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  1. RUBY-Red Siliques

    Type
    Blog Post
    ...markers for plant transformation fall into two main categories: antibiotic/herbicide resistance and fluorescent...culture), which is great for a wide variety of applications. But some techniques require you to select against...these mutant plants. Using RUBY to simplify the identification of these mutants will speed up my work and ...student studying plant development and cell-cell communication in the Nimchuk Lab in the Biology Department...

  2. Addgene's Top 10 Blog Posts of 2015

    Type
    Blog Post
    ...overjoyed to provide you with these fantastic educational resources and will be sure to keep our eyes open...used to generate inversions, deletions, and translocations. It also provides researchers with many different...repository use Cas9 to cut DNA, Addgene Science Communications Intern Mary Gearing explains how Cas9 homolog...make it easier to make gene edits at new genomic locations. 6. CRISPR 101: Non-homologous End Joining So ...

  3. Visualizing Genomic Loci with CRISPR-Sirius

    Type
    Blog Post
    ...The catalytically dead Cas9 protein (dCas9) is well known for its ability to bind DNA targets without...has been widely adapted for a wide variety of applications: base editing, CRISPR activation and inhibition... (B) CRISPR-Sirius used to visualize relative locations of the subtelomeric region of the pericentromeric...al. “CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.” Nature Methods 15 (2018)...

  4. Visualizing Translation at the Single Molecule Level

    Type
    Blog Post
    ... While ribosome profiling co-opts the physical location of the ribosome, TRICK (Translating RNA Imaging...development, the osk-TRICK reporter was double labeled, indicating translational repression. During later stages...ribosomes after initiation, to calculate a ribosome translocation rate of ~3.5 codons/second. They also explored...Resources the Addgene Blog Learn More about SunTag Catch up on Your GFP Background Choose the Brightest Fluorescent...

  5. Addgene Depositors Get More Citations

    Type
    Blog Post
    ...databases available, Web of Science. For each publication, Web of Science provides basic bibliographic ...Science, PLOS One, and PNAS. We then broke the publications from these journals into two groups: those containing...differences in citations due to the journal of publication. Table 1 provides an example calculation of the...Addgene in them. The adjustment is done within publication years. What do we find once we do this adjustment...

  6. Hot Plasmids - January 2023

    Type
    Blog Post
    ...antibodies may just not perform as well in one application as another, so it is always best to have options...for mEGFP-HRas (from Plasmid 18662). See the Applications section on the Anti-GFP [N86/8R] page for more...fluorescent proteins (FPs) necessary for many of these applications have lagged. Fixation, chemical staining, and...well-suited for the demands of advanced microscopy applications such as super resolution, electron, and expansion...

  7. DAP arrays for multiplex gene editing

    Type
    Blog Post
    ...packaged into viral vectors for potential in vivo applications or multiplex CRISPR screening.   Using tRNAs...multiplex genome engineering of crops or allow for sophisticated CRISPR screenings that would perturb the unprecedented...and efficient in plasmid and viral vectors. In applications when repetitive tRNA sequences must be avoided...construct DAP array for multiplex gene editing applications, we provide detailed manual and online design...

  8. 25 Work From Home Tips for Scientists

    Type
    Blog Post
    ...for all ages. Organize your data and prepare publications or your dissertation Organize data that you...these drafts and for a few model organisms, Micropublication will accept negative data or publish brief...brief, novel findings. Most Micropublications contain one figure. If you aren’t there yet, write introductions...introductions to potential publications or prepare a review article. These are both options that can be done...

  9. R Bodies: Membrane-Rupturing Microscopic Tools

    Type
    Blog Post
    ... modified to extend at different pH levels. Domesticating R bodies We have shown that all three of these...actuators that could be used in a variety of applications. For example, you could use them to lyse cells...matrices) in response to pH changes. Beyond these applications, purified R bodies could also perform as actuators...PubMed PMID: 26814170. Find Plasmids from This Publication at Addgene 4. Petroni, G., Spring, S., Schleifer...

  10. Management for Scientists: Delegating is Key

    Type
    Blog Post
    ...team manager must then facilitate appropriate communication between members of the team to ensure that no...of the overall project gets left undone or is duplicated. With each component of the project completed...clear outcomes in mind, you won’t be able to communicate these well to the task assignee and this is a...with most managerial responsibilities, good communication is at the heart of delegating for success.  ...

