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We narrowed to 876 results for: tra

Showing: 241 - 260 of 876 results

  1. Hot Biosensors 2022: Year-End Roundup

    Type
    Blog Post
    Published
    Dec. 6, 2022, 2:15 p.m.
    ...Modular fluorescence unit fused with TRansmembrane region-to-IntrAcellular loop linkers” (MTRIA for short),...-gTEMP plasmids here!   Lu K, et al. Intracellular Heat Transfer and Thermal Property Revealed by Kilohertz...new class of sensors for neuropeptides and neurotransmitters. Motivated to develop a biosensor for oxytocin...sensors based on GPCRs recognizing various neurotransmitters, neuropeptides and other ligands - almost ...inserting a circularly-permuted GFP into an intracellular loop of various G-protein-coupled receptors....fluorescent sensor for real-time measurement of extracellular oxytocin dynamics in the brain. Nat Methods....kinetics and localization for imaging synaptic transmission. bioRxiv 2022.02.13.480251. doi: 10.1101/2022.02.13.480251...

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

    Type
    Blog Post
    Published
    Sept. 14, 2016, 2:30 p.m.
    ...genes from a single transcript, or if you want to prevent read-thru transcription from resulting in the...developing a general translation initiation sequence known as the Species-Independent Translational Sequence (SITS...extensive sequences used for cloning into the final translated products. Negative selection markers built into...3509-3514. Tikhonova, Elena B., et al. "A transcription blocker isolated from a designed repeat protein...of which you can clone your gene of interest. Translation of the standardized leader peptide prevents secondary...encoding your gene of interest from affecting its translation initiation and instead makes initiation heavily...the production of a downstream peptide, the transcription terminators in this series are just the tool...

  3. Evolution of Lab Techniques

    Type
    Blog Post
    Published
    June 21, 2016, 2:30 p.m.
    ...techniques used to generate transgenic mouse lines, such as BAC transgenic or traditional knockins/knockouts, ...researchers generating transgenic animals may choose Southern blotting to screen founder transgenic animals for ...fragmented into smaller pieces, run on a gel, and transferred to a membrane for analysis through hybridization...for the inserted transgene because Southern blots have a lower false positive rate than real-time PCR (4...hydroxyl group required for the extension of a DNA strand (8). Adding a small amount of a single radiolabelled...regular nucleotides results in the synthesis of DNA strands of all possible lengths because extension is terminated...prevails. Sequencing whole genomes or profiling transcriptomes (RNAseq) require sequencing of many samples...

  4. Targeting HIV-1 with CRISPR: Shock and Kill or Cut it Out?

    Type
    Blog Post
    Published
    May 10, 2016, 2:30 p.m.
    ...’s lab at Temple University has demonstrated two potential strategies for CRISPR-HIV therapeutics - one...one using dCas9-SAM to activate HIV-1 transcription and destroy infected cells, the other using wild-type... no viral protein. To solve this problem, two strategies have been proposed. The first, “shock and kill...cytotoxicity or the immune response. The second strategy is the simple removal of the HIV-1 genome from...histone deacetylase (HDAC) inhibitors to increase transcription of the integrated HIV-1 genome. For a targeted...dCas9-VP64 fusion commonly used to activate transcription, but with two additional activation domains ...domains (MS2 and p65) to enhance transcriptional activation. Zhang et al. designed multiple gRNAs to target ...

  5. Evolution of Brainbow: Using Cre-lox for Multicolor Labeling of Neurons

    Type
    Blog Post
    Published
    April 24, 2015, 2:39 p.m.
    ...proteins, which are directly trafficked to cell membranes. Membrane trafficking of farnesylated derivatives... virus post-transcriptional regulatory element (WPRE), commonly used to increase transgene protein levels...has become very useful in lineage tracing; “Zebrabow” was used to trace the development of the corneal epithelium...Brainbow 3.0, 3.1, 3.2 plasmids References: Transgenic strategies for combinatorial expression of fluorescent...2013 May 5. PubMed. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish... also been applied to cell marking and lineage tracing in other systems, such as zebrafish and Drosophila...This system differs from Brainbow-1.0 in that transient Cre recombination is required to prevent constant...

