Assessment of the conservation priority status of South African estuaries for use in management and water allocation

The future health and productivity of South Africa's approximately 250 estuaries is dependent on two main factors: management and freshwater inputs. Both management and water allocation decisions involve trade-offs between conservation and various types of utilisation. In order to facilitate decision-making in both of these spheres, it is necessary to understand the relative conservation importance of different estuaries. This study devises a method for prioritising South African estuaries on the basis of conservation importance, and presents the results of a ranking based on the collation of existing data for all South African estuaries. Estuaries are scored in terms of their size, type and biogeographical zone, habitats and biota (plants, invertebrates, fish and birds). Thirtythree estuaries are currently under formal protection, but they are not representative of all estuarine biodiversity. We performed a complementarity analysis, incorporating data on abundance where available, to determine the minimum set of estuaries that includes all known species of plants, invertebrates, fishes and birds. In total, 32 estuaries were identified as 'required protected areas', including 10 which are already protected. An estuary's importance status (including 'required protected area' status) will influence the choice of management class and hence freshwater allocation under the country's new Water Act, and can be used to assist the development of a new management strategy for estuaries, which is currently underway. WaterSA Vol.28(2) 2002: 191-20

PPAR? Downregulation by TGF in Fibroblast and Impaired Expression and Function in Systemic Sclerosis: A Novel Mechanism for Progressive Fibrogenesis

The nuclear orphan receptor peroxisome proliferator-activated receptor-gamma (PPAR-γ) is expressed in multiple cell types in addition to adipocytes. Upon its activation by natural ligands such as fatty acids and eicosanoids, or by synthetic agonists such as rosiglitazone, PPAR-γ regulates adipogenesis, glucose uptake and inflammatory responses. Recent studies establish a novel role for PPAR-γ signaling as an endogenous mechanism for regulating transforming growth factor-ß (TGF-ß)- dependent fibrogenesis. Here, we sought to characterize PPAR-γ function in the prototypic fibrosing disorder systemic sclerosis (SSc), and delineate the factors governing PPAR-γ expression. We report that PPAR-γ levels were markedly diminished in skin and lung biopsies from patients with SSc, and in fibroblasts explanted from the lesional skin. In normal fibroblasts, treatment with TGF-ß resulted in a time- and dose-dependent down-regulation of PPAR-γ expression. Inhibition occurred at the transcriptional level and was mediated via canonical Smad signal transduction. Genome-wide expression profiling of SSc skin biopsies revealed a marked attenuation of PPAR-γ levels and transcriptional activity in a subset of patients with diffuse cutaneous SSc, which was correlated with the presence of a ''TGF-ß responsive gene signature'' in these biopsies. Together, these results demonstrate that the expression and function of PPAR-γ are impaired in SSc, and reveal the existence of a reciprocal inhibitory cross-talk between TGF-ß activation and PPAR-γ signaling in the context of fibrogenesis. In light of the potent anti-fibrotic effects attributed to PPAR-γ, these observations lead us to propose that excessive TGF-ß activity in SSc accounts for impaired PPAR-γ function, which in turn contributes to unchecked fibroblast activation and progressive fibrosis. © 2010 Wei et al

Evaluating the effects of catch-and-release angling on Cape stumpnose Rhabdosargus holubi in a South African estuary

Fisheries managers are increasingly promoting catch and release (C&R) as a means to manage recreational fish stocks. Several commonly used output regulations, including bag and size limits, require the mandatory release of captured fishes by anglers. In addition to mandatory C&R, conservation-conscious anglers have adopted voluntary C&R behaviour as a result of the noticeable declines in the populations of many fishery species and this behaviour is becoming increasingly popular among recreational anglers (Cooke et al. 2013a). The combination of mandatory and voluntary C&R behaviour is substantial, as Raby et al. (2014) estimated that 60% of fish captured in global recreational fisheries are released. In South Africa, Cowley et al. (2013) found that a large proportion (mean 74% [SD 7.3]) of the five most-dominant fishery species captured in the Sundays Estuary recreational fishery were released

Harmonisation and Between-Country Differences of the Lifetime of Experiences Questionnaire in Older Adults

Background: The Lifetime of Experiences Questionnaire (LEQ) assesses complex mental activity across the life-course and has been associated with brain and cognitive health. The different education systems and occupation classifications across countries represent a challenge for international comparisons. The objectives of this study were four-fold: to adapt and harmonise the LEQ across four European countries, assess its validity across countries, explore its association with brain and cognition and begin to investigate between-country differences in life-course mental activities. Method: The LEQ was administered to 359 cognitively unimpaired older adults (mean age and education: 71.2, 13.2 years) from IMAP and EU-funded Medit-Ageing projects. Education systems, classification of occupations and scoring guidelines were adapted to allow comparisons between France, Germany, Spain and United Kingdom. We assessed the LEQ's (i) concurrent validity with a similar instrument (cognitive activities questionnaire - CAQ) and its structural validity by testing the factors' structure across countries, (ii) we investigated its association with cognition and neuroimaging, and (iii) compared its scores between countries. Results: The LEQ showed moderate to strong positive associations with the CAQ and revealed a stable multidimensional structure across countries that was similar to the original LEQ. The LEQ was positively associated with global cognition. Between-country differences were observed in leisure activities across the life-course. Conclusions: The LEQ is a promising tool for assessing the multidimensional construct of cognitive reserve and can be used to measure socio-behavioural determinants of cognitive reserve in older adults across countries. Longitudinal studies are warranted to test further its clinical utility

