Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages

<p>Abstract</p> <p>Background</p> <p>Phosphatidylinositol 3-phosphate is involved in regulation of several key cellular processes, mainly endocytosis, signaling, nuclear processes, cytoskeletal remodelling, cell survival, membrane trafficking, phagosome maturation and autophagy. In most cases effector proteins bind to this lipid, using either FYVE or PX domain. These two domains are distributed amongst varied life forms such as virus, protists, fungi, viridiplantae and metazoa. As the binding ligand is identical for both domains, the goal of this study was to understand if there is any selectivity for either of these domains in different taxa. Further, to understand the different cellular functions that these domains may be involved in, we analyzed the taxonomic distribution of additional domains that associate with FYVE and PX.</p> <p>Results</p> <p>There is selectivity for either FYVE or PX in individual genomes where both domains are present. Fungi and metazoa encode more PX, whereas streptophytes in viridiplantae encode more FYVE. Excess of FYVE in streptophytes results from proteins containing RCC1and DZC domains and FYVE domains in these proteins have a non-canonical ligand-binding site. Within a taxonomic group the selected domain associates with a higher number of other domains and is thus expected to discharge a larger number of cellular functions. Also, while certain associated domains are present in all taxonomic groups, most of them are unique to a specific group indicating that while certain common functions are discharged by these domains in all taxonomic groups, some functions appear to be group specific.</p> <p>Conclusions</p> <p>Although both FYVE and PX bind to PtdIns(3)P, genomes of different taxa show distinct selectivity of encoding either of the two. Higher numbers of taxonomic group specific domains co-occur with the more abundant domain (FYVE/PX) indicating that group-specific rare domain architectures might have emerged to accomplish certain group-specific functions.</p

A qualitative assessment of natural and anthropogenic drivers of risk to sustainable livelihoods in the Indian Sundarban

In the Indian Sundarban, multiple attributes and interactions of natural hazards, exposure, and vulnerability pose severe threats to lives and livelihoods. Understanding the cause-and-effect relationships contributing to the risk of loss of sustainable livelihoods has become imperative but has not yet been holistically explored in a single study that provides a broader picture of all possible complex interactions. This study used the impact chain tool to holistically understand the risk that manifests as a result of interactions of hazards, exposure, and vulnerability. The secondary literature and authors’ observations helped us structure the first draft of the impact chain, which was further developed and validated through fourteen gender-disaggregated interviews with key informants and delta dwellers. This validation process identified the complex interconnections contributing to risk as experienced by experts and delta dwellers, which is seldom reflected through exclusively quantitative data. A quantitative analysis of the qualitative data strongly indicated that tropical cyclones, rainfall variability, and storms are the dominant hazards that affect social–ecological vulnerability manifested through mangrove degradation, land loss due to erosion, and embankment breaching. Social vulnerability is caused by processes and factors that are either directly or indirectly influenced by natural hazards and social–ecological factors. Processes such as increasing seasonal male migration, uncertain agricultural income, and a lack of hazard-resistant housing exacerbates social vulnerability. Embankment breaching, the salinization of land and water, land loss due to erosion, mangrove degradation, land conversion, and groundwater abstraction were identified as the fundamental threats that can lead to a loss of sustainable livelihoods of the people if left unaddressed

Development and characterization of large-scale simple sequence repeats in jute

Jute is an important crop of the Indian subcontinent and comprises tossa jute (Corchorus olitorius) and white jute (C. capsularis). The yield and fiber quality of this crop remained stagnant for many years and could not be improved through conventional plant breeding. Also, no effort has been made to develop molecular markers on a scale required for marker-assisted selection (MAS) to supplement conventional plant breeding. As a first step toward deploying MAS for jute improvement, 2469 simple sequence repeats (SSRs) were developed in tossa jute (JRO 524) using four SSR-enriched genomic libraries. A random subset of 100 SSRs (25 SSRs from each library) was used to detect polymorphism between the parental genotypes of each of the two recombinant inbred line (RIL) mapping populations. The RILs are being developed from JRO 524 × PPO4 (for fiber fineness) and JRC 321 × CMU 010 (for lignin content) crosses to prepare molecular maps and conduct quantitative trait loci (QTL) analyses. Both SSR length polymorphism and ± polymorphism (null alleles, i.e., presence and absence of specific SSR) were detected; 50 SSRs detected polymorphism between the two genotypes of tossa jute, whereas 45 SSRs detected polymorphism between the two genotypes of white jute. This SSR allelic polymorphism in jute is higher than that reported in other crops and is adequate for construction of genetic maps for QTL analysis. The large-scale SSRs will also prove useful in studying genetic diversity, population structure, and association mapping

Relativistic Electromagnetic Mass Models: Charged Dust Distribution in Higher Dimensions

Electromagnetic mass models are proved to exist in higher dimensional theory of general relativity corresponding to charged dust distribution. Along with the general proof a specific example is also sited as a supporting candidate.Comment: Latex, 7 pages. Accepted in Astrophysics and Space Scienc

Development of SSR markers and construction of a linkage map in jute

Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources. We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute

Assessing Vulnerability and Risk to Livelihoods in River Deltas Socio-ecological Systems: Alignment of the GDRI With Global Frameworks’ Indicators

