ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes

Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches

Background

Pyrazinamide is one of four first-line antibiotics used to treat tuberculosis; however, antibiotic susceptibility testing for pyrazinamide is challenging. Resistance to pyrazinamide is primarily driven by genetic variation in pncA, encoding an enzyme that converts pyrazinamide into its active form.

Methods

We curated a dataset of 664 non-redundant, missense amino acid mutations in PncA with associated high-confidence phenotypes from published studies and then trained three different machine-learning models to predict pyrazinamide resistance. All models had access to a range of protein structural-, chemical- and sequence-based features.

Results

The best model, a gradient-boosted decision tree, achieved a sensitivity of 80.2% and a specificity of 76.9% on the hold-out test dataset. The clinical performance of the models was then estimated by predicting the binary pyrazinamide resistance phenotype of 4027 samples harbouring 367 unique missense mutations in pncA derived from 24 231 clinical isolates.

Conclusions

This work demonstrates how machine learning can enhance the sensitivity/specificity of pyrazinamide resistance prediction in genetics-based clinical microbiology workflows, highlights novel mutations for future biochemical investigation, and is a proof of concept for using this approach in other drugs.

Identifying Adolescents at Highest Risk of ART Non-adherence, Using the World Health Organization-Endorsed HEADSS and HEADSS+ Checklists

Brief tools are necessary to identify adolescents at greatest risk for ART non-adherence. From the WHO's HEADSS/HEADSS+ adolescent wellbeing checklists, we identify constructs strongly associated with non-adherence (validated with viral load). We conducted interviews and collected clinical records from a 3-year cohort of 1046 adolescents living with HIV from 52 South African government facilities. We used least absolute shrinkage and selection operator variable selection approach with a generalized linear mixed model. HEADSS constructs most predictive were: violence exposure (aOR 1.97, CI 1.61; 2.42, p < 0.001), depression (aOR 1.71, CI 1.42; 2.07, p < 0.001) and being sexually active (aOR 1.80, CI 1.41; 2.28, p < 0.001). Risk of non-adherence rose from 20.4% with none, to 55.6% with all three. HEADSS+ constructs were: medication side effects (aOR 2.27, CI 1.82; 2.81, p < 0.001), low social support (aOR 1.97, CI 1.60; 2.43, p < 0.001) and non-disclosure to parents (aOR 2.53, CI 1.91; 3.53, p < 0.001). Risk of non-adherence rose from 21.6% with none, to 71.8% with all three. Screening within established checklists can improve identification of adolescents needing increased support. Adolescent HIV services need to include side-effect management, violence prevention, mental health and sexual and reproductive health.

Novel insights into the genetics, morphology, distribution and hosts of the global fish parasitic digenean Proctoeces maculatus (Looss, 1901) (Digenea: Fellodistomidae)

Larval stages of the widely distributed digenean species Proctoeces maculatus (Looss, 1901) were reported 40 years ago from South Africa in the common octopus, Octopus vulgaris Cuvier (Octopodidae). However, the absence of adult specimens and molecular data from this region has hindered a comprehensive understanding of its distribution. In this study, we collected three species of intertidal and near-shore marine fishes [Clinus superciliosus (L.) (Clinidae), Diplodus capensis (Smith) (Sparidae) and Sparodon durbanensis (Castelnau) (Sparidae)] along the South African coast and discovered adult specimens of P. maculatus at five localities. By employing a combination of morphological and molecular techniques, including 28S rDNA, 18S rDNA and COI mtDNA analyses, the first report of adult P. maculatus from South Africa is presented. The findings encompass a comprehensive morphological description and molecular data, illuminating the true distribution of this species in the region.

Exploring the connection between autophagy and heat-stress tolerance in Drosophila melanogaster

Mechanisms aimed at recovering from heat-induced damages are closely associated with the ability of ectotherms to survive exposure to stressful temperatures. Autophagy, a ubiquitous stress-responsive catabolic process, has recently gained renewed attention as one of these mechanisms. By increasing the turnover of cellular structures as well as the clearance of long-lived protein and protein aggregates, the induction of autophagy has been linked to increased tolerance to a range of abiotic stressors in diverse ectothermic organisms. However, whether a link between autophagy and heat-tolerance exists in insect models remains unclear despite broad ecophysiological implications thereof. Here, we explored the putative association between autophagy and heat-tolerance using Drosophila melanogaster as a model. We hypothesized that (i) heat-stress would cause an increase of autophagy in flies' tissues, and (ii) rapamycin exposure would trigger a detectable autophagic response in adults and increase their heat-tolerance. In line with our hypothesis, we report that flies exposed to heat-stress present signs of protein aggregation and appear to trigger an autophagy-related homoeostatic response as a result. We further show that rapamycin feeding causes the systemic effect associated with target of rapamycin (TOR) inhibition, induces autophagy locally in the fly gut, and increases the heat-stress tolerance of individuals. These results argue in favour of a substantial contribution of autophagy to the heat-stress tolerance mechanisms of insects.

Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.

Protective factors for adolescent sexual risk behaviours and experiences linked to HIV infection in South Africa: a three-wave longitudinal analysis of caregiving, education, food security, and social protection

BACKGROUND

Structural interventions are endorsed to enhance biomedical and behavioural HIV prevention programmes for adolescents. Aiming to inform future interventions, we evaluated longitudinal associations between six protective factors that link closely to existing structural HIV prevention interventions, and five sexual risk behaviours for HIV transmission in a cohort of adolescents in South Africa.

