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We narrowed to 393 results for: ARA-2

Showing: 41 - 60 of 393 results

  1. Sleeping Beauty Awakens for Genome Engineering

    Type
    Blog Post
    Published
    June 30, 2015, 2 p.m.
    ... of 2 components: 1) an SB transposase, the enzyme required for catalysis of transposition; and 2) a transposon...backbone. A separate plasmid contains the transposase gene (red) for expressing the transposase enzyme.2.) The... 2015 Feb 4. doi: 10.1002/biot.201400821. PubMed. 2. Mates L, et al. Molecular evolution of a novel hyperactive...efficiencies of stable gene transfer using SB100x were comparable to stable transduction efficiencies of integrating...

  2. The Effect of COVID-19 on Liu Lab Plasmid Requests From Addgene Data

    Type
    Blog Post
    Published
    July 16, 2020, 1:15 p.m.
    ...month, from 1/22/20–2/23/20, where there were zero plasmid requests. Afterwards, from 2/24/20–3/15/20 (the...Each paper has between 1–32 plasmids and a total of 2–2,590 requests. We received plasmid requests from ...observed between Jan. 1 and Mar. 1, 2020. Figure 2: A simple approximation of the effect of COVID-19 ...However, it is evident that if we believe that 1/22/20–2/23/20 are the more accurate dates of lockdown in China...cases being reported (right, red), likely due to quarantining {% video_player "embed_player" overrideable...modification also eases the interpretation of the parameters we infer, since scientific productivity is better... model to give uncertainty estimates for each parameter, we added log-normal noise to each of the terms...

  3. Rosella: A Fluorescent pH-Biosensor for Studying Autophagy

    Type
    Blog Post
    Published
    April 13, 2017, 2:30 p.m.
    ...Table 2 for more details on the effect of pH on the fluorescent properties of Rosella.   Table 2: Effect...in yeast. Autophagy,4(2), 205-213. doi:10.4161/auto.5331. PubMed PMID: 18094608 2. Sargsyan, A., Cai, J...environment like the vacuole or lysosome. See Table 2 for a summary of what color fluorescence Rosella emits...fluorescence accumulates in the vacuole. See Figure 2 for an example of what fluorescence looks like for..., Colosimo, L. K., Graham, T. E. (2015). Rapid parallel measurements of macroautophagy and mitophagy in...

  4. Grad School Advice Part 1: Picking a Lab and a Project

    Type
    Blog Post
    Published
    Sept. 1, 2016, 2:30 p.m.
    ...Introduction from Tyler 1:13 - 2:02 : Niroshi and Ben introduce themselves 2:03 - 3:22 : How did you end ...things get tough in the dreaded third year. Find Part 2 Here! We'd like to thank Niroshi and Ben for taking...senior graduate students, Ben Vincent and Niroshi Senaratne, from the Biological and Biomedical Sciences program...Biology, and he tweets @benjvincent.     Niroshi Senaratne is a graduate of the PhD program in Genetics and...

  5. CRISPR 101: Targeting RNA with Cas13a (C2c2)

    Type
    Blog Post
    Published
    Sept. 21, 2017, 2:07 p.m.
    ...question: C2c1, C2c2 and C2c3 (short for Class 2, candidate 1, 2, or 3). C2c1 and C2c3 are related to Cpf1,...et al. "Discovery and functional characterization of diverse class 2 CRISPR-Cas systems." Molecular cell...however cutting efficiency of Cas13a is reduced when 2 mismatches are present. The protospacer flanking sequence...PMC5127784. Find plasmids from this paper at Addgene. 2. East-Seletsky, Alexandra, et al. "Two distinct RNase... Leptotrichia shahii (LshCas13a) to begin to characterize this new effector (Abudayyeh et al., 2016). ... plant cells (Abudayyeh et al., 2017). They characterized Cas13a from Leptotrichia wadei (LwaCas13a), ...multiplexing; expressing 5 gRNAs simultaneously produces comparable gene knockdown to single gRNA expression. Although...

