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We narrowed to 490 results for: ARA-2

Showing: 141 - 160 of 490 results

  1. IBEX Knowledge-Base: A Data Resource for Multiplex Tissue Imaging

    Type
    Blog Post
    ...imaging of diverse tissues. Nature Protocols, 17(2), Article 2. https://doi.org/10.1038/s41596-021-00644-9 ...directly from the Zenodo dataset.     Figure 2: Screenshot showing reagent entries with associated... multiplexed: you can image over 65 different parameters using this method (see Movie S8 from Radtke et...

  2. Delivery Methods for Generating iPSCs

    Type
    Blog Post
    ...plasmid-based expression requires serial transfection of 1 or 2 plasmids that express the reprogramming factors of...for generating iPSCs by plasmid transfection where 2 of 11 clones tested had plasmid integration. Another...understanding the mechanisms of reprogramming, and 2) studies with clinical endpoints. In the first scenario...PubMed PMID: 27764162. PubMed Central PMCID: 5072705. 2. Sommer, Cesar A., and Gustavo Mostoslavsky. "The ...challenges." Journal of Cellular Physiology 228, no. 2 (2012): 267-75. PubMed PMID: 22767332.  3. Kim, Dohoon...PubMed PMID: 23546745. PubMed Central PMCID: 4176696. 2. Yusa, Kosuke, Roland Rad, Junji Takeda, and Allan...generation. Expert opinion on biological therapy, 10 2, 231-42. PubMed PMID: 20088717. PubMed Central PMCID...

  3. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    ...the light-inducible heterodimerizing cryptochrome 2 (CRY2) and calcium and integrin-binding protein 1 ...inactive, dead Cas9 protein (dCas9) fused to CIB1; and 2) the activator - the CRY2 photolyase homology region... fused to both the N- and C-termini of dCas9; and 2) CRY2FL-VP64, a fusion of full-length CRY2 and the...researchers saw an 11-fold increase in mRNA levels after 2 hr and a 400-fold increase after 30 hr. The system...authors fragmented Cas9 into N-terminal (residues 2-713, N713) and C-terminal (residues 714-1368, C714...nMagC714 instead of nMagHigh1-C714, generating paCas9-2. This change did not significantly alter the system...prior work, the Sato lab also showed that the paCas9-2 system could be spatially controlled and reversibly...

  4. DNA Purification Without a Kit

    Type
    Blog Post
    ...alkaline lysis plasmid miniprep Starting material: 2 mL bacterial culture Product: plasmid DNA This kit-free...protocol: 1) it solubilizes both DNA and agarose, and 2) it helps DNA stick to the glass. After binding DNA... had a similar level of sensitivity. Figure 2: Steps to purify DNA using a cellulose dipstick. Image...Academy of Sciences of the United States of America, 76 2, 615-9 . https://doi.org/10.1073/pnas.76.2.615  Zhou...rather a glass powder slurry that has a milk-like appearance. To make DNA stick to the glass particles in ....0007750  Vogelstein, B., & Gillespie, D.A. (1979). Preparative and analytical purification of DNA from agarose...

  5. Enhancing CRISPR Targeting Specificity with eSpCas9, SpCas9-HF1, & HypaCas9

    Type
    Blog Post
    ...target DNA strand separation is stabilized (2,3). Stable strand separation is maintained by 2 sets of interactions...formed by the Cas9 HNH and RuvC nuclease domains 2. Interactions between the target strand and the gRNA... Find plasmids from this publication at Addgene. 2. Nishimasu, Hiroshi, et al. "Crystal structure of ...basal strand separation. This decreased strand separation combined with the weak separation afforded by... 1: Strand separation and target DNA binding to the Cas9 nuclease. Stable strand separation is maintained...alanine substitutions throughout the groove in 32 separate Cas9 mutants. When tested for their ability to...M694A/Q695A/H698A). This new variant displays comparable on-target activity and similar or decreased off-target...

  6. Live and Let Dye: Self-Labeling Protein Tags

    Type
    Blog Post
    ...super-resolution or single-molecule techniques.   Figure 2: Two-color super-resolution imaging of ER and mitochondria...stimulated emission depletion (STED) nanoscopy. Scale bar, 2 μm. Inset shows comparison with standard confocal ...enables applications like multi-color imaging (Figure 2). If you’re working with purified proteins in vitro...Labeling in Living Cells. Chemistry & Biology, 15(2), 128–136. https://doi.org/10.1016/j.chembiol.2008.01.007...conjugates: A flexible chemical tag. Nature Methods, 2(4), Article 4. https://doi.org/10.1038/nmeth749  Strebinger... purified and labeled separately with different dyes. b) mDia1 and CP appearance at the filament tip from...the filament from (a-b), showing the appearance and disappearance of 649-mDia1 or 549-CP (upper, middle...

