Improving coastal livelihoods through sustainable aquaculture practices - a report to the collaborative APEC Grouper Research and Development Network

Wild-harvest fisheries for live reef fish are largely over-exploited or unsustainable because of over-fishing and the widespread use of destructive fishing practices such as blast and cyanide fishing. Sustainable aquaculture – such as that of groupers – is one option for meeting the strong demand for reef fish, as well as potentially maintaining or improving the livelihoods of coastal communities. This report from a short study by the STREAM Initiative draws on secondary literature, media sources and four diverse case studies from at-risk reef fisheries, to frame a strategy for encouraging sustainable aquaculture as an alternative to destructive fishing practices. It was undertaken as a component of the APEC-funded project Collaborative Grouper Research and Development Network (FWG/01/2001) to better understand how recent technical advances in grouper culture and other complementary work – including that of the Asia-Pacific Marine Finfish Aquaculture Network (APMFAN) hosted by NACA – could better support the livelihoods of poor coastal communities. (PDF contains 49 pages

The Effects of Pre-conditioning on Exercise-Induced Muscle Damage: A Systematic Review and Meta-analysis

Background: Several studies have utilised isometric, eccentric and downhill walking pre-conditioning as a strategy for alleviating the signs and symptoms of exercise-induced muscle damage (EIMD) following a bout of damaging physical activity. Objectives: This systematic review and meta-analysis examined the effects of pre-conditioning strategies on indices of muscle damage and physical performance measures following a second bout of strenuous physical activity. Data Sources: PubMed, CINAHL and Scopus. Eligibility Criteria: Studies meeting the PICO (population, intervention/exposure, comparison, and outcome) criteria were included in this review: (1) general population or “untrained” participants with no contraindications affecting physical performance; (2) studies with a parallel design to examine the prevention and severity of muscle-damaging contractions; (3) outcome measures were compared using baseline and post-intervention measures; and (4) outcome measures included any markers of indirect muscle damage and muscular contractility measures. Participants: Individuals with no resistance training experiences in the previous 6 or more months. Interventions: A single bout of pre-conditioning exercises consisting of eccentric or isometric contractions performed a minimum of 24 h prior to a bout of damaging physical activity were compared to control interventions that did not perform pre-conditioning prior to damaging physical activity. Study Appraisal: Kmet appraisal system. Synthesis Methods: Quantitative analysis was conducted using forest plots to examine standardised mean differences (SMD, i.e. effect size), test statistics for statistical significance (i.e. Z-values) and between-study heterogeneity by inspecting I2. Results: Following abstract and full-text screening, 23 articles were included in this paper. Based on the meta-analysis, the pre-conditioning group exhibited lower levels of creatine kinase at 24 h (SMD = − 1.64; Z = 8.39; p = 0.00001), 48 h (SMD = − 2.65; Z = 7.78; p = 0.00001), 72 h (SMD = − 2.39; Z = 5.71; p = 0.00001) and 96 h post-exercise (SMD = − 3.52; Z = 7.39; p = 0.00001) than the control group. Delayed-onset muscle soreness was also lower for the pre-conditioning group at 24 h (SMD = − 1.89; Z = 6.17; p = 0.00001), 48 h (SMD = − 2.50; Z = 7.99; p = 0.00001), 72 h (SMD = − 2.73; Z = 7.86; p = 0.00001) and 96 h post-exercise (SMD = − 3.30; Z = 8.47; p = 0.00001). Maximal voluntary contraction force was maintained and returned to normal sooner in the pre-conditioning group than in the control group, 24 h (SMD = 1.46; Z = 5.49; p = 0.00001), 48 h (SMD = 1.59; Z = 6.04; p = 0.00001), 72 h (SMD = 2.02; Z = 6.09; p = 0.00001) and 96 h post-exercise (SMD = 2.16; Z = 5.69; p = 0.00001). Range of motion was better maintained by the pre-conditioning group compared with the control group at 24 h (SMD = 1.48; Z = 4.30; p = 0.00001), 48 h (SMD = 2.20; Z = 5.64; p = 0.00001), 72 h (SMD = 2.66; Z = 5.42; p = 0.00001) and 96 h post-exercise (SMD = 2.5; Z = 5.46; p = 0.00001). Based on qualitative analyses, pre-conditioning activities were more effective when performed at 2–4 days before the muscle-damaging protocol compared with immediately prior to the muscle-damaging protocol, or 1–3 weeks prior to the muscle-damaging protocol. Furthermore, pre-conditioning activities performed using eccentric contractions over isometric contractions, with higher volumes, greater intensity and more lengthened muscle contractions provided greater protection from EIMD. Limitations: Several outcome measures showed high inter-study heterogeneity. The inability to account for differences in durations between pre-conditioning and the second bout of damaging physical activity was also limiting. Conclusions: Pre-conditioning significantly reduced the severity of creatine kinase release, delayed-onset muscle soreness, loss of maximal voluntary contraction force and the range of motion decrease. Pre-conditioning may prevent severe EIMD and accelerate recovery of muscle force generation capacity

