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

    Type
    Blog Post
    Published
    June 3, 2021, 1:15 p.m.
    ...Clinical and Developmental Immunology 2012:1–15 . https://doi.org/10.1155/2012/980250  Bates A, Power CA...Prospects of Antibody Fragments. Antibodies 8:28 . https://doi.org/10.3390/antib8020028  Bird R, Hardman ...antigen-binding proteins. Science 242:423–426 . https://doi.org/10.1126/science.3140379  Bradbury ARM,...display technologies. Nat Biotechnol 29:245–254 . https://doi.org/10.1038/nbt.1791  Deal CE, Balazs AB (...infection. Current Opinion in HIV and AIDS 10:190–197 . https://doi.org/10.1097/coh.0000000000000145  Gąciarz ...intrinsically stable scFv. PLoS ONE 12:e0189964 . https://doi.org/10.1371/journal.pone.0189964  Huston JS...the National Academy of Sciences 85:5879–5883 . https://doi.org/10.1073/pnas.85.16.5879  Leavy O (2016...

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

    Type
    Blog Post
    Published
    Sept. 28, 2020, noon
    ...sequence-specific antimicrobials. Nat Biotechnol 32:1146–1150 . https://doi.org/10.1038/nbt.3043 Bikard D, Jiang W, Samai...CRISPR-Cas system. Nucleic Acids Research 41:7429–7437 . https://doi.org/10.1093/nar/gkt520 Citorik RJ, Mimee M...RNA-guided nucleases. Nat Biotechnol 32:1141–1145 . https://doi.org/10.1038/nbt.3011 Cobb RE, Wang Y, Zhao...Engineered CRISPR/Cas System. ACS Synth Biol 4:723–728 . https://doi.org/10.1021/sb500351f Dong C, Fontana J, Patel...transcriptional reprogramming in bacteria. Nat Commun 9: . https://doi.org/10.1038/s41467-018-04901-6 Jiang W, Bikard...CRISPR-Cas systems. Nat Biotechnol 31:233–239 . https://doi.org/10.1038/nbt.2508 Leonard SP, Perutka J...Broad-Host-Range Plasmids. ACS Synth Biol 7:1279–1290 . https://doi.org/10.1021/acssynbio.7b00399 Li Q, Sun B,...

  3. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...Photoswitching Proteins (Vol. 2173, pp. 21–51). Springer US. https://doi.org/10.1007/978-1-0716-0755-8_2 Lehtinen, ...Frontiers in Cellular Neuroscience, 15, 778900. https://doi.org/10.3389/fncel.2021.778900 Mattis, J., ...microbial opsins. Nature Methods, 9(2), 159–172. https://doi.org/10.1038/nmeth.1808 References Abreu, N...Photoswitching Proteins (Vol. 2173, pp. 21–51). Springer US. https://doi.org/10.1007/978-1-0716-0755-8_2 Boyden, E....activity. Nature Neuroscience, 8(9), 1263–1268. https://doi.org/10.1038/nn1525 Gunaydin, L. A., Yizhar...optogenetic control. Nature Neuroscience, 13(3), 387–392. https://doi.org/10.1038/nn.2495 Marshel, J. H., Kim, Y...triggering perception. Science, 365(6453), eaaw5202. https://doi.org/10.1126/science.aaw5202 Mattis, J., Tye...

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

    Type
    Blog Post
    Published
    Sept. 3, 2020, 12:15 p.m.
    ...control of CRISPR–Cas9. Nat Methods 15:924–927 . https://doi.org/10.1038/s41592-018-0178-9  Hemphill J,...Cas9 Gene Editing. J Am Chem Soc 137:5642–5645 . https://doi.org/10.1021/ja512664v  Jain PK, Ramanan V,... Protectors. Angew Chem Int Ed 55:12440–12444 . https://doi.org/10.1002/anie.201606123  Kim JH, Rege M...gene expression control. Nat Methods 16:633–639 . https://doi.org/10.1038/s41592-019-0436-5 Mathony J, Hoffmann...of CRISPR‐Cas9. Angew Chem Int Ed 58:6285–6289 . https://doi.org/10.1002/anie.201900788 Nihongaki Y, Furuhata...neuronal differentiation. Nat Methods 14:963–966 . https://doi.org/10.1038/nmeth.4430 Nihongaki Y, Kawano...optogenetic genome editing. Nat Biotechnol 33:755–760 . https://doi.org/10.1038/nbt.3245 Nihongaki Y, Yamamoto...

