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  1. Quickest Way to Deposit Plasmids: The Deposit Spreadsheet

    Type
    Blog Post
    Published
    March 8, 2017, 3:15 p.m.
    ...our deposit spreadsheet to complete Step 1. Steps 2 and 3 are usually very easy — our tech transfer team...columns are shown in red in the spreadsheet (Figure 2) and are described in Table 1. Some cells have drop-down...Filling out and sending the deposit spreadsheet Figure 2: Example of the deposit spreadsheet showing the first...guide to our online data entry process. Figure 1: Begin the deposit process by clicking “Submit Online Deposit... our deposit spreadsheet?  Our plasmid deposit process can be broken down into four simple steps: Send... contact you if any issues arise during the QC process. As the depositing scientist, you will have the...information in a deposit spreadsheet. The data entry process On the Addgene home page, if you scroll over “Deposit...
  2. 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, ... Encouraged by the high efficiency and easy procurement of cr:tracrRNA reagents, we scaled up these tagging...
  3. Year of the Camelid: Antibody Style

    Type
    Blog Post
    Published
    May 9, 2024, 1:15 p.m.
    ...and a source of sdAbs (Figure 2) (Xu, et al., 2021).      Figure 2: Genetically modified mice offer... from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 595:278–282. https://doi.org/10.1038...? In the early years of sdAbs development, the process started with immunizing a camelid (usually llamas...
  4. Mouse Modeling, Part 2: Breeding and Crossing Mice

    Type
    Blog Post
    Published
    Aug. 6, 2019, 12:55 p.m.
    ...detect your targeting vector or gene of interest. 2. Breed your parental mice to generate F1 Once you’...maintain your parental strains throughout this process. In the F1 and later generations, mice that are...
  5. Hot Plasmids and Viral Preps - January 2021

    Type
    Blog Post
    Published
    Jan. 5, 2021, 2:15 p.m.
    ... Opto-Cre-Vvd is fast and can cut in as little as 2 hours.  Sheets, MB, et al., ACS Synth Biol. 2020....they investigated three Casɸ orthologs, Casɸ-1, Casɸ-2, and Casɸ-3. This system is notable for several reasons...a minimal PAM requirement. For instance, for Casɸ-2 the PAM sequence is 5’-TBN-3’ (where B is G, T, or...deposited by Leopold Parts. This library delivers 2 randomly paired guides per construct and allows a ...active site. The RuvC active site in Casɸ can both process crRNA and carry out the crRNA-guided DNA cutting...
  6. How-to: 5 Steps to a Great Panel Discussion

    Type
    Blog Post
    Published
    Oct. 22, 2014, 1:57 p.m.
    ... let the panelists introduce themselves. I do a 1-2 minute introduction. If you chose good panelists, ...take 5 minutes to introduce themselves and, voila, 1/2 of your time is gone with no interesting discussion...introductions. The moderator asks questions, calling on 1-2 panelist for each question in a way that elicits those...shift, they are checking out. If you can, plant 1-2 good questions with trusted audience members. A good... Your audience may have a lot of real or self-proclaimed experts on the topic at hand. You can use this...
  7. Quick Guide to Working with Drosophila Part 3: Genome Engineering in Flies

    Type
    Blog Post
    Published
    July 28, 2017, 1:30 p.m.
    ...are many docking sites available for integration. 2. How soon would you like your flies ready for use?...beautiful immunofluorescent images like in this paper (2). Metabolic assays such as Seahorse can be employed...PMID: 16547094. PubMed Central PMCID: PMC1526508. 2. H. Jiang,  et al. Cytokine/Jak/Stat signaling mediates...make a transgenic fly in order to study it. The process is fairly straightforward. Basically, you place... incorporated into the germline. To begin this process, you will first need to do some molecular cloning...
  8. AAV Vector Quality Control: Going the Extra Mile with NGS

    Type
    Blog Post
    Published
    Sept. 12, 2017, 1:44 p.m.
    ...extracted the DNA and processed the mixed sample in our pipeline (see Figure 2, sample 2). When we blindly... potential contaminants. The analysis is a 2-step process using Geneious software: First, the individual...quality, we undertake a rigorous quality control process. In 2016, we launched our viral service to continue...bacteria snuck into the prep during the production process? These questions are especially important when ...CHRM4 gene. When contamination is suspected, we proceed to de novo assembly of the unmapped reads, employing...answer your questions about our quality control process! The images in this blog post were created using...
  9. Making CRISPR Plasmids Using Fragmid

