We narrowed to 1,042 results for: URE

...noise and ensure you are measuring the events-of-interest. Sensors suitable for ER measurements include:... requiring only a simple measurement. However, single wavelength measurements are more susceptible to ... RE. Structure-and mechanism-guided design of single fluorescent protein-based biosensors. Nature chemical...subtype) and specific subcellular compartments for measurements. All of the sensors discussed below fall into...slower). GCaMPf may be suitable for very rapid measurements, like action potentials in neurons. jGCaMP7 ...additional versions are available to simultaneously measure calcium changes in the ER, cytosol and mitochondria...you combining your calcium reading with other measurements, specifically fluorescent ones? Many of the ...

...analyzes publications and figures using machine learning to extract important features such as influential ... top of the ever expanding body of biomedical literature! PubMed PubMed is the classic search engine ...eventually replace the existing version of PubMed.  Key features This new version has an improved search algorithm...updated. This Twitter list contains >300 Twitter literature bots, including a bot for biosensor papers, microbe...Semantic Scholar Semantic Scholar is an AI-backed literature search developed by the Allen Institute for Artificial...that are more relevant to your search terms. Key features Semantic Scholar has several ways to focus your... populated at the top of this filter. A unique feature of Semantic Scholar search results are the topic...

...to compare exposure times of our samples. A prominent, strong signal has a shorter exposure time than ... be essential to your new research project, but unsure which one will mark your target the best, or even...The strength is based on binding specificity and exposure time. We first have a negative control which does...align with what the atlases (mentioned above) and literature suggest, providing an expectation and comparison...imaged pattern does NOT align with the atlases/literature and is unrelated to the target protein, we categorize... goldilocks antibody selection process The exposure time of the primary antibody compared to negative...control also determines the signal’s strength. Exposure time is the amount of time the sample needs to...

...using cloning rings. A picture of a 60 mm dish ready for picking is shown in figure 1.   Find Additional... Protocol Pages Agarose cloning method procedure The procedure (illustrated in the YouTube video below...well plate is also prepared with about 200 ul of culture medium containing serum in each well. A 200 ul ...both Hepes and bicarbonate) is brought to room temperature and placed in the hood. The medium from a 10 ...is capped, swirled and tested for the correct temperature by placing on the wrist or cheek. Within less...warm but not hot- and still liquid- it is rapidly poured onto the middle of the plate, where it immediately...the agarose cloning method Test your agarose temperature. Cloning cells using an agarose overlay does ...

...editors for more details on how they work!) Figure 1: Base transitions are edits between the purine...side groups of DNA bases and leave the core ring structure intact, allowing them to make 4 out of the possible... Cas9 are sequence specificity and the R-loop structure. In order to bind DNA, Cas9 requires (1) a guide... a region of separate strands called an R-loop (Figure 2). This allows the guide RNA to base pair with...accessible on the outside of the enzyme. Figure 2: CRISPR R-loop. Created with BioRender.com. ...abasic sites with A's, producing C → A edits. Figure 3: Mechanism of cytosine transversion editors. ...experimented with adding different proteins to the CGBE architecture. They conducted a CRISPRi screen to identify...

...kinetics which are illustrated in figures 2 and 3.  Figure 2: Glutamate titration curves for ...from Aggarwal et al…, Supplementary Figure 3.   Figure 3: pH titration curves and ∆F/F0 for...recommend using the SGZ for in-culture work only, GPI anchors for in-culture work and 2P in vivo imaging,...using both 1-photon and 2-photon imaging.   Figure 1: 1P and 2P excitation and emission spectra of...iGluSnFR3 v857. Image adapted from Aggarwal et al., Figure 1   Increased versatility through two different...Image adapted from Aggarwal et al…, Supplementary Figure 2.   Improved trafficking and localization... constructs. Image adapted from Aggarwal et al… Figure 4. PDGFR is a C-terminal fusion to the PDGFR transmembrane...

