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We narrowed to 611 results for: sam

Showing: 161 - 180 of 611 results

  1. Plasmids 101: Methylation and Restriction Enzymes

    Type
    Blog Post
    ... experiment? The answer to both questions is the same--methylation! Read on to learn about how DNA methylation...companion endonucleases that recognizes and cleave the same DNA sequence if not methylated (if it comes from...Although not all prokaryotic DNA is methylated to the same level, the potential for methylation should be considered...any) of those sites will be methylated. Using the same example plasmid as above (which has the XbaI site...

  2. How to Keep a Lab Notebook for Bioinformatic Analyses

    Type
    Blog Post
    ...that you are in fact using the same data for all of your analyses. The same is true for scripts. Naming...files in a separate folder: You will often use the same data files for multiple analyses. Rather than copying... script as originalName_descriptionOfEdit in the same directory where it was run. This technique leaves...

  3. Giving gRNAs a Facelift - Synthetic and Beyond

    Type
    Blog Post
    ... when scientists talk about their precious RNA samples. RNA is inherently less stable than most macromolecules...CRISPR-Cas9 experiments – the “gRNA” – suffers from the same issues as your experimental RNA. To solve this problem...Another stabilizing sugar modification, found at the same site, is 2’-fluoro (2’-F), which substitutes a fluorine...protein and can increase on-target efficiency. In the same vein, locked nucleic acids or bridged nucleic acids...

  4. New Tool for Lineage Tracing: The ClonTracer Library

    Type
    Blog Post
    ...replicates would contain the same labels - i.e. they would always come from the same parent cells that represent...replicate groups, and treated these groups with the same drug regimen, they would find one of two outcomes...population (all barcodes can be amplified using the same sets of forward and reverse primers). The abundance...

  5. Plasmids 101: Cre-lox

    Type
    Blog Post
    ...two loxP sites, which can be located either on the same or on separate pieces of DNA. Both 13bp repeat sequences... sites: Inversion: If the loxP sites are on the same DNA strand and are in opposite orientations, recombination... reversed.   Deletion: If the sites face in the same direction, the sequence between the loxP sites is...sites undergo recombination with other sites of the same type, but are not cross-compatible. Using different...

  6. High Complexity Golden Gate Assembly with NEB’s DAD

    Type
    Blog Post
    ...don’t use the same overhang twice; (2) avoid palindromes; (3) no overhangs with the same three nucleotides...in a row; (4) no more than two nucleotides in the same position; (5) avoid overhangs with either 0% or ...71% (Pryor et al., 2020). And in 2022, using the same tools, they successfully assembled a 40 kb T7 phage...

  7. Illuminating Epigenetics with A FRET Based Biosensor

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    Blog Post
    ...corresponding gene products due to the same region, but not the same exact genes, being improperly silenced.... This is how most cells in the body contain the same DNA but have very different structure and function...present without any DNA changes, and both involve the same region of chromosome 15. They both result from the...

  8. Magnetic Control of Proteins: More than a Dream

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    Blog Post
    ...fluorescence when a small magnet was passed over the sample (Frank Hayward et al., 2024). The fluorescence ...intensity decreased whenever the magnet approached the sample (by less than 1%) and recovered after the magnet...expressing MagLOV while a magnet is waved under the sample. The imaged area measures approximately 82 mm across...Matsuoka, R., Kimura, S., Miura, T., Ikoma, T., & Kusamoto, T. (2023) Single-Molecule Magnetoluminescence...

  9. Of Myc and Men

    Type
    Blog Post
    ...between endogenous and exogenous versions of the same target. In the 1980s, Munro and Pelham set out to... ideal.  Unexpected connections Right around the same time that Munro and Pelham were devising their tagging...from this year.  But are we all really using the same antibody developed almost 40 years ago? Well…kinda...distributing monoclonal antibodies derived from the same hybridoma developed by Evans, et al. In other cases...

  10. CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments

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    Blog Post
    ...scientists design and analyze batches of CRISPR samples. We invite you to jump in and try it out, or take... databases, including primer3, biopython, bwa, samtools, bowtie, UCSC genome browser, Ensembl, and others...currently Crispor and Crispresso, that adhere to the same principles listed here. It employs biological best...productivity in the Biohub. We hope it will do the same for you. Send us your questions or comments to gdingle...

  11. Tips for a 1st time AAV user (by a Rookie AAV user)

    Type
    Blog Post
    ...particles that are present in an AAV prep. AAV samples are first DNaseI digested to remove any residual...technology or a TaqMan primer/probe set can be used and samples are quantified by comparing to an AAV standard ...AAV, remember to account for the dilution of the sample for the DNAseI digest. Use good sterile technique.... 2. Choi, V.W., Asokan, A., Haberman, R.A., & Samulski, R.J. (2007). Production of recombinant adeno-...

