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We narrowed to 888 results for: URE

Showing: 401 - 450 of 888 results
  1. Improving Transduction Efficiency with Exosome AAVs

    Type
    Blog Post
    Published
    March 14, 2019, 1:54 p.m.
    ...are secreted from the cellular membrane into the culture medium. AAV particles are either associated with...vexosomes (vector-exosomes), exosome AAVs, or exo-AAVs (Figure 1). The researchers discovered that these particles...differential centrifugation steps to separate cell culture supernatant containing exo-AVVs from producer cells...then to enrich the microvesicles containing AAVs (Figure 2). Since the development of the exo-AAV isolation...the production of exosomes or stabilize their structure or their interaction with AAVs (Schiller et al...model of glioblastoma (Volak et al. 2018). The structure of exosome AAVs is related to the use of microvesicles...
  2. Hot Plasmids - January 2023

    Type
    Blog Post
    Published
    Jan. 31, 2023, 2:15 p.m.
    ...and cytoplasmic (CKB1) RNA target. Adapted from Figure 3 Colognori et al 2022.   Find CRISPR Csm plasmids...lagged. Fixation, chemical staining, and light exposure can negatively affect FPs during these processes... also withstands denaturing conditions, high temperatures, and other chaotropic conditions better than...these preparations. After crystalizing the hfYFP structure, the group rationally designed GFP variants with...fluorescence in high molarity GdnHCl, at high temperatures, and in the presence of oxidizing agents. Adapted...Adapted from Fig. 2 Campbell et al, Nature Methods   Find YFP plasmids here!   Campbell, B.C., et ...
  3. Components of CRISPR/Cas9

    Type
    Blog Post
    Published
    Feb. 2, 2016, 5 p.m.
    ...cleave them leaving mature crRNAs bound to the Cas9/tracrRNA complex. D) The mature crRNA is used to guide...GAA, or GAT SpCas9-NG 3' NG  Staphylococcus aureus (SA); SaCas9 3' NNGRRT or NNGRR(N)  Acidaminococcus...the crRNA to Cas9 and facilitates processing of mature crRNAs from pre-crRNAs derived from CRISPR arrays...unique stretches of DNA between them “spacers” (see figure below). After years of research, we now know that...sequences required for processing pre-crRNA into mature crRNA and tracrRNA binding. The spacer regions,...
  4. Synthetic Photobiology: Optogenetics for E. coli

    Type
    Blog Post
    Published
    Sept. 8, 2015, 2:30 p.m.
    ...phosphorylation, promoting transcription (see figure below). Subsequent exposure to red light rapidly deactivates ...limited studies and can fluctuate with changing culture conditions. The use of low intensity light solves...promoting transcription of a GFP reporter. Subsequent exposure to red light rapidly deactivates the system. Version...systems The large dynamic range of these systems ensures that they can be used with many types of proteins...Scouras A, Ellington AD, Marcotte EM, Voigt CA. Nature. 2005 Nov 24;438(7067):441-2. PubMed. Find the...
  5. Using AAV for Neuronal Tracing

    Type
    Blog Post
    Published
    Aug. 9, 2018, 1:04 p.m.
    ...understanding the brain’s function is knowing its architecture, in particular the connections between different... uptake of these dyes in vivo, microinjection, pressure injection or iontophoresis (applying small electric...of RABV. This improvement resulted in a clearer picture of neuronal connectivity in the mammalian brain...but overall with rather low efficiency. Not all measures of transport efficiency are consistent which may...observations like these may be a starting point for future developments in the field of AAV vectors. Conclusion...achieve transgene delivery by targeting peripheral structures (such as injection into muscle) as opposed to...(2008). Concepts in the pathogenesis of rabies. Future Virol 3(5), 481–490. PubMed PMID: 19578477. PubMed...
  6. Fluorescent Proteins 101: Luciferases

