Development of an aquatic toxicity index for macroinvertebrates

A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science. School of Animal, Plant and Environmental Sciences of the University of the Witwatersrand. Johannesburg, 18 May 2018.Rapid biomonitoring protocols employing riverine macroinvertebrates in South Africa utilise the South African Scoring System version 5 (SASS5). The SASS5 was developed as part of the then River Health Programme (RHP) [now River Eco-status Monitoring Programme (REMP)]. The SASS5 index is a cost-effective procedure (utilising limited sampling equipment) that enables speedy evaluation of a riverine ecosystem’s health using macroinvertebrates as biological indicators of water quality and ecosystem health. As a result, the SASS5 (including earlier versions) has been widely accepted by water quality practitioners and is increasingly incorporated into Ecological Reserve determinations. However, the SASS is widely criticised for being a ‘red flag’ indicator of water quality and ecosystem health because it has the ability to show only whether a river is polluted (including the extent of pollution) or not, but cannot differentiate between pollutant types (whether chemical or physical). To trace the pollutants responsible for changes in water quality, practitioners are therefore required to conduct chemical-based water quality assessments. Chemical analyses can provide accurate measures of the magnitudes of chemical substances present in the river water but they do not readily translate into threshold limits supportive or protective of ecosystems. In South Africa the water quality threshold limits for aquatic ecosystems are provided by the South African water quality guidelines for aquatic ecosystems (volume 7). These guidelines provide threshold limits for the protection of the entire aquatic ecosystem constituting of fish, macroinvertebrates, microinvertebrates, algae and plants. These guidelines are therefore too broad for defining protection thresholds supportive of specific subcomponents (i.e. macroinvertebrates) of aquatic ecosystems. The Aquatic Toxicity Index (ATI) for macroinvertebrates was therefore developed for providing threshold limits for physical and chemical stressors protective of freshwater macroinvertebrates. The ATI is expected to aid water quality practitioners working in the Olifants River and catchments with similar land-uses in at least three ways. Firstly, in interpreting the magnitudes of physico-chemical water quality stressors by providing varying levels of protection (threshold limits) (i.e.PC99, PC95, PC90 and PC80) specific to freshwater macroinvertebrates. Secondly, the ATI is expected to aid in the compression of large volumes of water quality data into manageable quantities (descriptor words and grading symbols). Lastly, conventional water quality reports are replete with technical terminology and symbols emanating from water chemistry and ecotoxicology. While reporting of this kind is accessible to water resource specialists, it may constitute an obstacle for non-technical stakeholders (with no training or experience in water chemistry) like policy makers, political decision makers and the public. These groups generally have neither the time nor the training to study and understand a traditional, technical review of water quality data. Water quality indices are capable of eliminating technical language incurred in water quality reports; hence, they are viewed as necessary tools in reaching multiple audiences by bridging the gaps between the extremes of water quality monitoring and reporting. The ATI is expected to enhance not only accessibility and comprehensibility in all these instances, but utility in general too. Differently expressed, the ATI is expected to aid as a water quality-reporting tool that will help water quality practitioners and managers in communicating technical water quality data to multiple stakeholders even those without training and experience in water chemistry and ecotoxicology. The development of the ATI for macroinvertebrates was conducted in two phases. First, the derivation of Protection Concentrations (PCs). The PCs were obtained by fitting Species Sensitivity Distribution (SSD) curves on short-term (24-96 hours) median lethal (LC50) data for freshwater macroinvertebrates collected from databases and scholarly publications. Before the estimation of the PCs, the toxicity data had to undergo a preparatory process. This involved the conversion of metal stressors from total metal concentrations to dissolved fractions. Additionally, metal stressors whose toxicity is known to be dependent on water hardness (cadmium, chromium (III), copper, lead, nickel and zinc) were adjusted to reflect their toxicity at six different levels of water hardness using USEPA conversions algorithms. In addition, all ammonia data were converted to reflect the toxicity of ammonia as TAN at pH = 8 and temperature = 25°C. The second phase of the index development involved the allocation of index categories. This was to enable the discrimination of stressors’ magnitudes into classes. The final product is a five-point scale classification system (A to E) based on four PC levels (PC99, PC95, PC90 and PC80) for freshwater macroinvertebrates obtained by fitting Species Sensitivity Distribution (SSD) functions on the toxicity data. On development, the index was validated using water quality data, riverine macroinvertebrates survey data and flow data collected from the Olifants River catchment between 2015 and 2016. Eight study sites were covered, located in the upper and the lower Olifants system. Four of these were located in the Olifants River main stem and four from four tributaries (Klein Olifants, Blyde, Ga-Selati and Letaba rivers). The evaluation of the Olifants system based on the assessment of variable-by-variable indicated that Site S5 and S2 (lower Ga-Selati and Klein Olifants) were the most degraded sites in the study, respectively. In addition, the study indicated gross elevation of sulfate, nitrates, pH and copper. The evaluation of the Olifants system using the composite ATI for macroinvertebrates indicated that the system was generally in good condition. However, the identification of the lowest rating score indicated that temperature difference from reference conditions, sulfate, nitrate, zinc and lead were the main variables limiting the water quality of the Olifants system. In addition, the sensitivity analysis of the index conducted as part of the validation process of the index, indicated that temperature difference from reference conditions, sulfate and nitrate were the most important variables in the computation of the index. Investigations of the relationships between the ATI for macroinvertebrates, SASS5 metrics, MIRAI and measures of flow variability revealed negligible and statistically insignificant associations. These could mainly be attributed to three reasons. Firstly, sampling difficulty, this resulted from high density of filamentous algae and floating aquatic vegetation (posing physical obstructions to sampling) in the river. Such extraneous factors rendered the SASS5 sampling protocol (benthic/kick method), ineffective because of clogging of sampling net and loss of specimens in the sifting of aquatic plants for macroinvertebrates. Secondly, the filamentous algae interfered with the availability and suitability of habitat for aquatic invertebrates. For instance it covered stones biotopes (stones in current) forming a thick layer of algae on the stones thereby exhibiting the characteristics of vegetation biotopes for most sampling sites, a major impediment for the SASS5, a method that is largely dependent biotope availability. Thirdly, the SASS was developed for organic pollutants while the ATI for macroinvertebrates is largely driven by metal stressors. Because of toxicity data shortages for regional freshwater macroinvertebrates, a compromise between data availability and quality was considered. For example, toxicity data drawn from global sources were used as the base for the PCs and the index. Despite these limitations, the protection concentrations (numerical sensitivity values) that form the base of the index were comparable with published water quality benchmarks from literature and water quality jurisdictions. In addition, the index has the ability to summarise and discriminate (stressors in terms of concentrations and magnitudes) large quantities of water quality data to facilitate interpretation of the quality of a water’s ability to support freshwater macroinvertebrates. Keywords: Aquatic Toxicity Index, freshwater macroinvertebrates, water quality criteria, species sensitivity distribution, Olifants RiverLG201