  6. Plasmids 101: TOPO Cloning

    Type
    Blog Post
    Published
    Oct. 27, 2016, 2:30 p.m.
    ...different DNA strand comes along, it can attack this covalent bond thus joining the two DNA strands and releasing...planning to transform right away OR you can store the reaction at -20C overnight. 4. Transform TOPO Cloning...end cloning. So how does TOPO cloning work? As illustrated in the Figure below, the “A” overhang on the ...DNA sequence 5´-(C/T)CCTT-3' and digests double stranded DNA at this sequence. The energy from this breakage...stored as a covalent bond between the cleaved 3′ DNA strand and a tyrosyl residue of topoisomerase I (1). If...researcher to perform blue-white screening after transformation - self joining of the vector ends results in... minutes will not significantly improve the transformation efficiency).  5. Select and Analyze 10 White...

  7. CRISPR 101: Cytosine and Adenine Base Editors

    Type
    Blog Post
    Published
    Feb. 13, 2025, 2:15 p.m.
    ...the opposite strand). ABEs make an A to G change (or a T to C change on the opposite strand). Both are ...place on the free strand of DNA and converts a C to U without producing a double strand break. UGI = uracil...Repair CRISPR 101: Cytosine Transversion Editors CRISPR 101: Any Base Transversion Editors Learn about base...repair (HDR), the pathway for resolving DNA double-strand breaks (DSBs) preferred by researchers. Compared...are base transition editors: converting one purine base to the other or one pyrimidine base to the other...other. Figure 1: Base transition editors catalyze purine-to-purine or pyrimidine-to-pyrimidine base... indicate the change introduced to the opposite strand following base editing and DNA repair. Black arrows...

  8. Drew Endy Introduces the Biobrick Public Agreement Plasmid Collection

    Type
    Blog Post
    Published
    Dec. 12, 2013, 3:35 p.m.
    ...of DNA, transcription of DNA to make RNA, translation of RNA to make proteins. That's central to everything...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.... We have a strategy that organizes how we start the work, and it begins with the central dogma - replication...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... handle on precise, forward engineering of the central dogma at the genome scale, it's going to be tricky...

  9. FlipGFP, a novel fluorescence protease reporter to study apoptosis

    Type
    Blog Post
    Published
    May 21, 2019, 12:10 p.m.
    ...contains 11 β-strands and one central ɑ-helix that can be split into 3 parts: (1) β-strands 1-9 (β1-9) and... and the one ɑ-helix, (2) β-strand 10 (β10), and (3) β-strand 11 (β11). Each part contains components ...developed, such as the Forster resonance energy transfer (FRET)-based executioner caspase reporters. In...GFP (GFP1-9 and GFP10-11) by flipping a single β-strand of GFP, hence the name FlipGFP. FlipGFP increases...from β1-9 they will rapidly recombine with β1-9 strands nearby resulting in fluorescence within tens of...11 are antiparallel. To prevent binding, the β strands in FlipGFP were redesigned so that they are parallel...E5 and K5) that dimerize together and force the strands into a parallel conformation. Between β11 and one...

  10. Optimizing Donor DNA for Enhanced CRISPR Genome Editing

    Type
    Blog Post
    Published
    March 24, 2016, 2:30 p.m.
    ... of the four strands of the cleaved duplex, while the fourth strand (the released strand in Figure 1 below...discovered that single stranded donor DNA: Complementary to the released strand, 127bp in length, With...single or double stranded donor DNA with other design parameters. Example single stranded donor DNA and ...biological process in detail often suggests new strategies to manipulate that process. We began our research...investigations into the release of DNA post-cut. Using substrate DNA labeled on both sides of the break, we determined...presented in Figure 2. Figure 2: Single-stranded donor DNA interaction with the Cas9-DNA duplex...replacement without cutting Our in vitro results also demonstrated that catalytically inactive dCas9 produced a...

