Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

Background Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non‐invasive biodiversity monitoring. Aims In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of fish communities in two aquaculture ponds and to evaluate the detection sensitivity of this tool for low‐density species alongside highly abundant species. Materials & Methods This study was carried out at two artificially stocked ponds with a high fish density following the introduction and removal of two rare fish species. Results & Discussion When two rare species were introduced and kept at a fixed location in the ponds, eDNA concentration (i.e., proportional read counts abundance) of the introduced species typically peaked after two days. The increase in eDNA concentration of the introduced fish after 43 hrs may have been caused by increased eDNA shedding rates as a result of fish being stressed by handling, as observed in other studies. Thereafter, it gradually declined and stabilised after six days. These findings are supported by the highest community dissimilarity of different sampling positions being observed on the second day after introduction, which then gradually decreased over time. On the sixth day, there was no longer a significant difference in community dissimilarity between sampling days. The introduced species were no longer detected at any sampling positions on 48 hrs after removal from the ponds. eDNA is found to decay faster in the field than in controlled conditions, which can be attributed to the complex effects of environmental conditions on eDNA persistence or resulting in the vertical transport of intracellular DNA and the extracellular DNA absorbed by particles in the sediment. The eDNA signal and detection probability of the introduced species were strongest near the keepnets, resulting in the highest community variance of different sampling events at this position. Thereafter, the eDNA signal significantly decreased with increasing distance, although the signal increased slightly again at 85 m position away from the keepnets. Conclusions Collectively, these findings reveal that eDNA distribution in lentic ecosystems is highly localised in space and time, which adds to the growing weight of evidence that eDNA signal provides a good approximation of the presence and distribution of species in ponds. Moreover, eDNA metabarcoding is a powerful tool for detection of rare species alongside more abundant species due to the use of generic PCR primers, and can enable monitoring of spatial and temporal community variance

Identification of novel macrolides with antibacterial, anti-inflammatory and type I and III IFN-augmenting activity in airway epithelium

BACKGROUND: Exacerbations of asthma and COPD are triggered by rhinoviruses. Uncontrolled inflammatory pathways, pathogenic bacterial burden and impaired antiviral immunity are thought to be important factors in disease severity and duration. Macrolides including azithromycin are often used to treat the above diseases, but exhibit variable levels of efficacy. Inhaled corticosteroids are also readily used in treatment, but may lack specificity. Ideally, new treatment alternatives should suppress unwanted inflammation, but spare beneficial antiviral immunity. METHODS: In the present study, we screened 225 novel macrolides and tested them for enhanced antiviral activity against rhinovirus, as well as anti-inflammatory activity and activity against Gram-positive and Gram-negative bacteria. Primary bronchial epithelial cells were grown from 10 asthmatic individuals and the effects of macrolides on rhinovirus replication were also examined. Another 30 structurally similar macrolides were also examined. RESULTS: The oleandomycin derivative Mac5, compared with azithromycin, showed superior induction (up to 5-fold, EC50 = 5-11 μM) of rhinovirus-induced type I IFNβ, type III IFNλ1 and type III IFNλ2/3 mRNA and the IFN-stimulated genes viperin and MxA, yet had no effect on IL-6 and IL-8 mRNA. Mac5 also suppressed rhinovirus replication at 48 h, proving antiviral activity. Mac5 showed antibacterial activity against Gram-positive Streptococcus pneumoniae; however, it did not have any antibacterial properties compared with azithromycin when used against Gram-negative Escherichia coli (as a model organism) and also the respiratory pathogens Pseudomonas aeruginosa and non-typeable Haemophilus influenzae. Further non-toxic Mac5 derivatives were identified with various anti-inflammatory, antiviral and antibacterial activities. CONCLUSIONS: The data support the idea that macrolides have antiviral properties through a mechanism that is yet to be ascertained. We also provide evidence that macrolides can be developed with anti-inflammatory, antibacterial and antiviral activity and show surprising versatility depending on the clinical need

Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)

