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We narrowed to 573 results for: BASE

Showing: 151 - 200 of 573 results

  1. Uncovering Ancestral Bias in CRISPR Research

    Type
    Blog Post
    Published
    Nov. 29, 2022, 2:15 p.m.
    ...American, Africa, or South Asian) used in the screens based on the cells’ germline genetic variations. They ...generating genetic dependency data with an ancestry-based bias.   The correction process does not stop there...genome-wide screens, introducing bias into all work based on these and any other CRISPR screens using the ...variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries...Cancer Dependency Map (DepMap), a cancer dependency database used to make this information accessible to the...

  2. CRISPR 101: Targeting Non-Coding RNAs with CRISPR/Cas9

    Type
    Blog Post
    Published
    Nov. 14, 2024, 2:15 p.m.
    ...short ncRNAs, such as microRNAs that are around 20 base pairs long. Using a single guide RNA (sgRNA) to ...Figure 1: A schematic illustration of CRISPR/Cas9-based approaches to study ncRNAs. (A) Transcription start...your experiments, there are plenty of other CRISPR-based options that can target ncRNAs.  CRISPRi and CRISPRa...10.1126/science.1225829  Hazan J, Bester AC. CRISPR-Based Approaches for the High-Throughput Characterization...

  3. Your Lentiviral Plasmid FAQs Answered

    Type
    Blog Post
    Published
    April 23, 2014, 1:08 p.m.
    ...packaging systems have been developed over the years based on HIV-1; however, the 1st-generation vectors are...defines 2nd- or 3rd-generation transfer vectors based on whether or not they have a chimeric 5'LTR. Second-generation...? What percent of the vector components are HIV-based? A7: No single plasmid contains all the components...insertional mutagenesis. These risks are largely based upon the vector system used and the transgene insert...

  4. Creating accessible biology activities in schools with BioBits

    Type
    Blog Post
    Published
    Aug. 2, 2018, 12:56 p.m.
    ...While there are more and more molecular biology-based activities making their way into high school classrooms...BioBits ExplorerTM and BioBits BrightTM, biology kits based on freeze-dried, cell-free (FD-CF) components. Making...and is interested in developing synthetic biology based tools for science outreach and advocacy. You can...

  5. The Power Behind NGS Plasmid Validation: seqWell

    Type
    Blog Post
    Published
    April 19, 2017, 3:25 p.m.
    ...plexWell™ Library Preparation Technology for NGS-based sequencing and confirmation of Addgene’s large and...plexWell™ workflow also offers a highly efficient NGS-based alternative to Sanger sequencing because the sample... To date, this has resulted in high quality NGS-based assemblies for over 3000 plasmids in the Addgene...

  6. Addgene Receives NIH BRAIN Initiative Grant to Create Open-Access Recombinant Antibody Resource

    Type
    Blog Post
    Published
    May 25, 2021, 2:29 p.m.
    ...community.     Why recombinant antibodies? Animal-based methods for antibody production have several drawbacks..., 2015a, b). Recombinant antibodies are plasmid-based and offer numerous advantages, including more secure...Antibodies 101 blog post Learn more about plasmid-based recombinant monoclonal antibodies Resources on ...

  7. Early Career Researcher Toolbox: Free Tools for Science Writing

    Type
    Blog Post
    Published
    April 28, 2021, 1:15 p.m.
    ...and jargon Hemingway Editor  This is a free web-based tool for detecting the readability of your writing...or dissertations. Phrases are categorized either based on the section of a manuscript they might be found...to work with collaborators. Zotero is a desktop based program that’s compatible with Mac, Windows, and...directly import papers from web pages and academic databases.  Downloading Mendeley Cite lets you cite papers...

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

    Type
    Blog Post
    Published
    Oct. 4, 2018, 12:44 p.m.
    ...libraries utilize optimized sgRNAs that were designed based on the rules identified in Doench et al., 2014 to...assess library performance in viability screens. Based on these metrics the Brunello library was more effective...selected sgRNAs in this optimal window and ranked them based on their optimized sgRNA rules and potential off-target...Dolcetto library, sgRNAs were selected and ranked based on the previously established sgRNA rules and  potential...

