Biology subjects

Davies, K.

Publications and source records attributed to Davies, K..

24 records · Page 2Linked to original sources

bioRxiv2020

Developing mammary terminal duct lobular units have a dynamic mucosal and stromal immune microenvironment

The human breast and ovine mammary gland undergo a striking degree of postnatal development, leading to formation of terminal duct lobular units (TDLUs). In this study we interrogated aspects of sheep TDLU growth to increase understanding of ovine mammogenesis and as a model for the study of breast development. Mammary epithelial proliferation is significantly higher in lambs less than two months old than in peri-pubertal animals. Ki67 expression is polarized to the leading edge of the developing TDLUs. Intraepithelial ductal macrophages exhibit striking periodicity and significantly increased density in lambs approaching puberty. Stromal macrophages are more abundant centrally than peripherally. The developing ovine mammary gland is infiltrated by intraepithelial and stromal T lymphocytes that are significantly more numerous in older lambs. In the stroma, hotspots of Ki67 expression colocalize with large aggregates of lymphocytes and macrophages. Multifocally these aggregates exhibit distinct organization consistent with tertiary lymphoid structures. The lamb mammary gland thus exhibits a dynamic mucosal and stromal immune microenvironment and, as such, constitutes a valuable model system that provides new insights into postnatal breast development. Summary statementDevelopment of terminal duct lobular units in the sheep mammary gland involves distinct growth phases and macrophage and lymphocyte fluxes. Tertiary lymphoid structures are present subjacent to the mucosal epithelium.

developmental biology↗

bioRxiv2020

The effect of heat on SARS-CoV-2 viability and RNA integrity as determined by plaque assay, virus culture and real-time RT-PCR

The effect of heat on SARS-CoV-2/England/2/2020 viability was assessed by plaque assay and virus culture. Heating to 56{degrees}C and 60{degrees}C for 15, 30 and 60 minutes led to a reduction in titre of between 2.1 and 4.9 log10 pfu/ml but complete inactivation was not observed. At 80{degrees}C plaques were observed after 15 and 30 minutes of heating, however after 60 minutes viable virus was only detected following virus culture. Heating to 80{degrees}C for 90 minutes and 95{degrees}C for 1 and 5 minutes resulted in no viable virus being detected. At 56{degrees}C and 60{degrees}C significant variability between replicates was observed and the titre often increased with heat-treatment time. Nucleic acids were extracted and tested by RT-PCR. Sensitivity of the RT-PCR was not compromised by heating to 56{degrees}C and 60{degrees}C. Heating to 80{degrees}C for 30 minutes or more and 95{degrees}C for 1 or 5 minutes however, resulted in an increase of at least three Ct values. This increase remained constant when different dilutions of virus underwent heat treatment. This indicates that high temperature heat inactivation of clinical samples prior to nucleic acid extraction could significantly affect the ability to detect virus in clinical samples from patients with lower viral loads by RT-PCR.

microbiology↗

bioRxiv2020

Fidgetin-like 2 is a novel negative regulator of axonal growth and can be targeted to promote functional nerve regeneration after injury.

The microtubule (MT) cytoskeleton plays a critical role in axon growth and guidance. Here, we identify the MT severing enzyme fidgetin-like 2 (FL2) as a negative regulator of axonal regeneration and a potential therapeutic target for promoting neural regeneration after injury. Genetic knockout of FL2 in cultured adult dorsal root ganglion (DRG) neurons resulted in longer axons and attenuated growth cone retraction in response to inhibitory molecules. Given the axonal growth-promoting effects of FL2 depletion in vitro, we tested whether the enzyme could be targeted to promote regeneration in a rodent model of peripheral nerve injury. In the model used in our experiments, the cavernous nerves (CN) are either crushed or transected, mimicking nerve injury caused by radical prostatectomy (RP). As with patients, CN injury results in erectile dysfunction, for which there are presently poor treatment options. At the time of injury, FL2-siRNA or control-siRNA was applied to the site using nanoparticles or chondroitin sulfate microgels as delivery agents. Treatment significantly enhanced functional nerve recovery, as determined by cavernosometry (measurements of corporal blood pressure in response to electrostimulation of the nerve). Remarkably, following complete bilateral nerve transection, visible and functional nerve regeneration was observed in 7 out of 8 animals treated with FL2-siRNA. In contrast, no control-siRNA treated animals showed regeneration. These observations suggest a novel therapeutic approach to treat peripheral nerve injury, particularly injuries resulting from surgical procedures such as RP, where treatments depleting FL2 could be applied locally at the time of injury.