Biochar increases soil enzyme activities in two contrasting pastoral soils under different grazing management

Context: Soil enzyme activities are key regulators of carbon and nutrient cycling in grazed pastures. Aims: We investigated the effect of biochar addition on the activity of seven enzymes involved in the carbon, nitrogen and phosphorus cycles in a Sil-Andic Andosol and a Dystric Cambisol under permanent pastures. Methods: The study consisted of a one-year field-based mesocosm experiment involving four pastures under different nutrient and livestock practices: with and without effluent under dairy cow grazing on the Andosol, and with either nil or high phosphorus fertiliser input under sheep grazing on the Cambisol. Soil treatments were: (1) willow biochar added at 1% w/w; (2) lime added at the liming equivalence of biochar (positive control); (3) no amendments (negative control). Key results: Compared with the Cambisol, the Andosol had higher dehydrogenase, urease, alkaline and acid phosphatase and, especially, nitrate-reductase activities, aligning with its higher pH and fertility. In both soils, biochar addition increased the activity of all enzymes, except for acid phosphatase and peroxidase; lime addition increased peroxidase and nitrate-reductase activity. Conclusions: The increased enzyme activity was strongly positively correlated with soil biological activity following biochar addition. Biochar caused a 40-45% increase in cellulase activity, attributed to increased root biomass following biochar addition. The response in acid and alkaline phosphatase activity can be attributed to the impact of biochar and lime addition on soil pH. Implications: The results provide more insights in realising the potential benefits of biochar to the provision of ecosystem services for grazed pastures.fals

Effects of spatial data resolution on the modelling and mapping of soil organic carbon content in hill country grassland landscapes

Limited use has been made of spatially explicit modelling of soil organic carbon (SOC) in highly complex farmed landscapes to advance current mapping efforts. This study aimed to address this gap in knowledge by evaluating the spatial prediction of SOC content in the 0–75 mm soil depth in hill country landscapes in New Zealand (NZ) using point-based training data, along with topographic covariates and Sentinel 2 spectral band ratios using an automated set of machine learning (AutoML) tools in ArcGIS. Subsequently, it also focused on quantifying the effects of spatial data resolution (i.e., 1, 8, 15, and 25 m) in terms of predicted map accuracy. Farmlets with contrasting phosphorus fertilizer and sheep grazing histories located at the Ballantrae Hill Country Research Station, NZ were selected to conduct the research. Six candidate algorithms incorporated in the AutoML tools (i.e., XGBoost, LightGBM, linear regression, decision trees, extra trees, random forest) and ensemble model were utilized to model the spatial pattern of SOC content. The results show that the ensemble model that combine predictions of various algorithms applied for 1 m data resolution enables the highest performance and accuracy (i.e., R2 =.76, RMSE = 0.66%). Among the predictive variables used in the model, slope, wetness, and topographic position indices were found to be the most important topographical features that explain SOC patterns in the study area. Inclusion of spectral indices derived from remote sensing, including surface soil moisture and clay minerals ratio, made further improvement to the SOC content prediction. The study reveals that a decrease in the resolution of the geospatial data does not substantively affect the mean SOC content estimation of a farm-scale modelling. However, using coarser resolution data reduces the ability of the model to predict changes in the spatial pattern of SOC content across a hill country grassland landscape.fals

The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin

Viral infections are on the rise and drugs targeting viral proteins are needed. Viroporins constitute a growing groupof virus-encoded transmembrane oligomeric proteins that allow passage of small molecules across the membrane.Despite sparsity in viroporin structures, recent work has revealed diversity in both the number of transmembranehelices and oligomeric states. Here, we provide evidence that the small hydrophobic protein (SH) from mumps virusis a pentameric viroporin. From extensive biophysical data, a HADDOCK model of full-length SH shows its intracel-lular C-terminal region to form an extended structure crucial to stabilization of the pentamer. Heterologous expres-sion of wild-type SH and variants in Xenopus laevis oocytes reveals the viroporin as a chloride channel, with transportfacilitated by conserved hydroxyl-carrying residues lining the pore. The channel function of SH is inhibited by thesmall-molecule BIT225, highlighting the potential for antiviral targeting through SH

