Life Sciences

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DNA methylation plays a crucial role in development through inheritable gene silencing. Plants possess three types of DNA methyltransferases (MTases), namely Methyltransferase (MET), Chromomethylase (CMT) and Domains Rearranged Methyltransferase (DRM), which maintain methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far. Here, we report the identification and analysis of putative DNA MTases in five legumes, including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2) subfamilies based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2 represents a transfer RNA (tRNA) MTase. Structural comparison of all the MTases in plants with known MTases in mammalian and plant systems have been reported to assign structural features in context of biological functions of these proteins. The structure analysis clearly specified regions crucial for protein-protein interactions and regions important for nucleosome binding in various domains of CMT and MET proteins. In addition, structural model of DRM suggested that circular permutation of motifs does not have any effect on overall structure of DNA methyltransferase domain. These results provide valuable insights into role of various domains in molecular recognition and should facilitate mechanistic understanding of their function in mediating specific methylation patterns. Further, the comprehensive gene expression analyses of MTases in legumes provided evidence of their role in various developmental processes throughout the plant life cycle and response to various abiotic stresses. Overall, our study will be very helpful in establishing the specific functions of DNA MTases in legumes. © 2014 Garg et al.

(SoNS) School of Natural Sciences

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PLoS ONE

Genomic survey, gene expression analysis and structural modeling suggest diverse roles of DNA methyltransferases in legumes

Development of phosphate (P)-deficiency tolerant rice cultivars is constrained by lack of suitable, reproducible, and consistent seedling stage screening methods in breeding programs. This study reports the screening and characterization of M5 mutants derived from an ethyl methane sulfonate treated population of rice cv. Nagina 22 (N22) in low-P field (soil Olsen P 1.94-2.01 mg kg-1; alkaline Vertisol; pH 7.94) for high yield. The present study showed that seedling growth responses such as increase in root weight, root length, root/shoot weight, and dry weight in P-deficient medium can be taken as indices of low-P tolerance in mature plants in field. Total phosphorus content in seedlings showed an inverse relationship with total phosphorus content and low-P tolerance in mature plants in the field. But, phosphorus content in seeds and acid phosphatase activity in the seedling stage were positively correlated with survival and seed set in low-P field. In low-P field, plant height correlated most with yield per plant, and the number of productive tillers in mature plants was highly correlated with tiller number at vegetative stage. These mutants (NH776, NH710, and NH719) have agronomic importance because of their ability to grow and give higher yield than N22 in P-deficient field. © 2013 Taylor &amp; Francis.

Archives of Agronomy and Soil Science

Hydroponic experiment for identification of tolerance traits developed by rice Nagina 22 mutants to low-phosphorus in field condition

K-antigen capsule, a key virulence determinant of the oral pathogen Porphyromonas gingivalis, is synthesized by proteins encoded in a series of genes transcribed as a large polycistronic message. Previously, we identified a 77-base pair inverted repeat region with the potential to form a large stem-loop structure at the 59 end of this locus. PG0121, one of two genes flanking the capsule operon, was found to be co-transcribed with the operon and to share high similarity to the DNA binding protein HU from Escherichia coli. A null mutation in PG0121 results in down-regulation of transcription of the capsule synthesis genes and production of capsule. Furthermore, we have also shown that PG0121 gene can complement multiple deficiencies in a strain of E. coli that is deficient for both the alpha and beta subunits of HU. Here, we examined the biochemical properties of the interaction of PG0121 to DNA with the emphasis on the kinds of nucleic acid architectures that may be encountered at the 77-bp inverted repeat. We have concluded that although some DNA binding characteristics are shared with E. coli HU, HU PG0121 also shows some distinct characteristics that set it apart from other HU-like proteins tested to date. We discuss our results in the context of how PG0121 may affect the regulation of the K-antigen capsule expression. © 2014 Tjokro et al.

