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  1. Fluorescent Protein Guide: Biosensors

    Type
    Collection
    ...marking active neuron populations. Nat Commun. 2018 Oct 25;9(1):4440. Eric Schreiter Calcium AAV expression ...accumulation in bacteria. Biotechnol Biofuels. 2008 Jun 3. 1(1):11. Wolf Frommer Maltose Green fluorescent MBP-based...interneurons across vertebrate species. Nat Neurosci. 2016 Oct 31. Gordon Fishell Calcium GCaMP-X genetic encoded...indicator for neural activity imaging. J Neurosci. 2012 Oct 3;32(40):13819-40. Baljit Khakh , Douglas Kim , Loren...intracellular Zn(2+) homeostasis. Nat Methods. 2009 Oct;6(10):737-40. Maarten Merkx Zinc eZinCh-2 Zn2+ FRET... Secretion of Pancreatic Islets. Anal Chem. 2019 Oct 1;91(19):12212-12219. Huiwang Ai Zinc GZnP2 Cytosolic... Encoded Fluorescent Biosensor. Cell Metab. 2011 Oct 5;14(4):545-54. Gary Yellen NADH/NAD+ Peredox fluorescent...

  2. p53 Pathway

    Type
    Collection
    ...-phase expressed 1; also known as GTSE1 BAI-1 Brain-specific angiogenesis inhibitor 1 Bax BCL2-associated...inhibitor type 1), member 1 PERP TP53 apoptosis effector PIDD p53-induced death domain protein 1 PIGs Etoposide... Name 14-3-3-σ Stratifin Apaf-1 Apoptotic peptidase activating factor 1 ATM ATM serine/threonine kinase...kinase 4 or 6 CHK1 Checkpoint kinase 1 CHK2 Checkpoint kinase 2 Cop-1 Ring finger and WD repeat domain 2...receptor superfamily, member 10b E2F-1 E2F transcription factor 1 Fas Fas cell surface death receptor ...SESN1 SESN2 SESN3 Sestrins 1, 2, or 3 Siah Siah E3 ubiquitin protein ligase 1 TSC2 Tuberous sclerosis 2...p53 field. Brosh R, Rotter V. Nat Rev Cancer. 2009 Oct;9(10):701-13. PubMed PMID: 19693097 . The expanding...

  3. Zhang Lab CRISPR Page

    Type
    Collection
    ...Heidenreich 1, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F. Nat Biotechnol . 2015 Jan;33(1):102-6....2013.08.021. Epub 2013 Aug 29. Erratum in: Cell. 2013 Oct 10;155(2):479-80. PubMed . Genome engineering using...2281-308. doi: 10.1038/nprot.2013.143. Epub 2013 Oct 24. PubMed . Return to SpCas9 plasmids GeCKO Library...-6. doi: 10.1038/nbt.3055. Epub 2014 Oct 19. PubMed . In vivo genome editing using Staphylococcus aureus... Regev A, Feng G, Sharp PA, Zhang F. Cell . 2014 Oct 9;159(2):440-55. doi: 10.1016/j.cell.2014.09.014....SpCas9 alone without sgRNA. Full references are below. 1. SpCas9 (or SpCas9n, D10A nickase) + single guide ...screens. The libraries are available in two formats: 1 vector system - lentiCRISPR - sgRNA and SpCas9 together...

  4. Hot Plasmids - October 2022

    Type
    Blog Post
    ...protein sequence of the predecessor GEVIs (called ASAP 1 and 2), they found an indicator that is optimized ...several other constructs in plasmid form. Fig. 1: Summary of the approach and outcomes of the screen...

  5. University of Florida Serotype Testing Panel for the Eye and Brain

    Type
    Collection
    ...Donor-Variation and Implications in Genome Editing. Sci Rep . Oct 19;6:35495. PMID: 27759036 Other citations include...Donor-Variation and Implications in Genome Editing. Sci Rep . Oct 19;6:35495. PMID: 27759036 Rosario, et al. 2016. ...for any application TMN200 (200 mM sodium chloride, 1 mM magnesium chloride, 20 mM Tris at pH 8.0) Suitable...adeno-associated viral vector. Hum Gene Ther Methods . Feb;25(1):72-82. PMID: 24191859 Ye, et al. 2015. Safety and...

