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  1. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    ...recombinase polymerase amplification (RPA) using a commercially available amplification kit. In this case,... RNA is extracted and subject to isothermal amplification by primers that target the E and the N2 gene...reverse transcriptase to produce cDNA. Isothermal amplification is done at one constant temperature, eliminating...rapid detection.  Highlights: Cas13a is not catalytically active in the presence of two or more mismatches...that exhibit fluorescence upon cleavage. Upon amplification by the RPA primers, the Cas12a-crRNA binds to... SARS-CoV-2 detection, AIOD-CRISPR without preamplification was able to detect as low as 1.2 copies DNA..., field-deployable nucleobase detection and identification using FnCas9 (FELUDA) Sensitivity: – 110 femtomolar...

  2. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    ...ligation using SpyLigase Building off their SpyTag/SpyCatcher system for protein-peptide locking, Mark Howarth... a critical role in development and are often implicated in disease progression. One of the major challenges...challenges in signaling research is the inability to replicate the spatio-temporal precision with which signaling... of complex biological systems requires both a catalog of molecular players and contextualized knowledge...the most abundant forms of post-translational modifications in cells and research into its many roles in...Alex Schier's lab, designed for expression and purification of Cas9 protein in Rosetta E. coli. New Lentiviral...FokI-dCas9 expresses Fok1 nuclease domain fused to catalytically inactive Cas9 DNA-binding domain in mammalian...

  3. Targeted Mutagenesis with EvolvR

    Type
    Blog Post
    ...potential applications. Challenges of existing mutagenesis methods Several continuous diversification methods... challenging for users to achieve targeted diversification of all nucleotides within a defined region ...Chang Lab have created methods that introduce diversification by targeting a site of interest with dCas9 ...level of variation that can be introduced.   Diversification is limited due to the integration of oligonucleotide...increasing the standard mutation rate seen during DNA replication by 120-fold over background. Due to its modular...only ~2-fold over nCas9 levels. Two sets of modifications were also made to PolI3M to increase the mutation...more than one mutation near the target site. Applications of EvolvR The Dueber Lab used EvolvR to discover...

  4. How to Design Your gRNA for CRISPR Genome Editing

    Type
    Blog Post
    ...the optimal location. It is also important to have good information on the exact location of the TSS. ...appreciable levels of modification. Whole-genome sequencing of cells modified by CRISPR indicates that the consequences...specific base edit, or modulation of gene expression. Location and sequence are important considerations for ... gRNAs. For indels, it's not so important what location in the gene you target, but it is important that...fewer sequences to choose from). Finally, for HDR, location is much more important because you have to target...target site is far more constrained by the desired location of edit; efficiency decreases dramatically when...alternative to HDR for introducing edits. The same locational constraints are even more exquisite for the so-called...

  5. A Look at Addgene's QC Process

    Type
    Blog Post
    ... utilize an array of tools that rely on DNA amplification and manipulation to produce and edit plasmids...Potential points where DNA errors can be introduced, indicated by exclamation marks. Error points include places...places where DNA is being created, such as PCR amplification or bacterial growth. Created with BioRender....through the QC pipeline to resolve any issues.  Catching and addressing QC issues Addgene’s QC team has...has developed a process for identifying, categorizing, and resolving a variety of QC issues. This process...discrepancies can be caught prior to distribution. Catching these errors prevents future experimental issues...during analysis. These include topics such as: locations in a plasmid that are less likely to affect function...

  6. Rabies and Neuronal Tracing

    Type
    Blog Post
    ...able to replicate, and for a virus to cross a synapse from one cell to another, it must replicate. Modified...like how our stem cells are housed in specific locations and give rise to progenitors during growth and...infects one cell (the “starter cell”). It then replicates within that cell, and nascent RABV cross synapses...infection occurs, subsequent cycles of viral replication and retrograde transmission occur, spreading ...limitations. First, these high levels of viral replication are toxic. Second, infecting subsequently higher...spread monosynaptically from these cells. These modifications take advantage of the fact that RABV is an enveloped...G-deleted RABV will infect the starter cell. RABV replication will then occur and the G protein (supplied in...