  9. CRISPR 101: Targeting RNA with Cas13a (C2c2)

    Type
    Blog Post
    Published
    Sept. 21, 2017, 2:07 p.m.
    ...potential candidate genes that fell into 3 categories based on the architecture of the CRISPR protein in question...LshCas13a, on the other hand, uses only a short ~24 base crRNA that interacts with the Cas13a molecule through...spacer sequence and consists of a single A, U, or C base pair. In bacteria, once Cas13a has recognized and... the new development of Cas13b as a tool for RNA base editing,, and we are excited to see this group of...

  10. A Look Back at One Year of Plasmid Sharing for COVID-19 Research

    Type
    Blog Post
    Published
    July 12, 2021, 1:15 p.m.
    ...This version of the spike protein was developed based on 100 structure-guided spike designs and has improved...already developed nucleic acid detections tools based on Cas12a and Cas13  which could be repurposed for...JA, Finkelstein IJ, McLellan JS (2020) Structure-based design of prefusion-stabilized SARS-CoV-2 spikes... CM (2020) Open Sharing During COVID-19: CRISPR-Based Detection Tools. The CRISPR Journal 3:142–145. https...

  11. CRISPR Antimicrobials

    Type
    Blog Post
    Published
    May 3, 2016, 2:30 p.m.
    ...developed sequence-specific, antimicrobial, plasmid-based, CRISPR systems (Find the Citorik Plasmids here)...encoded quinolone resistance, mediated by a single base pair change in DNA gyrase, CRISPR phagemids were...crRNAs) targeting either genomic (blue) or plasmid-based sequences (red). Treating a mixed population, represented... al. recently engineered synthetic phages, each based on the well-studied T7 phage, to target various ...

  12. Plasmids 101: Protein tags

    Type
    Blog Post
    Published
    Dec. 11, 2014, 4:26 p.m.
    ...Though there are a number of chemical and peptide-based proteosome inhibitors, glutathione S-transferase...DYKDDDK 1 Affinity and Purification Good for antibody-based purification; has inherent enterokinase cleavage...residues improves solubility; good for antibody-based detection SUMO ~100 amino acid protein  12 Stability...1.4 Affinity and Purification Good for antibody-based purification Combo and cleavage tags Frequently...

  13. PEI Calculator for Planning AAV Packaging Transfections

    Type
    Blog Post
    Published
    Jan. 23, 2018, 2:04 p.m.
    ...names of the plasmids you plan to use Enter the base pair size of those plasmids Enter plasmid concentration...plasmid needed per dish or stack. Calculations are based on using 28 μg of total plasmid (Transfer, helper...

  14. Technologies Enabled by NanoLuc® Luciferase

    Type
    Blog Post
    Published
    Feb. 8, 2018, 12:17 p.m.
    ...science better when we share? NanoLuc® Luciferase-based tools are fantastic examples of technologies that...Nano-Lanterns to other cellular proteins. BRET-based biosensors utilizing NanoLuc® luciferase Many intracellular...powerful the FRET signal. In well-designed FRET-based biosensors, the intensity of the FRET signal can...Schmid, J.L., et al. (2016) CRISPaint allows modular base-specific gene tagging using a ligase-4-dependent...) Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing. Nature Comm. 7...

  15. Hot Plasmids: Spring 2025

    Type
    Blog Post
    Published
    June 3, 2025, 1:15 p.m.
    ...postsynaptic receptors and transporters. The intensity-based Glutamate-Sensing Fluorescent Reporter (iGluSnFR...The Abudayyeh-Gootenberg Lab developed this tool based on several new site-specific retrotransposon elements...can make a wide variety of genomic edits — single-base changes, small deletions, and large insertions up...insertion is scarless, unlike previous integrase-based approaches. Find STITCHR plasmids here! Fell, C...primates, and human tissue. Figure 6: Enhancer-based targeting of PV interneurons in mice. A) AAV expression...

