Explaining geographical variation in the isotope composition of mouse lemurs (Microcebus)

Aim We sought to quantify geographical variation in the stable isotope values of mouse lemurs (Microcebus) and to determine whether this variation reflects trophic differences among populations or baseline isotopic differences among habitats. If the latter pattern is demonstrated, then Microcebus can become a proxy for tracking baseline habitat isotopic variability. Establishing such a baseline is crucial for identifying niche partitioning in modern and ancient communities. Location We studied five species of Microcebus from eight distinct habitats across Madagascar. Methods We compared isotopic variation in C₃ plants and Microcebus fur within and among localities. We predicted that carbon and nitrogen isotope values of Microcebus should: (1) vary as a function of abiotic variables such as rainfall and temperature, and (2) covary with isotopic values in plants. We checked for trophic differences among Microcebus populations by comparing the average difference between mouse lemur and plant isotope values for each locality. We then used multiple regression models to explain spatial isotope variation in mouse lemurs, testing a suite of explanatory abiotic variables. Results We found substantial isotopic variation geographically. Ranges for mean isotope values were similar for both Microcebus and plants across localities (carbon 3.5–4.0‰; nitrogen 10.5–11.0‰). Mean mouse lemur and plant isotope values were lowest in cool, moist localities and highest in hot, dry localities. Rainfall explained 58% of the variation in Microcebus carbon isotope values, and mean plant nitrogen isotope values explained 99.7% of the variation in Microcebus nitrogen isotope values. Average differences between mouse lemur and plant isotope values (carbon 5.0‰; nitrogen 5.9‰) were similar across localities. Main conclusions Isotopic data suggest that trophic differences among Microcebus populations were small. Carbon isotope values in mouse lemurs were negatively correlated with rainfall. Nitrogen isotope values in Microcebus and plants covaried. Such findings suggest that nitrogen isotope values for Microcebus are a particularly good proxy for tracking baseline isotopic differences among habitats. Our results will facilitate future comparative research on modern mouse lemur communities, and ecological interpretations of extinct Holocene communities.     

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.     

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.     

Circadian regulation of visually evoked potentials in the domestic pigeon, Columba livia

The avian circadian and visual systems are integrally related and together influence many aspects of birds' behavior and physiology. Certainly, light cycles and their visual perception are the major zeitgebers for circadian rhythms, but do circadian rhythms affect vision? To assess whether visual function is regulated on a circadian basis, flash-evoked electroretinograms (ERGs) and vision-evoked potentials (VEPs) from the optic tectum (TeO) were recorded simultaneously in domestic pigeons at different circadian phases in a light-dark regime (LD) and in constant darkness (DD), while feeding activity was measured to determine circadian phase. In both LD and DD, the amplitudes of ERG b-waves were higher during the day than at night and latencies of a- and b-waves were longer at night. The median effective intensity for ERG a-wave was marginally higher during the day than during the night, indicating greater sensitivity at night, but this rhythm did not persist in DD. The amplitudes of TeO VEPs were also greater during the day, and latencies were greater at night in LD and DD. Together, the data indicate that a circadian clock regulates pigeon visual function at several integrative levels.     

Antiretroviral Therapy Reduces HIV Transmission in Discordant Couples in Rural Yunnan,China

Background

Although HIV treatment as prevention (TasP) via early antiretroviral therapy (ART) has proven to reduce transmissions among HIV-serodiscordant couples, its full implementation in developing countries remains a challenge. In this study, we determine whether China''s current HIV treatment program prevents new HIV infections among discordant couples in rural China.

Methods

A prospective, longitudinal cohort study was conducted from June 2009 to March 2011, in rural Yunnan. A total of 1,618 HIV-discordant couples were eligible, 1,101 were enrolled, and 813 were followed for an average of 1.4 person-years (PY). Routine ART was prescribed to HIV-positive spouses according to eligibility (CD4<350 cells/µl). Seroconversion was used to determine HIV incidence.

Results

A total of 17 seroconversions were documented within 1,127 PY of follow-up, for an overall incidence of 1.5 per 100 PY. Epidemiological and genetic evidence confirmed that all 17 seroconverters were infected via marital secondary sexual transmission. Having an ART-experienced HIV-positive partner was associated with a lower rate of seroconvertion compared with having an ART-naïve HIV-positive partner (0.8 per 100 PY vs. 2.4 per 100 PY, HR = 0.34, 95%CI = 0.12–0.97, p = 0.0436). While we found that ART successfully suppressed plasma viral load to <400 copies/ml in the majority of cases (85.0% vs. 19.5%, p<0.0001 at baseline), we did document five seroconversions among ART-experienced subgroup.

