Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa)

Background The response regulators represent the elements of bacterial two-component system and have been characterized from dicot plants like Arabidopsis but little information is available on the monocots, including the cereal crops. The aim of this study was to characterize type-A response regulator genes from rice, and to investigate their expression in various organs as well as in response to different hormones, including cytokinin, and environmental stimuli. Results By analysis of the whole genome sequence of rice, we have identified ten genes encoding type-A response regulators based upon their high sequence identity within the receiver domain. The exon-intron organization, intron-phasing as well as chromosomal location of all the RT-PCR amplified rice (Oryza sativa) response regulator (OsRR) genes have been analyzed. The transcripts of OsRR genes could be detected by real-time PCR in all organs of the light- and dark-grown rice seedlings/plants, although there were quantitative differences. The steady-state transcript levels of most of the OsRR genes increased rapidly (within 15 min) on exogenous cytokinin application even in the presence of cycloheximide. Moreover, the expression of the OsRR6 gene was enhanced in rice seedlings exposed to salinity, dehydration and low temperature stress. Conclusion Ten type-A response regulator genes identified in rice, the model monocot plant, show overlapping/differential expression patterns in various organs and in response to light. The induction of OsRR genes by cytokinin even in the absence of de novo protein synthesis qualifies them to be primary cytokinin response genes. The induction of OsRR6 in response to different environmental stimuli indicates its role in cross-talk between abiotic stress and cytokinin signaling. These results provide a foundation for further investigations on specific as well as overlapping cellular functions of type-A response regulators in rice

Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants

DNA topoisomerase 6 (TOP6) belongs to a novel family of type II DNA topoisomerases present, other than in archaebacteria, only in plants. Here we report the isolation of full-length cDNAs encoding putative TOP6 subunits A and B from rice (Oryza sativa ssp. indica), preserving all the structural domains conserved among archaebacterial TOP6 homologs and eukaryotic meiotic recombination factor SPO11. OsTOP6A1 was predominantly expressed in prepollinated flowers. The transcript abundance of OsTOP6A2, OsTOP6A3 and OsTOP6B was also higher in prepollinated flowers and callus. The expression of OsTOP6A2, OsTOP6A3 and OsTOP6B was differentially regulated by the plant hormones, auxin, cytokinin, and abscisic acid. Yeast two-hybrid analysis revealed that the full-length OsTOP6B protein interacts with both OsTOP6A2 and OsTOP6A3, but not with OsTOP6A1. The nuclear localization of OsTOP6A3 and OsTOP6B was established by the transient expression of their β-glucuronidase fusion proteins in onion epidermal cells. Overexpression of OsTOP6A3 and OsTOP6B in transgenic Arabidopsis plants conferred reduced sensitivity to the stress hormone, abscisic acid, and tolerance to high salinity and dehydration. Moreover, the stress tolerance coincided with enhanced induction of many stress-responsive genes in transgenic Arabidopsis plants. In addition, microarray analysis revealed that a large number of genes are expressed differentially in transgenic plants. Taken together, our results demonstrate that TOP6 genes play a crucial role in stress adaptation of plants by altering gene expression

Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice

Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P <0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation

Role of fine needle aspiration cytology in diagnosing leprosy: in a tertiary care hospital

Background: Leprosy, a chronic inflammatory granulomatous disease chiefly involving skin and peripheral nerves and occasionally other organ systems, caused by Mycobacterium leprae. It has tormented the human civilization through time immemorial. Leprosy remains a significant public health problem worldwide, especially in developing countries like India. The diagnosis of leprosy is not always easy because of long incubation period, over dependence of clinical expertise and a lack of rapid and simple diagnostic tool, patients remain undiagnosed for longer time. Fine needle aspiration (FNAC) technique is an inexpensive, rapid and accurate procedure for diagnosis of leprosy. We conducted a prospective study evaluating the ability of fine needle aspiration cytology in diagnosing and classifying leprosy lesions on Ridley-Jopling scale (R-J scale). The aim of this prospective study was to assess the usefulness of fine needle aspiration cytology in early diagnosis of leprosy, to identify specific cytological characteristics of diagnosis and to correlate the cytological smear findings with histopathology and to evaluate merits of relatively non-invasive procedure of FNAC over more invasive procedure - biopsy.Methods: The study is a hospital based prospective study carried out in the Department of Pathology and Department of Skin, Venereal Diseases, Leprosy, N.S.C.B. Medical College & Hospital, Jabalpur (M.P.) September 2010 to September 2013. Patients with new skin lesions were selected for the study. FNAC was performed and aspirates were evaluated for cytology using Hematoxylin and Eosin staining (H&E staining), Ziehl-Neelsen staining (ZN staining) and punch biopsy was collected.Results: Out of 50 cases, clinical and cytological correlation was seen in 88% tuberculoid leprosy, 93.7% of borderline tuberculoid, 33% of borderline lepromatous leprosy and 66% of lepromatous leprosy. While clinical with histopathological correlation revealed 100% specificity in tuberculoid leprosy, 100% in borderline tuberculoid, 66.6% in borderline lepromatous, 83.3% in lepromatous leprosy and 80% in indeterminate leprosy and 100% in histoid leprosy in our study. The overall cytodiagnostic accuracy has been 92% in present study.  Conclusion: Our study demonstrates that the combination of FNAC and ZN staining for Acid Fast Bacilli (AFB) can provide a rapid diagnosis in majority of leprosy suspected cases. FNAC is a safe, simple, rapid, less-invasive, OPD procedure for early diagnosis and classification of leprosy cases.

