Deployment of genetic and genomic tools toward gaining a better understanding of Rice-Xanthomonasoryzae pv. oryzae interactions for development of durable bacterial blight resistant rice

Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant’s defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world’s widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits

Phytoplankton assemblage and UV-protective compounds in the river Ganges

Interactions between physico-chemical parameters such as pH, temperature, nitrate, phosphate, alkalinity, acidity, biological oxygen demand (BOD), chemical oxygen demand (COD) and solar ultraviolet radiation (UVR) strongly affect aquatic ecosystems. Due to fluctuations in several environmental factors including river water pollution and UVR, organisms are under constant threat. However, phytoplankton protects themselves from environmental extremes by adopting several defense strategies including synthesis of photoprotective compounds such as scytonemin and mycosporine-like amino acids (MAAs).We investigated the presence of scytonemin and MAAs in phytoplankton of some polluted sites of one of the holy rivers of the world, the Ganges at Varanasi, India. We observed phytoplankton assemblages and studied certain environmental parameters which could possibly affect phytoplankton diversity in the river. Phytoplankton consisted mainly of 49 taxa of 34 genera belonging to Bacillariophyceae, Chlorophyceae, Cyanophyceae, and Chrysophyceae. The members belonging to Bacillariophyceae and Chlorophyceae were the two dominant classes, which comprised up to 75% of the total phytoplankton.Photoprotective compounds were isolated and characterized from phytoplankton. Electrospray ionization-mass spectrometry (ESI-MS) analysis of MAAs showed the presence of shinorine, palythinol, mycosporine-glycine and palythine. A high concentration of scytonemin was also observed with an absorption maximum at 386 nm in the studied phytoplankton

Phytoplankton assemblage and UV-protective compounds in the river Ganges

191-203Interactions between physico-chemical parameters such as pH, temperature, nitrate, phosphate, alkalinity, acidity, biological oxygen demand (BOD), chemical oxygen demand (COD) and solar ultraviolet radiation (UVR) strongly affect aquatic ecosystems. Due to fluctuations in several environmental factors including river water pollution and UVR, organisms are under constant threat. However, phytoplankton protects themselves from environmental extremes by adopting several defense strategies including synthesis of photoprotective compounds such as scytonemin and mycosporine-like amino acids (MAAs). We investigated the presence of scytonemin and MAAs in phytoplankton of some polluted sites of one of the holy rivers of the world, the Ganges at Varanasi, India. We observed phytoplankton assemblages and studied certain environmental parameters which could possibly affect phytoplankton diversity in the river. Phytoplankton consisted mainly of 49 taxa of 34 genera belonging to Bacillariophyceae, Chlorophyceae, Cyanophyceae, and Chrysophyceae. The members belonging to Bacillariophyceae and Chlorophyceae were the two dominant classes, which comprised up to 75% of the total phytoplankton. Photoprotective compounds were isolated and characterized from phytoplankton. Electrospray ionization-mass spectrometry (ESI-MS) analysis of MAAs showed the presence of shinorine, palythinol, mycosporine-glycine and palythine. A high concentration of scytonemin was also observed with an absorption maximum at 386 nm in the studied phytoplankton

Post-outburst evolution of bonafide FUor V2493 Cyg: A Spectro-photometric monitoring

We present here the results of eight years of our near-simultaneous optical/near-infrared spectro-photometric monitoring of bonafide FUor candidate `V2493 Cyg' starting from 2013 September to 2021 June. During our optical monitoring period (between October 16, 2015 and December 30, 2019), the V2493 Cyg is slowly dimming with an average dimming rate of $\sim$26.6 $\pm$ 5.6 mmag/yr in V band. Our optical photometric colors show a significant reddening of the source post the second outburst pointing towards a gradual expansion of the emitting region post the second outburst. The mid infra-red colors, on the contrary, exhibits a blueing trend which can be attributed to the brightening of the disc due to the outburst. Our spectroscopic monitoring shows a dramatic variation of the H$\alpha$ line as it transitioned from absorption feature to the emission feature and back. Such transition can possibly be explained by the variation in the wind structure in combination with accretion. Combining our time evolution spectra of the Ca II infra-red triplet lines with the previously published spectra of V2493 Cyg, we find that the accretion region has stabilised compared to the early days of the outburst. The evolution of the O I $\lambda$7773 \AA~ line also points towards the stabilization of the circumstellar disc post the second outburst.Comment: 34 pages, 12 figures, 6 tables, accepted for publication in Ap