  11. How to Keep a Lab Notebook for Bioinformatic Analyses

    Type
    Blog Post
    ..., specific goal for each analysis will help you locate relevant information in the future. Approach:...folders and files that you see on your desktop. The location of your master directory or folder for all of ...simple .txt document. Record the name, date, and location of all analyses (see above). Give every experiment.... She is particularly interested in science communication and epigenetics. Follow her on twitter @kc_palozola...

  13. 15 Years of Addgene: The Top 15 Plasmids

    Type
    Blog Post
    ...taken us on many adventures...From moving office locations three times, to opening our UK office in 2014,...cell types so it is useful in a wide range of applications. This plasmid was the top requested plasmid ...notice the “V2.0” at the end of this plasmid which indicates that there was a prior version of this plasmid...plasmid was called pLKO-Tet-On in the original publication but its name was subsequently changed to clarify...

  14. Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity

    Type
    Blog Post
    ...to generate a genomic alteration at a specific location, it must be accessible by Cas9. Our previous blog...off-target activity, which may be undesirable in many applications. At the time of our first blog post on choosing...CRISPR-Cas9 to increase its specificity." Nature communications 9.1 (2018): 3048. PubMed PMID: 30082838. PubMed...CRISPR-Cas12b for human genome editing." Nature communications 10.1 (2019): 212. PubMed PMID: 30670702. PubMed...

  15. Clear and Accessible Writing

    Type
    Blog Post
    ...principles we developed to use in our website and educational content conflicted with plain language guidelines...Stupid, overwhelmed, discouraged, tired…words that indicated there were many barriers between our audience ...readers.    Figure 1: An image from AAV Purification by Iodixanol Gradient Ultracentrifugation ...Figure 1 appears on our protocol page for AAV Purification by Iodixanol Gradient Ultracentrifugation. The...

  16. Viral Vectors 101: The AAV Retrograde Serotype

    Type
    Blog Post
    ...Tracers are typically delivered to a particular location and they either trace downstream from the soma...Others have noted a lack of transduction in catecholamine pathways from the spinal cord (Wang, 2018, Metcalfe...not yet understood, one thing is clear: this application opens a lot of doors in neuroscience. The retrograde...retrograde serotype also has promising therapeutic applications; it can enhance therapeutic delivery across ...

  17. Hot Plasmids - May 2022

    Type
    Blog Post
    ...of interest and, for in vivo work, generate a dedicated transgenic line. Using zebrafish as a model organism...off-target mutations. These plasmids contain catalytically inactive dCas9 and microbial SSAPs (dCas9-SSAP...clonal multiplexing of cells in live imaging application. Each visual barcode consists of a fluorescent...transcription response element (TRE) or kinase translocation reporters (KTRs). Find visual barcode plasmids...

  18. GPCRs: How Do They Work and How Do We Study Them?

    Type
    Blog Post
    ...constructed plasmids that can be used in peroxidase-catalyzed proximity labeling to quantifiably measure GPCR...In this technique, the receptor fused to APEX2 catalyzes the biotinylation of proteins near the GPCR. These...Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell 169:338-349.e11 . https...Kadowaki S, Haga T, Takaesu H, Mitaku S (2002) Identification of G protein-coupled receptor genes from the...

  19. Synthesized by Ginkgo Bioworks, Shared by Addgene: SARS-CoV-2 Plasmids for Many Expression Systems

    Type
    Blog Post
    ...other proteins that require post-translational modification may not be easily expressed in non-mammalian...constructs contain protein coding genes, tags, truncations, and codon optimizations similar to those found...are intended for the high level expression and purification of SARS-CoV-2 proteins for downstream experiments...wild type and codon optimized, full length and truncated versions of SARS-CoV-2 S (spike protein) cloned...

  20. Developing a cold tolerant E. coli using specialized chaperones

    Type
    Blog Post
    ...psychrophilic enzymes for milk processing, fruit juice clarification, meat tendering, and oligosaccharide synthesis...cultivating a nuanced understanding of the societal ramifications of laboratory science, and how it may best be...which received the Silver Medal in the Undergrad category at the iGEM Competition 2019. He has an active... interest in scientific writing and science communication, and is a fledgling (though infrequent) blogger...

  21. REPLACR Mutagenesis: Replacing In Vitro Recombination Methods

    Type
    Blog Post
    ... the steps of gel purification and in vitro recombination. Across all modifications described in Trehan...mutations, large deletions/insertions require complicated, often costly in vitro assembly methods. A new...recombination machinery, which facilitates easy genetic modification by homologous recombination. In most recombineering...

