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We narrowed to 876 results for: tra

Showing: 341 - 360 of 876 results

  1. Pushing the Limits of DNA Assembly

    Type
    Blog Post
    Published
    Sept. 6, 2017, 1:01 p.m.
    ...expression cassettes Traditionally, generating expression cassettes for yeast transformation can take 5 days...covalently joined, scarless DNA – perfect for transforma­­­tion or as a PCR template. Some of the applications...by using NEBuilder which requires only a single-stranded synthetic oligo to generate a single-guide RNA...RNA (sgRNA). Using only one single-stranded oligo, instead of the more typical two oligos, is more cost...annealing step usually used to create a double-stranded oligo. Generating an sgRNA construct becomes as...target region. Assembled plasmids can be directly transformed into E.coli for plating, screening and generation...inserted into a linearized cassette, ready for transformation into yeast that same day.  The field of synthetic...

  2. Components of CRISPR/Cas9

    Type
    Blog Post
    Published
    Feb. 2, 2016, 5 p.m.
    ...repeat region. B) RNase III, the tracrRNA and Cas9, bind to these transcripts and C) cleave them leaving mature...leaving a F) double-strand break. A “gRNA” is a researcher-designed hybrid of the tracrRNA and the crRNA. ...loci. 3. Cleave target DNA resulting in a double-strand break (DSB) Cas9 and its variants have two endonuclease...positions the nuclease domains to cleave opposite strands of the target DNA. Thus, the end result of Cas9...which defines the genomic target for Cas9, and the tracrRNA which acts as a scaffold linking the crRNA to ...for processing pre-crRNA into mature crRNA and tracrRNA binding. The spacer regions, on the other hand..., the “direct repeat region” combined with the tracrRNA forms the scaffold portion of a gRNA and the “...

  3. Choosing Your Fluorescent Proteins for Multi-Color Imaging

    Type
    Blog Post
    Published
    Oct. 9, 2014, 3 p.m.
    ...fluorescent proteins whose spectra overlap, there are techniques, like spectral unmixing, which can be used...Chroma Spectra Viewer comparing a standard Cy3 or Rhodamine filter set (Chroma #49004) to the spectra of ... the lighter colors; excitation spectra are blue and emission spectra are red. Neither is a perfect match...fluorescent proteins whose excitation and emission spectra differ sufficiently for them to be imaged in distinct...requires knowledge of their excitation and emission spectra, but a good rule of thumb is that both the peak...will want to compare the excitation and emission spectra of your protein with the filter sets or lasers ...emission filters and the excitation and emission spectra of the protein, so that the protein is well excited...

  4. Hot Plasmids - May 2022

    Type
    Blog Post
    Published
    May 26, 2022, 1:15 p.m.
    ...use of pre-existing transgenic lines, termed BLITZ (Biotin Labeling In Transgenic Zebrafish) (Xiong, et...“single-use” transgenic lines. Instead, researchers can generate and maintain transgenic lines that can...protein by a specific transcription response element (TRE) or kinase translocation reporters (KTRs). Find...interest and, for in vivo work, generate a dedicated transgenic line. Using zebrafish as a model organism, the...protein can then be co-expressed in essentially any transgenic zebrafish line expressing a GFP-tagged version...generational evolution of the AAV capsids (left) and transduction patterns (right).  Both AAV-PHP.eB and the AAV.CAP-B...mutations in mammalian cells. Long sequences traditionally have higher risks of off-target mutations. These...

  5. A Deep Dive into BioBuilder

    Type
    Blog Post
    Published
    Oct. 11, 2017, 1:44 p.m.
    ...Murray’s lab uses cellular extracts to perform transcription and translation in vitro, and the new BioBuilder...handful of local high school teachers receiving training modules in synthetic biology has grown into a ...cutting-edge research projects in synthetic biology and transforms them into modules that students and teachers ...droppers, centrifuge tubes, circuit parts, and lab-strains of bacteria to study — to conduct their hands-on...and test hypotheses. Students then use cellular extracts as a means to rapidly prototype DNA circuits and...resulted in a new BioBuilder book chapter and an illustrated, downloadable classroom poster — with both of...scientist mentors and the BioBuilderClub community. Registration is open through October 19. The BioBuilder Learning...