Prototype tasks: Improving crowdsourcing results through rapid, iterative task design

Low-quality results have been a long-standing problem on microtask crowdsourcing platforms, driving away requesters and justifying low wages for workers. To date, workers have been blamed for low-quality results: they are said to make as little effort as possible, do not pay attention to detail, and lack expertise. In this paper, we hypothesize that requesters may also be responsible for low-quality work: they launch unclear task designs that confuse even earnest workers, under-specify edge cases, and neglect to include examples. We introduce prototype tasks, a crowdsourcing strategy requiring all new task designs to launch a small number of sample tasks. Workers attempt these tasks and leave feedback, enabling the requester to iterate on the design before publishing it. We report a field experiment in which tasks that underwent prototype task iteration produced higher-quality work results than the original task designs. With this research, we suggest that a simple and rapid iteration cycle can improve crowd work, and we provide empirical evidence that requester “quality” directly impacts result quality

An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome.

Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a complex disease, with a spectrum of outcomes. Genomic, transcriptomic and methylation studies have revealed differences between Mtb lineages, likely to impact on transmission, virulence and drug resistance. However, so far no studies have integrated sequence-based genomic, transcriptomic and methylation characterisation across a common set of samples, which is critical to understand how DNA sequence and methylation affect RNA expression and, ultimately, Mtb pathogenesis. Here we perform such an integrated analysis across 22 M. tuberculosis clinical isolates, representing ancient (lineage 1) and modern (lineages 2 and 4) strains. The results confirm the presence of lineage-specific differential gene expression, linked to specific SNP-based expression quantitative trait loci: with 10 eQTLs involving SNPs in promoter regions or transcriptional start sites; and 12 involving potential functional impairment of transcriptional regulators. Methylation status was also found to have a role in transcription, with evidence of differential expression in 50 genes across lineage 4 samples. Lack of methylation was associated with three novel variants in mamA, likely to cause loss of function of this enzyme. Overall, our work shows the relationship of DNA sequence and methylation to RNA expression, and differences between ancient and modern lineages. Further studies are needed to verify the functional consequences of the identified mechanisms of gene expression regulation

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Principles and processes behind promoting awareness of rights for quality maternal care services: a synthesis of stakeholder experiences and implementation factors

BACKGROUND: Promoting awareness of rights is a value-based process that entails a different way of thinking and acting, which is at times misunderstood or deemed as aspirational. METHODS: Guided by the SURE framework, we undertook a secondary analysis of 26 documents identified by an earlier systematic review on promoting awareness of rights to increase use of maternity care services. We thematically analysed stakeholder experiences and implementation factors across the diverse initiatives to derive common elements to guide future efforts. RESULTS: Interventions that promote awareness of rights for maternal health varied in nature, methodological orientation, depth and quality. Materials included booklets, posters, pamphlets/ briefs and service standards/charters. Target populations included women, family members, communities, community structures, community-based and non governmental organizations, health providers and administrators, as well as elected representatives. While one initiative only focused on raising awareness, most were embedded within larger efforts to improve the accountability and responsiveness of service delivery through community monitoring and advocacy, with a few aiming to change policies and contest elections. Underlying these action oriented forms of promoting awareness of rights, was a critical consciousness and attitudinal change gained through iterative capacity-building for all stakeholders; materials and processes that supported group discussion and interaction; the formation or strengthening of community groups; situational analysis to ensure adaptation to local context; facilitation to ensure common ground and language across stakeholders; and strategic networking and alliance building across health system levels. While many positive experiences are discussed, few challenges or barriers to implementation are documented. The limited documentation and poor quality of information found indicate that while various examples of promoting awareness of rights for maternal health exists, research partnerships to systematically evaluate their processes, learning and effects are lacking. CONCLUSION: Rather than being aspirational, several examples of promoting awareness of women’s rights for quality maternity care services exist. More than mainly disseminate information, they aim to change stakeholder mindsets and relationships across health system levels. Due to their transformatory intent they require sustained investment, with strategic planning, concrete operationalization and political adeptness to manage dynamic stakeholder expectations and reactions overtime. More investment is also required in research partnerships that support such initiatives and better elucidate their context specific variations.ScopusIS