  6. Neurodegeneration Research Collection

    Type
    Collection
    ...between Rab12 and LRRK2 . Dhekne et al. Elife. 2023 Oct 24. See More CRISPR Tools Find CRISPR pooled libraries...target alpha-synuclein. Sastre et al. Sci Rep. 2023 Oct 18. Target neural oxytocin receptors using an AAV-CRISPR...dopaminergic activity in vivo. Sun et al. Nat Methods. 2020 Oct 21. Glutamate indicators with improved activation...one of three different inherited genes: Presenilin 1, Presenilin 2, and APP gene.The majority (>90%) of...

  7. 9 tips for a successful postdoctoral experience

    Type
    Blog Post
    ... postdoc fellowship. 1. Reverse engineer success On Day 1 of your postdoctoral experience, define what... of your postdoctoral training experience. If you're going to commit to doing a postdoctoral fellowship...contributed by Erik Snapp, the Director of Student and Postdoctoral Programs at theJanelia Research Campus of the...the Howard Hughes Medical Institute. Today's postdoctoral fellows (PFs) face a number of challenges ranging...academia - the main reason most people enter postdoctoral training. Similarly, there are several factors...you searched for and eventually identified a postdoctoral mentor. A good mentor typically writes the grants...of reference- the graduate school mentor, the postdoctoral mentor, and at least one more person that knows...

  8. Hot Plasmids - October 2020

    Type
    Blog Post
    ... inhibitory synapses in the brain.  Figure 1:Schematic diagram of different FingR constructs and...

  9. Botman-Teusink Yeast FP Collection

    Type
    Collection
    ...Saccharomyces cerevisiae. Microb Cell Fact. 2013 Oct 25;12:96. doi: 10.1186/1475-2859-12-96. PubMed 24161108...proteins in budding yeast. Sci Rep. 2019 Feb 19;9(1):2234. doi: 10.1038/s41598-019-38913-z. PubMed 30783202...

  10. Allen Institute for Cell Science Plasmid Collection

    Type
    Collection
    ...Rafelski SM, Gunawardane RN. Mol Biol Cell. 2017 Oct 15;28(21):2854-2874. doi: 10.1091/mbc.E17-03-0209...Institute ID Tag Protein Structure 87420 PXN-EGFP AICSDP-1 EGFP Paxillin Matrix Adhesions 87421 TUBA1B-mEGFP ...TJP1-mEGFP AICSDP-23 mEGFP Tight junction protein ZO-1 Tight junctions 91565 AAVS1-mEGFP AICSDP-35 mEGFP ...Centrioles 101782 LAMP1-mEGFP AICSDP-19 mEGFP LAMP-1 Lysosome 101783 MAP1LC3B-mEGFP AICSDP-25 mEGFP Autophagy-related...101786 ST6GAL1-mEGFP AICSDP-26 mEGFP Sialyltransferase 1 Golgi 109122 NPM1-mEGFP AICSDP-50 mEGFP Nucleophosmin... HIST1H2BJ-mEGFP AICSDP-52 mEGFP Histone H2B type 1-J Histones 109119 CTNNB1-mEGFP AICSDP-47 mEGFP Beta-catenin...

  11. Jaenisch Lab CRISPR Plasmids

    Type
    Collection
    ...Shivalila CS, Dadon DB, Jaenisch R. Cell Res. 2013 Oct;23(10):1163-71. doi: 10.1038/cr.2013.122. Epub 2013...plasmids can be ordered via the links below: Table 1. dCas9 Activators sgRNA Dual Expression ID Plasmid...