...content we store in them: music, emails, chats, pictures, and apps. Throughout my time as a graduate student...allowing you to upload anything from protocols to pictures of gels or even sketches to your notebook. The...saving trees! The Earth thanks you. 2. Gibco Cell Culture by Gibco Whenever I start to learn a new technique...I digress. When I started learning proper cell culture technique, I tried to find an app that could help...calculations. This is how I came across the Gibco Cell Culture app. Gibco organizes its app into four categories...are a lifesaver when your research requires cell culture and include a counter, lab timer, dilution calculator...calculator, and a couple of other nice features. This app also has a great educational section. This section...

... (see Figure 1). Oligo 2: Add 'ggcc' to the 5′ end of your reverse complement guide (see Figure 1). Perform... tissue culture-free heritable genome editing using RNA virus-based delivery in wheat. Nature Plants. ...single guide RNA (sgRNA) used in Cas systems. The structure is also reminiscent of sgRNAs, with reRNA containing...gene-edited plants without the need for tissue culture (Maher et al., 2020; Qiao et al., 2025). However...choice of promoter for ωRNA (reRNA) expression (see Figure 1). Both plasmids contain a hygromycin resistance...phosphorylation and annealing of the two oligos. Figure 1: Components of TnpB, schematic of pKb-TnpB1 and...transformation into plant cells. Conclusion & Future Directions TnpB represents a new generation of ...

... the process. Also refer to Figure 1 for a visual overview! Figure 1: General overview of the MoClo...dive directly into the pipetting! MoClo nomenclature and structure can be quite confusing for new users,...insert-to-vector ratio using the equation in Figure 3.    Figure 3: Calculation for the plasmid volume... MoClo a walk in the park.  Before you begin, be sure to check out Addgene’s MoClo guide for all the basics...assembly process to produce a multigene construct. Figure exemplifies the extraction and use of a coding ..., and have a clear vision of the final vector structure you want to achieve before starting your experiments...These overhangs are known as the common MoClo nomenclature. The overhangs are generated using type IIS ...

...solubility and stability (Figure 2).      Figure 2: Crystal structures of CRBNmidi alone (A) and...establishing CRBNmidi as a promising tool for future structure-guided drug design and studies of protein ...domains and is recommended for use in western blots (Figure 1). If you prefer to produce your own antibody ...chain are also available from Addgene!   Figure 1: Experimental validation for Anti-V5 [IPI-SV5...dimmer, showed greater photostability and also matured considerably faster, with expression levels comparable...comparable to GFP during early embryogenesis (Figure 3). mScarlet-I3 also offered clearer signals due to...autofluorescent tissues like the intestine. Figure 3: Expression of fluorophore-tagged GOLG-4 through...

...growing in requests faster than jGCaMP7 (Figure 5B).   Figure 5: A) GCaMP6, jGCaMP7, and jGCaMP8 viral...setup. Teams across Addgene have worked hard to ensure that the service has grown steadily, helped by ...our catalog had grown to 879 viral catalog items (Figure 1). The service caught on quickly in the scientific...distributed over 100,000 viral vector preps!   Figure 1: A) Cumulative AAV preps available in the Addgene... they’re delivering their payload to.   Figure 2: Numbers of AAV tools, by category, available...respectively, by substrates, light, or engineered ligands (Figure 2). Biosensors, which include calcium and voltage...explain why they are the most commonly requested (Figure 3). Over 400 biosensors were distributed in 2023...

...neuronal sub-cellular structures GFP is limited in its ability to label subcellular structures in the CNS. GFP...connections (Shepherd, 2004). Understanding the structure and function of these neural circuits is essential...experiments and visualize numerous molecules or structures at once (Shaner, 2007). In contrast to epitope...for the cells and affects the labeling of small structures like neurites. Like epitope tags, low FP expression...church of the Flying Spaghetti Monster; the smFP structure resembles images of the deity (see comparison ...processes. In contrast, smFPs can label fine neuronal structures with high fidelity and at lower concentrations...GFP. smFPs enable better labeling of these fine structures through their multiple, high-affinity binding...

...preparations are genome-containing (Figure 1).    Figure 1: Electron micrograph of an Addgene... by the temperature parameters. For example, we found that changing the annealing temperature of the PCR...viral vector solution, and generally these methods measure different characteristics of the solution. These... containing viral genomes. Physical titers are measured by quantifying the concentration of viral genomes... report the physical titer of a viral solution (Figure 2). Because physical titers are used for dosing...values mean and how they can be compared.   Figure 2: Label that comes on Addgene’s AAV aliquots. ...circled in red) report physical titer, which is measured by qPCR.   Physical titer is typically calculated...

