66 Matching Annotations
  1. Last 7 days
    1. Surprisingly, quorum sensing promotes V. cholerae virulence factor expression and biofilm formation at low cell density and represses these traits at high cell density

      Vibrio cholerae QS (high density) inhibits biofilm and virulence

    2. Quorum sensing is essential for chronic P. aeruginosa respiratory infection because it controls adhesion, biofilm formation, and virulence factor expression

      Psuedomonas aeruginosa QS induces biofilm formation

    1. ampicillin

      Why is this different from the conclusion and Fig 6a of - Dwyer, Daniel J., et al. “Antibiotics Induce Redox-Related Physiological Alterations as Part of Their Lethality.” Proceedings of the National Academy of Sciences, vol. 111, no. 20, May 2014, pp. E2100–09. www.pnas.org, doi:10.1073/pnas.1401876111.

    2. kanamycin

      This is obviously sensitive to Oxygen

    3. We conclude that these antibiotic exposures did not produce ROS

      Too strong of a conclusion. Did not produce the ROS that we tested for - should be the wording

  2. Jul 2019
    1. This is a direct result of the evolution of these antibiotics in microorganisms competing for resources, in which the production of antibiotics that target fast growing bacterial cells

      Great point! Antibiotics might have evolved to contain growth or population size rather than 'kill' the whole population

    1. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed.
  3. Jun 2019
    1. introduction of Cu to agricultural soil selects for Cu resistance, but also indirectly selects for antibiotic resistance in the Cu‐resistant bacteria
    1. response to antimicrobial agents can greatly vary, depending on the location of a particular cell within a biofilm community
    1. For example, bacteria could be engineered to seek out hazardous chemicals or heavy metals in the environment, perform cleanup and return to their origin to report on the number of hazardous sites encountered via analysis by microfluidic devices
    1. operating in the frequency domain can offer considerable advantages over steady-state designs in terms of information gathering and transmission
    1. less sensitive to environmental noise and exposure time than systems based on steady-state signals
    1. QS represses biofilm formation in both S. aureus and V. cholerae
    2. Pseudomonas aeruginosa is motile upstream (a QS-off phenotype), but forms biofilms downstream (a QS-on phenotype) in flowing networks

      Psuedomonas QS on => biofilms

    1. one to two AHL molecules per cell are sufficient to trigger autoinduction, suggesting that at very low AHL concentrations QS is intrinsically stochastic
  4. May 2019
    1. attB and attP sites are typically ≤ 50 bp with different inverted repeat sequences flanking 2 to 12 bp of complementary sequence, which includes the recombination crossover point
    1. the Tn5 transposon has been shown to be functional in a wide range of Gram-negative bacteria and to randomly insert into their genomes with high efficiency
    1. using recombinases can be challenging because their reactions are slow (requiring 2–6 h) and often generate mixed populations when targeting a multicopy plasmid
  5. Apr 2019
    1. the direct qPCR master mix, were added for direct qPCR.

      So no boiling or thermal cycling for lysis was done?

    2. we performed direct qPCR amplification

      After your thermal cycling for lysis?

    3. SYTO9
    4. we had initially added a higher concentration of the aforementioned components

      Does not make any sense to me

    5. induced

      Poor vocabulory, makes the paper very confusing to read

    6. qPCR components comprised
    7. bovine serum albumin (BSA; Sigma, St. Louis, MO, USA), to adsorb PCR inhibitors
    1. tudents must be registered for a minimum of 6 credit hours

      OISS says - "To maintain your status, undergraduate students must complete 12 hours and graduate students must complete 9 hours per semester."

    1. exopolysaccharide > flagella >N-acyl-homoserine lactones (AHLs) signaling molecules > extracellular protein > swarming motility
    1. using a commercially-available buffer that also requires a 15-minute incubation period prior to direct PCR
    1. organisms require physical lysis mainly based on heat,(31) pressure,(32) sonication with sound waves,(33) and bead milling.(34)
  6. Mar 2019
  7. www.microbiologyresearch.org www.microbiologyresearch.org
    1. The fluorescence signal atCT37±7 corre-sponds to the no-template-control andrepresents bacterial DNA contamination inthe commercially supplied reagents.
    1. insulation of minimal promoters was demonstrated

      (citation 35) excerpts σ70-dependent promoter cores are not modular in function and, therefore, are not a good choice for use in the bottom-up design of promoters

      promoter cores of PECF11 and PT7 are comparatively insensitive to the sequence context imposed by operators

      (fig 1) Natural promoters from bacteria and phages were genetically refined to identify insulated promoter cores (minimal promoters for which transcriptional activity is independent of sequence context). b Natural single operators were permuted and refined to create synthetic operators with diverse transcriptional regulation properties, designed to be free of spontaneous promoter activity. c and d Insulated promoter cores c and synthetic operators d were experimentally characterized and parameterized as transcriptional activation- and repression-dependent parameter databases, respectively, via biophysical modeling. e Genetic circuits including both basic genetic gates and complex transcriptional networks can be precisely designed using insulated transcriptional elements

    1. each with 80% power (chance) of achieving P < 0.05

      What is the meaning of this sentence?

    1. real-time information

      How does memory provide real-time information? It's an integral of all past information

  8. Feb 2019
    1. Several aspects influence PCR yield and specificity: reagents concentration, primer and amplicon length, template and primer secondary structure, or G+C content

      There are other overlooked factors here - presence of inhibitors, Tm of reaction compared to primer thermodynamics

  9. Dec 2018
    1. suggesting recent horizontal acquisitions

      Has been found in 2 species that have been sequenced.

      It is possible that it exists in other unsequenced species

    1. negative controls containing AF1000 cells devoid of plasmid yielded Ct numbers higher than 26 and were automatically censored by the LightCyclerTM software.

      What's the explanation for this!?

    1. a shrinking number of people have personal memories

      How is it that the virus still persists!? It is quite impressive

    2. peer-reviewed research

      The quality of peer-review is definitely at fault here. It could also undermine public faith in the peer-review process and the 'scientific community'

    3. the difference in how scientists and the general public perceive risk

      Information asymmetry

    4. a loss of personal freedom

      Personal freedom is quite a misconstrued concept. People miss the fact that vaccinations are not as personal as they seem to be. Vaccinations have a significant effect on the population through herd immunity.

      Can someone clarify in general, what the hell is personal freedom?

    1. observed reduction was likely an underestimate due to the bimodal circuit activation in each population

      Oh, it is not easy to grow just OFF cells!

      • Can we prevent them from turning ON for this measurement to be more precise?
    2. observation of hysteresis

      General definition - Hysteresis is the dependence of the state of a system on its history

  10. Nov 2018
    1. Partial charges and discharges that combine to 100% are counted as a single full cycle

      Really? I don't think anyone has tested partial charges and discharges. I would like to see a reference for this point!

    2. research says

      That is pretty weak evidence for such a strong statement

    1. push the technical limits of this information storage system

      I don't see anything new in this, technology wise. Cas1-2 will integrate any sequence, whether it codes for pixels or not

  11. Oct 2018
    1. But the bully-pulpit talk didn’t do much

      That's funny! I like the background of the legacy of George Bush!