In the UK, the native European otter ( Lutra lutra ) and invasive American mink ( Neovison vison ) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in decline due to population control and probable interspecific interaction with the otter. We explored the potential of DNA metabarcoding for investigating diet and niche partitioning between these mustelids. Otter spraints ( n = 171) and mink scats ( n = 19) collected from three sites (Malham Tarn, River Hull, and River Glaven) in northern and eastern England were screened for vertebrates using high-throughput sequencing. Otter diet mainly comprised aquatic fishes (81.0%) and amphibians (12.7%), whereas mink diet predominantly consisted of terrestrial birds (55.9%) and mammals (39.6%). The mink used a lower proportion (20%) of available prey ( n = 40 taxa) than the otter, and low niche overlap (0.267) was observed between these mustelids. Prey taxon richness of mink scats was lower than otter spraints, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter and mink consumed different prey taxa). Considering otter diet only, prey taxon richness was higher in spraints from the River Hull catchment, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter consumed different prey taxa at each site). Studies using morphological faecal analysis may misidentify the predator as well as prey items. Faecal DNA metabarcoding can resolve these issues and provide more accurate and detailed dietary information. When upscaled across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink

Low dose Btk inhibitors selectively block platelet activation by CLEC-2

Inhibitors of the tyrosine kinase Btk have been proposed as novel antiplatelet agents. In this study we show that low concentrations of the Btk inhibitor ibrutinib block CLEC-2-mediated activation and tyrosine phosphorylation including Syk and PLCγ2 in human platelets. Activation is also blocked in patients with X-linked agammaglobulinaemia (XLA) caused by a deficiency or absence of Btk. In contrast, the response to GPVI is delayed in the presence of low concentrations of ibrutinib or in patients with XLA, and tyrosine phosphorylation of Syk is preserved. A similar set of results is seen with the second-generation inhibitor, acalabrutinib. The differential effect of Btk inhibition in CLEC-2 relative to GPVI signalling is explained by the positive feedback role involving Btk itself, as well as ADP and thromboxane A2 mediated activation of P2Y12 and TP receptors, respectively. This feedback role is not seen in mouse platelets and, consistent with this, CLEC-2-mediated activation is blocked by high but not by low concentrations of ibrutinib. Nevertheless, thrombosis was absent in 8 out of 13 mice treated with ibrutinib. These results show that Btk inhibitors selectively block activation of human platelets by CLEC-2 relative to GPVI suggesting that they can be used at ‘low dose’ in patients to target CLEC-2 in thrombo-inflammatory disease

Significance of herpesvirus immediate early gene expression in cellular immunity to cytomegalovirus infection

Interstitial pneumonia linked with reactivation of latent human cytomegalovirus due to iatrogenic immunosuppression can be a serious complication of bone marrow transplantation therapy of aplastic anaemia and acute leukaemia1. Cellular immunity plays a critical role in the immune surveillance of inapparent cytomegalovirus infections in man and the mouse1−7. The molecular basis of latency, however, and the interaction between latently or recurrently infected cells and the immune system of the host are poorfy understood. We have detected a so far unknown antigen in the mouse model. This antigen is found in infected cells in association with the expression of the herpesvirus 'immediate early' genes and is recognized by cytolytic T lymphocytes (CTL)8. We now demonstrate that an unexpectedly high proportion of the CTL precursors generated in vivo during acute murine cytomegalovirus infection are specific for cells that selectively synthesize immediate early proteins, indicating an immunodominant role of viral non-structural proteins

Reactive oxygen species initiate luminal but not basal cell death in cultured human mammary alveolar structures: a potential regulator of involution

Post-lactational involution of the mammary gland is initiated within days of weaning. Clearing of cells occurs by apoptosis of the milk-secreting luminal cells in the alveoli and through stromal tissue remodeling to return the gland almost completely to its pre-pregnant state. The pathways that specifically target involution of the luminal cells in the alveoli but not the basal and ductal cells are poorly understood. In this study we show in cultured human mammary alveolar structures that the involution process is initiated by fresh media withdrawal, and is characterized by cellular oxidative stress, expression of activated macrophage marker CD68 and finally complete clearing of the luminal but not basal epithelial layer. This process can be simulated by ectopic addition of reactive oxygen species (ROS) in cultures without media withdrawal. Cells isolated from post-involution alveoli were enriched for the CD49f+ mammary stem cell (MaSC) phenotype and were able to reproduce a complete alveolar structure in subcultures without any significant loss in viability. We propose that the ROS produced by accumulated milk breakdown post-weaning may be the mechanism underlying the selective involution of secretory alveolar luminal cells, and that our culture model represents an useful means to investigate this and other mechanisms further

Barriers to living donor kidney transplantation in the United Kingdom: a national observational study.