  7. Quickest Way to Deposit Plasmids: The Deposit Spreadsheet

    Type
    Blog Post
    ...species can be indicated in the “Species Other” column. Relevant Mutations Indicate the amino acid...usually very easy — our tech transfer team will communicate with your organization’s technology transfer ...name and match the name as it appears in its publication or as it is commonly known in your lab. Plasmid...descriptive purpose focuses on the practical application of the plasmid and will help a scientist outside...reagent/antibody, unspecified, or other. If other, indicate type in “Vector Type Other” column. For example...or room temperature. Growth Strain Please indicate which growth strain Addgene should propagate your...For plasmids that contain the R6Kγ origin of replication, choose the Pir1 strain. If your plasmid cannot...

  8. Antibodies 101: Choosing the Right Isotype

    Type
    Blog Post
    ...your experiment (all well validated for your application, of course!) When the stars are aligned and the...factors that affect isotype choice. Target and application should be considered The first question you may... a strong signal and to work in a variety of applications. The desired specificity of your secondary antibody...affect my experiment?” Well, it depends on the application and target. If you are running a basic western...target is expressed at very low levels or your application requires a high degree of affinity, then species...considered when choosing an antibody. In some applications probing species-on-species, i.e. using a mouse...mouse IgG2a and rat IgG1 antibodies in the same application, using a Goat anti-mouse IgG2a cross-adsorbed...

  9. 7 Simple Strategies to Resolve Conflicts with Difficult Supervisors

    Type
    Blog Post
    ... series.  “The only healthy communication style is assertive communication.” - Jim Rohn, Author, Entrepreneur...I heard about supervisors in all of the above categories. In addition, I also learned about two other ...Assertiveness? An assertive person is able to communicate their ideas confidently while also considering...of the most frequent sources of conflict is miscommunication. For example, you might misunderstand your...the wrong direction. The best way to avoid miscommunication is to follow up after every meeting with an...workplace, these strategies will help you to communicate with confidence earn respect from your supervisor...in an email, there is a high likelihood of miscommunication, which can lead to even more conflicts. If...

  10. Plasmids 101: Optimizing Plasmid Yields

    Type
    Blog Post
    ...are, you’ll even have DNA left over for other applications, like PCR, cloning, transfection, or long-term...wash step or use a different strain. For most applications, Addgene uses and recommends DH5𝝰! This strain...cloning Bacterial strains adapted for protein purification use the cell’s resources to produce high levels...retransforming the plasmid into a strain meant for DNA purification. It sounds like extra work, but it will likely...your E. coli to ensure it is suitable for your application. We have previously reviewed many common lab ...partially specified by a plasmid’s origin of replication, but can also be affected by the plasmid size...the material used for inoculation. To further complicate matters, plasmid copy numbers are often ambiguous...

  11. 9 tips for a successful postdoctoral experience

    Type
    Blog Post
    ...need? Multiple first or corresponding author publications (published, not in preparation) A history of...The other items will follow. If you get more publications, you will be more competitive for fellowships...to write as well as mentor. Yet, even the most dedicated mentor is not always available for mentees due... project. Furthermore, Group Leader position applications require 3 letters of reference- the graduate...interests, complementary perspectives, a shared communication style. You “get” each other. The other factor...makes time for you, as needed, this is a strong indicator that this person cares about your science and ...spurious yet intriguing findings that fail to replicate. Plan experiments logically and strategically ...

  12. Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User)

    Type
    Blog Post
    ...and GFP-edited amplification products (BRAF-GFP duplex) and from GFP-edited amplification products (GFP-GFP... wanted to inactivate the gene BRAF (a kinase implicated in several human cancers) in A549 cells (a human...transduced with Cas9 expressing lentivirus at the indicated multiplicity of infection (MOI). Anti-vinculin...need to use FACS (like they did in the original publication). I thought I could see GFP expression with a...expression, but I didn’t. 2. In the original publication they see GFP expression in about 20% of their...an MOI of 0.3, as recommended by the original publication. Pro-Tip: 1. Use multiple gRNAs to target different...the 428 bp Surveyor nuclease cleavage product indicates a gene edit. GFP gRNA-transduced Cas9-A549 cells...

  13. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

    Type
    Blog Post
    ...and Jinfang Zhu. "Immunologic applications of conditional gene modification technology in the mouse." Current...contributed by Alessia Armezzani, scientific communication manager at genOway. A few decades ago, the brain...École Normale Supérieure de Lyon. Her love for educational science led her to pursue a teaching career, ..., and she now is a very happy scientific communication manager at genOway.     Acknowledgement:Through...Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein...): 7025-7030. PubMed PMID: 18614669. Belzung, Catherine, Marc Turiault, and Guy Griebel. "Optogenetics...Yizhar, and Karl Deisseroth. "The development and application of optogenetics." Annual review of neuroscience...

