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We narrowed to 208 results for: PHI-1

Showing: 61 - 80 of 208 results

  1. AAV Titers: Where Do They Come From And What Do They Mean?

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    Blog Post
    ...near-perfect physical-to-infectious particle ratio of 1:1 (Zeltner et al., 2010). However, for recombinant ...preparations are genome-containing (Figure 1).    Figure 1: Electron micrograph of an Addgene AAV...reported a physical-to-infectious particle ratio of 50:1 (Zeltner et al., 2010). The specific infectivity of... lot (if we still have it available). References 1. Fagone, Paolo, et al. "Systemic errors in quantitative... Human Gene Therapy, Part B: Methods 23.1 (2011): 1-7. PubMed PMID: 22428975. PubMed Central PMCID: PMC3640491...Image courtesy of David Bell and Svetla Stoilova-McPhie, Center for Nanoscale Systems, Harvard University...

  2. Harnessing Bacterial Toxins for Allelic Exchange

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    Blog Post
    ... requires selection. These two steps are (Figure 1): The initial plasmid integration step (the so-called...antibiotic resistance marker from the vector (abR, Figure 1). The resolution step (“double crossover”) which leads... loss of a specific phenotype (using sacB, Figure 1, further discussed below).  Counter-selectable marker...Current protocols in molecular biology 106.1 (2014): 1-16. PubMed PMID: 24733238. Additional resources on...performed the following modifications to pDS132 (Philippe et al., 2004): Replaced the sacB cassette with...PMID: 29760772. PubMed Central PMCID: PMC5946454. Philippe, Nadège, et al. "Improvement of pCVD442, a suicide...

  3. Scientific Reproducibility - Focusing on Solutions at the Minisymposium on Reproducibility

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    Blog Post
    ... handed out at the event). Program 0 - 1:24 - Intro 1:24 - 29:31 - Reproducibility Overview - Jeffrey... 49:45 0 1:18:45 - Reagent Development - Steven C. Almo, Institute for Protein Innovation  1:18:45 - 2...reproducibility As Jeffrey Flier points out in his talk (1:24 - 29:31), there are a variety of ways of defining...enterprise towards greater reproducibility. Cause 1: Inability to repeat previously performed experiments...the Institute for Protein Innovation (IPI) (49:45 - 1:18:45), there are also initiatives to create more ...found. Consider the hypothetical situation in Figure 1 where many scientists are performing similar experiments...Editor at Science) Edward J. Hall (Professor of Philosophy at Harvard University) Tony Cijsouw (Neuroscience...

  4. Tips for Screening with Yeast Two Hybrid Systems

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    Blog Post
    ... fusions that retain their individual activities (1). Researchers also discovered the modular format of...systems could be combined effectively (3). In Figure 1 for instance, the DBD of the fusion protein shown ...ubiquitin system has been devised (8). References 1. Casadaban M.J., Martinez-Arias A., Shapira S.K., ...now many variations, including many that use auxotrophic rescue genes as reporters and some that repress...example of the former. In this system, histidine-auxotrophic host strains are used to select for binding-dependent...

  5. CRISPR References and Information

    Type
    Collection
    ..., 2.4 MB Zhang GeCKO pooled library amplification 1 vector system: lentiCRISPR v2 2 vector system: lentiCas9...sites for S. pyogenes Cas9, S. aureus Cas9, S. thermophilus Cas9, N. meningitidis Cas9, or Cas12a from your...off-target binding and can work for S. pyogenes , S. thermophilus , or N. meningitidis Cas9 PAMs. Currently supports...

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

    Type
    Blog Post
    ...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,...these may require restriction fragment length polymorphism analysis, allele-specific PCR, T7EN1 cleavage...

  7. Comparing Cas9 to NgAgo: Can the Argonautes Best CRISPR?

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    Blog Post
    ...NgAgo takes a different approach, randomly removing 1-20 nucleotides from the cleavage site specified by...About NgAgo User's First Impressions Here References 1. Gao, Feng, Xiao Z. Shen, Feng Jiang, Yongqiang Wu... et al. characterized Argonaute from Thermus thermophilus (TtAgo), showing that this protein could cleave...orthologs similar to TtAgo and PfAgo, another thermophilic Argonaute. They identified NgAgo and showed ...