Conclusions

ART is associated with a 66% reduction in HIV incidence among discordant couples in our sample, demonstrating the effectiveness of China''s HIV treatment program at preventing new infections, and providing support for earlier ART initiation and TasP implementation in this region.     

The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions

The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro²¹⁶–Phe²²⁸ loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors.     

Edge effects on foliar stable isotope values in a madagascan tropical dry forest

Edge effects represent an inevitable and important consequence of habitat loss and fragmentation. These effects include changes in microclimate, solar radiation, or temperature. Such abiotic effects can, in turn, impact biotic factors. They can have a substantial impact on species, communities, and ecosystems. Here we examine clinal variations in stable carbon and nitrogen isotope values for trees along an edge-interior gradient in the dry deciduous forest at Ankarafantsika National Park. We predicted that soil respiration and differences in solar irradiance would result in stratified δ(13)C values where leaves collected close to the forest floor would have lower δ(13)C values than those growing higher up in the canopy. We also anticipated that plants growing at the savannah-forest boundary would have higher δ(13)C and δ(15)N values than plants growing in the forest interior. As expected, we detected a small but significant canopy effect. Leaves growing below 2 m from the forest floor exhibit δ(13)C values that are, on average, 1.1‰ lower than those growing above this threshold. We did not, however, find any relationship between foliar δ(13)C and distance from the edge. Unpredictably, we detected a striking positive relationship between foliar δ(15)N values and increasing distance into the forest interior. Variability in physiology among species, anthropogenic influence, organic input, and rooting depth cannot adequately explain this trend. Instead, this unexpected relationship most likely reflects decreasing nutrient or water availability, or a shift in N-sources with increasing distance from the savannah. Unlike most forest communities, the trees at Ampijoroa are growing in nutrient-limited sands. In addition to being nutrient poor, these well-drained soils likely decrease the amount of soil water available to forest vegetation. Continued research on plant responses to edge effects will improve our understanding of the conservation biology of forest ecosystems in Madagascar.     

Mortality among Methadone Maintenance Clients in China: A Six-Year Cohort Study

Objective

To assess the overall mortality of methadone maintenance treatment (MMT) clients in China and its associated factors.

Methods

A total of 1,511 MMT clients, all of whom enrolled in China''s first eight MMT clinics between March and December 2004, were included in this cohort study and followed for approximately six years, until June 2010. Mortality and its predictors were examined using Cox proportional hazards regression models.

Results

A total of 154 deaths were observed within 5,391 person-years (PY) of follow-up for an all-cause mortality rate of 28.6 per 1,000 PY. The leading causes of death were drug overdose (33.8%), HIV/AIDS-unrelated disease (21.4%), and HIV/AIDS (16.9%). The all-cause mortality rate of clients engaged in MMT for one year or less was roughly three times that of clients who stayed in MMT for four years or more (14.0 vs. 4.6, p<0.0001), HIV-positive subjects was nearly four times mortality rate than that of HIV-negative individuals (28.1 vs.6.8, p<0.0001). ART-naive HIV-positive subjects had approximately two times higher mortality rate than those receiving ART (31.2 vs. 17.3, <0.0001). After adjusting for confounding variables, we found that being male (HR = 1.63, CI: 1.03–2.57, p = 0.0355) and being HIV-positive (HR = 5.16, CI: 3.70–7.10, p<0.0001) were both associated with higher risk of death whereas increased durations of methadone treatment were associated with a lower risk of death (HR = 0.26, CI: 0.18–0.38, p<0.0001 for two to three years, HR = 0.08, CI: 0.05–0.14, p<0.0001 for four or more years).

Conclusion

Overall mortality was high among MMT clients in China. Specific interventions aimed at decreasing mortality among MMT clients are needed. Our study supports the need for keeping client at MMT longer and for expanding ART coverage and suggests the potential benefits of integrated MMT and ART services for drug users in China.     

Trends in hospital necropsy rates: Scotland 1961-74.

Examination of mortality statistic for Scottish hospitals showed that from 1961 to 1974 necropsy rates fell by almost 0-6% a year; by 1974, the rate over the whole country was 23% of hospital deaths. The fall resulted from a reduction in the number of necropsies and a coincident rise in the number of number of deaths in hospital. The necropsy rate fell with increasing age, was rather lower for women than men, and was lower for some diseases than others. There were considerable inaccuracies in the figures from which these trands were drawn, and these were in turn due to inaccurate recording of clinical and necropsy data. Examination of necropsy returns from the Scottish teaching hospital departments showed that, while a similar fall in necropsy rates was seen in some, there was no consistent pattern.