  6. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...derived from direct comparative analysis of microbial opsins. Nature Methods, 9(2), 159–172. https://doi.org...for controlling neuronal activity, channelrhodopsin-2 (ChR2), a blue light-activated cation channel, from...used in tandem with the opsin.      Figure 2: Diagram of excitatory (ChR2) activation by light ...) domains, phytochrome B (PhyB), and cryptochrome 2 (CRY2) (Zhang & Cui, 2015). When stimulated with light...Hegemann, P., & Bamberg, E. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane ...intracellular signaling pathways. Trends in Biotechnology, 33(2), 92–100. https://doi.org/10.1016/j.tibtech.2014.11.007...

  7. Plasmids 101: Dimers and Multimers

    Type
    Blog Post
    Published
    Jan. 10, 2023, 2:15 p.m.
    ...identification.   Fig. 2: Gel image of Plasmid 61564: pBAMD1-2 (~4.7 kb) digested with SpeI and... at ~3.6 kb and ~1.1 kb (lane 3). Uncut DNA (lane 2) has a band at <3 kb, which corresponds to the supercoiled...formation of plasmid multimers. Cell. 1976 Dec;9(4 PT 2):707-16. doi: 10.1016/0092-8674(76)90134-3. PMID: ...dimers in Escherichia coli K-12. Plasmid. 1989 Mar;21(2):138-41. doi: 10.1016/0147-619x(89)90057-7. PMID: ...Plasmids and Chromosomes. Microbiol Spectr. 2014 Oct;2(5). doi: 10.1128/microbiolspec.PLAS-0025-2014. PMID...Behavior of Plasmid DNA. Microbiol Spectr. 2015 Apr;3(2):10.1128/microbiolspec.PLAS-0036-2014. doi: 10.1128...: 21285356; PMCID: PMC3060453. Bazaral M, Helinski DR. Characterization of multiple circular DNA forms...

  8. Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User)

    Type
    Blog Post
    Published
    March 7, 2017, 3:30 p.m.
    ...transductions and use a range of reasonable MOIs. 2. Create a monoclonal Cas9-expression cell line. Especially...doing a screen. I made a few monoclonal lines (Figure 2) and I was surprised at how variable Cas9-expression...across the different cells (Figure 3).   Figure 2: Cas9 expression in monoclonal cell lines generated... expression Overview: By Western blotting (Figure 2, pool), I knew the cells expressed Cas9, but I didn... appear green despite having active Cas9 (see tip 2). Pro-Tips 1. To quantify Cas9 activity using this...Western blotting against GFP expression, but I didn’t. 2. In the original publication they see GFP expression...and I got clear bands using the conditions above. 2. Design your primers so that the digestion site isn...

  9. Flow Cytometry Readouts: Yes, No, and Everything in Between

    Type
    Blog Post
    Published
    Aug. 20, 2024, 1:15 p.m.
    ...low expression, and everything in between (Figure 2). These smears tend to occur when you are looking ...based on your experiment. You can see from Figure 2 that determining where to place your gate based on...the dot plot would be complicated.  Figure 2: (A) a smeary dot plot showing a range of antibody...plot in Figure 4 compared to the dot plot in Figure 2. Quantification using MFI makes it easier to identify...positive samples are clearly distinguishable as two separate populations. Created with biorender.com. Pro...with the baseline suggesting this sample has a comparable expression to the baseline/negative control. ...expression, using a histogram plot and MFI values to characterize your samples may allow for better interpretation...

  10. Genome-wide Screening Using CRISPR

    Type
    Blog Post
    Published
    Aug. 18, 2015, 2:30 p.m.
    ...gRNA-containing plasmid, or a 2-plasmid system in which Cas9 must be delivered separately.  Mutant cells are enriched...targeting a specific gene within the genome (see Fig. 2). Individual gRNAs are designed in silico using publicly...mouse, human, fly, E. coli, and T. gondii genes.  2) What genetic modification are you trying to make?...CRISPR libraries is a multi-step process (see Fig. 2). In most cases, CRISPR libraries are provided at ...uncontrolled cell growth, such as cancer. Figure 2: The CRISPR library must be amplified (A) to be used...If you've obtained a ready-to-use lentiviral preparation from Addgene, you can skip the steps above! Cells...