  8. Natural or synthetic? How Addgene’s dataset reveals trends in biological innovation

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    Blog Post
    ...is expanding rapidly.  References 1. Kunjapur, Aditya M., Philipp Pfingstag, and Neil C. Thompson. "Gene...from distantly related organisms. In 2006, less than 1% of the genes deposited at Addgene were synthetic.... student at the time, got involved. Along with Philipp Pfingstag, a visiting graduate student from TU ...

  9. When Fidelity Matters: A frank discussion about ligase fidelity

    Type
    Blog Post
    ...phosphorylated DNA termini to 3 ́-OH DNA termini (1-4). In vitro, ligases (notably T4 DNA ligase) are ... enzymology of DNA repair enzymes.     References 1. Shuman, Stewart, and Christopher D. Lima. "The polynucleotide...thermostable DNA ligase-encoding gene." Gene 109.1 (1991): 1-11. PubMed PMID: 1756968. 7. Lauer, G., et al. "Cloning...and even include profiling single nucleotide polymorphisms (SNPs) (5,12,13). For example, in the Ligase...sequence, and engineered expression of Thermus thermophilus DNA ligase, a homolog of Escherichia coli DNA...Identification of essential residues in Thermus thermophilus DNA ligase." Nucleic acids research 24.15 (1996...for characterization of resistance-mediating polymorphisms in African samples of Plasmodium falciparum....

  10. Cpf1: A New Tool for CRISPR Genome Editing

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    Blog Post
    ...guide for a refresher on CRISPR/Cas9.  Figure 1: Cpf1 is a single RNA-guided endonuclease of a class... than the multi-subunit complex employed by class 1 systems. A putative new class 2 nuclease, Cpf1 (CRISPR...that Cpf1 can tolerate mismatches at gRNA positions 1, 8, 9, and 19-23. Accordingly, the 3’ end of the gRNA...Most gRNAs directed low-frequency Cpf1 cleavage at 1-12 off-target sites; in contrast, SpCas9 may cleave...the diversity of CRISPR-based systems. References 1. Zetsche, Bernd, et al. "Cpf1 is a single RNA-guided... off-target editing rates, determined using sophisticated genome-wide analysis. At many of its computationally...

  11. Using Phosphoserine to Study Protein Phosphorylation

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    Blog Post
    ...follow her on Twitter @nieminm.   References 1. Cohen, Philip. "The origins of protein phosphorylation."...cellular proteins are modified through phosphorylation (1). However, the expansion of studies on protein phosphorylation...three components required for translation (Figure 1): A tRNA that recognizes a specific ‘open’ codon ... open reading frame (ORF) of interest (Figure 2). 1. The phosphoserine OTS The backbone of the phosphoserine...modification allowed the deletion of release factor 1, the protein responsible for terminating translation...Rinehart lab: pCRT7 NT TOPO E17TAG GFP and pGEX-6P-1. The pCRT7 NT TOPO vector contains a mutant pSer-containing...

  12. Addgene-Seeding Labs Plasmid Grant: Accelerating Science Globally - 5 Scientists, 4 Countries & 3 Continents!

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    Blog Post
    ... compounds with various antimicrobial activities (1). She has developed a fast endophyte screening system...us coordinate and promote the awards. References 1. Martinez-Klimova, Elena et al. “Endophytes as sources...antibiotic” Biochemical Pharmacology 2017 Jun 15;134:1-17. PubMed PMID: 27984002. 2. Bilan, Dmitry S. et ...working in a wide range of research fields and geographical locations. We are excited to see how all of ...

  13. Viral Vectors 101: Voltage Indicators

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    Blog Post
    ...depths (1 mm), important for certain applications such as in vivo tissue imaging.   Figure 1: Ace-mScarlet...sources – voltage-gated potassium channels found in Drosophila to phosphatases from sea squirts. This design... detector in this system was dipicrylamine, a lipophilic compound that distributes itself within the plasma...sensing) hydrolyzes a precursor dye to make it more lipophilic, increasing its affinity for the membrane, where... fluorescent component (i.e., when the dye is lipophilic and integrates into the membrane), the voltage...

