...previously developed small molecule degraders that achieve selective degradation of endogenous proteins (notably...Hippel-Lindau (VHL) to bring the endogenous degradation machinery into close proximity with the target protein, ...to co-opt the endogenous ubiquitin proteasome machinery to degrade any protein. We are particularly excited...FKBP12F36V-fusion and the ubiquitin proteasome machinery through binding with cereblon, leading to rapid...of N- or C-terminally FKBP12F36V-tagged fusion chimeras or locus-specific knock-in of FKBP12F36V. Detailed...your lab Confirm the functionality of your fusion chimeras For each protein-of-interest, it is important ... evaluate degradation of the FKBP12F36V-fusion chimera of interest. In the cell lines we have evaluated...

...Technique What It Locates ChIP-seq Proteins (for our example later, histones) ChiRP-seq RNA Hi-C DNA (genome-to-genome...Aneesh's research interests include proteomics, machine learning, and visualization for big biology. GPS...detect modified histones with “GPS for proteins,” ChIP-seq from Table 1. Because of DNA’s 3D geometry and...formula to a real-world experiment. We’ll start with ChIP-seq data from the ENCODE project, find enhancers...enhancers. A real-world experiment Suppose you run a ChIP-seq experiment (think “GPS for proteins”) for NANOG...transcription factor in embryonic stem cells (ESCs). Your ChIP-seq finds just over 13,000 significant binding peaks... (loops) and tertiary structures (globules) to achieve exquisite compaction—on the order of 700 terabytes...

...conditions. Common issues include photobleaching, non-specific binding, and quenching, which can be mitigated through...photostability, and most importantly, a photoswitching ability. This photoswitching refers to the ability to ‘toggle... must be taken to assess if proper staining is achieved. Fluorescent ligands have more flexibility due...peak wavelength can also decrease the rate of photobleaching. Interaction with receptors: Understanding ... technical manuals. Specific applications and matching dye/ligand choices For effective live-cell imaging.../doi.org/10.1007/s41048-017-0037-8 Lucidi, M., Capecchi, G., Visaggio, D., Gasperi, T., Parisi, M., Cincotti..., M., & Ghods, R. (n.d.). Comparison of the Photobleaching and Photostability Traits of Alexa Fluor 568...

...microscopy (FLIM) method. Acceptor photobleaching method The acceptor photobleaching method is simple but limited...when FRET occurs. By photobleaching the acceptor, you release the donor's quenching and the fluorescence...An EAMNET Teaching Module http://www.embl.de/eamnet/downloads/modules/FRET_teaching_module.pdf Day RN, ...brightness of a fluorophore pair, donor:acceptor stoichiometry, and cross-talk between the two fluorophore ...has five-fold less brightness than YFP. The stoichiometry of donor:acceptor is difficult to address especially...commonly used to measure FRET: the acceptor photobleaching method and the fluorescence lifetime imaging...

... was weird like that,” says Caitlin. A love of teaching also runs through Caitlin’s blood. “I come from...faculty members, I helped grad students who were teaching for the first time. I walk[ed them] through their...them advice, [and helped] proctor exams.” These teaching experiences led Caitlin back to being a student... signed up for a 10 week class at Iowa called “Teaching Your Research.” This course has participants take...ground up.”  Science writing and editing These teaching experiences definitely weighed in Caitlin’s post-grad...but in the end, writing won out. “I considered teaching at a liberal arts school but I’ve always enjoyed...off: “I spent about 6 months just editing and searching for a job and I stumbled upon eScience by luck...

...it’s true that adding histones and chromatin architecture to every diagram portraying some aspect of eukaryotic...when I recently attended the 2018 Chromosome Architecture and Chromosome Organization Keystone Symposium...but also specifically study it. They might be researching enhancer elements that control the transcription...posters I saw at the 2018 Keystone Chromosome Architecture and Chromosome Organization. These aren’t the...’re looking for on this list, please consider searching directly on our website. In-exhaustive Chromatin-related... that promotes homologous recombination. Gong F, Chiu LY, Cox B, Aymard F, Clouaire T, Leung JW, Cammarata...Crabtree GR Cell. 1998 Nov 25. 95(5):625-36. An architectural role for a nuclear noncoding RNA: NEAT1 RNA ...

