Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel

The AmtB channel passively allows the transport of NH(4) (+) across the membranes of bacteria via a “gas” NH(3) intermediate and is related by homology (sequentially, structurally, and functionally) to many forms of Rh protein (both erythroid and nonerythroid) found in animals and humans. New structural information on this channel has inspired computational studies aimed at clarifying various aspects of NH(4) (+) recruitment and binding in the periplasm, as well as its deprotonation. However, precise mechanisms for these events are still unknown, and, so far, explanations for subsequent NH(3) translocation and reprotonation at the cytoplasmic end of the channel have not been rigorously addressed. We employ molecular dynamics simulations and free energy methods on a full AmtB trimer system in membrane and bathed in electrolyte. Combining the potential of mean force for NH(4) (+)/NH(3) translocation with data from thermodynamic integration calculations allows us to find the apparent pK(a) of NH(4) (+) as a function of the transport axis. Our calculations reveal the specific sites at which its deprotonation (at the periplasmic end) and reprotonation (at the cytoplasmic end) occurs. Contrary to most hypotheses, which ascribe a proton-accepting role to various periplasmic or luminal residues of the channel, our results suggest that the most plausible proton donor/acceptor at either of these sites is water. Free-energetic analysis not only verifies crystallographically determined binding sites for NH(4) (+) and NH(3) along the transport axis, but also reveals a previously undetermined binding site for NH(4) (+) at the cytoplasmic end of the channel. Analysis of dynamics and the free energies of all possible loading states for NH(3) inside the channel also reveal that hydrophobic pressure and the free-energetic profile provided by the pore lumen drives this species toward the cytoplasm for protonation just before reaching the newly discovered site

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis

Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2°C), elevated pCO2(900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research

South African cause-of death profile in transition - 1996 and future trends

No Abstract

Unabated rise in number of adult deaths in South Africa

Mortality statistics are a fundamental cornerstone of the health status data needed for planning and monitoring the impact of health programmes. In developed countries, such data are generated through the death registration system, dating back to the 19th century in the case of the UK and Sweden. Until recently, South Africa’s death registration system was recognised as inadequate to provide such statistics for the majority of the population,1 but the postApartheid government has prioritised the collection of such statistics, as evidenced by a new-found collaboration between the Departments of Health and Home Affairs and Statistics South Africa.2 Registration of adult deaths improved from about 50% in 1990 to over 90% in 20003 as a result of the incorporation of the former homelands as well as national efforts to improve coverage. However, the production of timely cause of death statistics remains a challenge; the most recent year with full officially published statistics is 1996

Sea-weeding: Manual removal of macroalgae facilitates rapid coral recovery

Coral reef ecosystems globally are under threat, leading to declining coral cover and macroalgal proliferation. Manually removing macroalgae (i.e. ‘sea-weeding’) may promote local-scale coral recovery by reducing a biological barrier, though the impact of removal on community composition of benthic reef organisms has not been quantified. In this three-year study (2018–2021), fleshy macroalgae (predominantly Sargassum spp.) were periodically removed from 25 m2 experimental plots on two inshore fringing reefs of Yunbenun (Magnetic Island) in the central Great Barrier Reef. By the end of the study, coral cover in removal plots (n = 12 plots) assessed through in-field transects increased by at least 47% (2019 mean: 25.5%, 2021 mean: 37.4%), and macroalgal cover decreased by more than half. In contrast, in control plots (n = 12 plots), there was no change in macroalgal cover while coral cover remained stable (2019 mean: 16.4%, 2021 mean: 13.6%). Changes in benthic cover were supported by photoquadrat data, with Bayesian probability modelling indicating a 100% likelihood that coral cover more than doubled in removal plots over the study period, compared to only a 29% chance of increased coral cover in control plots. Synthesis and applications. Manual macroalgal removal can provide rapid benefits and enhance inshore coral reef recovery. Through involvement of community groups and citizen scientists, larger scale removal of macroalgae is a low-tech, high-impact, and achievable method for local reef management

