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  1. Hot Plasmids: FRET-Based Biosensors

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    Blog Post
    ... plasmids: Twitch sensors Griesbeck’s recent contribution to the field is a series of fluorescence resonance...which are available at Addgene, can be used for ratiometric in vivo imaging. Griesbeck explains, while these...both neuroscience and immunology. Don’t be shy: Ratiometric imaging for beginners Griesbeck says his calcium...beginners may have a tendency to shy away from ratiometric imaging, he recommends they give it a shot. “...practice optimizing the sensors involves plenty of trial and error. Transition metals also present challenges...dynamic range,” he says. Merkx recently applied this “trick” to the development of additional color variants...test.” References Thestrup et al. Optimized ratiometric calcium sensors for functional in vivo imaging...
  2. Reagent Repositories Are Speeding up Science During the Pandemic

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    Blog Post
    ... of times in 2 weeks. This is a striking example of the contributions that scientists are able to make... Figure 1: Biological repositories that distribute mouse strains, plasmids, cell lines, and much...Institutes of Biomedical Innovation, Health, and Nutrition in Japan. These results  will help researchers...investigation of this pathogen. The sharing and distribution of cell lines from repositories on opposite ...around the world. This scale of production and distribution is possible due to the dedicated facilities ...repositories’ capacity for storing, validating, and distributing such reagents are all ways in which the scientific...
  3. Crowdfight, a Platform to Boost Scientific Collaboration During COVID-19 and Beyond

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    Blog Post
    ...expert and the lack of credit for small contributions. We strive to eliminate these two barriers, creating...This post was contributed by Ignacio Amigo and María Hernández Sánchez from Crowdfight. In March 2020...between researcher and expert; 4) Credit all contributions.   Our volunteers are extremely diverse.... the project we are focusing on what we call “asymmetric collaborations.” These are transient partnerships...where a researcher makes a small but crucial contribution to someone else’s project. We think that these...A discussion about a protocol can save weeks of trial-and-error. A recommendation for the correct statistical...
  4. Developing a cold tolerant E. coli using specialized chaperones

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    Blog Post
    ...This post was contributed by Sreepadmanabh M, a member of the iGEM team from IISER Bhopal. Following ...The importance of psychrophilic enzymes From an industrial perspective, the enzymes obtained from psychrophiles...host The expression of recombinant proteins for industrial or research purposes requires stable host cells...either die out or grow so inefficiently that no industrial operation would ever consider them worth the ... Oleispira antarctica, and the P. haloplanktis Trigger Factor), that would allow the stable folding and...spirit with iGEM’s emphasis on holistic, community-centric science, our team has continuously engaged with...with a variety of stakeholders from industrial and commercial operators, government agencies, active researchers...
  5. Addgene’s Viral Service - Why Virus? Why Now?

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    Blog Post
    ...initiative since we started distributing plasmids in 2004. We’ve already distributed over 500 viral samples...In the middle of 2016 Addgene started distributing a small but growing catalog of ready-made AAV and ...the infrastructure capabilities to produce and distribute virus. Addgene is a 501(c)3 nonprofit and our...lead on operationalizing viral production and distribution, this project involved every Addgenie in the... to enable efficient, tracked production and distribution of viral samples. The Office Team made sure ... plasmid depositors and their institutions to distribute viral preps derived from plasmids in the repository...
  6. Mycoplasma Contamination: Where Does It Come From and How to Prevent It

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    Blog Post
    ...This post was contributed by guest blogger, Kaustubh Kishor Jadhav, a Research Assistant at MGMs Institute...enhance the growth of mycoplasmas. The serum is nutrient-rich and also the best source for mycoplasma proliferation... longer time. When they come in contact with a nutrient source, they start proliferating shortly. Once...to the liquid or semi-solid medium (containing nutrients essential for mycoplasma growth). Infected cell...culture. Once these cells detect mycoplasmas, they trigger a series of chemical reactions and this induces...mycoplasma and then specific enzymes are used which trigger cellular mechanisms that generate luminescence....fluoroquinolone ciprofloxacin, ciprobay, zagam, baytril, tetracycline, etc. are available for mycoplasma...
  7. Transferable Skills Guide: Teamwork