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

    Type
    Blog Post
    ... localized fusion proteins and do not require dedicated plasmids or constructs. It should be noted that...reached at high power may not translate to real applications in which far less power is used. For example...insight into the photostability in the intended application (Goedhart et al, 2012). The third issue relates...Selecting a photostable protein The issues with quantification of photobleaching rates can be summarized as...

  23. Plasmids 101: CcdB - The Toxic Key to Efficient Cloning

    Type
    Blog Post
    ...time-consuming aspects of traditional cloning is the identification of clones that actually contain your insert...technology. CcdB: A potent toxin... The ccdB gene, located on the F sex factor plasmid of E. coli, is part...enzyme-mediated disruption of ccdB, leading to positive identification of desired clones.   ...Becomes a powerful...which can then be used for downstream cloning applications. While these two strains ultimately perform ...

  24. Plasmid Tools for Microbiome Studies

    Type
    Blog Post
    ...modular suite of plasmids (pGT) with various replicative origins that can be used for broad or narrow ...Central PMCID: PMC5963681.  Meyer, Richard. "Replication and conjugative mobilization of broad host-range...growth dynamics in the gut microbiota." Nature communications 6 (2015): 10039. PubMed PMID: 26615910. PubMed...gut microbiota and host biomarkers." Nature communications 9.1 (2018): 3347. PubMed PMID: 30131493. PubMed...

  25. The Future of Research Symposium Boston 2015

    Type
    Blog Post
    ...University of Massachusetts Medical School. Graduate education programs are also beginning to address these issues...The panel discussion on Friday morning will be dedicated to Academic data and the Labor Market. On this...Sinche is a STEM career counselor, Director of Education for the Jackson Laboratory for Genomic Medicine...disease.  Outside the lab, he is interested in communicating science and in the intersection between science...

  26. Design Tips for Prime Editing

    Type
    Blog Post
    ...BioRender.com. The pegRNA specifies both the genomic location to be edited and the sequence of the edit, so ...its design changes for every new prime editing application. And optimizing its sequence is important, as...left), while pegRNAs that use other bases in this location bind to Cas9 with canonical sgRNA structure (right...structured motifs like mpknot, use the pegRNA Linker Identification Tool (pegLIT) to create linkers that minimize...

  27. Fluorescent Proteins 101: Introduction to FRET

    Type
    Blog Post
    ...sufficient spectral overlap, the fluorophores must be located within 1-10nm of each other and be oriented appropriately...decision easier. 1. Müller, Sara M., et al. "Quantification of Förster resonance energy transfer by monitoring...have enhanced the ability of labs to answer sophisticated questions about cellular processes. Currently...PMC18018. 2. Miyawaki, Atsushi, et al. "Fluorescent indicators for Ca2+ based on green fluorescent proteins ...

  28. Overcoming the Challenges of Lentiviral Production

    Type
    Blog Post
    ...prevent the formation of replication competent lentivirus (RCL). Replication competence can arise from...end-users, size of the transgene, and downstream applications should all be considered when choosing the correct... as resources available, cost and downstream applications. For example, while the PEG precipitation method...

  29. Plasmids 101: Modular Cloning

    Type
    Blog Post
    ...most obvious example of an individual part, this category also includes promoters, UTRs, terminators, etc...multi-purpose it can be. Let’s review a list of MoClo applications. Genetic circuits Most things in biology are...performing production and subsequent necessary modification of these chemical products. The flexible nature...genotype and phenotype is best described with “it’s complicated.” Applying MoClo Interested in using MoClo? You...

  30. Getting Started with Behavioral Neuroscience: Standardizing Experiments and Using Viral Vectors

    Type
    Blog Post
    ...there are two main decisions to make: 1. Which modification? and 2. Which viral vector should be used? Modifying...excitation or inhibition upon light (or drug) application.  Genetic manipulation can also reduce expression...recombinase on transgenic flox animals to introduce modifications at the DNA level in a temporally and locally... brain area, avoiding side effects from such modification in other areas. An alternative strategy is to...

  31. Hot Plasmids - October 2020

    Type
    Blog Post
    ... labeling proteins with different subcellular locations. Image from Goudeau et al., 2020. Goudeau... show a high proportion of blue fluorescence, indicating cell proliferation. BaF3 cells maintained in ...in high IL-3 showed mostly blue fluorescence, indicating a quick cell cycle. Cells that had IL-3 withdrawn...Hybrid for Multiplexed Editing and screening Applications (CHyMErA) Knockout Libraries express hybrid ...