  11. A Conference By Postdocs For Postdocs: Future of Research

    Type
    Blog Post
    Published
    Sept. 2, 2014, 3:05 p.m.
    ...of scientist training in the US and around the world. There are rumors that we are training too many scientists...few of these trainees are sufficiently prepared during their 6-12+ (!) years of training to get jobs. ...developing transferable skills to enable pursuit of these diverse opportunities after training. One of the... examples of science trainees taking a proactive role in their non-bench training. Grad students at Washington...academic administrators who are finding ways to provide new types of career preparedness training for their...the way we view the graduate school and postdoc training years. There is no doubt that there are too many...academia. Certainly funding for academic research and training is getting tighter and competition is fierce. ...

  12. MXS Chaining

    Type
    Blog Post
    Published
    Feb. 7, 2017, 3:30 p.m.
    ...constructs to visualize cell cycle dynamics, titrate inducible transgene expression, or a variety of other clever...throughput cloning strategies There are several high-throughput cloning strategies available for assembling...PubMed PMID: 25909630. PubMed Central PMCID: PMC4409215. 7. Swartz MN, Trautner TA, Kornberg A. Enzymatic ...incorporate each element into the final construct. This strategy can be used to build vectors with diverse functions...containing a unique fluorescent protein with minimal spectral overlap between them (Table 1). In each construct...expression) and a polyA signal (to terminate transcription) and the four constructs were then combined ...suited for particular downstream applications. The tradeoffs between various cloning methods are listed in ...

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

    Type
    Blog Post
    Published
    May 15, 2014, 3:33 p.m.
    ...detect a variety of intracellular conditions, including ion (such as Ca2+) concentrations and pH, using a ...Developmental/transgenic uses: Because of its stability, GFP can be used in lineage tracking capacities ...reporter for DNA double strand break repair, and to label pathogenic intracellular microbes to visualize...spontaneously and without additional co-factors, substrates, or enzymatic activity – it only requires the...folding at 37C, reduces aggregation at high concentrations T203Y Red-shifts the wavelength (yellow derivatives...K26R, Q80R, N146H, H231L, (and probably others) Neutral mutations    A multitude of applications Due...backbones for constructing fluorescent fusions. Transcription Reporter: Placing GFP under the control of a...

  14. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...control than is achieved by traditional pharmacologic methods. A number of strategies have been developed for... in the extracellular domain which activates the native signaling cascade of the intracellular part of...and Ca++ to passively enter the cell with the concentration gradient to depolarize it (Nagel et al., 2003...pumps that pass ions (Cl-, H+, Na+) against the concentration gradient and hyperpolarize the cell (Mattis ...activation by light showing ions flowing with the concentration gradient, and of activation inhibitory (ArCH...ArCH) proton pump passing ions against the concentration gradient. Created with BioRender.com.   Opto-G-protein...GPCR) regulate cellular function through multiple intra-cellular signaling cascades. Optical methods for...

  15. Plasmids 101: Dimers and Multimers

    Type
    Blog Post
    Published
    Jan. 10, 2023, 2:15 p.m.
    ...size, multimers may exhibit reduced transformation and transfection efficiency compared to the monomeric...1981). E. coli strains such as DH5α, HB101, NEB Stable, Stbl3, etc., are recA- mutant strains, and therefore... You can then gel extract the linearized band, ligate the plasmid, and re-transform the ligated plasmid... Elfinger M, Hartl D, Rudolph C. Transgene expression of transfected supercoiled plasmid DNA concatemers...multimeric forms (e.g. concatemers, dimers, trimers, tetramers). Since then, multimerization has been observed...the repeated plasmid sequence, giving greater concentration of cut DNA without changing the size. As a result...   Grow plasmids in recombinase-deficient strains Since plasmid multimerization is caused by homologous...