  5. Rett Syndrome: A History of Research and Therapeutic Outlooks

    Type
    Blog Post
    Published
    Nov. 19, 2020, 2:15 p.m.
    ...methyl-CpG-binding protein 2. Nat Genet 23:185–188 . https://doi.org/10.1038/13810 Amir RE, Zoghbi HY (2000...phenotype-genotype correlations. Am J Med Genet 97:147–152 . https://doi.org/10.1002/1096-8628(200022)97:2<147::aid-ajmg6...Syndrome and Related Disorders. Cell 152:984–996 . https://doi.org/10.1016/j.cell.2013.01.038 Guy J, Gan ...Model of Rett Syndrome. Science 315:1143–1147 . https://doi.org/10.1126/science.1138389 Le TTH, Tran NT...Human-Induced Pluripotent Stem Cells. Front Genet 10: . https://doi.org/10.3389/fgene.2019.00625 McGraw CM, Samaco... Function Requires MeCP2. Science 333:186–186 . https://doi.org/10.1126/science.1206593 Powers S, Miranda...MeCP2 null (S51.002). Neurology 92 (15 Supplement) . http://n.neurology.org/content/92/15_Supplement/S51.002...

  6. The PAM Requirement and Expanding CRISPR Beyond SpCas9

    Type
    Blog Post
    Published
    Aug. 20, 2020, 2:30 p.m.
    ...targeting with CRISPR–Cas13. Nature 550:280–284 . https://doi.org/10.1038/nature24049 Find plasmids from...high-fidelity genome-editing platform. Genome Biol 19: . https://doi.org/10.1186/s13059-018-1591-1 Cox DBT, Gootenberg...editing with CRISPR-Cas13. Science 358:1019–1027 . https://doi.org/10.1126/science.aaq0180 Find plasmids...endonucleases in human cells. Nat Biotechnol 34:863–868 . https://doi.org/10.1038/nbt.3609 Find plasmids from this...derived from Campylobacter jejuni. Nat Commun 8: . https://doi.org/10.1038/ncomms14500 Find plasmids from...altered PAM specificities. Nature 523:481–485 . https://doi.org/10.1038/nature14592 Find plasmids from...nucleases in human cells. Nat Biotechnol 34:869–874 . https://doi.org/10.1038/nbt.3620 Find plasmids from this...

  7. Viral Vectors 101: Pseudotyping

    Type
    Blog Post
    Published
    April 20, 2021, 2:30 p.m.
    ...Protein for Neutralization Assays. Viruses 12:513 . https://doi.org/10.3390/v12050513 Cronin J, Zhang X-Y,...Lentiviral Vectors through Pseudotyping. CGT 5:387–398 . https://doi.org/10.2174/1566523054546224 DePolo NJ, Reed...Inactivated by Human Serum. Molecular Therapy 2:218–222 . https://doi.org/10.1006/mthe.2000.0116 Gutierrez-Guerrero...for Research and Gene Therapy. Viruses 12:1016 . https://doi.org/10.3390/v12091016 Joglekar AV, Sandoval...Guises. Human Gene Therapy Methods 28:291–301 . https://doi.org/10.1089/hgtb.2017.084 Li Q, Liu Q, Huang...for enveloped viruses. Rev Med Virol 28:e1963 . https://doi.org/10.1002/rmv.1963 Mazarakis ND (2001) Rabies...delivery. Human Molecular Genetics 10:2109–2121 . https://doi.org/10.1093/hmg/10.19.2109 Sandrin V, Boson...

  8. Generating Mouse Models Using CRISPR/Cas9

    Type
    Blog Post
    Published
    July 12, 2016, 2:30 p.m.
    ...Using CRISPR/Cas Systems. Science 339:819–823 . https://doi.org/10.1126/science.1231143 Doench JG, Hartenian...gene inactivation. Nat Biotechnol 32:1262–1267 . https://doi.org/10.1038/nbt.3026 Gurumurthy CB, Takahashi...Embryos. Current Protocols in Human Genetics 88: . https://doi.org/10.1002/0471142905.hg1508s88 Leidy-Davis...CRISPR/Zygote Injection Approaches. Sci Rep 8: . https://doi.org/10.1038/s41598-018-33408-9 Mizuno N, Mizutani...Adeno-Associated Viral Vector. iScience 9:286–297 . https://doi.org/10.1016/j.isci.2018.10.030 Qin W, Kutny...Editing. Current Protocols in Mouse Biology 6:39–66 . https://doi.org/10.1002/9780470942390.mo150178 Qin W, ...Electroporation of Nuclease. Genetics 200:423–430 . https://doi.org/10.1534/genetics.115.176594 Yang H, Wang...