  14. Antibodies 101: Validation

    Type
    Blog Post
    ...intended application - Remember, just because your antibody performs as expected in one application does ...strategies for antibody validation in different applications. Here, I want to highlight the general suggestions...intentionally generalizable and not specific to certain applications or antibody targets. That said, not every strategy...will be suitable for every antibody or every application. The goal is to show that your antibody has been...strategy to use will depend on your intended application and available resources.     Figure 1...confident in your data. This is a good option for applications like immunohistochemistry on human tissues, ... for validating antibodies for immunocapture applications and is amenable to high-throughput analyses,...

  15. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    ...light has limited applications in vivo. UV and blue light is readily absorbed and scattered by the skin, so...strategies Publication System nickname Photoactivatable moiety Cas9 variatn CRISPR protein application Split...improvements to CRISPR technology since its initial applications for genome engineering in 2012.  Many of these...scientists to use light to externally control the location, timing, and reversibility of the genome editing...enzymatic activity. Photoactivatable genome modifications by NHEJ and HDR using split systems Later in...mutations via NHEJ (frequency of 20.5%) and induced modifications by HDR (frequency of 7.2%). The authors additionally...light (730 nm). This nucleotide triggers the translocation of the protein BldD to the nucleus. To couple...

  16. Tag Your Favorite Yeast Genes with Ease

    Type
    Blog Post
    ...insert will typically contain both a protein modification sequence and a selectable gene product for isolation...tags have been integrated. Simply design your amplification primers with the desired targeting homology—.... cerevisiae, looking at their performance in categories such as brightness, stability, and disruption...optimal FP combinations for use in yeast imaging, categorized by specific filter sets and experimental output...This collection is ideal for tandem affinity purification of protein complexes. John Pringle and Jürg ...deposited a large collection of plasmids for genome modification in yeast developed by Dr. Pringle’s former lab...collection of plasmids for a wide variety of genome modifications in S. Pombe, including full and partial gene...

  17. Course-Based Undergraduate Research Experiences (CUREs)

    Type
    Blog Post
    ... put it best when he stated, “the value of an education . . . is not the learning of many facts but the...possible to bring the kinds of transformative educational experiences afforded to those fortunate enough...which can lead to greater success in meeting educational goals (Kowalski et al., 2016; Scott, 2021). In...CUREs are beginning to transform undergraduate education in the sciences by making a greater number of ...scientific research more inclusive. CBE Life Sciences Education. 13(4):602-606. Brian, D. 1996, Einstein: A Life...positive STEM attitudes in CUREs. CBE Life Sciences Education. 21(4):ar74. Duboue, E., Kowalko, J., Keene, A...biochemistry laboratory: Part I – guided inquiry – purification and characterization of a fusion protein: Histidine...

  18. Negative Can Be Positive: Open AAV Data with Addgene

    Type
    Blog Post
    ...caudal NST. (A-C) Low-magnification images showing viral spread. (D-F)  High-magnification images immuno-stained... right AAV for your system or to successfully replicate published works. Of particular importance to these...improve our Addgene Data Hub, 76% of respondents indicated they wanted to see more negative data (Figure ...minimum n = 2, and well labeled high- and low-magnification images demonstrating vector performance) will...performance. Yet, most of the technical data needed to replicate and build on others’ results is available not ...information provided in openly accessible forms like publications. Why not get this data out there?  The Addgene...Sommer, J. M., Pierce, G. F., & Qu, G. (2005). Identification of factors that contribute to recombinant AAV2...

  19. Droplet Digital PCR for AAV Quantitation

    Type
    Blog Post
    ...take to achieve a clean NTC: Have a dedicated bench with a dedicated set of pipettes for ddPCR set-up. .... Each droplet contains the ingredients for amplification of the target DNA. This partitioning reduces...detection of the product. As an added benefit, replicates are built into the technology. One well (containing...droplet contains the material required for a mini amplification reaction to take place.  When the PCR is complete...number of cycles. After additional rounds of amplification, your fluorescence amplitude will increase, ... use ddPCR for AAV titration, there are many applications for the technology.  Droplet digital PCR is ...being used in the detection of microbes. Some applications include measuring viable probiotics and detecting...