Disasters have significant impacts on the progress towards achieving the Sustainable Development Goals (SDGs). However, the interlinkage between sustainable development and disaster risk reduction is not considered enough in risk assessment tools. A greater alignment with global frameworks would ease the monitoring while increasing the capacity to address data availability issues for indicator-based assessments. To bridge this gap, we use the Global Delta Risk Index (GDRI), which is composed of multiple components to assess risks to livelihoods: hazards, vulnerability, and exposure of social-ecological systems. The modular library of indicators of the GDRI has been further aligned with the Sustainable Development Goals (SDG) and the Sendai Framework for Disaster and Risk Reduction (SFDRR). To improve the accuracy of the risk assessment, the list of indicators has been weighted and scored through consultation with stakeholders. This research presents the initial results of a multi-hazard risk assessment that encompasses SDG and SFDRR indicators in three Asian river deltas: Ganges-Brahmaputra-Meghna, Mekong and Red River. This work aims at better informing risk management and supporting delta-level interventions to influence progress towards sustainability and resilience of river deltas

Climate change, migration and adaptation in deltas Key findings from the DECCMA projet

This work was carried out under the Collaborative Adaptation Research Initiative in Africa and Asia (CARIAA), with financial support from the UK Government’s Department For International Development (DFID) and the International Development Research Centre (IDRC), Canada.Deltas are home to 500 million people worldwide and known as a climate hange “hotspot” – a place where high exposure to climate stresses coincides with high levels of vulnerability. DECCMA has been undertaking research on climate and environmental change, migration and adaptation in three delta ystems: the transboundary Ganges-Brahmaputra-Meghna megadelta (comprising the Indian Bengal delta, as well as the bulk in Bangladesh), the Mahanadi delta in India, and the Volta in Ghana

Deltas, vulnerability and climate change ; migration and adaptation (DECCMA) CARIAA consortium final technical report 2018

This report summarises the main outcomes and learning from management and delivery of the nearly 5-year “DEltas, vulnerability and Climate Change; Migration and Adaptation” (DECCMA) project within the “Collaborative Adaptation Research Initiative in Africa and Asia” (CARIAA) programme. DECCMA considered climate change and deltas with a strong focus on adaptation and migration within deltas, including migration as an adaptation. It was committed to being gender-sensitive in research approach, data collection, and analysis. Globally deltas and their environs house 500 million (or 7 percent of global population) people on one percent of the land area, with a concentration of populated deltas at mid and low latitudes. Deltas are highly dynamic biophysically. This includes a high vulnerability to sea-level rise and climate change, and also subsidence (deltas sink), exacerbating global changes in sea level. Deltas are also socially dynamic, with changing land use, economies and strong trends of migration that have potential to be modified under future environmental and climate change

Aligning the Global Delta Risk Index with SDG and SFDRR global frameworks to assess risk to socio-ecological systems in river deltas

River deltas globally are highly exposed and vulnerable to natural hazards and are often over-exploited landforms. The Global Delta Risk Index (GDRI) was developed to assess multi-hazard risk in river deltas and support decision-making in risk reduction interventions in delta regions. Disasters have significant impacts on the progress towards the Sustainable Development Goals (SDGs). However, despite the strong interlinkage between disaster risk reduction and sustainable development, global frameworks are still developed in isolation and actions to address them are delegated to different institutions. Greater alignment between frameworks would both simplify monitoring progress towards disaster risk reduction and sustainable development and increase capacity to address data gaps in relation to indicator-based assessments for both processes. This research aims at aligning the GDRI indicators with the SDGs and the Sendai Framework for Disaster and Risk Reduction (SFDRR). While the GDRI has a modular indicator library, the most relevant indicators for this research were selected through a delta-specific impact chain designed in consultation with experts, communities and stakeholders in three delta regions: the Red River and Mekong deltas in Vietnam and the Ganges–Brahmaputra–Meghna (GBM) delta in Bangladesh and India. We analyse how effectively the 143 indicators for the GDRI match (or not) the SDG and SFDRR global frameworks. We demonstrate the interconnections of the different drivers of risk to better inform risk management and in turn support delta-level interventions towards improved sustainability and resilience of these Asian mega-deltas

Mitotic arrest by Melatonin

We are testing the hypothesis that migration of the newly formed mouth (i.e., oral membranellar band) in stentor is homologous to mitotic chromosomal movement and that both types of movement within single cells depend directly on microtubule elongation. The following compounds synchronously delay the migration of the oral membranellar band as an exponential function of concentration: Colcemid, podophyllotoxin, β-peltatin and vinblastine. Delay for these compounds can be described by the equation, y = kxn, where y is delay in hours and x is concentration of mitotic spindle inhibitor in moles/l. We discovered that the animal pineal gland hormone, melatonin (5-methoxy n-acetyl tryptamine), also specifically and reproducibly delays oral band regeneration according to an equation of this form. Thus we predicted that melatonin would arrest mitosis. We report here a colchicine-type disruption of the mitotic apparatus in onion root tips by melatonin. Two closely related tryptamine derivatives, n-acetyl serotonin and serotonin were inactive in both the stentor and onion assays: they neither delayed band migration in stentor as an exponential function nor induced mitotic arrest in onion