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We narrowed to 886 results for: URE

Showing: 181 - 200 of 886 results

  1. Fluorescent Proteins 101: Aptamer Fluorophores

    Type
    Blog Post
    Published
    April 11, 2017, 2:30 p.m.
    ...required longer exposure time than its protein equivalent and was less stable due its RNA nature, it paved ...including: Environments with higher temperatures, since proteins can denature while aptamers are more stable...form the base of the stem in an RNA stem-loop structure (see Fig. 1a). When the aptamer binds its ligand...laboratory took advantage of their deep knowledge of the nature of GFP fluorescence to create an improved fluorescent...fluorescent aptamer system. Knowing that GFP’s  structure stabilizes a 4-hydroxybenzylidene imidazolinone...cells. The new aptamer also has a higher melting temperature than its Spinach ancestors, and has a lower magnesium... its biosensor capabilities (see Fig. 1b). The future of aptamer fluorophores The Jaffrey lab and others...

  2. CRISPR-based Genome Editing Systems For Editing in E. coli

    Type
    Blog Post
    Published
    April 13, 2021, 1:15 p.m.
    ...Zhang, a Ph.D. candidate in the Yang Lab, Qi Li, a lecturer at Sichuan Normal University, Jieze Zhang, an ...plasmid that expresses the S. pyogenes Cas9, a temperature-sensitive replicon for self-curing, an arabinose... now take place. After editing, pTargetF can be cured from the cell by inducing expression of the sgRNA...other edits. Once you have all the edits you want, cure pCas9 by growing the cells at 37 °C.     The new...us to update the pCas/pTargetF system.   Figure 1: The editing process begins with the addition...DNA for editing to take place. Then plasmids are cured from the cell. Steps 1-1 and 1-2 can be done simultaneously..., 2) changed the replicon of pCas into a non-temperature-sensitive replicon, and 3) added the sacB gene...

  3. Multifunctional Neural Fibers: Modulation from Gut to Brain

    Type
    Blog Post
    Published
    Aug. 31, 2023, 1 p.m.
    .... These features enable the fibers to emit light for optogenetic purposes, measure temperature, study ... described, then measured electrophysiological potential afterwards. This measurement trended with expression... the fibers would need to be, as well as other features necessary for implantation in brain tissue. The...the wild west for fiber implants. Due to the soft nature of the intestines and the requirement for digestive...multiple channels and can also record tissue temperature proximal to the implanted fibers. As important...Alternatively, the system could be used to deliver or measure new variables. The sky is really the limit for ...wireless modulation of gut and brain neural circuits. Nature Biotechnology, 1–13. https://doi.org/10.1038/s41587...

  4. Plasmids 101: NGS Quality Control for Pooled Libraries

    Type
    Blog Post
    Published
    Oct. 26, 2017, 1:59 p.m.
    ...amplification and verification processes we use to ensure high-quality library distribution. You can also...library contains many plasmids, care must be taken to ensure that all of these plasmids are amplified and none...First, use enough DNA and competent bacteria to ensure all components of the library are represented. ...performing amplifications, and we use electroporation to ensure a good transformation efficiency. For a typical...Addgene still recommends plating the transformation mixture on solid media. The colonies are then scraped off...we created for the Brunello library is shown in Figure 2. You can use a small PCR product because the ...AUC of 0.5 representing perfect uniformity (see Figure 3A). Addgene finds that this representation is ...

  5. Photosensitizer Induced Cell Ablation with FAP-TAP MG-2I-dL5**

    Type
    Blog Post
    Published
    Sept. 19, 2017, 1:20 p.m.
    ...experimental settings: HEK293 cell culture and in live zebrafish. For cell culture experiments, only dL5**-expressing...just 1 minute of exposure. MG-2I-dL5** experienced minor bleaching after longer exposure times. Additionally... fluorogen that can be used to ablate cells in culture and in vivo.  Read on to learn more about this ...exposed to light stained dead within 30 minutes of exposure. 90 seconds of illumination were sufficient for...mCer3 cells present 96 hours post treatment (see figure 2). Induced cell death was confirmed by TUNEL staining...light. They found that KillerRed required longer exposure times (5 minutes vs 10 seconds) to achieve the...genetically targetable near-infrared photosensitizer. Nature Methods,13(3), 263-268. doi:10.1038/nmeth.3735....

