Variation Profile of the Orthotospovirus Genome

Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative- propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations across species. Remarkably, the highest nucleotide variation mapped to the intergenic region of RNA segments S and M, which fold into a hairpin. Secondary structure analyses showed that the hairpin is a dynamic structure with multiple functional shapes formed by stems and loops, contains sites under positive selection and covariable sites. A ccumulation and tolerance of mutations in the intergenic region is a general feature of orthotospoviruses and might mediate adaptation to host plants and insect vectors

Large Nabothian Cyst: A Rare Cause of Nulliparous Prolapse

Genital prolapse is commonly observed in postmenopausal and multiparous women, However, nulliparous women contribute to 2% of prevalence. We report a case of 21-year-old female who presented with a large nabothian cyst contributing to prolapse. This is the first case reported in the literature

Mutations in virus-derived small RnAs

RNA viruses exist as populations of genome variants. Virus-infected plants accumulate 21–24 nucleotide small interfering RnAs (siRnAs) derived from viral RnA (virus-derived siRnAs) through gene silencing. This paper describes the profile of mutations in virus-derived siRNAs for three members of the family Potyviridae: Turnip mosaic virus (tuMV), Papaya ringspot virus (pRSV) and Wheat streak mosaic virus (WSMV). for tuMV in Arabidopsis thaliana, profiles were obtained for mechanically inoculated rosette leaves and systemically infected cauline leaves and inflorescence. Results are consistent withselection pressure on the viral genome imposed by local and systemic movement. By genetically removing gene silencing in the plant and silencing suppression in the virus, our results showed that antiviral gene silencing imposes selection in viral populations. Mutations in siRnAs derived from a PRSV coat protein transgene in the absence of virus replication showed the contribution of cellular RnA-dependent RnA polymerases to the generation of mutations in virus-derived siRnAs. collectively, results are consistent with two sources of mutations in virus-derived siRNAs: viral RNA-dependent RNA polymerases responsible for virus replication and cellular RnA-dependent RnA polymerases responsible for gene silencing amplification

Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

<p>Abstract</p> <p>Background</p> <p>Genome-wide gene expression profiling and detailed physiological investigation were used for understanding the molecular mechanism and physiological response of <it>Gossypium herbaceum</it>, which governs the adaptability of plants in drought conditions. Recently, microarray-based gene expression analysis is commonly used to decipher genes and genetic networks controlling the traits of interest. However, the results of such an analysis are often plagued due to a limited number of genes (probe sets) on microarrays. On the other hand, pyrosequencing of a transcriptome has the potential to detect rare as well as a large number of transcripts in the samples quantitatively. We used Affymetrix microarray as well as Roche's GS-FLX transcriptome sequencing for a comparative analysis of cotton transcriptome in leaf tissues under drought conditions.</p> <p>Results</p> <p>Fourteen accessions of <it>Gossypium herbaceum </it>were subjected to mannitol stress for preliminary screening; two accessions, namely Vagad and RAHS-14, were selected as being the most tolerant and most sensitive to osmotic stress, respectively. Affymetrix cotton arrays containing 24,045 probe sets and Roche's GS-FLX transcriptome sequencing of leaf tissue were used to analyze the gene expression profiling of Vagad and RAHS-14 under drought conditions. The analysis of physiological measurements and gene expression profiling showed that Vagad has the inherent ability to sense drought at a much earlier stage and to respond to it in a much more efficient manner than does RAHS-14. Gene Ontology (GO) studies showed that the phenyl propanoid pathway, pigment biosynthesis, polyketide biosynthesis, and other secondary metabolite pathways were enriched in Vagad under control and drought conditions as compared with RAHS-14. Similarly, GO analysis of transcriptome sequencing showed that the GO terms <it>responses to various abiotic stresses </it>were significantly higher in Vagad. Among the classes of transcription factors (TFs) uniquely expressed in both accessions, RAHS-14 showed the expression of ERF and WRKY families. The unique expression of ERFs in response to drought conditions reveals that RAHS-14 responds to drought by inducing senescence. This was further supported by transcriptome analysis which revealed that RAHS-14 responds to drought by inducing many transcripts related to senescence and cell death.</p> <p>Conclusion</p> <p>The comparative genome-wide gene expression profiling study of two accessions of <it>G.herbaceum </it>under drought stress deciphers the differential patterns of gene expression, including TFs and physiologically relevant processes. Our results indicate that drought tolerance observed in Vagad is not because of a single molecular reason but is rather due to several unique mechanisms which Vagad has developed as an adaptation strategy.</p