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    Blog Post
    ...useless, and excess people who are not contributing will detrimentally affect a team’s morale and efficiency...member-by-association of the Development Team, and I contribute to the Management Team that steers the organization..., when it came time to update how we make and distribute kits, I helped assemble a crack team of Addgenies...times have you ever seen a scientific article attributed to a single author? I’ve seen so few in my 20...to make progress towards open-ended goals whose metrics for success are defined by ongoing mission fulfillment... can get since participation on such a team is strictly voluntary. New members could be recruited, but... teams when I’ve realized that I really can’t contribute anything. Purging team members does not have ...
  8. To Each HIS Own

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    Blog Post
    ...the polyhistidine tag? The polyhistidine tag is a string of 6 or more histidine residues expressed in frame...using these more selective substrates along with stringent wash conditions.   Find polyhistidine tag plasmids...   Fig 2:  A, The polyhistidine tag is a string of histidine amino acids on the N- or C- terminus...tag placement can affect protein function. B, The string of histidines in the tag is typically between 6...normal protein function, however longer histidine strings can increase that risk.    Number of residues...of the tag, with longer tags you can use more stringent wash conditions and remove more contaminants without...antibody, like this one developed by Dr. James Trimmer’s lab, to perform assays that they otherwise would...
  9. Hot Plasmids - March 2020 - base editors, GEVI, MoClo, and optogenetics

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    ...  AAV delivery of split base editors Article contributed by Jennifer Tsang AAVs are a great gene therapy...comparable to those currently used in human gene therapy trials. They further tested the base editors by correcting...genetically encoded voltage indicator Article contributed by Shreya Vedantam Genetically encoded voltage.... A MoClo toolkit for cyanobacteria Article contributed by Andrew Hempstead The Modular Cloning (MoClo... allows synthetic biologists to use Type IIS restriction sites to easily assemble multiple DNA fragments...applications including conversion of CO2 into water and electrical energy generation. Alistair McCormick’s lab recently...for precision in cell lineage tracing Article contributed by Erin Sanders CreLite, designed by the Eisenhoffer...
  10. Hot Plasmids May 2018 - Optogenetics, Decaffeination, Biosensors, and Fluorescent Protein Tools

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    ... optogenetics toolbox with CRY2clust Article contributed by Brook Pyhtila  Listen to the CRY2clust podcast...dynamics, higher sensitivity to light, and better distribution of clusters without accumulation in subcellular...that enables single-cell optogenetics Article contributed by Meghan Rego  Listen to the soCoChR podcast...        Synthetic decaffeination operon Article contributed by Angela Kaczmarczyk  Listen to the synthetic...enables the degradation of caffeine (1,3,7-trimethylxanthine) and its conversion into xanthine. The majority...live-cell imaging of biochemical activity Article contributed by Angela Holmes Jin Zhang’s lab is developing...the FLIM-FRET acceptor podcast segment Article contributed by Christina Mork The Murakoshi lab has developed...
  11. Antibodies 101: ELISA (Enzyme-linked Immunosorbent Assay)

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    Blog Post
    ...added to the wells. This reaction produces a colorimetric reaction that reflects the concentration of ... concentration or antibody specificity via a colorimetric reaction. Image from Boguszewska et al., 2019... concentration or antibody specificity via a colorimetric reaction. Image from Boguszewska et al., 2019...added and the reaction can be visualized via a colorimetric reaction. The direct ELISA is often used when...concentration of proteins in an ELISA well is based on a colorimetric reaction. Most commonly, this is a blue reaction...
  12. 5 Tips for Troubleshooting Viral Transductions

