Climate change, gender, youth and nutrition situation analysis - Ghana

Situation analysis of climate change, gender, youth and nutrition in Ghana

Strengthening Governance of Small-Scale Fisheries: An Initial Assessment of the Theory and Practice

Preferred citation for this report: Basurto, X., Virdin, J., Smith, H. and R. Juskus. 2017. Strengthening Governance of Small-Scale Fisheries: An Initial Assessment of Theory and Practice. Oak Foundation.Often hidden in national statistics, small-scale fisheries have been poorly measured at a global level, and in thepast often ignored in states' policy-making. Yet estimates suggest their aggregate global contribution tonutrition, food security and poverty eradication is massive. The most recent estimates available suggest thatsmall-scale fisheries account for over 90 percent of the world's commercial fishers, processors and otherpersons employed along the value chain, equivalent to over 108 million people. Roughly half areemployed in the ocean and the other half in inland fisheries—making small-scale fisheries far and awaythe ocean's largest employer (greater than oil and gas, shipping, tourism, etc.). This level of activitytranslates into a large portion of the global fish catch: an estimated 46 percent of the total, and 38 percentof the fish caught in the ocean. SSFs are also estimated to provide over half the animal protein intake inmany of the world's least developed countries, and over half of the fish for domestic consumption indeveloping countries more broadly. In sum, in many regions of the world SSFs provide both incomes tohelp reduce poverty and safety nets to help prevent it

Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation

High-throughput mass spectrometric (HT-MS) study is the method of choice for monitoring global changes in proteome. Data derived from these studies are meant for further validation and experimentation to discover novel biological insights. Here we evaluate use of relative solvent accessible surface area (rSASA) and DEPTH as indices to assess experimentally determined phosphorylation events deposited in PhosphoSitePlus. Based on accessibility, we map these identifications on allowed (accessible) or disallowed (inaccessible) regions of phosphoconformation. Surprisingly a striking number of HT- MS/MS derived events (1461/5947 sites or 24.6%) are present in the disallowed region of conformation. By considering protein dynamics, autophosphorylation events and/or the sequence specificity of kinases, 13.8% of these phosphosites can be moved to the allowed region of conformation. We also demonstrate that rSASA values can be used to increase the confidence of identification of phosphorylation sites within an ambiguous MS dataset. While MS is a stand-alone technique for the identification of vast majority of phosphorylation events, identifications within disallowed region of conformation will benefit from techniques that independently probe for phosphorylation and protein dynamics. Our studies also imply that trapping alternate protein conformations may be a viable alternative to the design of inhibitors against mutation prone drug resistance kinases

A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics

Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components

Environment sensing in spring-dispersed seeds of a winter annual Arabidopsis influences the regulation of dormancy to align germination potential with seasonal changes

Seed dormancy cycling plays a crucial role in the lifecycle timing of many plants. Little is known of how the seeds respond to the soil seed bank environment following dispersal in spring into the short-term seed bank before seedling emergence in autumn. Seeds of the winter annual Arabidopsis ecotype Cvi were buried in field soils in spring and recovered monthly until autumn and their molecular eco-physiological responses were recorded. DOG1 expression is initially low and then increases as dormancy increases. MFT expression is negatively correlated with germination potential. Abscisic acid (ABA) and gibberellin (GA) signalling responds rapidly following burial and adjusts to the seasonal change in soil temperature. Collectively these changes align germination potential with the optimum climate space for seedling emergence. Seeds naturally dispersed to the soil in spring enter a shallow dormancy cycle dominated by spatial sensing that adjusts germination potential to the maximum when soil environment is most favourable for germination and seedling emergence upon soil disturbance. This behaviour differs subtly from that of seeds overwintered in the soil seed bank to spread the period of potential germination in the seed population (existing seed bank and newly dispersed). As soil temperature declines in autumn, deep dormancy is re-imposed as seeds become part of the persistent seed bank

Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Supervised machine learning techniques have traditionally been very successful at reconstructing biological networks, such as protein-ligand interaction, protein-protein interaction and gene regulatory networks. Many supervised techniques for network prediction use linear models on a possibly nonlinear pairwise feature representation of edges. Recently, much emphasis has been placed on the correct evaluation of such supervised models. It is vital to distinguish between using a model to either predict new interactions in a given network or to predict interactions for a new vertex not present in the original network. This distinction matters because (i) the performance might dramatically differ between the prediction settings and (ii) tuning the model hyperparameters to obtain the best possible model depends on the setting of interest. Specific cross-validation schemes need to be used to assess the performance in such different prediction settings. In this work we discuss a state-of-the-art kernel-based network inference technique called two-step kernel ridge regression. We show that this regression model can be trained efficiently, with a time complexity scaling with the number of vertices rather than the number of edges. Furthermore, this framework leads to a series of cross-validation shortcuts that allow one to rapidly estimate the model performance for any relevant network prediction setting. This allows computational biologists to fully assess the capabilities of their models

Fisheries and Aquaculture and Their Potential Roles in Development: An Assessment of the Current Evidence

Commissioned by the International Sustainability Unity, this report investigates a number of innovative solutions that have been developed to deal with five key challenges that are impeding progress in achieving sustainable fisheries: overcapacity; perverse subsidies; poor governance; lack of data; and by-catch and discards. These key challenges are interlinked and affect the sustainability of fisheries both directly as well as indirectly by undermining instances of good management. Through 22 case studies demonstrating good practice, we explore how these challenges have been addressed around the world and how these approaches might be scaled up and applied in other fisheries. Each case study draws on published material and interviews with key people involved in the fishery. The main report draws lessons from these case studies

A Review of Indigenous Food Crops in Africa and the Implications for more Sustainable and Healthy Food Systems

Indigenous and traditional foods crops (ITFCs) have multiple uses within society, and most notably have an important role to play in the attempt to diversify the food in order to enhance food and nutrition security. However, research suggests that the benefits and value of indigenous foods within the South African and the African context have not been fully understood and synthesized. Their potential value to the African food system could be enhanced if their benefits were explored more comprehensively. This synthesis presents a literature review relating to underutilized indigenous crop species and foods in Africa. It organizes the findings into four main contributions, nutritional, environmental, economic, and social-cultural, in line with key themes of a sustainable food system framework. It also goes on to unpack the benefits and challenges associated with ITFCs under these themes. A major obstacle is that people are not valuing indigenous foods and the potential benefit that can be derived from using them is thus neglected. Furthermore, knowledge is being lost from one generation to the next, with potentially dire implications for long-term sustainable food security. The results show the need to recognize and enable indigenous foods as a key resource in ensuring healthy food systems in the African continent