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We narrowed to 606 results for: abo.2

Showing: 241 - 280 of 606 results

  1. Deep Dive: qPCR

    Type
    Blog Post
    ...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... should have a melting temperature 5-10 degrees above the primer and be at least 25 bp away from each ...

  2. How to Negotiate a Successful Lab Start Up Budget

    Type
    Blog Post
    ...identifying the resources needed to accomplish that goal. 2. Identify the tools in that timeline Avoid writing...based on experimental timelines and specific aims. 2. Then make decisions based on financial values. All...Would I be able to get access to these materials?” 2. Always negotiate for a win-win decision An institute...a successful negotiation and collaboration. We’d love to hear more about your experiences and opinions...can get away with using computer modeling and collaborations rather than using animals, then that’s a cost...associated with old equipment, like service repairs, labour costs, and loss of time, can exceed the cost of...Everything is negotiable. Try asking for discounts, collaborations, access to internal award applications, etc...

  3. Antibodies 101: Introduction to Immunofluorescence

    Type
    Blog Post
    ...into the several steps outlined below and in Figure 2. For a deeper dive into the steps and techniques, ...mounting sample on slides, and confocal   Figure 2: High-level overview of an indirect immunofluorescence...recognize the species of your primary antibody and 2) is conjugated to a fluorophore that suits your experiment... Learn about research applications of antibodies in Introduction to Antibodies Learn more about fluorescence...Stay tuned for a future blog post to learn more about these techniques!  Direct vs. indirect immunofluorescence...different approaches to be familiar with when talking about IF, direct and indirect. For direct IF, researchers...immunofluorescence procedure with key considerations about each step. Image created with BioRender.com   The first...

  4. Filming Science Videos in the Age of Social Distancing

    Type
    Blog Post
    ... 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... Production Specialist, I’m constantly thinking about ways to improve our productions to deliver the best...four months after I started with Addgene, I was about to have a check-in with my boss Jennifer. I had ... would be a couple months. Jennifer and I spent about an hour that morning scrambling. Everything we had...someone to be comfortable on camera while thinking about things like lighting, camera angle, and shot composition... allowing people to sit without having to worry about getting in close to mic them up. Monitor: I then...

  5. Plasmids 101: Plasmid Incompatibility

    Type
    Blog Post
    ...to plasmid loss (Diaz et al., 2015).  Figure 2: The partitioning problem. For low copy plasmids...of plasmid into a separate daughter cells (Figure 2) (Ebersbach et al., 2005). However, more recent studies...Plasmids. Microbiology and Molecular Biology Reviews 62(2): 434–464. Pubmed PMID: 9618448 Diaz R, Rech J, Bouet...101 blog posts Learn more about the origin of replication Find blog posts about plasmid cloning Resources... plasmids within the same bacterial cell, think about whether plasmid incompatibility will affect your...this is expanding as we obtain more genomic data about plasmids (Shintani et al., 2015). Now, bioinformatics...of the microbiological world. (Want to know more about these plasmid types? Read our Plasmids 101: Environmental...

  6. Twenty Years of Sharing: Expanding Accessibility

    Type
    Blog Post
    ...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 ...a less tangible form: knowledge and information about the materials in our repository. We started to increase...by making it easier to find materials and learn about them. As early as 2007, we began grouping similar...professors, stopping by to say, “Everything I know about virus, I learned from Addgene,” or “I learned to...seeing our resources shared via social media, on collaborators’ websites, or as a recommendation in a Reddit...

  7. Selecting Your Plasmid Purification Kit

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    Blog Post
    ... 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...columns we’ve been talking about!) are a significant source of waste in laboratories. To help combat this, ...dependent on many different factors as we detailed above, so be sure to pick what kit works best for you!...

  8. The PAM Requirement and Expanding CRISPR Beyond SpCas9

    Type
    Blog Post
    ...is unique compared to the rest of the genome and (2) the sequence is located just upstream of a Protospacer...pyogenes Cas9 variants with varying PAM sequences, 2) the use of Cas9 homologs derived from species other...Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell 163:759–771 . https://doi....Resources on the Addgene Blog  Read more about Cpf1 Read more about SaCas9 and AAV Check out our CRISPR Featured... and VRER) recognize novel PAM sequences (shown above). The VQR, EQR, and VRER Cas9 variants are capable...example, Cas9 from Staphylococcus aureus (SaCas9) is about 1 kilobase smaller than SpCas9, so it can be packaged...