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    Blog Post
    ... by ultracentrifugation (75,000 - 225,000 g for 1.5 – 4 hours at 4 °C). After ultracentrifugation, virus...integrity of your virus, perform a diagnostic restriction enzyme digest and compare it to some reliable...vectors) you can concentrate your virus by ultracentrifugation of the viral stock, followed by resuspension...packaging cell debris before proceeding to ultracentrifugation to avoid contaminating your transduction ...through a 0.45 µm or 0.22 µm filter) or by a centrifugation step (5 minutes at 300-500 g). After removing... to concentrate a virus solution without ultracentrifugation, you can reduce the volume of cell culture...
  13. Viral Vectors 101: Voltage Indicators

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    Blog Post
    ...and sensing electrical potential. Thankfully, there is a tool to measure these electrical events! Voltage...biological tools. Why Use Voltage Indicators? Electrical signals are integral to many facets of biology...muscle contraction – is directly related to the electrical impulse of the cardiac cells. To study this phenomenon...is carried out by action potentials which are electrical charges propagated through multiple cells to ...depends on the ability to monitor their signals – electricity! The research tools for studying voltage within...was dipicrylamine, a lipophilic compound that distributes itself within the plasma membrane as well. Another...
  14. Production of Virus in Insect Versus Mammalian Cells

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    Blog Post
    ...days Purification Ultracentrifugation (AAV); centrifugation (lenti) Centrifugation Titration time ~...using methods like ultracentrifugation, while lentivirus supernatants are centrifuged and filtered to eliminate...have a higher titer than a P1 virus. Pro-tip! Centrifuge the viral supernatant in between passages to ...straightforward — simply spin down the supernatant in a centrifuge to remove any unwanted cellular debris, as you...
  15. Simplify Cloning with in vivo Assembly

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    Blog Post
    ...This post was contributed by Jake Watson and Javier García-Nafría from the MRC Laboratory of Molecular...present even in common lab cloning strains. This intrinsic bacterial recombination pathway, referred to as... longer oligos, which could be avoided using restriction enzyme cloning, were more prohibitive at the ... doesn’t matter if the DNA is PCR amplified, restriction digested or even a synthesized gene. PCR is the... Mutagenesis is performed by designing primers astride the old codon, amplifying the whole vector. The...extending homologous sequences (to 25-30 bp). Tips and tricks for IVA cloning Use a sequence manager A sequence...IVA can be employed by cutting the vector with restriction enzymes and adding the corresponding homologous...
  16. Tips from the Repository Trenches: Using Barcodes to Track Samples

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    Blog Post
    ...colonies in petri dishes, but close to 80% of samples are received as DNA in a microcentrifuge tube. Once...sample enters Addgene’s lab, a series of events is triggered. Each step is tracked through barcoded tubes that...track all of our 40,000 samples available for distribution!    Check Out How We Think about Developing...The preferred E. coli strains for storage and distribution at Addgene are DH5α, NEB stable, ccdb survival...Each sample that is transformed is plated onto a petri dish plate that is also barcoded. The barcodes on... to be transformed with a micropulser using an electric charge to help the DNA enter the cells. Some samples...
  17. Important Considerations in Optogenetics Behavioral Experiments

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    Blog Post
    ...This post was contributed by guest blogger Derek Simon. The actual experiments you do will be determined...implanting an electrode and non-specifically electrically stimulating an ill-defined region of the brain...trained to “freeze” upon anticipation of a mild electric foot shock that has become associated with a visual...using HR was found to block the acquisition and retrieval of contextual fear memories [5].  In a modified...other regions of the brain may be involved in retrieval of remote contextual memories. This study is an...real-time inhibition), and behavioral (remote memory retrieval) specificity. Optogenetics can be used to more...2012): 159-172.5. Goshen I, et al. Dynamics of retrieval strategies for remote memories. Cell. 2011;147...
  18. Hot Plasmids: Summer 2024