Habitat and sex effects on behaviour in fawn-footed mosaic-tailed rats (Melomys cervinipes)

Habitat complexity reflects resource availability and predation pressure - both factors that influence behaviour. We investigated whether exploratory behaviour and activity varied in fawn-footed mosaic-tailed rats (Melomys cervinipes) from two habitats that were categorised differently based on vegetation. We conducted vegetation surveys to determine structural complexity and vegetation cover, confirming that an abandoned hoop-pine (Araucaria cunninghami) plantation forest was structurally less complex, with lower vegetation cover than a variable secondary rainforest. We then tested mosaic-tailed rats from both sites in four behavioural tests designed to assess exploratory and activity behaviours (open field, novel object, light-dark box, acoustic startle), predicting that rats from the less structurally complex habitat would be less exploratory, and show lower activity. Our results provide some evidence for a contextspecific trade-off between exploratory behaviour and predation risk in rats from the abandoned hoop pine plantation, as rats were less active, and showed a freezing strategy in the light-dark box. We also found context-specific sex differences in behaviour in response to a novel object and sound. Our results suggest that small-scale variation in habitat structure and complexity, as well as sex differences, is associated with variation in behaviour, most likely through effects on resource availability and/or predation risk

Revisiting Alkali Metals As a Tool to Characterize Patterns of Mosquito Dispersal and Oviposition.