  32. CRISPR in the Clinic

    Type
    Blog Post
    ... therapeutic potential in mice with a dominant cataract disorder caused by a single copy of a gene known...known as Crygc (Wu et al). They found that the cataracts phenotype could be rescued by zygote co-injection...substantial relief from both disorders. As of publication, submissions to the UK, EU, and USA federal drug...10.1186/s12943-022-01559-z Zarghamian P, Klermund J, Cathomen T. Clinical genome editing to treat sickle cell...

  33. Split Fluorescent Proteins for Studying Protein-Protein Interactions

    Type
    Blog Post
    ...some new and popular split-FP plasmids from our catalog to help you find the right split-FP plasmid for...pairs with N173 derived from Cerulean or Venus Identification of new fluorescent protein fragments for bimolecular...fluorescent proteins for protein labeling and signal amplification. Zhou S, Feng S, Brown D, Huang B. PLoS One....Huang Yellow Venus pBiFC-VN173, pBiFC-VC155 Identification of new fluorescent protein fragments for bimolecular...

  34. Simple CRISPR-based Epigenetic Editing: dCas9-directed DNA Demethylation

    Type
    Blog Post
    ...approach (spoiler alert: it’s dCas9… with no modifications). Ready to get started?   Figure 1:... when DNMT1 methylates the genome during DNA replication, it doesn’t methylate sites blocked by dCas9....for dCas9 to interfere with DNMT1 even through replication. The dCas9 also needs to be removeable, otherwise...vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions. Nat Biotechnol 34, 1060–1065. ...

  35. A Look Back at One Year of Plasmid Sharing for COVID-19 Research

    Type
    Blog Post
    ...a method that uses loop-mediated isothermal amplification after reverse transcription (RT-LAMP) and a ...receptor for SARS-CoV. The lab also found that cathepsins play a role in SARS-CoV infection and deposited...deposited plasmids for the expression of cathepsin S, L, and B. This became a great starting point for SARS-CoV..., Zengel JR, Sathyan V, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH,  Begeman A, Stark JC, Shon DJ...

  36. CRISPR 101: Anti-CRISPR Proteins Switch Off CRISPR-Cas Systems

    Type
    Blog Post
    ..., 2018). For example, AcrIIA4 mentioned above indicates that it’s the fourth Acr protein discovered that...viral particles that have the gene deletion could replicate when challenged with the S. islandicus CRISPR-...B, Bondy-Denomy J (2020) Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies....light-inducible Cas9 activity? Check out these these plasmids Catch Up on Your CRISPR Background with Our Guide Pages...

  37. Addgene's Cancer Collection Pages Connect the Research Community

    Type
    Blog Post
    ... millions of people die from cancer-related complications each year. Despite these grim statistics, new...any of these genes through several different applications such as fluorescent protein fusion studies and...Lemieux is a Scientist at Addgene with interests in education and scientific writing.     References 1. Martz...Martz, Colin A., et al. "Systematic identification of signaling pathways with potential to confer anticancer...

  38. Mobile-CRISPRi: Bringing CRISPRi to Diverse Bacteria

    Type
    Blog Post
    ...The vast majority of bacteria are undomesticated which limits the tools scientists can use to study them...the genome and is propagated during normal DNA replication and cell division. Mobile-CRISPRi does not disrupt...single-gene knockdown experiments. Mobile-CRISPRi applications Mobile-CRISPRi expands CRISPRi to non-model ...Elizabeth A., and Pamela A. Silver. "Harnessing undomesticated life." Nature microbiology 4.2 (2019): 212....

  39. Golden Gate Assembly Upgrades: More Fragments, Faster Assembly, and Higher Fidelity

    Type
    Blog Post
    ...upon growth on LB/Cam/X-gal/IPTG agar plates, indicating successful reconstruction of the coding sequence... sequence-dependent ligation efficiency and identification of mismatch-prone pairings. Using these 4 bp...Kucera is a Principal Development Scientist of Applications & Product Development focusing on DNA cloning...Optimization of Golden Gate assembly through application of ligation sequence-dependent fidelity and bias...

  40. Plasmids 101: 5 factors to help you choose the right cloning method

    Type
    Blog Post
    ...methodologies, with a special emphasis on these five categories. Please note that many of the following cloning...relies on site-specific recombination reactions catalyzed by BP Clonase and LR Clonase enzyme mixes. After...there is no need for restriction digests, gel purifications, or ligations. The general Gateway cloning protocol...Chaokun, et al. "FastCloning: a highly simplified, purification-free, sequence-and ligation-independent PCR ...