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    ...antibody (N206A/8 TC Supernatant). Image attribution: James Trimmer, UC Davis.   ...interact with the air-water interface (AWI) before vitrification, they can be completely denaturated (left) or...representative micrograph (C), particle orientation distribution and Fourier-shell correlation curve (D), and...protein. While the addition of LEAs may bias the distribution of particle orientations, this could be overcome...off-target editing. Cargo size limits are also less stringent for eVLPs than other viral delivery methods, allowing...anti-GFAP [N206A/8R] antibody shared by James Trimmer’s lab (Figure 5) as well as antibodies for identifying...
  19. Multiple Plasmids at a Low Price: Kits from Addgene

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    Blog Post
    ...study a matrix metalloproteinase: López-Pelegrín, Mar, et al. "A novel mechanism of latency in matrix metalloproteinases...Addgene. What you might not know is that Addgene distributes curated collections of plasmids as kits with ...This kit is designed to be used with Type IIS restriction enzymes and standardized primers to clone your... pExpression vectors) plasmids. The type IIS restriction sites used in these vectors are of low abundance...Biosafety of biotechnologically important microalgae: intrinsic suicide switch implementation in cyanobacterium...used to generate these fusions all use the same restriction enzymes for cloning. Furthermore, some plasmids...
  20. Reflections and Looking Ahead

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    ...collaboration. Together, we distributed 184,824 materials to 39,529 scientists across 86 countries. Even more remarkably...remarkably, 1,160 labs from 522 organizations in 41 countries enriched our repository with 15,020 new plasmids...part of the story. This year, we made significant strides in making science more accessible and reliable....thoroughly characterized antibodies, and our contributions to key research papers are already inspiring...Errington, T. M., Turn, R. E., Bandrowski, A., Trimmer, J. S., Rego, M., Freedman, L. P., Ferrara, F.,...
  21. Editor's Choice, September 2016

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    Blog Post
    ...of months. Read on to discover what new post contributed the most to this record breaking month and to... Apps for Lab Life This very useful post was contributed by guest blogger Sean Stacey from Eastern Tennessee...Phage Genomes for Host Binding Proteins," was contributed by guest blogger Jessica Sacher from the University...Disease, Running for FOP, Running for AJ,” was contributed by Kurt Swanson, husband of Addgene Director ...currently on my way back from a very successful Outreach Trip in San Francisco and would like to give my thanks...who spoke with me and deposited plasmids on this trip. Here’s to hoping that October is even more awesome...
  22. 2023 and 2024: Reflections and Looking Ahead

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    ... In 2023, Addgene distributed 188,729 materials to 39,844 scientists in 88 countries around the world....1,106 labs in 504 organizations from 37 different countries, into our repository, while expanding global access... access to our repository through our distributor partners, with the launch of antibodies in China and...Protein Innovation (IPI), in which Addgene will distribute recombinant antibodies (rAbs) developed at IPI... repository, partially through work with our distributors in China, Korea, Japan, India, and Brazil. Through...
  23. New Norepinephrine Indicators: nLightG and nLightR

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    Blog Post
    ... and were only available as green probes. The Patriarchi Lab aimed to overcome these limitations by developing...vivo experiments, and nLightG was successfully trialed in two-photon in vivo experiments. nLight indicators...nLightR, both generating a measurable signal after electrical stimulation with a single pulse, while nLightR...researchers looking to study norepinephrine, the Patriarchi lab continues to work on further improvements...nLightG. Many thanks to Mike Waring and Tommaso Patriarchi for their assistance with this blog post. References...Benke, D., Weber, B., Bohacek, J., Reiner, A., … Patriarchi, T. (2023). Sensitive multicolor indicators for...
  24. IBEX Knowledge-Base: A Data Resource for Multiplex Tissue Imaging

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    Blog Post
    ...includes 1049 community-validated reagents from 20 contributors, including 61 fluorescent probes, representing...for the performance of a reagent, e.g., antigen retrieval conditions, dye inactivation details, tissue preservation...   Figure 2: Screenshot showing reagent entries with associated metadata adapted from the Affinity...preservation, target tissue, detergent, antigen retrieval conditions, and more. Users can also recommend... showing the IBEX Knowledge-Base, with every contributor listed as an author.  The IBEX Knowledge-...and share their validation work. Everyone who contributes to the IBEX Knowledge-Base is named on the Zenodo...
  25. Hot Plasmids and Viral Preps - July 2021