... of temperature on total crop production and the production window. A two-way MANOVA could measure the..., you could test the impact of temperature, humidity, sunlight exposure time, and watering volume on total...power. Not sure if your data meets the assumptions of parametric tests? If you aren’t sure if your variance...outliers or data spread within those data sets. Measures of dispersion – standard deviation/error, variance...in a certain direction (i.e., you just want to measure if a sample is greater than a control), then a ...variable. A two-way ANOVA could test the effect of temperature and humidity on an outcome such as total crop... one-way ANOVA can test either the effect of temperature or humidity on crop production.   MANOVA The ...

... Figure 1: Schematic representations of the indicated unbiased genotyping options. Figure reproduced...other elements, including those relating to DNA structure (e.g. epigenetic modification, bulges) that may...conventional algorithms may not provide a full picture of the impact of CRISPR editing in the model cell...negatives Combining sequencing techniques can ensure validated experiments Unbiased detection methods...sequencing and in silico prediction should give a broad picture of all possible editing events in the genome; from...induced by CRISPR-Cas nucleases in human cells." Nature biotechnology 31.9 (2013): 822-826. PubMed PMID...reveals RNA-programmed Cas9 nuclease specificity." Nature biotechnology 31.9 (2013): 839-843. PubMed PMID...

...fluorescent protein mOrange2 (Figure 2). Figure 2: OCaMP structure and mechanism of action. Reproduced...brightness, ∆F/F0, or signal-to-noise ratio (Figure 3). Figure 3: One- and two-photon excitation and ... Figure 4: Calcium titration curves for OCaMP and various red and yellow GECIs measured with soluble...lasers available in your microscope setup. Figure 1: Excitation (dotted) and emission (solid) spectra...indicators spanning nearly the entire visible spectrum (Figure 1). The GCaMP series (e.g., jGCaMP8) remains the... yellow GECIs, OCaMP shows: Higher ΔF/F0 (the measure of signal change during calcium events), Greater...a CC-BY-NC-ND 4.0 International license. Figure 5: A) Simultaneous fluorescence (upper trace) and...

...downregulation. Figure 3 shows a histogram for a yes-no dot plot, like the one shown in Figure 1.  ...populations in the histogram plot in Figure 4 compared to the dot plot in Figure 2. Quantification using MFI makes...Before you read out your plots, you’ll want to make sure you’ve also adjusted voltage and compensated your...adjusting voltage: During data acquisition, make sure that the signal for the positive population is no...should overlap with the negative control population (Figure 1). Based on where the GFP- population ends, you... the total cells present in the gate.   Figure 1: Example of yes-no flow plot of the (negative...expression, low expression, and everything in between (Figure 2). These smears tend to occur when you are looking...

...Nishimasu H, Nureki O, Zhang F. Nature. 2015 Jan 29;517(7536):583-8. doi: 10.1038/nature14136. Epub 2014...Cas9’s crystal structure. “I thought maybe we could use information from the structure to guide and improve...technology. These libraries are lentiviral in nature, so please ensure that you are equipped and authorized to...genes, it is not possible to test each one and make sure it’s working. You can only do that screen with a... the SAM pooled library In a paper published in Nature in December, Konermann and her colleagues in Feng...-scale, knockout screening). As the Zhang lab's Nature paper reports, “Here we have shown that the SAM...Therapeutic uses in humans are also on the table. “In the future, there is potential there,” he says. "We have to...

...the purification procedure. Good indicators of DNA purity are the absorbance measurements at 230, 260, and...same. Before purifying a plasmid from a bacterial culture, it is important to consider your experiment.  ...Cloning grade DNA Transfection grade DNA Figure 1: Transformation introduces transformation grade...range). It can be extracted from small bacterial cultures (i.e. 2-3 ml) with or without commercially available...and DNA for transformation doesn’t need to be as pure as for other uses.   Cloning grade DNA Molecular...also dictate the required sizes of the bacterial cultures and commercial kits you will adopt for the extraction... cloning it is important that the preparation is pure from other nucleic acids (genomic DNA and RNA), ...

