Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties

Fragrance development in rice has been reported due to a 8-bp deletion in the exon 7 of badh2 gene located on Chromosome 8S. Multiplex markers targeting the functional InDel polymorphism was earlier reported for genotyping fragrance trait, but the marker was observed to be inconsistent and difficult to use. We have developed a simple, co-dominant, functional marker for fragrance trait, which can be resolved in an agarose gel and validated in Basmati and non-Basmati aromatic rice varieties and in a mapping population segregated for fragrance trait. The marker targets the InDel polymorphism in badh2 gene and amplifies 95 and 103 bp fragments in fragrant and non-fragrant genotypes, respectively. The newly developed marker was highly efficient in discriminating all fragrant and non-fragrant genotypes and showed perfect co-segregation with the trait of fragrance in the mapping population. We recommend the use of this simple, low-cost marker in routine genotyping for fragrance trait in large scale breeding materials and germplasm.     

Preparation of Gold Nanoparticles and their Applications in Anisotropic Nanoparticle Synthesis and Bioimaging

In this review, we highlight our recent achievements in using colloidal gold nanoparticles as building blocks for fabrication of anisotropic and multicomponent nanoparticles (e.g., nanoshells, semiconductor nanocrystals, and gold nanorods). The tunable optical properties of these nanoparticles are well suited for various biomedical and biophotonic applications.     

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

Translating a set of disease regions into insight about pathogenic mechanisms requires not only the ability to identify the key disease genes within them, but also the biological relationships among those key genes. Here we describe a statistical method, Gene Relationships Among Implicated Loci (GRAIL), that takes a list of disease regions and automatically assesses the degree of relatedness of implicated genes using 250,000 PubMed abstracts. We first evaluated GRAIL by assessing its ability to identify subsets of highly related genes in common pathways from validated lipid and height SNP associations from recent genome-wide studies. We then tested GRAIL, by assessing its ability to separate true disease regions from many false positive disease regions in two separate practical applications in human genetics. First, we took 74 nominally associated Crohn''s disease SNPs and applied GRAIL to identify a subset of 13 SNPs with highly related genes. Of these, ten convincingly validated in follow-up genotyping; genotyping results for the remaining three were inconclusive. Next, we applied GRAIL to 165 rare deletion events seen in schizophrenia cases (less than one-third of which are contributing to disease risk). We demonstrate that GRAIL is able to identify a subset of 16 deletions containing highly related genes; many of these genes are expressed in the central nervous system and play a role in neuronal synapses. GRAIL offers a statistically robust approach to identifying functionally related genes from across multiple disease regions—that likely represent key disease pathways. An online version of this method is available for public use (http://www.broad.mit.edu/mpg/grail/).     

Visualization of microarray gene expression data

Microarray gene expression data is used in various biological and medical investigations. Processing of gene expression data requires algorithms in data mining, process automation and knowledge discovery. Available data mining algorithms exploits various visualization techniques. Here, we describe the merits and demerits of various visualization parameters used in gene expression analysis.     

Microwave-assisted synthesis of antimicrobial dihydropyridines and tetrahydropyrimidin-2-ones: novel compounds against aspergillosis

Ten 4-aryl-1,4-dihydropyridine and three 4-aryl-1,2,3,4-tetrahydropyrimidin-2-one derivatives have been synthesized and examined for their activity against pathogenic strains of Aspergillus fumigatus and Candida albicans. Although none of the three compounds belonging to pyrimidin-2-one series showed any activity against two pathogens, two of the compounds of the dihydropyridine series, that is, diethyl 4-(4-methoxyphenyl)-2,6-dimethyl-1,4-dihydropyridin-3,5-dicarboxylate and dimethyl 4-(4-methoxyphenyl)-2,6-dimethyl-1,4-dihydropyridin-3,5-dicarboxylate, exhibited significant activity against A. fumigatus in disc diffusion, microbroth dilution and percent spore germination inhibition assays. The most active diethyl dihydropyridine derivative exhibited a MIC value of 2.92 microg/disc in disc diffusion and 15.62 microg/ml in microbroth dilution assays. The MIC(90) value of the most active compound by percent germination inhibition assay was found to be 15.62 microg/ml. The diethyl dicarboxylate derivative of dihydropyridine also exhibited appreciable activity against C. albicans. The in vitro toxicity of the most active diethyl dihydropyridine derivative was evaluated using haemolytic assay, in which the compound was found to be non-toxic to human erythrocytes even at a concentration of 625 microg/ml. The standard drug amphotericin B exhibited 100% lysis of erythrocytes at a concentration almost 16 times less than the safer concentration of the most active dihydropyridine derivative.     