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    Blog Post
    ...plant hormones strigolactones By Fabienne Furt Current methods used to detect strigolactones (SLs) are costly...build and validate a ratiometric fluorescent biosensor based on the parasitic Striga hermonthica SL receptor...editing in organoid Biosensors for detecting strigolactones The CRISPR Corner New ready-to-use viral preps... catalytic activity.  As SLs are also known to trigger seed germination of parasitic plants, this approach...
  26. Cellosaurus: A Cell Line Information Database

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    Blog Post
    ... submissions via email: [email protected] Entries include accession number, species, and assigned...cell lines profiled in the lab. You can browse entries by cell line groups, such as their vaccine production...collections.  Depending on available information, entries may also include whether a cell line is known to...programatically, their API allows fine grained query and retrieval of all the information in the resource.  This ...cells. Image courtesy of Josef Reischig.  Contributing to Cellosaurus Generated a new cell? Or finding...sent the updated information to the cell line distributor. A success all around! If you’re excited about...
  27. Plasmids 101: Walkthrough of Addgene’s Snapgene-Powered Quality Control Process

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    Blog Post
    ...sequencing results match sequence information contributed by the depositor, published backbone sequences...additional verification experiments: Primer and restriction digest design Some regions of plasmids are difficult...present in the plasmid, we might need to perform a restriction digest to confirm the size of the plasmid and...including our most popular primers and certain restriction enzymes, but you will also be able to create ...annotations and design additional experiments like restriction digests. We’ll have a tutorial showing all of...Basic Molecular Biology Protocols Diagnostic Restriction Digest Protocol ...
  28. Zebrafish as a Model for Behavior: Swimming into the Optogenetic Spotlight

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    ... Kolmer-Agduhr cells was sufficient to trigger the symmetrical tail movement unique to spontaneous slow...periodically beat their tails left and right in a symmetrical motion to move forward. This behavior is not ...behavior studies in action: Identifying neurons that trigger spontaneous swimming  Researchers at the Isacoff... zebrafish larvae to identify new neurons that trigger the CPG (central pattern generator) (Wyart et al... photostimulation in order to drive the full symmetrical response.  The function of Kolmer-Agduhr cells...
  29. The Blue Flame Award: Celebrating Addgene's Most Requested Depositors

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    ...the list weekly. The Blue Flame Award, first distributed this year, serves to congratulate researchers...one plasmid deposited at Addgene that has been distributed more than 100 times. We hope these desktop trophies... or personnel to constantly prepare them for distribution. One of the major advantages to depositing materials...Laboratory in Norwich, UK: “We’re very pleased to distribute our plasmids via Addgene. Given the increasing...world. “It’s easy to imagine how hard it is to distribute thousands of plasmids across the world from the...has made it possible to eliminate geographical restrictions in life science research." Claim Your Award ...
  30. Plasmids 101: Origin of Replication

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    ...pR6K ~15-20 R6K* C Stringent pACYC ~10 p15A B Relaxed pSC101 ~5 pSC101 C Stringent pBluescript ~300...of replication is referred to as "relaxed" or "stringent" depending on whether the ori is positively regulated... do you choose? Addgene Senior Scientist Marcy Patrick says researchers can ask themselves a few questions...copy number of a plasmid, other external factors contribute as well. These considerations are especially ...are temperature sensitive; others ori's can be "tricked" into amplifying more copies with the addition ...
  31. Hot Plasmids June 2018 - Reverse transcriptase, nanobody, and protein-DNA interaction tools

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    ...transport at the cell surface Article contributed by Marcy Patrick  Listen to the nanobody toolkit podcast...highly processive reverse transcriptase Article contributed by Will Arnold  Listen to the MarathonRT podcast...occupying a specific genomic locus: Caspex  Article contributed by Susanna Bachle  Listen to the Caspex podcast...occupying a specific genomic locus: C-BERST Article contributed by Klaus Wanisch  Listen to the C-BERST podcast...dCas9–APEX2 biotinylation at genomic elements by restricted spatial tagging), to confirm the composition ...
  32. Arabidopsis in Education: How the Arabidopsis Biological Resource Center Brings Plant Science to Life