METHODS

We used three rounds of data between 2014-2018 on 1046 adolescents living with HIV and 473 age-matched community peers in South Africa's Eastern Cape (Observations = 4402). We estimated sex-specific associations between six time-varying protective factors - number of social grants, education enrolment, days with enough food, caregiver supervision, positive caregiving, and adolescent-caregiver communication; and five HIV risk behaviours - multiple sexual partners, transactional sex, age-disparate sex, condomless sex, and sex on substances. HIV risk behaviours were analysed separately in multivariable random effects within-between logistic regression models that accounted for correlation of repeated observations on the same individual. We calculated prevalence ratios (PR), contrasting adjusted probabilities of HIV risk behaviours at 'No' and 'Yes' for education enrolment, and average and maximum values for the other five protective factors.

RESULTS

The sample mean age was 15.29 (SD: 3.23) years and 58% were girls. Among girls, within-individuals, increases from mean to maximum scores in positive caregiving were associated with lower probability of transactional sex (PR = 0.79; 95%CI = 0.67-0.91); in caregiver supervision were associated with lower probability of transactional sex (PR = 0.75; 95%CI = 0.66-0.84), and age-disparate sex (PR = 0.84; 95%CI = 0.73-0.95); in adolescent-caregiver communication were associated with higher probability of transactional sex (PR = 1.70; 95%CI = 1.08-2.32); and in days with enough food at home were associated with lower probability of multiple sexual partners (PR = 0.89; 95%CI = 0.81-0.97), and transactional sex (PR = 0.82; 95%CI = 0.72-0.92). Change from non-enrolment in education to enrolment was associated with lower probability of age-disparate sex (PR = 0.49; 95%CI = 0.26-0.73). Between-individuals, relative to mean caregiver supervision scores, maximum scores were associated with lower probability of multiple sexual partners (PR = 0.59; 95%CI = 0.46-0.72), condomless sex (PR = 0.80; 95%CI = 0.69-0.91), and sex on substances (PR = 0.42; 95%CI = 0.26-0.59); and relative to non-enrolment, education enrolment was associated with lower probability of condomless sex (PR = 0.59; 95%CI = 0.39-0.78). Among boys, within-individuals, increases from mean to maximum scores in positive caregiving were associated with lower probability of transactional sex (PR = 0.77; 95%CI = 0.59-0.96), and higher probability of condomless sex (PR = 1.26; 95%CI = 1.08-1.43); in caregiver supervision were associated with lower probability of multiple sexual partners (PR = 0.73; 95%CI = 0.64-0.82), transactional sex (PR = 0.63; 95%CI = 0.50-0.76), age-disparate sex (PR = 0.67; 95%CI = 0.49-0.85), and sex on substances (PR = 0.61; 95%CI = 0.45-0.78), and in days with enough food at home were associated with lower probability of transactional sex (PR = 0.91; 95%CI = 0.84-0.98).

CONCLUSION

Effective structural interventions to improve food security and education enrolment among adolescent girls, and positive and supervisory caregiving among adolescent girls and boys are likely to translate into crucial reductions in sexual risk behaviours linked to HIV transmission in this population.

Interactive effects of rising temperatures and urbanisation on birds across different climate zones: A mechanistic perspective

Climate change and urbanisation are among the most pervasive and rapidly growing threats to biodiversity worldwide. However, their impacts are usually considered in isolation, and interactions are rarely examined. Predicting species' responses to the combined effects of climate change and urbanisation, therefore, represents a pressing challenge in global change biology. Birds are important model taxa for exploring the impacts of both climate change and urbanisation, and their behaviour and physiology have been well studied in urban and non-urban systems. This understanding should allow interactive effects of rising temperatures and urbanisation to be inferred, yet considerations of these interactions are almost entirely lacking from empirical research. Here, we synthesise our current understanding of the potential mechanisms that could affect how species respond to the combined effects of rising temperatures and urbanisation, with a focus on avian taxa. We discuss potential interactive effects to motivate future in-depth research on this critically important, yet overlooked, aspect of global change biology. Increased temperatures are a pronounced consequence of both urbanisation (through the urban heat island effect) and climate change. The biological impact of this warming in urban and non-urban systems will likely differ in magnitude and direction when interacting with other factors that typically vary between these habitats, such as resource availability (e.g. water, food and microsites) and pollution levels. Furthermore, the nature of such interactions may differ for cities situated in different climate types, for example, tropical, arid, temperate, continental and polar. Within this article, we highlight the potential for interactive effects of climate and urban drivers on the mechanistic responses of birds, identify knowledge gaps and propose promising future research avenues. A deeper understanding of the behavioural and physiological mechanisms mediating species' responses to urbanisation and rising temperatures will provide novel insights into ecology and evolution under global change and may help better predict future population responses.