  9. Antibodies 101: Reading a Flow Plot

    Type
    Blog Post
    ...A-B+ cells. If you look at the dot plot in Figure 2, you might assume that all cell populations are positive... the different populations. In the case of Figure 2, one population is B- and another two are B+. Our ...are in the lower right corner.      Figure 2: This flow plot has two populations that are B+ and...series of one- or two-marker plots, like in Figure 3 above, until the population of interest has been successfully...  Of course, there are many more things to learn about when diving into flow cytometry data. There’s different... ways to use FSC and SSC, as briefly alluded to above. There’s many variations in how one can gate, select...

  10. Hot Plasmids: Fall 2024

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    Blog Post
    ...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...more feasible, the lab of Alessio Ciulli and collaborators developed CRBNmidi (Kroupova et al., 2024). ...stepwise, achieving mutation efficiencies of up to about 9% of colonies (102 to 104 times higher than traditional...Bentley Time to get flexible! Alex Dunn’s lab and collaborators have deposited a new mechanosensor called PILATeS...

  11. Scientific Peer-review: Providing Critical and Kind Feedback and Advocating for Open Science

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    Blog Post
    ... go back and finish the review.  Peer-review step 2: Detailed assessment After this initial assessment...salt-induced changes in root-to-shoot ratio in Arabidopsis, (2) expression patterns in plants with enhanced sodium...section-specific comments, I re-read what I wrote about the paper after my initial read, adjust my language...wish for The last thing that I wanted to mention about the peer-review, is that as a peer-reviewer, you...each peer-review, I try to mention what I liked about this paper and recognize the hard work that the .../visualization using R/Shiny. She is passionate about open science, BIG data analysis and sharing whatever...review article Resources on Addgene.org Learn about depositing plasmids pre-publication Find molecular...

  12. Early Career Researcher Toolbox: Free Tools for Science Writing

    Type
    Blog Post
    ...episode 2 "Organizing Literature" : I found out about Zotero here Dear Grad Student podcast episode 2 "Essential...frequency of use in black. This paper talks more about the development of the De-jargonizer.   Academic...with others which makes it easier to work with collaborators. Zotero is a desktop based program that’s compatible...Programming, & Productivity": This podcast talks about Mendeley, Zotero, and other citation managers and...the pomodoro technique": This podcast talks more about using the Pomodoro method in grad school Additional...

  13. Tips for CRISPR Gene Editing in Mice

    Type
    Blog Post
    ... 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...the pX330 plasmids used in the validation assay (above) and it is just as effective (Mashiko et al., 2014...Engineering with CRISPR Validate Your Genome Edit Learn about Non Homologous End Joining and Homology Directed...

  14. Even more elegant: Single injection CRISPR/Cas9 in C. elegans

    Type
    Blog Post
    ... one injection step! The entire protocol takes about 2-3 weeks but requires less than eight hours worth...for C. elegans genome modification. Figure 2: Schematic from Dickinson et al. (2015) illustrating... this species, namely, the robust HDR mentioned above, an accessible germline, and multiple selectable...modular system that requires very little hands-on labor and could facilitate the tagging of every protein...

  15. Hot Plasmids - September 2019 - CRISPR, Auxin Inducible Degradation, MerMAID Channelrhodopsins, and Genome Looping

    Type
    Blog Post
    ...target sites for editing. PAM sequences can be from 2-6 base pairs in length and follow the DNA sequence... Eric Perkins Mammalian genomic DNA is not just a 2-D linear molecule snaking through our cells’ nuclei... plasmids you need. If you'd ever like to write about a recent plasmid deposit please sign up here.    ...neurons. Earlier this year, the Hegemann lab and collaborators report their discovery of a new family of seven...

  16. New and Upcoming Viral Vectors - June 2019

    Type
    Blog Post
    ...  AAV9, AAVrg pAAV-hSyn-DIO-mCherry 37825 AAV1, 2, 5, 8, 9 (20 µL size serotype testing) pAAV-CAG-GFP...size serotype testing) pAAV-CAG-GFP 50465 AAV1, 2, 5, rg (20 µL size serotype testing) pAAV-hSyn-EGFP...vector name and serotype you’d like to be notified about. Controls Plasmid Serotype Name 37825  AAVrg...vectors 101 eBook Resources on Addgene.org Learn about Addgene's viral service Find viral protocols and...

  17. Plasmids 101: Broad Host Range Plasmids

    Type
    Blog Post
    ...host range plasmids. FEMS Microbiology Letters, 348(2), 87–96. https://doi.org/10.1111/1574-6968.12241  ...mobilization of broad host-range IncQ plasmids. Plasmid, 62(2), 57–70. https://doi.org/10.1016/j.plasmid.2009.05.001...negative hosts. Biotechnology and Bioengineering, 106(2), 326–332. https://doi.org/10.1002/bit.22695  Schmidhauser...plasmids may have high copy numbers and reduced metabolic load (Meyer 2009). Figure 1: Idealized ...

