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We narrowed to 490 results for: ARA-2

Showing: 121 - 140 of 490 results

  1. Controlling for Off-target Effects with a New Genome-wide CRISPR Screen Design

    Type
    Blog Post
    ...guide expression and dsDNA breaks. Figure 2: Non-targeting vs. safe-targeting guides. The genome-wide...target all protein-coding genes present in the genome; 2) non-targeting guides (red), which target no sequence...guides that had zero mismatch off-targets. Guides with 2-bp mismatch off-targets were only toxic if they had...tolerated than mismatches more distal to the PAM, and 2) guides with high GC content have greater off-target...PMID: 28474669. Pubmed Central PMCID: PMC5424143. 2. Tsai, Shengdar Q., et al. "GUIDE-seq enables genome-wide...effects. The flaws of RNAi screens are well characterized and strategies exist to control for these faults...also reproduced several previously observed characteristics that influence gRNA off-target activity: 1)...

  2. Tips for Getting a Faculty Position

    Type
    Blog Post
    ... this problem? (2-3 sentences) What will be the focus of your first grant? (1-2 sentences) ...of scientific success is publications and grants. 2. Write succinct and easy to understand documents A...consideration. 3. Present an easy to follow seminar See item 2. Attendees will include grad students (that are solicited...people would agree is important to understand. (1-2 sentences). For example: Distinguishing correctly ...emphatically deny that I have a magic formula to guarantee a reader the faculty job of his/her dreams. There...pitch that requires reading two pages or even a paragraph to get to the punch line is a terrible sales pitch...

  3. A Primer on Optogenetics: Introduction and Opsin Delivery

    Type
    Blog Post
    ...derived from direct comparative analysis of microbial opsins. Nature methods. 2012;9(2):159-72. doi: 10.1038...commonly used in optogenetics: 1) electrophysiology and 2) behavioral experiments. I’m not an electrophysiologist...choice in the brain region you wish to stimulate 2) Fabrication and implantation of the optical fiber...thoroughly elsewhere (here and here for instance) [2], [3]. Karl Deisseroth of Stanford University , one...reviews for a discussion of the different variants [1, 2, 4]. And, of course, the best way to learn about the...monitor expression at various time points (e.g. every 1-2 weeks over 8 weeks) in order to determine the optimal...(4):251-66. doi: 10.1038/nrn3171. PMID: 22430017. 2. Fenno L, et al. The development and application of...

  4. Hot Plasmids: Spring 2025

    Type
    Blog Post
    ...cell-attached recordings in primary visual cortex (V1) layer 2/3 (L2/3). B) Fluorescence from axonal boutons of neurons... generation and stable cell line creation (Figure 2). Looking for more? Explore our empty and EGFP retroviral...Lentiviral backbone plasmids here! Figure 2: Addgene cloned EGFP into pAG Lenti CMV N-HA Puro ...Glypicans are proteoglycans composed of a protein core, 2–4 glycosaminoglycans (GAG), and are (typically) tethered...either the optogenetic activator channelrhodopsin-2 or fluorescent reporter dTomato under the control ...deep-brain fiber photometry.  Figure 1: Characterization of iGluSnFR4 in mice. A) Scheme for two-photon...GPC4). All IPI antibodies undergo extensive characterization at IPI as well as community-led evaluation...

  5. Plasmids 101: Modular Cloning Applications and Kits

    Type
    Blog Post
    ... Multiple Introns.” Plant Communications, vol. 2, no. 2, Elsevier BV, Mar. 2021, p. 100135. Crossref, ...Constructs.” PLoS ONE, edited by Jean Peccoud, vol. 6, no. 2, Public Library of Science (PLoS), 18 Feb. 2011, p... vol. 5, no. 10, American Chemical Society (ACS), 2 May 2016, pp. 1059–69. Crossref, https://doi.org/10.1021...of Plant Genomes.” The Plant Genome, vol. 16, no. 2, Wiley, 9 Mar. 2023. Crossref, https://doi.org/10.1002...Crossref, https://doi.org/10.1186/s12870-020-02388-2. Stuttmann, Johannes, et al. “Highly Efficient Multiplex...Crossref, https://doi.org/10.1038/s41598-019-46171-2. Resources on Addgene.org Modular Cloning (MoClo....6b00337. Lee, Michael E., et al. “A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly...

  6. Grad School Advice Part 2: Building Community

    Type
    Blog Post
    ...these topics. Listen to Part 1 Here Listen to Part 2 here! Time : Topic 0:00 - 0:50 : Intro 0:51 - 3:08...series, we continue our conversation with Niroshi Senaratne and Ben Vincent from the Biological and Biomedical...Biology, and he tweets @benjvincent.     Niroshi Senaratne is a graduate of the PhD program in Genetics and...

