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We narrowed to 808 results for: Ran;

Showing: 261 - 280 of 808 results

  1. Viral Vectors 101: Viruses as Biological Tools

    Type
    Blog Post
    Published
    March 21, 2023, 1:15 p.m.
    ...one they have a high transduction efficiency and can effectively infect a wide range of cell types that ...used to achieve transient, high expression of the relevant cargo without the fear of random genomic integration... Packaging Capacity (>8kb) High Transduction Efficiency Transient Gene Expression High Immunogenecity...viral envelope, which fuses with the target cell’s membrane, allowing the viral particle access into the cell...that are typically ‘difficult to transfect’, such as primary cells. They can also be directly injected into...Immunogenicity Infects Non-Dividing Cells Transient Gene Expression Low Tropism for Mouse Cells and...out How to Get the Most from Your Lentiviral Transduction Additional Resources on Addgene.org Browse...

  2. CRISPR 101: Cas9 vs. The Other Cas(s)

    Type
    Blog Post
    Published
    Dec. 8, 2022, 2:15 p.m.
    ... it will proceed to generate a blunt DNA double strand break. Cas9 has been studied for genome engineering...an expanding number of others. Best for: a wide range of DNA edits.   Cas3 – The shredder What sets Cas3...locates its target sequence and initiates single stranded DNA degradation. Cas3 DNA digestion can proceed...convenient for targeting experiments requiring single strand DNA generation, such as homology directed-repair...therapeutic delivery.   Cas14 – Mini, but single strand mighty Unlike many other Cas enzymes, Cas14 targets...This makes it particularly useful in generating transient edits of signaling molecules (RNA) as opposed ...for targeting mRNA and useful as a mechanism of transient knockdown of gene expression. This system could...

  3. Teaching an Old DOG New Tricks: Controlling Protein Activity with GFP

    Type
    Blog Post
    Published
    Nov. 24, 2015, 3:30 p.m.
    ... to create a complete transcription factor, activating luciferase transcription. Tang et al. coined this...Connie Cepko’s lab allow researchers to activate transcription or Cre recombinase activity only in the presence...Using nanobodies to create GFP scaffolds for transcriptional activation The project began with a frustration... in their 293 cell culture system. In cells cotransfected with GFP and the GBPs, GFP linked the two GBPs...this system T-DDOG (Transcriptional Devices Dependent On GFP). In testing the specificity of their system... dsRed, mCherry, and TdTomato do not induce transcription. Thus, T-DDOGs can be used in combination with...T-DDOG results showed that GFP could regulate transcription in a cell-type specific manner, and Tang and...

  4. How to Design Your gRNA for CRISPR Genome Editing

    Type
    Blog Post
    Published
    Sept. 24, 2020, 1:15 p.m.
    ...-1 Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Cowan CA, Talkowski ME, Musunuru... efficacious to target the coding or non-coding strand of DNA. As a rule of thumb, we avoid target sites..., 2020). is not limited to single nucleotide transitions but still requires a nearby PAM, although these... modulating gene expression at the level of transcription – CRISPRa (activation) and CRISPRi (inhibition...most-efficacious to target a ~100nt window upstream of the transcription start site (TSS), while for CRISPRi, a ~100nt...of producing the guide (synthetic, in vitro transcription, or lentiviral delivery) can affect the accuracy...examined whenever possible when using knockout or transcriptional modulation approaches. Avoiding off-target ...

  5. Educational Planarian Tools for Teaching Developmental Biology Techniques

    Type
    Blog Post
    Published
    May 24, 2018, 1:20 p.m.
    ...remove one strand of the siRNA and are directed by complementarity to the remaining single stranded siRNA ...activity or their translation disrupted through physical blocking of the translation machinery. In the...WISH) for visualizing expression of genes. Double-stranded RNA (dsRNA)-mediated RNA interference (RNAi) to... by T7 promoters to allow for bidirectional transcription to create dsRNA. Students can produce DNA templates...the temporal and spatial localization of mRNA transcripts in tissue. This is useful for labeling specific...mixing with the liver paste, these E. coli are transformed with the appropriate plasmid and dsRNA expression...Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391 (1998...