    Type
    Blog Post
    Published
    Aug. 29, 2024, 1:15 p.m.
    ... components, such as your CRISPR enzyme or Pol 2 promoter. The options available in each class, or module...overhang specific to the type of module it is (Pol 2 protomer, Cas protein, ect...). Whatever individual... (KO, CRISPRa, CRISPRi, editing)   Figure 2: Selecting module fragments on the Fragmid website...Fragmid. Fragmid is a modular vector assembly process designed for a quick, plug-and-play approach to...of the design work out of the plasmid creation process. Each module of Fragmid represents a class of components..., the Fragmid website, which breaks the design process down into four easy steps, provides the real value...
  10. Educational Planarian Tools for Teaching Developmental Biology Techniques

    Type
    Blog Post
    Published
    May 24, 2018, 1:20 p.m.
    ...neoblast cells and the gene Prohormone convertase 2 (pc2) labels the central nervous system. Evaluating... characterized in an unrelated worm (C. elegans) [2]. Delivering dsRNA matching a specific mRNA sequence...223). Link: http://abt.ucpress.edu/content/79/3/208 2. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver... its expression. More specifically, during the process of RNAi, an enzyme dubbed Dicer cuts or “dices”...Phagocata morgani and Phagocata gracillis, the process is a little more complicated. These strains are...RNA inhibits gene expression in planarians." Proceedings of the National Academy of Sciences 100.suppl...
  11. Tips for arabidopsis transformation

    Type
    Blog Post
    Published
    Oct. 25, 2018, 1:23 p.m.
    ... Plant Methods. BioMed Central, 2(1), p. 19. doi: 10.1186/1746-4811-2-19. PubMed PMID: 17087829. PubMed...PMID: 24032037. PubMed Central PMCID: PMC3759027. 2 Harrison, S. J. et al. (2006) ‘A rapid and robust ...from later. The Arabidopsis transformation process The process itself is straightforward. When your agrobacterial...growth on antibiotic-containing media) A similar process occurs in nature; Agrobacterium tDNA insertion ...in hand, so it is pretty important to get this process right the first time. I’ll lay out some guidelines...Agrobacterium strain. Additionally, the transformation process can get a bit messy, so you want to make sure you...begin working in the T2 generation. The selection process itself can affect the growth of resistant plants...
  12. Plasmids 101: CcdB - The Toxic Key to Efficient Cloning

    Type
    Blog Post
    Published
    Dec. 8, 2016, 3:30 p.m.
    ...CcdB.” Biotechniques. 1996 Aug;21(2):320-3. PubMed PMID: 8862819. 2. Bahassi, EM., et al. “F plasmid CcdB... desired insert should not grow.   Figure 2: Image from http://teachline.ls.huji.ac.il/72682/tutorials...still express ccdB and therefore would die. This procedure dramatically reduces the number of clones that...recombinant plasmid and therefore makes the cloning process much more efficient, as one does not have to thoroughly...
  13. Pairing CombiGEM and CRISPR for Combinatorial Genetic Screening

    Type
    Blog Post
    Published
    April 12, 2016, 2:30 p.m.
    ...CombiGEM lentiviral vector backbone pAWp12 (Figure 2). Cloning from the pAWp28 storage vector to the pAWp12... before beginning your experiments. Figure 2: Strategy for assembling barcoded combinatorial gRNA...PMID: 25114216. PubMed Central PMCID: PMC4151723. 2. Doench, John G., et al. "Optimized sgRNA design to... massively parallel combinatorial genetics." Proceedings of the National Academy of Sciences 111.34 (2014... CRISPR-Cas9 screening enabled by CombiGEM." Proceedings of the National Academy of Sciences113.9 (2016...
  14. Antibodies 101: Stripping and Reprobing Western Blots

