...imaging method that uses iterative staining and chemical bleaching to allow for high-resolution imaging...not recommended reagents) along with information critical for the performance of a reagent, e.g., antigen... repository for reagents, protocols, panels, publications, software, and datasets. It’s also a great place... (2022). IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse...Germain, R. N. (2020). IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial...

...coming together, we can create a significant impact on both clinical care and public health for this current...match up scientists across fields with different technical knowledge that could help fight COVID-19. They...funding and volunteer opportunities, protocols, publications, and more to accelerate the pace of research...is based in Canada, much of the information is applicable to researchers worldwide. “COVID-19 has spread...

... postdocs, Kristin Krukenberg and Jessica Polka from Harvard Medical School and a long list of supporters...peer review and grant awards systems need to be radically overhauled.  Finally, the science publishing system...Associate Professor of Systems Biology at Harvard Medical School, titled her presentation “How to Train Your...and take action. More Reading: “Rescuing US biomedical research from its systemic flaws” by Bruce Alberts...

...this area will accelerate the launch of clinical applications. During the panel discussion, Dr. Mello...adaptive bacterial immunity and its potential applications in rewriting the genome. Their award acceptance... same Polish sub-dialect making their Skype communications extra fun) who shared first authorship on their...for billions of years (…) Bacteria are really sophisticated”.     New to CRISPR/Cas9 Technology? Learn ...

... Howarth’s lab at the University of Oxford is dedicated to generating new tools to manipulate biology ...able to grab on to proteins irreversibly in a genetically encoded way. SpyTag is nice and small, just 13... if there are forces acting on them. For the application we were looking at, magnetic isolation of circulating...out the cell capture system.) Cancer and other applications Addgene: What does this technology mean in the...this tool? Howarth: Polyproteins are useful for mechanical study of proteins by atomic force microscopy ...

...out that a PhD teaches analytical and critical thinking skills that are applicable to a variety of careers... Connie Cepko (Harvard Medical School), and Dr. George Church (Harvard Medical School) who took the time...

...of hues. While those tools are great for many applications, Verkhusha and his lab at Albert Einstein College...light. As the researchers described in Nature Communications last year, “The capability to control spectral...of specific wavelength and intensity allows for optical labeling and tracking of proteins, organelles, ...Verkhusha’s team reported another advance in the application of near-infrared fluorescent proteins, iRFP670... are always looking to improve upon existing genetically-encoded probes by making them brighter, more ...

...genes are truly dispensable or are the current identification methods missing something? Here we will review...review some time-tested gene identification systems that may have a leg up on their modern counterparts...throughout an organism’s genome. These reporters have historically been used extensively in fly, mouse, and yeast.... These are effective tools but neglect some biologically relevant situations. Tissue-specific genes...considerable distance away from a gene which can make identification of the gene itself difficult. The best trap...

...whether a cell line is known to be genetically manipulated, its anatomical origin, if cell line has ever been...is resistant to specific compounds, links to publication references, and cross-references with cell line....  For those wanting to access Cellosaurus programatically, their API allows fine grained query and retrieval...manually going through the pdfs of the 26,000 publications cited. If the information seems incomplete or...

...re proud to honor the creativity, passion, and dedication to sharing epitomized by the creators of these...plasmids through our repository since we know biological resource centers, including Addgene, positively...level system on our website:   A yellow flame indicates that a plasmid has been requested 20+ times   ...Since we so sincerely appreciate our depositor’s dedication to scientific sharing, we wanted to celebrate.... “Addgene has made it possible to eliminate geographical restrictions in life science research." Claim...

...demonstrate the most exciting application for ARG’s: in vivo imaging. Specifically, arg1 expressing E. coli... interpret signals from these reporters. Lack anatomical context/spatial localization: In vivo imaging...intestinal tract and has been used for 100 years to clinically treat enteric infection and inflammatory bowel...abdomen. arg1 signal, however, can be overlaid onto anatomical ultrasound imaging to show where the bacteria...