  16. Viral Vectors 101: Viruses as Biological Tools

    Type
    Blog Post
    Published
    March 21, 2023, 1:15 p.m.
    ...RNA cargo into their targets makes them attractive and tractable tools for genome engineering. Scientists... Packaging Capacity (>8kb) High Transduction Efficiency Transient Gene Expression High Immunogenecity...alternatives? Well, for one they have a high transduction efficiency and can effectively infect a wide...of cell types that are typically ‘difficult to transfect’, such as primary cells. They can also be directly...organisms. Finally, viral delivery is typically straightforward across applications, while electroporation ...derived from viruses that infect people in nature, extra safety measures, like replication incompetent viral...through nuclear localization signals which can traffic their viral particles inside the nucleus, without...

  17. Hot Plasmids Spring 2024

    Type
    Blog Post
    Published
    May 23, 2024, 1:15 p.m.
    ...RNA polymerase III transcript, the sgRNAs were encoded on the lentiviral minus strand in the 3’ LTR. These... Figure 6: Illustration of split fluorophore assay to test reconstitution via mRNA trans-splicing. A ... with tRNAs, which are cleaved out of the RNA transcript by endogenous processing enzymes (Figure 1). ...including modifications to the Cas9 or reverse transcriptase enzymes, inhibition of host cell proteins, and...(Figure 3).      Figure 3: HeLa cells transduced with SARS-CoV-2 nucleocapsid protein (Plasmid...modification of microglial immune cells is critical for central nervous system research; however, microglia are...are notoriously resistant to viral transduction. Through in vivo screening of human promoters, the Zhang...

  18. Four Base Editing Reporters to Monitor and Enrich Editing in Real-time

    Type
    Blog Post
    Published
    July 7, 2020, 1:15 p.m.
    ...reporter of transfection, which only report the efficiency of plasmid delivery to a cell. In contrast, TREE ... affecting protein translation of different reporter proteins. Protein translation requires the start ...compared to CRISPR/Cas9 edits that rely on double strand DNA breaks. Due to this inefficiency it is crucial...At the same time Cas9n cleaves the opposing DNA strain which results in two DSBs that can be repaired ...constitutively expressed to identify successfully transfected cells. C-to-T editing by the APOBEC-Cas9 editosome...that results in the restoration of fluorescence. Transient reporter for editing enrichment (TREE) The Wang...Wang and Brafman lab developed a transient reporter for editing enrichment (TREE) to purify single base...

  19. Fluorescent Proteins 101: Aptamer Fluorophores

    Type
    Blog Post
    Published
    April 11, 2017, 2:30 p.m.
    ...fluor. Transcribing and translating a protein fluorophore also takes time - bypassing translation altogether...expression strategies.” Chem Biol. 2015 May 21;22(5):649-60. PubMed PMID: 26000751. PubMed Central PMCID: ... PubMed Central PMCID: PMC3279232. 10. Song, Shiping, et al. “Aptamer-based biosensors.” TrAC Trends in...have used antibodies for diagnostics know how frustrating it can be to get a “bad batch”); Customizable...help reduce such background, thereby improving traditional visualization techniques. In addition, their ...biosensors. Aptabeacons Fluorescence resonance energy transfer (FRET) technology has been studied and used in...fluorescence-activated cell sorting (FACS) of E. coli transformed with aptamer libraries, the Jaffrey group selected...

  20. CRISPR-mediated Plant Base Editors

    Type
    Blog Post
    Published
    Jan. 3, 2019, 1:35 p.m.
    ...72 hours post-transformation/transfection in a transient assay. For stable transformation, regenerated ...Agrobacterium-mediated transformation. We also constructed smaller vectors suitable for transient assays using ...double-stranded DNA cleavage." Nature 533.7603 (2016): 420. PubMed PMID: 27096365. PubMed Central PMCID...creates a nick in the DNA by cutting only a single strand, dramatically reducing the likelihood of detrimental...of the desired T-A base pair. Figure 1: Transition mutation (C>T, G>A, A>G, and T>C) installation...deaminases (ecTadA), fused it with dCas9, and transformed it into E. coli harboring the defective CamR ...TadA*) that satisfactorily accepts DNA as its substrate (see figure 2).          The artificially evolved...
Showing: 241 - 260 of 876 results