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved

Genome-Wide Variation in Potyviruses

Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by hosts and vectors creates a footprint in areas of the genome involved in host adaptation. Here, we profiled genomic and polyprotein variation in all species in the genus Potyvirus. Results showed that the potyviral genome is under strong negative selection. Accordingly, the genome and polyprotein sequence are remarkably stable. However, nucleotide and amino acid substitutions across the potyviral genome are not randomly distributed and are not determined by codon usage. Instead, substitutions preferentially accumulate in hypervariable areas at homologous locations across potyviruses. At a frequency that is higher than that of the rest of the genome, hypervariable areas accumulate non-synonymous nucleotide substitutions and sites under positive selection. Our results show, for the first time, that there is correlation between host range and the frequency of sites under positive selection. Hypervariable areas map to the N terminal part of protein P1, N and C terminal parts of helper component proteinase (HC-Pro), the C terminal part of protein P3, VPg, the C terminal part of NIb (RNA-dependent RNA polymerase), and the N terminal part of the coat protein (CP). Additionally, a hypervariable area at the NIb-CP junction showed that there is variability in the sequence of the NIa protease cleavage sites. Structural alignment showed that the hypervariable area in the CP maps to the N terminal flexible loop and includes the motif required for aphid transmission. Collectively, results described here show that potyviruses contain fixed hypervariable areas in key parts of the genome which provide mutational robustness and are potentially involved in host adaptation

INTERNATIONALJOURNALOFENGINEERING SCIENCES&amp;MANAGEMENT A STUDY ON ENVIRONMENTAL ACCOUNTING WITH REFERENCE TO MANUFACTURING INDUSTRIES IN INDIA

ABSTRACT Our Vedas says environment should be respected as parent and should be loved as children, But in last few decade we can feel that environment is hampered and harmed at high degrees. Due to continuous rise in population deforestation is done to provide shelter which leads to green house effect and consequently ozone layer depletion. Manufacturing industries throw their waste in the rivers and ocean which pollutes water and those gases which are released by them are polluting the air. To develop industries the concerns need raw material which is provided by the environment. Many laws has been made to protect the environment but there is no such accounting system prepared which can calculate the how much goods and services are taken from the environment and how much is returned back. This research deals with the scope, challenges and prospects of environmental accounting

Genome-Wide Variation in Potyviruses

Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by hosts and vectors creates a footprint in areas of the genome involved in host adaptation. Here, we profiled genomic and polyprotein variation in all species in the genus Potyvirus. Results showed that the potyviral genome is under strong negative selection. Accordingly, the genome and polyprotein sequence are remarkably stable. However, nucleotide and amino acid substitutions across the potyviral genome are not randomly distributed and are not determined by codon usage. Instead, substitutions preferentially accumulate in hypervariable areas at homologous locations across potyviruses. At a frequency that is higher than that of the rest of the genome, hypervariable areas accumulate non-synonymous nucleotide substitutions and sites under positive selection. Our results show, for the first time, that there is correlation between host range and the frequency of sites under positive selection. Hypervariable areas map to the N terminal part of protein P1, N and C terminal parts of helper component proteinase (HC-Pro), the C terminal part of protein P3, VPg, the C terminal part of NIb (RNA-dependent RNA polymerase), and the N terminal part of the coat protein (CP). Additionally, a hypervariable area at the NIb-CP junction showed that there is variability in the sequence of the NIa protease cleavage sites. Structural alignment showed that the hypervariable area in the CP maps to the N terminal flexible loop and includes the motif required for aphid transmission. Collectively, results described here show that potyviruses contain fixed hypervariable areas in key parts of the genome which provide mutational robustness and are potentially involved in host adaptation