  14. Fluorescent Proteins 101: Introduction to FRET

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    Blog Post
    ...acceptor fluorophore. The typical steps in FRET are: 1. Donor fluorophore excitation by absorption of a photon... overlap, the fluorophores must be located within 1-10nm of each other and be oriented appropriately for... from various papers to make the decision easier. 1. Müller, Sara M., et al. "Quantification of Förster...diseases and even assist in drug discovery. References 1. Baird, Geoffrey S., et al. "Circular permutation ...have enhanced the ability of labs to answer sophisticated questions about cellular processes. Currently...

  15. Educational Planarian Tools for Teaching Developmental Biology Techniques

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    Blog Post
    ... hybridization experiments. A recent publication [1] from the Sánchez lab describes the plasmids and protocols...deposit) are described in the Sánchez lab publication [1] so that the students performing these experiments...can easily investigate in planarians. References 1. Alice Accorsi, Monique M. Williams, Eric J. Ross,...Proceedings of the National Academy of Sciences 100.suppl 1 (2003): 11861-11865. PubMed PMID: 12917490. PubMed...pp. 806-811. PubMed PMID: 9486653. 3. Newmark, Phillip A., et al. "Ingestion of bacterially expressed ...

  16. Nanoblades: Tiny CRISPR Ninjas for Genome Editing Difficult Cells

    Type
    Blog Post
    ...following four components into 293T cells. Figure 1: The key components of Nanoblades. Image from Mangeot...protein. A single Nanoblade particle can be loaded with 1-4 different gRNAs. Viral envelope proteins To alter... between ~50-70% for these four cell types (Table 1). Additionally, hiPSCs and mouse BM cells still behaved...hepatocytes  Myd88  ~50% Human HSCs  Myd88  ~50% Table 1: Nanoblades editing efficiencies of primary cells....accessible genome editing tool.   References Mangeot, Philippe E., et al. "Genome editing in primary cells and...

  17. Plasmids 101: Knockout/Knock-In Plasmids

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    Blog Post
    ... the example shown in Figure 1, large sequences corresponding to exons 1 and 3 of the targeted gene have...knock out exon 2 of a given gene.   Figure 1: A knockout targeting vector designed to insert a ... the Neomycin resistance (NeoR) gene between exon 1 and 3 of the targeted gene. Upon recombination, the...can be used to replace genes in yeast, mice, or Drosophila through homologous recombination. The concept...

  18. Celebrating One Million Plasmids Shared!

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    Blog Post
    ... @Addgene congrats for 1 million orders. @RothLabUNC accounts for 10,000 or 1%! — BryanRoth (@zenbrainest... scientific sharing community (check out the infographic below for stats on our plasmid deposits and requests...

  19. Cpf1 Update: Comparison to Cas9 and NgAgo

    Type
    Blog Post
    ...on-target and off-target editing efficiency Figure 1: Effects of (A) double and (B) single base pair gRNA-target...that Cpf1 can tolerate mismatches at gRNA positions 1, 8, 9, and 19-23. Accordingly, the 3’ end of the gRNA...Most gRNAs directed low-frequency Cpf1 cleavage at 1-12 off-target sites; in contrast, SpCas9 may cleave...fits into the genome editing landscape. References 1. Kim D, Kim J, Hur JK, Been KW, Yoon SH, Kim JS. Genome-wide... off-target editing rates, determined using sophisticated genome-wide analysis. At many of its computationally...

  20. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    ...attract fish for them to prey upon (Figure 1). Figure 1: The sea anemone's red color can be used ...synthetic biology. Journal of Biological Engineering, 12(1). https://doi.org/10.1186/s13036-018-0100-0 Murakoshi...expression in living cells. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-48604-4 Salih...surface of the chromoprotein Ultramarine with hydrophilic amino acids to reduce non-specific interactions...
Showing: 61 - 80 of 208 results