Risk of predation,hydrodynamic efficiency and their influence on school structure

Synopsis Laboratory studies were conducted on 15 schools of blackchin shiners, Notropis heterodon, to determine if they altered their structure in response to changing environmental demands. The hypothesis tested was that fish schools should sacrifice a flat, hydrodynamically efficient structure in favour of an unobstructed visual field in the presence of a predator by staggering in the vertical plane. Ten schools were exposed for two weeks to a simple environment with only a current. For the next two-week period a predator was added. Five control schools were exposed to the simple environment for both two-week periods. Six of the ten treated schools increased their staggering in the vertical dimension as predicted while none of the control schools changed. This result was suggestive that hydrodynamic advantages were sacrificed. Respirometer experiments indicated these fish were capable of achieving some hydrodynamic benefits from schooling but these benefits may be a function of fish size.     

Five pseudoknots are present at the 204 nucleotides long 3'' noncoding region of tobacco mosaic virus RNA.

The 104 nucleotides long 3' terminal region of TMV RNA was shown previously to contain two pseudoknotted structures (Rietveld et al. (1984), EMBO J. 3, 2613-2619). We here present evidence for the occurrence, within the 204 nucleotides long 3' noncoding region, of another highly structured domain located immediately adjacent to the tRNA-like structure of 95 nucleotides (Joshi et al. (1985) Nucleic Acids Res. 13, 347-354). A model for the three-dimensional folding of this region, containing three more pseudoknots, is proposed on the basis of chemical modification and enzymatic digestion. The existence of these three consecutive pseudoknots was supported by sequence comparisons with the RNA from the related tobamoviruses TMV-L, CcTMV and CGMMV. Coaxial stacking of the six double helical segments involved gives rise to the formation of a 25 basepair long quasi-continuous double helix. The results show that the three-dimensional folding of the 3' non-translated region of tobamoviral RNAs is largely maintained by the formation of five pseudoknots. The organisation of this region in the RNA of the tobamovirus CcTMV suggests that recombinational events among aminoacylatable plant viral RNAs have to be considered.     

Inherent asymmetry of the structure of F1-ATPase from bovine heart mitochondria at 6.5 A resolution.

ATP synthase, the assembly which makes ATP in mitochondria, chloroplasts and bacteria, uses transmembrane proton gradients generated by respiration or photosynthesis to drive the phosphorylation of ADP. Its membrane domain is joined by a slender stalk to a peripheral catalytic domain, F1-ATPase. This domain is made of five subunits with stoichiometries of 3 alpha: 3 beta: 1 gamma: 1 delta: 1 epsilon, and in bovine mitochondria has a molecular mass of 371,000. We have determined the 3-dimensional structure of bovine mitochondrial F1-ATPase to 6.5 A resolution by X-ray crystallography. It is an approximately spherical globule 110 A in diameter, on a 40 A stem which contains two alpha-helices in a coiled-coil. This stem is presumed to be part of the stalk that connects F1 with the membrane domain in the intact ATP synthase. A pit next to the stem penetrates approximately 35 A into the F1 particle. The stem and the pit are two examples of the many asymmetric features of the structure. The central element in the asymmetry is the longer of the two alpha-helices in the stem, which extends for 90 A through the centre of the assembly and emerges on top into a dimple 15 A deep. Features with threefold and sixfold symmetry, presumed to be parts of homologous alpha and beta subunits, are arranged around the central rod and pit, but the overall structure is asymmetric. The central helix provides a possible mechanism for transmission of conformational changes induced by the proton gradient from the stalk to the catalytic sites of the enzyme.     

Host-cell reactivation of ultraviolet-irradiated SV40 DNA in five complementation groups of xeroderma pigmentosum.

Host-cell reactivation of UV-irradiated double-stranded SV40 DNA was studied in BSC-1 monkey cells, normal human cells, heterozygous Xeroderma pigmentosum (XP) cells, representative cell strains of the five complemention groups of XP and in XP "variant" cells. The following percentages of survival of the plaque-forming ability of double-stranded SV40 DNA were found in XP cells compared with the value found in normal monkey and human cells: group A, 13%; group B, 30%; group C, 18%; group D, 14%; group E, 59%; and in the heterozygous XP cells almost 100%. The survival in XP "variant" cells was 66%. The survival of single-stranded SV40 DNA in BSC-1 cells was much lower than that of double-stranded SV40 DNA in XP cells of complementation group A, which possibly indicates that some repair of UV damage occurs even in XP cells of group A.     

