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  1. Last 7 days
  2. Nov 2022
    1. DNAPolymerase A

      Primase and DNA polymerase A work in close association.

    2. CDK2

      This is the S-phase CDK.

    3. Assembly of the pre-replicative complex
      • Replication origin licensing.
      • All of this occurs in G1 phase
    4. Orc complex

      Orc1-5 complex.

    5. Cdc6

      Cdc6 is only present in G1 phase.

    6. DNA replication pathway in humans. Orc complex binds the origin of replication.

    1. The initial sample consisted of 1 band. F = 0. 1st generation = The sample overall less dense, still one band. Intermediate density. dsDNA made of one strand heavy and one light. After 2 generations, there was a band for intermediate density and for strands of just light, N-14, dsDNA.

    2. Three methods of replication were initially hypothesized: * Conservative * Semi-conservative * Dispersive

      Semi-conservative method was eventually determined to be correct based on empirical evidence from Messelson & Stahl, in 1958.

    3. Parental strands consist of N-15 isotopes. Replicated daughter strands consist of N-14 isotopes. The CsCl ultracentrifugation process creates density gradient. This allows DNA fragments of different densities to migrate and form a band at the point at which their buoyant density equals that of the salt.

      1. E.coli grown in an heavy nitrogen, N-15, enriched medium
      2. Then transferred to N-14 based media to reproduce
      3. As several points in the experiment, cells were lysed and underwent ultracentrifugation through a CsCl concentration gradient
  3. Aug 2022
    1. Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature, 1–1. https://doi.org/10.1038/s41586-022-04474-x

  4. Dec 2021
  5. Oct 2021
  6. Jul 2021
    1. Short interview that covers the findings of a systematic review that aimed to identify the number of studies trying to replicate the outcomes of clinical decision support systems.

      Article being discussed in this piece: Coiera, E., & Tong, H. L. (2021). Replication studies in the clinical decision support literature-frequency, fidelity, and impact. Journal of the American Medical Informatics Association: JAMIA, ocab049. https://doi.org/10/gmb35n

  7. Jun 2021
  8. May 2021
    1. Braud, M., Gaboriaud, A., Ferry, T., Mardi, W. E., Silva, L. D., Lemouzy, M., Guttierrez, J., Petit, S., Szabelska, A., & IJzerman, H. (2021). COVID-19-related conspiracy beliefs and their relationship with perceived stress and pre-existing conspiracy beliefs in a Prolific Academic sample: A replication and extension of Georgiou et al. (2020). PsyArXiv. https://doi.org/10.31234/osf.io/t62s7

  9. Apr 2021
  10. Mar 2021
  11. Feb 2021
  12. Dec 2020
    1. All replication in R6K relies on the two essential components of a minimal replicon, the γ ori, and its cognate Rep, π protein, encoded by the pir gene
    1. Corker, K. S., Arnal, J., Bonfiglio, D. B. V., Curran, P. G., Chartier, C. R., Chopik, W. J., Guadagno, R., Kimbrough, A., Schmidt, K., & Wiggins, B. J. (2020). Many Labs 5: Registered Replication of Albarracín et al. (2008), Experiment 7. PsyArXiv. https://doi.org/10.31234/osf.io/qzspr

  13. Nov 2020
    1. Replication begins

      Rolling circle replication overview

      Replication begins when the Rep protein, which is encoded on the plasmid (ORF A), recognizes a specific site on the plasmid (double-strand origin, or DSO) and catalyzes the nicking of one DNA strand. The Rep protein remains bound to the 5′ phosphate after the nicking action. The newly released 3′ hydroxyl on the opposite end serves as a primer for DNA synthesis. The host DNA polymerase uses the unnicked circular strand as a template, so that a single replication fork moves around a plasmid until it regenerates the DSO. A second copy of Rep protein catalyzes the cleavage of the newly formed DSO, effectively releasing a single stranded copy of the plasmid. In the absence of Rep, the replication fork continues to move around the template, forming a single stranded concatemer. The single strand origin (SSO), a non-coding element that forms extensive secondary structure, is required for synthesis of the lagging strand. SSO sequences vary considerably among different RCR plasmids, but are extremely important for robust replication of the plasmid in the cell [10]. Here we describe the engineering of the pWV01 RCR origin to create pBAV1K-T5, a very broad-host range expression vector.

  14. Oct 2020
  15. Sep 2020
  16. Aug 2020
    1. Luban, J., Sattler, R., Mühlberger, E., Graci, J. D., Cao, L., Weetall, M., Trotta, C., Colacino, J. M., Bavari, S., Strambio-De-Castillia, C., Suder, E. L., Wang, Y., Soloveva, V., Cintron-Lue, K., Naryshkin, N. A., Pykett, M., Welch, E. M., O’Keefe, K., Kong, R., … Peltz, S. (2020). The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines. BioRxiv, 2020.08.05.238394. https://doi.org/10.1101/2020.08.05.238394

  17. Jul 2020
    1. Listens to changes in a PostgreSQL Database and broadcasts them over WebSocket. It works like this:the Phoenix server listens to PostgreSQL's replication functionality (using Postgres' logical decoding).it converts the byte stream into JSON.it then broadcasts over WebSocket.
  18. Jun 2020
  19. May 2020
  20. Apr 2020
  21. Feb 2020
    1. 0.506 (0.532)

      can we find any measures of dispersion here?

    2. For the 12 studies with an original p < 0.005, 10 (83%) replicated. For the 12 studies with an original p > 0.005, only 1 (8%) replicated. Further work is needed to test if prediction markets outperform predictions based only on the initial p-value, to test if the market also aggregates other information important for reproducibility.

      p values may capture all the information?

  22. Jan 2020
  23. Dec 2019
    1. "The replication crisis, if nothing else, has shown that productivity is not intrinsically valuable. Much of what psychology has produced has been shown, empirically, to be a waste of time, effort, and money. As Gibson put it: our gains are puny, our science ill-founded. As a subject, it is hard to see what it has to lose from a period of theoretical confrontation. The ultimate response to the replication crisis will determine whether this bout is postponed or not."

  24. Jul 2019
  25. Jun 2016
    1. etter writing continued as a medium for theinformal exchange of information and for requesting fellowscientists to replicate experiments (Manten, 1980, p. 8).

      replication happened outside of journals, via letter writing

  26. Mar 2016
    1. Schmidt, S. (2009). Shall we really do it again? The powerful concept of replication is neglected in thesocial sciences.Review of General Psychology, 13(2), 90–100.
    2. Evanschitzky, H., Baumgarth, C., Hubbard, R., & Armstrong, J. S. (2007). Replication research’s disturbingtrend.Journal of Business Research, 60(4), 411–415. doi

      replication research

  27. Jan 2015
    1. Teachers can save digital content to the built-in storage and up to 50 students at a time can connect to the Access Point to download or access documents, videos, or other files on their own devices even if there’s no internet signal.

      CouchDB replication anyone?

  28. Oct 2013