  18. New Acoustic Reporter Genes: Ultrasound Imaging of Gene Expression

    Type
    Blog Post
    ...under phase contrast starting day 2 after transfection.     Fig: 2: Expressing mARGAna in MDA-MB-231...engineering a cell line, cotransfect the mARG cassettes 2:1 (A:N-V) with PiggyBac transposase and outgrow the...you enjoy playing with our genes. Have fun!    About the authors: Marjorie Buss is a PhD student studying...

  19. Visualizing Translation at the Single Molecule Level

    Type
    Blog Post
    ...the reporter mRNA is labeled by PCP-mCherry (Figure 2). The 3’ UTR also contains a CAAX sequence to bind...PMC2746483 Find ribosome profiling plasmids at Addgene. 2. Halstead, James M., et al. “Translation. An RNA biosensor...Additional Resources the Addgene Blog Learn More about SunTag Catch up on Your GFP Background Choose the...

  20. Synthetic Photobiology: Optogenetics for E. coli

    Type
    Blog Post
    ...in Escherichia coli. Tabor JJ, Levskaya A, Voigt CA. J Mol Biol. 2011 Jan 14;405(2):315-24. doi: 10.1016...Marcotte EM, Voigt CA. Nature. 2005 Nov 24;438(7067):441-2. PubMed. Find the plasmids from this publication ...and Jeffrey Tabor have been working on making E. coli light responsive since 2005, when Tabor was working...these classic systems continue to be optimized by Tabor’s lab, making light-controlled gene expression in...for the computational problem of edge detection. Tabor et al. subsequently engineered a second photosensitive... and highest level of “output” signal, was only about 10-fold, precluding the study of gene expression...-component systems. Schmidl SR, Sheth RU, Wu A, Tabor JJ. ACS Synth Biol. 2014 Nov 21;3(11):820-31. doi...

  21. Four Factors that Differentiate the Stem Cell Field

    Type
    Blog Post
    ...Stem Cell Researcher Darrell Kotton 2. Stem cell scientists care about patients As any grad student who ... Yamanaka explained that it took 50 people nearly 2 years to create the first stem cell line that could...the Addgene Blog Learn about Efforts to Fight Rare disease with iPSCs Read About Addgene's Outreach Efforts...the first clinical trial with iPSCs with his collaborator Takahashi in 2014 – just 8 years after the OSKM...researchers special: 1. Stem cell scientists care deeply about ethics Ethics must play a prominent role in the ... a big picture perspective: Dr. Yamanaka talked about his clinical trial patients with advanced macular...proof that these researchers are thriving in a collaborative, rather than a combative, field. Of course they...

  22. Will You Be My Mentor? Finding and Asking for Mentoring Support

    Type
    Blog Post
    ...article in the Addgene Blog Mentoring series will cover 2 of the 7 mentoring questions I set out to answer. ...101-Building Relationships for Success”. Choose 1-2 tactics to try. One of my favorites is making the ...work if both parties are diligent about replying and thinking about good questions and answers. Professional...Sometimes, it is not who you know but who knows about you. I found some other great tips for finding mentors...Medical School researcher Connie Cepko to learn about her mentoring style. Mentors at home and away We...Catalyst Report “Making Mentoring Work” to learn about what makes a good mentoring program. If your organization...much less threatening! If they say no, don’t worry about it. It is a compliment to ask someone to share their...

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

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    Blog Post
    ...panning and scFv characterization.    Figure 2: Phage display starts with a pooled library of scFvs...the short epitope GCN4, also called a scaffold; and 2) a GCN4 binding scFv that’s fused to GFP. When the...Fv (Variable Domain) (scFv) Fragments. Antibodies 2:193–208 . https://doi.org/10.3390/antib2020193  Khantasup... Read about frankenbodies, an anti-HA scFv-based probe for fluorescent imaging. Learn more about antibodies...Köhler who developed hybridoma technology. But what about single chain fragment variables (scFvs)? scFvs weren...from inclusion bodies, it’s time-consuming and laborious.  To avoid this, one or more of these approaches...antibodies  Read about another reagent sharing platform for antibodies, the Developmental Studies Hybridoma...