  6. Trading Spaces - Visiting Scientist Edition

    Type
    Blog Post
    Published
    Aug. 22, 2023, 1 p.m.
    ...prior to your departure for the new placement. Make sure you read any relevant literature for the techniques... have structured visiting positions within defined labs which you can apply to. These structured types...institute and mentor that they may want to consider for future work placements. The chance to learn and collaborate...prior to arrival so that you can work together to ensure your expectations are reasonable, your reagents...Unless some of these logistics are covered by a structured visiting program, you will have to make arrangements...get the ball rolling! If you are applying to a structured program, they likely have guidelines to consult...don’t make your bench mentor wait on you!), make sure you are prepared (read any protocols the day before...

  7. The Advances Behind The World's First Personalized CRISPR Treatment

    Type
    Blog Post
    Published
    Sept. 16, 2025, 1:15 p.m.
    ...possible — and may contribute to more in the future. Figure 1: A timeline of CRISPR base editing advances...without DNA cleavage. Nature, 551(7681), 464–471. https://doi.org/10.1038/nature24644  Gaudelli, N. M., Lam...double-stranded DNA cleavage. Nature, 533(7603), 420–424. https://doi.org/10.1038/nature17946  Lander, E. S. (2016...receive a liver transplant — creating intense time pressure for the research team. Ultimately, the lifesaving...off-target editing. Base editing in the present—and future The final base editor that was administered to ...increased activity and therapeutic application. Nature Biotechnology, 38(7), 892–900. https://doi.org/...improved Cas domain compatibility and activity. Nature Biotechnology, 38(7), 883–891. https://doi.org/...

  8. Plasmids 101: Screens vs. Selections

    Type
    Blog Post
    Published
    Nov. 10, 2022, 2:15 p.m.
    ...yeast, are temperature sensitive screens. These involve raising or lowering the culture temperature to exacerbate...Selections do require there to be a culture condition that can apply enough pressure to select for variants of ...individually administered and then outcomes are measured. While the entire genome can be knocked out with... have a screen that doesn’t yield any hits. Make sure you plan ahead and consider these questions to save...though. A selection can take the form of varied temperature, nutrient availability, drugs, and much more....with screens. Selections require there to be a culture condition which eliminates manipulations that do...conditions which convey resistance to a drug. You could culture cells in the drug of interest at a lethal dose ...

  9. Hot Plasmids - February 2022

    Type
    Blog Post
    Published
    Feb. 22, 2022, 2:15 p.m.
    ...perturbation The Penn State Protein Ladder Engineered miniature CRISPR-Cas system for mammalian genome regulation...frankenbodies include mEGFP, mCherry, and HaloTag. Figure 1: (a) Anti-FLAG frankenbody (FB) construction ...advantageous to Cas9’s larger expression requirements (Figure 1), but Cas12a has generally been underutilized...finding acceptable variations in DR sequences. Figure 2: comparison of Cas 9 vs. Cas 12a expression cassettes...optimized toolkit furthers Cas12a’s potential in future genetic screens.   DeWeirdt PC, et al. Nat Biotechnol...commercial ladders which also provides a useful yet low-pressure teaching opportunity for lab members or students... to protein expression and purification. Figure 3: The Penn State Ladder run on SDS-Page gels. ...

  10. Viral Vectors 101: Inverted Terminal Repeats

    Type
    Blog Post
    Published
    Oct. 19, 2023, 1:15 p.m.
    ...(rAAV) vector (Figure 1). Everything else outside the ITRs gets left behind.    Figure 1: Recombinant...polyA signal. Created with biorender.com. ITR structure  WT ITRs are symmetrical 145-nucleotide sequences...palindromic arms (A-A’, B-B’, and C-C’) that give the feature its characteristic T-shape. The arrangement of ... the ITR, which can either be “flip” or “flop” (Figure 2). Additionally, the ITR contains a 4-nucleotide...target site for Rep proteins (Savvy et al. 2013). Figure 2: AAV2 wild type ITR in flip and flop orientation... B-B’, and C-C’ regions) and forms a T-shaped structure. The Rep binding element (RBE) and terminal resolution...FAQs Due to their high GC content and hairpin structures, ITRs are prone to replication errors and disruptive...

