Bharathidasan University

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.

Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.

The copper(II) complex [Cu(tdp)(ClO4)].0.5H2O (1), where H(tdp) is the tetradentate ligand 2-[(2-(2-hydroxyethylamino)ethylimino)methyl]phenol, and the mixed ligand complexes [Cu(tdp)(diimine)]+ (2-5), where diimine is 2,2'-bipyridine (bpy) (2), 1,10-phenanthroline (phen) (3), 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) (4), and dipyrido-[3,2-d:2',3'-f]-quinoxaline (dpq) (5), have been isolated and characterized by analytical and spectral methods. Complexes 1 and [Cu(tdp)(phen)]ClO4 (3) have been structurally characterized, and their coordination geometries around copper(II) are described as distorted octahedral. The equatorially coordinated ethanolic oxygen in 1 is displaced to an axial position upon incorporating the strongly chelating phen, as in 3. The solution structures of all the complexes have been assessed to be square-based using electronic absorption and electron paramagnetic resonance (EPR) spectroscopy. The interaction of the complexes with calf thymus DNA (CT DNA) has been explored by using absorption, emission, and circular dichroic spectral and viscometric studies, and modes of DNA binding for the complexes have been proposed. Absorption spectral (Kb = 0.071 +/- 0.005 (2), 0.90 +/- 0.03 (3), 7.0 +/- 0.2 (4), 9.0 +/- 0.1 x 10(5) M(-1) (5)), emission spectral (Kapp = 4.6 (1), 7.8 (2), 10.0 (3), 12.5 (4), 25.0 x 10(5) M(-1) (5)), and viscosity measurements reveal that 5 interacts with DNA more strongly than the other complexes through partial intercalation of the extended planar ring of the coordinated dpq with the DNA base stack. Interestingly, only complex 4 causes a B to A conformational change upon binding DNA. All the complexes hydrolytically cleave pBR322 supercoiled DNA in 10% DMF/5 mM Tris-HCl/50 mM NaCl buffer at pH 7.1 in the absence of an activating agent, and the cleavage efficiency varies in the order 5 > 3 > 2 > 4 > 1 with 5 displaying the highest Kcat value (5.47 +/- 0.10 h(-1)). The same order of cleavage is observed for the oxidative cleavage of DNA in the presence of ascorbic acid as a reducing agent. Interestingly, of all the complexes, only 5 displays efficient photonuclease activity through double-strand DNA breaks upon irradiation with 365 nm light through a mechanistic pathway involving hydroxyl radicals. The protein binding ability of 1-5 has been also monitored by using the plasma protein bovine serum albumin (BSA), and 4 exhibits a protein binding higher than that of the other complexes. Further, the anticancer activity of the complexes on human cervical epidermoid carcinoma cell line (ME180) has been examined. Interestingly, the observed IC50 values reveal that complex 4, which effects conformational change on DNA and binds to BSA more strongly, exhibits a cytotoxicity higher than the other complexes. It also exhibits approximately 100 and 6 times more potency than cisplatin and mitomycin C for 24 and 48 h incubation times, respectively, suggesting that 4 can be explored further as a potential anticancer drug. Complexes 4 and 5 mediate the arrest of S and G2/M phases in the cell cycle progression at 24 h harvesting time, which progress into apoptosis.

Duffing oscillator - bifurcation and chaos, analytic approaches chaotic dynamics of Bonhoeffer-Van der Pol (BVP) and Duffing-Van der POL (DVP) oscillators chaotic oscillators with Chua's diode controlling of chaos synchronization and secure communications.

Nanomedicine utilizes biocompatible nanomaterials for diagnostic and therapeutic purposes. The present study reports the use of Helicteres isora root extract for the synthesis of silver nanoparticles (AgNPs). The synthesized AgNPs were initially noticed through visual color change from yellow to reddish brown and further confirmed by surface plasmonic resonance (SPR) band at 450 nm using UV–visible spectroscopy. Morphology and size of AgNPs were determined by transmission electron microscopy (TEM) analysis. X-ray diffraction (XRD) study revealed crystalline nature of AgNPs. The prolonged stability of AgNPs was due to capping of oxidized polyphenols and carboxyl protein which was established by Fourier transform infrared spectroscopy (FTIR) study. In addition, the synthesized AgNPs were tested for antioxidant and antibacterial activities. It showed good antioxidant activity as compared to butylated hydroxytoluene (BHT) and ascorbic acid as standard antioxidant. It could be concluded that H. isora root extract can be used efficiently in the production of potential antioxidant and antibacterial AgNPs for commercial application.