  12. Antibody Plasmid Collection

    Type
    Collection
    ...Tomlinson I+J phagemid libraries. Immunol Lett. 2015 Oct;167(2):95-102. Joanna Bereta Sybody Generation Toolbox...phage display. J Immunol Methods. 2000 Aug 28;242(1-2):159-81. Carlos Barbas Vector system for expression...immunostaining. Biochem Biophys Res Commun. 2015 Jan 2;456(1):527-33. Gavin Wright pET-30-based vector dedicated...

  13. Tetracycline Inducible Expression

    Type
    Collection
    ...Pfleiderer K, Hillen W, Berens C. Biotechniques . 2004 Oct;37(4):546, 548, 550. PubMed . Optimization of the..., Klaver B, Berkhout B, Das AT. Gene Ther . 2006 Oct;13(19):1382-90. PubMed . Improved Tet-responsive ...Element On or off PI 26429 pLenti CMV rtTA3 Blast (w756-1) Lentiviral reverse tetracycline-controlled transactivator...

  14. Fujii Lab CRISPR Plasmids

    Type
    Collection
    ...gRNA-hIRF-1 #12 Expresses a guide RNA (gRNA) to target human IRF-1 promoter 61080 gRNA-hIRF-1 #12/pSIR ..._dCas9-2xAM_hIRF-1 Lentiviral plasmid expressing dCas9-2xAM and gRNA for human IRF-1 promoter. 98041 Sa-dCas9...interest. 98134 hIRF-1 gRNA #409 (Sa) Expresses a guide RNA (gRNA) to target human IRF-1 promoter for the ...system. 105283 hIRF-1 gRNA #351 (Sa) Expresses a guide RNA (gRNA) to target human IRF-1 promoter for the ...Yuno M, Suzuki Y, Sugano S, Fujii H. DNA Res. 2017 Oct 1;24(5):537-548. doi: 10.1093/dnares/dsx023. PubMed...LexA are subjected to affinity purification (Fig. 1). In enChIP, specific genomic regions are tagged with...plasmids or browse the Fujii Lab web page . Figure 1: iChIP general scheme Figure 2: enChIP general scheme...

  15. Plasmids for Stem Cell Research

    Type
    Collection
    ... 2018 Jul 6;9(1):2643. Otonkoski Lentivirus Human Expression of human Sox2, Nanog, Oct4, and Lin28 from...106(1):157-62. Jaenisch Lentivirus Mouse Doxycycline-inducible lentiviral expression of mouse Oct4, Sox2...Developmental Potential of iPSCs. Cell Stem Cell. 2019 Oct 30. pii: S1934-5909(19)30423-0. Schöler You can also...MicroRNA-Dependent Direct Conversion of Fibroblasts. Neuron. 2014 Oct 22;84(2):311-23. Yoo Fibroblasts Neurons Lentiviral...cell reprogramming. Stem Cell Res Ther. 2017 Jun 5;8(1):132. Zovein Replicating EBNA1 episome Human Non-integrating...transcription factors. Stem Cell Reports. 2015 Jan 13;4(1):25-36. Broccoli Fibroblasts Sensory Neurons Lentiviral...peripheral sensory neurons. Nat Neurosci. 2015 Jan;18(1):25-35. Baldwin Fibroblasts iTSCs Lentiviral Mouse...

  16. Rinehart Lab Phosphoprotein Reagents

    Type
    Collection
    ...library as GST-fusion peptides (“mode #1” expression). The mode #1 phosphosite library ( 111704 ) is available...Söll D, Isaacs FJ, Rinehart J. FEBS Lett . 2012. Oct 19;586(20):3716-22. PubMed (Link opens in a new window...standards for quantitative assessments. The mode #1 phosphosite library can be generated with either phosphoserine...available from Addgene. Screening kinases. The mode #1 phosphosite library can also be synthesized using ...pSerOTS-C1* (V70) Pooled Library 188526 iSPI_pSer_Subpool#1 Pooled Library 188527 iSPI_pSer_Subpool#2 Pooled Library...split mCherry 14-3-3β Pooled Library 111704 Mode #1 Library Pooled Library 111705 Mode #2 Library (14-...partial UAG codon reassignment and release factor 1 deletion. Heinemann IU, Rovner AJ, Aerni HR, Rogulina...

