Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies.     

Application of centrality measures in the identification of critical genes in diabetes mellitus

The connectivity of a protein and its structure is related to its functional properties. Many experimental approaches have been employed for the identification of Diabetes Mellitus (DM) associated candidate genes. Therefore, it is of interest to use var ious graph centrality measures integrated with the genes associated with the human Diabetes Mellitus network for the identification of potential targets. We used 2728 genes known to cause Diabetes Mellitus from Jensenlab (Novo Nordisk Foundation Center for Protein Research, Denmark) for this analysis. A protein-protein interaction network was further constructed using a tool Centralities in Biological Networks (CentiBiN) with 1020 nodes after eliminating the duplicates, parallel edges, self -loop edges and unknown Human Protein Reference Database (HPRD) IDS. We used fourteen centralities measures which are useful in identifying the structural characteristic of individuals in the network. The results of the centrality measures are highly correlated. Thus, we identified genes that are critically associated with DM. We further report the top ten genes of all fourteen centrality measures for further consideration as targets for DM.     

Structural characterization of BRCT-tetrapeptide binding interactions

BRCT(BRCA1) plays a major role in DNA repair pathway, and does so by recognizing the conserved sequence pSXXF in its target proteins. Remarkably, tetrapeptides containing pSXXF motif bind with high specificity and micromolar affinity. Here, we have characterized the binding interactions of pSXXF tetrapeptides using NMR spectroscopy and calorimetry. We show that BRCT is dynamic and becomes structured on binding, that pSer and Phe residues dictate overall binding, and that the binding affinities of the tetrapeptides are intimately linked to structural and dynamic changes both in the BRCT(BRCA1) and tetrapeptides. These results provide critical insights for designing high-affinity BRCT(BRCA1) inhibitors.     

Triterpenoids from walsura piscidia

A series of tirucallane (piscidinol A and B) and apotirucallane (piscidinol C–E) derivatives has been isolated from the leaves of Walsura piscidia. The fruit yielded a new tetranortriterpenoid, piscidofuran. The structures were assigned on the basis of ¹H NMR and ¹³C NMR evidence.     

Synthesis and characterization of high quantum yield and oscillator strength 6‐chloro‐2‐(4‐cynophenyl)‐4‐phenyl quinoline (cl‐CN‐DPQ) organic phosphor for solid‐state lighting

A novel blue luminescent 6‐chloro‐2‐(4‐cynophenyl) substituted diphenyl quinoline (Cl‐CN DPQ) organic phosphor has been synthesized by the acid‐catalyzed Friedlander reaction and then characterized to confirm structural, optical and thermal properties. Structural properties of Cl‐CN‐DPQ were analyzed by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR) spectroscopy, X‐ray diffraction technique (XRD) and scanning electron microscopy (SEM) and energy dispersive analysis of X‐ray (EDAX) spectroscopy. FTIR spectra confirmed the presence of different functional groups and bond stretching. ¹H–NMR and ¹³C–NMR confirmed the formation of an organic Cl‐CN‐DPQ compound. X‐ray diffraction study provided its crystalline nature. The surface morphology of Cl‐CN‐DPQ was analyzed by SEM, while EDAX spectroscopy revealed the elemental analysis. Differential thermal analysis (TGA/DTA) disclosed its thermal stability up to 250°C. The optical properties of Cl‐CN‐DPQ were investigated by UV–vis absorption and photoluminescence (PL) measurements. Cl‐CN‐DPQ exhibits intense blue emission at 434 nm in a solid‐state crystalline powder with CIE co‐ordinates (0.157, 0.027), when excited at 373 nm. Cl‐CN‐DPQ shows remarkable Stokes shift in the range 14800–5100 cm^?1, which is the characteristic feature of intense light emission. A narrow full width at half‐maximum (FWHM) value of PL spectra in the range 42–48 nm was observed. Oscillator strength, energy band gap, quantum yield, and fluorescence energy yield were also examined using UV–vis absorption and photoluminescence spectra. These results prove its applications towards developing organic luminescence devices and displays, organic phosphor‐based solar cells and displays, organic lasers, chemical sensors and many more.     

