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We narrowed to 798 results for: Cre

Showing: 201 - 220 of 798 results

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

    Type
    Blog Post
    Published
    Feb. 28, 2023, 2:15 p.m.
    ... complexity of the device increases, as does the price. With this increased complexity comes the need ...adapted and combined with creativity and feedback from the community to create state-of-the-art devices...via workshops, seminars, or hackathons greatly increases accessibility. Through this approach, the Planktoscope...Madagascar. Platforms that allow for on-going creativity with the construction plans. Appropriate open-source...sources within the next few years, with the goal of creating more transparent and reproducible science in the...

  2. Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity

    Type
    Blog Post
    Published
    Nov. 5, 2019, 1:28 p.m.
    ...approach, the Anna Cereseto Lab created pX-evoCas9, which they showed also increased specificity. Most recently...broader PAM specificity can target more sites. Created with BioRender.com. Specificity Specificity...multiple PAM sequences (NG, GAA, and GT), greatly increasing the number of genomic loci that can be targeted...developed SpCas9-HF1. Both of the enzymes showed decreased off-target activity relative to Cas9. Since then...accurate Cas9 (HypaCas9). This nuclease showed decreased or similar off-target activity, relative to eSpCas9..., et al. "Directed evolution of CRISPR-Cas9 to increase its specificity." Nature communications 9.1 (2018...

  3. Antibodies 101: Affinity Reagents

    Type
    Blog Post
    Published
    April 14, 2022, 1:15 p.m.
    ...new Antibody Guide and not just because I helped create it. But while antibodies, as the OG (as the kids...reagents we just didn't have the space to give proper credit to. Thankfully, as Addgene's resident blog editor...the majority of these alternative reagents are created in the lab, instead of generated in vivo, they ...Listed in no particular order.) Fab fragments are created through enzymatic cleavage of the variable region...in clinical applications. Fab fragments can be created in lab in situations where a suitable antibody ... fusion proteins similar to a Fab fragment but created through engineering instead of cleavage. They are...cheaper to make than antibodies. Minibodies are created by binding together two scFvs with a CH3 linker...

  4. Antibodies 101: Polyclonal Antibodies

    Type
    Blog Post
    Published
    July 14, 2021, 1:15 p.m.
    ...antibodies produced from its serum several weeks later. Created with biorender.com. To generate polyclonal ...additional booster immunizations every 2-3 weeks to increase the antibody titer. The titer is tested following...epitopes of the target protein. While this can increase background staining (see next section), it may...experimental protocol, using a polyclonal antibody increases the likelihood that one of the clones will still...crosslinking (ChIP) or fixation (IHC). Because of their increased sensitivity, polyclonal antibodies are particularly...epitopes of their target protein thereby greatly increasing signal amplification.  When to stay away from...population recognizes many different epitopes, increasing the likelihood of cross-reactivity with other...

  5. Adenoviral Vector Production and Troubleshooting

    Type
    Blog Post
    Published
    June 14, 2018, 11:44 a.m.
    ... Gen AdVs were designed to have increased cloning capacity, decreased  potential for the generation of...E4 are deleted in 2nd generation AdVs, thereby increasing cloning capacity to ~12 Kb. The ever popular ...generated high interest for gene therapy due their increased cloning capacity (up to 36 kb!), long-term transgene...AdEasyTM system is the most popular method for creating adenoviral vector constructs. It consists of 2...can be repeated multiple times (2-4 rounds) at increasing scale over the course of 1-2 weeks. Each round...of amplification should result in a 10-100-fold increase in virus. Purification (2 days) - Purification...

  6. 5 Tips for Troubleshooting Viral Transductions

    Type
    Blog Post
    Published
    Aug. 11, 2016, 2:23 p.m.
    ... prior to their transduction has been shown to increase AAV transduction efficiency by approximately 15...efficiency depends on viral titer Both of these can be increased by concentrating a viral stock. Different titering... virus-cell contact A variety of reagents can increase transduction efficiency. These reagents typically...reagent that is commonly used and has been shown to increase transduction efficiency by 10-fold (Davis et al...hematopoietic or primary cells), and has been shown to increase transduction efficiency by 1.5-fold (Stockschläder...12705861. 3. Chen, Sifeng, et al. "Freeze-thaw increases adeno-associated virus transduction of cells."... R. Morgan, and Martin L. Yarmush. "Polybrene increases retrovirus gene transfer efficiency by enhancing...

  7. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    Published
    Feb. 11, 2025, 2:15 p.m.
    ...different compositions of the Cascade complex. Created with BioRender.com.   The Cascade complex Cascade...Figure 2: Cascade complex from CRISPR type I-E. Created with BioRender.com. Thanks to this complex,...Tomoji Mashimo lab and the Tilmann Weber lab — to increase efficiency of these systems, though consistent...General overview of the Cascade-Cas3 mechanism. Created with BioRender.com.   The reeling mechanism...unwinding of dsDNA occur simultaneously, which creates a loop in the target strand that is cut occasionally...repair without the section between the two gRNAs, creating a deletion. However, there is the chance of a .... Future targets Cas3 has the potential to be incredibly useful in therapeutics. Imagine deleting a problematic...