  7. Mouse Modeling, Part 2: Breeding and Crossing Mice

    Type
    Blog Post
    ...detect your targeting vector or gene of interest. 2. Breed your parental mice to generate F1 Once you’...Instead, genetic engineering should be used to separately introduce each mutation independently into different...parental generation, they are likely to stay on separate chromosomes in future generations as well, a concept...

  8. Fluorescent Protein Guide: Empty Backbones

    Type
    Collection
    ...- Bacterial Expression mScarlet-I3 568 592 68 4.2 2 min Monomer pmScarlet-I3_C1 - Mammalian Expression... Vector - Mammalian Expression pENTR4-CLIPf (w877-2) - Gateway Entry Vector pET51b-His-TEV-CLIP-tag - ...and cloning of fusion proteins, along with key parameters to help you plan your experiment. Tables are ... like multicolor imaging with better spectral separation. Protein Excitation (nm) Emission (nm) Brightness...

  9. RNA Interference in Plant Biology: New Tools for an Old Favorite

    Type
    Blog Post
    ... analogs such as 2-fluoroadenine (2-FA), organisms with functional APT will convert 2-FA to cytotoxic ...selection of plants undergoing RNAi, and LIIbeta F 1-2 RNAi, which allows assembly of intron-spliced hpRNAs...nucleotides, resulting in death. In the presence of 2-FA, potent gene silencing of APT is required for survival...target of RNAi is expressed as inverted repeats separated by a loop region that facilitates the formation...the RNAi trigger delivering the RNAi trigger characterizing the RNAi phenotype. Although all these steps...amiRNAs based upon miRNA precursors of rice and Arabidopsis species, respectively. Short hairpin RNA (shRNA...plants, such as in the model flowering plant Arabidopsis thaliana (Li et al., 2013; Zhang et al., 2018...

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

    Type
    Blog Post
    ...then packaged into AAV’s protein shell, or capsid; 2) the pHelper plasmid which expresses adenovirus genes...takes ~3 hours to complete: 1 hours hands-on time and 2 hours for the qPCR run and data analysis. Refer to...quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Human ...therapy methods, 23 1, 18-28. PubMed PMID: 22428977. 2. Choi, V.W., Asokan, A., Haberman, R.A., & Samulski...concentrations of iodixanol to separate out contaminants from an impure AAV preparation. 15%, 25%, 40%, and 60%... doesn’t get too hot because then the PEG will separate into two phases. If this happens, the solution...

  11. Light Sheet Fluorescence Microscopy

    Type
    Blog Post
    ...Carballosa, et al, (2015) eNeuro, March/April 2015, 2(2) e0001-15.2015. Pubmed. Resources: http://openspim.org...orthogonal-plane fluorescence optical sectioning (OPFOS) (2). Arne Voie, David Burns and Francis Spelman focused...in LSFM. In LSFM the laser light sheet, typically 2-6  microns, illuminates only one thin plane of the...successful attempt to render fixed anatomical preparations transparent was done by Walter Spalteholtz (...Durchsichtigmachen von menschlichen und tierischen Praparaten. Leipzig: S. Hierzel.
 J.A Dent, A.G. Polson,...Pubmed. K. Chung, J. Wallace, S.Y. Kim, S. Kalyanasundaram, A.S. Andalman, T.J. Davidson et al. (2013)...

  12. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    ...Cas9 from Streptococcus pyogenes.   Figure 2:  Crystal structure of S. pyogenes Cas9 in the apo...NUC and REC lobes laying open like a book (Figure 2). The portion of the CTD that recognizes the PAM is...it doesn’t appear in the crystal structure (Figure 2) at all. When this crucial recognition region is disordered...regions, so crystal structures like those in Figures 2 and 3 don’t show these regions, even if they are present...itself at the bottom of the image. Stem loops 1 and 2 extend horizontally across both lobes. The guide RNA...is required for Cas9 nuclease function. Stem loops 2 and 3 are not strictly necessary for in vitro cleavage...open conformation, but highly flexible, as in Figure 2. The guide RNA is bound primarily by the REC lobe,...