  9. Viral Vectors 101: Producing Your rAAV

    Type
    Blog Post
    Published
    July 16, 2024, 1:15 p.m.
    .... Human Gene Therapy Methods, 23(1), Article 1. https://doi.org/10.1089/hgtb.2011.034 Benyamini, B., Esbin...Adeno-Associated Viral Vectors [Preprint]. Molecular Biology. https://doi.org/10.1101/2023.03.20.533580 Goodwin, M. ... Molecular Neurodegeneration, 15(1), Article 1. https://doi.org/10.1186/s13024-020-00361-z Grimm, D., ...recombinant AAV-2. Gene Therapy, 6(7), Article 7. https://doi.org/10.1038/sj.gt.3300946 Howard, D. B., &.... Human Gene Therapy Methods, 28(1), Article 1. https://doi.org/10.1089/hgtb.2016.180 Korte, J., Mienert.... Human Gene Therapy, 32(13–14), Article 13–14. https://doi.org/10.1089/hum.2020.120 Lock, M., Alvira,.... Human Gene Therapy Methods, 25(2), Article 2. https://doi.org/10.1089/hgtb.2013.131 Lock, M., McGorray...

  10. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    Published
    June 25, 2024, 1:15 p.m.
    ... Integrated in Parallel. Cell, 154(4), 914–927. https://doi.org/10.1016/J.CELL.2013.07.018 Anzalone, A...breaks or donor DNA. Nature, 576(7785), 149–157. https://doi.org/10.1038/s41586-019-1711-4 Chen, P. J.,...manipulation. Nature Reviews Genetics, 24(3), Article 3. https://doi.org/10.1038/s41576-022-00541-1 Kim, H. K.,...performance. Science Advances, 5(11), eaax9249. https://doi.org/10.1126/sciadv.aax9249 Koeppel, J., Weller... determinants. Nature Biotechnology 2023, 1–11. https://doi.org/10.1038/s41587-023-01678-y Li, X., Chen...epigenetic manipulation of prime editing. Cell. https://doi.org/10.1016/j.cell.2024.03.020 Mathis, N.,... learning. Nature Biotechnology, 41, 1151–1159. https://doi.org/10.1038/s41587-022-01613-7 Mathis, N.,...

  11. CRISPR Activators: A Comparison Between dCas9-VP64, SAM, SunTag, VPR, and More!

    Type
    Blog Post
    Published
    Oct. 6, 2020, 1:15 p.m.
    ...CRISPR-Cas system. Nucleic Acids Research 41:7429–7437 . https://doi.org/10.1093/nar/gkt520 Chavez A, Scheiman ...transcriptional programming. Nat Methods 12:326–328 . https://doi.org/10.1038/nmeth.3312 Chavez A, Tuttle M,...activators in multiple species. Nat Methods 13:563–567 . https://doi.org/10.1038/nmeth.3871 Konermann S, Brigham...engineered CRISPR-Cas9 complex. Nature 517:583–588 . https://doi.org/10.1038/nature14136 Perez-Pinera P, Kocak...transcription factors. Nat Methods 10:973–976 . https://doi.org/10.1038/nmeth.2600 Qi LS, Larson MH, Gilbert...Control of Gene Expression. Cell 152:1173–1183 . https://doi.org/10.1016/j.cell.2013.02.022 Sajwan S, Mannervik...system differ in target preference. Sci Rep 9: . https://doi.org/10.1038/s41598-019-54179-x Tanenbaum ME...

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

    Type
    Blog Post
    Published
    Dec. 14, 2021, 2:15 p.m.
    ...methylated somatic enhancers. Nat Genet 52, 819–827. https://doi.org/10.1038/s41588-020-0639-9.  Feinberg A...from their normal counterparts. Nature 301, 89–92. https://doi.org/10.1038/301089a0. Galonska C, Charlton...methyltransferase footprints. Nat Commun 9, 597. https://doi.org/10.1038/s41467-017-02708-5 Hrit J, Goodrich...activity and function in development. eLife 7:e34870. https://doi.org/10.7554/eLife.34870.  Kaas GA, Zhong C... and Memory Formation. Neuron 79, 6 P1086-1093. https://doi.org/10.1016/j.neuron.2013.08.032.  Morita ...catalytic domain fusions. Nat Biotechnol 34, 1060–1065. https://doi.org/10.1038/nbt.3658. Sapozhnikov DM, Szyf...methyltransferase with CRISPR/dCas9. Nat Commun 12, 5711. https://doi.org/10.1038/s41467-021-25991-9. Spruijt CG...