  24. Plasmids 101: Common Lab E. coli Strains

    Type
    Blog Post
    ...Table 2: Lab strains of E. coli Strain Natural resistance Primary Use Genotype ccdB Survival 2 T1R ...resistance to tetracycline Additionally, Table 2 provides a quick reference for some of the popular...thiamine metabolism Requires exogenous thiamine for growth ara disruption of arabinose metabolism pathway...little prokaryotic minions that carried out the labor-intensive process of replicating your new plasmid... Phage resistance gal Mutation in galactose metabolism pathway Cells cannot grow on galactose only ...repressed more   LacZ β-galactosidase activity abolished   lacY Lactose permease inactivated, lactose...plasmid stability recBCD Exonuclease V activity abolished Increased plasmid stability, reduced recombination...

  25. Cancer, Inflammation and Immunity - Harnessing the Body’s Defenses to Fight Cancer

    Type
    Blog Post
    ...represent a favorable state for tumor progression (Ref 2). Future treatments may need to target this immunosuppressive...cell 30.1 (2016): 147-160. PubMed PMID: 27411589. 2. Todoric, Jelena, Laura Antonucci, and Michael Karin...Cancer, Inflammation and Immunity and learn more about “... recent findings in basic immunology, cancer-immune...curing cancer in cross-disciplinary projects and collaborations. Summarized by Professor Michael Karin from...This was followed by a talk from Professor Karin about alcohol and obesity as driving factors for chronic...got a chance to talk with Dr. Friedmann-Morvinski about tools used to analyse the tumor microenvironment...community, contact [email protected] to find out more about our free deposit and distribution service! References...

  26. 5 Great Apps for Lab Life

    Type
    Blog Post
    ... there is no worry about misplacing your results or losing that lab notebook from 2 years ago. The free...notebooks you’re saving trees! The Earth thanks you. 2. Gibco Cell Culture by Gibco Whenever I start to learn...enzyme, or name to discover all the information about that restriction enzyme or share it via email with... this app. However, if you get quizzed randomly about a hazardous chemical and can’t find your lab’s MSDS... new researchers or students beginning to learn about biochemistry. The least this app will do is allow...

  27. Antibodies 101: Introduction to Gating in Flow Cytometry

    Type
    Blog Post
    ... intensity of the cell’s illumination (see Figure 2). H describes the maximum signal strength, while W...SSC-A, so most people use that setting. Figure 2: As the cell passes through the laser beam and causes...scale in proportion (while H and W do not; see Figure 2), single cell events will show up in a straight line...lymphocytes in a mouse tumor sample You made it! So much about the theoretical background. Let’s dive into the ...often choose a looser gate here. I am not worried about including irrelevant events in my analysis, as these...population, acquired from the previous gating pipeline, about 53% of my cells are dendritic cells and ~13% are...ve covered in this blog post. First, you learned about the types of scattering that occur when a cell is...

  28. CRISPR 101: Off-Target Effects

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    Blog Post
    ...sites would confound your experimental results and 2) perform targeted off-target measurements at those...experiments where only localization of the Cas occurs. 2 gRNA approach Off-targets that come from mutations...perform downstream characterization of, isolating 2 or 3 distinct clones to perform key experiments on...is an off-target effect. Should I be concerned about off-target effects? Depending on your experimental...this could be a huge concern, or nothing to worry about all. Let’s consider several scenarios below for ...Predicting off-target events As mentioned in the above section, there are gRNA softwares available which...diligence to ensure they are indeed a non-issue. Above we mentioned how to predict off-target frequency...

  29. Targeted Mutagenesis with EvolvR

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    Blog Post
    ...while increasing the standard mutation rate by only ~2-fold over nCas9 levels. Two sets of modifications ...10-3 mutations per nucleotide per generation, and (2) the addition of the thioredoxin-binding domain (TBD...blog Learn about other CRISPR methods for bacterial genome engineering   Learn more about lambda red ... genetic variants in bacteria. Read on to learn about the key components of EvolvR and its potential applications...

  30. Evolution of Lab Techniques

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    Blog Post
    ... 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...abundant in a sample. Whereas Southern blotting is labor intensive and requires a large amount of high-quality...DNA technologies that are now commonplace in laboratories. As scientific technologies rapidly progress...PMC4411503. Resources on the Addgene Blog Learn More about Restriction Cloning Get Tips on Analyzing DNA Sequencing...

  31. Visualizing Genomic Loci with CRISPR-Sirius

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    Blog Post
    ...that the signal to noise ratio can be increased from 2-fold (by CRISPRainbow) to 3-fold with CRISPR-Sirius...CNV) analysis of the U2OS cells.   Figure 2: CRISPR-Sirius tricolor labeling. (A) Diagram of sgRNA-Sirius...the Addgene blog Download our CRISPR eBook Learn about fluorescent protein-based tools Read all CRISPR ...