  11. Antibodies 101: Flow Cytometry Controls

    Type
    Blog Post
    Published
    June 6, 2024, 1:50 p.m.
    ... conjugated antibody. Compensation beads are a mixture between synthetic beads that can bind to a conjugated... your voltage using your single color controls (Figure 1A), instead of using your actual samples. They...the settings with experimental samples. Figure 1: Example flow plots for a single color control... may otherwise be difficult to separate out. In Figure 2, you can see that, without the FMO, it would ...population from the Ly6C positive population. Figure 2: An FMO gating example. The FMO sample (A) can...clear positive and negative population. If you’re unsure what your population will look like for a particular...provided by the antibody companies or check the literature. Pro tip! Early gates, like your live/dead markers...

  12. Viral Vectors 101: Viruses as Biological Tools

    Type
    Blog Post
    Published
    March 21, 2023, 1:15 p.m.
    ... from viruses that infect people in nature, extra safety measures, like replication incompetent viral ...the stomach flu), and many more. Their infectious nature allows them to easily deliver their “cargo” to ... make you sick…well, you feel it. But the same features that make these familiar viruses such a pain is...biological tools.   Viruses as biological tools In nature, viruses infect cells and organisms (which we refer...of cell the virus will target and fuse with. In nature, this determines which organisms and cells they...Institute. Its genome, however, isn’t enough to ensure the virus can replicate and spread. Instead, viruses...are required. We will be covering these safety measures in a separate, upcoming post. If a viral vector...

  13. 27 Hot Plasmids from 2016

    Type
    Blog Post
    Published
    Dec. 22, 2016, 3:03 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...under the control of the cI857 temperature-sensitive repressor. The temperature-controlled expression of the...crystallographic structures available in the PDB. Parton DL, Hanson SM, Rodríguez-Laureano L, Albanese SK...articles. These brief articles highlight the main features and applications of a partiular plasmid or set...arduous. The cloning process alone involves much literature searching, DNA synthesis, and plasmid assembly.... The pooled library, designed to be used with cultured Drosophila cells, targets 13,501 fly genes with...will create new traits in bacteria. Wang, et al. Nature. 2009. PubMed PMID: 19633652 Court, et al. Annu...

  14. Easi-CRISPR: Generating Knock-In and Conditional Mouse Models

    Type
    Blog Post
    Published
    April 5, 2018, 12:42 p.m.
    ...and one NHEJ-repaired indel, often occur. Figure 1: In conventional gene targeting (A), you must...be included in the final ssDNA template. Figure 2: Overview of ivTRT to generate an ssDNA repair...challenging for sequences with complex secondary structure. Today, multiple companies offer long single-stranded...directs cleavage right before the stop codon!  Figure 3: How to design a C-terminal insertion with Easi-CRISPR... To avoid re-cutting by Cas9 after editing, make sure that the repair template does not contain the wild...facing towards or away from each other.  Figure 4: How to design a conditional allele with Easi-CRISPR...you have a plasmid with your desired insertion feature (e.g., a fluorescent protein), you can amplify ...

  15. Building Global Connections with the International Mentorship Program USA-EUROPE

    Type
    Blog Post
    Published
    Nov. 6, 2015, 3:30 p.m.
    ...lives of people and society. Future generations of IMP Motivating future generations is key to the success...internationalization become a reality available to all youth, our future, around the world.   In many countries of the world...improvement) and bright students that will be the future of the country. Brain drain is a serious problem...build, together with the universities, a bright future. IMP provides matched one-on-one international ...support to increase the chances of success, but also nurture a supportive and protective environment where individuals...empowered to productively navigate through both their failures and their successes. Although all mentorship relationships...their immediate frontiers. Moreover, sharing a culture/country of origin with an international mentor ...