  6. Plasmids 101: Modular Cloning

    Type
    Blog Post
    Published
    March 12, 2024, 1:15 p.m.
    ...into… Transcription units (TUs), which are functional units composed of multiple parts transcribed together...a protein that regulated its own transcription, or the transcription of another gene? Now you have a genetic...As a plasmid repository, we are no strangers to cloning. If you’re reading this, then chances are you...hierarchical levels: individual DNA parts, transcriptional units, and multigene constructs. Let’s start...start by examining individual parts and transcriptional units. Individual parts are defined DNA sequences...assembled into larger functional units which are transcribed together. Image courtesy of Robert Hurt. ... with DNA, and these complexes regulate the transcription of specific genes. What if one of those genes...

  7. AAV Vector Quality Control: Going the Extra Mile with NGS

    Type
    Blog Post
    Published
    Sept. 12, 2017, 1:44 p.m.
    ...serotype. Additionally, we check viral transgene expression in transduced cells whenever possible. This post... for transgene expression. Once packaged in AAV, this pre-recombined DNA could lead to transgene expression... to these expected hits, we always get hits to “random” genes. Do these hits always mean the sample is...wanted to see how low we could go. We prepared a range of spiked samples from 0.1-20% and discovered that...find the optimal dose that allows for sufficient transgene expression but limits the likelihood of recombinase-independent...pioneering the systematic use of this new QC assay to guarantee that you receive the best AAV vectors for your...Broucque F, Robin C, Hebben M, Merten O-W, Blouin V, François A, Redon R, Moullier P, Léger A (2015) Advanced...

  8. Fluorescent Proteins 101: Visualizing Subcellular Structures & Organelles

    Type
    Blog Post
    Published
    June 22, 2017, 2:30 p.m.
    ...can be gained by understanding the location and transport of the protein within a living cell. Analyzing...Analyzing differences in protein localization and transport between healthy and diseased states can also provide...endoplasmid reticulum, modified in the golgi and then transported in vesicles via the secretory pathway to their...the end of their life cycle, proteins may be transported through the vesicles to the lysosome where they... of an organelle or involved in intracellular transport pathways, it is possible to map the internal organization...this case the cell needs to be fixed and the cell membrane permeabilized in order for the antibodies to reach...used markers for major mammalian organelles and transport pathways. It is best, though not always possible...

  9. Golden Gate Assembly Upgrades: More Fragments, Faster Assembly, and Higher Fidelity

    Type
    Blog Post
    Published
    Oct. 11, 2018, 12:30 p.m.
    ...number of transformants); the greater the number of inserts, the lower the number of transformants. To compensate...containing the transformants onto the selection plate. Figure 2 shows representative transformation plates obtained...high levels of transformants and low backgrounds – so much so that there was little range for detectable...the number of transformants while maintaining high levels of correct assemblies) translate to faster assembly...background by antibiotic selection. Screening of transformants by colony PCR confirmed the insertion of the...volume of the 1 ml outgrowth spread on each transformation plate can be manipulated to result in appropriate...

  10. xCas9: Engineering a CRISPR Variant with PAM Flexibility

    Type
    Blog Post
    Published
    March 28, 2018, 6:52 p.m.
    ...xCas9 for transcriptional regulation and base editing Hu et al. also engineered transcriptional activators...activating transcription. Sites containing NG, GAA, or GAT PAMs averaged 56-91% transcriptional activation... to create xCas9, an enzyme recognizing a broad range of PAMs like NG, GAA, and GAT, but also displaying...subunit ω. This construct is designed to activate transcription from the accessory plasmid (AP) encoding phage...could recognize a library PAM, it would induce transcription of gene III, permitting phage propagation and...spectinomycin resistance. xCas9 3.7 showed the broadest PAM range, recognizing NG, NNG, GAT, and CAA PAMs, while xCas9... xCas9 3.6 displayed the second best PAM range. Characterizing xCas9 in mammalian cells Hu et al. compared...