Mark-recapture methods constitute a set of classical ecological tools that are used to collect information on species dispersal and population size. These methods have advanced knowledge in disparate scientific fields, from conservation biology to pest control. Gathering information on the dispersal of mosquito species, such as Aedes aegypti, has become critical since the recognition of their role as vectors of pathogens. Here, we evaluate a method to mark mosquitoes that exploits the rare alkali metals rubidium (Rb) and caesium (Cs), which have been used previously to mark adult insects through feeding. We revised this method by adding Rb and Cs directly to water in which the immature stages of Ae. aegypti were allowed to develop. We then assessed the effect of Rb- and Cs-enriched water on fitness, survival and bioaccumulation in both adult females and their eggs. Results indicated that Cs had adverse effects on Ae. aegypti, even at low concentrations, whereas Rb at low concentrations had no measured effects on exposed individuals and accumulated at detectable levels in adult females. The method described here relies on passive uptake of Rb during immature stages, which has the benefit of avoiding handling or manipulation of the dispersive adults, which enables purer measurement of movement. Moreover, we demonstrated that Rb was transferred efficiently from the marked females to their eggs. To our knowledge, Rb is the only marker used for mosquitoes that has been shown to transfer vertically from females to eggs. The application of Rb rather than more traditional markers may therefore increase the quality (no impact on released individuals) and quantity (both adults and eggs are marked) of data collected during MR studies. The method we propose here can be used in combination with other markers, such as stable isotopes, in order to maximize the information collected during MR experiments

Strategies to increase port competitiveness

Improving the competitiveness of local businesses and their products within worldwide markets is a vital element for the long-term economic growth of a region. This paper presents a summary of ongoing research needs and outcomes formulated from a partnership between the University of Queensland and the Port of Brisbane Pty Ltd (PBPL), in order to facilitate international trade growth in Queensland and improve PBPL’s competitiveness. As part of this partnership with PBPL, we explore strategies to overcome inefficiencies in supply chain and infrastructure and discuss subsequent prospects for further investigation. The key goals of the partnership program for transport-related issues have been identified as: (i) providing a platform for freight actors trading through the port, in order to increase the performance of their logistics operations by adopting cooperative strategies; (ii) exploring modal shift opportunities to enhance the sustainability and the efficiency of the logistics operations of importers and exporters; (iii) facilitating improved inland supply chains for local export commodities through new trans-shipment points, back-loading opportunities, and logistics cost minimisation

Tiger on the prowl: invasion history and spatio-temporal genetic structure of the Asian tiger mosquito Aedes albopictus (Skuse 1894) in the Indo-Pacific

Background: Within the last century, increases in human movement and globalization of trade have facilitated the establishment of several highly invasive mosquito species in new geographic locations with concurrent major environmental, economic and health consequences. The Asian tiger mosquito, Aedes albopictus, is an extremely invasive and aggressive daytime-biting mosquito that is a major public health threat throughout its expanding range. Methodology/Principal findings: We used 13 nuclear microsatellite loci (on 911 individuals) and mitochondrial COI sequences to gain a better understanding of the historical and contemporary movements of Ae. albopictus in the Indo-Pacific region and to characterize its population structure. Approximate Bayesian computation (ABC) was employed to test competing historical routes of invasion of Ae. albopictus within the Southeast (SE) Asian/Australasian region. Our ABC results show that Ae. albopictus was most likely introduced to New Guinea via mainland Southeast Asia, before colonizing the Solomon Islands via either Papua New Guinea or SE Asia. The analysis also supported that the recent incursion into northern Australia's Torres Strait Islands was seeded chiefly from Indonesia. For the first time documented in this invasive species, we provide evidence of a recently colonized population (the Torres Strait Islands) that has undergone rapid temporal changes in its genetic makeup, which could be the result of genetic drift or represent a secondary invasion from an unknown source. Conclusions/Significance: There appears to be high spatial genetic structure and high gene flow between some geographically distant populations. The species' genetic structure in the region tends to favour a dispersal pattern driven mostly by human movements. Importantly, this study provides a more widespread sampling distribution of the species' native range, revealing more spatial population structure than previously shown. Additionally, we present the most probable invasion history of this species in the Australasian region using ABC analysis

A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (\u3ci\u3eOryza sativa\u3c/i\u3e)

Early vigor is an important trait for many rice (Oryza sativa L.)- growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ~360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, OsGA2ox7, which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single-nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37–0.53); however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice

