...transparent zebrafish embryo develops outside of the mother, making them ideal for studying vertebrate embryogenesis...similar processes occur over days inside the mother, the zebrafish is an ideal system to observe embryogenesis...zebrafish-specific gene expression databases that provide information about when and where genes are active...tools for zebrafish Random mutagenesis screens provided a major toehold into understanding how genes control...deactivation method in zebrafish are short, modified oligonucleotides called morpholinos. When injected into zygotes...applications and conclusions Zebrafish are also popular outside of developmental biology, and are particularly ... the biological question, and zebrafish are not ideal for every application. Disadvantages include their...

... sgRNAs. Its RNA-guided nature makes CRISPRa much simpler to implement in genome-wide screens over cDNA...components, and several sgRNAs must be screened to identify effective ones. Simplified in vivo delivery using... then isolated and their genomic DNA sequenced. Guide RNAs targeting several known and some unknown regulators...including microglia, astrocytes, and oligodendrocytes, provided that reporter genes specific to these cell types...of good flow cytometric antibodies for many CNS-resident cell types (microglia are a notable exception)...are often many more genetic strategies) and then consider whether traditional cDNA overexpression is suited... al. "CRISPR activation screens systematically identify factors that drive neuronal fate and reprogramming...

...always easy to identify the ideal codon for every amino acid across an entire polypeptide. Many researchers... growing polypeptide chain. One part of the tRNA contains the anticodon,  a three nucleotide sequence ...overview of peptide synthesis. A ribosome interacts with mRNA and charged tRNAs to build a peptide. Image ...Usage Tabulated from GenBank database (CUTG), that provides an electronic dataset for codon-usage of 257,468...synonymous codons based on an organism's codon bias. The idea is that scientists can make mutations throughout...

...). Genome-Wide Recessive Genetic Screening in Mammalian Cells with a Lentiviral CRISPR-Guide RNA Library..., targets 18,080 human genes with 64,751 unique guide sequences to enable both negative and positive selection...including Feng Zhang used the GeCKO library to identify genes essential for cell viability in cancer and...David Sabatini and Eric Lander, comprise 73,171 guide RNAs (gRNAs) covering a total of 7,114 human genes...target a smaller set of genes and it includes more guides per gene. The Sabatini/Lander library uses sequential...uses a 1 plasmid, single infection system. Genome wide mouse CRISPR library The Yusa lab has leveraged ...genes involved in bacterial toxin resistance, identifying 4 previously unknown genes.  “With this work,...

... cell lines used in scientific research are misidentified! Rigor and reproducibility of scientific data... cell lines. Cellosaurus Cellosaurus seeks to identify and describe all cell lines used in research, ...and collections. Importantly, Cellosaurus also identifies problematic cell lines: ones either suspected...or easily contaminated, as well as commonly misidentified lines. Browsing this feature to know if your...the known features and relevant literature, or to decide which line is best for your experiments. You can...and shared allele search preferences to help you identify proximal lines you care about. If you have cell...is as good a time as ever to find out the true identity of the line? Once you’re run your STR profiling...

...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ...approaches and organoid models, toolkits like this one provide new opportunities for investigating genetic mechanisms...2020.05.04.076067    Novel fluorescent enzyme biosensors provide direct, specific and sensitive detection of the... rather than on the fluorescence intensity, it provides a direct and quantitative detection of SLs. The...plants.  FnCas12a, unlike other Cas12a nucleases identified, functions at temperatures up to 43 °C and can... on NGG PAMs relative to wild type. A new genome-wide CRISPR knockout library from Xiaole Shirley Liu'...targets all mouse genes with 10 gRNAs per gene. The guides are optimized to maximize on-target cleavage and...

...Bleomycin glycopeptide Induces DNA breaks Bactericidal 5-100 ug/mL Erythromycin macrolide Blocks 50S...Resistance to antibiotics is a widely used tool in molecular biology, yet scientists rarely stop to think...when the cells are grown on selective media, and provides those bacteria with a pressure to keep your plasmid...Action*   Working Concentration** Kanamycin aminoglycoside Binds 30S ribosomal subunit; causes mis-translation...mis-translation Bactericidal 50-100 ug/mL Spectinomycin aminoglycoside Binds 30S ribosomal subunit; interrupts protein... Bactericidal 7.5-50 ug/mL Streptomycin aminoglycoside Inhibits initiation of protein synthesis ...Bacteriostatic 50-100 ug/mL in EtOH Polymyxin B polypeptide Alters outer membrane permeability Bactericidal...

