...rate of translation and thus protein expression. In fact studies have shown that translational efficiency...particular organism. Why is codon usage important? Translation and protein synthesis relies on transfer RNAs...efficiency is correlated with codon bias across all endogenous genes in E. coli and S. cerevisiae (Tuller et.... Image from Mariana Ruiz Villarreal. By the late 1980s, scientists even created a codon adaptation... 2000 the Ikemura lab created the Codon Usage Tabulated from GenBank database (CUTG), that provides an...on an organisms codon usage bias to increase translational efficiency and thus protein expression without...an organism that contains expression limiting regulatory elements or use a non-canonical code (Gustafsson...

...the resistant populations. In fact, 88% of the barcodes within the resistant populations were shared by...screening with lentiviral pooled shRNA libraries. Later, Bhang says, “When we developed this tool, there...library to determine whether or not cancer cell populations resistant to drug treatments arise during treatment...treatment or are preexisting in the parent population prior to the start of treatment. They hypothesized...hypothesized that, if they labeled the parent cell population using the library, propagated it, separated it into...cells that represent the preexisting resistant subpopulation 2. Resistant cells among the separate replicates...that are present at less than 0.1% of the total population are easily be missed. The ClonTracer library ...

...ratio calculators Lab math calculators These calculators can help you with common calculations performed...lab. Molarity calculator Promega's Biomath Calculators Primer resuspension calculator (sign-in required...sequences to sequences in a database ExPASy translation tool: Translates a DNA sequence using all six open reading... Cloning ligation reaction calculators These links can help you calculate how much insert and backbone...Annotates features, BLASTs, aligns, digests, and translates a sequence.   NEBCutter2: For finding restriction...information, such as expression patterns, post-translational modifications and polymorphisms Codon optimization...Addgene's Analyze Sequence tool.   DNA sequence manipulation tools  Sometimes DNA sequences need to be “cleaned...

... mk+) Unmethylated DNA not degraded, cell still can methylate DNA   hsdS(rk-,mk-) Unmethylated DNA not...from two individual isolates, the K-12 strain and the B strain. K-12 was isolated from a patient in 1920...pathway that cleaves methylated cytosine DNA Allows for uptake of foreign (methylated) DNA mrr, Δ(mcrC-mrr...that cleaves methylated adenine or cytosine DNA Allows for uptake of foreign (methylated) DNA recA, ...plasmids that should not be Dam or Dcm methylated, allows for methylation sensitive restriction enzymes to ...renaming samples throughout history. It was likely isolated in 1918 but was first referred to as “B strain...routine cloning, cloning unstable DNA, preparing unmethylated DNA, and more. Many mutations that make these...

...strands of the template DNA first have to be separated. This occurs by heating the dsDNA template to a point...categories of multiplex PCR:  Single template PCR reaction - one template is amplified using several forward... reverse primer sets.  Multiple template PCR - multiple templates with different primer pairs that align...invented in the early 1980s by Kary B. Mullis who later shared a Nobel Prize in Chemistry for his work. ... in temperature. Taq was first identified in the late 1960s during research at hot springs in Yellowstone...polymerase, PCR requires free nucleotides (dNTPs), template DNA to amplify from and unique single stranded... primers can anneal to the single stranded DNA template strands. DNA polymerase is also stable at this...

...As with DNA isolation, scientists commonly rely on RNA isolation kits to make their life easier. Recently... out. In this article, we cover the basics of isolating RNA without a kit. Tips for working with RNA (... today There are many alternative methods for isolating DNA without a kit. However, that isn’t the case...method. A major hurdle to developing protocols to isolate RNA was that RNases are commonly found in cells...upon cell lysis, RNA is degraded. To effectively isolate intact RNA, a fast, strong protein denaturant would...chance to break down RNA upon cell lysis.  In the late 1970’s, Chirgwin and colleagues showed that a strong...., 1979). They developed a protocol meant for isolating RNA from rat spleens in which they homogenized...

...detect proteins within a 96- or 384-well, flat-bottomed plate. The basic principle of an ELISA is that ...technique works by first coating the wells of a flat bottomed plate with a capture antibody that is specific ...experimental sample are bound to the wells of a plate instead of an antibody. Coating the wells with a...characterize antibodies against the antigen bound to the plate. Figure 3: Overview of using Direct ELISA...protein antigen is coated onto the wells of the plate. However, instead of detecting your protein using...absorbance of each well, which is measured using a microplate reader, is directly proportional to the amount... of enzyme present in the well and is used to calculate the amount of your protein of interest that is...

