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We narrowed to 886 results for: URE

Showing: 121 - 140 of 886 results

  1. Early Career Researcher Toolbox: Free Tools for Making Scientific Graphics

    Type
    Blog Post
    Published
    June 11, 2019, 1:16 p.m.
    ...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...

  2. The CRISPR Software Matchmaker: A New Tool for Choosing the Best CRISPR Software for Your Needs

    Type
    Blog Post
    Published
    Nov. 3, 2015, 3:30 p.m.
    ...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...

  3. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

    Type
    Blog Post
    Published
    Oct. 17, 2019, 12:28 p.m.
    ...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. ...

  4. Plasmids 101: Codon usage bias

    Type
    Blog Post
    Published
    Sept. 27, 2018, 1:09 p.m.
    ...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 (...

  5. QC Sequencing Technologies at Addgene

    Type
    Blog Post
    Published
    July 15, 2025, 1:15 p.m.
    ...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...

  6. Hot Plasmids - November 2023

    Type
    Blog Post
    Published
    Nov. 14, 2023, 3:35 a.m.
    ... 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...

  7. 15 Hot Plasmids from 2017

    Type
    Blog Post
    Published
    Jan. 9, 2018, 3:02 p.m.
    ...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...

  8. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    Published
    Sept. 3, 2020, 12:15 p.m.
    ...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...

  9. Illuminating Choices: A Guide to Selecting Fluorescent Dyes and Ligands

    Type
    Blog Post
    Published
    March 21, 2024, 1:15 p.m.
    ... 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 ...

  10. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    Published
    May 5, 2020, 1:15 p.m.
    ...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...

  11. Antibodies 101: Introduction to Immunofluorescence

    Type
    Blog Post
    Published
    Nov. 16, 2021, 2:15 p.m.
    ...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...

  12. Antibodies 101: Beyond Surface Labeling

    Type
    Blog Post
    Published
    June 27, 2024, 1:15 p.m.
    ...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;...

  13. Savvy Advocates Needed to Navigate a Scientific Enterprise in Flux

    Type
    Blog Post
    Published
    Sept. 13, 2016, 2:30 p.m.
    ...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, ...

  14. Scientific Reproducibility - Focusing on Solutions at the Minisymposium on Reproducibility

    Type
    Blog Post
    Published
    May 18, 2018, 7:32 p.m.
    ... 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...

  15. Exploring Applications of the Bioluminescent HiBiT Tag

    Type
    Blog Post
    Published
    Oct. 2, 2025, 1:15 p.m.
    ...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...

  16. Hot Plasmids: Spring 2025

    Type
    Blog Post
    Published
    June 3, 2025, 1:15 p.m.
    ...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 ...

  17. Viral Vectors 101: AAV Serotypes and Tissue Tropism

    Type
    Blog Post
    Published
    Jan. 16, 2025, 2:15 p.m.
    ...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, ...

  18. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...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...

  19. Plasmids 101: Restriction Cloning

    Type
    Blog Post
    Published
    Feb. 18, 2016, 3:42 p.m.
    ...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...

  20. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    Published
    Feb. 4, 2020, 2:15 p.m.
    ...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...
Showing: 121 - 140 of 886 results