  6. Luminescent Imaging with Nano-lanterns

    Type
    Blog Post
    Published
    May 25, 2017, 2:30 p.m.
    ... when supplied with a luciferase substrate, the luciferase transfers energy to the FP, resulting in a ...luminescent substrate is required for imaging, and it is important to verify that this substrate does not...luciferase has a low quantum yield, and when transiently expressed in cells, generates much less signal... principle of bioluminescence resonance energy transfer (BRET). Photons emitted by a Renilla luciferase...excitation light source. Instead, a luciferase substrate like coelenterazine is supplied in the culture...labeled tumors in freely moving mice injected intravenously with coelenterazine, with increased sensitivity... which is limited by depletion of luminescent substrate, they synthesized diacetyl coelenterazine-h. Unlike...

  7. Deep Dive: qPCR

    Type
    Blog Post
    Published
    Sept. 29, 2022, 1:15 p.m.
    ...increase as the DNA amplicon transitions from single-stranded to double-stranded, and finally, drop once more... by abundant transcripts, leading to falsely lowered levels for less abundant transcripts. However, adding...can even be used to detect a single copy of a transcript. But this sensitivity can sometimes cause as ...preferably weighted towards the ends of the primers. Concentration of primers should be between 100 and 400 nm ...optimal annealing temperature and optimal primer concentration; check for primer dimers; and validate assay...signals are produced by the presence of double-stranded DNA, when temperatures are high, signal intensity...reflecting the presence of primarily denatured (single-stranded) DNA. As the temperature drops, single intensity...

  8. An Integrin Antibody Toolkit from IPI

    Type
    Blog Post
    Published
    March 28, 2024, 1:15 p.m.
    ... signaling pathways and the linkage of intra- and extracellular environments. Found on nearly every cell...eight beta subunits. Both subunits have short intracellular ends and large ectodomains containing ligand-binding...the cell membrane, physically connecting the extracellular environment and the cytoskeleton. Most integrins...affinity for ligands. When integrins interact with extracellular ligands, their ectodomains can extend and open...mediating cell adhesion and migration, initiating intracellular signal cascades, and allowing agile responses...The actin cytoskeleton exerts tensile force, transmitted through the integrin, where it is resisted by...by the ligand embedded in the extracellular environment. This further stabilizes the extended open integrin...

  9. Proximity Labeling: A Powerful Tool for Protein Complex Purification and Proteomic Mapping

    Type
    Blog Post
    Published
    Dec. 2, 2019, 2 p.m.
    ... avidin, proximity labelling can capture weak/transient protein interactions as well as be used for both...after BioID became available, the Alice Ting Lab demonstrated that engineered ascorbate peroxidase (APEX),... is an enzyme-mediated proximity cell labeling strategy to detect cell-cell interactions in vivo (Ge et...2019). This technique relies on an S. auerus transpeptidase sortase A variant (mgSrtA), which is capable...36.9 (2018): 880. PubMed PMID: 30125270. PubMed Central PMCID: PMC6126969. Che, Yonglu, and Paul A. Khavari...27(8), 1188-1196. PubMed PMID: 26912792. PubMed Central PMCID: PMC4831873. Lam, Stephanie S., et al. "Directed...12.1 (2015): 51. PubMed PMID: 25419960. PubMed Central PMCID: PMC4296904. Martell, Jeffrey D., et al. ...

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

    Type
    Blog Post
    Published
    Dec. 8, 2022, 2:15 p.m.
    ...than the traditional SpCas9 enzyme (about a third of the size) and does not require a tracrRNA (it can ... it will proceed to generate a blunt DNA double strand break. Cas9 has been studied for genome engineering...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...it is also significantly smaller in size than traditional Cas9. Another similarity to Cas12a is that Cas14...and cleave RNA through the same mechanism as traditional spCas9. If you are looking to modify RNA, Cas9...