  11. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    Published
    Jan. 6, 2015, 5:21 p.m.
    ...Currently available from the Kim lab are 2 presynaptic and 2 postsynaptic targeting mGRASP plasmids. Additionally... cells were pulsed with 2µg/ml of Doxycycline for 2 hours, and imaged on the Keyence BZ-9000 fluorescence...work! Robinson et al., Dev Cell 2010 Feb 16;18(2):324-31. Cheeseman et al., J Cell Sci 2013 May 1...promotes the formation of an isopeptide bond between 2 peptide tags, SpyTag and KTag. The group demonstrated... of three sets of cloning vectors (Level 0, 1, or 2) which can be utilized in three successive assembly...1 modules can be similarly assembled into a Level 2 vector, thus forming a functional genetic circuit....circuit. Flexibility has been built into the Level 2 vectors to allow for additional iterations of Level 1 assembly...

  12. Using AAV for Neuronal Tracing

    Type
    Blog Post
    Published
    Aug. 9, 2018, 1:04 p.m.
    ...Baekelandt, V. (2007). Comparative analysis of adeno-associated viral vector serotypes 1, 2, 5, 7 and 8 in mouse...Yamamori, T. (2015). Comparative analyses of adeno-associated viral vector serotypes 1, 2, 5, 8 and 9 in marmoset...for retrograde transport has been found for AAV1, -2, -5, -7, -8 (Taymans et al., 2007), AAV1 (Hollis et... tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain. PLoS One 8:e76310...reveal novel hippocampal CA2 circuits. Nat Neurosci 17(2), 269–279. PubMed PMID: 24336151. PubMed Central PMCID... Mechanisms of Motility and Regulation. Neuron 84(2), 292–309. PubMed PMID: 25374356. PubMed Central PMCID...transduction efficiency of recombinant AAV serotypes 1, 2, 5 and 8 in the rat nigrostriatal system. J Neurochem...

  13. Fluorescent Proteins 101: Visualizing Subcellular Structures & Organelles

    Type
    Blog Post
    Published
    June 22, 2017, 2:30 p.m.
    ... to the lysosome where they are finally degraded (2, 3). Once you've created your fusion protein, it's...examples include the ImageJ plugins JACoP and Coloc 2, BioImageXD, and customized CellProfiler pipelines...colocalization analysis example is given in Figure 2 (adapted from 4) - Dunn et al. 2011 provides an in-depth...Since colocalization relies upon the detection of 2 independent fluorescent signals and their potential...here! References 1. Allen Institute Plasmid Pages 2. Cooper GM. 2000. The Cell: A Molecular Approach. ...Therefore, it can be beneficial to employ well-characterized marker proteins tagged with FPs to highlight...spectra of the selected FPs need to be sufficiently separated, most commonly FPs with red and green wavelengths...

  14. New Neuroscience Tool: The iGluSnFR3 Glutamate Sensor

    Type
    Blog Post
    Published
    April 7, 2022, 1:15 p.m.
    ...kinetics which are illustrated in figures 2 and 3.  Figure 2: Glutamate titration curves for the different...signals upon sensing glutamate using both 1-photon and 2-photon imaging.   Figure 1: 1P and 2P excitation...adapted from Aggarwal et al…, Supplementary Figure 2.   Improved trafficking and localization through...fluorescence intensity from the inserted GFP. After characterizing iGluSnFR in vitro, showing that it is selectively...response than its predecessors. The detailed characterization of the new variants is available here. Upgrades...

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

    Type
    Blog Post
    Published
    April 13, 2021, 1:15 p.m.
    ...plasmids are cured from the cell. Steps 1-1 and 1-2 can be done simultaneously. Image from Li et al., ...1) replaced the promoter of gRNA-pMB1 with PrhaB, 2) changed the replicon of pCas into a non-temperature-sensitive... pEcCas/pEcgRNA system in 4 E. coli K-12 strains, 2 E. coli B strains, 1 E. coli W strain, and 1 Tatumella...MUCICAT better, it is faster. Using MUCICAT only needs 2 newly constructed plasmids (pDonor and pQCascade) ...rounds of transformation in 30 days. Figure 2: (A) MUCICAT plasmids for multicopy integration. (...temperature-sensitive replicon for self-curing, an arabinose inducible lambda-red gene, and an IPTG-inducible...site of interest. The donor template is supplied separately. To use this system, you’d first introduce your...