    Type
    Blog Post
    Published
    Aug. 1, 2024, 1:15 p.m.
    ...incubation at 37 °C. Wash the membrane for 5–10 minutes 2–3x in fresh wash buffer such as PBS or TBST. Stringent...Purpose Tris HCl 62.5 mM Buffer SDS 2% (w/v) Detergent Β-mercaptoethanol (βME) 100...minutes at 50 °C. Wash the membrane for 5–10 minutes 2–6x in fresh wash buffer such as PBS or TBST. Note .... Dry nitrocellulose membranes are brittle, so proceed with caution. Unlike PVDF, they can be returned...remains, you may want to repeat your stripping procedure, perhaps using longer incubation times, or try...
  15. Negative Can Be Positive: Open AAV Data with Addgene

    Type
    Blog Post
    Published
    Sept. 6, 2022, 1:15 p.m.
    ...indicated they wanted to see more negative data (Figure 2.) At the same time, when scientists who support open...is not only housed, but encouraged.    Fig. 2: Results from a survey conducted by Addgene in 2021...detailed methods and image descriptions, a minimum n = 2, and well labeled high- and low-magnification images...gene therapy trials. Human Gene Therapy Methods, 26(2), 71–76. https://doi.org/10.1089/hgtb.2015.040 Initiative...expression can take months (or longer), yet the process is often not detailed in the primary literature...
  16. Technical Design of a Western Blot

    Type
    Blog Post
    Published
    Aug. 22, 2024, 1:15 p.m.
    .... 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...Tris-glycine 6–400 kDa Tris-glycine 100 V, 1–2 hours Easy and cheap to handcast Short shelf-life...–40 kDa Tris-tricine 30 V, 1 hour or 100 V, 1–2 hours Good separation, quality, and stability ...separation of proteins of different sizes.  Table 2: Recommended gel percentages for various protein sizes...are consistent and stable at room temperature for 1–2 years and are available in formulas specific to your...response over a broad dynamic range that typically spans 2–5 orders of magnitude, which includes a wide dynamic...
  17. 15 Hot Plasmids from 2017

    Type
    Blog Post
    Published
    Jan. 9, 2018, 3:02 p.m.
    ...NGG)  Editing window ~2 nt  85175  pBK-EE-BE3  SpCas9 (NGG)  Editing window ~2 nt  85176  pBK-YE2-...quantum yield of 0.54) and mScarlet-H with M164H (2-fold improvement in photostability compared to mScarlet...SpCas9 base editors with editing windows as small as 1-2 nucleotides! To reduce off-target effects associated...pBK-YE2-BE3  SpCas9 (NGG)  Editing window ~2 nt  85177  pBK-YEE-BE3  SpCas9 (NGG)  Lower on-target activity...activity than BE3; editing window ~1-2 nt  87438  pET42b-HF-BE3  HF-Cas9 (NGG)  Very low off-target activity...Ladders Are Awesome Tools: They are comprised of 2 plasmids, pPSU1 and pPSU2, that can be amplified affordably...libraries The Gross Lab at UCSF recently deposited 2 Bacillus subtilis libraries with Addgene – the B. ...
  18. FastCloning: A Newer, Simpler Cloning Technique

    Type
    Blog Post
    Published
    Nov. 1, 2016, 2:30 p.m.
    ...vector:insert ratio is used in the DpnI digestion and 2 µL of digest product are used in the transformation...Biology 38 (2016): 145-154. PubMed PMID: 27391134. 2. Li, Chaokun, et al. "FastCloning: a highly simplified...in vivo. Detailed FastCloning procedure To start the FastCloning process, the insert and vector are first...oldest of these techniques and is a multi-step process consisting of digestion, purification, ligation...techniques with higher efficiency and simpler procedures have been developed. Some of these include, TA...specific sequences. Read on to learn how easy this process is and to get tips for applying it in your own ...Ligation + - Transformation + + The FastCloning process in brief In FastCloning, you PCR both the vector...
  19. Production of Virus in Insect Versus Mammalian Cells