...sequences To design experiments for further plasmid verification Identifying plasmid features While our quality...promoters, selectable markers, tags, origins of replication, and fluorescent proteins that are already included...reference sequences. Using Snapgene for additional verification experiments: Primer and restriction digest design...repetitive regions. These regions require additional verification experiments that can be partially designed using... plasmid verification...

...be used to generate organoid cultures with a modification of interest. While the authors optimized the...mechanisms related to morphogenesis, cell fate specification, and human disease.     Sun, et al. bioRxiv...fluorescent biosensor based on the parasitic Striga hermonthica SL receptor HTL7. This novel type of biosensors...could be used in high throughput screening for agrochemical compounds that have the potential to regulate...parasitization of cereal crops. As a result, agricultural applications of these novel biosensors could have a major...

...protein transducers and that the potency and efficacy is typically non-uniform across the transducerome for...TRUPATH collection allows researchers to measure the physical association of combinations of different Gα, Gβ...well known and, as a result, a target of many pharmaceutical drugs, there is still only a partial understanding...Kadowaki S, Haga T, Takaesu H, Mitaku S (2002) Identification of G protein-coupled receptor genes from the...

...All Addgene depositors! Addgene was mentioned specifically in Dr. Zhang's introduction. His willingness...Cas9 that is improving the nuclease specificity dramatically and reducing off-target effects. Other young...scientists discussed new CRISPR delivery systems, modifications to the RNA components, and challenging target...discussed some of the many challenges of creating biological circuits, and I can only say this science is ... deposited and distributed – have changed so dramatically in the past 4 years. I kept busy for the whole...

...while constant regions are identical for antibodies within certain classification groups called isotypes....published, knockout validated, and work in your application. But…they are the same isotype and therefore ...antibodies are plasmid-based and are created synthetically or derived from hybridoma antibody sequences...antibodies affects binding properties. In Journal of Biological Chemistry (Vol. 269, Issue 17, pp. 13048–13055...

...template is supplied. Find Plasmids from the NgAgo Publication at Addgene Cas9 and NgAgo head to head NgAgo ...differences in cleavage efficiency. If this finding is replicated in larger studies, it will represent a key advantage...site specified by the gDNA. Depending on your application, this could be favorable or unfavorable. In a...PubMed PMID: 27136078. Find plasmids from this publication at Addgene. 2. Swarts, Daan C., et al.  “DNA-... PMCID: PMC4697943. Find plasmids from this publication at Addgene. 3. Swarts, Daan C., et al. “Argonaute...

...analyzing the gene’s function. The process is shown graphically in the following figure, in which we add EcoRI...amplify and design primers that will bind to and replicate it. The following image shows the ends of the ...need to use the reverse complement to get PCR amplification. We can start similarly, taking the final 18...reaction using a kit, such as the QIAquick PCR Purification Kit. The PCR product is now ready for restriction...your final plasmid by sanger sequencing. DNA replication by PCR has error rates that range from roughly...

...antibodies in your lab. Perhaps you’re even in that mythical place where antibodies are well-organized, documented... sample prep. This involves using heat and/or chemicals to break some of the bonds keeping the protein...epitope (right). Created withBioRender.com.   Biological Processes  If you’re feeling relieved that you...the available epitopes could be affected by, or critical to, the assay.   Next, look for antibodies that... also working for a Western because they both typically use denatured protein samples. If, however, you...

...AAV viral preps to easily find and share useful technical data. These data focus on experimental design ...these tools, which aren’t always easy to find in publications, so this is a much-needed community resource...resource of over 100 entries is driven by the dedicated community of data-contributing researchers who...exactly which strain you used so if they wish to replicate your experiment, they know exactly where to get... we’d like to give a shoutout to all of those dedicated scientists who have contributed to the AAV Data...

...culture), which is great for a wide variety of applications. But some techniques require you to select against...antibiotic. Successful editing of transformants then typically occurs in T0 plants (from callus) or T1 plants...cacti and beets. Betanin belongs to a different chemical family than the red/purple plant pigments found...these mutant plants. Using RUBY to simplify the identification of these mutants will speed up my work and ...student studying plant development and cell-cell communication in the Nimchuk Lab in the Biology Department...