  11. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    Published
    June 25, 2024, 1:15 p.m.
    ..., and deletions) without introducing DNA double-strand breaks (Anzalone et al., 2019; Chen & Liu, 2023...typically a Cas9 H840A nickase fused to a reverse transcriptase) together with a prime editing guide RNA (pegRNA...containing a primer binding site and a reverse transcription template (RTT). The design of the pegRNA has...provides users with different designs of pegRNAs, ranked by their PRIDICT/PRIDICT2.0 score. For the best...editing strategies) based on a DeepSpCas9 score ranking (Kim et al., 2019). PRIDICT saves time and resources...doi.org/10.1016/J.CELL.2013.07.018 Anzalone, A. V., Randolph, P. B., Davis, J. R., Sousa, A. A., Koblan, L....Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149–157...

  12. PITChing MMEJ as an Alternative Route for Gene Editing

    Type
    Blog Post
    Published
    Feb. 23, 2016, 3:30 p.m.
    ...genome edits. But have you heard of another double-stranded break repair mechanism: MMEJ (microhomology-mediated...primary methods for repairing DNA after a double-stranded break. HDR copies the sequence from a repair template...are chewed back to reveal homology, allowing the strands to anneal. DNA synthesis then fills in the gaps...5-25 bp) regions of homology flanking a double-stranded break yield precise deletion of the sequence between...locus flanking the GFP-Puro cassette. Three double stranded breaks are necessary for knock-in: one on either...an insertion locus-specific gRNA. These double stranded breaks allow for two sets of microhomologies (...PITCh-gRNA binding sites. This PITCh plasmic is cotransfected with a plasmid carrying Cas9, the PITCh-gRNA...

  13. Light Sheet Fluorescence Microscopy

    Type
    Blog Post
    Published
    July 16, 2015, 2:30 p.m.
    ...microscopy coupled with techniques that make tissues transparent are enabling microscopes to visualize the cellular...the cortico spinal tract, CST, spinal cord and cranial nerve afferents labelled with a AAV8 expressing...sectioning (OPFOS) (2). Arne Voie, David Burns and Francis Spelman focused a laser beam into a thin sheet ...of clear specimens and for in vivo imaging of transparent organisms. Advances in tissue clearing Similar...attempt to render fixed anatomical preparations transparent was done by Walter Spalteholtz (10).  He used...green fluorescent protein (GFP) (6).   The Dodt and Frank Bradke laboratories later developed the 3DISCO (...spinal cords by combining Ultramicroscopy with tetrahydrofuran-based tissue clearing (13,14). A few years ...

  14. Drew Endy Introduces the Biobrick Public Agreement Plasmid Collection

    Type
    Blog Post
    Published
    Dec. 12, 2013, 3:35 p.m.
    ...Science describing the development of “transcriptors,” transistor-like digital genetic switches that enable...comprised of well-characterized bacterial transcription and translation initiation elements. Open science with...dogma - replication of DNA, transcription of DNA to make RNA, translation of RNA to make proteins. That's...reliable gene expression via standard transcription and translation initiation." Nature Methods. 10, 354...cellular computing. These logic gates built from transcriptors are available at Addgene as a BIOFAB kit comprised...genetically encoded sensors. Those sensors could transduce otherwise invisible molecules into regulation ...

  15. AAVs in Retinal Gene Therapy

    Type
    Blog Post
    Published
    July 31, 2018, 12:55 p.m.
    ...and they had been shown to to transduce the retina but only transiently. However new viral vectors capable...adenovirus (AdV) and lentivirus (LV) are known to transduce retinal cells, AAV quickly became the vector of...due to its considerable immunogenicity and its transient expression. LV results in long term expression... in dividing and non-dividing cells due to its (random) integration into the genome, and its large DNA... packaging capacity is well suited for larger transgenes. Unfortunately it has limited tropism in the ...and the one used in Luxturna™, can efficiently transduce various types of retinal neurons. Nowadays a toolbox...engineered AAV serotypes that further expands the range of AAV properties is available. While only natural...