3'-N-Alkylamino-3'-deoxy-ara-uridines: a new class of potential inhibitors of ribonuclease A and angiogenin

In this study, we report the inhibition of ribonuclease A (RNase A) by certain aminonucleosides. This is the first such instance of the use of this group of compounds to investigate the inhibitory activity of this protein. The compounds synthesized have been tested for their ability to inhibit the ribonucleolytic activity of RNase A by an agarose gel-based assay. A tRNA precipitation assay and inhibition kinetic studies with cytidine 2',3'-cyclic monophosphate as the substrate have also been conducted for two of the compounds. Results indicate substantial inhibitory activity with inhibition association constants in the micromolar range. The experimental studies have been substantiated by docking of the aminonucleoside ligands to RNase A using AutoDock. We find that the ligands preferentially bind to the active site of the protein molecule with a favorable free energy of binding. The study has been extended to a member of the ribonuclease superfamily, angiogenin, which is a potent inducer of blood vessel formation. We show that the aminonucleosides act as potent inhibitors of angiogenin induced angiogenesis.     

A database of annotated tentative orthologs from crop abiotic stress transcripts

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.     

A systematic review and meta-analysis on the prevalence of infectious diseases of Duck: A world perspective

The Indian poultry industry is one of the fast-growing sectors of which duck farming plays an important role. Duck population in India is 33.51 million that is concentrated towards north-east and southern parts of the country who rears mainly for eggs and meat. Duck diseases are of great concern as they badly affect the financial status of the small, landless farmers. Databases such as Google Scholar, PubMed, J gate were used to search articles between 2000 and 2019 that showed the prevalence of viral, bacterial, and parasitic duck diseases. R open source software was used to derive forest plots by statistical analysis. Pooled prevalence estimates of duck diseases worldwide was found to be 20% (95%-CI:15–26). Also, continent-wise analysis of all duck diseases has revealed highest prevalence in North America, followed by Asia, Africa, Europe,Oceania and South America. This prevalence of data would be helpful to the policymakers to develop appropriate intervention strategies to prevent and control diseases in their respective locations.     

Mountain biodiversity conservation and management: a paradigm shift in policies and practices in the Hindu Kush-Himalayas

Mountains occupy 24% of the global land surface area and are home to 12% of the world’s population. They have ecological, aesthetic, and socioeconomic significance, not only for people living in mountain areas, but for those living beyond. Mountains need specific attention for their contribution to global goods and services, especially by developing and implementing mountain specific policies. Conservation policies have evolved from the protection of charismatic species, to habitat and ecosystem/landscape conservation, and, finally, to people-oriented conservation approaches. This paper, with particular reference to paradigm shifts in the Hindu Kush-Himalayan (HKH) region, discusses the evolution of conservation policies, developments in conservation practices, the status of protected area management, wetland conservation initiatives and the landscape approach, community-based conservation initiatives, and the convergence of policies and practices. In the HKH region, conservation efforts now adopt participatory approaches, implement policies of decentralised governance for biodiversity management, and empower local communities in biodiversity management. The paradigm shift in the policies and practices related to conservation has been gradual and has included the acceptance of communities as an integral part of national level conservation initiatives, together with the integration of many global conventions. There are many successful pilots in the HKH region that deserve upscaling by the countries from the region. Realising the importance of mountains as hotspots of biodiversity, and due to their role as providers of global goods and services, the Convention on Biological Diversity adopted the Programme of Work on Mountain Biodiversity. Such a decision specific to mountains provides enormous opportunities for both conservation and development. Recent challenges posed by climate change need to be integrated into overall biodiversity conservation and management agendas, especially in mountain areas. The HKH region has been identified as a blank spot for data by the Inter-Governmental Panel on Climate Change, indicating the need to develop regional database and sharing mechanisms. This is a tall task, but one that holds enormous opportunity for the HKH countries and institutions with regional mandates to address the emerging challenges of climate change on biodiversity conservation by reducing scientific uncertainty.