2‐(4‐Ethoxy phenyl)‐4‐phenyl quinoline organic phosphor for solution processed blue organic light‐emitting diodes

This paper reports the synthesis and characterization of 2‐(4‐ethoxyphenyl)‐4‐phenyl quinoline (OEt‐DPQ) organic phosphor using an acid‐catalyzed Friedlander reaction and the preparation of blended thin films by molecularly doping OEt‐DPQ in poly(methyl methacrylate) (PMMA) at different wt%. The molecular structure of the synthesized phosphor was confirmed by Fourier transform infra‐red (FTIR) spectroscopy and nuclear magnetic resonance spectra (NMR). Surface morphology and percent composition of the elements were assessed by scanning electron microscopy (SEM) and energy dispersive analysis of X‐rays (EDAX). The thermal stability and melting point of OEt‐DPQ and thin films were probed by thermo‐gravimetric analysis (TGA)/differential thermal analysis (DTA) and were found to be 80°C and 113.6°C, respectively. UV–visible optical absorption spectra of OEt‐DPQ in the solid state and blended films produced absorption bands in the range 260–340 nm, while photoluminescence (PL) spectra of OEt‐DPQ in the solid state and blended thin films demonstrated blue emission that was registered at 432 nm when excited at 363–369 nm. However, solvated OEt‐DPQ in chloroform, tetrahydrofuran or dichloromethane showed a blue shift of 31–43 nm. Optical absorption and emission parameters such as molar extinction coefficient (ε), energy gap (E_g), transmittance (T), reflectance (R), refractive index (n), oscillator energy (E₀) and oscillator strength (f), quantum yield (φ_f), oscillator energy (E₀), dispersion energy (E_d), Commission Internationale de l'Éclairage (CIE) co‐ordinates and energy yield fluorescence (E_F) were calculated to assess the phosphor's suitability as a blue emissive material for opto‐electronic applications such as organic light‐emitting diodes (OLEDs), flexible displays and solid‐state lighting technology.     

Synthesis of aminopyrazole analogs and their evaluation as CDK inhibitors for cancer therapy

We synthesized a library of aminopyrazole analogs to systematically explore the hydrophobic pocket adjacent to the hinge region and the solvent exposed region of cyclin dependent kinases. Structure-activity relationship studies identified an optimal substitution for the hydrophobic pocket and analog 24 as a potent and selective CDK2/5 inhibitor.     

Benzoxazine derivatives of phytophenols show anti-plasmodial activity via sodium homeostasis disruption

Development of new class of anti-malarial drugs is an essential requirement for the elimination of malaria. Bioactive components present in medicinal plants and their chemically modified derivatives could be a way forward towards the discovery of effective anti-malarial drugs. Herein, we describe a new class of compounds, 1,3-benzoxazine derivatives of pharmacologically active phytophenols eugenol (compound 3) and isoeugenol (compound 4) synthesised on the principles of green chemistry, as anti-malarials. Compound 4, showed highest anti-malarial activity with no cytotoxicity towards mammalian cells. Compound 4 induced alterations in the intracellular Na⁺ levels and mitochondrial depolarisation in intraerythrocytic Plasmodium falciparum leading to cell death. Knowing P-type cation ATPase PfATP4 is a regulator for sodium homeostasis, binding of compound 3, compound 4 and eugenol to PfATP4 was analysed by molecular docking studies. Compounds showed binding to the catalytic pocket of PfATP4, however compound 4 showed stronger binding due to the presence of propylene functionality, which corroborates its higher anti-malarial activity. Furthermore, anti-malarial half maximal effective concentration of compound 4 was reduced to 490?nM from 17.54?µM with nanomaterial graphene oxide. Altogether, this study presents anti-plasmodial potential of benzoxazine derivatives of phytophenols and establishes disruption of parasite sodium homeostasis as their mechanism of action.