neuroscience↗

bioRxiv2018

The predictive value of quantitative nucleic acid amplification detection of Clostridium difficile toxin gene for faecal sample toxin status and patient outcome

BackgroundLaboratory diagnosis of Clostridium difficile infection (CDI) remains unsettled, despite updated guidelines. We investigated the potential utility of quantitative data from a nucleic acid amplification test (NAAT) for C. difficile toxin gene (tg) for patient management.\n\nMethodsUsing data from the largest ever C. difficile diagnostic study (8853 diarrhoeal samples from 7335 patients), we determined the predicative value of C. difficile tgNAAT (Cepheid Xpert C.diff) low cycle threshold (CT) value for patient toxin positive status, CDI severity, mortality and CDI recurrence. Reference methods for CDI diagnosis were cytotoxicity assay (CTA) and cytotoxigenic culture (CTC).\n\nResultsOf 1281 tgNAAT positive faecal samples, 713 and 917 were CTA and CTC positive, respectively. The median tgNAAT CT for patients who died was 25.5 vs 27.5 for survivors (p = 0.021); for toxin-positivity was 24.9 vs 31.6 for toxin-negative samples (p<0.001) and for patients with a recurrence episode was 25.6 vs 27.3 for those who did not have a recurrent episode (p = 0.111). Following optimal cut-off determination, low CT was defined as [≤]25 and was significantly associated with a toxin-positive result (P<0.001, positive predictive value 83.9%), presence of PCR-ribotype 027 (P=0.025), and mortality (P=0.032). Recurrence was not associated with low CT (p 0.111).\n\nConclusionsLow tgNAAT CT could indicate CTA positive patients, have more severe infection, increased risk of mortality and possibly recurrence. Although, the limited specificity of tgNAAT means it cannot be used as a standalone test, it could augment a more timely diagnosis, and optimise management of these at-risk patients.

microbiology↗

bioRxiv2018

Simulation of enteric colonisation by and screening for Carbapenemase Producing Enterobacteriaceae using an in-vitro human gut model.

Introduction Introduction Methods Results Discussion Conclusion Appendix 1 Appendix 2 References Carbapenemase Producing Enterobacteriaceae (CPE) are increasing worldwide [1, 2] and pose a significant threat to public health. The burden of CPE infection is multifaceted, encompassing adjustment of treatment regimens [3, 4], increased duration of inpatient stay [5], associated morbidity [6] and mortality [5, 7, 8], in addition to the wider burden it poses on healthcare systems, with financial and societal implications [9]. The rapid spread of CPE within endemic areas [10] and in ...

microbiology↗

bioRxiv2018

Evidence for multifactorial processes underlying phenotypic variation in bat visual opsins

Studies of opsin genes offer insights into the evolutionary history and molecular basis of vertebrate color vision, but most assume intact open reading frames equate to functional phenotypes. Despite known variation in opsin repertoires and associated visual phenotypes, the genetic basis of such patterns has not been examined at each step of the central dogma. By comparing sequences, gene expression, and protein localization across a hyperdiverse group of mammals, noctilionoid bats, we find evidence that independent losses of S-opsin arose through disruptions at different stages of protein synthesis, while maintenance relates to frugivory. Discordance between DNA, RNA, and protein reveals that the loss of short-wave sensitivity in some lineages resulted from transcriptional and post-transcriptional changes in addition to degradation of open reading frames. These mismatches imply that visual phenotypes cannot reliably be predicted from genotypes alone, and connect ecology to multiple mechanisms behind the loss of color in vertebrates.

genomics↗