While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally ...determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.
This study was designed with the aim of establishing a comprehensive picture of the problems and needs of local communities in upholding sustainable livelihoods in the face of forest degradation and ...recommending how their livelihoods may be improved in the short and long term. Thus make them self-reliant by enhancing their resilience. Study Methodology: included a literature review and a household survey for a total of 443 household interviews. In addition, Focus Group Discussions (FGDs) and Key Informant Interviews (KIIs) were conducted with the rural population and other stakeholders respectively. Field visits were made to all the 8 sites in the two districts Serenje and Chitambo. The main constrain of sustainable livelihood in the communities, included, low levels of education and skills, low levels of asset holding, weak local institutions and unfavorable legal and institutional frameworks. But the respondents registered a wide variety of NTFPs based livelihoods obtained from forests resources (15). Most important usage includes land for cultivation, fuelwood, poles for construction, charcoal production and use of NTFPs (collection of mushrooms, wild fruits and nuts, caterpillars, honey production and medicinal plants). The livelihood activities remains largely subsistence and for safety net functions. Trade resulting into incomes generation is minimal, unstructured and therefore unsustainable. In conclusion: commercialization of NTFPS and PES activities may be the solution to sustainable livelihood and forest conservation. A range of specifically forest sector elements would also need to be addressed, including, entrepreneurship, market and skill development for forest product and services delivery; embracing these elements will also require new kinds of enhanced institutional arrangement.
Limestone remains the most exploited and crucial industrial mineral worldwide, hence mining activities within limestone quarries will imminently prevail. Quarrying for limestone is an economic ...necessity that is not only hazardous to humans but also one that invariably has deleterious effect on the environment. Information on the performance of tree species is important as plants are key in the revegetation of exhausted quarries. A comparison of field performance of Acacia xanthophloea, Schinus molle, Casuarina equisetifolia and Grevillea robusta was made in an exhausted limestone quarry in a semi-arid area, in Athi River, Kenya. The exhausted quarry was backfilled with the mine waste material and then leveled. Four blocks, each 25 m x 25 m, were established at the quarry site for tree planting and control, using the Randomized Complete Block Design (RCBD). Six months old seedlings of each species produced in a nursery were transplanted in the plots. The sequence of planting the four species was varied from block to block. One block was left unplanted for control. Growth performances were estimated by measuring tree height, diameter at the stem base (BD), and diameter at breast height (DBH). Seedling height (cm) and stem diameter (cm) were measured immediately after planting, and thereafter measurements were recorded every two weeks for a period of two years. To avoid border effect, the height and diameter of the middle 10 trees of each species in each block were measured, as these were less susceptible to external influence. The tree height from ground level to tip of the youngest leaf was determined using a tape measure. A Vernier caliper was used to measure basal stem diameter 1 cm above the soil surface. A line was painted on the trunk, to ensure repeat measurements are made at the same point for the diameter. To maintain consistency during data collection, a similar method was used for measurements of diameter at breast height (1m above soil). This commenced at the beginning of year II of planting when most trees had attained a height of at least 1.3 m. Diameter at breast height was measured immediately below a branch if this occurred at a height of 1 m. The study revealed that the time-species interaction was significant (p<0.001), indicating continuous tree growth for all the species. The tree species performance was varied. C. equisetifolia recorded the highest growth increments for the height (525.3 cm), BD (7.42 cm) and DBH (4.94 cm) and the highest growth rates for tree height (14.24 cm/month), BD (0.23 cm/month) and DBH (0.14 cm/month), indicating superior performance. This was followed by A. xanthophloea and S. molle. Grevillea robusta showed poor performance and recorded the lowest growth rates: tree height (1.35 cm/month), BD (0.017 cm/month) and DBH (0.023 cm/month). These results also indicated that there is species-specific response that may be due to different water- and nutrient-use strategies and growth patterns. From the study, C. equisetifolia has the best growth performance followed by A. xanthophloea. The two species are therefore recommended to be used in the rehabilitation of limestone quarries in similar semi-arid conditions.
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the ...Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144,000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
Improved sanitation leads to better environmental quality however threatened environments, population densities and inadequate finances are some of the challenges facing proper sanitation management. ...This paper sought to establish the effectiveness of policy, legal and institutional frameworks on promotion of sanitation management in Mavoko Municipality. Resident's awareness and compliance with policy instruments, role and responsibilities of Mavoko Municipality Residents and Service Providers and Political Champions were used to gauge the effectiveness of these policy instruments. Mavoko Municipality has low sewer network coverage with a deficit of 86% in sewerage treatment capacity as its existing sewerage treatment capacity stands at 192,000 m
3
against a required capacity of 1,407,000 m
3
. The study site covered the urbanizing areas within the Municipality. A cross-sectional study design was chosen and both primary and secondary data were collected. 385 house hold respondents were interviewed. Simple random and purposive sampling methods were used to administer questionnaires to standalone houses and comprehensive housing schemes. Key informant interviews with County and National Officials mandated with sanitation management related services were conducted using structured forms and interview guides. Findings indicate that existing policies and legal frameworks are not effective as they play little role in influencing policy for the promotion of appropriate sanitation management approaches. Political championing was negligible whilst County Government performed poorly in sanitation management. Commitment to providing sanitation services and building capacities and strengths of Service Providers and emerging Residential Neighbourhood Association is recommended to promote good practices in sanitation and environmental management.
Competitive and productive Special Economic Zones (SEZs)/ industrial Parks (IPs) of the future will be those that will abandon the wasteful linear development model and instead embrace a circular ...economy that is characterized with the circular flow of materials and energy. Doing this will not only lower pressure on the use of the country’s virgin raw materials but also contribute to the reduced carbon footprint of the SEZs/IPs by helping to divert wastes from the landfill. This paper investigated the spontaneous evolution of waste and by-product exchange at the agro-processing and garment clusters of the Athi River SEZ. These cluster based material exchanges evolved on their own largely as a result of the prevailing forces of material supply and demand. Though at its infancy, this emergency of industrial symbiosis at the economic zone has helped to demonstrate the social inclusion dimension of green growth through the creation of decent green jobs. The practice has also enabled participating firms to reduce their GHG emissions and lower their operational costs. The economic zone’s desire to fully embrace waste recovery, reuse and recycling as part of its deliberate efforts of advancing the ideals of a circular economy is currently being hampered by a lack of functional waste recovery, reuse, and recycling infrastructure. The proposed strengthening of University-Industry-Government (U-I-G) collaboration at the Athi River SEZ, will help promote eco-innovation that forms the cornerstone of the economic zone’s improved productivity and competitiveness. The paper sought to unravel the enabling policy interventions that need to be put in place so as to accelerate the transformation of the country’s economic zones into environmentally friendly Eco-Industrial Parks (EIPs) capable of attracting green foreign direct investments (FDIs). It also tackled the barriers that need to be overcome by key stakeholders so that the country’s SEZs/ IPs can adopt a development trajectory that enjoys low-emission levels, efficiently uses its resources, and is socially inclusive through the creation of decent green jobs.
PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, ...PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics. Availability and Implementation: PDBImages is available as an npm package from https://www.npmjs.com/package/pdb-images. The source code is available from https://github.com/PDBeurope/pdb-images. Contact: mvaradi@ebi.ac.uk, sameer@ebi.ac.uk
PDF