  17. PCR Applications for Copy Number Variation Assays

    Type
    Blog Post
    ...falciparum multidrug resistance-1 gene (pfmdr1). J Parasitol. 2011 Oct;97(5):939-42. doi: 10.1645/GE-2792.1...-87. doi: 10.1016/j.mimet.2005.09.007. Epub 2005 Oct 10. PMID: 16216354 ...against the limitations of the assay.      Fig. 1: A schematic representation of Sybr Green chemistry...Methods Mol Biol. 2018;1768:143-160. doi: 10.1007/978-1-4939-7778-9_9. PMID: 29717442. Arya M, Shergill IS...gamma receptor genes FCGR3A and FCGR3B. PloS one, 10(1), e0116791. https://doi.org/10.1371/journal.pone.0116791...

  18. Synthetic Photobiology: Optogenetics for E. coli

    Type
    Blog Post
    ...;3(11):820-31. doi: 10.1021/sb500273n. Epub 2014 Oct 11. PubMed. Find the plasmids from this publication...315-24. doi: 10.1016/j.jmb.2010.10.038. Epub 2010 Oct 28. PubMed. Find the plasmids from this publication...red light rapidly deactivates the system. Version 1 of this far-red/red light-responsive system is spread...

  19. Viral Vectors 101: Types of viruses

    Type
    Blog Post
    ...Retroviruses and cancer. Rev Infect Dis. 1982 Sep-Oct;4(5):1015-25. DOI: 10.1093/clinids/4.5.1015 Lee C.S...Application of Viruses to Biotechnology. Viruses. 2021 Oct 14;13(10):2073. DOI: 10.3390/v13102073 Resources ...efficiently with adenovirus and AAV.   Table 1: Types of viruses and their features Choosing ...

  20. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

    Type
    Blog Post
    ...Weissman JS. Cell. 2014 Oct 23;159(3):647-61. doi: 10.1016/j.cell.2014.09.029. Epub 2014 Oct 9.     ...endogenous genes and it consists of three components: 1. A nucleolytically inactive Cas9-VP64 fusion; 2. A... the top 10 hits.” Two-way CRISPR screening In October, Jonathan Weissman’s lab introduced additional ...

  21. CRISPR Protocol for Genomic Deletions in Mammalian Cell Lines [Video]

    Type
    Blog Post
    ... determines fetal hemoglobin level. Science 2013 Oct 11;342(6155):253-257. PubMed. 3. Canver MC, Bauer...harness non-homologous end joining repair (NHEJ) [1]. Our initial work was with TALENs, in collaboration...from the University of Pennsylvania.     References: 1. Lee HJ, Kim E, Kim JS. Targeted chromosomal deletions...using zinc finger nucleases. Genome Res. 2010 Jan;20(1):81-89. PubMed. 2. Bauer DE, Kamran SC, Lessard S,...

  22. Protocol - Over-Agar Antibiotic Plating

    Type
    Protocol
    ... resistance) Procedure Day 1 Prepare carbenicillin to a concentration of 1 mg/mL – 4 mg/mL in LB medium...determine optimal antibiotic concentration. Last Update: Oct. 27, 2017 Protocol Video Watch the protocol video...lawn of E. coli and no apparent selection. 150 µL of 1 mg/mL Carbenicillin plated over-agar Plate shows several...over-agar Plate shows less individual colonies than the 1 mg/mL plate and effective selection. 150 µL of 4 mg...several individual colonies with smaller size than the 1 mg/mL and 2 mg/mL plates and effective selection. ...

