.... Eight years later, scientists isolated pink, purple, and blue chromoproteins isolated from reef-building...reach zooxanthellae, the coral’s symbiotic dinoflagellates that are photosynthetic (Salih et al., 2000...experiment worked just by looking at the cells on the plate. For example, if your plasmid contains a gene encoding...directly use in bacteria, where most genetic manipulations start. Anthony Forster’s lab used codon optimization... Chromoprotein expression from bacteria on agar plate. Image: Liljeruhm et al., 2018. For each chromoprotein...exchange. These vectors contain a toxin gene (regulated by a rhamnose-inducible promoter) and a chromoprotein...Dove SG, Takabayashi M, Hoegh-Guldberg O (1995) Isolation and Partial Characterization of the Pink and Blue...

...solution of benzyl alcohol and methyl salicylate which was later modified by others to produce Murray’...major advances in light microscopy, particularly related to the neurosciences.  These developments in microscopy...single gold particles with diameters less than 4nm. Lateral view of a cleared rat pons, medulla and the first...using optical projection tomography (OPT)  (12) and later Hans-Ulrich Dodt’s lab pioneered the use of light...) (6).   The Dodt and Frank Bradke laboratories later developed the 3DISCO (3-dimensional imaging of solvent...tetrahydrofuran-based tissue clearing (13,14). A few years later, Karl Deisseroth’s lab developed CLARITY, which ...relied on the use of transgenic mice in which a subpopulation of neurons are brightly labeled with GFP (e....

...tumors, which can lead to new cancer targets and related biomarkers . Data from such screens are often uploaded...Unexpected results Their results showed 96 strongly correlated genetic dependencies that were clearly associated... they looked for a biological explanation, a relationship between the genetic dependencies they identified... ancestries. While there were some exciting relationships identified, 48% were found to be artificial,...bias into their experiments instead of a true correlation.   It turned out there was indeed a bias, and...diversity of genetic variation across the human population. Rather, it primarily reflects European ancestry... to guides in the Broad’s Genomic Perturbation Platform Avana library (used by the Cancer Dependency Map...

...their resistance genes throughout the bacterial population. But what if we could specifically target only...successfully resensitized a beta-lactam resistant population to the antibiotic, despite this resistance gene...plasmid-based sequences (red). Treating a mixed population, represented here by cells of different colors...given genomic or plasmid sequence from a mixed population without affecting the other bacteria. Targeting...small pools of antibiotic resistant cells could repopulate the environment after treatment. The phagemid...antibiotics can be used to target the sensitive population. Yosef et al.’s proof-of-concept work targeted...infected by the lysogenic phage, rendering the population sensitive to antibiotics. Created with BioRender.com...

... and whether you are inoculating from a frozen stock or a colony from an LB plate. In my hands, a 5 mL...mL starter culture inoculated from a colony on a plate will reach an optimal density in 18-24 hours. I...Arabidopsis, from studying transcriptional and translational dynamics of genes and proteins in living plants... seeds from the pool you will be selecting from later. The Arabidopsis transformation process The process... T1 plants from each transformation. I like to isolate a minimum of five. You have no control over how..., check out Harrison et al., 2006. Tips: Don’t plate seeds too densely during selection: this will increase...difficult. Don’t leave your plants on selective plates for too long: even resistant plants will be affected...

...transcription and epigenetic regulation. To elucidate molecular mechanisms of regulation of genome functions, ...mechanisms of genome functions such as epigenetic regulation and transcription by using locus-specific chromatin...manner. To achieve this goal, it is necessary to isolate specific genomic regions while retaining molecular... step of knocking-in. In 2013, we showed that isolation of a single copy genomic locus is feasible by ...enChIP, specific genomic regions can be easily isolated for identification of associated proteins, RNAs...that enChIP will markedly accelerate research of regulation mechanisms of genome functions in the hope of... of the reasons why we have only three biology-related Nobel prizes, out of which only one was done in...

...has seen before, showing how DNA sequences are translated into amino acids. And I was astonished that the...basis of shuttle vectors, which can function in unrelated host species, even from completely different kingdoms...eukaryotic cells, but would prefer to grow, clone, and manipulate their vectors in fast-growing bacteria first....consider how to keep it there. In fast-growing populations of cells, the vector needs to replicate alongside...alongside its host, or it will be lost from the population. A bacterial chromosome has a single origin of...replication machinery. A shuttle vector designed for unrelated bacteria should include oris for both target species...selection, but these resistance systems don’t always translate to eukaryotes. For example, beta-lactam antibiotics...