... The conventional approach has typically been to either systematically delete/overexpress endogenous genes... interference (CRISPRi) model consists of a catalytically dead Cas9 protein (dCas9) that lacks endonuclease...Western Ontario studying plant-based recombinant pharmaceuticals. Follow him on Twitter @AdamChinFatt     References...library of characterized aptamers and supporting publication: http://www.freebase.com/base/aptamer Cruz-...

...particle to infect a cell, it has to come into physical contact with that cell. Since there is a limited... by an anterograde AAV was shown to drop off drastically with lower titers. As you can see in figure 2...AAV-mediated gene expression in a target cell. Practical considerations If you have high quality AAV, you...Integration. Molecular therapy : the journal of the American Society of Gene Therapy. 2008;16(7):1189-1199.... Protocols for Work with Virus Watch Our AAV Purification Video ...

... Writing schedule tools How to write a lot: A practical guide by Paula J. Silvia  This book has tips for...app lets you track habits, like writing. It’s basically the equivalent of crossing off days on the calendar...suggestions Hemmngway makes (it wasn’t designed for technical writing), it’s great at flagging passive voice...jargon, this tool can help you avoid overusing technical terms when writing for a general audience. The...goal of the phrase, such as being cautious, being critical, or defining terms. The phrases in Phrasebank ...

...Collaboration and creativity are pivotal in writing publications/grants too. As described by several works (Wuchty...backgrounds.” This work outlines the need for clear communication, fair credit through authorship, and acceptance...remotely. The authors stress the fact that “miscommunication, a lack of leadership, and inappropriate tools...approaches can lead to frustration, delay of publication, or even the termination of a project.” Take ...setting. Check out the blog post “Fostering Communication in Remote Collaborations” to get more ideas....

...imaging apoptosis in animals." Journal of the American Chemical Society (2019). PubMed PMID: 30821975. Additional...cell death" plays a pivotal role in an array of biological processes including development, the immune system...study apoptosis in vivo, scientists have used genetically encoded fluorescent executioner caspase reporters... reporter for imaging apoptosis in vivo." Cell chemical biology 23.7 (2016): 875-882. PubMed PMID: 27447051...

... Connie Cepko (Harvard Medical School) , and Dr. George Church (Harvard Medical School) for taking the...environment for research is totally dependent on communication amongst the team so getting everyone talking...your department, and online. The Howard Hughes Medical Institute (HHMI) offers some great resources for...Scientists, including their "Making the Right Moves: A Practical Guide to Scientifıc Management for Postdocs and...

... the steps of gel purification and in vitro recombination. Across all modifications described in Trehan...effects of inactivating/activating mutations. In biomedical research, modeling patient mutations using SDM...mutations, large deletions/insertions require complicated, often costly in vitro assembly methods. A new...recombination machinery, which facilitates easy genetic modification by homologous recombination. In most recombineering...

...North Carolina, Connie Cepko’s lab from Harvard Medical School, and Jonathan Ting’s lab from the Allen ...directions. I would like to thank them for their time, dedication, advice and encouragement. Why virus? Why did...educational materials, and provides viral vector technical service (details about virus production protocols...word out about this new resource and providing fantastically useful educational content on viral vectors....the impression that it took a lot of work and dedication to do this well ... because it did. So finally...

...remotely as an Addgene Science Communication Intern. Developing science communication skills, while also learning...panel about “Social Media for Science Communication” at the American Society for Cell Biology (ASCB) 2018...Twitter Learn about using Reddit for science communication ...

...activate essentially any gene,” she says. The technical leap from mutating and deactivating a gene or ... and it consists of three components: 1. A nucleolytically inactive Cas9-VP64 fusion; 2. A sgRNA incorporating...distinct effector domains that work together synergistically, modeled after natural transcription activation...demonstrated in a paper in Cell that they could typically achieve 90-99% knockdown with minimal off-target...more about the rules.” He said that there is no theoretical limit on the number of genes that can be manipulated...