Pond Acoustic Sampling Scheme: A draft protocol for rapid acoustic data collection in small waterbodies

1. Freshwater conservation is vital to the maintenance of global biodiversity. Ponds are a critical, yet often under‐recognized, part of this, contributing to overall ecosystem functioning and diversity. They provide habitats for a range of aquatic, terrestrial, and amphibious life, often including rare and declining species.
2. Effective, rapid, and accessible survey methods are needed to enable evidence‐based conservation action, but freshwater taxa are often viewed as “difficult”—and few specialist surveyors are available. Datasets on ponds are therefore limited in their spatiotemporal coverage.
3. With the advent of new recording technologies, acoustic survey methods are becoming increasingly available to researchers, citizen scientists, and conservation practitioners. They can be an effective and noninvasive approach for gathering data on target species, assemblages, and environmental variables. However, freshwater applications are lagging behind those in terrestrial and marine spheres, and as an emergent method, research studies have employed a multitude of different sampling protocols.
4. We propose the Pond Acoustic Sampling Scheme (PASS), a simple protocol to allow a standardized minimal sample to be collected rapidly from small waterbodies, alongside environmental and methodological metadata. This sampling scheme can be incorporated into a variety of survey designs and is intended to allow access to a wide range of participants, without requiring complicated or prohibitively expensive equipment.
5. Adoption of this sampling protocol would enable consistent sound recordings to be gathered by researchers and conservation organizations, and allow the development of landscape‐scale surveys, data sharing, and collaboration within an expanding freshwater ecoacoustic community—rather than individual approaches that produce incompatible datasets. The compilation of standardized data would improve the prospects for effective research into the soundscapes of small waterbodies and aid freshwater conservation efforts.

     

Will an Unsupervised Self-Testing Strategy for HIV Work in Health Care Workers of South Africa? A Cross Sectional Pilot Feasibility Study

Background

In South Africa, stigma, discrimination, social visibility and fear of loss of confidentiality impede health facility-based HIV testing. With 50% of adults having ever tested for HIV in their lifetime, private, alternative testing options are urgently needed. Non-invasive, oral self-tests offer a potential for a confidential, unsupervised HIV self-testing option, but global data are limited.

Methods

A pilot cross-sectional study was conducted from January to June 2012 in health care workers based at the University of Cape Town, South Africa. An innovative, unsupervised, self-testing strategy was evaluated for feasibility; defined as completion of self-testing process (i.e., self test conduct, interpretation and linkage). An oral point-of-care HIV test, an Internet and paper-based self-test HIV applications, and mobile phones were synergized to create an unsupervised strategy. Self-tests were additionally confirmed with rapid tests on site and laboratory tests. Of 270 health care workers (18 years and above, of unknown HIV status approached), 251 consented for participation.

Findings

Overall, about 91% participants rated a positive experience with the strategy. Of 251 participants, 126 evaluated the Internet and 125 the paper-based application successfully; completion rate of 99.2%. All sero-positives were linked to treatment (completion rate:100% (95% CI, 66.0–100). About half of sero-negatives were offered counselling on mobile phones; completion rate: 44.6% (95% CI, 38.0–51.0). A majority of participants (78.1%) were females, aged 18–24 years (61.4%). Nine participants were found sero-positive after confirmatory tests (prevalence 3.6% 95% CI, 1.8–6.9). Six of nine positive self-tests were accurately interpreted; sensitivity: 66.7% (95% CI, 30.9–91.0); specificity:100% (95% CI, 98.1–100).

Interpretation

Our unsupervised self-testing strategy was feasible to operationalize in health care workers in South Africa. Linkages were successfully operationalized with mobile phones in all sero-positives and about half of the sero-negatives sought post-test counselling. Controlled trials and implementation research studies are needed before a scale-up is considered.     