Insights into Architects’ Future Roles in Off-Site Construction

Today’s construction industry is overflowing with new ideas about its future. Off-Site Manufacture and Construction (OSCM) is at the heart of the modern construction industry. Much has been written about the state and context of OSCM in different countries regarding its perceived benefits and barriers to implementation. Off-site production (OSP) plays an important role in improving fragmented construction processes. Although most OSP research targets the attitudes and practices of OSP adoption, there is limited understanding of the philosophical issues underpinning OSP-related architecture. The roles of the architects’ personal philosophies are neglected and this hampers their implementation of OSCM (which has had a largely technical focus). This paper explores the traditional thinking patterns of architects in China and predicts possible future roles for them. It then conceptualizes an “architectural work” mode and a “building product” mode of design and construction and identifies the shortcomings of architects in an OSCM environment. The arguments made are based on practitioners’ perceptions and the first author’s practical experiences of leading several real-life projects in recent years. The findings reveal the implications and significance of the transformation from an “architectural work” mode to a “building product” mode. We foresee a study approach that focuses on the order and rules for OSCM, resulting in architects’ existing mindsets being changed to thinking patterns and design methodologies better suited to OSCM

A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

Understanding past dispersal and breeding events can provide insight into ecology and evolution, and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal, and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m), and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance

PLoS Negl Trop Dis

BackgroundWithin the last century, increases in human movement and globalization of trade have facilitated the establishment of several highly invasive mosquito species in new geographic locations with concurrent major environmental, economic and health consequences. The Asian tiger mosquito, Aedes albopictus, is an extremely invasive and aggressive daytime-biting mosquito that is a major public health threat throughout its expanding range.Methodology/Principal findingsWe used 13 nuclear microsatellite loci (on 911 individuals) and mitochondrial COI sequences to gain a better understanding of the historical and contemporary movements of Ae. albopictus in the Indo-Pacific region and to characterize its population structure. Approximate Bayesian computation (ABC) was employed to test competing historical routes of invasion of Ae. albopictus within the Southeast (SE) Asian/Australasian region. Our ABC results show that Ae. albopictus was most likely introduced to New Guinea via mainland Southeast Asia, before colonizing the Solomon Islands via either Papua New Guinea or SE Asia. The analysis also supported that the recent incursion into northern Australia\ue2\u20ac\u2122s Torres Strait Islands was seeded chiefly from Indonesia. For the first time documented in this invasive species, we provide evidence of a recently colonized population (the Torres Strait Islands) that has undergone rapid temporal changes in its genetic makeup, which could be the result of genetic drift or represent a secondary invasion from an unknown source.Conclusions/SignificanceThere appears to be high spatial genetic structure and high gene flow between some geographically distant populations. The species' genetic structure in the region tends to favour a dispersal pattern driven mostly by human movements. Importantly, this study provides a more widespread sampling distribution of the species\ue2\u20ac\u2122 native range, revealing more spatial population structure than previously shown. Additionally, we present the most probable invasion history of this species in the Australasian region using ABC analysis.28410388PMC540602

Tofacitinib, an oral janus kinase inhibitor: pooled efficacy and safety analyses in an Australian rheumatoid arthritis population

In Australia, there is an unmet need for improved treatments for rheumatoid arthritis (RA). Tofacitinib is an oral Janus kinase inhibitor for the treatment of RA. To provide an overview of key study outcomes for tofacitinib in Australian patients, we analyzed the efficacy and safety of tofacitinib in the Australian subpopulation of global RA phase III and long-term extension (LTE) studies. Data were pooled from the Australian subpopulation of four phase III studies and one LTE study (database not locked at cut-off date: January 2016). Patients in the phase III studies received tofacitinib 5 or 10 mg twice daily (BID), placebo (advancing to tofacitinib at months 3 or 6), or adalimumab, with background methotrexate or conventional synthetic disease-modifying antirheumatic drugs. Patients in the LTE study received tofacitinib 5 or 10 mg BID. Efficacy endpoints were American College of Rheumatology (ACR) 20/50/70 response rates, and change from baseline in the Disease Activity Score in 28 joints, erythrocyte sedimentation rate [DAS28-4(ESR)] and Health Assessment Questionnaire-Disability Index (HAQ-DI) scores. Safety endpoints included incidence of adverse events (AEs), serious AEs, and discontinuations due to AEs. AEs of special interest and laboratory parameters were analyzed in the LTE study. Across phase III studies (N = 100), ACR response rates and improvements in DAS28-4(ESR) and HAQ-DI scores were numerically greater with tofacitinib vs. placebo at month 3, and increased until month 12. The results were sustained in the LTE study (N = 99) after 60 months' observation. In general, the efficacy and safety profiles of tofacitinib were similar to those of the global RA population. In Australian patients with RA, tofacitinib therapy demonstrated sustained efficacy and consistent safety over ae 60 months' treatment. Pfizer Inc. NCT00960440; NCT00847613; NCT00856544; NCT00853385; NCT00413699