  20. pSiM24: Simplifying Plant Genetic Engineering

    Type
    Blog Post
    ...for both transient and stable gene expression applications in plants. This smaller, easily customizable...Agrobacterium are termed binary vectors because they must replicate in two species: Agrobacterium and E. coli. Like.... coli. However, they also need to be able to replicate in Agrobacterium to ensure that they are maintained... Thus, binary vectors contain two origins of replication, one each for E. coli and Agrobacterium, along...bases each. By switching the E. coli origin of replication and codon-optimizing the Agrobacterium ORI, they...constitutively active M24 promoter has been modified with duplicated enhancer domains and characterized in studies...these properties of pSiM24 are suitable for many applications, the plasmid can also be customized due to its...

  21. Antibodies 101: Flow Cytometry

    Type
    Blog Post
    ... it passes through and scatters in different directions. The degree of scatter is captured by detectors...Light that scatters sideways to the path that it was initially traveling is called side scatter (SSC) and...granulocytes in a plot of forward scatter (FSC) versus side scatter (SSC). Users can gate around their...protein composition. It is used for a variety of applications such as measuring target protein expression ...expression levels, assessing post-translational modifications, determining cell health, analyzing cell cycle stages...size and complexity, measured using visible light scatter The optical system has both visible and fluorescent...as it was initially traveling is called forward scatter (FSC) and provides information about the relative...

  22. CRISPR 101: Targeting RNA with Cas13a (C2c2)

    Type
    Blog Post
    ...use, functional in most species, and has many applications. That said, SpCas9 is not the only game in town... makes this molecule unique, and the various applications of Cas13a. The origins of Cas13a: An RNA cleaving...53 potential candidate genes that fell into 3 categories based on the architecture of the CRISPR protein... is analogous to the PAM sequence for Cas9, is located at the 3’ end of the spacer sequence and consists...discussed below. Subscribe to CRISPR Blog Posts Applications of Cas13a   Figure 1: Using Cas13a as...) is amplified using Recombinase Polymerase Amplification (RPA) or Reverse-transcription RPA (RT-RPA),...fluorophore. The fluorescent signal can be used as an indicator to determine whether the target sequence is present...

  23. Tips for Writing a Good Cover Letter

    Type
    Blog Post
    ...excellent communication skills” try giving an example, like “I have extensive communication experience...usually yes! A good cover letter won’t hurt your application, but it can certainly help you stand out.  In...letter is vital, particularly in fields where communication and writing are key skills. Other fields, often...consider cover letters an important part of the application. Even within an organization, there can be variance...good cover letter!) As with any part of the job application process, it's a good idea to talk to people in... to proactively address questions about your application. These could be logistical, like briefly explaining...explaining a gap in your job history or sharing relocation plans. They can be skills-based: if you're switching...

  24. Overcoming the AAV Size Limitation for CRISPR Delivery

    Type
    Blog Post
    ...described above showed successful target modification, indicating that AAV is a good delivery vehicle for... with AAV. This system fuses catalytically dead dCas13b to the catalytic domain of RNA deaminase ADAR2...overall packaging capacity but necessitating purification and co-infection of two AAVs. Cas9 orthologs...Streptococcus thermophilus and a rationally-designed truncated Cas9. Unfortunately, certain drawbacks limit the...that limits the number of targetable loci, and truncated Cas9 has much lower efficiency than its wild-type...the AAV-SaCas9-sgRNA constructs mediate genome modification, but they did so without a substantial immune...ADAR2. Constructs containing the ADAR2 truncation ADAR2DD(delta984-1090) are approximately 4.1 kb in length...

  25. Finding nucleic acids with SHERLOCK and DETECTR

    Type
    Blog Post
    ...activated” Cas13 produces a quantifiable signal that indicates the presence of your targeted nucleic acid. To...amplified using RPA (recombinase polymerase amplification) or reverse transcriptase (RT)-RPA, respectively...RNA for subsequent detection by Cas13. This amplification step in combination with the ssRNA reporter ... introduced in 2017 so the lab made further modifications to improve their detection system. They named... SHERLOCKv2 uses far less primer in the pre-amplification step allowing for greater quantitation without...hour. Find the SHERLOCK plasmids at Addgene! Applications of the SHERLOCK detection system The Zhang lab...portability. This method can be used for an array of applications including clinical diagnostics (e.g. pathogen...

