Impact of seed size on seed yield of kabuli chickpea (Cicer arietinum L.)

A study was conducted during Rabi 2008–09 to evaluate the impact of seed size on seed yield of kabuli chickpea genotypes. Three groups of seed size viz., group 1 (20–30 g), group 2 (30.1–40 g) and group 3 (>40 g) per 100-seed comprising of 18, 99 and 25 genotypes, respectively were used for this study. The estimates of different parameters of three different group of seed size showed that seed yield decreased with the increase in seed size. The correlation and regression coefficient was positive for the group 1 while negative for other two groups of large seed size which further confirmed this observation. It was also observed from the results that seed size up to 30 g/100-seed was useful to realize maximum seed yield

Polymorphisms of MTHFR and MTR genes are not related to susceptibility to childhood ALL in north India

Background:Acute lymphoblastic leukemia (ALL) is the most worldwide common type of childhood cancer. Methylenetetrahydrofolate reductase (MTHFR) and 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) participate in folate pathways and are known as critical factors for DNA integrity as well as DNA hypomethylation. The aim of this work is to investigate frequency of MTHFR (677C→T and 1298A→C) and MTR (2756A→G) polymorphisms and their interaction with respect to possible effect on risk of childhood ALL among North Indian population. Procedure: A case control study from has been conducted on bone marrow and peripheral blood samples from 125 ALL patients and 100 sex-age matched healthy controls using PCR-RFLP method. Results: No statistically significant differences were observed for different genotypes between patients and controls (p>0.05). Significant difference for the risk of ALL in individuals having genotype of MTHFR 677TT (OR=0.61, 95% CI=0.21–1.77) and MTHFR 1298CC (OR=0.56, 95% CI=0.18–1.68) was not observed. The correlation of SNP of MTR gene and risk of ALL was not observed, too. Conclusions: The differences in distribution of possible combined genotypes of MTHFR (677C→T, 1298A→C) and MTR (2756A→G) between ALL patients and controls were statistically insignificant

Genetic Variability of Pigeonpea (Cajanus cajan (L.) Millsp.) for Water Logging and Salinity Tolerance under in vitro and in vivo Conditions

Pigeonpea (Cajanus cajan (L.) Millsp.) genotypes acquired from diverse sources, were screened for water logging and salinity tolerance under laboratory and field conditions. Analysis of variance revealed significant differences among the genotypes for various traits. Based on seedling vigor index, six genotypes (AL 1756, AL 1849, AH-06-7, H-2000-14, H-2003-14, ICP 5028) were found highly tolerant, 10 tolerant, 24 moderately tolerant, 12 sensitive and eight highly sensitive to water logging. In case of salinity treatment, seven genotypes (AL 1849, AH-06-7, H-2000-14, H-2001-25, H-2003-14, ICP 5028, JBP 110B) were found tolerant, 14 moderately tolerant, 17 sensitive and 22 highly sensitive. Mean values for germination percentage, seedling length, seedling dry weight and seedling vigor index were generally lower in salinity treatment than water logging treatment. Based on results of laboratory studies, 28 genotypes were screened in pot/field for tolerance to water logging and salinity and were categorized on the basis of plant survival percentage after treatments. Based on plant survival, four genotypes (AL 15, AL 1849, H-2000-14, H-02-28) were found highly tolerant, five tolerant, nine moderately tolerant, four sensitive and six were found highly sensitive in water logging treatment. In case of salinity treatment, six genotypes were found tolerant, five moderately tolerant, three sensitive and 14 were found highly sensitive. Based on higher plant survival (%) under both water logging and saline conditions, common genotypes were identified for their further use in breeding programme

The prevalence and risk factors for human Brucella species infection in a cross-sectional survey of a rural population in Punjab, India

Brucellosis is an important neglected zoonosis. Effective cattle vaccines are available but are infrequently used in India, where rural households commonly own one or two cattle as sources of protein and income. We assessed the prevalence of infection and risk factors in humans

On the elliptical flow in asymmetric collisions and nuclear equation of state

We here present the results of elliptical flow for the collision of different asymmetric nuclei (10Ne20 +13 Al27, 18Ar40 +21 Sc45, 30Zn64 +28 Ni58, 36Kr86 +41 Nb93) by using the Quantum Molecular Dynamics (QMD) model. General features of elliptical flow are investigated with the help of theoretical simulations. The simulations are performed at different beam energies between 40 and 105 MeV/nucleon. A significant change can be seen from in-plane to out-of-plane elliptical flow of different fragments with incident energy. A comparison with experimental data is also made. Further, we predict, for the first time that, elliptical flow for different kind of fragments follow power law dependence ? C(Atot)? for asymmetric systems

