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  1. Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More

    Type
    Blog Post
    ...Why have zebrafish become such a popular model organism? Zebrafish (Figure 1) were initially recognized...reasons that zebrafish have been embraced as a model organism, I’ll outline a few of the available genetic resources...reason for the success of zebrafish as a model organism is its amenability to genetic manipulation. Tools...Europe, and China. In addition, the Zebrafish Model Organism Database ZFIN actively curates information on ...Generating zebrafish transgenics Creating transgenic organisms by introducing foreign DNA into the genome is ...fertilized zebrafish zygote transforms into an organism with a clearly established body plan including...pinhead—contribute to the “sculpting” of tissues and organs during embryo development. Single cell sequencing-based...

  2. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    ... Resources and references More resources on addgene.org  Addgene's CRISPR Guide Addgene's CRISPR 101 ...Reviews Microbiology, 20(11), 641–656. https://doi.org/10.1038/s41579-022-00739-4 References Bravo, J....CRISPR–Cas9. Nature, 603(7900), 343–347. https://doi.org/10.1038/s41586-022-04470-1 Cofsky, J. C., Soczek...Structural & Molecular Biology, 29(4), 395–402. https://doi.org/10.1038/s41594-022-00756-0 Jiang, F., & Doudna,...Annual Review of Biophysics, 46, 505–529. https://doi.org/10.1146/annurev-biophys-062215-010822 Nishimasu...and Target DNA. Cell, 156(5), 935–949. https://doi.org/10.1016/j.cell.2014.02.001 Osuka, S., Isomura, ...CRISPR–Cas9. The EMBO Journal, 37(10), e96941. https://doi.org/10.15252/embj.201796941 Pattanayak, V., Lin, S....

  3. Reagent Repositories Are Speeding up Science During the Pandemic

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    Blog Post
    ...investigate the susceptibility of cells from different organisms to SARS-CoV-2 (Chu et al., 2020). An additional...mechanisms to maintain and grow these critical organizations should be a fundamental part of the scientific... study. The Lancet Microbe 1:e14–e23 . https://doi.org/10.1016/s2666-5247(20)30004-5 McCray PB Jr, Pewe...Syndrome Coronavirus. JVI 81:813–821 . https://doi.org/10.1128/jvi.02012-06 Ou X, Liu Y, Lei X, Li P, ...cross-reactivity with SARS-CoV. Nat Commun 11: . https://doi.org/10.1038/s41467-020-15562-9 Subbarao K, Roberts ...SARS? Trends in Microbiology 14:299–303 . https://doi.org/10.1016/j.tim.2006.05.007 (2020) Open for outbreaks...outbreaks. Nat Biotechnol 38:377–377. https://doi.org/10.1038/s41587-020-0499-y Additional resources on the...

  4. Predicting Adverse Reactions to Monoclonal Antibody Drugs

    Type
    Blog Post
    ... the effects of the drug on the actual cells or organ system. This allows scientists to get a more definitive...Patients. Frontiers in Immunology, 13. https://www.frontiersin.org/articles/10.3389/fimmu.2022.885672Piché, ...Assessment (pp. 519–542). Academic Press. https://doi.org/10.1016/B978-0-12-417144-2.00027-5van Brummelen...Challenges. The oncologist, 21(10), 1260–1268. https://doi.org/10.1634/theoncologist.2016-0061WHO. International...Frontiers in drug discovery, 2, 952326. https://doi.org/10.3389/fddsv.2022.952326Joubert, M. K., Deshpande...Biotherapeutics. PloS one, 11(8), e0159328. https://doi.org/10.1371/journal.pone.0159328Groell, F., Jordan,...Pharmazeutische Verfahrenstechnik e.V, 130, 128–142. https://doi.org/10.1016/j.ejpb.2018.06.008Lu, RM., Hwang, YC., ...

  5. How to Design Your gRNA for CRISPR Genome Editing

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    Blog Post
    ...prime editors. Nat Biotechnol 38:824–844 . https://doi.org/10.1038/s41587-020-0561-9 Dempster JM, Pacini C...dependency data sets. Nat Commun 10: . https://doi.org/10.1038/s41467-019-13805-y Doench JG (2017) Am ...genetic screens. Nat Rev Genet 19:67–80 . https://doi.org/10.1038/nrg.2017.97 Hanna RE, Doench JG (2020) ...experiments. Nat Biotechnol 38:813–823 . https://doi.org/10.1038/s41587-020-0490-7 Radzisheuskaya A, Shlyueva...repression. Nucleic Acids Res 44:e141–e141 . https://doi.org/10.1093/nar/gkw583 Rees HA, Liu DR (2018) Base ...living cells. Nat Rev Genet 19:770–788 . https://doi.org/10.1038/s41576-018-0059-1 Veres A, Gosis BS, Ding... Sequencing. Cell Stem Cell 15:27–30 . https://doi.org/10.1016/j.stem.2014.04.020 Yang L, Guell M, Byrne...