...unique changes in their spectral properties upon exposure to a specific wavelength of light. PA-FPs can ...fluorescence, to a brighter fluorescent state by exposure to a specific wavelength of light. The switch ...switches from green to red fluorescence. mEosFP exposure to UV light causes an irreversible cleavage near...formation of mEosFP’s chromophore requires a temperature below 30°C and this is not ideal for experiments...emission of green fluorescence, but then further exposure to blue light also inactivates the chromophore...state. Dronpa can be reversibly reactivated by exposure to UV light. The fact that blue light both activates...photons are being emitted, making it easier to capture a clear image above background. The majority of...

...applications.   Figure 1: Live-cell labeling strategies. The green structure represents a fluorophore... end up linked to whatever molecule you choose (Figure 1). Just express the fusion protein and add a specific...fluorophore or other useful ligand, gray structure is the protein of interest, and black is the fusion tag ...-tag construct can help you better detect dim structures or low levels of expression with the same imaging...super-resolution or single-molecule techniques.   Figure 2: Two-color super-resolution imaging of ER and... enables applications like multi-color imaging (Figure 2). If you’re working with purified proteins in...colors depending on the needs of your experiment (Figure 3). And using self-labeling tags makes updating...

... to ensure all plasmids pass our high-quality standards and contain the expected plasmid features.  ...based on SnapGene’s “Common Feature” library — with some additional features added by the QC team — and...the plasmid to ensure our assembly result is accurate The gene/insert or any major feature highlighted by...Nobody’s perfect! This is a platitude I’m sure we have all heard. It’s a truth that extends to both people...optimizing experiments, to false conclusions.  Figure 1. Potential points where DNA errors can be introduced... Figure 2. Addgene’s basic QC process. Created with BioRender.com. Once Addgene receives deposited...resolving a variety of QC issues. This process ensures that any potential sequence discrepancies can be...

... alert the day of the procedure. Mice move much more quickly than cell cultures do, and tired researchers... some nerves. Following safety procedures and practicing safety culture, however, can let you work with...risks and how to minimize them. Built-in safety features   When viruses were first being engineered as ...still enter (and thus infect) cells, this safety feature prevents the virus from replicating and spreading... including yourself as the researcher.   Figure 1: Separation of retroviral packaging components...precautions to take, and if something does happen, ensure you can receive appropriate treatment and/or monitoring...monitoring. Virus-specific concerns   In nature, some viruses are more dangerous than others, and the...

...present in the sample (APC in the case of Figure 1). In Figure 1A, the population needs to be shifted towards.... Let's look at an experimental example in Figure 2. Figure 2A shows the sample prior to compensation....the populations move, as in Figure 2, following compensation. Figure 3: Flow plot for a double positive... a compensation value between the two channels (Figure 1A). Applying compensation means you are telling...values later in your analysis, unlike voltages.  Figure 1A shows a single-color APC control, with APC and... a straight line and are only positive for APC (Figure 1B). For single-color samples, you can only change...would decrease the compensation value.   Figure 1: Compensation example with single color control...

...also stable at this temperature and can bind to the primers.  Extension- The temperature is then raised slightly...slightly to Taq polymerase’s ideal temperature (70-75oC). At this temperature Taq polymerase can synthesize...and the use of a fluorometer feature built into the thermocycler to measure that fluorescent output. With...resistant enzyme that can withstand changes in temperature. Taq was first identified in the late 1960s during...separation of the two DNA strands.  Annealing- The temperature is then dropped to a range in which the forward...forward and reverse primers are stable. At this temperature the primers can anneal to the single stranded...the target DNA quickly and accurately.  Figure 1: Steps in PCR reaction   This process of ...