  16. Technique: Probe Phage Genomes for Host Binding Proteins

    Type
    Blog Post
    Published
    Sept. 29, 2016, 2:30 p.m.
    ...glycosyl groups, and other modifications to their bases in order to protect their DNA from host cell nucleases...proteins in the (all-too-common) event that homology-based searches return no candidates. Our strategy: Express...in the presence of certain modifications to DNA bases.  Ligate and transform your resultant plasmid libraries...Adapting drug approval pathways for bacteriophage-based therapeutics."Frontiers in Microbiology 7 (2016)...Raleigh. "Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses." Chemical Reviews...

  17. Pushing the Limits of DNA Assembly

    Type
    Blog Post
    Published
    Sept. 6, 2017, 1:01 p.m.
    ...you through both experimental and primer design based on fragment sequences and the polymerase used in...joining of multiple mutations spread over thousands of base pairs. Cloning sgRNAs Generating constructs to produce...Cloning Gibson Assembly and Other Long-Homology Based Cloning Methods Screen Plasmids by Colony PCR Addtional...

  18. Addgene Depositors Get More Citations

    Type
    Blog Post
    Published
    April 20, 2017, 2:30 p.m.
    ...plasmids and those without, we adjust our estimates based on the journal that published the articles.  That...Addgene plasmids as if they comprised 10 percent. Based on this new re-weighting, we can compare citations...Addgene is achieving its goal of making plasmid-based science more accessible…and accruing more citations..., we went to one of the largest bibliographic databases available, Web of Science. For each publication...number of citations the paper receives. From the database we pulled the journals from 2005 to 2015 in areas...

  19. Building and Validating Recombinant Antibodies: A Case Study

    Type
    Blog Post
    Published
    April 5, 2022, 1:20 p.m.
    ...plasmids used to generate these antibodies were based off of a large collection of mouse monoclonal antibodies...Antibodies?  One of the benefits of using a plasmid based system for expression of R-mAbs is that it can easily...Additional Resources on the Addgene blog:  Plasmid-Based Recombinant Antibodies  Plasmids 101: Secondary ...

  20. REPLACR Mutagenesis: Replacing In Vitro Recombination Methods

    Type
    Blog Post
    Published
    Feb. 10, 2016, 3:30 p.m.
    ...genomic SDM relatively straightforward, but plasmid-based SDM has lagged behind. While commercial kits are...PCR is used to splice together two PCR amplicons based on sequence homology, and the subsequent product...primers also have some homology to each other; ~17 bases is optimal. After being treated with DpnI to digest...

  21. Synthetic Photobiology: Optogenetics for E. coli

    Type
    Blog Post
    Published
    Sept. 8, 2015, 2:30 p.m.
    ...limited to neuroscience. In fact, precise light-based control of biological processes is highly useful...better fine-tune the level of output gene expression based on the input light intensity. In addition to these...strains of E. coli, as well as with other plasmid-based systems, which will enable the assembly of larger...

  22. Kiran Musunuru on the Newest TALEN Genome-Editing System

    Type
    Blog Post
    Published
    Dec. 10, 2013, 3:13 p.m.
    ...a DNA-binding domain to recognize any desired 15 base pair sequence in the genome in rapid fashion. The...All you do to create a protein that binds those 15 base pairs is take four plasmids out of the library in...genome-editing system for generating human stem cell-based disease models." Cell Stem Cell. 12, 238-251 (7 ...

  23. Alex Chavez on MD PhDs, CRISPR, Gene Drives, & More

    Type
    Blog Post
    Published
    Nov. 15, 2016, 3:30 p.m.
    ...and what work he's planning on doing with CRISPR-based gene drives focusing on safety and the ability to...Board with a particular interest in generating Cas9 based tools to enable facile control of DNA and RNA.   ...

  24. Transferable Skills Guide: Teamwork

    Type
    Blog Post
    Published
    Nov. 28, 2017, 2 p.m.
    ... knowledge base is going to necessarily need a diverse group of people to provide that base. Sometimes... Mission accomplished! One example of a mission-based team in academia would be your school’s post-doc...Let’s think about some of the advantages of team-based work: Nobody knows everything anymore John F. Kennedy... post, so here are just a few critical features based on my own experience: Leadership Few things are ...

