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We narrowed to 281 results for: hal.1

Showing: 61 - 80 of 281 results

  1. Reagent Repositories Are Speeding up Science During the Pandemic

    Type
    Blog Post
    Published
    Aug. 4, 2020, 1:15 p.m.
    ...available from their original sources. Figure 1: Biological repositories that distribute mouse strains... from Reproducibility for Everyone. Case study 1: Cell lines Many of the reagents used to investigate...COVID-19: an observational study. The Lancet Microbe 1:e14–e23 . https://doi.org/10.1016/s2666-5247(20)30004... J, Jia HP, Halabi C, Sigmund CD, Meyerholz DK, Kirby P, Look DC, Perlman S (2006) Lethal Infection of...

  2. Fluorescent Proteins 101: Luciferases

    Type
    Blog Post
    Published
    July 22, 2025, 1:15 p.m.
    ...available. Table 1 compares some general advantages and disadvantages of each approach. Table 1: Properties...alternatives to fluorescent proteins. Figure 1: Firefly, from Wikimedia Commons. The North American...Renilla reniformis), click beetle (Pyrophorus plagiophthalamus), deep-sea copepod (Gaussia princeps), Japanese...None No Click Beetle Red (CBR)(Pyrophorus plagiophthalamus) Natural or codon-optimized 613 (luciferin...

  3. Top Requested Lentivirus and AAV of 2016

    Type
    Blog Post
    Published
    Jan. 6, 2017, 3:56 p.m.
    ...visualizing hM4D(Gi)-mCherry in fixed tissue. References 1. Aschauer DF, Kreuz S, Rumpel S. Analysis of transduction...efficiency, tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain. PLoS One. 2013...PMC3069789. 3. Kügler S, Kilic E, Bähr M. Human synapsin 1 gene promoter confers highly neuron-specific long-...makes generation of high titer Cas9 lentiviruses challenging. This cytotoxicity also causes growth rate variability...):337-47. PubMed PMID: 12595892. 4. Sanjana NE, Shalem O, Zhang F. Improved vectors and genome-wide libraries...

  4. Hot Plasmids Spring 2024

    Type
    Blog Post
    Published
    May 23, 2024, 1:15 p.m.
    ...or nuclear expression of BFP2.     Figure 1: CROPseq-multi uses two sgRNAs with internal barcodes...transcript by endogenous processing enzymes (Figure 1). To ensure this tRNA processing only occurs on the...served as positive control (cis-ctrl). v1, vector 1; v2, vector 2; BD, binding domain; SDS, splice donor...)genome editing and gene therapy. Nat Commun., 14(1), 6578. https://doi.org/10.1038/s41467-023-42386-0...earlier Voltron indicators (a fusion of Ace2N and HaloTag, Figure 4), they determined that an A122D mutation...changing the dye that becomes conjugated with its HaloTag domain.  Find Voltron2 plasmids here! Abdelfattah...

  5. Truncated gRNAs for Regulating Gene Expression

    Type
    Blog Post
    Published
    Jan. 10, 2017, 3:37 p.m.
    ...while its nucleolytic activity is eliminated (Fig. 1) (1, 3). The gRNA can be further modified by incorporation... Podcast Interview with Alex Chavez Figure 1: Schematic of native (nuclease-competent) Cas9 interacting...which Cas9 protein is directed to which target site (1). Although this is possible, this strategy suffers...sequence or regulating gene expression.     References 1. Esvelt, Kevin M., et al. "Orthogonal Cas9 proteins...different perturbations. Consider, for instance, the challenge of attempting to simultaneously and selectively...

  6. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...dual-color control of neurons. Nature Communications, 12(1), 1–20. https://doi.org/10.1038/s41467-021-24759-5 Zhang...to consider when choosing one.     Figure 1: Example of an experimental optogenetic setup. A light... 21–51). Springer US. https://doi.org/10.1007/978-1-0716-0755-8_2 Lehtinen, K., Nokia, M. S., & Takala... 21–51). Springer US. https://doi.org/10.1007/978-1-0716-0755-8_2 Boyden, E. S., Zhang, F., Bamberg, E...nn1525 Gunaydin, L. A., Yizhar, O., Berndt, A., Sohal, V. S., Deisseroth, K., & Hegemann, P. (2010). Ultrafast... Augustin, S., Sauter, K., Papagiakoumou, E., Gottschalk, A., Soba, P., Emiliani, V., Engel, A. K., Hegemann...

  7. Mobile-CRISPRi: Bringing CRISPRi to Diverse Bacteria

    Type
    Blog Post
    Published
    April 4, 2019, 12:53 p.m.
    ...active for greater than 50 generations. Figure 1: Mobile-CRISPRi's modular components. Image from Peters...on a non-selective plate. Most bacteria tested had 1 transfer in every ~100 to 1,000 colonies, but some...including E. faecalis and P. mirabilis, had only ~1 transfer per 1,000,000 colonies. Higher transfer rates...which creates a challenge when studying them since their complete knockdown is lethal. Incomplete or titratable... to lab-adapted bacteria because it has been challenging to introduce CRISPRi machinery into diverse bacteria...