Understanding accelerators to improve SDG-related outcomes for adolescents-An investigation into the nature and quantum of additive effects of protective factors to guide policy making

Recent evidence has shown support for the United Nations Development Programme (UNDP) accelerator concept, which highlights the need to identify interventions or programmatic areas that can affect multiple sustainable development goals (SDGs) at once to boost their achievement. These data have also clearly shown enhanced effects when interventions are used in combination, above and beyond the effect of single interventions. However, detailed knowledge is now required on optimum combinations and relative gain in order to derive policy guidance. Which accelerators work for which outcomes, what combinations are optimum, and how many combinations are needed to maximise effect? The current study utilised pooled data from the Young Carers (n = 1402) and Child Community Care (n = 446) studies. Data were collected at baseline (n = 1848) and at a 1 to 1.5- year follow-up (n = 1740) from children and young adolescents aged 9-13 years, living in South Africa. Measures in common between the two databases were used to generate five accelerators (caregiver praise, caregiver monitoring, food security, living in a safe community, and access to community-based organizations) and to investigate their additive effects on 14 SDG-related outcomes. Predicted probabilities and predicted probability differences were calculated for each SDG outcome under the presence of none to five accelerators to determine optimal combinations. Results show that various accelerator combinations are effective, though different combinations are needed for different outcomes. Some accelerators ramified across multiple outcomes. Overall, the presence of up to three accelerators was associated with marked improvements over multiple outcomes. The benefit of targeting access to additional accelerators, with additional costs, needs to be weighed against the relative gains to be achieved with high quality but focused interventions. In conclusion, the current data show the detailed impact of various protective factors and provides implementation guidance for policy makers in targeting and distributing interventions to maximise effect and expenditure. Future work should investigate multiplicative effects and synergistic interactions between accelerators.

Art-based reflections from 12 years of adolescent health and development-related research in South Africa

This paper presents empirical and methodological findings from an art-based, participatory process with a group (n = 16) of adolescent and young advisors in the Western Cape Province of South Africa. In a weekend workshop, participants reflected on their participation in 12 years of health and development-related research through theatre, song, visual methodologies and semi-structured interviews. Empirical findings suggest that participants interpreted the group research encounter as a site of empowerment, social support and as a socio-political endeavour. Through song, theatre and a mural illustration, they demonstrated that they value 'unity' in research, with the aim of ameliorating the conditions of adolescents and young people in other parts of South Africa and the continent. Methodological findings document how participants deployed art-based approaches from South Africa's powerful history of activism, including the struggle against apartheid, the fight for anti-retroviral therapy and more recent social movements towards decolonization.

Adolescent Motherhood and HIV in South Africa: Examining Prevalence of Common Mental Disorder

The mental health of adolescents (10–19 years) remains an overlooked global health issue, particularly within the context of syndemic conditions such as HIV and pregnancy. Rates of pregnancy and HIV among adolescents within South Africa are some of the highest in the world. Experiencing pregnancy and living with HIV during adolescence have both been found to be associated with poor mental health within separate explorations. Yet, examinations of mental health among adolescents living with HIV who have experienced pregnancy/parenthood remain absent from the literature. As such, there exists no evidence-based policy or programming relating to mental health for this group. These analyses aim to identify the prevalence of probable common mental disorder among adolescent mothers and, among adolescents experiencing the syndemic of motherhood and HIV. Analyses utilise data from interviews undertaken with 723 female adolescents drawn from a prospective longitudinal cohort study of adolescents living with HIV (n = 1059) and a comparison group of adolescents without HIV (n = 467) undertaken within the Eastern Cape Province, South Africa. Detailed study questionnaires included validated and study specific measures relating to HIV, adolescent motherhood, and mental health. Four self-reported measures of mental health (depressive, anxiety, posttraumatic stress, and suicidality symptomology) were used to explore the concept of likely common mental disorder and mental health comorbidities (experiencing two or more common mental disorders concurrently). Chi-square tests (Fisher’s exact test, where appropriate) and Kruskal Wallis tests were used to assess differences in sample characteristics (inclusive of mental health status) according to HIV status and motherhood status. Logistic regression models were used to explore the cross-sectional associations between combined motherhood and HIV status and, likely common mental disorder/mental health comorbidities. 70.5% of participants were living with HIV and 15.2% were mothers. 8.4% were mothers living with HIV. A tenth (10.9%) of the sample were classified as reporting a probable common mental disorder and 2.8% as experiencing likely mental health comorbidities. Three core findings emerge: (1) poor mental health was elevated among adolescent mothers compared to never pregnant adolescents (measures of likely common mental disorder, mental health comorbidities, depressive, anxiety and suicidality symptoms), (2) prevalence of probable common mental disorder was highest among mothers living with HIV (23.0%) compared to other groups (Range:8.5–12.8%; Χ² = 12.54, p = 0.006) and, (3) prevalence of probable mental health comorbidities was higher among mothers, regardless of HIV status (HIV & motherhood = 8.2%, No HIV & motherhood = 8.2%, Χ² = 14.5, p = 0.002). Results identify higher mental health burden among adolescent mothers compared to never-pregnant adolescents, an increased prevalence of mental health burden among adolescent mothers living with HIV compared to other groups, and an elevated prevalence of mental health comorbidities among adolescent mothers irrespective of HIV status. These findings address a critical evidence gap, highlighting the commonality of mental health burden within the context of adolescent motherhood and HIV within South Africa as well as the urgent need for support and further research to ensure effective evidence-based programming is made available for this group. Existing antenatal, postnatal, and HIV care may provide an opportunity for mental health screening, monitoring, and referral.