  6. Hot Plasmids - May 2022

    Type
    Blog Post
    ...https://doi.org/10.7554/eLife.64631  Goertsen D, et al. Nature Neuroscience. 2022. https://doi.org/10.1038...proteomic mapping in both cell culture and whole organisms (see our 2019 overview). Until recently, the approach...dedicated transgenic line. Using zebrafish as a model organism, the Parton Lab recently created a flexible system...Given that the liver is an immunologically active organ, this advance is likely to afford the ability to...Goertsen D, et al. Nature Neuroscience. 2022. https://doi.org/10.1038/s41593-021-00969-4.   dCas9-SSAP with ...here! Wang et al. Nat Cell Biol. 2022. https://doi.org/10.1038/s41556-021-00836-1 Visual barcodes for...here! Kaufman, et al. 2022. Nature Comm.https://doi.org/10.1038/s41467-022-30008-0      ...

  7. Communicating Your Science With Help From ComSciCon

    Type
    Blog Post
    ...paper or preparing a presentation, it's easy to forget that you have a much bigger job than merely telling... at Addgene, ComSciCon, and many more great organizations. At ComSciCon, our primary mission is to strengthen...respective fields. To help attendees launch new organizations that will extend opportunities to practice science...education initiatives like BiteScis (https://bitescis.org/) and amazing graduate student writing collaboratives...collaboratives like Oceanbites (https://oceanbites.org/) have already grown out of our workshops. If you'... create them.  Seek out collaborations with organizations that practice science communication or start...Facebook, Instragram, or send an email to info@comscicon.org. Many thanks to our guest blogger, Nathan Sanders...

  8. A Practical Guide to Optimizing AAV DIO and FLEx Vector Expression

    Type
    Blog Post
    ... vector you are using. Contact Addgene (help@addgene.org), or the supplier of your vector, to obtain this...in the Mouse Brain. PLoS ONE 8:e76310. https://doi.org/10.1371/journal.pone.0076310 Burger C, Gorbatyuk... System. Molecular Therapy 10:302–317. https://doi.org/10.1016/j.ymthe.2004.05.024 Dudek AM, Pillay S,...Independent of AAV Receptor. J Virol 92. https://doi.org/10.1128/jvi.02213-17 Fischer KB, Collins HK, Callaway...Proc Natl Acad Sci USA 116:27001–27010. https://doi.org/10.1073/pnas.1915974116 Guerin K, Rego M, Bourges...Extracts. Human Gene Therapy 31:664–678. https://doi.org/10.1089/hum.2019.277 Lavin TK, Jin L, Lea NE, Wickersham...Concentrations. Front Synaptic Neurosci 12. https://doi.org/10.3389/fnsyn.2020.00006 O’Carroll SJ, Cook WH,...

  9. Hot Plasmids February 2024

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    Blog Post
    ...–9. https://doi.org/10.1038/s41592-023-02085-6. PMID: 38036853. Preprint: https://doi.org/10.21203/rs.3...–4. https://doi.org/10.1038/s41587-023-02018-w. PMID: 38081970. Preprint: https://doi.org/10.21203/rs.3...Biotechnology, 10.1038/s41587-023-01756-1. https://doi.org/10.1038/s41587-023-01756-1. PMID: 37095348. ...from StayGold. ResearchSquare (Preprint). https://doi.org/10.21203/rs.3.rs-3188559/v1.  Neurogenetic alchemy... Nanotechnology, 18, 1241–1251 (2023). https://doi.org/10.1038/s41565-023-01419-x. PMID: 37430038. Endothelial-specific...primates. Nature Communications, 14(1), 3345. https://doi.org/10.1038/s41467-023-38582-7. PMID: 37291094.   ...

  10. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    ...steps. Molecular Cell, 70(3), 385-394.e3. https://doi.org/10.1016/j.molcel.2018.03.031 Xiao, Y., Luo, M.,... Cascade and Cas3. Science, 361(6397). https://doi.org/10.1126/science.aat0839 Yoshimi, K., & Mashimo,... Gene and Genome Editing, 3–4, 100013. https://doi.org/10.1016/j.ggedit.2022.100013 O’Brien, R. E., Bravo...Cascade. Molecular Cell, 83(5), 746-758.e5. https://doi.org/10.1016/j.molcel.2023.01.024 Morisaka, H., Yoshimi...human cells. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-13226-x Cameron, P., Coons, ...Nature Biotechnology, 37(12), 1471–1477. https://doi.org/10.1038/s41587-019-0310-0 Makarova, K. S., Wolf...Reviews Microbiology, 13(11), 722–736. https://doi.org/10.1038/nrmicro3569 Additional resources on the...