    Type
    Blog Post
    Published
    July 22, 2025, 1:15 p.m.
    ...and alternatives to fluorescent proteins. Figure 1: Firefly, from Wikimedia Commons. The North...reaction in its abdomen to produce yellow-green light (Figure 2). Despite the title of this post, this reaction...photon; no chemical reaction takes place. Figure 2: Simplified chemical reaction catalyzed by luciferase...luciferase gene, and expression of luciferase is measured via the light produced. A similar approach can...luciferase or alternative substrates can permit measurements of luminescence from live cells. Luciferase ...with experiments that supply both substrates and measure luciferase output at different wavelengths. Addgene...
  7. Clear and Accessible Writing

    Type
    Blog Post
    Published
    Feb. 15, 2024, 2:15 p.m.
    ...densities are captured at the 17%, 25%, and 60% layers, and genome-containing virions are captured at the 40%...pun intended.)  Steps to clear writing Let’s use Figure 1 as our example. Remember, our goal is to use ...same information as sighted readers.    Figure 1: An image from AAV Purification by Iodixanol ...What are they hoping to get from it? The image in Figure 1 appears on our protocol page for AAV Purification...group to share with the rest of the workshop.  For Figure 1, Addgene chose this alt text: "The left panel...
  8. Viral Vectors 101: Types of viruses

    Type
    Blog Post
    Published
    June 6, 2023, 1:15 p.m.
    ...cell line cultures. Lentivirus Lentivirus is a type of retrovirus and shares many common features with gamma-retrovirus... gamma-retrovirus including genome architecture, host integration, and its association with disease. The...cell types. Altogether, AAV has many excellent features for human gene therapy and is currently being ...types of interest. This is a particularly nice feature as organ-specific injections, or the location of...   Table 1: Types of viruses and their features Choosing a virus Now that we’ve reviewed the...
  9. Hot Plasmids - May 2022

    Type
    Blog Post
    Published
    May 26, 2022, 1:15 p.m.
    ...powerful approach for proteomic mapping in both cell culture and whole organisms (see our 2019 overview). Until...doi.org/10.7554/eLife.64631  Goertsen D, et al. Nature Neuroscience. 2022. https://doi.org/10.1038/s41593... applies both positive and negative selective pressures for novel capsids. In a continuation of that work...Find M-CREATE plasmids here!  Goertsen D, et al. Nature Neuroscience. 2022. https://doi.org/10.1038/s41593... factors, including limitations of number of flourescent proteins that can be inserted into a cell without...visual barcode plasmids here! Kaufman, et al. 2022. Nature Comm.https://doi.org/10.1038/s41467-022-30008-0...
  10. Screening for Successful Genome Editing with Digital PCR

    Type
    Blog Post
    Published
    March 30, 2017, 2:30 p.m.
    ...negative (digital) signal at the end of the reaction (Figure 1). Partitions that did not contain any target ...precision. This means digital PCR provides an absolute measure of target abundance, does not require standard ...directly at the predicted double strand break site (Figure 2A). The single molecule resolution of digital...completely “blind” to this very important difference (Figure 3). If you are interested in harnessing the power...requires target DNA sequencing to confirm the exact nature of your mutations. A great description of the plethora...induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology 31, 822–826 (2013). PubMed PMID: ...
  11. A Novice's Perspective on Neuroscience - SfN2017

    Type
    Blog Post
    Published
    Dec. 15, 2017, 2:07 p.m.
    ...scientists and nonscientists alike). My only in-depth exposure to neuroscience prior to this conference was a.... This was not at all the case. The conference featured people who work in sociology, behavior, and artificial... session organized by Story Collider and which featured a talk about the different parts of the brain ...getting into neuroscience from the mol bio side you’re sure to have many opportunities to learn about and develop...website and on the Addgene blog to get some ideas for future experiments and to find tools that will make your...Ed Boyden on Optogenetics, Neuroscience, and the Future of Neuroengineering Primer on Optogenetics Resources...
  12. Q&A with Karen Katz and Carl Paratore, the Newest Members of the Addgene Board of Directors

    Type
    Blog Post
    Published
    Feb. 19, 2019, 1:36 p.m.
    ...important considerations for the future of open science? What about the future of open science are you most...do you hope Addgene will accomplish in the near future? Katz: I’m excited that Addgene is continuing to...those “what could go wrong scenarios” and making sure we have adequate process and controls in place to... particular area or profession, you need to make sure you have learned and mastered the fundamentals.   ...was a founding member of Mass Medical Angels, a venture mentor at MIT and served on the Boards of BioBuilder...
  13. Sharing is Caring: But How to Distribute Open Hardware?