...your own figures Google Drawings Google Drawings is similar to using PowerPoint to draw figures. It’s part...useful for drawing figures with lots of elements. It took some playing around to figure out all the settings...project my team & I have poured our hearts into for 2 yrs) has 200K+ figures by 95K+ scientists 👨🏽‍🔬...when writing posts. Since then I’ve realized my figures are just as important, if not more important, than...drawing tools, so it’s harder to draw intricate figures, like a brain or a mouse. Vectr Vectr is like a... Vectr to be fairly intuitive and I was making figures quickly. Inkscape Inkscape is the most similar...Illustrator out of the three options for drawing your own figure discussed in this post. It’s open source and available...

...design goals. Examples:  “feature aware”, “SNP aware”, “secondary structure aware”, and “microhomology...collective utility, it’s easy to fault the lack of features in a single application. The question is then,... solve, and finally how we might proceed in the future. When we think of designing experiments using CRISPR...have broken down the tools into the individual features that make each tool unique. The CRISPR Software...Software Matchmaker is composed of these features and enables you to select the tool(s) based on your project...advanced functionality, it seems these kinds of features are delegated to other more suitable software ... removing repetitive tasks and/or by providing features to help with the post-design process such as primer...

...activates halorhodopsins to silence neuronal activity (Figure 1) (Wiegert et al., 2017). How to get an opsin...into the correct orientation to be transcribed (Figure 2) (Sharma and Zhu, 2014). How does FLEx enable...promoter only in specific neuronal cells. FLEx ensures, therefore, spatial accuracy and strong opsin expression... functional topography of the neural circuit architecture of the brain regions associated with motivated...on developmental biology at the École Normale Supérieure de Lyon. Her love for educational science led...genetically targeted optical control of neural activity." Nature neuroscience 8.9 (2005): 1263. PubMed PMID: 16116447...: PMC2820367. Deisseroth, Karl. "Optogenetics." Nature methods 8.1 (2011): 26. PubMed PMID: 21191368. ...

...short-read sequencing are highlighted in Figure 2. Figure 2: Overview of short-read sequencing technology...pnas.74.12.5463  Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26... that’s not the only technology Addgene uses to ensure accuracy of deposited plasmids. To resolve QC issues...recognized and recorded as a DNA strand is synthesized (Figure 1). Sanger sequencing requires four separate reactions... “trace” file to determine the sequence. Figure 1: Overview of Sanger sequencing technology. Created...by synthesis, but modifies the original Sanger procedure to improve throughput by increasing the number...puzzle pieces together. Once they have the full picture of the puzzle, the QC team compares it to the plasmid...

... and in vitro applications.   Figure 2: Modular features of DIRECTED particles where the fusion...-the-art. PE6b was very efficient for short, unstructured templates and significantly reduced undesired...efficient at complex edits, such as long or highly structured templates. Cas9 variants PE6e–g often had even...varied depending on the specific edit.   Figure 1: Choosing the best PE6 variant for your application...type-specific delivery by modular envelope design. Nature Communications, 14(1), 5141. https://doi.org/10.1038...therefore been trafficked between locations). Figure 3: A) LOV-Turbo becomes active when illuminated... control of proximity labeling in living cells. Nature Methods, 20(6), 908–917. doi: 10.1038/s41592-023...

...codon optimality reveals hidden signatures of cotranslational folding." Nature structural & molecular biology20.2...but some possible reasons include: Metabolic pressures - it takes cellular resources to produce tRNAs...Protein folding - If a protein is encoded by a mixture of codons with highly and poorly charged tRNAs,...codons are associated with specific secondary structures in 10 closely related yeast strains. Adaptation...properly. You might then think, “Okay, I’ll just make sure the abundances of the codons I choose for the host...Angov et al., 2008), but there are still many more features to consider when designing a full gene. A non-...Restriction sites Sequences prone to create secondary structures in RNA transcripts Effects on transcription (...

...repository, but be sure to let us know if you'd like to write about your plasmids in a future blog post. No...found at Addgene and in Figure S12 of the publication. Agudelo D, et al. Nature Methods. 2017. PubMed ...Rees H, et al. Nature Communications. 2017. PubMed PMID: 28585549 Kim Y, et al. Nature Biotechnology. ...GABA-ergic interneurons here. Dimidschstein J, et al. Nature Neuroscience. 2016. PubMed PMID: 27798629 Listen...Find PhoCl plasmids at Addgene. Zhang W, et al. Nature Methods. 2017. PubMed PMID: 28288123 Listen to...used as tools to learn about the influence of structure on an FP’s properties. pBAD-LSSmCherry1 is a long... Plasmid ID Plasmid Name Cas9 Variant Speacial Features 85169  pJL-SaBE3  SaCas9 (NNGRRT)    85170...