Parental morph combination does not influence innate immune function in nestlings of a colour-polymorphic African raptor

Conditions experienced during early life can have long-term individual consequences by influencing dispersal, survival, recruitment and productivity. Resource allocation during development can have strong carry-over effects onto these key parameters and is directly determined by the quality of parental care. In the black sparrowhawk (Accipiter melanoleucus), a colour-polymorphic raptor, parental morphs influence nestling somatic growth and survival, with pairs consisting of different colour morphs ('mixed-morph pairs') producing offspring with lower body mass indices, but higher local apparent survival rates. Resource allocation theory could explain this relationship, with nestlings of mixed-morph pairs trading off a more effective innate immune system against somatic growth. We quantified several innate immune parameters of nestlings (hemagglutination, hemolysis, bacteria-killing capacity and haptoglobin concentration) and triggered an immune response by injecting lipopolysaccharides. Although we found that nestlings with lower body mass index had higher local survival rates, we found no support for the proposed hypothesis: neither baseline immune function nor the induced immune response of nestlings was associated with parental morph combination. Our results suggest that these immune parameters are unlikely to be involved in providing a selective advantage for the different colour morphs' offspring, and thus innate immunity does not appear to be traded off against a greater allocation of resources to somatic growth. Alternative hypotheses explaining the mechanism of a low nestling body mass index leading to subsequent higher local survival could be related to the post-fledgling dependency period or differences in dispersal patterns for the offspring from different morph combinations.

Relationships with caregivers and mental health outcomes among adolescents living with HIV: a prospective cohort study in South Africa

BACKGROUND

Mental health problems may impact adherence to anti-retroviral treatment, retention in care, and consequently the survival of adolescents living with HIV. The adolescent-caregiver relationship is an important potential source of resilience. However, there is a lack of longitudinal research in sub-Saharan Africa on which aspects of adolescent-caregiver relationships can promote mental health among adolescents living with HIV. We draw on a prospective longitudinal cohort study undertaken in South Africa to address this question.

METHODS

The study traced adolescents aged 10-19 initiated on antiretroviral treatment in government health facilities (n = 53) within a health district of the Eastern Cape province. The adolescents completed standardised questionnaires during three data collection waves between 2014 and 2018. We used within-between multilevel regressions to examine the links between three aspects of adolescent-caregiver relationships (caregiver supervision, positive caregiving, and adolescent-caregiver communication) and adolescent mental health (depression symptoms and anxiety symptoms), controlling for potential confounders (age, sex, rural/urban residence, mode of infection, household resources), n=926 adolescents.

RESULTS

Improvements in caregiver supervision were associated with reductions in anxiety (0.98, 95% CI 0.97-0.99, p=0.0002) but not depression symptoms (0.99, 95% CI 0.98-1.00, p=.151), while changes in positive caregiving were not associated with changes in mental health symptoms reported by adolescents. Improvements in adolescent-caregiver communication over time were associated with reductions in both depression (IRR=0.94, 95% CI 0.92-0.97, p<.0001) and anxiety (0.91, 95% CI 0.89-0.94, p<.0001) symptoms reported by adolescents.

CONCLUSIONS

Findings highlight open and supportive adolescent-caregiver communication and good caregiver supervision as potential factors for guarding against mental health problems among adolescents living with HIV in South Africa. Several evidence-informed parenting programmes aim to improve adolescent-caregiver communication and caregiver supervision, and their effect on depression and anxiety among adolescents living with HIV should be rigorously tested in sub-Saharan Africa. How to improve communication in other settings, such as schools and clinics, and provide communication support for caregivers, adolescents, and service providers through these existing services should also be considered.

Violence prevention accelerators for children and adolescents in South Africa: A path analysis using two pooled cohorts

BACKGROUND

The INSPIRE framework was developed by 10 global agencies as the first global package for preventing and responding to violence against children. The framework includes seven complementary strategies. Delivering all seven strategies is a challenge in resource-limited contexts. Consequently, governments are requesting additional evidence to inform which 'accelerator' provisions can simultaneously reduce multiple types of violence against children.

METHODS AND FINDINGS

We pooled data from two prospective South African adolescent cohorts including Young Carers (2010-2012) and Mzantsi Wakho (2014-2017). The combined sample size was 5,034 adolescents. Each cohort measured six self-reported violence outcomes (sexual abuse, transactional sexual exploitation, physical abuse, emotional abuse, community violence victimisation, and youth lawbreaking) and seven self-reported INSPIRE-aligned protective factors (positive parenting, parental monitoring and supervision, food security at home, basic economic security at home, free schooling, free school meals, and abuse response services). Associations between hypothesised protective factors and violence outcomes were estimated jointly in a sex-stratified multivariate path model, controlling for baseline outcomes and socio-demographics and correcting for multiple-hypothesis testing using the Benjamini-Hochberg procedure. We calculated adjusted probability estimates conditional on the presence of no, one, or all protective factors significantly associated with reduced odds of at least three forms of violence in the path model. Adjusted risk differences (ARDs) and adjusted risk ratios (ARRs) with 95% confidence intervals (CIs) were also calculated. The sample mean age was 13.54 years, and 56.62% were female. There was 4% loss to follow-up. Positive parenting, parental monitoring and supervision, and food security at home were each associated with lower odds of three or more violence outcomes (p < 0.05). For girls, the adjusted probability of violence outcomes was estimated to be lower if all three of these factors were present, as compared to none of them: sexual abuse, 5.38% and 1.64% (ARD: -3.74% points, 95% CI -5.31 to -2.16, p < 0.001); transactional sexual exploitation, 10.07% and 4.84% (ARD: -5.23% points, 95% CI -7.26 to -3.20, p < 0.001); physical abuse, 38.58% and 23.85% (ARD: -14.72% points, 95% CI -19.11 to -10.33, p < 0.001); emotional abuse, 25.39% and 12.98% (ARD: -12.41% points, 95% CI -16.00 to -8.83, p < 0.001); community violence victimisation, 36.25% and 28.37% (ARD: -7.87% points, 95% CI -11.98 to -3.76, p < 0.001); and youth lawbreaking, 18.90% and 11.61% (ARD: -7.30% points, 95% CI -10.50 to -4.09, p < 0.001). For boys, the adjusted probability of violence outcomes was also estimated to be lower if all three factors were present, as compared to none of them: sexual abuse, 2.39% to 1.80% (ARD: -0.59% points, 95% CI -2.24 to 1.05, p = 0.482); transactional sexual exploitation, 6.97% to 4.55% (ARD: -2.42% points, 95% CI -4.77 to -0.08, p = 0.043); physical abuse from 37.19% to 25.44% (ARD: -11.74% points, 95% CI -16.91 to -6.58, p < 0.001); emotional abuse from 23.72% to 10.72% (ARD: -13.00% points, 95% CI -17.04 to -8.95, p < 0.001); community violence victimisation from 41.28% to 35.41% (ARD: -5.87% points, 95% CI -10.98 to -0.75, p = 0.025); and youth lawbreaking from 22.44% to 14.98% (ARD -7.46% points, 95% CI -11.57 to -3.35, p < 0.001). Key limitations were risk of residual confounding and not having information on protective factors related to all seven INSPIRE strategies.