  25. 3 Tips to Improve HDR Efficiency for CRISPR Editing in Human Cells

    Type
    Blog Post
    Published
    Sept. 5, 2017, 1:58 p.m.
    ... et al) we were very excited to set up a CRISPR-based editing platform in our lab. Our goal was to use...binding sequence, we recommend changing several bases as close to the PAM as possible (see below to find...Ludwig-Maximilians-University Munich. His lab develops iPSC-based models of neurodegenerative and neurovascular diseases...of Alzheimer’s disease by developing novel iPSC-based model systems.     References 1. Cong, Le, et al...

  26. Plasmids 101: Broad Host Range Plasmids

    Type
    Blog Post
    Published
    April 11, 2024, 1:15 p.m.
    ...are functionally differentiated from one another. Based on their structural elements, oris interact with...proteins within different host organisms. pBBR1-based plasmids and plasmids in incompatibility groups ...campestris pv. malvacearum, Zymomonas mobilis pBBR1 based pBBR1  Gram-negative  Alcaligenes eutrophus...constitutive and IPTG-inducible integron promoter-based expression systems for Escherichia coli and Agrobacterium...

  27. AAV Titers: Where Do They Come From And What Do They Mean?

    Type
    Blog Post
    Published
    Nov. 15, 2017, 3 p.m.
    ...infectious titer of a viral vector stock can vary based on transduction target and can also be altered by...titer is typically calculated by two popular PCR-based methods: Quantitative PCR (qPCR) Digital droplet...not widely used today (Fagone et al., 2012). PCR-based methods are robust, easy, fast, and convenient. ...quantified with a different primer pair. Ct values vary based on the amount of starting material in the PCR because...

  28. Site Directed Mutagenesis by PCR

    Type
    Blog Post
    Published
    Aug. 2, 2016, 2:30 p.m.
    ...of the desired mutation (usually 1-3 mismatched bases) is sufficient for your primers to successfully ...a minor extension can usually ensure that the 3’-base(s) do not form secondary structures. The introduction...feature used in TA-cloning). Such non-complementary bases at the 3’-end interfere with plasmid reconstitution...et al. "Predicting DNA duplex stability from the base sequence." Proceedings of the National Academy of...

  29. Getting the Most from Your Lentiviral Transduction

    Type
    Blog Post
    Published
    April 7, 2016, 2:30 p.m.
    ...the best possible results for any tissue culture-based experiment, labs should routinely test for mycoplasma...detector cell lines, ELISA, fluorometry, or PCR-based approaches to detect even low levels of contamination...detection, Uphoff et. al. outline a do it yourself PCR-based approach complete with freely available positive...concentration and titration of pseudotyped HIV-1-based lentiviral vectors."Nature protocols 4.4 (2009):...

  30. How to Negotiate a Successful Lab Start Up Budget

    Type
    Blog Post
    Published
    Sept. 1, 2015, 2:30 p.m.
    ... decisions based on experimental timelines and specific aims. 2. Then make decisions based on financial...instructions on creating a budget, making decisions based on that budget, and negotiating in regards to the...will need, and how long it will take to publish based on these findings. Most often we suggest estimating...

  31. Screening for Successful Genome Editing with Digital PCR

    Type
    Blog Post
    Published
    March 30, 2017, 2:30 p.m.
    ...allows classification of individual target molecules based on their mutation status. The drop-off probe is ...References 1. Miyaoka, Y. et al. Isolation of single-base genome-edited human iPS cells without antibiotic..., Berman, J. R. & Postovit, L.-M. A Digital PCR-Based Method for Efficient and Highly Specific Screening...

  32. A Quick Guide to a Career in Software Product Management

    Type
    Blog Post
    Published
    Nov. 24, 2020, 2:15 p.m.
    ...contributed by guest blogger, Rachel Rubinstein, a field-based software product manager at Oxford Nanopore Technologies... messy if you’re not on top of it. In a science-based software PM role, having a good understanding of...Rubinstein! Rachel Rubinstein is currently a Field-based Product Manager at Oxford Nanopore Technologies ...