Nanoparticles are of great importance in development and research because of their application in industries and biomedicine. The development of nanoparticles requires proper knowledge of their fabrication, interaction, release, distribution, target, compatibility, and functions. This review presents a comprehensive update on nanoparticles' toxic effects, the factors underlying their toxicity, and the mechanisms by which toxicity is induced. Recent studies have found that nanoparticles may cause serious health effects when exposed to the body through ingestion, inhalation, and skin contact without caution. The extent to which toxicity is induced depends on some properties, including the nature and size of the nanoparticle, the surface area, shape, aspect ratio, surface coating, crystallinity, dissolution, and agglomeration. In all, the general mechanisms by which it causes toxicity lie on its capability to initiate the formation of reactive species, cytotoxicity, genotoxicity, and neurotoxicity, among others.

Abstract In order to demarcate the ground water potential zones of Marudaiyar basin different thematic maps such as, lithology, landforms, lineaments and surface water bodies at a 1: 50000 scale were prepared, using remotely-sensed data as well as drainage density and slope classes from Survey of India topographical sheets. In addition, a soil map at 1:50000 scale covering the study area was generated from a 1:250000 scale soil map prepared by the Soil Survey and Landuse Organization by regrouping the soil types based on their hydrological characteristics. All the thematic layers were integrated and analysed using a model developed with logical conditions in the geographical information system (GIS). The ground water potential zones map generated through this model was verified with the yield data to ascertain the validity of the model developed. The verification showed that the ground water potential zones demarcated through the model are in agreement with the bore well yield data collected in the field. Since the present approach was built with logical conditions and reasoning, this approach can be successfully used elsewhere with appropriate modifications. Thus, the above study has clearly demonstrated the capabilities of remote sensing technique and GIS in demarcation of the different ground water potential zones, particularly in such a diverse geological set up.

The interaction of copper(II/I) complexes of a few 2,9-dimethyl-1,10-phenanthrolines with calf thymus DNA has been investigated using absorption and circular dichroic spectral and electrochemical techniques and viscometry. The observation of the usual hypochromism and the novel hyperchromism in the absorption spectra of [CuI(bcp)2]+ [bcp = 2,9-dimethyl-4,7-diphenyl-1,10- phenanthroline] and [CuI(dpsmp)2]3- [dpsmp2- = 2,9-dimethyl-4,7-bis(sulfonatophenyl)-1,10-phenanthroline] respectively in the presence of DNA and the increase in viscosity of DNA at low loadings of both these complexes have been interpreted in terms of bridging of a pair of DNA duplexes by the complex species. These tetrahedral copper(I) complexes, which lack minor groove binding because of substituents at the 4- and 7-positions of phen ring, are efficient in bridging the duplexes. The electrochemical behaviors of [CuI(dmp)2]+ [dmp = 2,9-dimethyl-1,10-phenanthroline] and [CuI(bcp)2]+ bound to DNA have been compared with that of the analogous sulfonated complex [Cu(dpsmp)2]2-/3-. The DNA binding constants determined reveal that dpsmp2- complex is engaged in DNA binding less intimately than the bcp complex. While Coulombic interactions are clearly more important than other types of interactions for the former, nonclassical hydrophobic interactions for the latter. The Hill analysis of the absorbance data obtained as a function of added DNA reveals Hill coefficients greater than unity, which may be construed as evidence for cooperative binding of the copper complexes to B-DNA.

Pure ZnO and Neodymium (Nd) doped ZnO nanoparticles (NPs) were synthesized by the co-precipitation method. The synthesized nanoparticles retained the wurtzite hexagonal structure. From FESEM studies, ZnO and Nd doped ZnO NPs showed nanorod and nanoflower like morphology respectively. The FT-IR spectra confirmed the Zn-O stretching bands at 422 and 451 cm(-1) for ZnO and Nd doped ZnO NPs respectively. From the UV-VIS spectroscopic measurement, the excitonic peaks were found around 373 nm and 380 nm for the respective samples. The photoluminescence measurements revealed that the broad emission was composed of ten different bands due to zinc vacancies, oxygen vacancies and surface defects. The antibacterial studies performed against extended spectrum β-lactamases (ESBLs) producing strains of Escherichia coli and Klebsiella pneumoniae showed that the Nd doped ZnO NPs possessed a greater antibacterial effect than the pure ZnO NPs. From confocal laser scanning microscopic (CLSM) analysis, the apoptotic nature of the cells was confirmed by the cell shrinkage, disorganization of cell wall and cell membrane and dead cell of the bacteria. SEM analysis revealed the existence of bacterial loss of viability due to an impairment of cell membrane integrity, which was highly consistent with the damage of cell walls.