  13. Plasmid-based Recombinant Monoclonal Antibodies: What They Are and Why You Should Be Excited About Them

    Type
    Blog Post
    Published
    May 4, 2021, 1:15 p.m.
    ...enhanced multiplex immunolabeling of brain. eLife 8: . https://doi.org/10.7554/elife.43322 Baker M (2015) Reproducibility...Blame it on the antibodies. Nature 521:274–276 . https://doi.org/10.1038/521274a Begley CG, Ellis LM (2012...preclinical cancer research. Nature 483:531–533 . https://doi.org/10.1038/483531a Bradbury A, Plückthun ...antibodies used in research. Nature 518:27–29 . https://doi.org/10.1038/518027a Bradbury AM, Plückthun...validate recombinants once. Nature 520:295–295 . https://doi.org/10.1038/520295b Bradbury ARM, Trinklein... functional variable regions. mAbs 10:539–546 . https://doi.org/10.1080/19420862.2018.1445456 Crosnier...mouse monoclonal antibodies. BMC Biology 8:76 . https://doi.org/10.1186/1741-7007-8-76 Greenfield, E.A...

  14. Viral Vectors 101: The Retroviral Lifecycle

    Type
    Blog Post
    Published
    July 27, 2023, 1:15 p.m.
    ...retroviruses. Microbiological Reviews, 56(3), 375–394. https://doi.org/10.1128/MR.56.3.375-394.1992. PubMed PMID...Current State and Perspectives. Viruses, 13(7), 1288. https://doi.org/10.3390/v13071288. PMID: 34372494. Prussin...Environmental Science & Technology Letters, 2(4), 84. https://doi.org/10.1021/ACS.ESTLETT.5B00050. PubMed PMID...of the United States of America, 54(1), 137–144. https://doi.org/10.1073/PNAS.54.1.137. PubMed PMID: 4285422...precursor protein. The EMBO Journal, 16(16), 5113–5122. https://doi.org/10.1093/EMBOJ/16.16.5113. PubMed PMID:...virus DNAs. Journal of Virology, 14(5), 1132–1141. https://doi.org/10.1128/JVI.14.5.1132-1141.1974. PubMed.... Journal of Molecular Biology, 79(1), 163–183. https://doi.org/10.1016/0022-2836(73)90277-5. PubMed PMID...

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

    Type
    Blog Post
    Published
    March 21, 2024, 1:15 p.m.
    ...dopamine D2/D3 receptors. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-78827-9 Breen, C. J...fluorescence-based ligand-binding assay. Scientific Reports, 6. https://doi.org/10.1038/srep25769 Grimm, J. B., & Lavis...Vol. 19, Issue 2, pp. 149–158). Nature Research. https://doi.org/10.1038/s41592-021-01338-6 Grimm, J. B... vivo imaging. Nature Methods, 14(10), 987–994. https://doi.org/10.1038/nmeth.4403 Hayashi-Takanaka, Y... partner for live cell imaging. PLoS ONE, 9(9). https://doi.org/10.1371/journal.pone.0106271 Heinrichs...fluorescent dyes. Nature Cell Biology, 11(S1), S7–S7. https://doi.org/10.1038/ncb1939 Liu, X., Yang, L., Long...mammalian cells. Biophysics Reports, 3(4–6), 64–72. https://doi.org/10.1007/s41048-017-0037-8 Lucidi, M., ...

  16. Finding nucleic acids with SHERLOCK and DETECTR

    Type
    Blog Post
    Published
    April 16, 2020, 1 p.m.
    ...RNA-targeting CRISPR effector. Science 353:aaf5573 . https://doi.org/10.1126/science.aaf5573 Broughton JP, ... detection of SARS-CoV-2. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0513-4 Chen JS, Ma ...-stranded DNase activity. Science 360:436–439 . https://doi.org/10.1126/science.aar6245 Gootenberg JS,... with CRISPR-Cas13a/C2c2. Science 356:438–442 . https://doi.org/10.1126/science.aam9321 Gootenberg JS,... Cas13, Cas12a, and Csm6. Science 360:439–444 . https://doi.org/10.1126/science.aaq0179 Myhrvold C, Freije...diagnostics using CRISPR-Cas13. Science 360:444–448 . https://doi.org/10.1126/science.aas8836 Niewoehner O, ...CRISPR-associated protein Csm6. RNA 22:318–329 . https://doi.org/10.1261/rna.054098.115 Shmakov S, Abudayyeh...