... protein is up or downregulated, examine a protein’s stability or post-translational modifications, or...aureus. Its isolation by affinity chromatography and its use as an immunosorbent for isolation of immunoglobulins...immobilized antibodies, or immunoglobulins, to isolate a specific protein out of a complex mix. Using ...suitable for all applications, such as protein isolation from serum. In this case, Protein A and Protein... assay, an antibody against the tag is used to isolate the protein of interest. The wide availability ...experiments using a tagged protein may not be translatable to the endogenous system and will need to be...modification. Similarly, RNA IP (RIP) can be used to isolate proteins that bind to RNA, though the details of...

...identification system for the isolation of base-edited cell populations. To develop this method the lab... affecting protein translation of different reporter proteins. Protein translation requires the start ...edited cells without the need for single cell isolation and downstream sequencing (Standage-Beier et al...and Brafman lab showed that GFP positive cells isolated with TREE have a significantly higher frequency...base-editor (C>T conversion) they could induce the translation of any detectable protein, not just fluorescent...base-editing reporter. As the initiation of protein translation at the start codon ATG is universal, the Dow ...Dow lab successfully used GO to induce the translation of an array of different reporters including mScarlet-I...

...hedgehog signalling pathway, which is a key regulator of all bilateral animal development. SHH plays a key role...Cancer Institute! Sonic Hedgehog, an important regulator of embryonic development The largest conference...publication, Ivics et al 1997. Spaghetti Squash, a regulator of cellular contraction You may think that a gene...component of the fly actomyosin cytoskeleton that regulates cellular contraction. This network is composed...vessels). Spaghetti squash (Sqh) is the Drosophila Regulatory Light Chain (RMLC) of nonmuscle myosin II (Karess... Jordan and Karess, 1997), which contains the regulatory regions that are necessary for myosin activity...Roger Karess. "Myosin light chain–activating phosphorylation sites are required for oogenesis in Drosophila...

...intensity. Researchers use later steps in this chain (blue) to infer or calculate things about earlier ones... normalization and loading controls needed for relative quantification of a western blot — and why you...can you accurately compare different lanes? In relative quantification, the POI bands are normalized to...protein concentration in your sample would directly correlate to protein abundance on your membrane, which would...multiple sources of error (red) influence these relationships and must be addressed with separate controls...accurately quantified In western blotting, the relationship between protein abundance and band intensity... BioRender.com. To see why this S-shaped relationship poses problems for proteins of very different...

...phenotype. Incubating the phage display library with plate-bound antigen helps select for high affinity scFvs...bacteriophages. This library is incubating with plate-bound antigen to select for scFvs with high affinity...the non-oxidizing cytoplasm of bacteria, scFvs accumulate in insoluble inclusion bodies. While it’s possible... has led to their application for basic and translational research.  Basic research applications of scFvs...generate since it’s genetically encoded.   Translational applications of scFvs: Just like antibodies...scFvs are also used for eye diseases, such as age-related macular degeneration (AMD) since direction injection...cell. When a CAR has an scFv that binds cancer-related antigens, binding of the scFv part of the receptor...

...recipient, the only antibiotic resistant colonies isolated are those where the allelic exchange vector has...that contained one of eight bacterial toxin genes isolated from E. coli or Psuedomonas aeruginosa. These ...the transcriptional activator rhaS. To allow manipulation of bacteria without an endogenous rhamnose regulon...synthetic ribosome binding site (using the online calculator from the Salis group) (Espah Borujeni et al.,...designed with the help of the DNA tuner program) (Latynski and Valentovich 2014). We routinely clone the ...facilitate the cloning of toxic products. To allow manipulation of naturally chloramphenicol-resistant strains...Anirudh S. Channarasappa, and Howard M. Salis. "Translation rate is controlled by coupled trade-offs between...