  16. How Exercise Purges Stress and Keeps Depression at Bay

    Type
    Blog Post
    Published
    Nov. 25, 2014, 4:02 p.m.
    ...expression of kynurenine aminotransferases, to enhance the conversion of kynurenine into kynurenic acid. That...That’s key because, unlike kynurenine, kynurenic acid can’t cross the blood-brain barrier. By lowering...muscles led to another clue: differences in the kynurenine pathway of tryptophan degradation. It turns out...lowering circulating levels of kynurenine in the body, the brain is protected from stress-induced biochemical...brain’s physiological demands,” they write. “In the future, these may lead to treatments for a variety of ...References: Skeletal muscle PGC-1α1 modulates kynurenine metabolism and mediates resilience to stress-...

  17. Tips for a 1st time AAV user (by a Rookie AAV user)

    Type
    Blog Post
    Published
    Oct. 23, 2018, 11:49 a.m.
    ...pellet for the remainder of the cultures and later maxiprep only the cultures with intact ITRs. I use a spreadsheet...proper packaging of AAV, but also form secondary structures that are prone to deletion from the transfer ...this issue. One way is to grow multiple bacterial cultures of your AAV transfer plasmid at 30 °C instead ...like to miniprep 5 mL of my AAV transfer plasmid cultures and then screen with SmaI digests. I freeze the...PEI transfections. It saves me time and helps me figure out if I have enough plasmid to complete my experiment... viral particles for efficient gene transfer. I figure it’s better to have a bit extra AAV than to have... skip the PEG precipitation of the HEK293 cell culture supernatant because it’s time consuming to prepare...

  18. Hot Plasmids and Viral Preps - May 2021

    Type
    Blog Post
    Published
    May 18, 2021, 1:15 p.m.
    ...synthetases.     Figure 2: Specific binding of scFVs to cognate aaRS antigens as measured by suspension ...encapsulating the protein of interest (Figure 3).   Figure 3: Schematic representation of the MPyV...domain (RBD) of the viral spike protein.   Figure 1. (A) SARS-CoV-2 RBD DMS Library generation and...resolved fluorescence, and suspension bead assay (Figure 2). After finding no cross-reactivity, antibody...within seconds. A CRISPR-based lineage tracing tool captures rare clones that represent 0.001% of the population...found a way to use the accumulation of indels to measure time. These plasmids with different promoters driving...anti-CRISPRs were identified that inhibit the S. aureus Cas9, a Cas protein that is smaller and easier ...

  19. Light Sheet Fluorescence Microscopy

    Type
    Blog Post
    Published
    July 16, 2015, 2:30 p.m.
    ...enabling microscopes to visualize the cellular architecture of whole tissues in 3D with unprecedented detail...thin sheet to illuminate a fluorescent sample and captured the reflected light using a different objective...Ultramicroscope was developed using a stereomicroscope to capture large field-of-views (6). For more comprehensive... on several other LSFM configurations’ various features see (4,7).   Light sheet fluorescence microscopy...methods will greatly aid our understanding of the structure-function relationship of the central nervous system...Jährling, C.P. Mauch,  K. Deininger, et al. (2007). Nature Methods, 4, 331–336. Pubmed. P. Keller, M.B. Ahrens...Neuron, 85, 462-483. Pubmed. E.H.K. Stelzer. (2015). Nature Methods, 12, 23–26. Pubmed. M. Weber, M. Mickoleit...

  20. Antibodies 101: Validation

    Type
    Blog Post
    Published
    March 24, 2022, 1:15 p.m.
    ...your experiments. Capture MS Strategies This approach uses immunoprecipitation to capture proteins from a...been planning, it is a good idea to pause and make sure that your antibody has been appropriately validated...recognition of the target antigen. You want to make sure that your antibody binds to what you expect it to...application and available resources.     Figure 1: Table summarizing the IWGAV five proposed antibody...information for some antibodies, which makes it hard to ensure that you have unique antibodies. An additional ...and then uses mass spectrometry to identify the captured proteins. If the antibody is specific, then you...approach is ideal for validating antibodies for immunocapture applications and is amenable to high-throughput...
Showing: 181 - 200 of 886 results