...cloning and the FNLCR Combinatorial Cloning Platform (CCP); the latter of which greatly enhances the utility...assembly cloning platform called GMAP (Gibson assembly-based modular assembly platform). GMAP is based ... that locus to be methylated. This powerful tool has been used to direct methylation to and lower expression...method, called STARR-seq (self-transcribing active regulatory region sequencing) that tests enhancer sequences...enhancers function independently of their position relative to a transcription start site. In STARR-seq, randomly...researchers to screen the entire genome for genes that regulate a wide variety of phenotypes, including but not...the resulting lentiviral library to generate a population of HEK293FT cells expressing a single gRNA targeting...

...transfection into plates containing selection agent at different densities, then dispose of the plates that do ...) to transition from a 48-well cell plate to a 96-well assay plate. We generally freeze at least 2 ampules...rapidly isolate individual cell clones with different expression characteristics from a population of transfected...became frustrated with using glass cloning rings to isolate colonies of antibiotic-resistant cells; during ...cloning rings, the remainder of the colonies on the plate dried out and died. The alternative to cloning rings... rings, dilution cloning into 96-well plates, is extremely time- and resource-consumptive, since only ...cell can give rise to single clones, and thus many plates must be examined for single clones and then handled...

...technology can be used to isolate a specific subset of cells in a population in a procedure termed fluorescence...stream oscillates to generate droplets that are charged as they pass through a metal deflection plate. Each...lymphocytes and “gate” that population for further analysis. Since different populations of immune cells express...desired cell population for further analysis. In this example, the lymphocyte population is selected and...analyze a specific subset of cells in a complex population. Have you spent hours in the biosafety cabinet...cytometry allows users to analyze single cells in a population. Single cells are passed through the path of ...target protein expression levels, assessing post-translational modifications, determining cell health, analyzing...

...and negative populations. Oftentimes, you’ll be presented with a trend of two populations with basically...within a clear negative population. When you’re interested in measuring a population based on a fluorescent...two stains in relation to each other. Using a quadrant gate, I can divide my cell population into DN, DP...experiments you’ll be working with a heterogeneous cell population, for example from a processed piece of tissue...But even if you are analyzing a homogenous cell population in culture, it is normal to observe diversity...Figure 3 you can see how I gated out my lymphocyte population from a tumor sample. Many cell types can be found... I can however clearly identify my lymphocyte population (10.7% of all recorded events) based on their...

...occur directly after any 3’ regulatory elements, such as the polyadenylation or poly(A) signal. While many...purpose and mechanism of polyadenylation vary across cell types, but polyadenylation generally serves to promote...which promotes both polyadenylation and termination. Out of those listed, the SV40 late polyA and rbGlob ...export and translation processes as well.   Figure 2: The conserved eukaryotic polyadenylation signal...efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. Molecular...working with plasmids! What are termination and polyadenylation? The role of the terminator, a sequence-based...half-life, and ultimately gene-expression. Polyadenylation is the post-transcriptional additional of multiple...

...Tends to resist promoter down regulation due to methylation or deacetylation. Ubc General expression mRNA...controlled by still other regulatory factors: enhancers, boundary elements, insulators, and silencers; however...pET vectors. Very tightly regulated by the lac operators. Good for modulating gene expression through varied...Good for rapid regulation and low basal expression; however, not well-suited for modulating gene expression...repressor 10x, thus tightening regulation of lac promoter. Good for modulating gene expression through varied...and -10 region from lac. Very tight regulation. Good for modulating gene expression through varied inducer...cells and typically only in the same or closely related species from which they were derived. Similarly...

...and plate transformants for isolated colonies (150-200 per plate) across 20 fresh selective plates. Step...gently down onto a plate of colonies. Mark the orientation of each membrane on its plate before moving on...on. Then peel each membrane off the plate (saving the plate so you can regrow the lifted colonies overnight...therapeutics, which is also gaining a lot of new traction lately (1, 2), depends on knowledge of the structure(s... a given fragment size to be selected for by manipulating the nebulization time and pressure. Nebulization...a hose to a nitrogen gas tank with a pressure regulator. Other methods for physical shearing exist as ...working with DNA that is refractory to enzymatic manipulation, amplifying phage DNA with phi29 polymerase ...

...disorders. A series of studies carried out on an isolated population in Sweden found that paternal grandfathers...in their DNA methylation patterns, either large increases or decreases. Hypermethylation of CpG islands... (pcDNA3-K9 histone methylation reporter) and K27 (pcDNA3-K27 histone methylation reporter) positions ...to recognise lysine 27 methylation. When tested in living cells where methylation of these sites was controlled...significantly different FRET levels between unmethylated and methylated states. Thus, this system is a reliable... transcription and inactivate them. Global hypomethylation, on the other hand, has also been implicated...immunoprecipitation, fluorescent in-situ hybridization, methylation-sensitive restriction enzyme digestion, DNA adenine...

...thus individual laser stimulation is essential. In terms of the laser stimulation itself, the output of...cable is threaded through—and fixed to—an optical insulator called a ferrule (below). The fiber optic cable...significant amount of equipment, most of which is relatively cheap). Several protocols have been written outlining...the dorsal/ventral location of your region of stimulation (the z-axis bregma coordinate). Because the light...it enters tissue, placement above the site of stimulation guarantees that the majority of the opsins will...should be about 0.4-0.5mm above the site of your stimulation. The scatter effect is also an important consideration...during the entire protocol, otherwise optical stimulation will be erratic, opsin activation/inactivation...