  7. Viral Vectors 101: An Introduction to AAV

    Type
    Blog Post
    ..., AAV2/8 has a type 2 ITR and a type 8 serotype. Almost all vectors contain type 2 ITRs, which comes from...differentiated, non-dividing cells.   Figure 2: DNA rescue and transduction of a conventional single-stranded...quantitative PCR-based method for the titration of AAV-2 vector stocks."Molecular Therapy 6.2 (2002): 272. ...names of AAVs contain two numerical designations, separated by a slash, that indicate the ITR and serotype...

  8. Plasmids 101: FLEx Vectors

    Type
    Blog Post
    ...conditional knock-in cassette. As shown in Figure 2, the cassette should contain a reporter DNA sequence...a targeted neuronal population.    Figure 2 (modified from Schnutgen et al. Nat Biotech 2003):...cellular level in the mouse. 2003 PubMed PMID: 12665802. 2. Branda, CS and Dymecki, SM. Talking about a Revolution... SM. 2008. A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range ...will be greatly reduced, allowing for clearer characterization of the location, morphology, and circuit mapping...

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

    Type
    Blog Post
    ...the induction of transcription factors 1 and 2. See Aranda-Díaz et al. for more information. The El-Samad...difficult-to-manipulate primary cells, achieving knockdown within 1-2 hr of reagent delivery. TRIM-Away is suitable for ...factor 1 controls expression of transcription factor 2, which directly controls expression of a reporter ...knockout techniques. Find the plasmids from Aranda-Díaz et al. Aranda-Díaz, et al. ACS Synth Biol. 2017. Pubmed...demonstrate independent control of gene expression, Aranda-Díaz et al transformed yeast with both a GAL4/estradiol...each other, these systems can be used together. Aranda-Diaz et al additionally show that it is possible...places reporter expression under the control of two separate synthetic transcription factors in series and ...

  10. Advanced Uses of Cre-lox and Flp-FRT - A Neuroscientist’s View

    Type
    Blog Post
    ...FLP and Cre for additional control   Figure 2: Expression of a morphological marker (eYFP) and synaptic...Sternson. 2008. “A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-Range ...PMID: 18614669. PubMed Central PMCID: PMC2593125. 2. Buchholz, F, P O Angrand, and A. Francis Stewart....The FLP Recombinase of the Saccharomyces Cerevisiae 2 Micron Plasmid Attaches Covalently to DNA via a Phosphotyrosyl...structure of 13 base pair palindromic repeats separated by an 8 bp asymmetric core. Recombination between...recombinase. The high concentration of FLEx vectors guarantees that most cells are transfected with all labeling... knockout of a target gene and expression of a separate gene. In these mouse lines, gene knockout can ...

  11. A Practical Guide to Optimizing AAV DIO and FLEx Vector Expression

    Type
    Blog Post
    ...one of lox2272 sites will now be sandwiched between 2 loxp sites and is excised by Cre (Figure 1). This ...flank the transgenes (non-homologous pairs) (Figure 2.). They found that almost all off-target expression...exercise caution when using them.    Figure 2. Schematic diagram showing the mechanism of spontaneous... Tropism and Axonal Transport of AAV Serotypes 1, 2, 5, 6, 8 and 9 in the Mouse Brain. PLoS ONE 8:e76310... Pseudotyped with Viral Capsids from Serotypes 1, 2, and 5 Display Differential Efficiency and Cell Tropism...and volumes to determine the optimal injection parameters needed to transduce your cells of interest. Using...Once you have determined the optimal injection parameters for the serotype that best transduces your cells...

  12. CRISPR 101: Cytosine Transversion Editors

    Type
    Blog Post
    ...Nature Cell Biology, 26(2), 294–304. https://doi.org/10.1038/s41556-023-01342-2 Koblan, L. W., Arbab, M...adjacent DNA to create a region of separate strands called an R-loop (Figure 2). This allows the guide RNA to...order to bind DNA, Cas9 requires (1) a guide RNA, (2) a complementary DNA sequence, and (3) a protospacer-adjacent...accessible on the outside of the enzyme. Figure 2: CRISPR R-loop. Created with BioRender.com. Base...), 35–40. https://doi.org/10.1038/s41587-020-0592-2 Additional Resources on the Addgene blog CRISPR 101...while Cas9 is bound, keeping the two DNA strands separate and preventing repair based on the complementary...The structure formed by Cas9 binding to DNA and separating the two strands. The guide RNA base pairs to ...

  13. Plasmids 101: E. coli Strains for Protein Expression

    Type
    Blog Post
    ...increase multimer formation Δ(ara-leu)7697 ΔlacX74 ΔphoA PvuII phoR araD139 ahpC galE galK rpsL F′[lac+ ...gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10--TetS)2 [dcm] R(zgb-210::Tn10--TetS) General protein expression...recommended for toxic proteins BL21-A1 Tetracycline Arabinose-inducible expression of T7 RNAP; IPTG may still... expression F- ompT lon hsdSB (rB- mB-) gal dcm araB::T7RNAP-tetA General protein expression  BLR ...expression strain to make sure they are compatible. An arabinose-inducible plasmid will not express in an IPTG ...