...CRY2PHR-activator fusion floats freely, depicted in the figure below. Once triggered by blue light, the CRY2 and...31X. By using a slit pattern during blue light exposure (470nm), the researchers showed that expression...created a photoactive Cas9 tool, as shown in the figure below. Their most successful design utilized Magnet...on and off. As one might expect from the modular nature of Cas9, Nihongaki et al. showed that it was possible...reach deeper tissues. Additionally, high intensity exposure can cause DNA damage. Far-red light, however, ...to create photoswitchable spCas9, dCas9, and S. aureus Cas9 (saCas9) proteins, showing the versatility... variant of AcrIIA4 (CASANOVA). As shown in the figure below, in the absence of light, Cas9 is bound by...

... of fluorescent dyes/ligands Figure 1: Example structures of fluorophores, fluorescent dyes, and...visualization of both organic tissues and cell cultures, opening biological interiors to many inquisitive... and fluorescent ligands. Figure created with BioRender.com. Fluorescence refers to the emission ...Fluorescent dyes and ligands vary in their chemical structure, leading to differences in their excitation and...ability to retain fluorescent intensity during exposure to light, is another factor to consider. If your...your application requires longer periods of exposure, you’ll want a more photostable fluorophore. Factors...recruitment to receptors, indicating their agonistic nature. The potency and efficacy of these ligands can ...

...a separate fix/perm cytosolic procedure in that case.     Figure 3: For intracellular labeling...antibody through the biotin-streptavidin interaction (Figure 1a). This interaction brings the fluorophore in...plasmids and biotin plasmids at Addgene!     Figure 1: Indirect detection of target markers can be ...(“anti-rabbit”) region of the primary antibody (Figure 1b). As above, the advantage of this system is ...which would label everything but the CD8+ T cells (Figure 2). Even better, we can use the same fluorophore... gating on the negative population.     Figure 2: Dump gating labels all unwanted cell lineages...membrane but inside the cell. Due to their chemical nature, antibodies cannot penetrate the cell membrane;...

...guest bloggers Shravanti Surest from Iowa State University. Shravanti Suresh is a PhD candidate who investigates...This post was contributed by Shravanti Suresh from Iowa State University. Since its appearance, SARS-...19 and some serological tests to determine past exposure. However, the limited availability of reagents... turn to other technologies like CRISPR. Figure 1: An overview of the general schematic of CRISPR...with streptavidin, the lateral flow strip first captures the streptavidin portion of the probe via biotin...probe that is cut will continue to flow and be captured by an antibody further along on the strip. Highlights...Isothermal amplification is done at one constant temperature, eliminating the need for thermocyclers. This...

...primary is conjugated to a fluorophore (Figure 1).   Figure 1: Comparison between how direct immunofluorescence...confocal   Figure 2: High-level overview of an indirect immunofluorescence procedure with key considerations...within a cell,” “Does this disease change the architecture of my cells,” or “How does this mutation impact...non-fluorescent visualization methods. Stay tuned for a future blog post to learn more about these techniques!.... For this strategy to work, it is important to ensure that you are using secondaries with fluorophores...divided into the several steps outlined below and in Figure 2. For a deeper dive into the steps and techniques...involve multiple smaller steps that all help to ensure that antibodies can access their target and that...

...Symposium and Workshop, organized by Future of Research, Academics for the Future of Science, and the MIT Graduate... More information can be found at http://futureofresearch.org/advocating-for-science-boston-2016/. Sign...Science Symposium Boston 2016 Changes since the Future of Research Symposia Ongoing challenges facing...et al, PNAS 2014; Taylor, eLife, 2016). Several Future of Research (FoR) symposia held across the USA ...science to date. Advocacy opportunities for the future No matter your opinion on these changes, it is ...institutional responses to the FLSA ruling. Similarly, from purely a salary perspective, while this is a move in the...For those advocating in this area, keeping the pressure on for further increases will be challenging, ...

