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Shiv Nadar University

(SoNS) School of Natural Sciences

Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea. © 2018, The Author(s).

World University root node

Life Sciences

Fulltext

Scientific Reports

Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance

DNA methylation is widely known to regulate gene expression in eukaryotes. Here, we unraveled DNA methylation patterns in cultivated chickpea to understand the regulation of gene expression in different organs. We analyzed the methylation pattern in leaf tissue of wild chickpea too, and compared it with cultivated chickpea. Our analysis indicated abundant CG methylation within gene-body and CHH methylation in intergenic regions of the chickpea genome in all the organs examined. Analysis of differentially methylated regions (DMRs) demonstrated a higher number of CG context DMRs in wild chickpea and CHH context DMRs in cultivated chickpea. We observed increased preponderance of hypermethylated DMRs in the promoter regions and hypomethylated DMRs in the genic regions in cultivated chickpea. Genomic location and context of the DMRs correlated well with expression of proximal genes. Our results put forth a positive correlation of promoter hypermethylation with increased transcript abundance via identification of DMR-associated genes involved in flower development in cultivated chickpea. The atypical correlation observed between promoter hypermethylation and increased transcript abundance might be dependent on 24-nt small RNAs and transcription factors binding to the promoter region. This study provides novel insights into DNA methylation patterns in chickpea and their role in regulation of gene expression. © 2018 The Author(s).

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea

We consider a class of systems where N identical particles with positions q1,⋯,qN and momenta p1,⋯,pN are enclosed in a box of size L and exhibit the scaling U(Lr1,⋯,LrN)=α(L)U(r1,⋯,rN) for the associated potential energy function U(q1,⋯,qN). For these systems, we propose an efficient implementation of the Wang-Landau algorithm for evaluating thermodynamic observables involving energy and volume fluctuations in the microcanonical description and temperature and volume fluctuations in the canonical description. This requires performing the Wang-Landau simulation in a scaled box of unit size and evaluating the density of states corresponding to the potential energy part only. To demonstrate the efficacy of our approach as example systems, we consider Padmanabhan's binary star model and an ideal gas trapped in a harmonic potential within the box. © 2018 American Physical Society.

Physics

Physical Review E

Efficient implementation of the Wang-Landau algorithm for systems with length-scalable potential energy functions

In this paper we study seminormed double sequence spaces of a four-dimensional matrix and Musielak–Orlicz function over n-normed spaces. We explore some interesting inclusion relations, algebraic and topological properties of these spaces. © 2018, The Author(s).

Mathematics

Journal of Inequalities and Applications

Seminormed double sequence spaces of four-dimensional matrix and Musielak–Orlicz function

Fluorescent probes for simultaneous detection of multiple organelle specific analytes in cancer cells are essential for bioimaging applications. During abnormalities in cells, among other important parameters (metal ions, reactive oxygen species (ROS), enzymes, etc.) pH and Zn2+ are also altered in cells. Herein, we report the formation of nanoparticles of the fluorescent molecules based on carbazole-bipyridine conjugates (CBL1-3) and their use as nanoprobes to simultaneously detect Zn2+ and pH variations in lysosome. Upon increasing the pH from 4–6, these probes form nanoparticles with increased size and enhanced fluorescence at 510 nm. Among CBL1-3, nanoparticles of CBL2 upon Zn2+ binding, exhibit pH responsive intensity change only at lysosomal pH window at 610 nm and become silent above pH 7. Fluorescent imaging experiments on cancer cells revealed that the CBL2 nanoprobe is capable of localizing at lysosomes and facilitates the detection of endogenous Zn2+ and pH variations. Furthermore, the lysosomal Zn2+ variation with external stimuli induced programmed cell death was visualized using the nanoprobe. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Chemistry

ChemistrySelect

pH-Controlled Nanoparticles Formation and Tracking of Lysosomal Zinc Ions in Cancer Cells by Fluorescent Carbazole–Bipyridine Conjugates

This paper deals with the problem of finding an integer solution to a linear complementarity problem (LCP). Chandrasekaran et al. [1] introduced the class I of integral matrices for which the corresponding LCP has an integer solution for every integral vector q, for which it has a solution and proved that for some well-known matrix classes principal unimodularity forms a necessary and sufficient condition for inclusion in the class I. In this paper, we identify some more well-known matrix classes for which principal unimodularity forms a necessary and sufficient condition for inclusion in the class I. The concept of total dual integrality is utilized to obtain a necessary and sufficient condition for existence of an integer solution to LCP with a hidden K-matrix. We interconnect the concept of Hilbert basis with principal unimodularity of a matrix and the corresponding complementary cones. A necessary and sufficient condition is given for the existence of an integer solution of a linear fractional programming problem by using its LCP formulation. © 2018 Elsevier Inc.

Linear Algebra and Its Applications

Total dual integrality and integral solutions of the linear complementarity problem

Verhandlungen der Deutschen Physikalischen Gesellschaft

Low temperature heat capacity measurements on the mixed-valence iridate BaInIrO

In this paper we will highlight how a simple vacuum energy dominated inflection-point inflation can match the current data from cosmic microwave background radiation and predict large primordial tensor to scalar ratio, r∼O(10-3-10-2), with observable second order gravitational wave background, which can be potentially detectable from future experiments, such as DECi-hertz Interferometer Gravitational wave Observatory (DECIGO), Laser Interferometer Space Antenna (eLISA), cosmic explorer (CE) and big bang observatory (BBO).