  33. Sharing is Caring: But How to Distribute Open Hardware?

    Type
    Blog Post
    Published
    Feb. 28, 2023, 2:15 p.m.
    ...of imaging data (ILASTIK), or the popular plugin-based image process framework FIJI are just three of the...to the biological protocol, and assembly designs based around the use of commercially available tools and...provides a potential conflict between traditional IP-based models and the use of taxpayer money to support ...

  34. Delivery Methods for Generating iPSCs

    Type
    Blog Post
    Published
    April 17, 2018, 1:37 p.m.
    ... efficiencies ranking as low, medium or high is based on the reprogramming efficiencies reported in González...Non-replicating Plasmids: Generating iPSCs with plasmid-based expression requires serial transfection of 1 or ...Replicating oriP/Epstein-Barr nuclear antigen-1 (EBNA1) based episomes: These plasmids carry the origin of replication...DNA methylation. Another downside of using EBNA1 based vectors is that the plasmid can hang around for ...behave. iPSCs are typically tested with molecular-based assays first. These methods less rigorously assesses...Transgene Expression Mediated by a Sendai Virus-Based Vector Using a Nonstructural C Protein and Endogenous...

  35. Plasmid Preps: Different Purity, Different Quantities, Different Uses

    Type
    Blog Post
    Published
    June 16, 2020, 1:25 p.m.
    ... of DNA you need, and at which level of purity. Based on these premises we can classify a plasmid preparation...will adopt for the extraction. Restriction enzyme based approaches can require several hundreds of nanograms...

  37. How Do I Place an Addgene Order Using a PO Number?

    Type
    Blog Post
    Published
    Feb. 27, 2020, 2:15 p.m.
    ... your website? Many vendors will process orders based on a purchase order, which is an official document...depositing institutions. Addgene cannot fulfill orders based on PO documents that are sent to us by fax or email...

  38. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    Published
    Jan. 6, 2015, 5:21 p.m.
    ...resistance cassette) in pUC19 based entry vectors, as well as the pGreen-IIS based destination vectors. To ...CRISPR family of plasmids by offering a lentivirus-based mechanism for sgRNA delivery and providing a means...ACS Synth Biol 2013 Sep 20;2(9):537-41. DREADD-based chemogenetic technologies After several years...up to six DNA fragments at a time. This method (based on the Golden Gate technology) exploits the ability...reconstitution across synaptic partners) technique based on functional complementation between two non-fluorescent...tags in the FP sequence for separation from Cre-based Brainbow-expressing cells. Autobow plasmids are ...The expression plasmids for a given species are based on the same backbone to permit expression levels...

  39. RaPID Detection of RNA-protein Interactions

    Type
    Blog Post
    Published
    Aug. 16, 2018, 12:40 p.m.
    ...resolution for in vivo work. APEX2, a faster peroxidase-based labeling approach, is an alternative option but ...signaling. Limitations of RaPID Like other BirA*-based proximity labeling methods, RaPID cannot distinguish...reported by other research groups that performed BirA*-based affinity purification mass spec experiments. These...

  40. Hot Plasmids April 2018 - Protein Degradation, Nanoscopy, FIRE-Cas9, and Yeast Expression Tools

    Type
    Blog Post
    Published
    April 23, 2018, 2 p.m.
    ...protein degradation. Enter TRIM-Away - an antibody-based system developed by the James and Schuh labs. Clift...endocytosis is further complicated by the reliance on pH-based biosensors used to detect the maturation of neutral... Crabtree’s lab has developed a new CRISPR/Cas9-based system to study epigenetic modulation. While catalytically...

  41. Mouse Modeling, Part 1: Genetically Engineered Mice

    Type
    Blog Post
    Published
    July 11, 2019, 1:26 p.m.
    ...recombination of the targeting vector. CRISPR/Cas9-based systems have been developed for generating knockin... for gestation. All three can introduce multiple base pair deletions, but CRISPR/Cas9 can also introduce...in which the conditional recombination can occur based on the cells in which Cre is expressed.  Several...