  26. Early Career Researcher Toolbox: Free Tools for Making Scientific Graphics

    Type
    Blog Post
    ...software that let me create graphics that better communicated the science in my blog posts. This post highlights...free tools which will hopefully also help you communicate your science, whether it’s in presentations, ...number of drawing tools, so it’s harder to draw intricate figures, like a brain or a mouse. Vectr Vectr ...without the watermark, which are better suited for publications, if you sign up for a paid account.  I’m proud... free medical images organized into four main categories: anatomy and the human body, cellular biology...appropriate credit, provide a link to the license, and indicate if changes were made to the images. This requirement...easier to give attribution, than for journal publications. Google Image Search Google image search is ...

  27. Viral Vectors 101: Parts of the AAV Packaging Plasmid

    Type
    Blog Post
    ...Rep78/68 play a key role in AAV genome replication. Replication initiates from the AAV genome ITRs on ...contains the proteins needed for the virus to replicate,  and the transfer plasmid which contains the ...aka the RepCap plasmid encodes two genes: the replication (rep) gene and the capsid (cap) gene. In wild-type...its products. Created with BioRender.com   Replication (rep) gene The rep gene encodes four proteins...proteins that are required for viral genome replication and packaging: Rep78, Rep68, Rep52, and Rep40. Rep gene... generate a 3’ hydroxyl group needed for DNA replication, Rep78/68 binds the Rep binding element (RBE)...nicked by its endonuclease domain. Following replication, Rep78/68 stays attached to the AAV genome and...

  28. Summer SciComm: Science Storytelling

    Type
    Blog Post
    ...formal scientific communications, they are fantastic fodder for science communication. The trick is to ... is far from the only way to communication science. Science communicators also use the hero’s journey,...this small glimpse into the world of science communication and can use what you've learned to share your...Finding Conflict in Science  In all science communication, what you are doing is telling a (nonfiction...details often aren’t included in scientific communications, but they’re firmly part of the story to the...conflict gives you an easy framework with which to communicate your science. The act of building towards your...your results right at the beginning of your communication, use conflict to get your audience invested ...

  29. Antibodies 101: Normalization and Loading Controls for Western Blots

    Type
    Blog Post
    ...normalization and loading controls needed for relative quantification of a western blot — and why you might want ...accurately compare different lanes? In relative quantification, the POI bands are normalized to the loading...other errors in experimental design and gel quantification. Figure 3: In a perfect world, protein...and it’s also problematic for computational quantification. Outside the linear detection range, band intensity...common error associated with Western blotting quantification” (Gilda & Gomes, 2013). To address this source... Gilda & Gomes, 2013. Figure 7: Semi-quantification of liver lysate using different loading controls...concentration of β-actin in panel A. Indeed, the quantification in panel B is not especially linear. In panel...

  30. Optimizing Donor DNA for Enhanced CRISPR Genome Editing

    Type
    Blog Post
    ... reagent. This interplay falls into two broad categories and thus, causes two types of editing outcomes...altering its function). HDR is crucial for certain applications, for example, correcting the allele that causes... dissociation rates and discovered that the catalytically active form of the nuclease dissociates very...we measured identical dissociation rates for catalytically inactive dCas9 molecules. We followed these ...Our in vitro results also demonstrated that catalytically inactive dCas9 produced a “bubble” structure...nucleofection The in vivo editing experiments in this publication were performed using a technique called nucleofection...Additonal Corn Lab Members who worked on this publication:         References 1. Richardson, Christopher...

  31. Synthetic Photobiology: Optogenetics for E. coli

    Type
    Blog Post
    ...consistent, and controllable pulses of light. Complicated patterns of light intensity and wavelength can... also be used to engineer new pathways with sophisticated gene expression controls. Most cell types do...light; these two systems can be coexpressed for sophisticated control of gene expression. An E. coli light-sensitive...; only two plasmids are required per system. Applications of these systems The large dynamic range of ...suitable for various scientific or engineering applications.   References Refactoring and optimization ...Oct 11. PubMed. Find the plasmids from this publication at Addgene. Synthetic biology: engineering Escherichia...:441-2. PubMed. Find the plasmids from this publication at Addgene. A synthetic genetic edge detection...

  32. 15 Hot Plasmids from 2017

    Type
    Blog Post
    ... plasmid or group of plasmids' functions and applications. We hope that these articles make it easier ...FLIM (Fluorescence Lifetime Imaging Microscopy) applications. To demonstrate the power of mCyFP1, the Lin... Coselection efficiency is so high that some applications may permit working with edited “pools” of cells...showed high editing efficiencies with AsCpf1, indicating that ouabain coselection is a robust and flexible...be found at Addgene and in Figure S12 of the publication. Agudelo D, et al. Nature Methods. 2017. PubMed...potential of base editing for precise genome modification. Plasmid ID Plasmid Name Cas9 Variant Speacial...(NGG)  Very low off-target activity; protein purification vector  87439  pCMV-HF-BE3  HF-Cas9 (NGG) ...

