...on-site, but now we were presented with a new challenge: automating the bioinformatics steps needed to...input to the next via a Nextflow concept known as channels. Since a Nextflow process can utilize any scripting...process.  Next, we specified the input and output channels for the initial process and tested it by running...number of input file names or filtered the input channel to only use the first n items. To be sure, we went...first, to make sure we understood the concept of channels and implemented the input declaration correctly...faster runtime and decreased cost compared to purchasing and maintaining our own infrastructure. Our patchwork...

...sensitivity Longer protocolIncreased chance of cross-reactivityChallenging to develop assay Competitive...antibodies. Assay development, however, can be challenging since scientists must first identify two independent...Disadvantages Direct Fast and simple protocolReduced chance of cross-reactivity Higher level of background...availability Longer protocolLess specificityIncreased chance of cross-reactivity Sandwich High specificityHigh...Competitive Appropriate for small moleculesReduced chance of cross-reactivity Less sensitivityLess specificityLimited...

... of the fly (Pfeiffer et al., 2010). Yeast (Saccharomyces cerevisiae) Yeast, one of the simplest eukaryotic...as Parkinson’s disease (PD). PD is primarily characterized by protein misfolding that leads to a build-...invaluable in understanding the basic molecular mechanisms underlying the disease (Menezes et al., 2015)... development, cell signaling, aging, and mechanotransduction to name a few. For example, Andrew Leifer....5 (2011): 190-195. Liu, Wei, et al. "From Saccharomyces cerevisiae to human: The important gene co‑expression... PubMed PMID: 26712014. Pandey, Udai Bhan, and Charles D. Nichols. "Human disease models in Drosophila...

...Stochastic multicolor labeling is a popular technique in neuroscience and developmental biology. This... persistently fluorescent during development. Stochastic multicolor labeling systems, many based on Brainbow...even axons of up to 100 microns in length. Some challenges of the Brainbow system are that it does not use...for improving the level of detail possible for stochastic multicolor labeling of the brain. Labeling Drosophila... researchers who developed Tetbow. Conclusion Stochastic multicolor cell labeling systems allow single...Harbor Protocols 2011.1 (2011): pdb-prot5546. Richardson, Alexander, et al. "Visualizing the Fate of Transplanted...

...nature. Once the bond is formed it is unaffected by changes in pH, temperature or organic solvents. Uses of...it is added to. Biotin also has an exposed side chain that can be easily manipulated to make reactive ...vivo. Biotinylation reagents Biotin’s exposed side chain can be cross-linked to amino acid functional groups... terminus of a DNA sequence during a Polymerase Chain Reaction (PCR) by using a biotinylated primer. Biotin...substrate (Holden and Cremer, 2003). References 1. Chapman-Smith, A., & Cronan, J. E. “Molecular Biology of...129 (2009a): 477–484. PubMed PMID: 10064313. 2. Chapman-Smith, A., & Cronan, J. E. “The enzymatic biotinylation...

...: In one of my favorite books, Michael Ende’s Momo, the title character endears herself to the nearby ...lack thereof): Information sharing gets more challenging the bigger an organization gets, and creating...communication that gets sent out through multiple channels is not reasonable or sustainable. That said, when...village (and to the reader) by simply listening. Chances are, you know someone like this, even if you’re...these people yourself.  Fig 1: Quote from Michael Ende, courtesy of morefamousquotes.com A good...

...to simultaneously test how multiple amino acid changes affect a protein of interest’s function. This technique...combination and possibly discover unexpected epistatic changes in protein activity. See Natarajan et al for an...mutagenic primers to introduce all desired codon changes (step 1 in the image above). A second universal...This results in the final product having a codon change present on both strands of the plasmid. The ssDNA...in your research? References 1. Natarajan, Chandrasekhar, et al. "Epistasis among adaptive mutations ... Mccullum, E. O., Williams, B. A., Zhang, J., & Chaput, J. C. (2010). “Random Mutagenesis by Error-Prone...

...genome editing without a nuclease Although the mechanism of incorporation is not well understood, researchers...double strand break repair, it has proven more challenging to develop high efficiency CRISPR-based approaches...Schofield, 2015; Moser and Hirsch, 2016; Epstein and Schaffer, 2017) Hopefully you’ve been able to check out...research currently focuses on determining the mechanisms and consequences of cohesin gene inactivation...27280971. 10. Epstein, Benjamin E., and David V. Schaffer. "Combining engineered nucleases with adeno-associated...Medicine, CRISPR, and Genome Engineering. Springer, Cham, 2017. 29-42. PubMed PMID: 29130152. PubMed Central...

...may be familiar with popular light-sensitive ion channels used to control activities like neuronal signaling...activity. Researchers have designed a variety of photoswitchable elements into many other types of proteins....under blue light BcLOV4 undergoes a conformational change and binds the plasma membrane under blue light ...The authors demonstrated its use to probe cell mechanics, vesicle transport, and cell division, but given...family signaling pathways. Rho guanine-nucleotide exchange factors (GEFs) activate their partner Rho GTPase...formation, cell contraction, or other morphological changes, depending on the specific Rho GTPase/GEF pair ...