...down RNA upon cell lysis.  In the late 1970’s, Chirgwin and colleagues showed that a strong protein denaturant...denaturant, guanidinium thiocyanate, did just this (Chirgwin et al., 1979). They developed a protocol meant...ultracentrifugation altogether. Chomczynski and Sacchi showed that RNA could be effectively separated ...method are still widely used today (Chomcynski and Sacchi, 2006).  View our protocol for RNA extraction! ...ammonium sulfate on the activity of ribonuclease A. Biochimica et Biophysica Acta (BBA) - Enzymology 341:484.... https://doi.org/10.1016/0005-2744(74)90240-x Chirgwin JM, Przybyla AE, MacDonald RJ, Rutter WJ (1979...https://doi.org/10.1021/bi00591a005 Chomczynski P, Sacchi N (1987) Single-Step Method of RNA Isolation by...

...Pubmed PMID 23887178. 7. Watabe-Uchida M1, Zhu L, Ogawa SK, Vamanrao A, Uchida N. Whole-brain mapping of direct... of us learned in biology is that the body’s architecture and plumbing are important. We started with ...oxygenates the body. However, in neuroscience, this architecture is frequently still an open question. The connections...way, but rather just labels the whole brain. To achieve labeling of only first-order connections to the...cell type specificity of the starter cell can be achieved by using EnvA-pseudotyped RABV, and only expressing...supplied in trans. Monosynaptic RABV spread can be achieved by modifying the wild-type RABV genome, which ...populations in two specific brain regions (Watabe-Uchida et al., 2012). They could also quantify the strength...

...formerly known as Pichia pastoris). If your goal is protein isolation, then the MoClo Pichia Kit will get ...discuss. If you can think it, MoClo might help you achieve it! MoClo applications and specialized tools Synthetic...a broad range of parts, including copy number machinery, chromosomal integration modules, and many more...to study the effects of protein degradation on chimeric antigen receptor signaling (Kim et al., 2024)....can dream up an experiment, MoClo can help you achieve it! More recently, a CRISPR MoClo kit termed Fragmid...fungi, bacteria, protists, plants, and animals (Chiasson et al., 2019). Many plasmid elements such as promoters...Ulrike, et al. “A Modular Toolkit for Generating Pichia Pastoris Secretion Libraries.” ACS Synthetic Biology...

...fluorophores to block out of focus fluorescence from reaching a detector or restricting fluorescence to specific...fluorescent light passes through a pinhole before reaching the detector. The pinhole is specifically placed... the focal volume. This leads to more rapid photobleaching and a reduction in signal intensity. 2-Photon...Photon microscopes restrict excitation (and bleaching) to a single focal point. This is accomplished by ...the sample is excited at one time, limiting photobleaching. Similar to widefield, the entire field of ...coverslip (4). Essentially, an optical section is achieved that boosts contrast by filtering out emission...photons, a higher signal to noise ratio can be achieved (6). Super-resolution techniques such as Structured...

...spectrometry (IP/MS) and chromatin immunoprecipitation (ChIP). In IP/MS, a target protein is first immunoprecipitated...identify the interacting proteins. Similarly, in ChIP-seq assays, chromatin fragments that are bound by... patterns of the target protein. Both IP/MS and ChIP-seq methods provide a wealth of information about...all-purpose “tag antibody” can be used for downstream IP/ChIP assays. Creating epitope-tagged clonal cell lines...Using our 96-format pipeline, we can routinely achieve 5-30% tag knock-in efficiency across different ...clonal knock-in lines that we now use for IP and ChIP assays. Tag 96 genes at a time using Custom Synthetic...transfection/delivery step needs to be optimized to achieve high knock-in efficiency. To calculate the tagging...

...molecule-mediated chromatin immunoprecipitation (enChIP) because any engineered DNA-binding molecule, such... the IRF-1 locus. Figure 1: Schematic of enCHIP. Image from Fujita and Fuji, 2013. Prior to...molecule (Hoshino and Fujii, 2009). Other forms of enChIP, that do not use dCas9, require Zinc-finger or ...purification of a specific genomic region, other forms of enChIP, and additional research conducted in the Hodaka...molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR." Biochemical and biophysical research...molecule-mediated chromatin immunoprecipitation (enChIP)." Scientific reports 3 (2013): 3171. PubMed PMID...associated with telomeres using a combination of enChIP and RNA sequencing." PLoS One 10.4 (2015): e0123387...