  8. Pooled Library Amplifications

    Type
    Blog Post
    Published
    May 30, 2024, 1:30 p.m.
    ...Factors to consider when creating a pooled library amplification protocol. Created with BioRender.com. ...Re-transformation of the SPLINTR Libraries (PDF, 401 KB) Screening Zhang Lab - Multiplexed Overexpression of Regulatory...et al. Nat Protoc. 2017 with modifications Screening pCMV-Rep78/68 Scanning Saturation Mutagenesis...Amplification and Sequencing Protocol (DOCX, 32 KB) Screening Rinehart Lab Iterative Synthetically Phosphorylated...-Cas9 knockout and transcriptional activation screening, a protocol paper by the Zhang lab, and the Broad...More resources on the Addgene blog Genome-Wide Screening Using CRISPR Preparing Pooled Libraries NGS Quality...

  9. CRISPR 101: Mammalian Expression Systems and Delivery Methods

    Type
    Blog Post
    Published
    Sept. 24, 2015, 2:30 p.m.
    ...expression? Are you trying to create a single point mutation? Do you want to create a fusion with a reporter...include a homology directed repair (HDR) template to create knock-ins, point mutations, or to add a tag, you...vivo. A common choice for conducting genome-wide screens using CRISPR. AAV transduction Only compatible...Transient expression of CRISPR components, expression decreases as RNA is degraded within the cell. Can be used...Transient expression of CRISPR components, expression decreases as gRNA and Cas9 protein are degraded within the...validated tools.  Special thanks to Joel McDade for creating the Expression Systems table. Marcy Patrick contributed...

  10. CRISPR 101: RNA Editing with Cas13

    Type
    Blog Post
    Published
    July 31, 2020, 12:30 p.m.
    ...and found that 50 nt spacers increase editing efficiency but also increase off-target editing within the...1090), which decreases the REPAIRv1 construct size from 4,473 bp to 4,152 bp without decreasing editing efficiency..., which deaminate adenosine to inosine in RNA, creating a functional A->G change. They fused ADAR deaminase...to dPspCas13b, but observed low RNA editing. To increase A->G editing, they employed hyperactive ADAR constructs... they hoped to destabilize ADAR-RNA binding to decrease off-targets. Of the tested constructs, ADAR2DD...

  11. Droplet Digital PCR for AAV Quantitation

    Type
    Blog Post
    Published
    Jan. 16, 2020, 2:18 p.m.
    ...generation oil are moved through small channels to create a water-in-oil emulsion containing approximately...the number of positive droplets as the dilutions increase. The ddPCR software uses the ratio of positive...parameters, here are a few things you can try: Increase the number of cycles. After additional rounds ...amplification, your fluorescence amplitude will increase, leading to greater separation of your positive...droplets. No more than 50 cycles is recommended. Decrease your ramp rate. A rate of 2C/s is recommended ... the droplets, but you can go as low as 1C/s. Increasing the elongation time to 2 minutes and the denaturation...denaturation time to 1 minute has been shown to increase droplet separation (Witte et al., 2016). This is...

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

    Type
    Blog Post
    Published
    Aug. 9, 2016, 2:30 p.m.
    ...CRISPR screen to disrupt these enhancers. The third and final step is to conduct our CRISPR screen. We start... the marvel of DNA compaction, an enhancer can increase the expression of a gene that is millions of base...stem cells, and conclude with a targeted CRISPR screen that can disrupt these enhancers. A real-world ...that have NANOG binding sites 2. Design a CRISPR screen to target and disrupt the NANOG enhancers 3. CRISPR...you’re interested in designing your own CRISPR screens for enhancers, check out the Appendix. Conclusion...precision medicine. We can apply this knowledge to create targeted disease therapies with minimal side-effects...

  13. Fluorescent Proteins 101: Green Fluorescent Protein (GFP)

    Type
    Blog Post
    Published
    May 15, 2014, 3:33 p.m.
    ...Fluorescent Protein (GFP) has likely existed in creatures such as jellyfish for millions of years; however...physiological processes. Re-engineering GFP to increase its range of color and application Almost as.... Tsien described an S65T point mutation that increased the fluorescence intensity and photostability ...derivatives Mutation Known Function S65T Increased fluorescence, photostability, and a shift of the... the major excitation peak to 488 nm F64L Increased folding efficiency at 37C Y66W Causes the chromophore...Blue-shifts the wavelength (blue derivatives) Y145F Increases quantum yield for BFP Y145A and H148D Stabilizes...to identify particular cell populations in drug screens, to visualize micrometastases in nude mice in cancer...

  14. Harnessing TnpB for Genome Editing: A Compact and Versatile Tool for Your Research

    Type
    Blog Post
    Published
    July 29, 2025, 1:15 p.m.
    ...downstream of the TAM, creating staggered double-strand breaks like those created by Cas12a. Applications...TnpB from Deinococcus radiodurans (Dra2TnpB) to create a genome editing system for plants (Karmakar et... proteins with additional enzymes or domains (increasing the overall size), using TnpB as the core nuclease... using your method of choice. Step 5: Colony Screening Use Primer 92F (5′-cattacgcaattggacgacaac-3′)...′) and Oligo 2 (specific to your target) to screen colonies via PCR. A 354-bp product confirms successful...insertion. Alternatively, use M13R and Oligo 2 to screen. A 667-bp product confirms successful insertion...