...transcriptional regulator to modulate expression at that locus. The use of regulators allows a greater...that can recruit various transcriptional regulators (Zalatan et al. 2015).  These scaffolds are stretches...promoter to modulate dCas9 expression, multiple scRNA transcriptional programs can be regulated with dCas9...University of Western Ontario. Adam summarizes Zalatan JG, et al.'s recent paper, "Engineering Complex...differentiation or metabolism. Our attempts to manipulate these cellular behaviors often fall short with...shifted in recent years toward tinkering with regulatory networks and multiplex gene control. However,...approaches are often met with the challenges of regulatory bottlenecks and their scope is limited by the...

...modifications exist in the template DNA. There are several unique HDR mechanisms, but all templated-repair pathways...fix a broken relationship. Pardo B, et al. Cell Mol Life Sci (2009). PubMed. Regulation of DNA double-strand...along the way. HDR uses homologous sequence as a template for repair and is thus the more accurate mechanism...process is generally error-free provided the DNA template used for repair is identical to the original DNA...one strand of the homologous DNA donor and can template repair off the other strand; this results in the...mechanism that notably does not require a donor template and thus won’t be covered in detail here. Classical...pathway, the 3’ ends invade an intact homologous template to serve as a primer for DNA repair synthesis,...

... region that has mono-methylated and acetylated histones, but not tri-methylated histones, functions as...denote enhancers as follows: (mono_methylation + acetylation) - tri_methylation In the next section we’ll ... me3, and ac – denoting mono-methylation, tri-methylation, and aceylation, respectively (these are chemical...sequencing to measure the relative proportion of guide RNAs (gRNAs) across the population. Recall that guide ...inclusive markers of regulatory regions in the genome, including enhancers, promoters, insulators, and more. I...It Locates ChIP-seq Proteins (for our example later, histones) ChiRP-seq RNA Hi-C DNA (genome-to-genome...tried and true method of finding enhancers by isolating genomic regions that are bound to modified proteins...

...gene-function relationships in defined substructures of the CNS as well as individual neuronal populations.  The...some unknown regulators of neuronal differentiation were enriched in the CD8+ population, as expected....neurons, forming the neuronal circuits that will later be refined through experience. However, studying...complicated by the lack of precise genetic tools for modulating gene expression in the central nervous system...using CRISPRa to target individual genes can be relatively laborious because multiple plasmids/viruses are...generated from the same gene but with different untranslated or coding regions. Typically, each gene isoform...can be targeted anywhere in the genome, it is relatively straightforward to use CRISPRa to selectively...

...know if you are actually stimulating or inhibiting the targeted neuronal population prior to behavioral testing...receive different types of stimulation may help to refine and optimize your stimulation parameters as well. ... and stimulate them for 30min to an hour and observe what happens. You never know how stimulation of a...personally interested in include: intracranial self-stimulation (ICSS) and place preference. The lab I work in... electrode and non-specifically electrically stimulating an ill-defined region of the brain. With the ...particular hole (the active hole) induces laser stimulation of the chosen brain circuit, while a nose-poke...different patterns and the animal only receives stimulation in one of the two chambers (see image below)....

...the model organisms which I use to study gene regulation during developmental processes, CRISPR/Cas9 allows...but currently requires additional experimental manipulation. In some cases, injection of Cre is required...mutation must be removed, which can be done by isolating animals with particular visible phenotypes. These...following a report that one can use linear repair templates (ie. PCR-derived dsDNA) with 30-60 basepair homology...ribonucleoprotein complex with linear DNA as repair templates which reduces time to generate edits to only four...but require variable amounts of experimental manipulation and screening.  A co-selection strategy for ...be obtained in eight days. The only animals on a plate, other than the parental animal, are rescued progeny...

...developing a general translation initiation sequence known as the Species-Independent Translational Sequence (SITS... fuse custom PUF proteins to a translational repressor to down-regulate a gene of interest. You can generate...: 1147. Cooke, Amy, et al. "Targeted translational regulation using the PUF protein family scaffold....extensive sequences used for cloning into the final translated products. Negative selection markers built into...Tikhonova, Elena B., et al. "A transcription blocker isolated from a designed repeat protein combinatorial library...of which you can clone your gene of interest. Translation of the standardized leader peptide prevents secondary...encoding your gene of interest from affecting its translation initiation and instead makes initiation heavily...

...Forward and reverse screens involve manipulating or mutagenizing a population (typically cells or small organisms...screens, there is random or unknown manipulation of the population. This is contrary to reverse screens...disease as the input population. For these experiments, the goal is to identify manipulations which either enhance...in that only survivable manipulations are assessed, rather than all manipulation events. To put it another...looking at cells that can survive. Instead, all manipulations are assessed, regardless of whether they enhance... is assessed. The two most common methods of manipulation are genetic knockout mutations and treatment...consider these questions to save yourself a headache later on. Enhancer and suppressor screens These types ...

...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...