  33. Hot Plasmids - January 2023

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    Blog Post
    ...is always best to have options.      Fig. 2: Addgene’s western blot for mEGFP-HRas (from Plasmid...the presence of oxidizing agents. Adapted from Fig. 2 Campbell et al, Nature Methods   Find YFP plasmids... minutes of FUS.  Similar constructs to the one above can be made for expressing your favorite T-cell ...

  34. Form Your Own Peer Mentoring Group: A How-To Guide for Scientists

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    Blog Post
    ...The groups in these programs typically consist of 1-2 mentors and 3-5 mentees who meet together for an 8... together. If you all work at the same place, a 1-2 hour lunch on a regular schedule might work. If not...for Scientists Series. I have been thinking a lot about Mentoring for over 10 years. Many successful scientists...Medical School researcher Connie Cepko to learn about her mentoring style. While working on this project...postdocs I have started to talk to trainees more about peer mentoring. They want to find mentors to help... questions I get is, “What are we going to talk about?” There are an infinite number of ideas on the internet...from a lab, career or industry of interest – learn about their career paths and get their advice. Attend ...

  35. Expanding the Targeting Scope and Editing Efficiency of Adenine Base Editors

    Type
    Blog Post
    ... systems to engineer better and faster ABEs (Fig. 2). These systems allow for rapid continuous protein...and less stringent phage selection. Figure 2: Phage-assisted evolution of base-editing activity...posts on base editing Read more about CRISPR Learn all the basics about CRISPR in our CRISPR 101 blog series...both changes simultaneously with 54% efficiency, about 7 times higher than ABE7.10. However, the increased...change C to T, G to A, A to G, and T to C, represent about two-thirds of known pathogenic point mutations. ...

  36. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

    Type
    Blog Post
    ...VP64 fusion; 2. A sgRNA incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2; 3. The MS2...that screen with a system you are really confident about working for most genes and individual targeting ... system, Konermann explained, was new knowledge about Cas9’s crystal structure. “I thought maybe we could...RNA we use. What we have to do now is learn more about the rules.” He said that there is no theoretical...References & Further Reading: For more information about SAM, including a tool for getting optimized guide...

  37. Advice for Starting a Biotech Company from a Grad Student turned Entrepreneur

    Type
    Blog Post
    ...go anywhere. The team should initially consist of 2-3 individuals that are aligned in vision and outcomes... the technology. This transition takes around 1 – 2 years. The product is the measure of success. Technology...transitioned away from the bench and became all about finding the best product-market fit for this set...Notably, the team must have an upfront conversation about its goals and vision for the company; this will ...section! And read on for more great information about starting a biotech company. Suggested reading The...of Sample6) for taking the time to speak with us about the biotech startup process and work environment...

  38. Troubleshooting and Optimizing a Western Blot

    Type
    Blog Post
    ... that all look exactly alike.      Figure 2: Reagent gradient. Here, the lanes are lightly marked...guide. The gel is then removed from the membrane (2) and the membrane is cut so each lane is its own piece...in the bands, you may want to consult Tables 1 and 2 in our Technical Design of a Western Blot post to ...the antibody’s dynamic range. Specifically, the 1:2, 1:1, and No dilution samples all have approximately...conditions are 4 °C overnight or room temperature for 1–2 hours, there is some evidence that antibodies may ...re in the right place! In this post, we’ll talk about western blot optimization and troubleshooting.   ...can be informative, so spend some time thinking about which type of gradient can help answer your particular...

  39. 7 Tips to Secure a STEAM Internship This Summer

    Type
    Blog Post
    ...and scholarships in different subject areas!    2. Resume and cover letter know-how  Tailor your resume...4. Letters of recommendation wisdom  Reach out to 2-3 individuals in your professional circle to vouch...Rose is passionate about outreach among low-income communities to educate parents about resources that can...automated filters of consideration. If you are worried about any eligibility provision, don’t guess. Simply reach...

  40. Stabilized Bacterial Promoters: Constant Gene Expression at any Copy Number

    Type
    Blog Post
    ...per cell increases 4-5 fold (for pUC plasmids) or ~2 fold (for p15a, R6K, and ColE2 plasmids) as cell division...biotechnology 36.4 (2018): 352. PubMed PMID: 29553576. 2. Kittleson, Joshua T., Sherine Cheung, and JChristopher...is useful for many metabolic engineering and synthetic biology goals. In metabolic engineering, the expression...or can interfere with the precision needed in metabolic engineering or other synthetic biology circuits...
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