    Type
    Blog Post
    Published
    Nov. 5, 2024, 8:32 p.m.
    ...) 38 kb Cells HEK-293T Sf9 Time to collection 2–4 days 5–10 days Purification Ultracentrifugation...Centrifugation Titration time ~1 day (AAV); ~1 week (lenti) 2–10 days Initial titers Higher Lower Resources... a factory to produce adeno-associated virus type 2 vectors. Human Gene Therapy, 13(16), 1935–43. https...takes a little bit longer in insect cells. Processing Processing of your baculovirus is straightforward —...cell preparations, which we talk about below. Processing The viral supernatant is typically collected ... couple days to increase yield. The collection process is a cycle of collecting the media and adding fresh... fresh media every 12 to 24 hours. Processing the virus-containing supernatant will depend on the virus...
  20. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    Published
    Sept. 3, 2020, 12:15 p.m.
    ...the light-inducible heterodimerizing cryptochrome 2 (CRY2) and calcium and integrin-binding protein 1 ...inactive, dead Cas9 protein (dCas9) fused to CIB1; and 2) the activator - the CRY2 photolyase homology region... fused to both the N- and C-termini of dCas9; and 2) CRY2FL-VP64, a fusion of full-length CRY2 and the...researchers saw an 11-fold increase in mRNA levels after 2 hr and a 400-fold increase after 30 hr. The system...authors fragmented Cas9 into N-terminal (residues 2-713, N713) and C-terminal (residues 714-1368, C714...nMagC714 instead of nMagHigh1-C714, generating paCas9-2. This change did not significantly alter the system...prior work, the Sato lab also showed that the paCas9-2 system could be spatially controlled and reversibly...
  21. The Importance of High Titer for AAV Transductions

    Type
    Blog Post
    Published
    March 1, 2018, 2:11 p.m.
    ...drastically with lower titers. As you can see in figure 2, the expression from the 5x1011 titer was essentially... roughly 6-fold increase in expression [3, Figure 2]. Note how expression increases exponentially with...international 61.1 (2002): S9-S15. PubMed PMID: 11841606. 2. Schultz BR, Chamberlain JS. Recombinant Adeno-associated...healthy as can be to prepare them for the arduous process of generating viral particles. Limit tube transfer...
  22. Predicting Adverse Reactions to Monoclonal Antibody Drugs

    Type
    Blog Post
    Published
    Feb. 13, 2024, 2:15 p.m.
    ...various components of the immune system. Figure 2: In-vitro models for immunogenicity prediction of ...drug reaction. This system would somewhat act like a 2-step verification. All approaches have their own limitations...Future Enhancements. Frontiers in drug discovery, 2, 952326. https://doi.org/10.3389/fddsv.2022.952326Joubert...approach cannot replicate the complexity of antigen processing events that take place within an antigen-presenting...
  23. Opto-Nanobodies: Using Light to Manipulate Cell Signaling and Protein Purification

    Type
    Blog Post
    Published
    Nov. 19, 2019, 2:08 p.m.
    ...non-specific proteins, and then elute YFP.  Option #2: Opto-Nanobodies (OptoNBs) purification You skip adding...blue lights. Which option do you choose?  Option #2 may sound like fiction, but light-controlled protein...experiments.  AsLOV2 Inertion Site mCherry #1 mCherry #2 GFP Loop 1 dark-induced dark-induced dark-induced...with a flip of a light switch would improve this process. The team used nickel-coated agarose beads coated...
  24. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    Published
    May 22, 2018, 1:38 p.m.
    ...research experiences to undergraduate students (1, 2), but educators face significant challenges in designing... by western blotting in other experiments (Figure 2).   Complementation reveals conservation of function...Biology Education: A Call to Action, Washington, DC. 2. President's Council of Advisors on Science and Technology... controlled by the GAL1 promoter. The cloning procedure adds both V5 and His6 epitope tags to the C-termini...successfully analyze Met protein complementation. In the procedure diagrammed in Figure 3, students first transform...
  25. Deep Dive: Statistical Tests (Comparisons)

    Type
    Blog Post
    Published
    March 7, 2023, 2:15 p.m.
    ...typically, normal (bell curve) or skewed (see Fig. 2). Assumptions – characteristics of a data set; ...levels of variance among data.     Fig. 2: Examples of data distribution profiles.   Parametric... positive is much higher than if you only look at 2 or 3 pairwise comparisons. Similar to family-wise ...statistical facets of reproducibility. Adv Physiol Educ. 40(2): 248-252 (2016). 0.1152/advan.00042.2016 Finch, W...Simulation Study. Front. Appl. Math. Stat. Volume 2 (2016). doi.org/10.3389/fams.2016.00002  ...Bonferroni Correction and the Benjamini-Hochberg procedure are designed to reduce false positive rates and...
  26. The AAVantages of AAV in CRISPR Screens