  13. MXS Chaining

    Type
    Blog Post
    ...listed in Table 2. For example,  chaining-based cloning methods require that the separate modules combined... TagBFP 399nm/ 456nm histone 2B (H2B) Chromatin 2 Cerulean 433nm/ 475nm Lyn-tag (derived from the tyrosine-protein...based (chaining-based) cloning. The modules (Figure 2) are contained in individual plasmids and are each...suitable for combining endogenous sequences. Table 2: High Throughput Cloning Strategies Method Technology...PMID: 20205762. PubMed Central PMCID: PMC2822740. 2. Engler C, Kandzia R, Marillonnet S. A one pot, one...

  14. Truncated gRNAs for Regulating Gene Expression

    Type
    Blog Post
    ...the absence of genome editing (Fig. 2 and 3) (5, 3). Figure 2: Gene activation with nuclease-competent... PMC3844869. 2. Chari, Raj, et al. "Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library...shown to exhibit more limited activity than SpCas9 (2). In many cases this is due both to lower relative...importantly, most Cas9 orthologs are less well characterized than the conventionally used SpCas9 (derived...

  15. No Llamas Required - Synthetic Nanobodies Against Membrane Proteins

    Type
    Blog Post
    ...select for optimal sybody candidates. Figure 2: Outline of the process for selection of sybodies ...identify and isolate sybodies targeting the SARS-CoV-2 Receptor Binding Domain found on the membrane-bound...Generation Toolbox kit. Find the Seeger lab's SARS-CoV-2 sybodies! References Geertsma ER (2013) FX Cloning...2020) Synthetic nanobodies targeting the SARS-CoV-2 receptor-binding domain. BioRxiv.  https://doi.org...production of tag-free proteins for further characterization and analysis. In a rapid response to the COVID...Versatile High-Throughput Cloning System for Characterization of Enzyme Variants. In: Methods in Molecular...

  16. Important Considerations in Optogenetics Behavioral Experiments

    Type
    Blog Post
    ... will repeatedly nose-poke at the active hole [1, 2].    Place preference/place aversion also models reinforcement...spend most of its times in the opposite chamber) [2]. Laser activation is usually controlled automatically...two different ways 1) your hypothesis is wrong or 2) there is some problem with the technical implementation...PMID: 21716290. Pubmed Central PMCID: PMC3775282. 2. McDevitt, Ross A., et al. "Serotonergic versus nonserotonergic...the chosen brain circuit, while a nose-poke at a separate hole (inactive hole) does not. If activation of... help to refine and optimize your stimulation parameters as well. Inhibition of neuronal activation is...contextual fear memories [5].  In a modified behavioral paradigm, the authors found that precise but not prolonged...

  17. Antibodies 101: Chimeric Antibodies

    Type
    Blog Post
    ...use 2 different secondaries for your antibody pair and visualize both targets in parallel (Fig. 2). For...successfully visualize both proteins.     Figure 2: Two primary antibodies with the same isotype can ...be converted? Isotype conversion is a unique characteristic of recombinant antibodies. Recombinant antibodies...

  18. Optimizing Donor DNA for Enhanced CRISPR Genome Editing

    Type
    Blog Post
    ...mechanism of action are presented in Figure 2. Figure 2: Single-stranded donor DNA interaction with...Nature biotechnology (2016). PubMed PMID: 26789497.  2. Lin, Steven, et al. "Enhanced homology-directed human... et al 2016) revealed some of the biophysical parameters that can influence the HDR/NHEJ decision. Our...or double stranded donor DNA with other design parameters. Example single stranded donor DNA and a presumptive...

  19. Addgene’s Newest Way to Speed Your Research: The Cloning Grade DNA Service

    Type
    Blog Post
    ... be directly used in the research on the SARS-CoV-2. Nine of the overall plasmid selection will be open... cloning grade DNA beta project We will ship you  2 µg of DNA in 20 µl of Tris buffer suitable for molecular...plasmid without spending time and resources in preparative experiments.  We’re excited to begin offering...etc. and/or directly long term storage. Every preparation is quality controlled through next generation...

  20. Antibodies 101: Flow Cytometry

    Type
    Blog Post
    ...cell types will separate into distinct populations on a FSC versus SSC plot (Figure 2).  A user can then...B cell marker) to separate the B cell and T cell into distinct populations (Figure 2). An immunologist...termed fluorescence activated cell sorting or FACS (2). By analyzing single cells instead of the population...expression. A routine flow cytometry experiment uses 2 or 3 different fluorescent colors each measuring a... B cells, plasma cells or others.   Figure 2: Due to differences in their size and complexity, ...the desired parameter. A droplet containing a cell that is positive for a desired parameter is collected...both cell surface and intracellular proteins in parallel, then stain the surface protein first, fix and...
Showing: 121 - 140 of 490 results