    Type
    Blog Post
    Published
    Feb. 28, 2023, 2:15 p.m.
    ...provided by the manufacturers and enables customized experiments. Projects such as the OpenFlexure Microscope...modify the device for individual experiments. Manufacturers rarely provide the construction plans or CAD...accessible open-source hardware. Projects such as the OpenFlexure microscope or open-source modular optical toolbox...documentation, which facilitates the reproduction of the structure in a similar way to the biological protocol, and...et. al, "Robotic microscopy for everyone: the OpenFlexure microscope," Biomed. Opt. Express 11, 2447-2460...
  14. Antibodies 101: Monoclonal Antibodies

    Type
    Blog Post
    Published
    June 29, 2021, 1:15 p.m.
    ...focus on antibodies that recognize proteins. Figure 1: Steps in the generation of hybridomas for monoclonal...fused to myeloma cells at a 1:1 ratio and then cultured in a special medium called HAT. This medium selects...antibodies are particularly useful when you want to ensure that the antibody binds to a specific region of... during your experiment, then you’d want to make sure that you choose an antibody that recognizes an epitope...polyclonal antibodies - which are a heterogenous mixture of antibodies that recognize many different epitopes...plasmid to create a recombinant antibody.     Figure 2: Changes to the heavy chain or light chain genes...
  15. Antibodies 101: Conjugation

    Type
    Blog Post
    Published
    March 26, 2024, 1:15 p.m.
    ...types. Be sure to check the spectral properties of the fluorophores you are considering to make sure that ... peptides, like an Fc-binding domain (Figure 1).  Figure 1: Examples of sites on antibodies used...process quick and easy. Before getting started, be sure to check that your antibody’s buffer is compatible...2017) Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14:865–868. https...
  16. Transferable Skills Guide: Cross-team Communication

    Type
    Blog Post
    Published
    Nov. 21, 2019, 1:53 p.m.
    ...the biggest project I’d seen in my already long tenure at Addgene. I would work with our research team...of what we discussed and decided. I needed to a) figure out the sources of miscommunication and b) find... steps towards solving this problem by 1) making sure we qualified these words when we discussed them ...Creating this guide was relatively easy. I took a picture of virtually every container we used, then for ...team identify possible points of confusion in the future. Improving cross team communication, be it in ...productive. Higher Productivity. Taking active measures in improving cross team communication has helped...
  17. Plasmid Tools for Microbiome Studies

    Type
    Blog Post
    Published
    June 27, 2019, 12:25 p.m.
    ... is limited and many microbes are difficult to culture outside of their natural environment. Thus, the...Pamela Silver’s lab developed a synthetic mark and recapture strategy for bacteria to count cell divisions....generations can be determined. The lab used DCDC to measure growth rate of E. coli for over 10 generations ...reveals growth dynamics in the gut microbiota." Nature communications 6 (2015): 10039. PubMed PMID: 26615910...engineering of the mammalian gut microbiome in situ." Nature methods 16.2 (2019): 167. PubMed PMID: 30643213... analyzing gut microbiota and host biomarkers." Nature communications 9.1 (2018): 3347. PubMed PMID: 30131493...
  18. RANbodies: Reporter Nanobody Fusions

    Type
    Blog Post
    Published
    April 10, 2018, 12:56 p.m.
    ...sequence, making them easy to harvest from cell culture media. Their His tags allow for further purification...for your RANBody While all three reporters stain cultured cells and tissue sections, some reporters are ...secondary antibody. Table 1: Summary of the Key Features of HRP, Spaghetti Monster, and Chicken IgY Domain...Tyramide signal amplification of HRP Staining cultured cells and tissue sections Amplifying weak signals...versions Labeled anti-HA or -Myc antibody Staining cultured cells and tissue sections When detected with a...(Y) Labeled Anti-Chicken IgY antibody Staining cultured cells and tissue sections Great for multicolor...
  19. RNA Extraction Without A Kit