    Type
    Blog Post
    Published
    Feb. 4, 2025, 2:15 p.m.
    ...handled at BSL-1, while lentivirus requires a BSL-2 setup. This requires a less involved setup when working...infection rates in your experiment. Figure 2: Visual representation of common AAV serotypes used..., 10(1). https://doi.org/10.1038/s41467-019-12449-2 Pupo, A., Fernández, A., Low, S. H., François, A.,... — in vivo, in vitro, and ex vivo. The general process of these screens is the same: Deliver CRISPR library... mice and slightly less red tape for approval processes. Additionally, while both AAV and lentivirus have... AAV also has psuedotypes. Psuedotyping is the process of making a hybrid AAV, with the genome from one...
  27. Plasmids 101: Control Plasmids

    Type
    Blog Post
    Published
    April 9, 2015, 3:29 p.m.
    ...the result in Figure 1 could look like this: Figure 2: Expression of Plasmid B (as internal control) This...down expression of Gene X but, as shown in Figure 2, this was likely due to the original transfection ...PMID: 20074371. PubMed Central PMCID: PMC2817684. 2. Replicates and repeats—what is the difference and...transfection, transfection reagent, or transfection process) may have on the target cells. One transfection... the transfection reagents or the transfection process itself has any cytotoxic effects on the target ... optimization of the transfection reagents and process. It is important to note that optimal experimental...
  28. How Dry Ice Affects Viral Vector Sample pH & How to Avoid It

    Type
    Blog Post
    Published
    June 20, 2017, 2:30 p.m.
    ...pH visible at the sample interface upon thaw (Fig. 2). Before thawing, all the samples were at the control...showed that AAV infectivity was not altered by a short 2-hour exposure to pH as low as 2.5 (Potter et al., ...Methods. 2013 Apr;10(4):278-9. PubMed PMID: 23538862. 2. Potter M, Lins B, Mietzsch M, Heilbronn R, Van Vliet...always looking for ways to improve our shipment processes. After reading a publication describing how short...
  29. Fluorescent Tagging of Endogenous Genes with SapTrap

    Type
    Blog Post
    Published
    Oct. 12, 2017, 2:26 p.m.
    ...digestion of the destination vector with SapI yields 2 sites- the first site accepts the sgRNA target sequence...marker, and connector to be released (Fig. 1, Step 2-3). Since donor plasmids of the same type will produce... a gRNA vector that targets the gene of interest, 2) a plasmid to specify the reading frame of the insertion...scientists have been able to study many cellular processes, including mitosis, mitochondrial fission/fusion...insertions can only be detected by labor-intensive processes like PCR or by evaluating visual phenotypes. Improving...
  30. Cloning Mammalian Cells with the Agarose Method

    Type
    Blog Post
    Published
    Sept. 7, 2017, 12:17 p.m.
    ...3 plates at different densities for selection). A 2% agarose solution is then melted (and thereby sterilized...96-well assay plate. We generally freeze at least 2 ampules each of 4 clones with different levels of ...of agarose, which is then overlaid with the firmer 2% agarose gel solution discussed above for picking.... Protocol Pages Agarose cloning method procedure The procedure (illustrated in the YouTube video below...
  31. Important Considerations in Optogenetics Behavioral Experiments

    Type
    Blog Post
    Published
    Oct. 1, 2015, 2:30 p.m.
    ... 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...neuronal activation and is a sufficient readout to proceed with your behavioral experiments. Comparison of...
  32. Technique: Probe Phage Genomes for Host Binding Proteins

    Type
    Blog Post
    Published
    Sept. 29, 2016, 2:30 p.m.
    ... is also gaining a lot of new traction lately (1, 2), depends on knowledge of the structure(s) a given...per plate) across 20 fresh selective plates. Step 2: Express random phage DNA fragments in E. coli Now...microbiology 23.4 (2015): 185-191. PubMed PMID: 25708933. 2. Cooper, Callum J., Mohammadali Khan Mirzaei, and ... biology 34 (2015): 69-77. PubMed PMID: 26275959. 2. Weigele, Peter, and Elisabeth A. Raleigh. "Biosynthesis...useful for the biotech industry, which is in the process of capitalizing on phage RBPs as diagnostic tools...DNA fragments with live host cells Now you can proceed with incubating this membrane with your cells of...
  33. Antibodies 101: Introduction to Immunofluorescence

