondary antibodies, allowing us to only image...

...). Figure 3: pegRNAs whose 3′ extension begins with a C base can cause unwanted base pairing (...BioRender.com. What to edit The sequence you choose to install can influence the success of your prime edit. If...sgRNA is designed to bind only after the edit is installed. This reduces concurrent nicks, which lowers indel...so that nicking only occurs after the edit is installed on the opposite strand. Created with BioRender.com...

...indicators (GECIs) are fluorescent proteins linked to calcium binding proteins (e.g., calmodulin or troponin... changes with Ca while another wavelength is insensitive. Additional red sensors based on mRuby (jRCaMP1...Addgene.org Addgene’s AAV Guide Fluorescent Proteins: Biosensors Addgene’s Viral Services  Resources...

...students and postdocs broadly – and thus PI’s and institutions in turn. The first is the passing and upcoming...the NIH recommended pay scale – used by many institutions to set postdoc wages. The second event of note...simply being able to categorize all postdocs at institutions, will be challenging. At the same time, there...level, FoR is currently compiling a database of institutional responses to the FLSA ruling. Similarly, from...

...postdoctoral fellows with Jim Collins and Peng Yin at the Wyss Institute (Harvard University), we developed...Perhaps most striking is that there were seven institutions involved in the effort. This inclusive and open...biomolecular tools can distinguish between global strains of the Zika virus (Asian-, African- and American-lineages...

... Rho-independent termination is also known as intrinsic termination, and it relies on the formation of...tail targets the RNA to the degradosome, which contains enzymes that cut RNA not protected by secondary...complex and involves two RNA polymerase-associated proteins, CPSF and CstF, which are responsible for recruiting...Cell. 1987. PMID: 3568131.  Hager S, Frame FM, Collins AT, Burns JE, Maitland NJ. An Internal Polyadenylation...

... Khan Khilji, a PhD student at the Max Planck Institute of Colloids and Interfaces. Here are some tips...split cells Don’t be lazy about splitting cells, instead try to form a routine. Twice a week often works...take a vial of the ‘mint condition’ master stock instead of ‘borrowing’ cells that have already been passaged...soon be joining her PhD lab at the Max Planck Institute of Colloids and Interfaces. Sana is particularly...

...helper plasmids or the cell genome can be packaged inside the vectors during production. These impurities...removed during the purification step because they are inside the virus itself. While these impurities are generally...NGS at Addgene to sequence all the DNA packaged inside the viral particles (Figure 1). Briefly, packaged...to the contaminant. Each contig is then BLASTed against the NCBI nucleotide collection database, and it...

...these therapeutics. Jesse Bloom’s lab at the Fred Hutchinson Cancer Research Center developed a pooled plasmid...created a novel nanocompartment for transporting proteins in yeast by using murine polyomavirus virus-like...VLPs ). This artificial nanoparticle can protect proteins from unfavorable interactions in the cell, improving...zCas9i cloning kit is a plant cloning kit that contains a series of vectors and DNA modules for assembly...

...department during the application process. Many institutions recommend that you reach out to potential advisors...you can’t visit. By talking with people at the institution, you can get a better sense of the environment...answer process can also help you to see if the institution is right for you outside of just the program ...options are very handy in moments like that! For instance, during my application cycle, two schools on opposite...

...November 18, 2016): Researchers from a variety of institutions recently reported their inability to recapitulate... and development before it can truly be pitted against CRISPR head-to-head.  Exciting features of NgAgo...and fussy to optimize. One reason could be the instability of the supposedly alien 5’-phosphorylated ssDNA...Burgess, Shawn., et al. "Questions about NgAgo." Proteins & Cell (2016). 3. "NgAgo: Genome-editing by a ...

...D-F)  High-magnification images immuno-stained against dopamine beta-hydroxylase (DBH, magenta) to label...and that it often provides incredibly valuable insight into one’s work. As a community, we must therefore...remove the stigma around sharing negative data and instead focus on getting this information out into the ... A., Hsu, R., Kalwani, L., Sierra-Mercado, D., Robinson, J. O., Outram, S., Koenig, B. A., Pereira, S....

...labs of David Root and John Doench at the Broad Institute have developed human genome-wide CRISPRko (knock...CRISPRi libraries utilize an engineered Cas9, which contains multiple point mutations in the nuclease domain...potential off-target effects. The Dolcetto library contains two sets of sgRNAs; A, the top 3 ranked sgRNAs... sequences can also be modified to include RNA domains that recruit additional transcription factors. ...

...antimicrobials could become our newest line of defense against bacteria. Created with BioRender.com. ...resistance using multiple approaches. Major restaurant chains including Chipotle and Panera Bread have pledged... just the method needed to jumpstart the fight against antibiotic resistance. Advantages of CRISPR over...strategy can help us win back ground in the fight against bacterial superbugs. References 1. Citorik, Robert...