  8. Which Fluorescent Protein Should I Use?

    Type
    Blog Post
    Published
    May 20, 2014, 2:06 p.m.
    ...biological questions. The two most common uses are: 1) to test the expression level in a specific system...brightness is compared to that of EGFP which is set as 1. Some proteins are very dim (e.g. TagRFP657, which...Photostability can be as short as 100ms (EBFP) or as long as 1 hour (mAmetrine1.2). However, for most FPs it is a...be split into two halves, which are non-fluorescent on their own. If the two halves are in close proximity...determine the proximity of two proteins fused to the halves of the split FP. This technique is also is also...

  9. Three Key Considerations for Precise Neuronal Targeting Using AAV Technologies

    Type
    Blog Post
    Published
    Nov. 27, 2019, 2:03 p.m.
    ...from the paper for designing experiments with AAV: 1. Getting your viral vector into your cell of interest... administration routes for neuroscience see Table 1 from the paper. 2. Manipulate your cell of interest...information from a region. In the example shown in Figure 1, injected retrograde AAVs at one location result in...development, learning, and behavior poses many challenges in neuroscience with many brain regions, neuronal...

  10. Clear and Accessible Writing

    Type
    Blog Post
    Published
    Feb. 15, 2024, 2:15 p.m.
    ...intended.)  Steps to clear writing Let’s use Figure 1 as our example. Remember, our goal is to use words...information as sighted readers.    Figure 1: An image from AAV Purification by Iodixanol Gradient...are they hoping to get from it? The image in Figure 1 appears on our protocol page for AAV Purification ... share with the rest of the workshop.  For Figure 1, Addgene chose this alt text: "The left panel is a...scientific paper, you may feel it’s overwhelming or challenging. So instead, let’s focus on practicing with a...

  11. Early Career Researcher Toolbox: Social Media for Scientists

    Type
    Blog Post
    Published
    Dec. 11, 2018, 12:46 p.m.
    ...how scientists connect on Twitter that I realized 1) a lot of scientists are using social media professionally... but my consistent writing for the Addgene blog (~1-2 blog posts per month) and use of Twitter and LinkedIn... have tips for using social media as a scientist. 1. "5 Ways Scientists SHOULD Be Using Twitter" podcast...of interest. Hopefully through these links, I’ve: 1) convinced you social media can positively impact ...professional development, and while it’s not challenging to use, it’s hard to know where to begin. To ...

  12. Simplify Cloning with in vivo Assembly

    Type
    Blog Post
    Published
    Oct. 18, 2018, 12:37 p.m.
    ...two-step, 2 hr protocol prior to transformation (Figure 1). As this approach requires no special reagents or...with linearized vector backbone. DpnI digestion - 1 μl DpnI is added to the PCR mix to remove parental...confirm primer design.  Use minimal template DNA Use 1 ng of PCR template DNA to minimize false positive ... by PCR, so we usually add DMSO (3%) and Betaine (1 M) to the PCR mix. When PCR is not possible Some plasmids...Twitter @jakefwatson and @JGarciaNafria.  References 1. Jones, Douglas H., and Bruce H. Howard. "A rapid ... to amplify away from the insertion site. Encode half the new sequence at the 5’ end of each primer, with...

  13. Choosing the B(right)est Fluorescent Protein: Photostability

    Type
    Blog Post
    Published
    June 8, 2017, 2:30 p.m.
    ...various cyan fluorescent proteins is depicted in figure 1. Of note, the photobleaching rate does not depend ...to be used with the fluorescent protein. In figure 1 we provide an example of such a comparison between...the variants is comparable (lower panel of figure 1). To avoid changes in excitation power, it is important...the power 2-fold does not reduce photobleaching by half. How exactly the photobleaching rate depends on ...described by the t½, which is the time after which half of the initial fluorescence intensity remains. The...

  14. Pairing CombiGEM and CRISPR for Combinatorial Genetic Screening

    Type
    Blog Post
    Published
    April 12, 2016, 2:30 p.m.
    ..., including those found at Addgene! Figure 1: Strategy for assembling the barcoded gRNA library...pool-clone them into the pAWp28 storage vector (Figure 1): Forward oligo: 5’- CACCGNNNNNNNNNNNNNNNNNNNGTTTGGGTCTTCGAGAAGACCTATTCXXXXXXXXC... He can be contacted at [email protected].   References 1. Cheng, Allen A., Huiming Ding, and Timothy K. Lu....2015; Koike-Yusa et al., 2014; Ma et al., 2015; Shalem et al., 2014; Wang et al., 2014), knock down (Gilbert... 26190106. PubMed Central PMCID: PMC4559080. 8. Shalem, Ophir, et al. "Genome-scale CRISPR-Cas9 knockout...