  41. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    ...genome editing technology that allows precise modifications of DNA (replacements, small insertions, and ...configurations can be used to introduce specific target modifications. Since this means we could design hundreds to...affects prime editing outcomes across many genomic locations. In our study, we used the TRIP (Thousands of ...to chromatin data from over a thousand genomic locations. This allowed us to train ePRIDICT (Figure 3),...

  42. The Scientific Conference Poster Session: Tips for Success

    Type
    Blog Post
    ...but will also give you a chance to slow down and catch your breath before diving in to the next figure....don’t fully understand the question, ask for clarification. Having them reframe or elaborate their thought...system, and is interested in a career in science communication.       Resources on the Addgene blog Read other... other posts on scientific communication Find more tips for scientific networking Read this blog post ...

  43. No Llamas Required - Synthetic Nanobodies Against Membrane Proteins

    Type
    Blog Post
    ...Starting with libraries and a biotinylated (for purification purposes) protein target of interest, the protocol...-30) of sybody candidates are sequenced for identification. All unique sybodies can be subcloned into ...2020) Generation of synthetic nanobodies against delicate proteins. Nature Protocols 15:1707–1741. https...Light to Manipulate Cell Signaling and Protein Purification RANbodies: Reporter Nanobody Fusions Plasmids...

  44. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    ... sequencing are more definitive, but visual identification is a good place to start before taking on more...resources are limited or for bioart and teaching applications. Find a chromoprotein for your experiment! ...events: The plasmid carrying the desired genetic modification integrates into the genome (Figure 3). Here,...of Allelic-Exchange Vectors for the Scarless Modification of Proteobacterial Genomes. Applied and Environmental...

  45. Transgenic Organisms, Cas9 Gene Drives, and Appropriate Safeguards

    Type
    Blog Post
    ...strategies is strongly advised. The effects are multiplicative, and there are very few gene drive experiments...An accidental release could delay real-world applications against scourges such as malaria and dengue ...about gene drives can be found in the referenced publications. Thank you to our guest blogger! An inventor...2003). PubMed. Esvelt, K. M., Smidler, A. L., Catteruccia, F. & Church, G. M. Concerning RNA-guided gene...

  46. Better Dyeing Through Chemistry & Small Molecule Fluorophores

    Type
    Blog Post
    ...Subsequent advances in fluorescent proteins have replicated many of the properties once exclusive to small-molecules...phosphopantetheinyltransferase) – These enzymes catalyze the covalent attachment of a fluorophore ligand...labels for fixed-cell imaging, not for live-cell applications. Thus, these fluorophores are often bulky and...the Addgene Blog Learn About Other Protein Tags Catch Up on Your Fluorescent Protein Background Which ...

  47. INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons

    Type
    Blog Post
    ... and have been adapted for a wide variety of applications - as mutagenesis tools for genetic studies (... The process also creates a 5-bp target-site duplication (TSD), a hallmark characteristic of the Tn7-family...the new streamlined VchINT system was shown to catalyze insertion of mini-transposons up to 10 kb in size...at one or multiple desired genomic loci. Many applications of these systems have already been demonstrated...

  48. CRISPR 101: Making a Knock-In Cell Line

    Type
    Blog Post
    ...cut site location Position your CRISPR cut site as close as possible to the knock-in location. HDR depends...sequence to be incorporated at a precise genomic location, with little to no room for error. It’s no surprise...nutrients in their media, they will not undergo DNA replication, so make sure you are keeping an eye on those...

  49. Uncovering Ancestral Bias in CRISPR Research

    Type
    Blog Post
    ...Dependency Map cancer cell lines (left). Heatmap indicating the breakdown of ancestry associated dependencies...machinery where to cut.      Fig. 2: Heatmap indicating loci where SNPs reside on sgRNA target sequences...Understanding the impact Fig. 3: Histograms indicating the frequency (x-axis) which SNPs map to thetargeting...same reference genomes and libraries. Further complicating the issue is the long and ugly history of reporting...

  50. Getting to Know Expansion Microscopy

    Type
    Blog Post
    ...with an abundance of protocols and examples of applications from across disciplines now available. In this...experiment or evaluating ExM images in a new publication.         Why Expansion Microscopy?  Traditional...microscopes sounds great, right? But there is always a catch - some limitation of the technique that users should...Tissue expansion is not compatible with in vivo applications and there’s just not much to be done about that...
Showing: 601 - 650 of 1030 results