  12. Light Sheet Fluorescence Microscopy

    Type
    Blog Post
    ...beam into a thin sheet to illuminate a fluorescent sample and captured the reflected light using a different...laser and the reflected light travel through the same objective lens. Using this method, these authors...microns, illuminates only one thin plane of the sample surrounding the focal plane of the detection lens...problem is to illuminate and acquire images of a sample from two opposing sides and merge the images, such...

  13. Simplify Cloning with in vivo Assembly

    Type
    Blog Post
    ...laboratory. All procedures are performed using the same three step protocol:  Fragment generation - Any...events, all linear fragments need to get into the same cell. For simple cloning requiring just one or two...vector and insert with separate primer pairs in the same PCR. Add homologous sequences to one of the primer...simply by adding all the necessary primers to the same PCR mix. Pairs of primers will amplify the whole...

  14. Using AAV for Neuronal Tracing

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    Blog Post
    ...al., 2008) AAV6 (Towne et al., 2010), AAV8, -9 (Masamizu et al., 2011); AAV5 (Aschauer et al., 2013). Anterograde...PMCID: PMC5529245. Choi, V.W., McCarty, D.M., and Samulski, R.J. (2005). AAV Hybrid Serotypes: Improved Vectors...PMC2895694. Hollis, E. R. 2nd, Kadoya, K., Hirsch, M., Samulski, R. J., and Tuszynski, M. H. (2008). Efficient...PMID: 25374356. PubMed Central PMCID: PMC4269290. Masamizu, Y., Okada, T., Kawasaki, K., Ishibashi, H., Yuasa...PubMed Central PMCID: PMC5572074. Salegio, E.A., Samaranch, L., Kells, A.P., Mittermeyer, G., San Sebastian...

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

    Type
    Blog Post
    ...reintroduction, inversion and re-inversion happen at the same probability. Continuous inversion of the DNA sequence...recombination can only occur between target sites of the same sequence in FLEx vectors, the DNA sequence that ...neuron and its synapse should be visualized at the same time from two different plasmids this approach becomes...connectivity before and after the gene knockout in the same mouse.   Scientists always strive for more....

  16. Fluorescent Proteins 101: Aptamer Fluorophores

    Type
    Blog Post
    ...and subsequently leading to a positive signal. The same effect can be achieved for a fluorophore that relies...context of a paired fluorophore protein. Years later, Samie Jaffrey’s laboratory took advantage of their deep... Jaffrey lab asked:  Could an RNA aptamer do the same thing? Using the HBI derivative 3,5-difluoro-4-hydroxybenzylidene...· February 2008. 11. Svensen, Nina and Jaffrey, Samie R. “Fluorescent RNA Aptamers as a Tool to Study ...

  17. Save Time with Transient Plant Leaf Transformations

    Type
    Blog Post
    ...thanks to our guest blogger Samuel Mortensen from Northeastern University. Samuel Mortensen is a PhD candidate...This post was contributed by Samuel Mortensen, a PhD candidate at Northeastern University. Working with...19457242. PubMed Central PMCID: PMC2693113. Mortensen, Samuel, et al. "EASI transformation: An efficient transient...

  18. CRISPR-based Genome Editing Systems For Editing in E. coli

    Type
    Blog Post
    ...our metabolic engineering case study of N-acetylglucosamine biosynthesis, we constructed a strain library...rounds of transformation to complete the N-acetylglucosamine strain library construction in 8 days. To ...numbers. (D) The effect of gene dosage on N-acetylglucosamine concentration. Image from the Yang lab. ... a lecturer in the College of Life Sciences that same year. Her research is focused on the escape mechanism...

  19. Antibodies 101: Reading a Flow Plot

    Type
    Blog Post
    ... are represented as a series of dot plots in the same order. However, in an actual flow cytometry run,...parallel.  Let’s imagine we’re looking for cells in a sample that are negative for marker A and positive for... proxy for nucleic complexity of the cell.  The sample will have been labeled using a panel of markers... dots. In a contour plot, each line contains the same number of events. Thus, contour lines that are close...

  20. Using Phosphoserine to Study Protein Phosphorylation

    Type
    Blog Post
    ... purified from the system, researchers can run samples on SDS-PAGE gels containing Phos-Tag, a small molecule...non-phosphorylated serine at the TAG codon of the same expression vector used for phosphoserine incorporation...incorporation of serine) population of protein using the same expression plasmid. This is a particularly important...express the completely wild type protein from the same plasmid.  Upon verifying that serine phosphorylation...
Showing: 161 - 180 of 611 results