CONCLUSION

In this cohort study, we found that positive and supervisory caregiving and food security at home are associated with reduced risk of multiple forms of violence against children. The presence of all three of these factors may be linked to greater risk reduction as compared to the presence of one or none of these factors. Policies promoting action on positive and supervisory caregiving and food security at home are likely to support further efficiencies in the delivery of INSPIRE.

Fabrication of monodispersed copper oxide nanoparticles with potential application as antimicrobial agents

Cuprous oxide nanoparticles (Cu2O NPs) were fabricated in reverse micellar templates by using lipopeptidal biosurfactant as a stabilizing agent. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive x-ray spectrum (EDX) and UV-Vis analysis were carried out to investigate the morphology, size, composition and stability of the nanoparticles synthesized. The antibacterial activity of the as-synthesized Cu2O NPs was evaluated against Gram-positive B. subtilis CN2 and Gram-negative P. aeruginosa CB1 strains, based on cell viability, zone of inhibition and minimal inhibitory concentration (MIC) indices. The lipopeptide stabilized Cu2O NPs with an ultra-small size of 30 ± 2 nm diameter exhibited potent antimicrobial activity against both Gram-positive and Gram-negative bacteria with a minimum inhibitory concentration of 62.5 µg/mL at pH5. MTT cell viability assay displayed a median inhibition concentration (IC50) of 21.21 μg/L and 18.65 μg/mL for P. aeruginosa and B. subtilis strains respectively. Flow cytometric quantification of intracellular reactive oxygen species (ROS) using 2,7-dichlorodihydrofluorescein diacetate staining revealed a significant ROS generation up to 2.6 to 3.2-fold increase in the cells treated with 62.5 µg/mL Cu2O NPs compared to the untreated controls, demonstrating robust antibacterial activity. The results suggest that lipopeptide biosurfactant stabilized Cu2O NPs could have promising potential for biocompatible bactericidal and therapeutic applications.

Flower orientation in Gloriosa superba (Colchicaceae) promotes cross-pollination via butterfly wings

BACKGROUND AND AIMS

Complex modifications of angiosperm flowers often function for precise pollen placement on pollinators and to promote cross-pollination. We explore the functional significance of the unusually elaborate morphology of Gloriosa superba flowers, which are divided into one hermaphrodite meranthium and five male meranthia (functional pollination units of a single flower).

METHODS

We used controlled pollination experiments, floral measurements, pollen load analyses and visitor observations in four populations of G. superba in South Africa to determine the breeding system, mechanism of pollination and role of flower in the promotion of cross-pollination.

KEY RESULTS

We established that G. superba is self-compatible, but reliant on pollinators for seed production. Butterflies, in particular the pierid Eronia cleodora, were the primary pollinators (>90 % of visitors). Butterflies brush against the anthers and stigma during nectar feeding and pollen is carried on their ventral wing surfaces. Butterfly scales were positively correlated with the number of pollen grains on stigmas. We demonstrate that the styles were orientated towards clearings in the vegetation and we confirm that the highest proportion of initial visits was to hermaphrodite meranthia pointing towards clearings.

CONCLUSIONS

The flower morphology of G. superba results in effective pollen transfer on the wings of butterfly visitors. The style-bearing hermaphrodite meranthium of the flowers orientates towards open spaces in the vegetation, thus increasing the probability that butterflies land first on the hermaphrodite meranthium. This novel aspect of flower orientation is interpreted as a mechanism that promotes cross-pollination.

Consistent Provisions Mitigate Exposure to Sexual Risk and HIV Among Young Adolescents in South Africa

Exposure to sexual risk in early adolescence strongly predicts HIV infection, yet evidence for prevention in young adolescents is limited. We pooled data from two longitudinal South African surveys, with adolescents unexposed to sexual risk at baseline (n = 3662). Multivariable logistic regression tested associations between intermittent/consistent access to eight provisions and reduced sexual risk exposure. Participants were on average 12.8 years, 56% female at baseline. Between baseline and follow-up, 8.6% reported sexual risk exposure. Consistent access to caregiver supervision (OR 0.53 95%CI 0.35-0.80 p = 0.002), abuse-free homes (OR 0.55 95%CI 0.37-0.81 p = 0.002), school feeding (OR 0.55 95%CI 0.35-0.88 p = 0.012), and HIV prevention knowledge (OR 0.43, 95%CI 0.21-0.88 p = 0.021) was strongly associated with preventing early sexual risk exposure. While individual factors reduced the odds of sexual risk exposure, a combination of all four resulted in a greater reduction, from 12.9% (95%CI 7.2-18.7) to 1.0% (95%CI 0.2-1.8). Consistent access to provisions in early adolescence may prevent sexual risk exposure among younger adolescents.