  33. A Deep Dive into BioBuilder

    Type
    Blog Post
    ...and consultant whose work is focused on education and education policy. Additional Resources on the Addgene...that routinely hit the inbox at the BioBuilder Educational Foundation. With a goal of “bringing tomorrow...BioBuilder answers the call by offering a variety of educational programs all focused on current questions and...effectively contribute as part of a team.” As a seasoned educator, Kuldell also knew that the best days in the classroom...As a result, Kuldell launched the BioBuilder Educational Foundation in partnership with high school teachers...grown into a recognized name in the field of STEM education worldwide. The BioBuilder curriculum is now taught...critical thinking, persistence, teamwork, and communication. And as a program focused on an emerging scientific...

  34. Viral Vectors 101: Types of viruses

    Type
    Blog Post
    ...injections, or the location of a specific cell type doesn’t always lend itself to direct application of virus. ...addition of a helper virus or plasmid allows it to replicate episomally, essentially remaining an extrachromosomal...extrachromosomal part of the host genome that can replicate and divide along with the endogenous DNA. AAV also...gamma-retro viruses. This is large enough for many applications, but in some cases multiple AAVs (co-infection...and AAV. If you’re wondering more about what applications these viruses are good for, we have plenty of...Adenovirus-Mediated Gene Delivery: Potential Applications for Gene and Cell-Based Therapies in the New...Gammaretroviral vectors: biology, technology and application. Viruses. 2011 Jun;3(6):677-713. DOI: 10.3390...

  35. Back to Bacteria: CRISPR gRNA Multiplexing Using tRNAs

    Type
    Blog Post
    ...biological pathways;  to observe a phenotype, the modification of multiple genes is often necessary. Guide ...recognition and cleavage. This sequence flexibility indicates that gRNAs could be incorporated into these constructs...the 5’ end. PTG construct schematics. Scissors indicate cleavage sites. After confirming gRNA cleavage...) How many loci can Cas9 modify? To test the application of this system to gRNA multiplexing, Xie et al...deletion with 4-20% frequency at the four loci, indicating that Cas9 can be guided to at least 8 distinct...multiplexing further illustrates the potential of PTGs. Applications of PTGs The major advantage of the PTG system... Mar 2. PubMed. Find the plasmids from this publication at Addgene Other Techniques for gRNA Multiplexing...

  36. Dos & Don'ts When Publishing a Scientific Manuscript

    Type
    Blog Post
    ...should I choose? Writing a research paper for publication in a scientific journal requires several considerations...detailed information on lab resources, such as catalogue numbers and manufacturers’ details for antibodies...Information Framework (NIF) called the Resource Identification Initiative. During this project, authors are...likely that researchers have enough information to replicate your experiments, making research more reproducible...the reproducibility and reliability of science publications. Peer reviewing To make sure your manuscript...happens before the manuscript is accepted for publication and is, in most cases, blind (meaning you don...revised before it can be published, this can delay publication and manuscripts may go through several rounds...

  37. Hot Plasmids: Spring 2025

    Type
    Blog Post
    ...Here's what you'll find in this post: Glutamate indicators with increased sensitivity and tailored deactivation...viral preps targeting interneurons Glutamate indicators with increased sensitivity and tailored deactivation...popular choice for a variety of synaptic imaging applications. Find iGluSnFR4 plasmids here! Aggarwal, A...., Iyer, R., … Podgorski, K. (2025). Glutamate indicators with increased sensitivity and tailored deactivation...DNA vector that contains everything needed to replicate inside a host cell but with space to insert your...This requires both targeting a specific genome location and isolating the interacting proteins. Lucky ...immunoprecipitation. The top panel depicts the identification of heat-shock proteins at the FOS gene promoter...

  38. RaPID Detection of RNA-protein Interactions

    Type
    Blog Post
    ...methods Not in a native context. While native purification preserves RNA structure and naturally occurring...used the Contamination Repository for Affinity Purification (CRAPome), to identify highly biotinylated background...research groups that performed BirA*-based affinity purification mass spec experiments. These background proteins...subtracted from Ramanathan et al.’s RaPID datasets. Applications of RaPID RaPID sounds like a nifty technique...help answer? Ramanathan et al. outline three applications of RaPID: Discovery. To discover novel RNA-... that QKI is a host protein critical to Zika replication. Human genetic disease. RaPID can also be used...binding patterns. Hereditary Hyperferritinemia-Cataract Syndrome (HHCS), a disease characterized by increased...