  11. Sharing Your Lab Protocols: Using Apps to Save Time & Track Your Experiments

    Type
    Blog Post
    ...About Developing Lab Management Software    Organizing and sharing your updated protocols So that’s ... mobile) tools are available for scientists to organize and share their scientific protocols. Here are...lab protocols online Addgene Website: http://www.addgene.org/ If you’re working with plasmids and you decide...submit an updated protocol? Just email us at help@addgene.org and we will be happy to upload your newest resources...Supplemental Document”: gRNA_Cloning Vector (deposited by George Church’s lab). Addgene has also cataloged a variety... Protocol Online Website: http://www.protocol-online.org/ Protocol Online is one of the early protocol...streamline your lab management and you want the works: organizing reagent storage and inventory, managing orders...

  12. Don’t FRET: Bimolecular Fluorescence Complementation Makes Visualizing Protein-Protein Interactions Easy

    Type
    Blog Post
    ... such resources in less genetically tractable organisms lags behind. BiFC can also be used to screen for...interactions in live Drosophila. eLife 7. https://doi.org/10.7554/elife.38853 Hu C-D, Chinenov Y, Kerppola...Complementation. Molecular Cell 9:789–798. https://doi.org/10.1016/s1097-2765(02)00496-3 Kerppola TK (2006... living cells. Nat Protoc 1:1278–1286. https://doi.org/10.1038/nprot.2006.201 Kerppola TK (2013) Bimolecular...Spring Harb Protoc 2013:pdb.prot076497. https://doi.org/10.1101/pdb.prot076497 Kim Y, Jung JP, Pack C-G...Saccharomyces cerevisiae. Genome Res 29:135–145. https://doi.org/10.1101/gr.231860.117 Kodama Y, Hu C-D (2012) Bimolecular...update and future perspectives. Biotech 53. https://doi.org/10.2144/000113943 Additional resources on the Addgene...

  13. The Importance of a Fun Workplace: Company Culture at Addgene

    Type
    Blog Post
    ... priority and have organized many events over the years. To keep the organizational side of things from...Use it! 8. Organize If you’re doing an event that requires people to be in groups, organize your troops...event! Addgene company culture At Addgene we organically developed the philosophy of  “work hard, play... in getting the fun started. I’m aware that  “organizing the fun” sounds a little neurotic, but hey- sometimes...posters, megaphone, or your company’s intranet. Don’t forget about the power of simple word of mouth - be sure... her operational responsibilities, she enjoys organizing team building events at Addgene and cultivating...

  14. CRISPR 101: Cytosine Transversion Editors

    Type
    Blog Post
    ...proteins. Nature Communications, 12(1), 1384. https://doi.org/10.1038/s41467-021-21559-9 Huang, M. E., Qin, Y.... Nature Cell Biology, 26(2), 294–304. https://doi.org/10.1038/s41556-023-01342-2 Koblan, L. W., Arbab...Nature Biotechnology, 39(11), 1414–1425. https://doi.org/10.1038/s41587-021-00938-z Koblan, L. W., Doman... Nature Biotechnology, 36(9), 843–846. https://doi.org/10.1038/nbt.4172 Kurt, I. C., Zhou, R., Iyer, S...cells. Nature Biotechnology, 39(1), 41–46. https://doi.org/10.1038/s41587-020-0609-x Yang, C., Dong, X., Ma...Baden-Wurttemberg, Germany), 9(26), e2202957. https://doi.org/10.1002/advs.202202957 Yuan, T., Yan, N., Fei, ...methods. Nature Communications, 12(1), 4902. https://doi.org/10.1038/s41467-021-25217-y Zhao, D., Li, J., Li...