...and increased tariffs present an unprecedented challenge to the scientific research ecosystem, not just...concerned about these developments. These abrupt changes threaten to slow transformative biological discoveries...years to come. We Are Here to Help Despite these challenges, Addgene remains steadfast in our mission to ...resilience and creativity in the face of funding challenges. By strengthening our commitment to collaboration... invite researchers to share how these funding changes are impacting your work and what support would ...

...known about bioluminescent organisms and their characteristic radiance for some time – there are records ...after that, in 1994, Prasher’s collaborator Martin Chalfie expressed GFP in exogenous organisms (E. coli, ...and later C. elegans) for the first time. After Chalfie’s work, scientists really started to take notice... Roger Tsien resulted in much of our current mechanistic understanding of GFP’s function. His lab described...Nobel Prize in chemistry was awarded to Shimomura, Chalfie, and Tsien for their work on GFP. This great honor...

...alterations in gene expression, but causality and mechanisms remain unclear. Today, targeted epigenetic modification...could identify the target genes of previously uncharacterized enhancers. The popular TALEN-based LITE system...H3K27ac histone modification at specified loci. Charles Gersbach’s lab has deposited mammalian expression...sorting and selection of transduced cells. Grant Challen’s lab also created constitutive (pCMV-dCas9-D3A)...publication at Addgene. Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander...Fowler T, Rees R, Kramer A, Martens A, Edwards JR, Challen GA (2016) Reprogrammable CRISPR/Cas9-based system...

... technology was invented to introduce specific changes into the mouse genome. With these early technologies...Mice. My first CRISPR mouse experiment Everything changed with the advent of CRISPR in 2013 (Cong et al.,...CRISPR-Cas9 is an acquired immune system in bacteria and archaea. As you know well if you’ve been following the ...sends out an “SOS” signal and cellular repair mechanisms rush in to repair the damage. If all they can...form of an oligonucleotide or plasmid), precise changes can be made in the genome via the homology directed...repair pathway (HDR), be it a single nucleotide change, insertion of a reporter gene, or replacement of...

...Magenta. Or you can use Color>Split Channels and then Color>Merge Channels into whatever combination of colors...antibody Secondary antibody SCN1A sodium channels anti-pan-Nav R-mAb K58/35R (Mouse IgG2a) Goat... (Mouse IgG1) Goat anti-mouse IgG1 Kv2.1 channel anti-Kv2.1 KC (Rabbit IgG polyclonal) Goat ...images of each labeled target as different color channels and analyze the results. Depending on the goal...rather than red-green). Even better, show each channel in individual panels, then the multicolor overlay...

... some challenges during my internship, but nothing could have prepared me that those challenges would ...always been interested in the ways that I could change the world around me. My strong interest in the ...exploring my different interests but also a way of challenging what I am used to. Brandon Solis, marketing...structured career because our mindsets and needs can change. Having been at Addgene for a month, I can say ...

...Cloning, Fluorescent Voltage Indicators, and Photoswitchable Proteins by Cary Valley, Shreya Vedantam, Michelle...fluorescent proteins at Addgene. 7. Designing Your Chalk Talk for the Academic Job Interview by Erik Snapp...blogger Erik Snapp breaks down how to prepare a chalk talk for an academic job interview including defining... research vision, organizing your vision into a chalk talk, and tips for practicing.  6. The Fluorescent...insertions, deletions, and all possible base-to-base changes.   1. Plasmids 101: Transformation, Transduction...

...from Zygosaccharomyces rouxii), B2 (from Zygosaccharomyces bailii) and B3 (from Zygosaccharomyces bisporus...as low toxicity. FLP/FRT recombinases (from Saccharomyces cerevisiae) had been used successfully in Drosophila... Kotelevtseva N, King K, Davis JR, Mullins LJ, Chapman KE, Dunbar DR, Mullins JJ. Nucleic Acids Res. 2007...

...selection. Knock-in events tend to be rare, and the challenge with any experiment is in efficient recovery of...increase in knock-in efficiency, presumably by channeling DNA breaks into the homologous recombination ... template design The Meyer lab meticulously characterized several aspects of editing. First, they devised...injected animal.  PAM sequence considerations For changes 5’ to the PAM, sequences corresponding to the same...Prize included Jennifer Doudna and Emmanuelle Charpentier for their pioneering CRISPR/Cas9 work (now recognized...proteins associated with a given genomic locus (CRISPR-ChAP-MS) could further transform the range of experiments...

...Matthew J. Niederhuber, a graduate student at UNC Chapel Hill. Chromatin immunoprecipitation followed by...interactions, the reliance on fixation does increase the chance of false-positives, as proteins may appear to be...rely on nuclei extraction. They report that this change offers a significant improvement and simplification...especially in situations when it is technically challenging to collect large numbers of cells or when a high... student at the University of North Carolina in Chapel Hill, where he studies enhancers and blogs about...

... suggest changes to our social media strategy. We ended up implementing some of these changes and seeing...my current projects and personal interests. We chatted about social media analytics and summer travel ...at once. I was able to do something that was challenging while helping us share our resources better with...video production, and keeping inventory of our merchandise collection. While most days I was up to my neck...