IMPACT ASSESSMENT OF ICDS FOOD FORTIFICATION IN THE STATE OF UTTAR-PRADESH

Background and Objective: The concept of food fortification is relatively uncommon in India. Hence, sometimes due to ignorance or due to paucity of research to assess the impact of fortifying supplementary food in large feeding programmes, there is an apprehension that fortification may either lead to imbalance of nutrients in the body or may not really improve the nutritional status of people consuming marginal diets. This has lead to a prudent approach in taking bold decisions to fortify the ICDS supplementary food to reduce micronutrient malnutrition in different states. The current research planned to provide empirical evidence on the impact of fortified ICDS supplementary food through a well-conducted community based research study among the children between 12-59 months under programmatic conditions in state of Uttar Pradesh.&nbsp;Methods: The sampling design adopted was quasi experimental design under programme conditions. The study was taken up in Kanpur dehat district of UP. The block where fortified food was to be initiated constituted the experimental universe where as those blocks where &nbsp; fortified food was not to be initiated form the control universe. &nbsp;One block namely Maitha was taken as Experimental block and Rajpur as Control block. &nbsp;The base line was done in both the blocks. However, no intervention with fortified food could take place in Maitha and hence substituted by neighboring block Rasulabad. This block was named as benchmark block. Later after six months; benchmark survey was done in Rasulabad block. An end line survey was done after one year of intervention in all three blocks. At the base line, care was taken that experimental block and control block match in terms of socio economic and demographic parameters. Later, while substituting Maitha by Rasulabad at bench mark stage, it was assured that these two blocks matched in terms of socio economic and demographic parameters.The sample size worked out as 750 which were selected in the form of 30 villages and 25 children per village.&nbsp;30 villages from each of these blocks were selected by Probability Proportion to population Size (PPS). From the each selected village, 25 children were selected for the anthropometrics measurement and dietary intake, 10 children for clinical examinations and 5 for the bio-chemical examinations. The sample design as well as the sample selection for endline assessment as well as for bench mark assessment was similar to those as was used in the baseline assessment.&nbsp;Results and Discussion: The majority of the children surveyed in these blocks belonged to lower socio-economic groups and the underprivileged sections of the society. There were considerable improvements in anemia in all these blocks. There is significant improvement in serum retinol levels of children at the end line stage in both the blocks. It is observed that there is significant improvement in Serum levels of children at the benchmark stage. Prevalence of severe malnutrition declined considerably in Maitha and Rajpur though it remained almost static in Rasulabad, giving further support to earlier observations on anemia. Only few (about 15%) children were taking home supplementary food and rest beneficiaries were consuming food at the AWCs. The paper show significant decline in the levels of anemia, vitamin A deficiency and malnutrition levels, an attempt was made to correlate these with the extent of food consumed.&nbsp;Interpretation and Conclusion: The findings reveal that fortified panjiri has been effective in improving anemia, serum retinol and nutritional status. It is also revealed that short duration of intervention is as effective as prolonged interventions. &nbsp;There are other studies also indicating that fortification of foods with iron has produced improvements in iron status. In India, where double fortification of salt, with iodine and iron, has the potential to prevent both iron and iodine deficiencies and has been effective for improved hemoglobin concentrations

Computational analysis of miRNA-target community network reveals cross talk among different metabolisms

To date, only a few conserved miRNAs have been predicted in hexaploid (AABBDD) bread wheat and till now community behavior among miRNA is still in dark. Analysis of publically available 1287279 ESTs from NCBI resulted 262 putative pre-miRNAs and 39 novel mature miRNAs. A total 22,468 targets were identified on 21 chromosomes. MiRNA target community was identified for genomes with different levels of cross talks. Gene ontology of these community targets suggests their differential involvement in different metabolisms along with common and stringent involvement in nitrogen metabolism