...disrupt normal cell biology and make it hard to capture true protein behavior. Traditional epitope knock-ins...Together, these limitations create challenges for measurements needed to move discoveries from the lab bench...reconstitutes a fully functional luciferase enzyme (Figure 1). Addition of substrate generates a proportionate...research questions before creating knock-ins.  Figure 1: Schematic of HiBiT tagging technology.   ...autofluorescence from the plates or media, which can obscure weak signals; photobleaching from the excitation...more than substrate addition and a simple add-mix-measure method. NanoBiT® luciferase activity is compatible...letting you track endogenous protein activity and measure responses to therapeutics in real time. Let's take...

...Glypican Collection here! Figure 3: General glypican domain structure. Glypicans are proteoglycans ... no UTR sequence added to the genome (Figure 4). Figure 4: STITCHR consists of a nicking Cas9 ... FOS gene promoter and the MYC locus (Figure 5). Figure 5: TurboCas protein labeling compared ...synapses and deep-brain fiber photometry.  Figure 1: Characterization of iGluSnFR4 in mice. A) Scheme...choice. After hearing about researchers' favorite features and limitations of existing backbones, we're excited...viral generation and stable cell line creation (Figure 2). Looking for more? Explore our empty and EGFP... own Lentiviral backbone plasmids here! Figure 2: Addgene cloned EGFP into pAG Lenti CMV N-HA ...

...between strains of one species, so be sure to check the literature and validate your choice of AAV vector...Tropism depends on many variables, so be sure to check the literature for previous work in your experimental...adeno-associated virus infection. Nature, 530(7588), 108–112. https://doi.org/10.1038/nature16465 Tervo, D. G. R., Hwang...allowing them to target particular cell types. Figure 1: Diagram of AAV components. Created with BioRender.com...vectors have both distinctive capsids and genomic structures. The viral capsid is the key that lets AAVs “...mixing, matching, and modifying capsid and genomic structures. For example, rAAV pseudotypes mix the genome... by Addgene are pseudotypes using the genomic structure of AAV2, so they are formally called rAAV2/1, ...

...factors to consider when choosing one.     Figure 1: Example of an experimental optogenetic setup...activity or gene expression. Experimental output is measured and quantified. Created with BioRender.com. ...either excite or inhibit neuronal activity upon exposure to light within a specific range of wavelengths... be used in tandem with the opsin.      Figure 2: Diagram of excitatory (ChR2) activation by light...engineered receptor that change shape with light exposure to activate them. PORTLs use a similar concept...when a signaling pathway is unknown.      Figure 3: Chimeric OptoXR incorporating rhodopsin undergoes...that may go awry in a disease state.      Figure 4: Example of an intracellular signaling pathway...

... notes on how lab procedures were actually performed, potentially curtailing future confusion (and hours...community-editable fluorescent protein database ReFigure: Save Scientific Figures into Dashboards and Share Your Insights...reproducibility issues in the biological sciences and featured speakers from academia, industry, nonprofits, ...reproducible if its findings can be predictably applied to future work. Importantly, no one should expect that every...Failed attempts to apply irreproducible results to future work cost both time and money with estimates reaching...doing an experiment wrong. However, even simple procedures like pouring a plate or running a gel have intricacies...initiatives to create more reliable reagents for future research. I’ve talked to many researchers who have...

...10 minutes, but check with your enzyme’s manufacturer to ensure that you’re cutting for the proper duration... the ligation mixture with backbone alone; 2. Transformation containing ligation mixture with insert and...proper orientation. You then add ligase to the mixture to covalently link the backbone and insert and,... phosphatase) are commonly used. Follow the manufacturer’s instructions.   2. Isolate Your Insert and...unfortunately you can’t just throw the digestion mixtures together. You need to isolate your insert and ...charged DNA through the gel. As indicated in the figure on the left, your digested DNA (and undigested ... the Bitesize Bio Blog and their associated manufacturers websites. These stains require you to either...