Multiwavelength study of the transient X-ray binary IGR J01583+6713

We have investigated multiband optical photometric variability and stability of the H$\alpha$ line profile of the transient X-ray binary IGR J01583+6713. We set an upper limit of 0.05 mag on photometric variations in the {\it V} band over a time scale of 3 months. The H$\alpha$ line is found to consist of non-Gaussian profile and quite stable for a duration of 2 months. We have identified the spectral type of the companion star to be B2 IVe while distance to the source is estimated to be $\sim$ 4.0 kpc. Along with the optical observations, we have also carried out analysis of X-ray data from three short observations of the source, two with the {\it Swift}--XRT and one with the {\it RXTE}--PCA. We have detected a variation in the absorption column density, from a value of 22.0 $\times$ 10$^{22}$ cm$^{-2}$ immediately after the outburst down to 2.6 $\times$ 10$^{22}$ cm$^{-2}$ four months afterwards. In the quiescent state, the X-ray absorption is consistent with the optical reddening measurement of E(B - V) = 1.46 mag. From one of the {\it Swift} observations, during which the X-ray intensity was higher, we have a possible pulse detection with a period of 469.2 s. For a Be X-ray binary, this indicates an orbital period in the range of 216--561 days for this binary system.Comment: 22 pages, 8 figures, accepted for publication in MNRA

Identification of NAD interacting residues in proteins

Background: Small molecular cofactors or ligands play a crucial role in the proper functioning of cells. Accurate annotation of their target proteins and binding sites is required for the complete understanding of reaction mechanisms. Nicotinamide adenine dinucleotide (NAD+ or NAD) is one of the most commonly used organic cofactors in living cells, which plays a critical role in cellular metabolism, storage and regulatory processes. In the past, several NAD binding proteins (NADBP) have been reported in the literature, which are responsible for a wide-range of activities in the cell. Attempts have been made to derive a rule for the binding of NAD+ to its target proteins. However, so far an efficient model could not be derived due to the time consuming process of structure determination, and limitations of similarity based approaches. Thus a sequence and non-similarity based method is needed to characterize the NAD binding sites to help in the annotation. In this study attempts have been made to predict NAD binding proteins and their interacting residues (NIRs) from amino acid sequence using bioinformatics tools. Results: We extracted 1556 proteins chains from 555 NAD binding proteins whose structure is available in Protein Data Bank. Then we removed all redundant protein chains and finally obtained 195 non-redundant NAD binding protein chains, where no two chains have more than 40% sequence identity. In this study all models were developed and evaluated using five-fold cross validation technique on the above dataset of 195 NAD binding proteins. While certain type of residues are preferred (e.g. Gly, Tyr, Thr, His) in NAD interaction, residues like Ala, Glu, Leu, Lys are not preferred. A support vector machine (SVM) based method has been developed using various window lengths of amino acid sequence for predicting NAD interacting residues and obtained maximum Matthew's correlation coefficient (MCC) 0.47 with accuracy 74.13% at window length 17. We also developed a SVM based method using evolutionary information in the form of position specific scoring matrix (PSSM) and obtained maximum MCC 0.75 with accuracy 87.25%. Conclusion: For the first time a sequence-based method has been developed for the prediction of NAD binding proteins and their interacting residues, in the absence of any prior structural information. The present model will aid in the understanding of NAD+ dependent mechanisms of action in the cell. To provide service to the scientific community, we have developed a user-friendly web server, which is available from URL http://www.imtech.res.in/raghava/nadbinder/

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Background: Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study. Results: Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified. Conclusion: The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling–uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought

Mucin (Muc) expression during pancreatic cancer progression in spontaneous mouse model: potential implications for diagnosis and therapy.

BACKGROUND: Pancreatic cancer (PC) is a lethal malignancy primarily driven by activated Kras mutations and characterized by the deregulation of several genes including mucins. Previous studies on mucins have identified their significant role in both benign and malignant human diseases including PC progression and metastasis. However, the initiation of MUC expression during PC remains unknown because of lack of early stage tumor tissues from PC patients. METHODS: In the present study, we have evaluated stage specific expression patterns of mucins during mouse PC progression in (Kras(G12D);Pdx1-Cre (KC)) murine PC model from pancreatic intraepithelial neoplasia (PanIN) to pancreatic ductal adenocarcinoma (PDAC) by immunohistochemistry and quantitative real-time PCR. RESULTS: In agreement with previous studies on human PC, we observed a progressive increase in the expression of mucins particularly Muc1, Muc4 and Muc5AC in the pancreas of KC (as early as PanIN I) mice with advancement of PanIN lesions and PDAC both at mRNA and protein levels. Additionally, mucin expression correlated with the increased expression of inflammatory cytokines IFN-γ (p \u3c 0.0062), CXCL1 (p \u3c 0.00014) and CXCL2 (p \u3c 0.08) in the pancreas of KC mice, which are known to induce mucin expression. Further, we also observed progressive increase in inflammation in pancreas of KC mice from 10 to 50 weeks of age as indicated by the increase in the macrophage infiltration. Overall, this study corroborates with previous human studies that indicated the aberrant overexpression of MUC1, MUC4 and MUC5AC mucins during the progression of PC. CONCLUSIONS: Our study reinforces the potential utility of the KC murine model for determining the functional role of mucins in PC pathogenesis by crossing KC mice with corresponding mucin knockout mice and evaluating mucin based diagnostic and therapeutic approaches for lethal PC