  15. Antibodies 101: The Four ELISAs and When to Use Them

    Type
    Blog Post
    Published
    July 25, 2024, 1:15 p.m.
    ...level of antigen in the sample. This figure was created with BioRender.com  Direct ELISAs A direct ... bind non-specifically to assay components and increase background staining. Direct ELISAs also lack the... antibody. Incorporating a secondary antibody increases the sensitivity of the assay, since multiple secondary... both primary and secondary incubation steps, increasing the workload and time commitment for users. This...antibodies for the capture and detection steps, which increases the specificity of the assay. The assay is also...antibody availability Longer protocolLess specificityIncreased chance of cross-reactivity Sandwich ... High specificityHigh sensitivity Longer protocolIncreased chance of cross-reactivityChallenging to develop...

  16. Neuronal labeling with Spaghetti Monster

    Type
    Blog Post
    Published
    Aug. 14, 2018, 12:42 p.m.
    ...USA have used AAV1 and AAV2 serotypes in order to create an atlas of the mouse brain. This atlas enables...antibody recognition of epitope tags. Thus they have created antigenic protein tags called “spaghetti monster... FPs fused to multiple epitope tags. Indeed, to create the smFPs Looger’s team strategically inserted ...antibody-based amplification of their signals is weak and increases background fluorescence. Furthermore, many of ...instance, smFPs have been used to visualize “thorny excrescence” (TE) spines in the Hippocampal CA3 pyramidal...sites and primary antibody-based detection, smFPs create much brighter signals for weakly expressed proteins...: Making the journey from axon to nucleus AAVs CREATEd for gene delivery to the CNS and PNS Resources...

  17. The PAM Requirement and Expanding CRISPR Beyond SpCas9

    Type
    Blog Post
    Published
    Aug. 20, 2020, 2:30 p.m.
    ...s lab performed a series of positive selection screens in bacteria to identify mutants of S. pyogenes ...sequences (Kleinstiver et al. 2015). From these screens, they identified four novel SpCas9 variants with...some cleavage with an NGA PAM. This variant may increase the specificity of genome modifications at DNA...allows for expanded PAM recognition as well as increased specificity and lower off-target activity (Hu ...proteins has and will continue to dramatically increase the number of CRISPR applications. The first non-Cas9...formation of “sticky ends” rather than the blunt ends created by Cas9. Cas12a  displays lower off-target editing...) system fuses Cas13b to RNA deaminase ADAR2 to create a specific RNA editor. Cas13 enzymes are advantageous...

  18. Designing Your Chalk Talk for the Academic Job Interview

    Type
    Blog Post
    Published
    March 12, 2019, 1:37 p.m.
    ...significant knowledge gap in your field or even creating a new field. A knowledge gap is an impediment ...of experiments or a laundry list of molecules to screen has unclear utility. You cannot predict what will... have no hook. A battery of new assays for your screen result may or may not actually help. Ultimately...distinguish mechanistic questions from open ended screens and data collection. Organize your research vision...want to know the answer to your research problem. Creating a coherent unified story and model can help make...Consider going beyond the whiteboard. You may wish to create a sculpture or print a 3D model to better illustrate... His interests include the quality control of secretory proteins in the Endoplasmic Reticulum, optimization...

  19. Plasmids 101: Broad Host Range Plasmids

    Type
    Blog Post
    Published
    April 11, 2024, 1:15 p.m.
    ...they function in nature can inform us on how to create better recombinant vectors. In this blog post, ...provide tips on how we can harness those features to create broad host range recombinant vectors.  A plasmid... host range in plasmids? Not all plasmids were created equally. Only a handful of plasmids have been identified..., from broad host range plasmids can be used to create recombinant vectors that can replicate in different...vinelandii, Brevibacterium methylicum, Caulobacter crescentus, Desulfovibrio vulgaris, Erwinia carotovora, ..., Bordetella spp., Brucella spp., Caulobacter crescentus, Escherichia coli, Gluconacetobacter xylinus,...recombinant vectors can be modified further to increase the range of hosts in which proteins can be expressed...

  20. To Codon Optimize or Not: That is the Question

    Type
    Blog Post
    Published
    Nov. 12, 2020, 2:15 p.m.
    ...Villarreal. By the late 1980s, scientists even created a codon adaptation index (CAI) that is based on... (Sharp and Li, 1987). In 2000 the Ikemura lab created the Codon Usage Tabulated from GenBank database...interest based on an organisms codon usage bias to increase translational efficiency and thus protein expression...across an entire polypeptide. Many researchers have created codon-optimization algorithms/resources (Athey ...study, codon optimization resulted in a 6-9 fold increase in expression of these channels providing scientists...to codon optimize? Although codon optimization increases protein production in certain systems, synonymous...optimization may not always be the optimal strategy for increasing protein production. If you are trying to express...
Showing: 201 - 220 of 798 results