A biochemical analysis of the interaction of Porphyromonas gingivalis HU PG0121 protein with DNA

Background: There has been increasing interest recently in the plasticity of mesenchymal stem cells (MSCs) and their potential to differentiate into neural lineages. To unravel the roles and effects of different growth factors in the differentiation of MSCs into neural lineages, we have differentiated MSCs into neural lineages using different combinations of growth factors. Based on previous studies of the roles of insulin-like growth factor 1 (IGF-1) in neural stem cell isolation in the laboratory, we hypothesized that IGF-1 can enhance proliferation and reduce apoptosis in neural progenitor-like cells (NPCs) during differentiation of MSCs into NCPs.We induced MSCs differentiation under four different combinations of growth factors: (A) EGF + bFGF, (B) EGF + bFGF + IGF-1, (C) EGF + bFGF + LIF, (D) EGF + bFGF + BDNF, and (E) without growth factors, as a negative control. The neurospheres formed were characterized by immunofluorescence staining against nestin, and the expression was measured by flow cytometry. Cell proliferation and apoptosis were also studied by MTS and Annexin V assay, respectively, at three different time intervals (24 hr, 3 days, and 5 days). The neurospheres formed in the four groups were then terminally differentiated into neuron and glial cells.Results: The four derived NPCs showed a significantly higher expression of nestin than was shown by the negative control. Among the groups treated with growth factors, NPCs treated with IGF-1 showed the highest expression of nestin. Furthermore, NPCs derived using IGF-1 exhibited the highest cell proliferation and cell survival among the treated groups. The NPCs derived from IGF-1 treatment also resulted in a better yield after the terminal differentiation into neurons and glial cells than that of the other treated groups.Conclusions: Our results suggested that IGF-1 has a crucial role in the differentiation of MSCs into neuronal lineage by enhancing the proliferation and reducing the apoptosis in the NPCs. This information will be beneficial in the long run for improving both cell-based and cell-free therapy for neurodegenerative diseases. © 2014 Huat et al.; licensee BioMed Central Ltd.

BMC Neuroscience

IGF-1 enhances cell proliferation and survival during early differentiation of mesenchymal stem cells to neural progenitor-like cells

miRNAs are some of the key epigenetic regulators of gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up- and downregulation of the oncogenic and tumor suppressor miRNAs, respectively. The levels of aberrantly expressed oncogenic miRNAs can be downregulated in different ways. Similarly, restoration of tumor suppressor miRNAs to their normal levels can be achieved using miRNA mimics. However, the use of miRNA mimics is limited by their reduced biostability and function. We have studied the hybridization thermodynamics of the miRNA 26a (11-mer, including the seed sequence) guide strand with the mRNA (11-mer) target strand in the absence and presence of AfPiwi protein. We have also inserted locked nucleic acids (LNAs) and 2-O-methyl-modified nucleotides into the guide strand, in a walk-through manner, to assess their effect on the binding efficiency between guide and target RNA. Insertion of LNA and 2-O-methyl-modified nucleotides into the guide strand helped to strengthen the binding affinity irrespective of the position of insertion. However, in the presence of AfPiwi protein, these modifications reduced the binding affinity to different extents depending on the position of insertion. Insertion of a modification leads to an increase in the enthalpic contribution with an increased unfavorable entropic contribution, which negatively compensates for the higher favorable enthalpy. © 2014 American Chemical Society.

Biochemistry

Understanding the effect of locked nucleic acid and 2- O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein

Serologic characterization of autoantibodies helps in the management and monitoring of the course of autoimmune hemolytic anemia (AIHA). The purpose of this study was to evaluate gel centrifugation test (GCT) cards for immunoglobulin G (IgG) titer and determination of IgG subclasses IgG1 and IgG3 and their influence on hemolysis. Eighty direct antiglobulin test (DAT)-positive patients were examined with the help of GCT cards for IgG titer and IgG subclasses. The results were correlated with the presence and absence of hemolysis. A statistically significant (p < 0.005) association of hemolysis with increasing anti-IgG titer was observed. When IgG titer was 30 or less, 28 (50.91%) patients had no hemolysis, whereas 15 (93.75%) patients had features of hemolysis when titer was at least 300. Statistically significant (p < 0.005) association of subclass of IgG (IgG1, IgG3) coating the red blood cells with intravascular hemolysis was also seen. Twenty-nine (80.56%) patients had evidence of hemolysis when IgG1 or IgG1-IgG3 both were present. Gel technology is helpful to demonstrate red blood cell-bound autoantibodies and their characterization with regard to class, subclass, and titer. This information is useful to identify patients with AIHA who are at risk of severe hemolysis with adverse prognosis.