...clusters under blue light Check out our Optogenetics Guide to learn more about how these modules work, and ...important components of the cytoskeleton. They provide cells with physical structure, separate chromosomes...microtubules, Opto-katanin will surely be useful for a wide variety of experiments. Opto-RhoGEFs manipulate ...by Rho family signaling pathways. Rho guanine-nucleotide exchange factors (GEFs) activate their partner...system (Mahlandt et al., 2023). These Opto-RhoGEFs provide a reversible and non-invasive way to activate a...efficiency in mammalian cells and in vitro, opening up a wide realm of possibilities. The CRY2-SuperPLD module...membrane or lysosomes (the earlier article also provided CIB constructs for targeting Golgi, ER, and endosome...

...tissue is identifying the cells you are studying. Antibodies can help reveal cellular identities by targeting...while also supporting imaging, making it easy to identify dozens or hundreds of particles surrounding each... A) Schematic of workflow. B) Detail of spacer peptides (3HB: 11-nm 3-helix bundle; SAH: 60-nm single ...with MagIC-cryo-EM. Nucleosome-like particles identified by Topaz software (green circles), magnetic bead...its chaperone NPM2, but the technique should be widely applicable to other targets. The modular system..., M., Kamath, N., … & Weissman, J. S. (2024). Brainwide silencing of prion protein by AAV-mediated delivery...Samelson, A. J., … & Weissman, J. S. (2021). Genome-wide programmable transcriptional memory by CRISPR-based...

...in bacteria, so many that it may be difficult to decide which path to take. A quick and easy way to introduce... the Lambda bacteriophage, is arguably the most widely and productively used  (Thomason et al., 2014)....In recent years, CRISPR-Cas9 technology has also aided in the creation of scarless mutations, both in stand-alone...What are the counter-selectable markers used to identify double crossovers? The most commonly used counter-selection...the genome. Subsequent selection on sucrose will identify double crossovers. This can be an efficient method...unmarked mutants, but it frequently requires considerable optimization to ensure strong counter-selection...Central PMCID: PMC4862005. Jiang, Wenyan, et al. "RNA-guided editing of bacterial genomes using CRISPR-Cas systems...

...proper formation of the disulfide bond between the VL and VH domains. This bond provides stability and solubility...recombinant antibody. They are ~25 kDa single polypeptides that contain the variable light chain (VL) and... two chains are connected by a flexible linker peptide that is usually 15-20 amino acids long and made...lethal to animals.  In the clinic, scFvs’ size also provides advantages over antibodies (Ahmed et al., 2012...oxidizing periplasm of bacteria to allow for proper disulfide bond formation.  expression in strains of bacteria... concentrations in the eye with minimal systemic side effects. scFvs are part of engineered chimeric antigen...determining regions and frameworks contribute to the disulfide bond independent folding of intrinsically stable...

...or developmental characteristics that make them ideal for studying in a laboratory environment. We’ve ...manipulation and genetics research. Plasmids are ideal tools for studying genetic modification for their... E. coli biotin ligase, BirA, has been used to identify and study protein-protein interactions in proximity...pathological developments (Vieira et al., 2019) Besides their ability to regenerate, the axolotl has several...several attractive characteristics that make them an ideal model organism; they are relatively simple to maintain...have large, easily modifiable embryos, which is ideal for observing and manipulating the entire developmental...scientific history, highly characterized genome, and widespread utilization, Arabidopsis has made significant...

...others. Another peptide-based strategy uses an enzyme to covalently label the peptide with a fluorophore... Balla. "Live cell imaging of phosphoinositides with expressed inositide binding protein domains." Methods...University of Amsterdam). GFP is the most popular, most widely used genetically encoded fluorescent probe. Several...proteins as described above. The smallest tags are peptides that are engineered to bind specifically and with...homology domains can be used to detect specific phosphoinositides (Varnai and Balla, 2008) (Figure 2). RNA production...the continuous effort of numerous scientists world-wide.   Many thanks to our guest blogger, Joachim Goedhart...PubMed PMID: 10748019.  8. Lotze, Jonathan, et al. "Peptide-tags for site-specific protein labelling in vitro...