...devastating afflictions. Elia Di Schiavi - Spinal muscular atrophy Dr. Elia Di Schiavi is a Research Scientist ...mechanisms behind the disease are unclear. Dr. Di Schiavi plans on using C. elegans as a model to identify...disruption. As part of his work in C. elegans, Dr. Di Schiavi will use Addgene plasmids to characterize smn1 ...behind SMN1 and its interaction partners, Dr. Di Schiavi will be able to better choose which genes and pathways...SMN1 and its partners in mouse cell lines. Dr. Di Schiavi hopes that these studies will accelerate the development...Website.  We are proud to provide support to Drs Di Schiavi and Nabavi and will continue to work to help those...

...photoswitches Photoactivation of Cas9 can also be achieved using single-chain fusion proteins by fusing Cas9...was from the lab of Michael Lin, who developed a chimeric protein consisting of Cas9 and a photo-dissociable...control over Cas9 activity. Dominik Niopek’s lab achieved this by fusing the anti-CRISPR Acr protein, AcrIIA4...resulting system was coined as CRISPR–Cas9 activity switching via a novel optogenetic variant of AcrIIA4 (CASANOVA...-mediated CRISPR labeling to study chromatin architecture (Hoffman et al., 2020). Fluorescent dCas9 proteins...can potentially alter the genome and chromatin architecture, it is useful to regulate the time in which ...tRNA synthetase pair which would add the PCK upon reaching the amber stop codon, TAG. (To learn more about...

...that you come into the lab wishing there was a machine that could make your life a hundred times easier...off our hands. Good news! There is probably a machine or robot out there that does exactly what you want...lot of time. Enter the Biomek FXP! We wanted a machine that would improve our transformation protocol ...played a factor in our decision to go with this machine, but we also really liked that Beckman was flexible...apart before plating. With this fine piece of machinery we have been able to transform 96 samples in about...lab team. Enter the Liquid Handler!     This machine fits on a table top and can be easily programmed...t electronic but it is one of the most helpful machines I have used in the lab. It’s especially useful...

...about how I could combine all of these roles by reaching out to my school district not just as a dad, but...presentations. If you’re a scientist thinking about reaching out to your community’s schools, here are a few...recent experiences. STEM in elementary schools - catching them early I’m fortunate to live in a town with... means to request funding for events, consider reaching out to it. PTAs have more flexibility than the...but I also tried not to be an alarmist.  The overarching guideline for all of these questions, and for...community as a scientist. Perhaps you have young children and you want to make sure their STEM education...regardless of race or ethnicity. Perhaps you don’t have children but are interested in testing your SciComm skills...

... in China. They were also able to help with sharing information through the use of popular Chinese social...have partnered with six distributors (Table 1), in China, Korea, Japan, Brazil, India, and Mexico. Table ... Country Served Beijing Zhongyuan 2012 China Summit Pharmaceuticals International 2013 ...agreement with a distributor for that country. In China, direct shipments weren’t able to clear import control...In 2023 alone, viewers spent over 22,000 hours watching these and other videos on Addgene’s YouTube channel... We’ve learned that increased accessibility is achieved through interconnected incremental changes. It...

...CRISPR-Cas9-assisted genome editing in Escherichia coli. Acta Biochimica et Biophysica Sinica. https://doi....Yang, a professor in synthetic biology from the Chinese Academy of Sciences. In the Yang lab, we’re continually...dehydrogenase and generated a strain that could achieve glucose dehydrogenase expression that is 2.6 times...guest bloggers! Qi Li obtained her Ph.D. from the Chinese Academy of Sciences (CAS) Center for Excellence...Ph.D. from Shanghai Institute of Biochemistry, Chinese Academy of Sciences. He joined Shanghai Institutes...Yang J, Yang S (2015) Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System. Appl ...

...organisms!) Escherichia coli One of the most recognizable and utilized model organisms is Escherichia coli. ...introductory teaching and research environments (Idalia & Bernardo, 2017).  Escherichia coli. Image...2017). Escherichia coli as a Model Organism and Its Application in Biotechnology. In Escherichia coli -...used mammalian model in medical research with an archive of information and data that has yet to be produced...

...afternoon during the child-rearing years, learning “lots of interesting things from children, their classmates...work-life balance. How do you celebrate your lab’s achievements? Tom Ellis highlights the importance of acknowledging...Although hard work and perseverance are required to achieve success in the lab, it is important to take the...along the way. Take time to celebrate the lab’s achievements and enjoy time with friends and family. And ... this series about how they manage their labs, achieve success, and have fun with their lab. Further ...