...purified viral vector solution (which contains viral capsid proteins) as opposed to purified DNA. This may...see below), since each viral particle typically contains one viral genome. Other than a theoretical maximum...mitigated by using purified viral DNA as the template instead of the intact AAV particle. Finally, the precision...

...medical journal. Decades later and after years of painstaking work trying to isolate the causative gene for...recently used the CRISPR/Cas9 system to both precisely insert the MECP2-R270X mutation into the MECP2 gene in...fine-tuning dosage so that enough wild-type MECP2 is made inside the cells, but this is exciting progress in tackling...:2<147::aid-ajmg6>3.0.co;2-o Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY (2013) An AT-Hook...

...growing polypeptide chain. One part of the tRNA contains the anticodon,  a three nucleotide sequence complementary...become extremely useful in expressing functional proteins in hosts that do not naturally express that gene...host you are using or come from an organism that contains expression limiting regulatory elements or use...10.1038/nsmb1031 Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias and heterologous protein expression...

...with the replicon- the part of the plasmid that contains the origin of replication and the replication ...inhibiting translation of replication machinery proteins, or directly inhibit replication by binding to...walking” the same plasmids to one daughter cell, instead of partitioning each type of plasmid into a separate...2015) Imaging centromere-based incompatibilities: Insights into the mechanism of incompatibility mediated...

...reproducibility is limited in two ways – only data inside the ELN is reproducible, and only the highly restricted...Goettingen, and several other large research institutions. The following graphic depicts the ways in which...banks and sequencing files is likely stored in institutional and lab servers specifically designed to hold...illustrated in this video, and to data stored on institutional and lab servers. Connectivity to other tools...

...Transition mutation (C>T, G>A, A>G, and T>C) installation by base editors. Pathways that compete with ...developed plant adenine base editor (ABE) vectors to install A>G or T>C mutations in the plant genome. We constructed...probably due to the presence of nucleosome or other proteins. You can detect base editing as early as 48-72...Ag-biotechnologist in the National Rice Research Institute, Cuttack, Odisha, India. Currently Kutubuddin ...

...process that isn’t as simple as it seems. Take, for instance, the GCaMP-encoding viral vectors available in...service. While they were both requested, GCaMP6 remains the more requested option, and jGCaMP8 appears ...compared to other AAVs preps from 2016–2023. B) Inset showing distribution of only GCaMP6, jGCaMP7, and...our own repository data, giving us significant insight into which vectors are likely to be of most use...

...every experiment, an investigator needs a standard against which the results can be compared; results from...single experiment wherein Plasmid A (encoding shRNA against human Gene X in backbone Y) was transfected into...included as these provide the baseline/standard against which other samples can be compared. The Empty ...For example, in the experiment above, Plasmid A contains an shRNA that targets human Gene X and human cells...

...within living cells. By coupling fluorophores to proteins, pioneers of this technique were able to directly...FRET-based biosensors, and interactions between DNA and proteins. FRET, in theory, is an easy technique, but it...to studying an unknown interaction between two proteins, these parameters are difficult to overcome but...FRET_teaching_module.pdf Day RN, Davidson MW. Fluorescent proteins for FRET microscopy: monitoring protein interactions...

...serotype that works great in a GABA neuron, for instance, may not transduce the adjacent norepinephrine...differences in tropism between animal species or even strains of the same species. What works well in a mouse...recommended to optimize to the “lowest number required” instead of using the first amount that looks effective....Moullier, P. (2002). Lack of an Immune Response against the Tetracycline-Dependent Transactivator Correlates...

...turning transcription OFF. Despite their bacterial origins, Tet systems function well in mammalian cells, ...including the “middle” ADH1 promoter pADH1m, which maintains activity during the late ethanol consumption phase...results in chimeric GAL80-repressible and GAL80-insensitive activators of lexAop. This system is commonly...modular vector for ease of use! Conclusion This post contains only a brief overview of some of the most common...

...came as an undergrad at Worcester Polytechnic Institute. Though some WPI students chose to go the solo...matter whether that other person really is acting against the team’s interests or not; once that seed of ... to be invited onto a team. Make one yourself. Instead of thinking “What’s my angle on attacking this ... Eric J. Perkins...

...scientist” conjured up images of men like Albert Einstein and Bill Nye in their lab coats handling glassware...solve global problems. Biomedical research, for instance, contributes heavily to medical practice, and ...relatives suffering from similar diseases. Others were inspired by the imminent threat of climate change to study...interesting questions and your excitement will in turn inspire the people around you. Be proactive Rather than...