...improves upon them. Methods for studying autophagy Biochemical assays Long-lived protein degradation: This...radioactivity in the culture supernatant (this is indicative of protein degradation). To control for protein...’s slow and only measures bulk autophagy. Morphological assays Electron microscopy: Electron microscopy...studying autophagy. This method relies on the identification of autophagic structures based on morphology...available from Addgene. References 1. Rosado, C., Mijaljica, D., Hatzinisiriou, I., Prescott, M., & Devenish...

...time-consuming aspects of traditional cloning is the identification of clones that actually contain your insert...enzyme-mediated disruption of ccdB, leading to positive identification of desired clones.   ...Becomes a powerful...ccdB and therefore would die. This procedure dramatically reduces the number of clones that do not contain...which can then be used for downstream cloning applications. While these two strains ultimately perform ...and ccdB Survival strains have been developed specifically with ccdB-containing vectors in mind, any plasmid...

... year, narrow by article type (review, patent, clinical study, research article etc). There are also numerous...looking for a particular protocol or are trying to replicate an experiment, the methods section probably won...conclusions. In any case, the reader should give a critical eye to all results in the relation to how they...is science’s way of validating work prior to publication, it doesn’t mean that there are no mistakes or... biochemistry instructor in the Department of Biological Sciences at Louisiana State University. She is...

...when it comes to targeting precision and practical application. If the CRISPR/Cas9 system is not effective...but directly incorporating very long ncRNAs is impractical. Instead, tags or stop elements can be inserted...can cleave single-stranded RNA using gRNAs to specifically edit or degrade targeted lncRNAs. The Cas14 ...lncRNAs with high specificity, particularly in applications requiring smaller delivery systems (Zibitt et...

...including RNPs for indel formation via NHEJ, precise modification with Homology Directed Repair (HDR), CRISPR ...potential to be used for other types of CRISPR applications. Let’s take a look at the key components of ... which means they are non-infectious and non-replicative. Nanoblades are produced by transfecting the ...cytoplasm or pronucleus of the zygote which is both technically challenging and can negatively impact zygote ...with Cas9-sgRNA ribonucleoproteins." Nature communications 10.1 (2019): 45. PubMed PMID: 30604748. PubMed...

...biologists and computer scientists learning and communicating with one another.      Currently our main focus...our worms.  We are on the lookout for genome modifications that do not exist in the CGC library but that...makeup of the bacterial species in the gut of the domesticated housecat, and seeing how that makeup differs...cats with the goal of optimizing the health of domesticated cats and learning about feline microbiomes. ...and the reagents are too expensive to make it practical - but we have members looking at how to re-use...

...Chavez, researchers at the Wyss Institute for Biologically Inspired Engineering. CRISPR/Cas9 technology... addition to its utility in making targeted modifications to DNA, Cas9 can be reprogrammed to serve as... a gene of interest, they have been shown to dramatically alter levels of expression. Cas9’s ability to...Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease." Nature biotechnology ...Options for CRISPR Genotyping Cas9 Activators: A Practical Guide Additional Resources on Addgene.org Check...

...genes for drug discovery or to understand the intricacies of molecular pathways. These screens have gotten...diseases, as you can target your library to a significant degree using different types of AAV. Expression...into the genome, CRISPR may increase this rate. Specifically, portions of the AAV genome can integrate at...multi-plasmid system, where you have one AAV vector dedicated to expressing Cas9, while the other houses the...integration into CRISPR-induced DNA breaks. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-...

...The vast majority of bacteria are undomesticated which limits the tools scientists can use to study them...the genome and is propagated during normal DNA replication and cell division. Mobile-CRISPRi does not disrupt...single-gene knockdown experiments. Mobile-CRISPRi applications Mobile-CRISPRi expands CRISPRi to non-model ...Elizabeth A., and Pamela A. Silver. "Harnessing undomesticated life." Nature microbiology 4.2 (2019): 212....PMC6424567. Peters, Joseph E. "Tn7." Mobile DNA III. American Society of Microbiology, 2015. 647-667. PubMed...