14 Matching Annotations
  1. Last 7 days
    1. Bacterial cultures were first centrifuged at 15,000 x g for 10 min at 4 °C in a tabletop centrifuge (Heraeus Megafuge 16R, Thermo Scientific, Waltham, USA) to remove bacterial mass. The supernatants were filtered through 0.22 µm PES bottle top filters (Fisher Brand, New Hampshire, USA) and concentrated approximately 10-fold by tangential flow filtration (VivaFlow 200, 100 kDa cutoff, polyethersulfone, Sartorius, Göttingen, Germany). The concentrate was then ultracentrifuged for 2 h at 150,000 xg and 4 °C in a Beckman Optima LE-80K (Beckman Coulter, Brea, USA). The supernatant was discarded, and the pellet was washed twice in 1 mL ultrapure water. Afterward, the BMV pellet was resuspended in 1 mL ultrapure water and stored at 4 °C for a maximum of 1 week.

      Would you expect a difference in vessicle stability or selective depletion more labile vesicles (e.g., smaller/unsaturated or protein-rich)?

    1. Incorporation and detection of nitrile-labeled proteins in live bacterial cells

      How stable is this signal over time in live cells (v FTIR for instance)? Would it be possible to obtain in vivo kinetic data over a multi hour run?

  2. Jun 2025
    1. This model framework also more readily permits the integrated modeling of evolutionary therapy. These frameworks can assist calculations for optimal stochastic control and adaptive therapy in the presence of experimentally motivated drug and micro-environmental-dependent ecological cell interactions.

      One potential extension would seem to be considering scenarios where fitness is not strictly determined by heritable genetic states but rather by transient transcriptional or epigenetic programs. For example, stress-induced transcriptional states conferring temporary antibiotic tolerance at significant fitness costs or stochastic activation of drug-tolerant persister states in tumor cells. Have you considered incorporating such phenotypic switching dynamics, possibly modeled as Markov transitions between transient states with distinct fitness and ecological interaction coefficients?

  3. May 2025
    1. We observed mutations that replaced the wildtype base in all cells of the population as well as mixed sequences, i.e., not all copies of the target gene carried the mutation (data not shown).

      What was the ratio of fixed mutations to mixed sequences and how did you determine target depth of coverage (minimum VAF)?

  4. Apr 2025
    1. The method provided reliable MIC values for several strains of E.coli and K.pneumoniae and three types of antibiotics, including ampicillin from penicillin family, kanamycin from aminoglycoside family and levofloxacin from fluoroquinolone family.

      The table above (table 1) shows that levofloxacin MIC measured by Raman and E-test are similar. Levofloxacin exhibits concentration dependent killing which, in theory would be easier to measure in a rapid 1.5 hour test like the one proposed here. You mention ampicillin was also tested but I don't see that data here. This would be interesting to compare beacause ampicillin pharmacodynamics operate on a time > MIC principle, and so it would be even more impressive to detect resistance with a rapid, 1.5 hour test.

  5. Mar 2025
    1. But the efficacy of TILs was borderline when compared to CAR-T therapy. This may be because TILs are restricted to recognizing antigens bounded by the major histocompatibility complex (MHC), whereas CAR-T cells can target antigens without such limitation

      Could this also be due to differences in stage of disease treated in the two TIL studies reviewed relative to the CAR-T studies? French and NCT00200577 are also much smaller than the CART-T studies (88 v over 300 patients in most cases).

    1. Moreover, only a few studies examined the place of kin and cultural connection for parent and child in direct and moderated pathways(as in Howes & Obregon, 2009). Investment inindicatingsocio-culturalcontext withinfuturelongitudinalcohortdesignsis key to understanding overt and subliminalprotective influences on relational life

      Would this include studies assessing impact of number of attachment relationships an infant or child develops, beyond situations with one primary-carer?

    2. Of these, the majority (k=49; 89%)specificallymeasuredattachmentobservationallywith the Strange Situation Procedure (SSP; Ainsworth et al., 1978)or by theAttachment Q-Set(AQS; Waters, 1995).

      Did any of these studies include measurement of concordance between Strange Situation Procedure (SSP) and Attachment Q-Set (AQS)?

  6. Jan 2025
    1. We designed the image magnification at the CCD camera to be low (4.8 to 9.6 times) so that signal from a relatively large volume within the sample could be integrated in a single CCD pixel

      With the objectives used, what area does a CCD pixel cover? Is this cellular level resolution for the HepG2 cells (diameter ~20µm) and could cellular resolution for smaller cells, e.g. E. coli (diameter ~2µm) also be achieved?

    1. To test whether additional pathways may also be involved in the cell death induced by R4VPL3-1

      Have you noted any mechanisms of ferroptosis resistance that align with those seen previously, such as GSH and CoQ pathway activation (Wang et al. 2024 10.20517/cdr.2024.127)?

    2. We identified that R4VPL3-1 induced lipid peroxidation, as evident by positive 4HNE immuno-staining, suggesting that the R4VPL3-1 indeed induced ferroptosis.

      Is it clear that R4VPL3-1 is specifically inducing lipid peroxidation and ferroptosis or could this be a secondary effect of cell death due to RNF4 degradation?

  7. Dec 2024
    1. We then filtered out non-informative clusters with a median combined mitochondrial and ribosomal fraction higher than 50%

      From Figure S1, it seems ddqcR identified a 2-14% mitochondrial UMI contribution threshold for the intestinal cell clusters. How many non-informative clusters with high mitochondrial + ribosomal (<50%) fractions were removed in the subsequent integration and filtering process?