Shifted distribution baselines: neglecting long-term biodiversity records risks overlooking potentially suitable habitat for conservation management

Setting appropriate conservation measures to halt the loss of biodiversity requires a good understanding of species' habitat requirements and potential distribution. Recent (past few decades) ecological data are typically used to estimate and understand species' ecological niches. However, historical local extinctions may have truncated species-environment relationships, resulting in a biased perception of species' habitat preferences. This may result in incorrect assessments of the area potentially available for their conservation. Incorporating long-term (centuries-old) occurrence records with recent records may provide better information on species-environment relationships and improve the modelling and understanding of habitat suitability. We test whether neglecting long-term occurrence records leads to an underestimation of species' historical niche and potential distribution and identify which species are more vulnerable to this effect. We compare outputs of species distribution models and niche hypervolumes built using recent records only with those built using both recent and long-term (post-1500) records, for a set of 34 large mammal species in South Africa. We find that, while using recent records only is adequate for some species, adding historical records in the analyses impacts estimates of the niche and habitat suitability for 12 species (34%) in our dataset, and that this effect is significantly higher for carnivores. These results show that neglecting long-term biodiversity records in spatial analyses risks misunderstanding, and generally underestimating, species' niches, which in turn may lead to ill-informed management decisions, with significant implications for the effectiveness of conservation efforts. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Response time of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph

To avoid predation, many species rely on vision to detect predators and initiate an escape response. The ability to detect predators may be lower in darker light conditions or with darker backgrounds. For birds, however, this has never been experimentally tested. We test the hypothesis that the response time of avian prey (feral pigeon Columbia livia f. domestica) to a simulated hawk attack (taxidermy mounted colour-polymorphic black sparrowhawk Accipiter melanoleucus) will differ depending on light levels or background colour. We predict that response will be slower under darker conditions, which would translate into higher predation risk. The speed of response of prey in relation to light level or background colour may also interact with the colour of the predator, and this idea underpins a key hypothesis proposed for the maintenance of different colour morphs in polymorphic raptors. We therefore test whether the speed of reaction is influenced by the morph of the hawk (dark/light) in combination with light conditions (dull/bright), or background colours (black/white). We predict slowest responses to morphs under conditions that less contrast with the plumage of the hawk (e.g. light morph under bright light or white background). In support of our first hypothesis, pigeons reacted slower under duller light and with a black background. However, we found no support for the second hypothesis, with response times observed between the hawk-morphs being irrespective of light levels or background colour. Our findings experimentally confirm that birds detect avian predators less efficiently under darker conditions. These conditions, for example, might occur during early mornings or in dense forests, which could lead to changes in anti-predator behaviours. However, our results provide no support that different morphs may be maintained in a population due to differential selective advantages linked to improved hunting efficiencies in different conditions due to crypsis.

Brain evolution in Proboscidea (Mammalia, Afrotheria) across the Cenozoic

As the largest and among the most behaviourally complex extant terrestrial mammals, proboscideans (elephants and their extinct relatives) are iconic representatives of the modern megafauna. The timing of the evolution of large brain size and above average encephalization quotient remains poorly understood due to the paucity of described endocranial casts. Here we created the most complete dataset on proboscidean endocranial capacity and analysed it using phylogenetic comparative methods and ancestral character states reconstruction using maximum likelihood. Our analyses support that, in general, brain size and body mass co-evolved in proboscideans across the Cenozoic; however, this pattern appears disrupted by two instances of specific increases in relative brain size in the late Oligocene and early Miocene. These increases in encephalization quotients seem to correspond to intervals of important climatic, environmental and faunal changes in Africa that may have positively selected for larger brain size or body mass.

Scent chemistry is key in the evolutionary transition between insect and mammal pollination in African pineapple lilies

Volatile emissions may play a key role in structuring pollination systems of plants with morphologically unspecialised flowers. Here we test for pollination by small mammals in Eucomis regia and investigate whether its floral scent differs markedly from fly- and wasp-pollinated congeners and attracts mammals. We measured floral traits of E. regia and made comparisons with insect-pollinated congeners. We observed floral visitors and examined fur and faeces of live-trapped mammals for pollen. We determined the contributions of different floral visitors to seed set with selective exclusion and established the breeding system with controlled pollination experiments. Using bioassays, we examined whether mammals are attracted by the floral scent and are effective agents of pollen transfer. Eucomis regia differs from closely related insect-pollinated species mainly in floral scent, with morphology, colour and nectar properties being similar. We found that mice and elephant-shrews pollinate E. regia, which is self-incompatible and reliant on vertebrates for seed production. Mammals are strongly attracted to the overall floral scent, which contains unusual sulphur compounds, including methional (which imparts the distinctive potato-like scent and which was shown to be attractive to small mammals). The results highlight the important role of scent chemistry in shifts between insect and mammal pollination systems.

Screening and supporting through schools: educational experiences and needs of adolescents living with HIV in a South African cohort

BACKGROUND

Many adolescents living with HIV remain disconnected from care, especially in high-prevalence settings. Slow progressors-adolescents infected perinatally who survive without access to lifesaving treatment-remain unidentified and disconnected from heath systems, especially in high-prevalence settings. This study examines differences in educational outcomes for ALHIV, in order to i) identify educational markers for targeting HIV testing, counselling and linkages to care, and ii) to identify essential foci of educational support for ALHIV.