  39. Announcing the Winners of the 2021 Michael Davidson and Roger Tsien Commemorative Conference Awards

    Type
    Blog Post
    ... Haoyi Qiu He Tian Every two years, we seek applications for awards to early career scientists using ...virtual conference attendance. We also opened up applications to research technicians and undergraduate researchers...mercaptopyruvate sulfurtransferase (MPST) which catalyzes the desulfuration of 3-mercaptopyruvate and generates...the chromophore that are susceptible to redox modification, the MPST hydrosulfide can be transferred to... and CNO silencing. (D) Immunohistochemistry verification of the dual virus expression in CR neurons of...where she engineers genetically encoded voltage indicators. Tian developed a video-based high-throughput...archaerhodopsin‑derived genetically encoded voltage indicator which had improved performance in live mouse brains...

  40. Summer Fun at Addgene!

    Type
    Blog Post
    ...Summer Science Communication Series. We’ll be covering the basics of science communication, tips and tricks...science with others, and introducing science communication as a research field. And there will even be ...be a few tips for scientific communication (manuscripts, talks, etc…!)  Deep Dives You probably are familiar... Dives” series comes in! We’ll take a common application or concept and go beyond the basics - diving ...you’re ready for the next steps on some common applications, join us as we get into the weeds on some of... the end of this month! We’ll be sharing our educational resources and tips and tricks for those new to...media endeavors - in between some much-deserved vacations, sunshine, and beach trips, of course.    *not...

  41. Plasmids 101: The Wide World of Natural Plasmids

    Type
    Blog Post
    ...Shareck et al., 2004). Plasmid categorization is complex Plasmid classification has shifted over the years...us! A plasmid is a small piece of DNA that can replicate independently from its host’s chromosome. Although...genes between bacteria can also have serious implications for public health. Bacteriocin plasmids: microbial...poisoning, the difference is virulence plasmids! This category includes genes that help bacteria invade hosts...years, and new classifications are still being created as whole-genome sequencing becomes more relevant (... common plasmid features, such as origins of replication and promoters, check out our other Plasmids 101...Redondo-Salvo, S., & de la Cruz, F. (2023). Plasmid classifications. Plasmid, 126, 102684. https://doi.org/10.1016...

  42. Adapting Toehold Switches to Detect Zika Virus

    Type
    Blog Post
    ... journal Cell just six weeks later. The Zika publication timeline I think we can speak for all the authors...research, but the urgent need for the test did catalyze our resolve to get the work done as quickly as... dozen versions of the toehold switches and amplification primers. This helped make sure that we had a...this includes primer directed isothermal RNA amplification, new toehold switch designs, CRISPR/Cas9-mediated...our electronic reader that provides portable quantification of diagnostic results.  Our approach now detects...directly from infected monkey blood plasma without purification or concentration of the virus. Future work Going...focused on developing cell-free synthetic biology applications for human health and the environment.     Alexander...

  43. Early Career Researcher Toolbox: Finding Relevant Papers

    Type
    Blog Post
    ...show all publications by an author, total number of citations, and the number of publications that heavily...read the abstract or full text of the paper, publication date, a relevance score, and type of article....that term. You can also set up alerts for new publications from a particular author. Saving papers Papers... work, so it’s also a good place to look for publications. Bonus: papers have to be summarized in 280 ...organizations, and universities often tweet about publications in the fields of research they support. Monitoring...Artificial Intelligence. Semantic Scholar analyzes publications and figures using machine learning to extract...your search to a specific window of time for publication. To help you quickly identify papers with greater...

  44. Illuminating Epigenetics with A FRET Based Biosensor

    Type
    Blog Post
    ...Mechanisms of epigenetic modifications The main mechanism of epigenetic modification is chromatin remodeling...literally means ‘on top of the genome’). Epigenetic modifications can result in phenotypic changes without any...any change in genotype. Epigenetic modifications play a large role in turning genes ‘off’ and ‘on’, signaling...two main mechanisms, either through histone modifications, which can influence the transcription of genes...hypomethylation, on the other hand, has also been implicated in the development and progression of cancer ...enzyme digestion, DNA adenine methyltransferase identification, and bisulfite sequencing. However none of ...can be used for in-situ research of dynamic modifications in real-time, posing a huge challenge to studying...

