Socio-ecological drivers of fish biomass on coral reefs: the importance of accessibility, protection and key species

Coral reefs have the greatest biodiversity of any ecosystem on the planet and support ecosystem goods and services to million people who depend directly on them for food, economic income, coastal protection and cultural values. There is a clear consensus that accessibility through road networks and infrastructure expansion is a main driver of ecosystem conditions, with the most accessible resources being most at risk. Yet to date measuring the extent to which coral reefs are accessible to humans is strictly limited to examining the linear distance between fishing grounds and markets or ports. However, linear distance ignores ragged coastlines, road networks and other features that can affect the time required to reach fishing grounds from a human settlement. This thesis presents a double challenge: (i) developing new metrics of accessibility that account for seascape heterogeneity to better assess human impacts on coral reefs; and (ii) evaluating the importance of coral reef accessibility, in interactions with their management, to explain variations of fish biomass. First, I estimated the travel time between any given coral reef and human populations and markets based on the friction distance which is related to transport surfaces (paved road, dirt road, water) influencing transportation costs and the effective reach from human settlements. I found that travel time is a strong predictor of fish biomass. Second, using a downscaling of the travel time approach I illustrated how market proximity can affect the behavior of fishermen and, ultimately, trigger changes in marine resource exploitation in North-Western Madagascar. Market access appears as a critical step toward a long-term management of coral reef fisheries. Third, travel time was used to build a human gravity index, defined as human population divided by the squared travel time, to better assess the level of human pressure on any reef of the world. Then, gravity was used to assess the effectiveness of marine reserves given the level of human pressure. The results highlighted critical ecological trade-offs in conservation since reserves with moderate-to-high human impacts provide substantial gains for fish biomass while only reserves located where human impacts are low can support populations of top predators like sharks which are otherwise absent from coral reefs. Fourth, I developed a new Community-Wide Scan (CWS) approach to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to fish biomass and coral cover on Indo-Pacific reefs. Among about 400 fishes, I identified only a limited set of species (51), belonging to various functional groups and evolutionary lineages, which promote biomass and coral cover; such key species making tractable conservation targets. Within the context of global changes and biodiversity loss, the thesis challenges the sustainable and efficient management of coral reef socio-ecological systems with accessibility being the cornerstone but also the main danger in a near future where roads will expand and coastal human populations will grow

Підвищення інвестиційної привабливості підприємств житлово-комунального господарства України на основі використання закордонного досвіду

Мета роботи - підвищення інвестиційної привабливості підприємств житлово-комунального господарства на основі можливостей використання закордонного досвіду реформування

Secure local aquatic food systems in the face of declining coral reefs

Coral reefs are harbingers of environmental change. In this issue of One Earth, Eddy et al. analyze long-term declines in reef condition and fish catches. Here, we highlight how policies that secure coral reefs as local food systems can safeguard diverse, nutrient rich diets and support vulnerable social-ecological systems

NIPTmer : rapid k-mer-based software package for detection of fetal aneuploidies

Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/.Peer reviewe

Managing fisheries for maximum nutrient yield

Wild-caught fish are a bioavailable source of nutritious food that, if managed strategically, could enhance diet quality for billions of people. However, optimising nutrient production from the sea has not been a priority, hindering development of nutrition-sensitive policies. With fisheries management increasingly effective at rebuilding stocks and regulating sustainable fishing, we can now begin to integrate nutritional outcomes within existing management frameworks. Here, we develop a conceptual foundation for managing fisheries for multispecies Maximum Nutrient Yield (mMNY). We empirically test our approach using size-based models of North Sea and Baltic Sea fisheries and show that mMNY is predicted by the relative contribution of nutritious species to total catch and their vulnerability to fishing, leading to trade-offs between catch and specific nutrients. Simulated nutrient yield curves suggest that vitamin D, which is deficient in Northern European diets, was underfished at fishing levels that returned maximum catch weights. Analysis of global catch data shows there is scope for nutrient yields from most of the world's marine fisheries to be enhanced through nutrient-sensitive fisheries management. With nutrient composition data now widely available, we expect our mMNY framework to motivate development of nutrient-based reference points in specific contexts, such as data-limited fisheries. Managing for mMNY alongside policies that promote access to fish could help close nutrient gaps for coastal populations, maximising the contribution of wild-caught fish to global food and nutrition security

Oligomeric Status and Nucleotide Binding Properties of the Plastid ATP/ADP Transporter 1: Toward a Molecular Understanding of the Transport Mechanism

Background: Chloroplast ATP/ADP transporters are essential to energy homeostasis in plant cells. However, their molecular mechanism remains poorly understood, primarily due to the difficulty of producing and purifying functional recombinant forms of these transporters. Methodology/Principal Findings: In this work, we describe an expression and purification protocol providing good yields and efficient solubilization of NTT1 protein from Arabidopsis thaliana. By biochemical and biophysical analyses, we identified the best detergent for solubilization and purification of functional proteins, LAPAO. Purified NTT1 was found to accumulate as two independent pools of well folded, stable monomers and dimers. ATP and ADP binding properties were determined, and Pi, a co-substrate of ADP, was confirmed to be essential for nucleotide steady-state transport. Nucleotide binding studies and analysis of NTT1 mutants lead us to suggest the existence of two distinct and probably inter-dependent binding sites. Finally, fusion and deletion experiments demonstrated that the C-terminus of NTT1 is not essential for multimerization, but probably plays a regulatory role, controlling the nucleotide exchange rate. Conclusions/Significance: Taken together, these data provide a comprehensive molecular characterization of a chloroplas

Rights and representation support justice across aquatic food systems

Injustices are prevalent in food systems, where the accumulation of vast wealth is possible for a few, yet one in ten people remain hungry. Here, for 194 countries we combine aquatic food production, distribution and consumption data with corresponding national policy documents and, drawing on theories of social justice, explore whether barriers to participation explain unequal distributions of benefits. Using Bayesian models, we find economic and political barriers are associated with lower wealth-based benefits; countries produce and consume less when wealth, formal education and voice and accountability are lacking. In contrast, social barriers are associated with lower welfare-based benefits; aquatic foods are less affordable where gender inequality is greater. Our analyses of policy documents reveal a frequent failure to address political and gender-based barriers. However, policies linked to more just food system outcomes centre principles of human rights, specify inclusive decision-making processes and identify and challenge drivers of injustice

Rights and representation support justice across aquatic food systems

Injustices are prevalent in food systems, where the accumulation of vast wealth is possible for a few, yet one in ten people remain hungry. Here, for 194 countries we combine aquatic food production, distribution and consumption data with corresponding national policy documents and, drawing on theories of social justice, explore whether barriers to participation explain unequal distributions of benefits. Using Bayesian models, we find economic and political barriers are associated with lower wealth-based benefits; countries produce and consume less when wealth, formal education and voice and accountability are lacking. In contrast, social barriers are associated with lower welfare-based benefits; aquatic foods are less affordable where gender inequality is greater. Our analyses of policy documents reveal a frequent failure to address political and gender-based barriers. However, policies linked to more just food system outcomes centre principles of human rights, specify inclusive decision-making processes and identify and challenge drivers of injustice

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems