...Colorful CRISPR technologies are helping researchers visualize the genome and its organization within the nucleus...nucleus, also called the 4D nucleome. Visualizing specific loci has historically been difficult, as techniques...CRISPR labeling techniques allowed researchers to visualize nearly any single genomic locus, and recent advances...Image from Ma et al, 2016. Using dCas9 to visualize genomic loci in vivo The flexibility of CRISPR...

...Rojas. A question worthy of a PhD: How do you visualize protein turnover within a neuron? For my PhD I...context. In other words, I needed a method for visualizing protein turnover in situ in neurons. The classic...turnover of individual proteins in situ.  For the visualization of specific proteins in situ immunocytochemistry...within that pool. Therefore, it is not possible to visualize the localization of protein synthesis. Alternatively... protein tags can be used to facilitate the visualization of specific proteins in cells. Tagged protein...back then still unpublished, that allowed the visualization of specific de novo synthesized proteins in ...Frankfurt am Main and perform similar experiments. Visualizing newly synthesized proteins with FUNCAT Professor...

...these visualization tools is CRISPR-Sirius, the brightest CRISPR-based tool to date for visualizing genomic...past few years, dCas9 has also become a robust visualization tool to study the spatial and temporal arrangement...cells. Previous iterations of genomic loci visualization tools using CRISPR In 2015, Thoru Pederson’s...developed a dCas9-based multicolor labeling system to visualize chromosomal loci in human cells (Ma et al., 2015... While CRISPRainbow allows for simultaneous visualization of sites on different chromosomes in living ...They improved on previous CRISPR-based loci visualization tools by increasing gRNA stability. First, they...they began with the Broccoli aptamer system to visualize the gRNA in living cells. Broccoli aptamers are...

...of various stimuli on global translation, but a visual technique to study translation remained elusive...destination co- or post-translationally. TRICK: Visualizing the first round of translation While ribosome...membrane, it’s not appropriate for use with mRNAs usually translated in a specific compartment. Despite these...

...requested plasmids, or trends of requests over time. Visualizing the data So, after downloading my plasmid request...request data, I started to explore how I could visualize the aggregated data. Plotting the data in interactive...

...protein of interest is to make it detectable. Visualization can be achieved using fluorescent microscopy...from the fusion itself to the wild-type protein visualized with a fluorescently-tagged antibody. By employing..., to use inert fluorescent protein fusions to visualize subcellular structures. For example, you might...appropriate quantification methods and tools. It is usually not enough to examine your images using subjective...

...antibody probe, scientists can now more easily visualize single molecules and newly formed proteins.  ...specificity towards a HA epitope from the CDRs.  To visualize proteins of interest tagged with the HA epitope... created a versatile tool that can be used to visualize a wide range of protein dynamics in vivo. In the...Additional resources on the Addgene blog Learn about visualizing protein turnover Download the fluorescent protein...

...method for directly visualizing PPIs in cells. The ease with which BiFC can be visualized makes it amenable...Fortunately, a complementary method exists for visualizing protein-protein interactions (PPIs): Bimolecular...BiFC only uses a single fluorescent protein to visualize PPIs. This fluorescent protein (FP) is split into...complementation BiFC has been used to directly visualize PPIs that regulate numerous cellular functions....38853 Hu C-D, Chinenov Y, Kerppola TK (2002) Visualization of Interactions among bZIP and Rel Family Proteins...fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells. Nat...

...developed visual barcodes for clonal multiplexing of cells in live imaging application. Each visual barcode... reduced error rate for long sequence knock-ins Visual barcodes for live cell clonal multiplexing Improving...2022. https://doi.org/10.1038/s41556-021-00836-1 Visual barcodes for live cell clonal multiplexing by: ...different fluorescent proteins, and inserting each visual barcode into its own subclone, they were able to... using freeware.    Fig. 4: Images of 12 visual barcodes in use in A375 cell line. Image from Kaufman...allowing for up to 20-plex experiments with one visual barcode per cell and up to 200-plex with two barcodes... or kinase translocation reporters (KTRs). Find visual barcode plasmids here! Kaufman, et al. 2022. Nature...

...neuroscience research. The use of genetic tools for visualizing and perturbing circuits together with the development...expressed. As these epitopes tags have no intrinsic visual signal, they cannot be detected directly in live...also use multiple FPs in single experiments and visualize numerous molecules or structures at once (Shaner...multi-color imaging experiments, the second color is usually provided by red fluorescent proteins such as tdTomato...using smFPs and standard neuronal tracers. 2. Visualization of neuronal sub-cellular structures GFP is limited...structures. For instance, smFPs have been used to visualize “thorny excrescence” (TE) spines in the Hippocampal...appear to be very effective probes for finely visualising sub-cellular structures or low-abundance proteins...