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    ... This post was contributed by guest blogger Courtney Price, the Education & Outreach Specialist for the...mission is to collect, preserve, reproduce and distribute seeds, DNA and other resources for Arabidopsis...100,000 samples to researchers and educators in 60 countries each year. Introducing Arabidopsis Arabidopsis...fluorescent lights. Other experiments require only seeds, petri dishes, and filter paper. Another benefit of using...learning. Whether visiting classrooms, hosting field trips, conducting teacher workshops, or staffing a booth...partnerships have grown to include local school districts, professional education associations, and local...
  33. Celebrate Open Data Day with Addgene’s AAV Data Hub!

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    ...resource of over 100 entries is driven by the dedicated community of data-contributing researchers who use...This word cloud (using wordart.com) represents contributed data on brain injection site from the AAV data...recently used Addgene AAV tools, we invite you to contribute your data to grow this resource for the community...opportunity to cite the image to give proper attribution.  We hope that this provides a clear overview...to all of those dedicated scientists who have contributed to the AAV Data Hub. If you haven’t yet, we encourage...
  34. FLEx Technology and Optogenetics: Flipping the switch on gene expression with high spatial and temporal resolution

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    ...This post was contributed by Alessia Armezzani, scientific communication manager at genOway. A few decades...Hegemann, 1991). These proteins control the flow of electric charges across cell membranes and maintain membrane...neurons have in common? Neuronal stimulations are triggered by the movement of ions across the axon's membrane... is reached and the neuron fires, sending the electrical signal down the axon (Lodish et al., 2000). Most...light activates channelrhodopsins that, in turn, trigger neural excitation, whereas yellow light activates...stimulations, they simultaneously recorded the electrical impulses of discrete subpopulations of this brain...Through a partnership with genOway, we are able to distribute materials containing FLEx technology. Read the...
  35. Important Considerations When Using AAVs

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    ...This post was contributed by guest blogger Katrina Armstrong, a Neurophysiology Msc Student at the University...communities. Many thanks to our guest blogger Katrina Armstrong. Katrina Armstrong is a Neurophysiology Msc Student...better (3). Brain Region  Optimal Serotype Striatum AAV5>AAV9>AAV8>AAV1>AAV6>AAV2 Hippocampus AAV9...will depend upon which section you’re looking at (striatum, hippocampus and cortex) within the mouse brain...serotonin in movement. Follow her on twitter @katrinaboards.   References 1. Russell, David W. "AAV vectors...
  36. 22 Hot Plasmid Technologies from 2014

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    ...intensity, excitation and emission spectra. The lab of Dimitri Deheyn recently identified a family of GFP proteins... that they can be imported to the mitochondrial matrix. Gottlieb’s lab has used an inducible MitoTimer...into Golden Gate entry vectors via traditional restriction enzyme cloning, TA cloning, or annealing of oligonucleotides...team at the Institute of Science and Technology Austria, decided to take a novel approach to control for...activity levels and limited sensitivity under the stringently low expression conditions necessary to avoid ...chemogenetic technologies After several years of distributing his Designer Receptors Exclusively Activated...cloning strategy, MoClo, which uses the Type IIS restriction enzymes BsaI and BpiI/BbsI to efficiently assemble...
  37. Plasmids 101: Screening Strategies Used in Plasmid Cloning

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    Blog Post
    ...use restriction digest to screen your clones, but there are many other ways to choose restriction enzymes...blue-white screen. Image from Stefan Walkowski.   Restriction digest Another way to distinguish between colonies...inserts from those that do not is by using a restriction digest. The key is to be strategic about your...route, check out our protocol video on using restriction digests to analyze plasmids, which can help you... you visualize this process, or visit our restriction analysis blog post. Colony PCR Colony PCR can...
  38. Clear and Accessible Writing