...continuing to copy the template rather than dissociating).  MarathonRT, isolated from Eubacterium rectale...fields of biology and enable the conversion of RNA templates to DNA but suffer from several important shortcomings...structured HCV genome (~9.6 kb of highly structured template!). MarathonRT also faithfully transcribes RNA ...protein fused with GFP, YFP, mCerulean, or other related fluorophores. Find all of the nanobody toolkit ...biotin. The biotin-labeled proteins can then be isolated and analysed. In this work, the authors specifically...discovery of proteins involved in transcriptional regulation and chromatin structure at your locus of choice...technology, which they call C-BERST (dCas9–APEX2 biotinylation at genomic elements by restricted spatial tagging...

...with ssDNA repair templates. Their work demonstrates that different repair template strategies activate...using dsDNA templates achieving ~1-10% efficiency. Easi-CRISPR uses a long ssDNA template to increase ...These complementary goals are aimed at improving translation of CRISPR technology, but they would also bring...working with CRISPR than just designing a repair template that contains your desired edit, and I want to...CRISPR updates on our blog to keep current with the latest and greatest! Addgene resources 3 Tips to Improve...Editing in Human Cells Hands-on tips for repair template design from guest bloggers Dominik Paquet and ...

...mentor. How do you make the most of this new relationship? Consider adding formality and active goal setting... setting to your mentoring relationships, so that you can reap rewards in the form of reaching career ... career path is a great start to a mentoring relationship, but if you don’t take this past the chatting...meetings and setting the direction in a mentoring relationship falls on the shoulders of the Mentee. A Mentor...progress over the course of an ongoing mentoring relationship (in a book or online). Mentee: Make a list of...secret of accountability To make a mentoring relationship really productive, the most important step you...on setting SMART goals using a Development Plan template. A Development Plan or mentoring journal will ...

...efficiency of Cas9 cleavage is relatively high while the efficiency of HDR is relatively low, meaning that most...without double-strand breaks (DSBs) or donor DNA templates.  Figure 1: An overview of prime editing...summarize the major ones in Addgene’s repository later in the post. Advantages of prime editing Less constrained...homology-directed repair Homology-directed repair (HDR) stimulated by double strand breaks has been widely used ...increase activity, enhance binding between the template and primer binding site, increase processivity...remake that strand using the edited strand as the template. The PE3 system does just this by including an...PE = prime editor; RTT = reverse transcriptase template; PBS = primer binding site. Image from Doman et...

... can rupture E. coli spheroplasts to release encapsulated proteins. Video by ACS. For a more cartoony ...thousands of times by propagating through an enormous lattice of identical subunits. A brief history of R bodies...coli in the 1980s  (Kanabrocki et al 1986). Much later, it was shown that putting the operon under a strong...mutants that couldn’t extend at a normal pH and later realized that these mutations clustered in a particular...their ability to penetrate other barriers (like vasculature or extracellular matrices) in response to pH ... response to environmental conditions. More speculatively, R bodies might endow divergent organisms with...Protein Piston That Breaks Membranes to Release Encapsulated Cargo. ACS Synth. Biol. (2016). doi:10.1021/...

...transduced by lentivirus and have been difficult to manipulate genetically. To solve this issue, Sarah Teichmann...disease is driven by atherogenic lipoproteins that accumulate within the vascular wall. ApoB, the main structural...lipoproteins, shuttles lipoproteins through the circulatory systems, but can also lead to the formation of... of ApoB-LPs has been shown to have a strong correlation with cardiovascular disease and indirect measurement...in vivo model to identify drug candidates that modulate ApoB-LP size and concentration, Steven Farber ...that the system is active in E. coli and closely related species, is amenable to use with other bEBP/UAS...and the system may not be adaptable to distantly related species from E. coli. This tool should serve as...

... AAV Targeting and manipulating specific, genetically-defined neuronal populations with intersectional...calcium sensors and GABA sensors) Calcium sensors The latest calcium sensors from Janelia (jGCaMP7) continue...potential, GCaMP7s is approximately twice as bright, relative to baseline fluorescence, as the GCaMP7f variant...useful for imaging signaling activity in large populations of densely-labeled neurons because background...all our biosensors inventory, and check out our latest vectors below: pGP-AAV-syn-jGCaMP7f-WPRE (104488...Optogenetics continues to be a useful method for manipulating specific neurons. We recently packaged a soma-targeted...specificity of influence measurements by reducing photostimulation of the axons and dendrites of non-targeted...