  15. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    Published
    Jan. 6, 2015, 5:21 p.m.
    ...expression. Brown et al., Genesis 2014 Jan;52(1):39-48. APEX2 for proteomic mapping and electron...engineering cells that lack release factor one (RF-1; Bacterial strain EcAR7) and minimizing the set of... of human mitogen-activated ERK activating kinase 1 (MEK1) with either one or two phosphoserine residues...comprised of three sets of cloning vectors (Level 0, 1, or 2) which can be utilized in three successive assembly... vectors are directionally assembled into a Level 1 vector creating a single transcriptional unit (Ex:...coding region, and terminator). Next, up to six Level 1 modules can be similarly assembled into a Level 2 ...vectors to allow for additional iterations of Level 1 assembly if necessary. Combining multiple Level 2 ...

  16. Deciphering the Mysteries of Behavior with Viral Vectors

    Type
    Blog Post
    Published
    Sept. 17, 2019, 12:40 p.m.
    ...production of the pro-inflammatory cytokine interleukin IL-1 beta in the dorsal raphe nucleus (DRN), a region thought... a transgenic mouse harbouring a Cre-dependent IL-1 beta overexpression cassette. Expression of Cre in...in these neurons turns on overexpression of IL-1 beta. They tested the mice in a series of behavioral ...risky), or a closed arm (safe). Mice with higher IL-1 beta production spent more time in the open arm and... part of the apparatus, it turned out that the IL-1 beta overexpressing mice spent more time in the risky...stay tuned!  References Alpár, Alán, et al. "Hypothalamic CNTF volume transmission shapes cortical noradrenergic...

  17. Technical Design of a Western Blot

    Type
    Blog Post
    Published
    Aug. 22, 2024, 1:15 p.m.
    ...Tris-tricine 2.5–40 kDa Tris-tricine 30 V, 1 hour or 100 V, 1–2 hours Good separation, quality, and stability...lot to cover, so let's dive in!      Figure 1: The technical decisions to make when designing a ...assay. The most common options are 4 °C overnight or 1–2 hours at room temperature (RT). Most people choose...overnight at 4 °C and their secondary antibody for 1–2 hrs at room temperature, which allows them to reduce...weight of the proteins you’re interested in. Table 1 lists the most common types of gels for SDS-PAGE running...gel chemistry and/or specialty gel options. Table 1: Types of gels  Gel Type Protein sizes Running... Tris-glycine 6–400 kDa Tris-glycine 100 V, 1–2 hours Easy and cheap to handcast Short shelf-life...

  18. Illuminating Choices: A Guide to Selecting Fluorescent Dyes and Ligands

    Type
    Blog Post
    Published
    March 21, 2024, 1:15 p.m.
    ...principles of fluorescent dyes/ligands Figure 1: Example structures of fluorophores, fluorescent dyes... dopamine D2/D3 receptors. Scientific Reports, 10(1), 21842. https://doi.org/10.1038/s41598-020-78827-...for bacterial imaging . Microbiology Spectrum, 12(1), e0369023. https://doi.org/10.1128/spectrum.03690...Biochimica et Biophysica Acta - Biomembranes, 1838(1 Pt A), 15–33. https://doi.org/10.1016/j.bbamem.2013.09.005...interchangeable labeling using the HaloTag® system, the new Janelia Fluor HaloTag Ligands expand the self-labeling... self-labeling proteins would be SNAP-tag® and HaloTag®. These consist of a genetically encoded enzyme...Hayashi-Takanaka et al., 2014). Other dyes may prove challenging to stain intracellular compartments in in vivo...

  19. Antibodies 101: Single Chain Fragment Variables (scFvs)

    Type
    Blog Post
    Published
    June 3, 2021, 1:15 p.m.
    ...the other (Sandomenico et al., 2020). Figure 1: Comparison between the IgG antibody and scFv. ...intensity of a tagged protein. SunTag has two components: 1) a protein of interest that’s tagged with 10-24 copies...Application. Clinical and Developmental Immunology 2012:1–15 . https://doi.org/10.1155/2012/980250  Bates A,...without disulfide bonds, made by molecular evolution 1 1Edited by I. A. Wilson. Journal of Molecular Biology... the body or self antigens, and toxins that are lethal to animals.  In the clinic, scFvs’ size also provides...plasmid in bacteria (Ahmed et al., 2012). One challenge of bacterial expression is the proper formation...

  20. 27 Hot Plasmids from 2016

    Type
    Blog Post
    Published
    Dec. 22, 2016, 3:03 p.m.
    ...a rate of up to 1 per 500-1000 bp. In comparison, the DNA replication error rate is 1 per 109 bp. Unlike...Transcriptional Output-TANGO (PRESTO-TANGO) to screen the NCC-1 library of approved drugs against the entire kit; ...generated 5 common 30bp overlap sequences (Sites #1-5). Each overlap site encodes a unique restriction...First, GMAP-compatible backbones for lentivirus LV 1-5 and retrovirus RV 2-5 were constructed. The authors...is multiplex automated genome engineering (MAGE) (1). MAGE uses recombineering (2) to simultaneously incorporate...of GFP (SEP) by a 9 amino-acid linker (see Figure 1). The key to the biosensor lies in pH: DsRed is relatively...inactivate SEP and leave only DsRed to fluoresce (1). With variants that can be targeted to specific cellular...
Showing: 61 - 80 of 281 results