...formation of disulfide bridges, glycosylation and acetylation to create functional, stable proteins. Protein...used to manipulate DNA), or in medicine (e.g. insulin). Proteins, unlike DNA which can be relatively easily...cells with your DNA template of choice and allowing these cells to transcribe, translate and modify your ...transcribed into messenger RNA (mRNA). mRNA can then be translated at the ribosome into polypeptide chains that ...proteins are then modified via an array of post-translational modifications including protein folding, formation...proteins from mRNA and the addition of post-translational modifications Learn more molecular biology ...mammalian proteins that require multiple post-translation modifications for proper protein function. Most...

... the biotinalatable tag on dCas9 with a BioTAP-tag. The BioTAP-tag is a 69 aa long biotinylation targeting...Jul 2, 2020. Promoters may be the star of gene regulation, but enhancers and chromatin looping play important...important supporting roles. Enhancers are cis regulatory DNA sequences that, when bound by transcription...thousands of base pairs away from the gene they regulate, but are brought in proximity by the looping of...CAPTURE (CRISPR Affinity Purification in situ of Regulatory Elements) method. The original CAPTURE method...2020). CRISPR Affinity Purification in situ of Regulatory Elements: The original CAPTURE method The original...the dCas9 to the loci of interest and dCas9 is biotinylated by BirA. From here, the CAPTURE method is similar...

...antibody manipulation), then expression is likely sufficient for successful optical stimulation.  It is...Gore BB, et al. Manipulating gene expression in projection-specific neuronal populations using combinatorial...technique is remarkably straightforward to learn and relatively cheap (compared to many other technologies and...electrophysiology to prove that your optogenetic manipulations are generating action potentials (or lack there...assess the effectiveness of your optogenetic manipulations (though a reviewer will probably ask for electrophysiology...circuit of interest in promoting reward is a self-stimulation experiment wherein mouse initiated optogenetic...in a reward sensation and subsequent repeated stimulation. A spatial memory task, on the other hand, would...

...possible to build gene regulatory RSMs (GRSMs, the subset of RSMs that regulate gene expression) that ...massive amount of information regarding which regulatory proteins, signaling molecules, mutations, and...individual bacterial cells to form colonies on a plate and then we performed colony PCR on the register...sequencing.  A less straightforward, but more population-wide (as opposed to single-cell) approach is ...a particular application makes it difficult to isolate single registers or if it requires reading so many...necessarily have to be based on transcriptional regulation, as long as they can control recombinase activity...post-transcriptional recombinase activation via RNA toehold riboregulation could be a promising strategy for linking RSM...

...Kinases: they regulate many proteins, with ~1/3 of human proteins predicted to be phosphorylated on at least...least one site. Phosphorylation is particularly important for regulating signal transduction and measuring...predict. Slower Dephosphorylation Rates: FRET-based reporters can have slower dephosphorylation rates than ... signal (NES), both which are phosphorylatable. Prior to phosphorylation, the KTR localizes to the nucleus... of the nucleus depending on its phosphorylation status. The relative ratio of cytoplasmic vs. nuclear...hypothesized to be caused by FRET reporters having phosphorylated conformations that are less phosphatase-accessible...nucleus, but following phosphorylation bNLS activity is suppressed and NES activity is enhanced, leading...

...differentiate the Ly6C negative population from the Ly6C positive population. Figure 2: An FMO gating...clear positive and negative population. If you’re unsure what your population will look like for a particular...Markers that define more specific cell populations, often used in the later gates, are more likely to require...or isotype controls, which we’ll describe a bit later. Single Colors Single color controls contain, as...artificial positive (bound) and negative (unbound) population. The benefit of beads is that they do not require...allows you to more easily and accurately gate populations that may otherwise be difficult to separate out...commonly used markers that define broader cell populations (e.g., CD4, CD8b, CD11b, CD19), are less likely...