  11. The Breast Cancer Microenvironment: A Tumor’s Backstage Team

    Type
    Blog Post
    Published
    Jan. 31, 2019, 1:32 p.m.
    ...microenvironment. This results in increased expression of transforming growth factor-β signaling, possibly inducing...tumor microenvironment is the immune cells. The contradiction is strong in this one. After all, the system...let’s take a look at exosomes. Proficient in transportation, exosomes are tools of communication and provide... (micro RNA) and other molecules that can be transferred to other cells, inducing epigenetic changes in...in targeted cells. In this case, exosomes may transport miRNA from drug-resistant cells to sensitive ones...enzyme that controls apoptosis and regulates transcription. Without TKA1, cells proliferate and cannot ...2009). Then, scientists began focusing on the extracellular matrix and fibroblasts. With each cell mechanism...

  12. Choosing the B(right)est Fluorescent Protein: Aggregation Tendency

    Type
    Blog Post
    Published
    June 15, 2017, 2:30 p.m.
    ... on size is ultracentrifugation. Sedimentation equilibrium analytical ultracentrifugation yields an affinity... In corals, the red fluorescent proteins form tetramers. In general, fluorescent proteins have a natural...in some applications (e.g. labeling of cells or tracking promotor activity), but it is problematic in applications...oligomers can be analyzed by several techniques. Gel filtration and SDS-PAGE under non-denaturing conditions ...will depend on the homodimer affinity and the concentration of the protein solution. During the experiment...affinity and has been used to demonstrate that yellow fluorescent protein homodimerization is characterized...Zacharias et al, 2002), meaning that at this concentration 50% of the protein forms dimers. Finally, spectroscopic...

  13. Hot Plasmids February 2024

    Type
    Blog Post
    Published
    Feb. 20, 2024, 2:45 p.m.
    ...Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain...AAV9-X1.1 efficiently transduce brain endothelial cells across diverse mice strains and rats. Figure from...StayGold variants AAV.CAP-Mac for systemic gene transfer in primate brains Endothelial-specific AAV delivery...electroporation or poor cellular entry with other transfection methods. The Junwei Shi Lab addressed this problem...Editing (PAGE). They fused the Cas enzyme to cell-penetrating peptides and co-incubate it with an “assist peptide...multiplexed guides. Figure 1: A) Cell-penetrating Cas9, fused to HIV TAT, Myc and SV40 Nuclear ...breaching the blood-brain barrier and delivering a transgene, with neuron bias observed in young macaques and...

  14. Cloning Mammalian Cells with the Agarose Method

    Type
    Blog Post
    Published
    Sept. 7, 2017, 12:17 p.m.
    ...growth rate/transfection efficiency is not known, this is easily achieved by splitting transfected cells into...specific cell line, and its transfection efficiency. We often trypsinize the transfected cells on the day after...Many years ago, people in the laboratory became frustrated with using glass cloning rings to isolate colonies... cell lines we most commonly work with, require extra serum to survive at low densities - adding to the...biology-grade agarose containing physiological concentrations of salts and glucose. If we circled well-separated...Agarose cloning method procedure The procedure (illustrated in the YouTube video below) is simple: After ...after transfection into plates containing selection agent at different densities, then dispose of the plates...

  15. Fluorescent Proteins 101: Fluorescent Protein Timers

    Type
    Blog Post
    Published
    May 4, 2017, 2:30 p.m.
    ...production of dsRed E5. This timer predictably transitions from green to red fluorescence (500 to 580 nm...elegans embryos. However, this initial timer was a tetramer with a propensity to aggregate in cells (Tsuboi... expression time but independent of protein concentration. Calibration curves correlating this ratio to...have realized how problematic aggregation-prone tetrameric fluorescent proteins can be. Cytotoxicity, improper...to red (see Table 1 for emission and absorption spectra). Subach et al’s directed mutagenesis also produced...Miyatsuka et al.) Distinguish between models for trafficking to the lysosome by fusing Medium-FT to LAMP-2A...structure and a particular biological event (trafficking to a subcellular location, start of gene expression...

