Molecular characterisation of group A streptococcus isolates recovered from the north-west of Pretoria, South Africa

Background. Group A streptococcus (GAS) is a human pathogen responsible for a wide range of invasive and non-invasive infections. Pharyngitis caused by GAS may have complications such as acute rheumatic fever subsequently leading to rheumatic heart disease (RHD). RHD continues to have high morbidity and mortality and affects millions of children and young adults, mostly in developing countries. An effective preventive vaccine against GAS may reduce the morbidity and mortality. A 30-valent M-protein-based vaccine is currently at the clinical trials stage of development. Potential vaccine coverage will depend on the geographical distribution of GAS emm (M protein) types.Objectives. To determine the emm types of GAS isolates circulating in the north-west of Pretoria, South Africa.Methods. Throat swabs were collected from patients aged 3 - 20 years presenting with pharyngitis at one local clinic. In addition, GAS clinical isolates were collected from the National Health Laboratory Service diagnostic laboratory. Emm genotyping was done on the GAS isolates by amplification of the emm gene followed by sequencing of the 5′ portion of the gene. The emm types were correlated with the types in the vaccine.Results. A total of 54 GAS isolates were collected, comprising 19 pharyngitis and 35 clinical isolates. We found 15 different emm types among the 43 GAS isolates that were successfully sequenced. Eleven isolates (20%) could not be typed. The most prevalent emm type was 92 (26%), which is part of the 30-valent vaccine. This was followed by emm 25 and 75, each accounting for 12% of the isolates. Up to 67% of the emm types are not covered in the 30-valent vaccine.Conclusions. Fifteen emm types were identified, of which 92 was the most prevalent. It is concerning that 67% of the emm types are not covered in the vaccine currently under development. It is recommended that surveillance studies be extended to include other parts of the country in order to expand knowledge of the circulating emm types

An unusual coordination polymer containing Cu+ ions and featuring possible Cu⋯Cu `cuprophilic' inter­actions: poly[di-μ-chlorido-(μ4-3,5-di­amino­benzoato-κ4O:O′:N:N′)tricopper(I)(3 Cu—Cu)]

We thank the Higher Education Commission of Pakistan (grant No. 1-3/PM-PDFP-II/2006/22) for financial support.Peer reviewedPublisher PD

Hydrothermal synthesis and crystal structure of poly[bis- (μ3-3,4-diaminobenzoato) manganese], a layered coordination polymer

Acknowledgements The EPSRC National Crystallography Service (University of Southampton) is thanked for the intensity data collection. Funding information We thank the Higher Education Commission of Pakistan (grant No. 1–3/PM-PDFP-II/2006/22) for financial supportPeer reviewedPublisher PD

Effect of parallel electric fields on whistler mode waves in Jupiter's magnetosphere

Observation of auroral hiss at Jupiter by Voyager I has been suggested as being directly related to regions of parallel electric field and auroral particle precipitation. The effect of a parallel electric field on whistler mode propagation in Jupiter's magnetosphere has been studied. The dispersion relation for whistler mode waves in an isothermal one-component electron plasma in the presence of a parallel electric field has been used to study the growth of whistler mode waves propagating in the Jovian magnetosphere. The growth rates have been computed by using the observed plasma parameters at 5.6 Rj . The growth rate, which is found to be a maximum in the equatorial magnetosphere, is reduced to zero in the absence of the electrostatic field. This has lead us to conclude that, in the case of isothermal magnetosplasma, the growth rate is induced by the electrostatic field.         ARK: https://n2t.net/ark:/88439/y007466 Permalink: https://geophysicsjournal.com/article/16 &nbsp

Effect of water and straw management practices on methane emissions from rice fields: A review through a meta-analysis

[EN] Rice fields contribute substantially to global warming of the atmosphere through emission of methane (CH4). This article reviews the state of the art of factors affecting CH4 emissions in rice fields, focusing on soil organic matter content and water management practices. A quantitative relationship between these factors was established through a meta-analysis based on a literature survey. This relationship can be useful to update emission factors used to estimate CH4 in the National Emission Inventories. Methane emissions in rice fields can be as much as 90% higher in continuously flooded rice fields compared with other water management practices, independent from straw addition. Water management systems that involve absence of flooding in total or for part of the growing period such as midseason drainages, intermittent flooding, and percolation control, can reduce CH4 emissions substantially. Moreover, CH4 emissions increase with the amount of straw added up to 7.7 t/ha for continuously flooded soils and up to 5.1 t/ha for other water regimes. Above these levels, no further increase is produced with further addition of straw. With regard to rice straw management mitigation strategies, recommended practices are composting rice straw, straw burning under controlled conditions, recollecting rice straw for biochar production, generation of energy, to be used as a substrate, or to obtain other byproducts with added value. This review improves the understanding of the relationship between straw application rate, water regimes, and CH4 emissions from rice fields to date. This relationship can help to select the most appropriate management practices to improve current mitigation strategies to reduce atmospheric CH4. © 2012 Mary Ann Liebert, Inc.This study was financially supported by Fundacio´n Agroalimed from the Consellerı´a de Agricultura of Valencia, Spain and the Vicerrectorado de Investigacio´n of the UPV (Programa de Apoyo a la Investigacio´n y Desarrollo, PAID06-11 Program, Project No. 1950).Sanchís Jiménez, EM.; Ferrer Roglán, M.; Torres, AG.; Cambra López, M.; Calvet Sanz, S. (2012). Effect of water and straw management practices on methane emissions from rice fields: A review through a meta-analysis. Environmental Engineering Science. 29(12):1053-1062. https://doi.org/10.1089/ees.2012.0006S10531062291