...spectrometry to identify a mass shift proportional to a single phosphate moiety on the peptide of interest...databases of post-translational modifications, identifies a staggering ~250,000 phosphorylation events ...incorporation of phosphoserine (as described below) provides researchers with a valuable tool for understanding...extension and translation of the pSer-incorporated polypeptide. These three components were shown to effectively...mutation. This emphasizes the advantages of bona fide pSer-incorporation into recombinant proteins as ...between different proteins. Beyond these standard considerations, it is important to determine how much phosphorserine...and non-phospho-bands will give the researcher an idea of the purity of pSer-incorporated to non-phosphorylated...

...Park et al., 2019). This provided an engineering road map of sorts, giving an idea of the stiffness the fibers...Resources on Addgene.org Optogenetics guide Chemogenetics guide BRAIN initiative plasmid collection ...cumbersome systems during experiments – neither ideal for the intrepid researcher. There existed, therefore...that could continuously monitor multiple systems. Ideally this tool would be wireless, able to monitor outcomes...important as its capabilities are the practical considerations of actually using it - the device has a rechargeable...indeed stable for continuous monitoring. On the gut side of things, the authors optigenetically and chemically...

...Addgene blog Important Considerations When Using AAVs Three Key Considerations For Precise Neuronal Targeting...your next AAV experiment, use these questions as a guide for designing your future injection experiments....injection and detection methods. For example, you can provide location, titer dose (Example: 1E13 GC/mL) and ...experiment, read our blog post on important considerations when using AAVs. Experimental results: These...Frontiers in Neuroanatomy and summarized some considerations for precise neuronal targeting using AAV on...to give proper attribution.  We hope that this provides a clear overview of what you need to submit data...tracing Resources on Addgene.org Read our AAV guide Browse all  AAV vectors Find ready-to-use AAV preps...

....” Subscribers to Scientific America would be considered the interested public and it would be safe to...scientific or science communication. A Tweet is still considered scientific communication if the language is aimed...communication.  Formal education is education that is provided through a structured environment such as the classroom...will.  Informal education is education that is provided, typically ad hoc, for learners who can choose... only used in the field and terminology that is widely used but has a very specific use-case (definition...the context of disease testing, it can still be considered jargon in most other uses. Many laypeople would...communication work does not explicitly exclude people outside of the original recipients. Instead, it targets...

...make her work understandable to people both inside and outside the scientific community. We’re excited to...making their own fluorescent protein technologies widely available to the research community. To honor their... proteins in which Dronpa domains flanked either side of an enzyme’s active site. In these fusions, ultraviolet...domains could be placed in amino acid loops on either side of an enzyme’s active site and still block enzyme... will be able to use similar designs to create a wide variety of enzymes and proteins with inducible activity...post. Fatima Enam: Biosensors for human milk oligosaccharides Fatima Enam is currently a graduate student...fluorescent protein-based biosensors for Human Milk Oligosaccharides (HMOs). HMOs are thought to play an important...

...meeting with no idea why you are there. Make the most of everyone’s time by considering the level of meeting...meetings spent on details that do not yet need to be decided. Figure out what you need to accomplish to get .... Team Meetings: For standing team meetings, provide agenda sections for each person to add a bullet...meetings tend to fill the shape of their container. Consider whether you actually need a full hour to achieve...the time down to an hour or less and are able to provide more timely feedback on each other’s projects. ...each of your meeting types (see above). We’ve provided some tips above for what works well at Addgene...FInd Tips on Picking a Research Project Read Other Inside Addgene Posts Resources on the Addgene Website...

...not identical, to their defined recognition sequence. Most enzyme manufacturers make High Fidelity versions...from a colleague down the hall, it is always a good idea to take some time to confirm that you are working...gel correspond to the predicted sizes. Watch this video for a quick overview of how to analyze a restriction...accurately visualize the full size of your construct. Consider buffer and temperature compatibility when digesting...avoid this issue. For your gel: Add ethidium bromide (EtBr) to your gel before pouring it. EtBr binds...your sample settles in the gel well and the dyes provide a visual reference point so you can easily assess...Molecular Biology Reference Find More Protocols and Videos      ...