METHODS

Quantitative interviews with N = 1063 adolescents living with HIV and N = 456 HIV-free community control adolescents (10-19 year olds) included educational experiences (enrolment, fee-free school, school feeding schemes, absenteeism, achievement), physical health, cognitive difficulties, mental health challenges (depression, stigma, and trauma), missing school to attend clinic appointments, and socio-demographic characteristics. Voluntary informed consent was obtained from adolescents and caregivers (when adolescent < 18 years old). Analyses included multivariate logistic regressions, controlling for socio-demographic covariates, and structural equation modelling using STATA15.

RESULTS

ALHIV reported accessing educational services (enrolment, free schools, school feeding schemes) at the same rates as other adolescents (94, 30, and 92% respectively), suggesting that school is a valuable site for identification. Living with HIV was associated with poorer attendance (aOR = 1.7 95%CI1.1-2.6) and educational delay (aOR1.7 95%CI1.3-2.2). Adolescents who reported educational delay were more likely to be older, male, chronically sick and report more cognitive difficulties. A path model with excellent model fit (RMSEA = 0.027, CFI 0.984, TLI 0.952) indicated that living with HIV was associated with a series of poor physical, mental and cognitive health issues which led to worse educational experiences.

CONCLUSION

Schools may provide an important opportunity to identify unreached adolescents living with HIV and link them into care, focusing on adolescents with poor attendance, frequent sickness, low mood and slow learning. Key school-based markers for identifying unreached adolescents living with HIV may be low attendance, frequent sickness, low mood and slow learning. Improved linkages to care for adolescents living with HIV, in particular educational support services, are necessary to support scholastic achievement and long-term well-being, by helping them to cope with physical, emotional and cognitive difficulties.

Structural and biochemical characterization of Plasmodium falciparum Hsp70-x reveals functional versatility of its C-terminal EEVN motif

Plasmodium falciparum, the main agent of malaria expresses six members of the heat shock protein 70 (Hsp70) family. Hsp70s serve as protein folding facilitators in the cell. Amongst the six Hsp70 species that P. falciparum expresses, Hsp70-x (PfHsp70-x), is partially exported to the host red blood cell where it is implicated in host cell remodeling. Nearly 500 proteins of parasitic origin are exported to the parasite-infected red blood cell (RBC) along with PfHsp70-x. The role of PfHsp70-x in the infected human RBC remains largely unclear. One of the defining features of PfHsp70-x is the presence of EEVN residues at its C-terminus. In this regard, PfHsp70-x resembles canonical eukaryotic cytosol-localized Hsp70s which possess EEVD residues at their C-termini in place of the EEVN residues associated with PfHsp70-x. The EEVD residues of eukaryotic Hsp70s facilitate their interaction with co-chaperones. Characterization of the role of the EEVN residues of PfHsp70-x could provide insights into the function of this protein. In the current study, we expressed and purified recombinant PfHsp70-x (full length) and its EEVN minus form (PfHsp70-xT ). We then conducted structure- function assays towards establishing the role of the EEVN motif of PfHsp70-x. Our findings suggest that the EEVN residues of PfHsp70-x are important for its ATPase activity and chaperone function. Furthermore, the EEVN residues are crucial for the direct interaction between PfHsp70-x and human Hsp70-Hsp90 organizing protein (hHop) in vitro. Hop facilitates functional cooperation between Hsp70 and Hsp90. However, it remains to be established if PfHsp70-x and hHsp90 cooperate in vivo.

Describing the diurnal relationships between objectively measured mother and infant physical activity

BACKGROUND

Evidence for the importance of accumulating sufficient physical activity in the early years is mounting. This study aimed to determine the relationship between maternal and infant objectively measured physical activity, and to examine the diurnal interactions between these behaviours while accounting for potential covariates.

METHODS

Mothers and infants (n = 152 pairs; infants aged 3-24 months) were recruited from Soweto, South Africa, and physical activity was measured using a wrist worn accelerometer (Axivity AX3, Axivity Ltd., Newcastle-upon-Tyne, UK) for 3-7 days. Mothers completed sleep diaries recording night time-in-bed (used as a proxy for nocturnal sleep status) for themselves and their infant; and reported times during which their infant was in their personal care (caregiver status) for each day during the measurement period. Significant correlates of infant physical activity, as well as the interactions between mother's physical activity, day of the week, sleep status, and caregiver status, were included in panel regression analyses with infant physical activity as the outcome.

RESULTS

There was an equal distribution of boys and girls, and their age ranged from 2.6 to 24.5 months. The majority of mothers (73%) did not spend any time apart from their infant. During weekdays, the combined effect of mother's physical activity (β=0.11), the interactions between mother's physical activity and caregiver status (β=0.17), and sleep status (β= - 0.04) on infant physical activity was β=0.24; while during weekend days this association was β=0.21; and was largely moderated by the interaction between the mother being with the infant and her activity levels (β=0.23), but partly attenuated by mother's physical activity independent of other variables (β= - 0.04). For each hour of the day, for both mother and infant, peaks of physical activity were higher when the mother was not the primary caregiver.

CONCLUSIONS

Infant physical activity levels were strongly associated with their mother's activity levels particularly during the week; this relationship was stronger when mothers were more active while looking after their infant. Mothers should be encouraged to be active when looking after their children, particularly during the week, and to provide infants with as much opportunity to be active as possible.