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    Blog Post
    ...from AAV Purification by Iodixanol Gradient Ultracentrifugation First, you’ll want to identify the reader...for AAV Purification by Iodixanol Gradient Ultracentrifugation. The reader may be, for example, a graduate...between a gradient tube before and after ultracentrifugation so that a scientist can extract virus from...interfaces between layers are blurred after centrifugation and the syringe needle is inserted bevel-up...profile photo of an iodixanol gradient after ultracentrifugation. The interfaces between layers are muddled...illustrates a gradient tube before and after ultracentrifugation. The viral supernatant migrates through increasingly...
  39. CasPEDIA: A Functional Classification of Cas Enzymes

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    Blog Post
    ...make efforts to keep it updated with new entries and update entries as research progresses, but you are invited...Additionally, the Phylogeny tool allows users to browse entries by the current phylogenetic nomenclature and discover... database, and all researchers are invited to contribute to it! The CasPEDIA Consortium will, of course... invited to reach out to suggest new entries or even new features to the tool. Resources and References...References References Adler, B., Trinidad, M., Bellieny-Rabelo, D., et al. (2023). CasPEDIA Database: A Functional...
  40. GPCRs: How Do They Work and How Do We Study Them?

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    Blog Post
    ...coupled with heterotrimeric G proteins on the intracellular side of the cell membrane. Heterotrimeric G proteins...in signal transduction pathways and consist of a trimer of three subunits: alpha (Gα), beta (Gβ), and gamma...the GPCR allows for binding of a new inactive heterotrimeric G protein complex and subsequently another ...elucidate the role of 14 of the 16 non-visual heterotrimeric G proteins that can be activated downstream... alpha, 2 beta, and 4 gamma subunits of the heterotrimeric G protein complex that can be used to detect...
  41. Hot Plasmids December 2018 - C. elegans RNAi, TurboID, Detecting Viral Outbreaks, and Protein Binding Specificity Tools

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    Blog Post
    ...construct for C. elegans gene knockdown Article contributed by Alyssa Cecchetelli  Listen to the C. elegans... labeling with TurboID and miniTurbo Article contributed by Eric Perkins  Listen to the TurboID and miniTurbo...compartments is via proteomics--the study of the distribution and interactions of proteins within these structures...small-molecule substrate to map the spatiotemporal distribution and interaction networks of specific proteins...Changing the way we detect viral outbreaks Article contributed by Izzy Mueller  Listen to the viral detection... reveals novel peptide ligand motifs Article contributed by Michael Lemieux  Listen to the SH3 domain ...
  42. Improved Plasmid Maps Powered by SnapGene

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    Blog Post
    ...identify. Improved Restriction Enzyme Handling - SnapGene’s software positions restriction enzyme annotations...paste functionality. Restriction Enzymes Here you'll find a table of restriction enzymes that cut the...previous mapping software and now includes Type IIS restriction enzymes that are commonly used for Golden Gate...clicking on column heads. Clicking on a particular restriction enzyme here also highlights it in the “Map” and...
  43. Using AAV for Neuronal Tracing

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    ...strengthened during memory formation and memory retrieval. In neuronal tracing experiments, brain tissue...Traditional tracing compounds either produce a colorimetric product or are fluorescent. While dyes usually...pressure injection or iontophoresis (applying small electric currents via inserted electrodes) may be applied...both antero- and retrograde labelling, synaptic restriction as well as controlled monosynaptic and polysynaptic...polysynaptic spreading. AAV vectors cover some of these attributes and their use has allowed for the visualization...recombinant AAV serotypes 1, 2, 5 and 8 in the rat nigrostriatal system. J Neurochem 109, 838–845. PubMed PMID...PMID: 19727139. Ugolini, G., Kuypers, H.G., and Strick, P.L. (1989). Transneuronal transfer of herpes ...
  44. Addgene: The First Twenty Years