Impacts of Sediments on Coral Energetics: Partitioning the Effects of Turbidity and Settling Particles

Sediment loads have long been known to be deleterious to corals, but the effects of turbidity and settling particles have not previously been partitioned. This study provides a novel approach using inert silicon carbide powder to partition and quantify the mechanical effects of sediment settling versus reduced light under a chronically high sedimentary regime on two turbid water corals commonly found in Singapore (Galaxea fascicularis and Goniopora somaliensis). Coral fragmentswere evenly distributed among three treatments: an open control (30% ambient PAR), a shaded control (15% ambient PAR) and sediment treatment (15% ambient PAR; 26.4 mg cm22 day21). The rate of photosynthesis and respiration, and the dark-adapted quantum yield were measured once a week for four weeks. By week four, the photosynthesis to respiration ratio (P/R ratio) and the photosynthetic yield (Fv/Fm) had fallen by 14% and 3–17% respectively in the shaded control,contrasting with corals exposed to sediments whose P/R ratio and yield had declined by 21% and 18–34% respectively. The differences in rates between the shaded control and the sediment treatment were attributed to the mechanical effects of sediment deposition. The physiological response to sediment stress differed between species with G. fascicularis experiencing a greater decline in the net photosynthetic yield (13%) than G. somaliensis (9.5%), but a smaller increase in the respiration rates (G. fascicularis = 9.9%, G. somaliensis = 14.2%). These different physiological responses were attributed, in part, to coral morphology and highlighted key physiological processes that drive species distribution along high to low turbidity and depositional gradients

Disturbance and the Dynamics of Coral Cover on the Great Barrier Reef (1995–2009)

Coral reef ecosystems worldwide are under pressure from chronic and acute stressors that threaten their continued existence. Most obvious among changes to reefs is loss of hard coral cover, but a precise multi-scale estimate of coral cover dynamics for the Great Barrier Reef (GBR) is currently lacking. Monitoring data collected annually from fixed sites at 47 reefs across 1300 km of the GBR indicate that overall regional coral cover was stable (averaging 29% and ranging from 23% to 33% cover across years) with no net decline between 1995 and 2009. Subregional trends (10–100 km) in hard coral were diverse with some being very dynamic and others changing little. Coral cover increased in six subregions and decreased in seven subregions. Persistent decline of corals occurred in one subregion for hard coral and Acroporidae and in four subregions in non-Acroporidae families. Change in Acroporidae accounted for 68% of change in hard coral. Crown-of-thorns starfish (Acanthaster planci) outbreaks and storm damage were responsible for more coral loss during this period than either bleaching or disease despite two mass bleaching events and an increase in the incidence of coral disease. While the limited data for the GBR prior to the 1980's suggests that coral cover was higher than in our survey, we found no evidence of consistent, system-wide decline in coral cover since 1995. Instead, fluctuations in coral cover at subregional scales (10–100 km), driven mostly by changes in fast-growing Acroporidae, occurred as a result of localized disturbance events and subsequent recovery

Extraction of pure components from overlapped signals in gas chromatography-mass spectrometry (GC-MS)

Gas chromatography-mass spectrometry (GC-MS) is a widely used analytical technique for the identification and quantification of trace chemicals in complex mixtures. When complex samples are analyzed by GC-MS it is common to observe co-elution of two or more components, resulting in an overlap of signal peaks observed in the total ion chromatogram. In such situations manual signal analysis is often the most reliable means for the extraction of pure component signals; however, a systematic manual analysis over a number of samples is both tedious and prone to error. In the past 30 years a number of computational approaches were proposed to assist in the process of the extraction of pure signals from co-eluting GC-MS components. This includes empirical methods, comparison with library spectra, eigenvalue analysis, regression and others. However, to date no approach has been recognized as best, nor accepted as standard. This situation hampers general GC-MS capabilities, and in particular has implications for the development of robust, high-throughput GC-MS analytical protocols required in metabolic profiling and biomarker discovery. Here we first discuss the nature of GC-MS data, and then review some of the approaches proposed for the extraction of pure signals from co-eluting components. We summarize and classify different approaches to this problem, and examine why so many approaches proposed in the past have failed to live up to their full promise. Finally, we give some thoughts on the future developments in this field, and suggest that the progress in general computing capabilities attained in the past two decades has opened new horizons for tackling this important problem