  14. Retrograde AAV viral preps

    Type
    Collection
    ...sensor Jonathan Ting 83899 pAAV-mDlx-GCaMP6f-Fishell-2 mDlx GCaMP6f expression under the control of the mDlx...final viral vector preparation. In some cases, in vivo testing of these viral preparations was performed by...Addgene is producing ready-to-use viral vector preparations in a retrograde serotype from the Alla Karpova...David Schaffer laboratories. These viral vector preparations were produced with the rAAV2-retro helper plasmid...-Ef1a-mCherry-IRES-Cre EF1a Cre and physically-separate mCherry expression Recombinases Karl Deisseroth...pAAV-EF1a-mCherry-IRES-Flpo EF1a Flpo and physically-separate mCherry expression Recombinases Karl Deisseroth...GCaMP6f-P2A-nls-dTomato Syn GCaMP6f and physically separate nuclear dTomato Calcium sensor Jonathan Ting 51083...

  15. Predicting Adverse Reactions to Monoclonal Antibody Drugs

    Type
    Blog Post
    ...various components of the immune system. Figure 2: In-vitro models for immunogenicity prediction of ...drug reaction. This system would somewhat act like a 2-step verification. All approaches have their own limitations...Future Enhancements. Frontiers in drug discovery, 2, 952326. https://doi.org/10.3389/fddsv.2022.952326Joubert...ADAs can inactivate the drug and increase drug clearance, lowering its efficacy and increasing the risk...Efforts to predict T cell epitopes focus on characterizing those epitopes as CD8 or CD4 epitopes, as well...

  16. Year of the Camelid: Antibody Style

    Type
    Blog Post
    ...and a source of sdAbs (Figure 2) (Xu, et al., 2021).      Figure 2: Genetically modified mice offer... from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 595:278–282. https://doi.org/10.1038...2024 the International Year of Camelids. The declaration is intended to raise awareness of the economic...

  17. Hot Plasmids and Viral Preps - January 2021

    Type
    Blog Post
    ... Opto-Cre-Vvd is fast and can cut in as little as 2 hours.  Sheets, MB, et al., ACS Synth Biol. 2020....they investigated three Casɸ orthologs, Casɸ-1, Casɸ-2, and Casɸ-3. This system is notable for several reasons...a minimal PAM requirement. For instance, for Casɸ-2 the PAM sequence is 5’-TBN-3’ (where B is G, T, or...deposited by Leopold Parts. This library delivers 2 randomly paired guides per construct and allows a ...crRNA-guided DNA cutting, unlike other well-characterized Cas enzymes, which rely on multiple active sites...

  18. Viral Vectors 101: What is a Virus (and a Viral Vector)?

    Type
    Blog Post
    ...developed around how they replicate (Figure 2). Figure 2: Baltimore replication classes. Image credit...safer viral vectors that can be used in BSL-1 or BSL-2 labs. Viral vectors are viruses that have been genetically...genes for the required proteins are packaged in separate plasmids and expressed via cells cultured with...

  19. Viral Vectors 101: Calcium Sensors

    Type
    Blog Post
    ...calcium biosensor, so that the (1) binding of calcium, (2) allosteric rearrangements of the sensor, and (3) ...user-controlled illumination with violet light and (2) exposure to increased intracellular calcium. It has...dynamics in vivo. Neuroscience Research. 2021 Aug 1;169:2-8. Suzuki J, Kanemaru K, Iino M. Genetically encoded...experiment with a sensor that is tuned to your parameters.   Kinetics How fast is the process you would...used calcium reporters with different kinetic parameters. There are three GCaMP types based on their kinetics...available with improved kinetic and sensitivity parameters. Sensitivity and Localization The calcium concentrations...to go. Pro tip: Vectors with ready-to-use AAV preparations are labeled with the green virus particle on...

  20. Pairing CombiGEM and CRISPR for Combinatorial Genetic Screening

    Type
    Blog Post
    ...CombiGEM lentiviral vector backbone pAWp12 (Figure 2). Cloning from the pAWp28 storage vector to the pAWp12... before beginning your experiments. Figure 2: Strategy for assembling barcoded combinatorial gRNA...PMID: 25114216. PubMed Central PMCID: PMC4151723. 2. Doench, John G., et al. "Optimized sgRNA design to...has been successfully applied to functionally characterize combinatorial gene knockouts generated via multiplexed...antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics." Proceedings of the National...PMC3972032. 10. Wong, Alan SL, et al. "Massively parallel high-order combinatorial genetics in human cells...
Showing: 141 - 160 of 490 results