Immunohematology

Demonstration of IgG subclass (IgG1 and IgG3) in patients with positive direct antiglobulin tests

Ionospheric perturbations in possible association with the earthquake occurred on 25 March 2013 in India-Oceania region (magnitudes ≈ 6.0) is investigated on the basis of subionospheric propagation data from the NWC transmitter(19.8 kHz) on the North West Cape, Australia to a VLF receiving station at Agra, India. The local nighttime VLF amplitude data are extensively investigated during the period, ±15 days of the earthquake, in which the trend (nighttime average amplitude), dispersion and nighttime fluctuation are analyzed. It is found that a clear precursory ionosphere perturbation is detected, about 12 days before the main shock, which is characterised by the simultaneous decrease in the trend and increase in nighttime fluctuation. Possible seismo-ionospheric mechanisms to demonstrate the physics that how ionosphere starts to feel these earthquakes are discussed. © 2014 IEEE.

2014 31th URSI General Assembly and Scientific Symposium, URSI GASS 2014

Sub-ionospheric vlf propagation anomalies associated with the earthquake on 25 March 2013

Porteresia coarctata is a wild relative of rice with capability of high salinity and submergence tolerance. The transcriptome analyses of Porteresia can lead to the identification of candidate genes involved in salinity and submergence tolerance. We sequenced the transcriptome of Porteresia under different conditions using Illumina platform and generated about 375 million high-quality reads. After optimized assembly, a total of 152 367 unique transcript sequences with average length of 794 bp were obtained. Many of these sequences might represent fragmented transcripts. Functional annotation revealed the presence of genes involved in diverse cellular processes and 2749 transcription factor (TF)-encoding genes in Porteresia. The differential gene expression analyses identified a total of 15 158 genes involved in salinity and/or submergence response(s). The stress-responsive members of different TF families, including MYB, bHLH, AP2-EREBP, WRKY, bZIP and NAC, were identified. We also revealed key metabolic pathways, including amino acid biosynthesis, hormone biosynthesis, secondary metabolite biosynthesis, carbohydrate metabolism and cell wall structures, involved in stress tolerance in Porteresia. The transcriptome analyses of Porteresia are expected to highlight genes/pathways involved in salinity and submergence tolerance of this halophyte species. The data can serve as a resource for unravelling the underlying mechanism and devising strategies to engineer salinity and submergence tolerance in rice. © 2013 The Author.

DNA Research

Deep Transcriptome Sequencing of Wild Halophyte Rice, Porteresia coarctata, Provides Novel Insights into the Salinity and Submergence Tolerance Factors

Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Plant Biotechnology Journal

Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance

Fifteen mango genotypes were characterized for their flowering behaviour under Delhi conditions during 2011-12. Dushehari, Langra and Primor de Amoreira showed very early panicle initiation, i.e., before 10th February. However, Erwin and Husnara had very late panicle initiation, i.e., after 3rd March. Totapari Red Small, Pusa Arunima and Janardan Pasand had flowering during 10-20th February. Whereas, Zill, Tommy Atkins, Sensation, Neelum, Mallika, Amrapali and Bhadauran initiated panicles during 21st February to 3rd March. The maximum duration of flowering was noticed in Primor de Amoreira (41.5 days). However, the minimum duration of flowering was noticed in Husnara (13.0 days) followed by Erwin (14.5 days). Flowering duration was more than 20 days but less than 30 days in Amrapali, Sensation, Bhadauran, Mallika, Totapari Red Small and Janardan Pasand. Total number of flowers ranged between 133.30 in Bhadauran to 506.10 in Tommy Atkins. In general, per cent hermaphrodite flowers was less in early emerged panicles compared to late emerged panicles in all mango genotypes. A scheme of hybridization was suggested on the basis of flowering duration employing these mango genotypes. The effective period of mango hybridization using diverse parental mango genotypes was found to be from 3rd week of February to mid March under Delhi conditions. © 2015, Horticulture Society of India. All rights reserved.