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

    Type
    Blog Post
    Published
    May 15, 2014, 3:33 p.m.
    ...physiological processes. Re-engineering GFP to increase its range of color and application Almost as soon as its...backbones for constructing fluorescent fusions. Transcription Reporter: Placing GFP under the control of a...promoter in a given cell type. This type of transcription reporting was among the earliest uses of GFP...GFP. Fluorescence resonance energy transfer (FRET): This is used to study the interactions between two ...ion (such as Ca2+) concentrations and pH, using a range of strategies such as FRET, calmodulin, and others... gene of interest, or expressed from the same transcript as the gene of interest, but after an internal...expressing GFP from cells that are not. Developmental/transgenic uses: Because of its stability, GFP can be used...

  17. Antibodies 101: Reading a Flow Plot

    Type
    Blog Post
    Published
    Feb. 6, 2024, 3:13 p.m.
    ...conceptualize where the populations are, try drawing a quadrant over the plot that divides it into four, using...different populations by imagining (or drawing) a quadrant over the dot plot. Created with biorender.com....Biorender! While a helpful visualization tool, a quadrant will often be too clean for real-world data. Most...and debris. The side scatter roughly measures granularity, a proxy for nucleic complexity of the cell.  ...these populations, I suggest using the imaginary quadrant to help (Figure 5). Even though this real-world...real-world data is far messier than biorender plots, quadrants can still help me as a reader if I'm struggling...strategy from Barlow-Anacker et al., 2017, with quadrants to help visualize the different populations. Used...

  18. Viral Vectors 101: Parts of the AAV Packaging Plasmid

    Type
    Blog Post
    Published
    Dec. 3, 2020, 2:15 p.m.
    ...proteins needed for the virus to replicate,  and the transfer plasmid which contains the viral genome. In today...and cap are expressed from a separate plasmid in trans, freeing up space in the viral genome so that a ...Replication initiates from the AAV genome ITRs on the transfer plasmid, which contain regions of dsDNA. To generate...capsid. Rep proteins are also involved in the transcriptional regulation of the AAV p40 promoter which drives...promoter. Alternative splicing and differing translational start sites generate the three VP proteins. ...Assembly-Activating Protein (AAP) and the recently discovered Membrane Associated Accessory Protein (MAAP) from an alternative...out this blog post to learn more about the AAV transfer plasmid! References: Naso MF, Tomkowicz B, ...

  19. FastCloning: A Newer, Simpler Cloning Technique

    Type
    Blog Post
    Published
    Nov. 1, 2016, 2:30 p.m.
    ...products are then transformed directly into chemically competent E. coli and transformants selected with ... for further purification before transformation. After transforming cells, you should perform colony ...consisting of digestion, purification, ligation, and transformation. While restriction cloning is still routinely...+ + Gel Purification + - Ligation + - Transformation + + The FastCloning process in brief In ...for this procedure to work properly. Directly transform chemically competent cells with the digested mixture...-cycle PCR leads to the most colonies after transformation. When a 1:1 vector:insert ratio is used in ... and 2 µL of digest product are used in the transformation, >70% of the colonies are correct. Good luck...

  20. Antibody Neutralization Response Against Pseudoviruses Expressing SARS-CoV-2 Spike Protein Variants

    Type
    Blog Post
    Published
    June 22, 2021, 1:15 p.m.
    ...vaccines differed depending on the variants (Garcia-Beltran et al., 2021). Antibodies from individuals who ...and B.1.351 variants tested. Image from Garcia-Beltran et al., 2021 with permission.   The spike variant...represent lineages and variants that are actually transmitting out in the world” says Balazs. “By combining...quantified in terms of luminescence. Image from Garcia-Beltran et al., 2021 with permission.   Mutations ...with various pseudotyped virus. Image from Garcia-Beltran et al., 2021 with permission.   Difference ...https://doi.org/10.1038/s41586-021-03471-w Garcia-Beltran WF, Lam EC, Astudillo MG, Yang D, Miller TE, Feldman...Nitido AD, Murali MR, Alter G, Charles RC, Dighe A, Branda JA, Lennerz JK, Lingwood D, Schmidt AG, Iafrate...
Showing: 261 - 280 of 808 results