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    Blog Post
    ...March 2015, Addgene reached the 500,000 plasmids distributed milestone! We were thrilled to see the impact...one plasmid deposited at Addgene that has been distributed more than 100 times.   “I really like this award... labs worldwide use our plasmids. I hope they contribute to great discoveries!” — Julien Béthune, Professor...Flame Award on Bluesky. In 2016, we also began distributing ready-to-use viral vectors from some of our ...supportive educational resources. By 2017, we had distributed 1,000 ready-to-use viral vector preps. Today,...citations of individual items in our repository, a tribute to how many discoveries have been made because ...
  45. Troubleshooting Your Plasmid Cloning Experiment

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    Blog Post
    ...your cloning strategy: Restriction enzyme digestion Be mindful of the restriction enzymes you chose. Make...This post was contributed by Oskar Laur, head of the custom cloning core at Emory University, and Paolo...which technique you are going to adopt (i.e. restriction cloning, Gibson Assembly, Golden Gate etc.), ... fragments of the size you expect, check the restriction pattern of the enzymes you chose, and verify ...hopefully have some new strategies to tackle that tricky cloning project. Good luck with your experiment...
  46. Plasmid Tools for Microbiome Studies

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    Blog Post
    ...translation by sequestering the RBS, but binding of the “trigger RNA” (in this case, biomarker RNA or 16S rRNA isolated...can also detect expression of toxin mRNA from Clostridium difficile. As mRNA expression cannot be identified...fluorescent markers to visualize localization and distribution of gut bacteria without fixation or preparation... count cell divisions. The technique, called distributed cell division counting (DCDC), relies on the ... for both in vitro and in vivo studies. Find distributed cell division counting plasmids here References...PMCID: PMC2752045. Myhrvold, Cameron, et al. "A distributed cell division counter reveals growth dynamics...
  47. Addgene's Tips for Plasmid Quality Control

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    Blog Post
    ... added level of confidence in the plasmids we distribute through our quality control processes. Every ... Addgene, we collect data on every plasmid we distribute through our deposit process, and then we carefully...functional mutations, antibiotic resistance, restriction sites used during cloning, and most importantly...sequencing reactions in parallel. We have a few tricks to simplify the process. First, nearly all of our...sequencing from the exact same stock that we store and distribute from. Of course, your culture should always be...sequencing reads? Tell us your favorite sequencing tricks in the comments section below.  Additional Resources...
  48. Viral Vectors 101: Virus Safety

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    Blog Post
    ... caps, compatible with your centrifugation speed, to cover the centrifuge bins. These have to be added...okay to add another level of protection! When centrifuging viruses (a necessary step during production)...significant risk for aerosol contamination. As most centrifugation has to be done outside of a biosafety cabinet... and removed in a biosafety cabinet. For ultracentrifugation, heat sealed tubes can be used for extra ... spinning down lentivirus, you’ll need to use centrifuge bin covers, which you should open in the biosafety...
  49. Adeno Associated Virus (AAV) for Cell and Gene Therapy

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    Blog Post
    ...183 gene therapy trials (http://www.abedia.com/wiley/vectors.php). These clinical trials have been directed...This post was contributed by guest blogger Harshana S De Silva Feelixge. Gene therapy technologies ...gene therapies from conceptual design to clinical trials involve identifying a therapeutic gene, finding...most naturally occurring viruses used in clinical trials, wild type AAV is not associated with any pathogenicity...While basic research and other ongoing clinical trials support the utility of AAV as a broadly applicable...
  50. Experimenting in an Open Source lab: from CRISPR to Cats

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    Blog Post
    ...science has become increasingly restricted to academic and industrial labs, but recently there has been ...The following post was contributed by Derek Jacoby from Makerspace Victoria, CA Over the decades science...possible that we’ll find something interesting and contribute it back to the kittybiome project, but the primary...generally funded on a membership model - everyone contributes each month - with only occasional supplementation...would otherwise be discarded. For instance, the centrifuge in the picture had a broken controller and would...
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