    Type
    Blog Post
    Published
    March 24, 2020, 1:15 p.m.
    ...and work quickly to mitigate RNA degradation. Make sure to use DEPC-treated or RNAse free water. If using...water, autoclave the water to inactivate the DEPC.  Ensure that plasticware or glassware used is RNase free...or more large, expensive ultracentrifuge.  Figure 1: An outline of the different steps in RNA extraction...you need really clean RNA, it’s important to make sure that when extracting, to only take the aqueous layer... from) on your resuspended RNA sample will help ensure DNA contamination is not an issue.  References...thiocyanate–phenol–chloroform extraction: twenty-something years on. Nature Protocols 1:581–585. https://doi.org/10.1038/nprot...
  20. The Breast Cancer Microenvironment: A Tumor’s Backstage Team

    Type
    Blog Post
    Published
    Jan. 31, 2019, 1:32 p.m.
    ...understood, a team of researchers lead by Takayuki Kogure (Kogure et al., 2011) believes that miRNA may decrease...metastasis." Nature 527.7578 (2015): 329. PubMed PMID: 26524530. PubMed Central PMCID: PMC4788391. Kogure, Takayuki...Microenvironments are cellular regions with specialized structures. Tumors are surrounded by microenvironments and...instead of repressing them, making it even harder to cure cancer. To understand how cancer cells influence...
  21. Hot Plasmids - October 2020

    Type
    Blog Post
    Published
    Oct. 13, 2020, 1:15 p.m.
    ...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...
  22. How to Prepare for an Industry Interview

    Type
    Blog Post
    Published
    July 9, 2020, 1:15 p.m.
    ...process. Industry interviews, however, were more structured. I met with several individual and/or small groups...a theme too, which is something not inherently captured by the STAR method. I like to think of the theme...evaluations, professional development, and company culture.  It’s also a good idea to prepare 1-2 unique questions... of your work, such as improving a process or procedure, solving a problem, or making a key decision. ...hours, which was a lot of extraversion for me. Make sure to get enough sleep the night before. Have your ... professional  First impressions matter, so make sure yours counts. Dress professionally but still like...
  23. A Guide to Designing a Scientific Poster: Content, Layout, and More

    Type
    Blog Post
    Published
    Oct. 22, 2019, 12:20 p.m.
    ...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...
  24. Engaging with science and society at pgEd

    Type
    Blog Post
    Published
    Sept. 20, 2018, 12:17 p.m.
    ... 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 ...
  25. A New Generation of Adenine Base Editors Improves Editing in Primary Human Cells

    Type
    Blog Post
    Published
    May 7, 2020, 1:15 p.m.
    ... without DNA cleavage. Nature 551:464–471 . https://doi.org/10.1038/nature24644 Gaudelli NM, Lam DK, Rees... editors (ABE) mediate A•T-to-G•C base changes (Figure 1), but it can be challenging to make these base...and dCas to the genomic DNA of interest  Figure 1. When ABEs are in action they bind DNA so that...NG-Cas9 (PAM: NG) to create NG-ABE8.xm/d and the S. aureus Cas9 (PAM: NNGRRT) to create Sa-ABE8.x-m/d. With...increased activity and therapeutic application. Nature Biotechnology. https://doi.org/10.1038/s41587-020...
  26. Plasmids 101: In-house NGS Plasmid Quality Control Now at Addgene

    Type
    Blog Post
    Published
    April 6, 2021, 12:30 p.m.
    ...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....
  27. 6 Tips for Grant Writing

    Type
    Blog Post
    Published
    Oct. 18, 2016, 2:30 p.m.
    ... the lynch pin that results in your success or failure and demands attention, practice, and honing of ...otherwise why would you be interested in it?) so make sure that comes across. Check out some in-depth grant...you were awarded money to carry out research, be sure to make it clear what the outcome of the work was... the successful use of your preliminary data to secure further funding. Make it clear that you intend ...productive with the granting agency’s investment. 6. Failure is part of the process, keep your head up! It’...an IDP Get Tips on Keeping Up With Scientific Literature  ...
  28. CRISPR 101: Multiplex Expression of gRNAs