...compositions of Cascade. Although seemingly ubiquitous in nature, they are largely underutilized in research settings...mostly a consequence of Cascade's complexity. Figure 1: Schematic of Class 1 CRISPR types. Class 1 includes... systems utilize with type I-F Cascades. Figure 2: Cascade complex from CRISPR type I-E. Created...tools has been challenging. It can be difficult to ensure comparable expression of all components of Cascade...making cuts every so often. Cutting both strands ensures that there isn’t a template strand left behind ...behind that the cell can use to repair. Figure 3: General overview of the Cascade-Cas3 mechanism. Created...components can make Cas9 easier to work with than Cas3. Future targets Cas3 has the potential to be incredibly...

...MagLOV’s structure changes under magnetic field. Such changes could be harnessed or enhanced for future MagLOV-based...control of biological systems (Wheeler et al., 2016; Duret et al., 2019). But the field has sometimes seen ...1%) and recovered after the magnet was removed (Figure 1). At first, Andrew and Maria were skeptical. ... since the initial report in 2023.)     Figure 1: Fluorescence intensity of EGFP-FlavinTag in ...change of ~75% in response to the magnetic field (Figure 2); they named this variant MagLOV. Andrew was ...and didn’t need any added cofactors.      Figure 2: Fluorescence intensity and ΔF/F of MagLOV, a...magnet is waved under the sample. The imaged area measures approximately 82 mm across. Video courtesy of ...

...which attract fish for them to prey upon (Figure 1). Figure 1: The sea anemone's red color can be used...aeBlue, amilCP, tsPurple, and gfasPurple) (Figure 2). Figure 2: Chromoprotein expression from bacteria...fluoresce at very low levels. Chromoproteins in nature Compared to the history of fluorescent proteins... chromoproteins lost color overnight in liquid culture, though expressing the chromoproteins from the ...chromoprotein plasmid that combines the most desirable features: intense color, fast maturation, and low fitness...     Chromoproteins for allelic exchange Figure 3: pTOX plasmids expressing amilCP and tsPurple...genetic modification integrates into the genome (Figure 3). Here, the chromoprotein is expressed and gives...

... active for greater than 50 generations. Figure 1: Mobile-CRISPRi's modular components. Image from...it integrates into the trnS-leu2 locus.   Figure 2: Introducing Mobile-CRISPRi into bacteria. Top...However, the rate of transfer was variable. They measured transfer rates by comparing the number of colonies...several bacteria associated with human disease (S. aureus, Klebsiella pneumoniae, and P. aeruginosa) in addition...isolated from cheese. Knockdown efficiency, as measured by knockdown of a constitutely expressed RFP reporter...median knockdown of ~40-fold across all species measured. Beyond understanding the basic biology of bacteria...pathogens) were grown in presence of trimethoprim, cultures treated with a folA gRNA were more sensitive to...

... resource. Nature Protocol Exchange Website: http://www.nature.com/protocolexchange/ Nature Protocol Exchange...for iOS and Android). A neat feature of protocols.io is the checklist feature which allows you to check ...process so you’ll have a record of your work. This feature further simplifies lab work if you like to bring...an open online protocol repository hosted by the Nature Publishing Group. Like the previously mentioned...and create lists of your favorite protocols for future reference. The exchange currently boasts over 2,500...links to protocols on their own websites. We're not sure how frequently it's being updated now, but there...access to protcols from external vendors, such as Nature Protcols and NEB. Quartzy Website: https://www....

...Martin, B., & Shendure, J. (2022). Precise genomic deletions using paired prime editing. Nature Biotechnology...editing world. The approach, originally published in Nature, is a “search-and-replace” genome editing technique... breaks (DSBs) or donor DNA templates.  Figure 1: An overview of prime editing. Created with BioRender.com...Liu lab contributed an improved prime editing “architecture” that can be combined with any of the PE2-PE5...prime editing as efficient as possible. Figure 2: Decision tree for selecting a PE6 variant. PE...2023, under a CC BY 4.0 license. epegRNAs: Structured RNAs with improved stability Traditional sgRNAs...of large DNA sequences with twin prime editing. Nature Biotechnology, 40(5), 731–740. https://doi.org/...