BACKGROUND: Living donor kidney transplantation (LDKT) provides more timely access to transplantation and better clinical outcomes than deceased donor kidney transplantation (DDKT). This study investigated disparities in the utilization of LDKT in the UK. METHODS: A total of 2055 adults undergoing kidney transplantation between November 2011 and March 2013 were prospectively recruited from all 23 UK transplant centres as part of the Access to Transplantation and Transplant Outcome Measures (ATTOM) study. Recipient variables independently associated with receipt of LDKT versus DDKT were identified. RESULTS: Of the 2055 patients, 807 (39.3%) received LDKT and 1248 (60.7%) received DDKT. Multivariable modelling demonstrated a significant reduction in the likelihood of LDKT for older age {odds ratio [OR] 0.11 [95% confidence interval (CI) 0.08-0.17], P < 0.0001 for 65-75 years versus 18-34 years}; Asian ethnicity [OR 0.55 (95% CI 0.39-0.77), P = 0.0006 versus White]; Black ethnicity [OR 0.64 (95% CI 0.42-0.99), P = 0.047 versus White]; divorced, separated or widowed [OR 0.63 (95% CI 0.46-0.88), P = 0.030 versus married]; no qualifications [OR 0.55 (95% CI 0.42-0.74), P < 0.0001 versus higher education qualifications]; no car ownership [OR 0.51 (95% CI 0.37-0.72), P = 0.0001] and no home ownership [OR 0.65 (95% CI 0.85-0.79), P = 0.002]. The odds of LDKT varied significantly between countries in the UK. CONCLUSIONS: Among patients undergoing kidney transplantation in the UK, there are significant age, ethnic, socio-economic and geographic disparities in the utilization of LDKT. Further work is needed to explore the potential for targeted interventions to improve equity in living donor transplantation

Corrosion and tribological performance of quasi-stoichiometric titanium containing carbo-nitride coatings

Zr, Nb and Si doped TiCN coatings, with (C+N)/(metal + Si) ratios of approximately 1, were deposited on stainless steel and Si wafer substrates using a cathodic arc technique in a mixture of N2 and CH4 gases. The coatings were comparatively analysed for elemental and phase composition, adhesion, anticorrosive properties and tribological performance at ambient and 250 °C. Zr, Nb and Si alloying contents in the coatings were in the range 2.9–9.6 at.%. All the coatings exhibited f.c.c. solid solution structures and had a 〈1 1 1〉 preferred orientation. In the adhesion tests conducted, critical loads ranged from 20 to 30 N, indicative of a good adhesion to substrate materials. The Ti based coatings with Nb or Si alloying elements proved to be resistant to corrosive attack in 3.5% NaCl and of these coatings the TiNbCN was found to have the best corrosion resistance. TiCN exhibited the best tribological performance at 250 °C, while at ambient temperatures it was TiNbCN. Abrasive and oxidative wear was found to be the main wear mechanism for all of the coatings. Of the tested coatings, TiNbCN coatings would be the most suitable candidate for severe service (high temperature, corrosive, etc.) applications

Atmospheric Evolution

Earth's atmosphere has evolved as volatile species cycle between the atmosphere, ocean, biomass and the solid Earth. The geochemical, biological and astrophysical processes that control atmospheric evolution are reviewed from an "Earth Systems" perspective, with a view not only to understanding the history of Earth, but also to generalizing to other solar system planets and exoplanets.Comment: 34 pages, 3 figures, 2 tables. Accepted as a chapter in "Encyclopaedia of Geochemistry", Editor Bill White, Springer-Nature, 201