Polymyxin B inhibits the chaperone activity of Plasmodium falciparum Hsp70

Heat shock protein 70 (Hsp70) is a molecular chaperone that plays an important role in cellular proteostasis. Hsp70s are also implicated in the survival and pathogenicity of malaria parasites. The main agent of malaria, Plasmodium falciparum, expresses six Hsp70s. Of these, two (PfHsp70-1 and PfHsp70-z) localize to the parasite cytosol. Previously conducted gene knockout studies suggested that PfHsp70-z is essential, and it has been demonstrated that small-molecule inhibitors targeting PfHsp70-1 cause parasite death. For this reason, both PfHsp70-1 and PfHsp70-z are potential antimalarial targets. Two cyclic lipopeptides, colistin and polymyxin B (PMB), have been shown to bind another heat shock protein, Hsp90, inhibiting its chaperone function. In the current study, we investigated the effect of PMB on the structure-function features of PfHsp70-1 and PfHsp70-z. Using surface plasmon resonance analysis, we observed that PMB directly interacts with both PfHsp70-1 and PfHsp70-z. In addition, using circular dichroism spectrometric analysis combined with tryptophan fluorescence measurements, we observed that PMB modulated the secondary and tertiary structures of Hsp70. Furthermore, PMB inhibited the basal ATPase activity and chaperone function of the two Hsp70s. Our findings suggest that PMB associates with Hsp70 to inhibit its function. In light of the central role of Hsp70 in cellular proteostasis and its essential role in the development of malaria parasites in particular, our findings expand the library of small-molecule inhibitors that target this medically important class of molecular chaperones.

Environmental drivers of viral community composition in Antarctic soils identified by viromics

BACKGROUND

The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region.

METHODS

Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution.

RESULTS

We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure.

CONCLUSIONS

The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.

One Size Fits All? The Validity of a Composite Poverty Index Across Urban and Rural Households in South Africa

Composite indices have been prominently used in poverty research. However, validity of these indices remains subject to debate. This paper examines the validity of a common type of composite poverty indices using data from a cross-sectional survey of 2477 households in urban and rural KwaZulu-Natal, South Africa. Multiple-group comparisons in structural equation modelling were employed for testing differences in the measurement model across urban and rural groups. The analysis revealed substantial variations between urban and rural respondents both in the conceptualisation of poverty as well as in the weights and importance assigned to individual poverty indicators. The validity of a 'one size fits all' measurement model can therefore not be confirmed. In consequence, it becomes virtually impossible to determine a household's poverty level relative to the full sample. Findings from our analysis have important practical implications in nuancing how we can sensitively use composite poverty indices to identify poor people.

Relationship Between HIV Coinfection, Interleukin 10 Production, and Mycobacterium tuberculosis in Human Lymph Node Granulomas

BACKGROUND

 Human immunodeficiency virus type 1 (HIV)-infected persons are more susceptible to tuberculosis than HIV-uninfected persons. Low peripheral CD4+ T-cell count is not the sole cause of higher susceptibility, because HIV-infected persons with a high peripheral CD4+ T-cell count and those prescribed successful antiretroviral therapy (ART) remain more prone to active tuberculosis than HIV-uninfected persons. We hypothesized that the increase in susceptibility is caused by the ability of HIV to manipulate Mycobacterium tuberculosis-associated granulomas.

METHODS

 We examined 71 excised cervical lymph nodes (LNs) from persons with HIV and M. tuberculosis coinfection, those with HIV monoinfection, and those with M. tuberculosis monoinfection with a spectrum of peripheral CD4+ T-cell counts and ART statuses. We quantified differences in M. tuberculosis levels, HIV p24 levels, cellular response, and cytokine presence within granulomas.

RESULTS

 HIV increased M. tuberculosis numbers and reduced CD4+ T-cell counts within granulomas. Peripheral CD4+ T-cell depletion correlated with granulomas that contained fewer CD4+ and CD8+ T cells, less interferon γ, more neutrophils, more interleukin 10 (IL-10), and increased M. tuberculosis numbers. M. tuberculosis numbers correlated positively with IL-10 and interferon α levels and fewer CD4+ and CD8+ T cells. ART reduced IL-10 production.

CONCLUSIONS

 Peripheral CD4+ T-cell depletion correlated with increased M. tuberculosis presence, increased IL-10 production, and other phenotypic changes within granulomas, demonstrating the HIV infection progressively changes these granulomas.

Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi

BACKGROUND

Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree death. The decline of orchards infected with P. cinnamomi occurs much faster when exposed to flooding, even if flooding is only transient. Flooding is a multifactorial stress compromised of several individual stresses, making breeding and selection for tolerant varieties challenging. With more plantations occurring in marginal areas, with imperfect irrigation and drainage, understanding the response of avocado to these stresses will be important for the industry.

RESULTS

Maintenance of energy production was found to be central in the response to flooding, as seen by up-regulation of transcripts related to glycolysis and induction of transcripts related to ethanolic fermentation. Energy-intensive processes were generally down-regulated, as evidenced by repression of transcripts related to processes such as secondary cell-wall biosynthesis as well as defence-related transcripts. Aquaporins were found to be down-regulated in avocado roots exposed to flooding, indicating reduced water-uptake under these conditions.

CONCLUSIONS

The transcriptomic response of avocado to flooding and P. cinnamomi was investigated utilizing microarray analysis. Differences in the transcriptome caused by the presence of the pathogen were minor compared to transcriptomic perturbations caused by flooding. The transcriptomic response of avocado to flooding reveals a response to flooding that is conserved in several species. This data could provide key information that could be used to improve selection of stress tolerant rootstocks in the avocado industry.