Emergence of a peak in early infant mortality due to HIV/AIDS in South Africa

Objectives: South Africa has among the highest levels of HIV prevalence in the world. Our objectives are to describe the distribution of South African infant and child mortality by age at fine resolution, to identify any trends over recent time and to examine these trends for HIV-associated and non HIV-associated causes of mortality. Methods: A retrospective review of vital registration data was conducted. All registered postneonatal deaths under 1 year of age in South Africa for the period 1997–2002 were analysed by age in months using a generalized linear model with a log link and Poisson family. Results: Postneonatal mortality increased each year over the period 1997–2002. A peak in HIV-related deaths was observed, centred at 2–3 months of age, rising monotonically over time. Conclusion: We interpret the peak in mortality at 2–3 months as an indicator for paediatric AIDS in a South African population with high HIV prevalence and where other causes of death are not sufficiently high to mask HIV effects. Intrauterine and intrapartum infection may contribute to this peak. It is potentially a useful surveillance tool, not requiring an exact cause of death. The findings also illustrate the need for early treatment of mother and child in settings with very high HIV prevalence

Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function

The MYC genes encode nuclear sequence specific–binding DNA-binding proteins that are pleiotropic regulators of cellular function, and the c-MYC proto-oncogene is deregulated and/or mutated in most human cancers. Experimental studies of MYC binding to the genome are not fully consistent. While many c-MYC recognition sites can be identified in c-MYC responsive genes, other motif matches—even experimentally confirmed sites—are associated with genes showing no c-MYC response. We have developed a computational model that integrates multiple sources of evidence to predict which genes will bind and be regulated by MYC in vivo. First, a Bayesian network classifier is used to predict those c-MYC recognition sites that are most likely to exhibit high-occupancy binding in chromatin immunoprecipitation studies. This classifier incorporates genomic sequence, experimentally determined genomic chromatin acetylation islands, and predicted methylation status from a computational model estimating the likelihood of genomic DNA methylation. We find that the predictions from this classifier are also applicable to other transcription factors, such as cAMP-response element-binding protein, whose binding sites are sensitive to DNA methylation. Second, the MYC binding probability is combined with the gene expression profile data from nine independent microarray datasets in multiple tissues. Finally, we may consider gene function annotations in Gene Ontology to predict the c-MYC targets. We assess the performance of our prediction results by comparing them with the c-myc targets identified in the biomedical literature. In total, we predict 460 likely c-MYC target genes in the human genome, of which 67 have been reported to be both bound and regulated by MYC, 68 are bound by MYC, and another 80 are MYC-regulated. The approach thus successfully identifies many known c-MYC targets and suggests many novel sites. Our findings suggest that to identify c-MYC genomic targets, integration of different data sources helps to improve the accuracy

Multiple effects of silymarin on the hepatitis C virus lifecycle

Silymarin, an extract from milk thistle (Silybum marianum), and its purified flavonolignans have been recently shown to inhibit hepatitis C virus (HCV) infection, both in vitro and in vivo. In the current study, we further characterized silymarin's antiviral actions. Silymarin had antiviral effects against hepatitis C virus cell culture (HCVcc) infection that included inhibition of virus entry, RNA and protein expression, and infectious virus production. Silymarin did not block HCVcc binding to cells but inhibited the entry of several viral pseudoparticles (pp), and fusion of HCVpp with liposomes. Silymarin but not silibinin inhibited genotype 2a NS5B RNA-dependent RNA polymerase (RdRp) activity at concentrations 5 to 10 times higher than required for anti-HCVcc effects. Furthermore, silymarin had inefficient activity on the genotype 1b BK and four 1b RDRPs derived from HCV-infected patients. Moreover, silymarin did not inhibit HCV replication in five independent genotype 1a, 1b, and 2a replicon cell lines that did not produce infectious virus. Silymarin inhibited microsomal triglyceride transfer protein activity, apolipoprotein B secretion, and infectious virion production into culture supernatants. Silymarin also blocked cell-to-cell spread of virus. CONCLUSION: Although inhibition of in vitro NS5B polymerase activity is demonstrable, the mechanisms of silymarin's antiviral action appear to include blocking of virus entry and transmission, possibly by targeting the host cell