  45. The Materials Science of Optogenetics Experiments

    Type
    Blog Post
    ...There are several important considerations with fabrication of the fiber optics needed for optogenetics. ... for the implant depends on the dorsal/ventral location of your region of stimulation (the z-axis bregma...emitted from the end of the fiber optic implant scatters a great deal once it enters tissue, placement ...0.5mm above the site of your stimulation. The scatter effect is also an important consideration when ...Lasers can be purchased through Laserglow, which caters to optogenetics users and adjusts the lasers appropriately...require stimulation only under certain contexts/locations in the test apparatus and thus individual laser...inactivation kinetics. For example, the light-gated cation channel, Channelrhodopsin 2 (ChR2), exists in several...

  46. A Guide to Getting Started in Undergrad Research

    Type
    Blog Post
    ...entire page dedicated to different career options from science policy to science communication and much ...), about their experiences. Research requires dedication and effort, so building a strong understanding...critically about whether it’s something you want to dedicate your time and energy to. How can I make the most... feel less confident in their abilities and qualifications. Studies on imposter syndrome have also found...universities often have scholarships and funds dedicated for undergraduates interested in doing research...the experience would improve my scientific and application writing skills, and ended up with the award. ...fantastic for broadening your experiences! These applications can be highly competitive, so asking for help...

  47. Hot Plasmids: Summer 2025

    Type
    Blog Post
    ...between mGold2s and mGold2t depending on the application. Figure 1: Super-resolution imaging...fused to mVenus, mGold2s, or mGold2t. Bottom: Quantification of photostability. Image reused from Lee & ...fluorescent proteins for extended imaging. Nature Communications, 16(1), 3241. https://doi.org/10.1038/s41467...available for tracking cell lineage, different applications require careful selection or design to ensure...for gene therapy and ex vivo cell engineering applications and is especially well-suited for lung cells...tool for circuit tracing and other neuroscience applications (Figure 4). Check out our blog post on AAV serotypes... Figure 4: AAV6 and AAV11 tropism and applications. A) AAV6 is reported to have broad tissue tropism...

  48. CRISPR Methods for Bacteria: Genome Engineering, CRISPRa, CRISPRi, Base Editing, and More

    Type
    Blog Post
    ...for successful modifications, efficiency can be low, especially for larger modifications. What’s the solution...several potential CRISPR applications. First, CRISPR can be used to target locations in the genomes of pathogenic...tools available for bacteria and some of the applications for which they’ve been used. The beginnings ... of Enterobacteriaceae, without the need for modification. This finding suggests that the system may be...eukaryotes (Qi et al., 2013). As in other systems, catalytically dead (dCas9) targeted to a promoter or gene ...responsive promoter to drive expression of a catalytically dead Cas9 enzyme allows reversible repression...Bikard et al., 2013). By targeting either a catalytically dead Cas9 (dCas9) alone or a dCas9 fused to ...

  49. Lentiviral Vector Uses and Overview

    Type
    Blog Post
    ...many CRISPR applications, and they’ve also had success in clinical gene therapy applications. Read on to...to learn more about the current (and future) applications of lentiviral vectors! Lentiviral vector history...original system, the possibility of creating a replication-competent virus via recombination between the...of recombination events necessary to create a replication-competent virus. Second, Tat is eliminated through...barcoding libraries have been used for complex applications like lineage tracing in heterogeneous tumors...2015: lentiCRISPR v2, used both for targeted modification and genome-wide screening.   Lentiviral vectors...developed integrase-deficient lentiviral vectors for applications that require the large genetic capacity of a...

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

    Type
    Blog Post
    ...emission wavelengths, which are pivotal in their application in biotechnology (Grimm & Lavis, 2022). These... substrates/peptides and antibodies. Example applications of this include coupling to an antibody, whereby...whereby excitation of blue light will indicate where FITC is bound through green light emission. Key considerations...typically bind to. Stability of fluorescence: For applications that involve ranges of pH, and significant lengths...light, is another factor to consider. If your application requires longer periods of exposure, you’ll want...degrees of β-arrestin-2 recruitment to receptors, indicating their agonistic nature. The potency and efficacy...descriptions, or technical manuals. Specific applications and matching dye/ligand choices For effective...
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