Outlooks of Nanotechnology in Organic Farming Management

Technological advances are getting monitored with time, and science suggests nanotechnology as the emerging future. This even holds correct with human food consumption for health benefits, where organic farming is a better solution for the rising population and is even supported by major countries instead of using chemical fertilisers and pesticides. Nanotechnology provides a platform where nanoparticles help in better management for organic farming by using it as nano fertilisers, nanocides, nano biosensors, nano growth promoters, etc. These nanomaterials can be synthesised by three different mechanisms namely; chemical, physical, and biological methods. Since the chemical and physical mode of synthesis does not follow the criteria of organic farming and have their drawbacks. Hence, the biological method, also known as the green synthesis of nanomaterials fulfills the requirement of organic farming and has achieved the attention of researchers. Extracts of plant parts (stems, roots, leaves, flowers and, fruits) and different microbes, including bacteria, fungus, and mycorrhiza can be used as a base material for the synthesis of nanoparticles under green synthesis mode. The vision behind the green synthesis of nanoparticles was to curb the hazardous effects of chemically synthesised nanoparticles. In the present review, green synthesis of major elements of organic farming namely; nano fertilisers, nano-pesticides, and nano growth promoters, their modes of transportation, their advantages, and disadvantages in organic farming are discussed

Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa)

Auxin exerts pleiotropic effects on plant growth and development by regulating the expression of early auxin-responsive genes of auxin/indoleacetic acid (Aux/IAA), small auxin-up RNA, and GH3 classes. These genes have been studied extensively in dicots like soybean and Arabidopsis. We had earlier characterized a cDNA of the first monocot member of Aux/IAA family from rice. The achievement of the large scale rice genome sequencing combined with the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encyclopedia provided us the opportunity to draw up the first comprehensive list of Aux/IAA genes in a monocot. By screening the available databases, we have identified 31 Aux/IAA genes having high sequence identity within the conserved domains I, II, III, and IV. The genomic organization as well as chromosomal location of all the Oryza sativa indoleacetic acid (OsIAA) genes is reported. The rice Aux/IAA proteins can be classified in two groups (A and B) on the basis of their phylogenetic relationship with Arabidopsis Aux/IAA proteins. An evolutionary pattern of the rice Aux/IAA genes has been discussed by analyzing their structure (exon/intron organization) and duplications. Interestingly, the duplication of rice Aux/IAA genes was found to be associated with chromosomal block duplication events in rice. The in-silico analysis has been complemented with real-time polymerase chain reaction analysis to quantify transcript levels of all Aux/IAA family members. OsIAA genes showed differential and overlapping organ-specific expression patterns in light- and dark-grown seedlings/plants. Although auxin enhanced the transcript abundance of most of the OsIAA genes, the effect was more pronounced on OsIAA9, 14, 19, 20, 24, and 31. These results provide a foundation for future studies on elucidating the precise role of rice Aux/IAA genes in early steps of auxin signal transduction

Statistical media optimization studies for growth and polydroxybutyrate (PHB) production by Pseudomonas spp.

Using glucose as carbon source and mustard cake and yeast extract as nitrogen sources bacterial isolate Pseudomonas B2 exhibited a maximum PHB recovery of 0.620 (in terms of O.D.) and PHB weight of 0.27g/L in 96 h. To determine the possibility of growth potential of Pseudomonas spp., it was grown in different carbon sources like fructose, glucose, maltose, mannitol etc. and it was found that glucose yielded good growth and PHB production. In order to incorporate cost effective nitrogen and carbon source, mustard cake and cotton cake as nitrogen source and molasses as carbon were used in medium. Statistical media optimization design was used to optimize the culture conditions for maximizing the PHB production. A maximum of 0.37 g/L of PHB and 0.746 (O.D.) PHB recoveries were obtained using optimized concentrations. Batch kinetics can be used for model development, which will make possible simulation of nutrient limited cultivation(s) for over accumulation of PHB. FTIR studies confirmed the presence of PHB

High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties