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We narrowed to 1,025 results for: URE

Showing: 511 - 540 of 1025 results

  1. Plasmids 101: In-house NGS Plasmid Quality Control Now at Addgene

    Type
    Blog Post
    ...a large undertaking. Priority number one was to ensure that this changeover had no impact on our ability... Since we’ve successfully grown the plasmid in culture to prepare it for sequencing, we feel confident...proteins, and selectable markers by detecting common features using Snapgene. If we find information that differs...many of you will be familiar with our efforts to ensure access to high quality, ready-to-use viral preps...Sequencing (CPS) workflow and yield sufficient data to capture the entire viral genome. The full details of that...it on to our new MiSeq and set up the run making sure to note the appropriate barcode for each sample....

  2. Engaging with science and society at pgEd

    Type
    Blog Post
    ... are to figure out the best way to shepherd technologies through thorny ethical issues, ensure that everyone...communities, which is in turn crucial if we want to make sure that everyone can be informed and empowered to make...public engagement efforts, including giving public lectures, writing science articles for a lay readership...organizations (often volunteer-based) that put on public lectures, science cafés or science festivals, and getting...events will be important both in preparing you for future work in these areas, and in helping you decide ...

  3. Hot Plasmids - October 2020

    Type
    Blog Post
    ...tools to tease out the details underlying brain structure and function, with the advent of each tool expanding...excitatory and inhibitory synapses in the brain.  Figure 1:Schematic diagram of different FingR constructs...protein products have distinct localizations. Figure 2: Split-wrmScarlet labeling proteins with different...more red than blue (Eastman et al., 2020). Figure 3: BaF3 cells were transduced with H2B-FT virus...which depend on IL-3 to proliferate. The cells cultured with a low dose of IL-3 showed reduced proliferation...proliferation and had a greater number of red cells as measured by flow cytometry. Cells grown in high IL-3 showed...

  4. A Guide to Designing a Scientific Poster: Content, Layout, and More

    Type
    Blog Post
    ...You’ve analyzed the data and generated beautiful figures. And, you can’t wait to tell your story. But, before...accomplished with an exciting title and attractive figures. Next, the poster should be legible from a distance...central box, often used for displaying all of one’s figures, or at least the majority of the visual data. This...poster sections like the introduction, methods, and figures flank the central region, and a scannable barcode...potentially more catchy, but it can be trickier to make figures fit nicely into circular shapes rather than a square...you select for the background, you’ll want to make sure that the color of your font is compatible. Use high-contrast...

  5. CRISPR 101: Multiplex Expression of gRNAs

    Type
    Blog Post
    ... multiple gRNAs on the same plasmid, you’ll make sure that each cell that gets the plasmid contains all...blog post about multiplexing with Cpf1.   Figure 1: Multiplexing allows researchers to express multiple... illustrated in the schematic below.   Figure 2: gRNA target sequences (colored rectangles) are... Note: depending on which method you use, the procedure will vary slightly.   Two Golden Gate options...need to supply it with another plasmid.   Figure 3: Comparison of Multiplex Strategies including...chromosomal rearrangements with the CRISPR/Cas9 system.” Nature 516(7531) (2014): 423-7. PubMed PMID: 25337876....nucleases for highly specific genome editing.”  Nature Biotechnology 32(6) (2014): 569-576. PubMed PMID...

  6. Common Injection Routes in Mice

    Type
    Blog Post
    ...intermediate to advanced and finally, to expert.   Figure 1. Visual representation of common injection routes... injections require a little bit of practice to ensure the proper injection site has been located and ...instillation” or “gavage,” as they do not require any punctures. Intratracheal instillation Intratracheal instillation...delivery is also common. Due to the intubation, this procedure is considered quite invasive. Restraint: anesthesia...similar to its intratracheal counterpart, as both procedures target the lungs. The main differences are that...on the end, which prevents accidental tears or punctures to the throat. The feeding tube can be flexible...

  7. Transferable Skills Guide: Managing a Team

    Type
    Blog Post
    ...a formal training for new managers and I had a “Eureka” moment while reviewing the results of my Myers-Briggs...easily identify what to delegate and to whom (make sure that person has time for it!). Then schedule a meeting... I still need to check myself sometimes to make sure I am delegating well, but it does get easier over...able to go to your manager for advice if you’re not sure how to face a particular situation. But keep in ...reason!).  Try to buffer them from unnecessary pressure “coming from above”, which is when other skills.... Three Rules for Managing a Successful Team. Naturejobs blog by Joanne Kamens  Are Good Managers Born...

  8. Plasmids 101: Protein Expression

    Type
    Blog Post
    ...into polypeptide chains that make up the primary structure of proteins. Most proteins are then modified via...localization or purify proteins to study their structure, interactions and functions. Proteins can also...easily synthesized, must be produced using complex mixtures derived from cells or using live cells. There ... expressions systems do require demanding cell culture conditions compared to other systems. Insect expression...consuming and that insect cells require demanding culture conditions similar to mammalian expression systems...expression. Plant systems share many of the same features and processing requirements as mammalian cell ...

  9. Experimenting with New Careers while in Grad School

    Type
    Blog Post
    ...University School of Medicine. It’s not always easy to figure out what you want to do after graduate school, ...experience taught me something about myself and my future career. If it wasn’t something I liked – well, ...the labs in our program to write short, funny, picture-filled blog posts about their research? Then we.... I gained a concrete example to use to promote future attempts and learned a bit about recruiting scientists...shape, was when I started volunteering. I wasn’t sure yet what a career in science outreach would look... disappointed graduate students because I wasn’t sure what I wanted to do. A few weeks into volunteering...

  10. Drew Endy Introduces the Biobrick Public Agreement Plasmid Collection

    Type
    Blog Post
    ...as part of President Barack Obama's Winning the Future Initiative. Endy's team made news in March with...plasmid kits, the Biobricks Public Agreement, and the future of the bioeconomy. Addgene: What do these BIOFAB...life, then this new language needs to be free. The future of synthetic biology Addgene: You've described ...visualization. Addgene: What do you envision for the future as this programming language is put into practice...therapeutic space. If you were to look forward to the future of the bioeconomy it's less clear, but the way ...standard transcription and translation initiation." Nature Methods. 10, 354-360 (10 March 2013). ...

  11. Transferable Skills Guide: Identifying Your Transferable Skills

    Type
    Blog Post
    ...issues raised by team members, and plan for the future of the team. All while still paying bills and having...These skills will be useful anywhere I work in the future; they are transferrable across most, if not all...you’re sitting in the lobby of (hopefully) your future employer. Your heart is pounding, you’re short ...communication style, your potential teammates want to be assured that you will contribute openness, clarity, approachability...your boss needs someone to step up, when a new venture presents itself even outside of work, consider ... these skills you’ve used in your own work - I’m sure you’ve used many! Teamwork Collaborating with others...

  12. CRISPR 101: RNA Editing with Cas13

    Type
    Blog Post
    ...rescue known pathogenic alleles, or introduce a premature stop codon to render an RNA nonfunctional. In ..., like ADAR2DD(E488Q). They also adjusted the structure of the guide RNA by introducing a C opposite the...delivery.  Find the RESCUE RNA editing plasmids here! Future directions Building on previous RNA targeting work...Omar O., et al. “RNA targeting with CRISPR-Cas13.” Nature 550(7675) (2017):280-284. PMID: 28976959. Find...enable guide-RNA processing and RNA detection." Nature 538(7624) (2016):270-273. PubMed PMID: 27669025...Resources on the Addgene Blog Check out our CRISPR Featured Topic Page Learn about RNA Targeting with Cas13a...

  13. New Optimized Genome-wide CRISPRko, CRISPRi, and CRISPRa Libraries

    Type
    Blog Post
    ...approximately 1,900 sgRNAs and identified sequence features and adjustments that improved sgRNA activity and...libraries (see below). Let’s take a look at the features and advantages of the optimized human CRISPR libraries...scientists to conduct genome-wide screens in standard cultured cells as well as more difficult conditions such...sgRNAs for CRISPR-Cas9–mediated gene inactivation." Nature biotechnology 32.12 (2014): 1262. PubMed PMID: ...and minimize off-target effects of CRISPR-Cas9." Nature biotechnology 34.2 (2016): 184. PubMed PMID: 26780180...activation by an engineered CRISPR-Cas9 complex." Nature517.7536 (2015): 583. PubMed PMID: 25494202. PubMed ...

  14. Negative Can Be Positive: Open AAV Data with Addgene

    Type
    Blog Post
    ...providing many of the details not generally captured in the literature, scientists can use the Data Hub to compare... process is often not detailed in the primary literature, and as a result can leave scientists under-informed...both excellent at infecting our target neurons (Figure 1). However, this one set of experiments didn’t...indicated they wanted to see more negative data (Figure 2.) At the same time, when scientists who support...Initiative, F. B. (2019). Setting your data free. Nature, 5–7. O’Connor, D. M., Lutomski, C., Jarrold, M...

  15. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

    Type
    Blog Post
    ...Chromatin folds into secondary structures (loops) and tertiary structures (globules) to achieve exquisite... enhancers with the help of genome math. Figure 1: Genome math illustrated. Intersect (left) and...which genes influence the survival of our cell culture is the foundation of modern drug discovery and ...periodically use next-generation sequencing to measure the relative proportion of guide RNAs (gRNAs) across...for further details. DNA is a 3D Fractal Figure 2: DNA compaction. Graphics courtesy of beyondthedish...

  16. Using Video to Share Your Science: We Share Science

    Type
    Blog Post
    ...discipline to solve them on their own. According to a Nature News Article, since the 1980s researchers have ... of all of this appears to be that video is the future in terms of communicating ideas. In 2012, for example...and a few other disciplines leading the way, the future of complementing published research with video ... helps researchers go beyond citation rates to measure the impact of their contribution. It offers a 5...pin/7439 Research Website: https://umaine.edu/aquaculture/ The goal of the WeShareScience project is to...Richard. "Interdisciplinary research by the numbers." Nature 525.7569 (2015): 306-307. 3. Spicer, Scott. "Exploring...

  17. Four Base Editing Reporters to Monitor and Enrich Editing in Real-time

    Type
    Blog Post
    ... without DNA cleavage. Nature 551:464–471 . https://doi.org/10.1038/nature24644 Glaser A, McColl B, Vadolas...APOBEC-Cas9n-UGI complex. So how exactly does this work? Figure 1: APOBEC- and Cas9-mediated editing (ACE) reporter...mCherry positive cells (Martin et al., 2019). Figure 2: Editing efficiencies using base editing reporters...visualized and sorted via flow cytometry. Figure 3: Targeting pEF-BFP with a cytidine deaminase ...detectable protein, not just fluorescent proteins. Figure 4: Reporters in Gene On include a mScarlet reporter...

  18. Plasmids 101: Plasmid Incompatibility

    Type
    Blog Post
    ...antisense RNAs inhibit plasmid replication.   Figure 1: The replication problem. Iterons are repeated...the same RepA molecules, forming a “handcuff” structure that physically blocks replication machinery when...actually does, and neither plasmid is maintained (Figure 1).  The partitioning problem Plasmid incompatibility...leading to plasmid loss (Diaz et al., 2015).  Figure 2: The partitioning problem. For low copy plasmids...type of plasmid into a separate daughter cells (Figure 2) (Ebersbach et al., 2005). However, more recent...Partition-associated incompatibility caused by random assortment of pure plasmid clusters. Molecular Microbiology 56:1430...

  19. Bioinformatics at Addgene

    Type
    Blog Post
    ...From the beginning, one of Addgene’s goals was to ensure the scientific community obtained high-quality ... programs to a uniform language.  The modern architecture of Nextflow included built-in support for containers...convenient compatibility with our internal software infrastructure; however, it is not necessary to use containers...input channel to only use the first n items. To be sure, we went through much trial and error to learn the...with our bbduk process.    At first, to make sure we understood the concept of channels and implemented...compared to purchasing and maintaining our own infrastructure. Our patchwork collection of scripts evolved...

  20. Avoiding the Dark Side of Fluorescent Protein Fusions with mOX FPs

    Type
    Blog Post
    ...experiments or even negatively impact cells (see Figure 1). When behaving properly, FPs enable researchers...inappropriate disulfide bonds in the secretory pathway (Figure 1) [4,6–8]. Additionally, FPs that encode N-glycosylation...from properly exiting the ER and fluorescing (see Figure 2) [5].  When using FPs containing two cysteine...experiments, please consider the following: How can one ensure that an FP fusion with a non-cytosolic protein ...cellular compartments including the secretory pathway (Figure 2), the inner membrane space of mitochondria and...proteins optimized for diverse cellular environments." Nature communications 6 (2015). Pubmed PMID: 26158227....

  21. Plasmids 101: The Promoter Region – Let's Go!

    Type
    Blog Post
    ...bacteriophage lambda Can be temperature regulatable  Often paired with the temperature sensitive cI857 repressor...replication are necessary to replicate plasmids and make sure the cells maintains it. Here, we'll cover the promoter...transcribed from the RNAP III promoters. This post features promoters for general RNAP II and RNAP III transcription...retroviral constructs and we will discuss these in a future post on viral vector parts. Promoter specificity...type of RNA transcript, you will also need to make sure your plasmid has a promoter suited to working in...

  22. New Educational Resource: The Addgene Videos Page

    Type
    Blog Post
    ...below: How-to videos Our How-To videos feature screen-capture footage to help you navigate Addgene’s ..., we have also created video protocols.  These feature step-by-step instructions to navigate various lab...biotech nonprofit? In our Career Video series, we feature interviews with real Addgenies who have a variety...Addgene.  You’ll hear all about their career paths, future goals, and get some useful career advice.  Our ...

  23. An Integrin Antibody Toolkit from IPI

    Type
    Blog Post
    ...biomedical research and drug development. Integrin structure and conformational complexity There are 24 known...With the right research reagents, researchers can measure this conformational change to investigate the role...specific integrins in cellular processes.   Figure 1: Integrins can shape into three conformations...much lower affinity than their open states (C). Figure courtesy of IPI. IPI anti-integrin toolset IPI...biology talks on the IPI website and stay informed on future events by signing up for the IPI newsletter. The...characterization of subtype-specific β1 integrin mechanics. Nature Communications, 13(1), 7471. https://doi.org/10.1038...

  24. CRISPR 101: Validating Your Genome Edit

    Type
    Blog Post
    ...Make sure to check out our validated gRNAs to avoid rolling the dice on a new gRNA in the future! References...target cells with Cas9. Hooray! Now it’s time to make sure your genome edits went according to plan. In this...validation on your bulk population. This way you can ensure you aren’t looking for a needle in a haystack before...sgRNA-Cas9 combo. Pro tip: When designing your PCR, ensure there is at least ~200 base pairs of sequence flanking... inserted or deleted accordingly. Pro tip: make sure your PCR amplicon isn’t too large so that you can...

  25. Deep Mutational Scanning with One Pot Saturation Mutagenesis

    Type
    Blog Post
    ...desired variants of a protein. Applying a selective pressure winnows the pool down to plasmids expressing variants...High-throughput DNA sequencing is then used to measure the frequency of each variant during the selection...plasmid will be degraded by ExoIII. See the below figure for an example like this. 2) When your gene of ...to remove the BbvCI site(s). Overall, the key features of the one-pot saturation mutagenesis method are..."Plasmid-based one-pot saturation mutagenesis." Nature Methods 13.11 (2016): 928-30. PubMed PMID: 27723752... a Large Scale Using Deep Mutational Scanning.” Nature Protocols 9.9 (2014): 2267–2284. PubMed PMID: 25167058...

  26. Adeno-associated Viruses (AAVs) for Genome Editing

    Type
    Blog Post
    ...applications.  Third, even in the most optimized tissue-culture based system, the efficiency of gene editing is...limitations, the AAV approach is best suited for tissue culture based approaches that require modification of only...mutations of a gene into the endogenous allele in cultured cells. AAV genome editing combined with targeted...T-cells and hematopoietic stem cells respectively. Future researchers could apply this technique to efficiently...Hirata. "Human gene targeting by viral vectors." Nature genetics 18.4 (1998): 325. PubMed PMID: 9537413...editing via postnatal administration of AAV vector cures haemophilia B mice." Scientific Reports 7.1 (2017...

  27. Transferable Skills Guide: Time Management

    Type
    Blog Post
    ...Scientists. Back when I used to do mammalian cell culture, I would often respond to friends asking me to ...achieving your goals. However, you should have a good mixture of useful tasks that can be accomplished quickly...Monitoring task progress. For this, I always make sure I have explicit goals in mind for the endpoints ...extensively, my lack of desire to go sit in the tissue culture hood may have prevented me from splitting cells...splitting cells boring, hanging out in the tissue culture room also gave me time to listen to some of my ...any other time management suggestions, please be sure to note them in the comments! Additional Resources...

  28. Using Phosphoserine to Study Protein Phosphorylation

    Type
    Blog Post
    ...to recapitulate the true steric and charge-based nature of the phosphoryl-modification; they are both much...defined three components required for translation (Figure 1): A tRNA that recognizes a specific ‘open’ codon...encoding the open reading frame (ORF) of interest (Figure 2). 1. The phosphoserine OTS The backbone of the...be optimized for parameters such as induction temperature and length of induction, which will vary between...Philip. "The origins of protein phosphorylation." Nature cell biology4.5 (2002): E127-E130. PubMed PMID:... permits programmable protein phosphorylation." Nature communications 6 (2015). PubMed PMID: 26350500....

  29. What's New in CRISPR - May 2019

    Type
    Blog Post
    ...editing efficiency. Read the paper in Nature Find the SECURE base editors All-in-one AAV delivery ...inhibition Covalent tethering of DNA template to Cas9 SECURE base editors Nme2Cas9 CRISPR interference in Candida...genome as a negative control. Read the paper in Nature Communications Find the E. coli genome-wide CRISPR...plasmids Selective curbing of unwanted RNA editing (SECURE) base editors Keith Joung’s lab recently found ...

  30. Your Top Requested Plasmid in 2016!

    Type
    Blog Post
    ...popular any one of them will become. One thing is for sure, as is obvious from our most requested plasmid, ...modified for viral trasduction (see the Zhang Lab's Nature Protocols Paper for more information). V2.0 This...included in this plasmid's name are some additional features. The first and most imporant is that, upstream...these variants, as well as links to the Zhang Lab's Nature Protocols Publication describing them here. References...Genome engineering using the CRISPR-Cas9 system." Nature protocols 8.11 (2013): 2281-2308. PubMed PMID: ...
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