...an shRNA to downregulate expression of miR124a, a regulatory RNA that negatively regulates BDNF levels...Christian Lüscher. "Refining deep brain stimulation to emulate optogenetic treatment of synaptic pathology...their involvement is activating, inhibiting, or modulating. Viral vectors, in contrast, are considerably...considerably more versatile and specific in how they manipulate neuronal function, with far fewer side effects compared...animal has been exposed to morphine or other stimulating drugs, it develops an enhanced propensity for...connection between neuroinflammation and anxiety by modulating the production of the pro-inflammatory cytokine..., or passive floating on the water surface. The latter reflects a state of behavioral despair, and the...

...example Tuller et al. found that translation efficiency is well correlated with codon bias in both E. coli...therefore may need fewer resources for the entire translation process. For example, during high growth rate...rate conditions, E. coli preferentially upregulates production of tRNAs that recognize codons found in highly...tRNAs, different regions of the protein may be translated at different rates. The ribosome will move quickly...the ribosome stalls, this may give the swiftly translated regions a chance to fold properly. For example...with specific secondary structures in 10 closely related yeast strains. Adaptation to changing conditions...codon preferences online). Even if the gene is translated, it may not function properly. This is the result...

... Single-stranded DNA repair templates Short single-stranded DNA templates have been shown to improve the...laboratory mouse. It’s also made targeted insertions relatively simple in C. elegans and bacteria. But CRISPRing...from low efficiency when a standard dsDNA repair template is used. The original design for creating a conditional...targeting two intronic regions and two repair templates in order to insert two loxP sites. Since two double-strand...ameliorate this problem. Briefly, you design your donor template to include a T7 promoter upstream of the left ...vitro transcription, and use the IVT product as a template for reverse transcription to create your ssDNA...promoter will not be included in the final ssDNA template. Although effective, ivTRT may be more challenging...

... constructs. In multiple HIV-1 latent T cell lines, as well as a latent microglial line, treatment with...doesn’t completely disappear; it just hides in latently infected cells. To truly cure HIV-1, researchers... levels due to the viral reservoirs located in latently infected cells. Although ART-treated patients ...disease. This increased disease risk is attributed to latent HIV reservoirs, chronic inflammation, and negative...doesn’t see any threat to which it should respond. Latently infected cells evade immune detection because ...first, “shock and kill”, aims to reactivate the latent HIV so that infected cells will produce viral proteins...joined together. Clonal Cas9/gRNA-expressing cell populations were also immune to HIV-1 reinfection. Importantly...

... are enriched relative to controls using Split-BioID-GFP and BioID run on six unrelated proteins. One ...These interactions are often modeled as binary relationships, i.e. protein A interacts with protein B; but...controllable version of the proximity-dependent biotinylation technique BioID. The key advantage of Split-...BioID, BirA* is fused to a bait protein and it biotinylates proteins that are within a ~10 nm radius of ...biotin. When proteins Y and Z part ways, BirA* biotinylation activity ceases. After biotin tagging of proteins... PPIs are identified via mass spec analysis. Biotinylated proteins are considered possible interaction...different levels of fusion protein expression and biotinylation depending on which terminus of the bait proteins...

...promoter or the coding sequence and the template or non-template strand, among other parameters. .  Stanley...introduced along with an oligonucleotide repair template. Through recombineering, the locus of interest...interest is modified to match the repair template, and the locus cannot be recognized by the spacer-derived ... contains the specific gRNA(s), and the repair template is supplied as a dsDNA fragment. Each round of...with XbaI to insert extra elements, like a repair template, using Gibson Assembly or restriction enzyme cloning...does not function in bacteria, most efforts to regulate gene expression were limited to inducible promoters...CRISPR offers a much more user-friendly way to modulate gene expression. The Marraffini lab and Qi lab...

...relying on correlations between actual antibody labeling and expected labeling. Correlation cannot prove...practice to combine correlation with other approaches when possible. Finally, correlation of -omics data ...a powerful tool to delineate cell populations and to study relative protein expression. Its reliability...against markers of the human blood leukocyte populations, as well as a pragmatic approach to determining...and the abundance of the epitope in the sample, relative to cross-reactive antigens – that is, an antibody...images showing the staining intensity in the KO population (pink histogram) compared to the WT cells (green...shows separation between the wild-type and the KO population (Figure 1), further optimization can be performed...