  23. Plasmids 101: Dimers and Multimers

    Type
    Blog Post
    ... of colicinogenic factor E-1 from Proteus mirabilis. Biochemistry. 1968 Oct;7(10):3513-20. doi: 10.1021...Plasmids and Chromosomes. Microbiol Spectr. 2014 Oct;2(5). doi: 10.1128/microbiolspec.PLAS-0025-2014. ...indicates the presence of a multimer.   Fig. 1: The monomer of Plasmid 12259: pMD2.G (depicted on...plasmid sequencing services using long-read sequencing (1-25 kb), such as Oxford Nanopore sequencing or PacBio...10017-26. doi: 10.1074/jbc.M110.176636. Epub 2011 Feb 1. PMID: 21285356; PMCID: PMC3060453. Bazaral M, Helinski...Methods Mol Biol. 2009;582:11-25. doi: 10.1007/978-1-60761-340-4_2. PMID: 19763938. Maucksch C, Bohla A...

  25. Molecular Biology Protocol - Restriction Digest of Plasmid DNA

    Type
    Protocol
    ...restriction digestion reaction could look like this: 1 µg DNA 1 µL of each Restriction Enzyme 3 µL 10x Buffer...definition: one unit of enzyme will cut 1 µg of DNA in a 50 µL reaction in 1 hour. Using this ratio, you can .... For diagnostic digests, 1-2 hours is often sufficient. For digests with >1 µg of DNA used for cloning...of a plasmid by diagnostic digest . Last Upload: Oct. 11th, 2016 Protocol Video Watch the video below ...ng of DNA, while molecular cloning often requires 1 µg of DNA. The total reaction volume usually varies...tube at appropriate temperature (usually 37 °C) for 1 hour. Always follow the manufacturer’s instructions...

  26. Hot Plasmids: FRET-Based Biosensors

    Type
    Blog Post
    ...self-associating fluorescent domains. ACS Chem Biol. 2013 Oct 18;8(10):2133-9. doi: 10.1021/cb400427b. Epub 2013...variants. This resulted in the construction of redCALWY-1, a red-shifted FRET sensor for zinc using variants...

  27. Viral Vectors 101: Biosensors

    Type
    Blog Post
    ...Introduction to Biosensors. Essays Biochem. 2016 Jun 30;60(1):1-8. DOI: 10.1042/EBC20150001 Leopold, A. V., Shcherbakova...Applications. Frontiers in Cellular Neuroscience. 2019 Oct Vol. 13; 1662-5102. DOI: 10.3389/fncel.2019.00474...

  28. Plasmids for Endogenous Gene Tagging in Human Cells

    Type
    Blog Post
    ...Last updated on Oct 14, 2020 by Seth Kasowitz. This post was contributed by the gene editing team at ...Collection Fluorescent tagging strategy Figure 1: Gene editing is the addition of a useful coding sequence...plasmid design strategy. A donor plasmid contains 1 kb homology arms matching the gene of interest, a ...Institute website at alleninstitute.org. References 1. Roberts, Brock, et al. "Systematic gene tagging using...

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

    Type
    Blog Post
    ... the F plasmid ccdB killer gene”. Gene. 1994 Oct 11;148(1):71-4. PubMed PMID: 7926841. 4. Bernard, P.,...succumb to the toxicity of CcdB.   Figure 1: Image from Bernard, P., et al. showing the pKIL 18...submit a guest blog entry of your own! References 1. Bernard, P. “Positive Selection of Recombinant DNA...

  30. Lentiviral Vector Uses and Overview

    Type
    Blog Post
    ...HIV-1 were transduced with a lentiviral vector containing an antisense sequence against the HIV-1 envelope...U, Takahashi M, Gage FH, Verma IM. J Virol. 1998 Oct;72(10):8150-7. PubMed PMID: 9733856. PubMed Central...Trono and collaborators turned to the lentivirus HIV-1, well-known to infect non-dividing cells. The first...plasmids. The packaging plasmid carried a mutated HIV-1 provirus that couldn’t package itself due to a few...plasmid encoded the desired transgene flanked by HIV-1 long terminal repeats (LTRs) that facilitate viral... targeting and tracing cells in the brain (Figure 1). 2nd generation lentiviral packaging system The graphic...infectivity, is often used as a substitute for HIV-1 Env, which can only infect CD4+ cells. 3rd generation...
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