  42. Antibodies 101: Conjugation

    Type
    Blog Post
    Published
    March 26, 2024, 1:15 p.m.
    ...change, so they are typically used in microscopy-based assays like immunohistochemistry, though they are....  Biotin Biotin is used in a range of antibody-based assays. Biotin itself is not visible or capable ...But hopefully, this introduction provides a good base from which to dive deeper!References and resources...instruments, each other, and your target. I love FPbase’s Spectra Viewer tool for comparing different fluorophores...

  43. What's New in CRISPR - November 2021

    Type
    Blog Post
    Published
    Nov. 18, 2021, 2:15 p.m.
    ...is less than half the size of the Cas9 or Cas12a based systems, making it well suited for AAV packaging...was shown to be effective for CRISPR activation, base editing, and genome editing in mammalian cells. ...had the highest activity for gene activation  and base editing, whereas a different set of mutations (the...

  44. Troubleshooting and Optimizing a Western Blot

    Type
    Blog Post
    Published
    Sept. 17, 2024, 1:15 p.m.
    ...gradient with different concentrations of your protein-based buffer (FBS, milk, etc.) against the same amount...instead of concentrations. Most labs use protein-based buffers, so here’s a quick tip: Keep a bottle of...even give gelatin a shot.  Remember that protein-based blockers degrade fairly quickly, even at 4 °C, so...peroxidase protein (HRP), have a limited dynamic range based on the solution used to expose them. You’ll need...(if available) and note in analysis Plasmid-based proteins: plasmid sequence not accurate Check ...and/or concentration Try a different protein-based buffer (eg, milk instead of BSA) Nonspecific...buffer/adjust lysing buffer strength Sonication based lysing protocol Subcellular fractional kit or...

  45. Fluorescent Proteins 101: When GFP lets you down

    Type
    Blog Post
    Published
    Aug. 23, 2018, 12:05 p.m.
    ...diffusion rates. Smaller genetically encoded probes are based on cofactor binding proteins as described above....the His tag and several others. Another peptide-based strategy uses an enzyme to covalently label the ...: 9759496.  3. Buckley, Anthony M., et al. "LOV-based reporters for fluorescence imaging." Current opinion...PMC3129320.  18. Mastop, Marieke, et al. "A FRET-based biosensor for measuring Gα13 activation in single...protein are available (Cranfill et al., 2016 and FPbase.org). A number of variants remain fluorescent under...

  46. Multiple Plasmids at a Low Price: Kits from Addgene

    Type
    Blog Post
    Published
    Sept. 14, 2016, 2:30 p.m.
    ...expression of many different genes was predictable based solely on the promoters and Shine-Delgarno sequences...Illumina sequencing libraries using a 2-step PCR-based protocol and are compatible with single-end or paired-end...segments that can be engineered to bind specific RNA bases. By swapping out these different modular repeat ... the variant PUF segments required to bind any 8 base RNA sequence. The segments are provided in Gateway...

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

    Type
    Blog Post
    Published
    Nov. 6, 2015, 3:30 p.m.
    ...Medical School/Brigham and Women’s Hospital (BWH). Based on her experience co-directing Mentor Circle Programs...-Europe professional collaborations, setting up bases and contacts with Spanish laboratories to start ...key to the success of this program. As we build a base of former mentees, we encourage them to get involved...consulting firm focused on new health care models based on integrative and eco-social health strategy, and...their degree. Students filled in a pre-program, baseline self-assessment survey to determine their expectations...expectations of the program and their baseline skills. Mentors were Spanish scientists (MD, PhD and MD/...defining expectations of the program and their baseline skills and a post-program self-assessment, participants...

  48. Microbes: Look, Listen, and Tell

    Type
    Blog Post
    Published
    Aug. 28, 2018, 12:04 p.m.
    ... after I arrived, I was looking through a paper-based, affordable, and portable microscope called the ... known as gas vesicles) as acoustic biomolecule-based dyes. This technology is widely applicable as bacterial...
Showing: 151 - 200 of 573 results