...(AAV), have been used for tracing and visualizing motor, visual, and auditory neuronal circuitry in vivo...away from the site of application and aid in visualization of the morphology of individual neurons, including...colorimetric product or are fluorescent. While dyes usually spread unidirectionally, there are some reports...that their diffusion across the synaptic cleft is usually severely impaired, and only few reports exist about...number of connections, or the “connectome”, to be visualized in a uniform and standardized way (Oh et al.,...An additional desirable property for network visualization would be the ability to spread trans-synaptically...attributes and their use has allowed for the visualization of single connection networks within the rodent...

...to high Uses visuals, audios, and text. Incredibly immersive and flexibility to visualize and contextualize...often more suited for cartoons or graphics for visuals. However, it’s much more challenging to design ...from smartphones with low data requirements.  No visuals. Variety of hosting platforms can splinter audience... digitally and physically. Easy to incorporate visuals if needed. Traditional media formats are quite ...  Photography Medium (high for microscopy) Visually compelling. Easy to convey a large number of details...contextualize. Graphics/cartoons (no words) Low Visually compelling and flexible. Can be used to illustrate...

...non-model organisms. Therefore, transient methods are usually the first choice for investigating gene function...In the plant sciences “transient transformation” usual means that neither a stable cell line or plant is... re-invent the wheel. Test different leaf ages Usually younger leaves work better. Not every leaf is equally...with histochemical GUS-staining is a very useful visual reporter (Figure 2). The GUS enzyme cleaves a substrate...which will then form a blue precipitate. GUS is usually the first choice for establishing a new transformation...substrate to produce bioluminescence. Luciferases usually have shorter mRNA and protein half-lives then GUS.... Syringe infiltration (D'Aoust et al., 2009): Usually a syringe without a needle is used to inject an...

...sound to visualize bacteria in the lab, I was excited to learn about creative approaches to visualize bacteria...microbes through a microscope is not the only way to visualize them. You can also “hear” them. Addgene depositor... as bacterial expression of dyes allows dye visualization in vivo using ultrasound (for an example see...showcased complex connections and ideas in various visualized approaches from hand-drawn comics (Dr. Sanja ...interesting and approachable!   The grand finale of visual impressions was delivered by the ASM Agar Art Winners...

...ELISA or Western Blotting, but it allows you to visualize a target of interest within an intact cell, tissue...these terms refer to the use of antibodies to visualize a target within an intact sample, a cell in the... case of IHC. IF is used specifically when we visualize the antibodies using fluorescence (for some background... also refer to assays using non-fluorescent visualization methods. Stay tuned for a future blog post to...direct IF, researchers use a single antibody to visualize their target. These antibodies are generated against...fluorescent molecule allowing one to “directly” visualize their target. In contrast, indirect IF requires...antibodies conjugated to distinct fluorophores to visualize multiple targets at once. An advantage of multiplexing...

...the insert ended up in the direction you want - usually by Sanger sequencing or further restriction digests... use a voltage difference across a gel matrix (usually agarose) to pull your negatively charged DNA through... individually. There are a variety of ways to visualize the DNA in your gel (this table is not inclusive...all gel stains):  Stain Pre or Post Run? Visualization Sensitivity (ng DNA) SYBR Safe Pre and Post...respectively). Some of the above stains require you to visualize your DNA using UV light – please note that UV ...personal protective equipment should be worn when visualizing using UV as it can cause damage to the eyes and...backbone alone plate). Unsuccessful ligations will usually result in few colonies on both plates (unsuccessful...

...the dynamic or working range of a given reagent (usually an antibody).      Figure 1: A protein ...number of helpful suggestions.  Gels Gel issues usually come down to voltage and time. Make sure to load...seeing a smiley face at an appropriate voltage (usually 10–15 V/cm of gel), your gel may be overheating...protein tag or an IgG binding site, allowing you to visualize them with a conjugated antibody. If you do not...with 20% methanol, and place over a light box to visualize proteins after transfer. Troubleshooting The ...with specific blockers, and the manufacturer will usually include recommended blocking conditions on the ... antibodies, the recommended dilution range is usually between 1:5,000 and 1:200,000. Check the manufacturer...

...studies, which are evinced by the Tet system and visualization of single molecules via targeted fluorescent...2013 August 20th; 14(1). TRICK: A method for visualizing the first round of translation in living cells...anticipate that this tool can also be used to visualize translocations, genome rearrangements and cancer-associated...GFP, BFP and mCherry), the authors were able to visualize simultaneously several parts of the genome and...variety of experiments including subcellular visualization of 6 different organelles, a cell cycle indicator...proteins have been used as subcellular markers to visualize the dynamics and interactions between the endoplasmic...These fusion proteins can act as markers for visualization of subcellular structure, for performing live-cell...

...marker, studying protein-protein interactions, visualizing promoter activity, and much more. Read on to ...C-terminus of a protein, which allows the scientist to visualize when and where the gene is expressed. Click here...cells in order to understand their activity and visualize the effects of alterations to this activity. Learn...put under control of promoters of interest, to visualize the developmental stage at which these promoters...particular cell populations in drug screens, to visualize micrometastases in nude mice in cancer studies...to label pathogenic intracellular microbes to visualize host/pathogen interactions.   Do you have a favorite...