    Type
    Blog Post
    Published
    Nov. 16, 2021, 2:15 p.m.
    ...   Figure 2: High-level overview of an indirect immunofluorescence procedure with key considerations... several steps outlined below and in Figure 2. For a deeper dive into the steps and techniques, see Im...recognize the species of your primary antibody and 2) is conjugated to a fluorophore that suits your experiment...primary antibodies is a time consuming and expensive process. Consider the vast number of possible primary antibodies...Performing an immunofluorescence experiment The process to perform IF can be broadly divided into the several...specific 3-dimensional epitopes. Different sample processing steps can alter epitopes in different ways, so...secondary antibody you use, so as long as the sample processing steps used in a non-fluorescent IHC/ICC assay...
  34. Droplet Digital PCR for AAV Quantitation

    Type
    Blog Post
    Published
    Jan. 16, 2020, 2:18 p.m.
    ... qPCR is that the results can vary by a factor of 2. This means that if you set up two identical assays...amplitude measured for each droplet in each well (Figure 2). A clean ddPCR should have a clear separation between...as low as 1C/s. Increasing the elongation time to 2 minutes and the denaturation time to 1 minute has ...one is needed. For these reasons, we are in the process of transitioning our titering method from qPCR ...information needed for your PCR experiment. The process to titrate AAV by ddPCR begins with diluting the...
  35. Transferable Skills Guide: Cross-team Communication

    Type
    Blog Post
    Published
    Nov. 21, 2019, 1:53 p.m.
    ...discussed them in meetings and 2) creating a pictorial guide for our engineers (Fig. 2). Creating this guide was...communication has helped Addgene move from completing 2-3 large projects a year, on average, to completing... academic lab or your workplace, is an ongoing process. It is never really done. But if you implement ...
  36. The Future of Research Symposium Boston 2015

    Type
    Blog Post
    Published
    Oct. 20, 2015, 2:30 p.m.
    ...Quotes taken directly from participants (summarized in 2) touched upon many problems in this area: “ [The] ...PMID: 24733905. Pubmed Central PMCID: PMC4000813. 2. McDowell, Gary S., et al. "Shaping the Future of ...A fair deal for PhD students and postdocs." Elife 2 (2013): e01139. Pubmed PMID: 24137543. Pubmed Central...biomedical research from its systemic flaws." Proceedings of the National Academy of Sciences 111.16 (2014...
  37. Neuronal labeling with Spaghetti Monster

    Type
    Blog Post
    Published
    Aug. 14, 2018, 12:42 p.m.
    ...experiment using smFPs and standard neuronal tracers. 2. Visualization of neuronal sub-cellular structures...similar proteins. For example, N-cadherin (cadherin-2) is a postsynaptic cell adhesion protein that plays...PMID: 25915120. PubMed Central PMCID: PMC4573404. 2. Shepherd, G.M. (2004). In "The synaptic organization...central nervous system (CNS) orchestrates complex processes enabling organisms to control their movements ...tendency to brightly label somata but not neuronal processes. In contrast, smFPs can label fine neuronal structures...
  38. Viral Vectors 101: Calcium Sensors

    Type
    Blog Post
    Published
    Aug. 10, 2023, 1 p.m.
    ...calcium biosensor, so that the (1) binding of calcium, (2) allosteric rearrangements of the sensor, and (3) ...user-controlled illumination with violet light and (2) exposure to increased intracellular calcium. It has...dynamics in vivo. Neuroscience Research. 2021 Aug 1;169:2-8. Suzuki J, Kanemaru K, Iino M. Genetically encoded...to your parameters.   Kinetics How fast is the process you would like to monitor? Neurons, for example...
  39. DAP arrays for multiplex gene editing