ESTABLISHING A PLATFORM FOR SPRAY DRYING INHALABLE VACCINES IN SOUTH AFRICA

Mycobacterium bovis BCG is the current vaccine for tuberculosis (TB). However, BCG as it is currently administered shows highly variable efficacy in protecting adults against TB. The natural route of infection of TB is via inhalation of bacilli-containing aerosols and it is postulated that immunization by the natural route of infection may lead to a greater immunity given the fact that the lungs are the primary target of infection. By eliciting both local and systemic immune responses, it is anticipated that an inhaled form of BCG will offer greater protection against pulmonary TB. Current commercial BCG vaccine preparations are filled as bacterial suspensions in vials, dried through lyophilization and stabilized through refrigeration with a one year shelf life. However, freeze-dried BCG does not exhibit a particle form conducive for delivery via the aerosol route and must be injected. Spray drying studies by Harvard University and Medicine in Need (MEND) scientists have demonstrated that BCG could be spray dried into a viable aerosol with up to 1 year of stability under refrigerated conditions, with the potential for room temperature stability. To support the further preclinical development of the BCG aerosol for application in the developing world, MEND established a state-of-the-art Biosafety level 3 spray drying facility with local expertise in South Africa, where the vaccine will be produced for an IND-enabling toxicology study meeting OECD Good Laboratory Practice (GLP) requirements. Frozen BCG bulk is spray dried and the resulting dry powder is characterized in terms of viability and aerosol properties. The dried BCG aerosol is then aseptically filled into capsules using a semi-automatic filling device for delivery using a low-cost hand-held inhaler. In conclusion, the spray drying technology was successfully transferred from Harvard University to the MEND facility in Pretoria. MEND is developing local expertise and infrastructure to support further preclinical and clinical development of BCG for inhalation

Geography : the state of the discipline in South Africa (2000 - 2001)

The research team presents the findings of a comprehensive investigation into the status and role of Geography as an academic discipline in South Africa. The paper begins by placing the discipline in historical and epistemological context. Extensive and intensive interviews were conducted with geographers at all South African universities and, on a smaller scale, in the workplace. Information was also gleaned from an array of documents. Comments on the characteristics of university departments, general school education, the geography research environment the geographer in the workplace are given. Emerging trends, many of which relate to recent socio-political change, show that contemporary emphasis is on applied geography, specific fields of specialisation, the accommodation of Environmental Science and Environmental Management, skills training and on curriculum development with a marked vocational orientation. As geographers continue addressing national and international environmental and social issues in their professional endeavours, they are alerted to critical concerns voiced with conviction by practising geographers. In the final analysis a positive conclusion is reached and the academic merit and status of the discipline is confirmed

The effect of prey identity and substrate type on the functional response of a globally invasive crayfish

Biological invasions threaten biodiversity on a global scale, therefore, developing predictive methods to understand variation in ecological change conferred is essential. Trophic interaction strength underpins community dynamics, however, these interactions can be profoundly affected by abiotic context, such as substrate type. The red swamp crayfish (Procambarus clarkii) has successfully invaded a number of freshwater ecosystems. We experimentally derive the Functional Response (FR) (density dependent predation) of the red swamp crayfish preying upon both a benthic prey; chironomid larvae, and a pelagic prey; Daphnia magna, on a no substrate control, sand, and gravel substrates to determine whether (1) there is a higher impact on prey that are benthic, and (2) whether the presence of different substrate types can dampen the interaction strength. We apply and demonstrate the utility of the Functional Response Ratio (FRR) metric in unravelling differences in ecological impact not obvious from traditional FR curves. Procambarus clarkii is capable of constantly utilising high numbers of both benthic and pelagic prey items, showing a Type II functional response under all scenarios. The presence of gravel and sand substrate each independently decreased the magnitude FR upon D. magna. Though, with regards to chironomid larvae the FR curves showed no difference in magnitude FR, the FRR reveals that the highest impact is conferred when foraging on sand substrate. This reinforces the need for impact assessments to be contextually relevant

An evaluation of the current extent and potential spread of Black Bass invasions in South Africa

Black Bass, a collective name for members of the centrarchid genus Micropterus, are native to North America, but have been introduced globally to enhance recreational angling. This study assessed the distribution of Micropterus salmoides, M. dolomieu and M. punctulatus in South Africa using both formal (survey-based) and informal (tournament data and social media) information sources. Analysis of the distribution data showed habitat bias between the data sources. Survey data from formal information sources were dominated by locality records in riverine environments while those derived from informal information sources focused more on lacustrine habitats. Presence data were used to develop niche models to identify suitable areas for their establishment. The predicted distribution range of M. salmoides revealed a broad suitability over most of South Africa, however, the Cape Fold Ecoregion and all coastal regions were most suitable for the establishment for both M. dolomieu and M. punctulatus. Flow accumulation and precipitation of coldest quarter were the most important environmental variables associated with the presence of all Black Bass species in South Africa. In addition, anthropogenic disturbance such as agricultural activities were associated with the presence of both Smallmouth Bass and Spotted Bass. An extensive area-based invasion debt was observed for all Micropterus spp. The potential for further spread of Black Bass in South Africa is of ecological concern because of their impact on native biota