  16. Advice on Career Paths and the Green Card Process for International Researchers and Entrepreneurs

    Type
    Blog Post
    Published
    Dec. 20, 2017, 2:33 p.m.
    ...the non-profit sector are transferrable to industry such as technology transfer, communications, medical.../experience, i.e. a research role, for a Ph.D. trained scientist. If the candidate is ultimately looking... on projects with an international scope (i.e. strategy/management consulting firms), sponsor more H-1Bs...and therefore the academic H-1B visa cannot be transferred to an industry position. If you cannot get an...management, collaboration management, grant administration, clinical operations, and so on. Candidates...patents and letters of recommendation. EB-1A extraordinary ability category The EB-1A - is similar to national...expertise in field). Publicity in major media and/or trade journals: You the individual must be named in the...

  17. In Vivo Biotinylation of Bacterial Fusion Proteins

    Type
    Blog Post
    Published
    Jan. 25, 2018, 2:09 p.m.
    ...ligand (after subtracting out non-specific binding). Historically, glutathione-S-transferase (GST) fusion...Vanderbilt Eye Institute and Tonia Rex's lab. A common strategy to determine the binding kinetics of a purified... avidin (or its derivatives streptavidin and neutravidin) is for all practical purposes covalent. Therefore...so, theoretically, saturated avidin could form tetramers of biotinylated protein. However, oligomerization...for improved biotinylation selectivity A common strategy to biotinylate proteins involves amine-reactive...subsequently purify the fusion protein from a bacterial extract. The MBP tag can be removed using Xa protease. ...joyful that getting to the final step and the transformed bacteria refuse to grow. Eventual success was...

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

    Type
    Blog Post
    Published
    Aug. 18, 2023, 4:15 p.m.
    ...reverse transcribe their gRNA into DNA, which is then transcribed into mRNA before being translated into ...genome types that can be either double stranded (ds) or single stranded (ss) (ie, dsDNA, ssDNA, dsRNA, positive... of virus. RNA genomes can be transcribed into mRNA, directly translated into proteins, or, in the case...looking for molecular biology tools, a very useful trait. Virus structure While all viruses have a genome...2016 Viruses with DNA genomes can either follow central dogma (gDNA to RNA to proteins) or require an intermediary...generally still kill the infected cell.) This is in contrast to bacteria and eukaryotes, which use a binary...and envelope), has a “gutted” genome with genes central to the replication process removed. This means ...

  19. Rett Syndrome: A History of Research and Therapeutic Outlooks

    Type
    Blog Post
    Published
    Nov. 19, 2020, 2:15 p.m.
    ...discovery, Addgene and RSRT have consolidated and centralized a collection of molecular biology tools so that...maturation (Tillotson & Bird, 2019) and is a global transcriptional regulator of thousands of genes. Studies have...have suggested roles in transcriptional repression, activity dependent de-repression, chromatin remodeling...groove of AT-rich DNA sequences to regulate transcription (Baker et al., 2013). Mutations that affect .... Much research is now focused on therapeutic strategies that use gene replacement therapy, gene editing...editing, MECP2 reactivation, RNA editing, RNA trans-splicing, and protein replacement to reverse the impacts...in animal models, Rett syndrome is a strong translational candidate for gene replacement therapy. In 2014...

  20. Finding nucleic acids with SHERLOCK and DETECTR

    Type
    Blog Post
    Published
    April 16, 2020, 1 p.m.
    ...amplification) or reverse transcriptase (RT)-RPA, respectively. RPA is coupled with T7 transcription to convert amplified... specificity to detect nucleic acids at low concentrations and/or are too expensive, time-consuming, and... method termed DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR) (Chen et al., 2018). Both SHERLOCK...mutation of interest. Together SHERLOCK and DETECTR demonstrate the power of CRISPR-based diagnostics. SHERLOCK...almost anywhere as lateral flow strips are easy to transport and work rapidly, providing reliable results in... the SHERLOCK detection system The Zhang lab demonstrated that SHERLOCK could reliably distinguish between...    DETECTR- DNA Endonuclease Targeted CRISPR Trans Reporter Cas12a (Cpf1) is a CRISPR Cas variant that...
Showing: 341 - 360 of 876 results