    Type
    Blog Post
    Published
    July 7, 2022, 1:15 p.m.
    ... as muscular dystrophies, heart disease, and type 2 diabetes, across four different types of human cells...(#186715) and hCtRNA_VT (#186716).   Fig. 2: Comparison of previous representative dual-gRNA architectures...array  Although CRISPR-Cas12a, with abilities to process and release its own gRNAs from a single array, ...efficient base editing and prime editing, is unable to process its own array but is the key component to enable...minimal size. To do so, they harnessed the tRNA processing mechanism, which is conserved in all living organisms...individual gRNAs are released by endogenous tRNA processing machineries, specifically, RNaseZ and RNaseP....additional promoter, which is followed by tRNA processing to release individual gRNAs for gene editing....
  40. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

    Type
    Blog Post
    Published
    Oct. 17, 2019, 12:28 p.m.
    ...upstream of an opsin gene (e.g., channelrhodopsin-2, ChR2) fused to a reporter gene (e.g., mCherry) to...the correct orientation to be transcribed (Figure 2) (Sharma and Zhu, 2014). How does FLEx enable strong... Abdallah, Khaled, et al. "Adeno-associated virus 2/9 delivery of Cre recombinase in mouse primary afferents...Deniz, et al. "A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range ...optogenetics to study physiological and behavioral processes (Abdallah et al., 2018; Deubner et al., 2019)....induces reanimation from general anesthesia." Proceedings of the National Academy of Sciences 113.45 (2016...
  41. Hot Plasmids: Fall 2024

    Type
    Blog Post
    Published
    Nov. 21, 2024, 1:30 p.m.
    ...improve solubility and stability (Figure 2).      Figure 2: Crystal structures of CRBNmidi alone...fluorescent tags in Caenorhabditis elegans. Genetics, 228(2), iyae126. https://doi.org/10.1093/genetics/iyae126...are essential tools for visualizing biological processes in vivo. However, mScarlet’s slow maturation rate...like the C. elegans embryo, where developmental processes happen within a few hours. In order to use the...addition to the toolkit for visualizing cellular processes in C. elegans: mScarlet3 for applications needing...
  42. What's Your Organism? Expanding Genomic Tools via the NSF EDGE Program

    Type
    Blog Post
    Published
    May 2, 2019, 12:41 p.m.
    ...presented in a series of quick (10 minute) or very quick (2 minute) talks so we got to hear from everyone. Addgene...evolutionary tree at least 6-7 times and on at least 2 separate continents. Mimulus (Andrea Sweigart) Monkeyflowers...Organisms, Part 1 Five Popular Model Organisms, Part 2 ...’ll choose to study Crepidula atrasolea or Prochlorococcus with your next project. Gymnotiformes and Mormyridae...evolution in immunology, neurobiology, and more. Prochlorococcus (Penny Chisholm) This cyanobacterium is the...need to grow to get a recombinant because this process is expensive. They are using a cool fluorescent...
  43. Filming Science Videos in the Age of Social Distancing

    Type
    Blog Post
    Published
    May 20, 2021, 1:15 p.m.
    ... Figure 2: Ironing boards. Good as a WFH desk, and as a video control center.   Cycle 2: Zooming ...ironing board, giving it the perfect height (Fig. 2). We recorded video using a simple, external video...doesn’t, and trying all over again. Here’s that process!   Figure 1: The Design-Build-Test-Learn...gear, and walking everyone through the recording process was going to be time consuming and difficult. Finding...in the future, but we were finally refining the process down to a place I could be happy with it. Cycle...
  44. Evolution of Brainbow: Using Cre-lox for Multicolor Labeling of Neurons

    Type
    Blog Post
    Published
    April 24, 2015, 2:39 p.m.
    ...delicate axonal and dendritic processes not previously visible with Brainbow-1 and -2. The general structure ...Brainbow mouse neural labeling system. Brainbow-1 and -2 have been further refined to create Brainbow 3.2. ...M-CFP expression; these deletions are defined using 2 loxP variants (only identical loxP sites can mediate... each fluorophore. Third, Brainbow-1 and Brainbow-2 each contained a “default” state; for example, Brainbow...
  45. Selecting Your Plasmid Purification Kit