Intimate Partner Femicide in South Africa in 1999 and 2009

Background

Death is the most extreme consequence of intimate partner violence. Female homicide studies with data on the perpetrator–victim relationship can provide insights. We compare the results of two South African national studies of female homicide with similar sampling done 10 y apart.

Methods and Findings

We conducted a retrospective national survey using a weighted cluster design of a proportionate random sample of 38 mortuaries to identify homicides committed in 2009. We abstracted victim data from mortuary and autopsy reports, and perpetrator data from police interviews. We compared homicides of women 14 y and older in 2009 with previously published data collected with the same methodology for homicides committed in 1999.The study found that the rate of female homicide per 100,000 female population in 2009 was 12.9 (95% confidence interval [CI]: 9.3, 16.5), compared to 24.7 (95% CI: 17.7, 31.6) in 1999. The incidence rate ratio of 0.54 (95% CI: 0.20, 0.84) reflects a significantly lower rate in 2009. The rate of intimate partner femicide was 5.6/100,000 in 2009 versus 8.8/100,000 in 1999, with an incidence rate ratio of 0.63 (95% CI: 0.24, 1.02), indicating no difference between rates. Logistic regression analysis of homicide characteristics showed that the odds ratio of suspected rape among non-intimate femicides in 2009 compared to 1999 was 2.61 (95% CI: 1.23, 4.08) and among intimate partner femicides it was 0.84 (95% CI: 0.50, 1.42). The OR of homicide by gunshot was 0.54 (95% CI: 0.30, 0.99) in 2009 versus 1999. There was a significant drop in convictions of perpetrators of non-intimate femicide in 2009 versus 1999 (OR = 0.32 [95% CI: 0.19, 0.53]). Limitations of the study include the relatively small sample size and having only two time points.

Conclusions

Female homicide in South Africa was lower in 2009 than 1999, but intimate partner femicide and suspected rape homicide rates were not statistically different. The cause of the difference is unknown. The findings suggest that South Africa needs greater efforts nationally to implement evidence-based violence prevention. Please see later in the article for the Editors'' Summary     

TB Incidence in an Adolescent Cohort in South Africa

Background

Tuberculosis (TB) is a major public health problem globally. Little is known about TB incidence in adolescents who are a proposed target group for new TB vaccines. We conducted a study to determine the TB incidence rates and risk factors for TB disease in a cohort of school-going adolescents in a high TB burden area in South Africa.

Methods

We recruited adolescents aged 12 to 18 years from high schools in Worcester, South Africa. Demographic and clinical information was collected, a tuberculin skin test (TST) performed and blood drawn for a QuantiFERON TB Gold assay at baseline. Screening for TB cases occurred at follow up visits and by surveillance of registers at public sector TB clinics over a period of up to 3.8 years after enrolment.

Results

A total of 6,363 adolescents were enrolled (58% of the school population targeted). During follow up, 67 cases of bacteriologically confirmed TB were detected giving an overall incidence rate of 0.45 per 100 person years (95% confidence interval 0.29–0.72). Black or mixed race, maternal education of primary school or less or unknown, a positive baseline QuantiFERON assay and a positive baseline TST were significant predictors of TB disease on adjusted analysis.

Conclusion

The adolescent TB incidence found in a high burden setting will help TB vaccine developers plan clinical trials in this population. Latent TB infection and low socio-economic status were predictors of TB disease.     

Gender Differences in Homicide of Neonates,Infants, and Children under 5 y in South Africa: Results from the Cross-Sectional 2009 National Child Homicide Study

BackgroundHomicide of children is a global problem. The under-5-y age group is the second largest homicide age group after 15–19 y olds, but has received little research attention. Understanding age and gender patterns is important for assisting with developing prevention interventions. Here we present an age and gender analysis of homicides among children under 5 y in South Africa from a national study that included a focus on neonaticide and infanticide.ConclusionsHomicide of children is an extreme form or consequence of violence against children. This national study provides one of the first analyses of neonaticide and infanticide by age and gender and shows the failure of reproductive and mental health and social services to identify and help vulnerable mothers. Multi-sectoral prevention strategies are needed.