Age and growth of Cape stumpnose Rhabdosargus holubi (Pisces: Sparidae) in the Eastern Cape, South Africa

Rhabdosargus holubi (Steindachner, 1881) is a small (maximum size = 450 mm total length; Heemstra and Heemstra 2004) sparid that is distributed along the south-east coast of Africa from St Helena Bay, South Africa, to Maputo, Mozambique (Götz and Cowley 2013). Spawning occurs in the nearshore marine environment primarily during winter, specifically May–August in KwaZulu-Natal (KZN) (Wallace 1975) and July–February in the South-Eastern Cape (Whitfield 1998). Individuals reach 50% sexual maturity at approximately 150 mm standard length (SL) in the Eastern Cape (Whitfield 1998). The early life stages are transported by the south-westward-flowing Agulhas Current, and recruit as post-flexion larvae and early juveniles into estuaries during late winter and early summer (Blaber 1974). The warm temperatures and high nutrient levels in estuaries favour fast growth (Blaber 1973a), and fish spend their first year of life in these environments, migrating back out to sea after reaching approximately 120 mm SL. Some individuals remain trapped in closed estuaries, where they may reach sizes greater than 200 mm SL (James et al. 2007a). Rhabdosargus holubi is the dominant estuarine-dependent marine teleost species recorded in permanently open and temporarily open/closed estuaries in the warm-temperate region, which spans the south, south-east and east coast of South Africa (Harrison 2005). The species is also an important component of the linefishery in many SouthAfrican estuaries (10–15.6% by number) (Pradervand and Baird 2002), particularly in Eastern Cape estuaries (Cowley et al. 2003). These figures underestimate the presence of R. holubi, as most individuals making use of estuaries are young, feeding predominately on filamentous macroalgae and diatom flora, and are generally too small to be caught with hook and line (De Wet and Marais 1990). James et al. (2007b) showed that R. holubi made up 34–92% of the annual seine-net catch in the East Kleinemonde Estuary. Rhabdosargus holubi is also important in the KZN shorebased linefishery, representing 4.6% of the total landed catch (Dunlop and Mann 2012)

Development of a Halotolerant Community in the St. Lucia Estuary (South Africa) during a Hypersaline Phase

Background: The St. Lucia Estuary, Africa’s largest estuarine lake, is currently experiencing unprecedented freshwater deprivation which has resulted in a northward gradient of drought effects, with hypersaline conditions in its northern lakes. Methodology/Principal Findings: This study documents the changes that occurred in the biotic communities at False Bay from May 2010 to June 2011, in order to better understand ecosystem functioning in hypersaline habitats. Few zooplankton taxa were able to withstand the harsh environmental conditions during 2010. These were the flatworm Macrostomum sp., the harpacticoid copepod Cletocamptus confluens, the cyclopoid copepod Apocyclops cf. dengizicus and the ciliate Fabrea cf. salina. In addition to their exceptional salinity tolerance, they were involved in a remarkably simple food web. In June 2009, a bloom of an orange-pigmented cyanobacterium (Cyanothece sp.) was recorded in False Bay and persisted uninterruptedly for 18 months. Stable isotope analysis suggests that this cyanobacterium was the main prey item of F. cf. salina. This ciliate was then consumed by A. cf. dengizicus, which in turn was presumably consumed by flamingos as they flocked in the area when the copepods attained swarming densities. On the shore, cyanobacteria mats contributed to a population explosion of the staphylinid beetle Bledius pilicollis. Although zooplankton disappeared once salinities exceeded 130, many taxa are capable of producing spores or resting cysts to bridge harsh periods. The hypersaline community was disrupted by heavy summer rains in 2011, which alleviated drought conditions and resulted in a sharp increase in zooplankton stock an

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

A quick guide for building a successful bioinformatics community

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB)

All-cause and liver-related mortality risk factors in excessive drinkers: Analysis of data from the UK biobank

Background: High alcohol intake is associated with increased mortality. We aimed to identify factors affecting mortality in people drinking extreme amounts of alcohol. Methods: We obtained information from the UK Biobank on approximately 500,000 participants aged 40–70 years at baseline assessment in 2006–2010. Habitual alcohol intake, lifestyle and physiological data, laboratory test results, and hospital diagnoses and death certificate data (to June 2020) for 5136 men (2.20% of male participants) and 1504 women (0.60%) who reported consuming ≥80 or ≥50 g/day, respectively, were used in survival analysis. Results: Mortality hazard ratios for these excessive drinkers, compared to all other participants, were 2.02 (95% CI 1.89–2.17) for all causes, 1.89 (1.69–2.12) for any cancer, 1.87 (1.61–2.17) for any circulatory disease, and 9.40 (7.00–12.64) for any liver disease. Liver disease diagnosis or abnormal liver function tests predicted not only deaths attributed to liver disease but also those from cancers or circulatory diseases. Mortality among excessive drinkers was also associated with quantitative alcohol intake; diagnosed alcohol dependence, harmful use, or withdrawal syndrome; and current smoking at assessment. Conclusions: People with chronic excessive alcohol intake experience decreased average survival, but there is substantial variation in their mortality, with liver abnormality and alcohol dependence or other alcohol use disorders associated with a worse prognosis. Clinically, patients with these risk factors and high alcohol intake should be considered for early or intensive management. Research can usefully focus on the factors predisposing to dependence or liver abnormality