    Type
    Blog Post
    Published
    May 27, 2025, 1:15 p.m.
    ... environmental sustainability in mind (Table 2). Table 2: Sustainability features highlighted in plasmid...debris”; and then clean-up the plasmid DNA (Figure 2). For most kits, the steps for lysing cells and removing...together — no mixing and matching!   Figure 2: Plasmid isolation workflows are similar across kits...that can arise during the plasmid purification process. One is the possibility of damaging the plasmid...carrying over contaminants from the plasmid prep process into the final plasmid eluate. Possible contaminants...contaminants can sneak in from almost any step of the process and include things like genomic DNA, RNA, proteins...
  46. Deep Dive: qPCR

    Type
    Blog Post
    Published
    Sept. 29, 2022, 1:15 p.m.
    ...indicating primer dimers. (c) A double peak indicating 2 amplicons. Image credits (respectively): Zuzanna K...details for reproducibility’s sake!   Fig. 2: Setting up triplicates in multiple configurations...used method is the Standard Curve method. See Table 2, (adapted from Wong, 2018) for a comparison of different...Statistically defined log-linear phase   Table 2: A comparison of different qPCR analysis methods. ... for RNA quantitation. Biotechniques. 2000 Aug;29(2):332-7. doi: 10.2144/00292rv02. PMID: 10948434.Taylor...Getting your RQ value isn’t the end of your analysis process. You’ll still need to do statistical analysis to...Gene Expression Analysis During iPS Reprogramming Process. Sci Rep 8, 8716 (2018). https://doi.org/10.1038...
  47. Adeno Associated Virus (AAV) for Cell and Gene Therapy

    Type
    Blog Post
    Published
    Nov. 7, 2017, 1:59 p.m.
    ...AAVs in the clinic Thus far, AAV vectors AAV1, AAV-2, AAV1-AAV2 hybrids, AAV-6, AAV-7, AAV-8, AAV-9 and...neutralizing antibodies against some AAV types, AAV1, 2, 3 and 5 are thought to be as high as 70% among the... 10.24 (2003): 1999-2004. PubMed PMID: 14566358.  2. Hirsch, M. L., et al. "Self-complementary AAV mediates...vectors Learn about Addgene AAV Quality Control Process Resources on Addgene.org Find ready-to-use AAV...
  48. Evolution of Lab Techniques

    Type
    Blog Post
    Published
    June 21, 2016, 2:30 p.m.
    ... is the genetic test used for sickle cell anemia (2). Southern blotting, in conjunction with restriction...program) can then reproduce the DNA sequence (Figure 2). Accuracy and accessibility led to the widespread...biology98.3 (1975): 503-517. PubMed PMID: 1195397. 2. Chang, Judy C., and Yuet Wai Kan. "A sensitive new...recording DNA abundance throughout the amplification process, rather than just at the end as in standard PCR...became the workhorses of molecular biology." Proceedings of the National Academy of Sciences 102.17 (2005...restriction endonuclease of Hemophilus influenzae." Proceedings of the National Academy of Sciences 68.12 (1971...sequencing with chain-terminating inhibitors." Proceedings of the National Academy of Sciences 74.12 (1977...
  49. Twenty Years of Sharing: Expanding Accessibility

    Type
    Blog Post
    Published
    Nov. 21, 2024, 10:47 p.m.
    ...China, Korea, Japan, Brazil, India, and Mexico. Table 2: Addgene distributors Distributor Partnership...distribution after we partnered with them (Figure 2). In others, the distributor helped solve an issue...temperature for the duration of their journey. Figure 2: Annual distribution of items to countries with a ...import and export regulations, differing customs processes, and the distances the packages needed to travel...addgene.org. Currently, we’re evaluating our depositor process to identify and reduce barriers for scientists ...
  50. Tips for CRISPR Gene Editing in Mice

    Type
    Blog Post
    Published
    June 28, 2016, 10:59 a.m.
    ... than control, 3; same as control (Cetn1/sgRNA1), 2; darker than control, 1; very dark). Brighter fluorescence...you can hold off on genotyping until the pups are 2-4 weeks old and use the ear tag method (creating different...PMID: 24253446. PubMed Central PMCID: PMC3875854. 2. Mashiko, Daisuke, et al. "Generation of mutant mice...a post that goes into the mouse genome editing process in a bit more detail in the coming weeks, but, ...Target Mouse Genes To begin the in vitro screening process, you should first develop primers to the approximately...
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