  15. CRISPR 101: Any Base Transversion Editors

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    Blog Post
    ... Nature Biotechnology, 42(4), 638–650. https://doi.org/10.1038/s41587-023-01821-9 He, Y., Zhou, X., Chang.... Molecular Cell, 84(7), 1257-1270.e6. https://doi.org/10.1016/j.molcel.2024.01.021 Tong, H., Liu, N.,...National Science Review, 10(8), nwad143. https://doi.org/10.1093/nsr/nwad143 Tong, H., Wang, H., Wang, X...glycosylase. Nature Communications, 15(1), 4897. https://doi.org/10.1038/s41467-024-49343-5 Tong, H., Wang, X., ...Nature Biotechnology, 41(8), 1080–1084. https://doi.org/10.1038/s41587-022-01595-6 Ye, L., Zhao, D., Li...Nature Biotechnology, 42(10), 1538–1547. https://doi.org/10.1038/s41587-023-02050-w Yi, Z., Zhang, X., Wei...glycosylase. Nature Communications, 15(1), 6397. https://doi.org/10.1038/s41467-024-50012-w Additional Resources...

  16. Hot Plasmids Spring 2024

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    Blog Post
    ...screens. bioRxiv 2024.03.17.585235; doi: https://doi.org/10.1101/2024.03.17.585235.   Improved prime editor...RNA-binding protein. Nature. 2024 Apr 3. doi: https://doi.org/10.1038/s41586-024-07259-6. PMID: 38570691. Antibodies...monoclonal antibody. Virology. 558, 28–37. https://doi.org/10.1016/j.virol.2021.01.003. PMID: 33714753. ...emitting at 525 nm. Image reused from https://www.janelia.org/open-science/voltron-and-positron.  Both...2023) Neuron, 111(10), 1547–1563.e9. doi: https://doi.org/10.1016/j.neuron.2023.03.009. PMID: 37015225.  ...Virus. bioRxiv 2023.12.12.571321; doi: https://doi.org/10.1101/2023.12.12.571321.  Revolutionizing Gene...vitro and in vivo, including in human retinal organoids and live mice. Importantly, REVeRT avoids the ...

  17. Multicolor Animals: Using Fluorescent Proteins to Understand Single Cell Behavior

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    Blog Post
    ... (XFP) of different colors to label an organ or entire organism. Because each cell can have multiple copies...The ability to track single cell dynamics at the organism level has been made possible by tools that allow.... Genes encoding the fluorescent proteins are organized in tandem with a single promoter, but only the...developed for tracking various cell types and organisms and for improving the level of detail possible...that allow for multicolor labeling of an entire organism or a specific tissue. XFPs are introduced using...systems allow single cell dynamics in a variety of organisms to be observed in more detail than ever before...fluorescent proteins topic page Resources on Addgene.org Browse Addgene’s fluorescent protein collection...

  18. Transferable Skills Guide: Conflict Resolution

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    Blog Post
    ...critical in the business world. Companies and organizations that avoid all conflict can fall into “groupthink...individuals involved, and also for the labs, organizations, or businesses as a whole. When I’m attempting... sharing gets more challenging the bigger an organization gets, and creating new avenues of communication...should be communicated is necessary in a large organization, because confirming that every person has read...attempting to resolve conflicts within a given organization, it can help tremendously to have as much context... solutions that benefit themselves and their organization. Resolving conflicts is great, but avoiding ...Thomas-Kilmann Conflict Model, courtesy of https://managementweekly.org/thomas-kilmann-conflict-resolution-model...

  19. Genetically-encoded Sparse Cell Labeling - A SPARC of Innovation

    Type
    Blog Post
    ...specifically manipulate a cell type of interest in an organism, all cells of that type are affected. Previous...versatile and can be applied across cell types and organisms by replacing the transcription factor binding ...the PhiC31 recombinase can work in other model organisms including mouse and fish, SPARC is likely generalizable...in Drosophila. Nature Methods 9:47–55 . https://doi.org/10.1038/nmeth.1800 Isaacman-Beck J, Paik KC, Wienecke... proportions of cells. bioRxiv 788679; https://doi.org/10.1101/788679 Lin R, Wang R, Yuan J, Feng Q, Zhou...neurons. Nature Methods 15:1033–1036 . https://doi.org/10.1038/s41592-018-0184-y Additional resources...controlling gene expression in flies Resources on Addgene.org Find fluorescent protein plasmids at Addgene...

  20. Addgene's a Nonprofit? Nonprofit Awareness Day 2017

    Type
    Blog Post
    ...nonprofit" organization what do you think of? Maybe the term brings to mind a social service organization like... about a local food pantry or community arts organization. Many people are surprised to learn that Addgene...nonprofits do with their revenue. A nonprofit organization cannot distribute profits to private individuals...as a nonprofit, we attract partnerships with organizations that share our community-oriented values. Addgenies...Meron, Michael Lo., Michael Le., Michel, Michelle, Morgan, Natashia, Nicole, Olivia, Pamela, Racheal, Ramsey...Addgene Board Member, Connie Cepko Resources on Addgene.org Learn More About Our Mission Meet the Addgene...
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