  17. Plasmids 101: Broad Host Range Plasmids

    Type
    Blog Post
    Published
    April 11, 2024, 1:15 p.m.
    ...Journal of Biological Chemistry, 273(14), 8447–8453. https://doi.org/10.1074/jbc.273.14.8447  Jain, A., & Srivastava...plasmids. FEMS Microbiology Letters, 348(2), 87–96. https://doi.org/10.1111/1574-6968.12241  Keen, N. T., ...in Gram-negative bacteria. Gene, 70(1), 191–197. https://doi.org/10.1016/0378-1119(88)90117-5  Lale, R....Molecular Biology (Clifton, N.J.), 765, 327–343. https://doi.org/10.1007/978-1-61779-197-0_19  Meyer, R...host-range IncQ plasmids. Plasmid, 62(2), 57–70. https://doi.org/10.1016/j.plasmid.2009.05.001  Meyer, ...Molecular & General Genetics: MGG, 152(3), 129–135. https://doi.org/10.1007/BF00268809  Prior, J. E., Lynch...Biotechnology and Bioengineering, 106(2), 326–332. https://doi.org/10.1002/bit.22695  Schmidhauser, T. J....

  18. Viral Vectors 101: Integrase-Deficient Lentiviral Vectors

    Type
    Blog Post
    Published
    May 13, 2025, 1:15 p.m.
    ...and applications. Gene Therapy, 17(2), 150–157. https://doi.org/10.1038/gt.2009.135. PubMed PMID: 19847206...Expression. Viruses: Essential Agents of Life, 147–175. https://doi.org/10.1007/978-94-007-4899-6_7. PubMed Central...human cells. Nature Biotechnology, 31(9), 822–826. https://doi.org/10.1038/nbt.2623. PubMed PMID: 23792628...Journal of Clinical Investigation, 118(9), 3143–3150. https://doi.org/10.1172/JCI35798. PubMed PMID: 18688286...infection. Journal of Virology, 70(2), 721–728. https://doi.org/10.1128/JVI.70.2.721-728.1996. PubMed ...genes and local hotspots. Cell, 110(4), 521–529. https://doi.org/10.1016/s0092-8674(02)00864-4. PubMed ...American Society of Gene Therapy, 17(8), 1316–1332. https://doi.org/10.1038/mt.2009.122. PubMed PMID: 19491821...

  19. Prime Editing: Adding Precision and Flexibility to CRISPR Editing

    Type
    Blog Post
    Published
    Jan. 13, 2025, 9:49 p.m.
    ... editing. Nature Biotechnology, 40(5), 731–740. https://doi.org/10.1038/s41587-021-01133-w Anzalone, A...breaks or donor DNA. Nature, 576(7785), 149–157. https://doi.org/10.1038/s41586-019-1711-4 Chen, P. J.,...editing outcomes. Cell, 184(22), 5635-5652.e29. https://doi.org/10.1016/j.cell.2021.09.018 Choi, J., Chen... editing. Nature Biotechnology, 40(2), 218–226. https://doi.org/10.1038/s41587-021-01025-z Doman, J. L...efficient prime editors. Cell, 186(18), 3983-4002.e26. https://doi.org/10.1016/j.cell.2023.07.039 Lin, Q., Jin...in plants. Nature Biotechnology, 39(8), 923–927. https://doi.org/10.1038/s41587-021-00868-w Nelson, J. ...efficiency. Nature Biotechnology, 40(3), 402–410. https://doi.org/10.1038/s41587-021-01039-7 Pandey, S.,...

  20. Plasmids 101: Gram Negative and Positive Bacteria

    Type
    Blog Post
    Published
    Aug. 2, 2022, 1:15 p.m.
    ...(red/pink) staining. Image credit: Mark Perkins https://www.flickr.com/photos/occbio/7092385559 For...these resources.   Bruckner, M. Gram Staining. https://serc.carleton.edu/microbelife/research_methods...Protocols. American Society for Microbiology (2005). https://asm.org/getattachment/5c95a063-326b-4b2f-98ce-...Positive vs Gram Negative. Technology Networks (2019) https://www.technologynetworks.com/immunology/articles...) a000414 (2010). Cleveland Clinic. Gram Stain. https://my.clevelandclinic.org/health/diagnostics/22612...gram-stain Hardy, J. Gram’s Serendipitous Stain. https://hardydiagnostics.com/wp-content/uploads/2016/05...
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