  16. CasPEDIA: A Functional Classification of Cas Enzymes

    Type
    Blog Post
    Published
    Jan. 25, 2024, 2:15 p.m.
    ...systems: a burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2), 67–83. https://doi.org...resource that provides summary information on Class 2 Cas enzymes. The information is organized in wiki ...this content and much, much more.     Fig. 2 – List of resources and properties for a Cas entry...Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes [Preprint]. Biochemistry, Biophysics... your hits, you can easily sort them by other parameters, such as E-value for protein sequence searches...

  17. Easi-CRISPR: Generating Knock-In and Conditional Mouse Models

    Type
    Blog Post
    Published
    April 5, 2018, 12:42 p.m.
    ...of conventional gene targeting is lowered to about 2-3 months. But certain models remain more difficult...included in the final ssDNA template. Figure 2: Overview of ivTRT to generate an ssDNA repair template... floxed conditional allele requires you to target 2 loxP sites to intronic regions 0.5 - 0.8 kb apart....Typically, Easi-CRISPR works best with insertions of 2 kb or less. Luckily, most of the commonly used cassettes... induction systems (ttA or rtTA) are between 1 to 2 kb in length. There are plenty of Addgene plasmid ...create the ssDNA construct as described in Figure 2.  You can also use Addgene plasmids to purify Cas9...ribonucleoprotein (RNP) complexes of Cas9 protein and the separated guide RNA components (crRNA and tracrRNA) for ...

  18. Hassle-free 96-well Format Epitope Tagging Using Cas9 Ribonucleoprotein

    Type
    Blog Post
    Published
    June 28, 2018, 3:01 p.m.
    ...purify IVT sgRNA in the lab. Figure 2: Cas9 RNP complexed with 2-part cr:tracrRNA tags genes more effectively...into stem cells. Cells are allowed to recover for 2-5 days and then analyzed for tagging efficiency using...IVT sgRNA) approach (Dewari et al. 2018 and Figure 2). Not only is the cr:tracrRNA approach highly efficient...cell suspension, transfect and let cells recover for 2-5 days.Note: We use the Nucleofection method for delivery...success was ~%50. If you get low knock-in efficiency (<2% positive by ICC for the tag) or do not see any cells...PMID: 28096221. PubMed Central PMCID: PMC5312033. 2. Dewari PS, Southgate B, Mccarten K, Monogarov G, ...assembling csRNPs in a 96-well plate format and tested parallel tag knock-in for 96 different genes in a single...

  19. Viral Vectors 101: AAV Variables That Matter

    Type
    Blog Post
    Published
    June 1, 2023, 1:15 p.m.
    ...testing your AAV.  Figure 2: Comparison of AAV serotypes 1, 2, 5, 6, 8, and 9 in two different ...Yamamori, T. (2015). Comparative analyses of adeno-associated viral vector serotypes 1, 2, 5, 8 and 9 in marmoset...) your experimental conditions and measurements; (2) the cells you’re targeting; (3) how much expression... Tropism and Axonal Transport of AAV Serotypes 1, 2, 5, 6, 8 and 9 in the Mouse Brain. PLOS ONE, 8(9),... Comparison of four promoters. Gene Therapy, 28(1–2), 56–74. https://doi.org/10.1038/s41434-020-0169-1...site  (Kanaan et al., 2017), axonal transport  (Murlidharan et al., 2014), and postsynaptic transmission ... 1–41. https://doi.org/10.3390/cells12050785 Murlidharan, G., Samulski, R. J., & Asokan, A. (2014). Biology...

  20. Visualizing Your Plasmid Request Data

    Type
    Blog Post
    Published
    April 11, 2023, 4 p.m.
    ...with request data to the dashboard (Fig. 2).     Figure 2: Insert showing the upload function for... the date of downloading the CSV is shown (figure 2) and the dashboard displays the data in a standardized...microscopy (University of Amsterdam). He develops, characterizes, and uses genetically encoded fluorescent probes...
Showing: 41 - 60 of 393 results