    Type
    Blog Post
    Published
    Sept. 10, 2020, 11:45 a.m.
    ... 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...
  29. Common Injection Routes in Mice

    Type
    Blog Post
    Published
    Jan. 22, 2025, 9:42 p.m.
    ...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...
  30. Plasmids 101: Protein Expression

    Type
    Blog Post
    Published
    June 7, 2018, 1:17 p.m.
    ...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 ...
  31. Transferable Skills Guide: Managing a Team

    Type
    Blog Post
    Published
    Jan. 30, 2018, 2:42 p.m.
    ...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...
  32. Experimenting with New Careers while in Grad School

    Type
    Blog Post
    Published
    Feb. 25, 2016, 3:30 p.m.
    ...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...
  33. Drew Endy Introduces the Biobrick Public Agreement Plasmid Collection

    Type
    Blog Post
    Published
    Dec. 12, 2013, 3:35 p.m.
    ...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). ...
  34. Negative Can Be Positive: Open AAV Data with Addgene

    Type
    Blog Post
    Published
    Sept. 6, 2022, 1:15 p.m.
    ...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...
  35. CRISPR 101: RNA Editing with Cas13

    Type
    Blog Post
    Published
    July 31, 2020, 12:30 p.m.
    ...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...
  36. New Optimized Genome-wide CRISPRko, CRISPRi, and CRISPRa Libraries

    Type
    Blog Post
    Published
    Oct. 4, 2018, 12:44 p.m.
    ...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 ...
  37. Transferable Skills Guide: Identifying Your Transferable Skills

    Type
    Blog Post
    Published
    Jan. 11, 2018, 3:29 p.m.
    ...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...
  38. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

    Type
    Blog Post
    Published
    Aug. 9, 2016, 2:30 p.m.
    ...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...
  39. Bioinformatics at Addgene

    Type
    Blog Post
    Published
    July 14, 2022, 1:15 p.m.
    ...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...
  40. Four Base Editing Reporters to Monitor and Enrich Editing in Real-time

    Type
    Blog Post
    Published
    July 7, 2020, 1:15 p.m.
    ... 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...
  41. Plasmids 101: Plasmid Incompatibility

    Type
    Blog Post
    Published
    March 31, 2020, 1:15 p.m.
    ...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...
  42. Using Video to Share Your Science: We Share Science

    Type
    Blog Post
    Published
    Nov. 3, 2016, 2:30 p.m.
    ...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...
  43. Avoiding the Dark Side of Fluorescent Protein Fusions with mOX FPs

    Type
    Blog Post
    Published
    Oct. 27, 2015, 3 p.m.
    ...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....
  44. Plasmids 101: The Promoter Region – Let's Go!

    Type
    Blog Post
    Published
    April 3, 2014, 8:05 p.m.
    ...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...
  45. New Educational Resource: The Addgene Videos Page

    Type
    Blog Post
    Published
    June 16, 2017, 2 p.m.
    ...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 ...
  46. An Integrin Antibody Toolkit from IPI

    Type
    Blog Post
    Published
    March 28, 2024, 1:15 p.m.
    ...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...
  47. CRISPR 101: Validating Your Genome Edit

    Type
    Blog Post
    Published
    Nov. 3, 2022, 12:15 p.m.
    ...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...
  48. Deep Mutational Scanning with One Pot Saturation Mutagenesis

    Type
    Blog Post
    Published
    Feb. 22, 2017, 3:30 p.m.
    ...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...
  49. Adeno-associated Viruses (AAVs) for Genome Editing

    Type
    Blog Post
    Published
    March 27, 2018, 1:32 p.m.
    ...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...
  50. Transferable Skills Guide: Time Management

    Type
    Blog Post
    Published
    Dec. 5, 2017, 1:52 p.m.
    ...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...
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