Merkel cell carcinoma (MCC) is a rare but highly aggressive cutaneous neuroendocrine tumor. Merkel cell polyomavirus (MCPyV) may contribute to tumorigenesis in a subset of tumors via inhibition of tumor suppressors such as retinoblastoma (RB1) by mutated viral T antigens, but the molecular pathogenesis of MCPyV-negative MCC is largely unexplored. Through our MI-ONCOSEQ precision oncology study, we performed integrative sequencing on two cases of MCPyV-negative MCC, as well as a validation cohort of 14 additional MCC cases (n = 16). In addition to previously identified mutations in TP53, RB1, and PIK3CA, we discovered activating mutations of oncogenes, including HRAS and loss-of-function mutations in PRUNE2 and NOTCH family genes in MCPyV-negative MCC. MCPyV-negative tumors also displayed high overall mutation burden (10.09 ± 2.32 mutations/Mb) and were characterized by a prominent UV-signature pattern with C > T transitions comprising 85% of mutations. In contrast, mutation burden was low in MCPyV-positive tumors (0.40 ± 0.09 mutations/Mb) and lacked a UV signature. These findings suggest a potential ontologic dichotomy in MCC, characterized by either viral-dependent or UV-dependent tumorigenic pathways.

By constructing the general six-parameter bright two-soliton solution of the integrable coupled nonlinear Schr\"odinger equation (Manakov model) using the Hirota method, we find that the solitons exhibit certain novel inelastic collision properties, which have not been observed in any other $(1+1)$-dimensional soliton system so far. In particular, we identify the exciting possibility of switching solitons between modes by changing the phase. However, the standard elastic collision property of solitons is regained with specific choices of parameters.

We present the exact bright one-soliton and two-soliton solutions of the integrable three coupled nonlinear Schrödinger equations (3-CNLS) by using the Hirota method, and then obtain them for the general N-coupled nonlinear Schrödinger equations ( N-CNLS). It is pointed out that the underlying solitons undergo inelastic (shape changing) collisions due to intensity redistribution among the modes. We also analyze the various possibilities and conditions for such collisions to occur. Further, we report the significant fact that the various partially coherent solitons discussed in the literature are special cases of the higher order bright soliton solutions of the N-CNLS equations.

Green synthesis of nanoparticles using seaweeds are fascinating high research attention nowadays and also gaining center of attention in biomedical applications. In this work, we have synthesized biocompatible and functionalized silver nanoparticles using an aqueous extract of seaweed Enteromorpha compressa as a reducing as well as stabilizing agent and their efficient antimicrobial and anticancer activity are reported here. The UV–vis spectra of AgNPs showed the characteristics SPR absorption band at 421 nm. The chemical interaction and crystalline nature of the AgNPs were evaluated by FT-IR and XRD studies. The XRD result of AgNPs shows typical Ag reflection peaks at 38.1°, 44.2°, 64.4° and 77.1° corresponding to (111), (200), (220) and (311) Bragg’s planes. The surface morphology and composition of the samples were observed by HRTEM, EDS and SAED pattern analyses. Spherical shaped Ag nano structures were observed in the size ranges between 4 and 24 nm with clear lattice fringes in the HRTEM image. This report reveals that seaweed mediated synthesis of AgNPs and sustained delivery of Ag ions to the bacterial and fungal surface have been reducing their growth rate which was evaluated by well diffusion assay. The synthesized AgNPs showed favorable cytotoxicity against Ehlrich Ascites Carcinoma (EAC) cells with IC50 value was recorded at 95.35 μg mL−1. This study showed cost effective silver nanoparticles synthesis with excellent biocompatibility and thus could potentially be utilized in biomedical and pharmaceutical applications.

The Landau-Lifshitz-Gilbert (LLG) equation is a fascinating nonlinear evolution equation both from mathematical and physical points of view. It is related to the dynamics of several important physical systems such as ferromagnets, vortex filaments, moving space curves, etc. and has intimate connections with many of the well-known integrable soliton equations, including nonlinear Schrödinger and sine-Gordon equations. It can admit very many dynamical structures including spin waves, elliptic function waves, solitons, dromions, vortices, spatio-temporal patterns, chaos, etc. depending on the physical and spin dimensions and the nature of interactions. An exciting recent development is that the spin torque effect in nanoferromagnets is described by a generalization of the LLG equation that forms a basic dynamical equation in the field of spintronics. This article will briefly review these developments as a tribute to Robin Bullough who was a great admirer of the LLG equation.

Cannonball ( Couroupita guianensis ) is a tree belonging to the family Lecythidaceae. Various parts of the tree have been reported to contain oils, keto steroids, glycosides, couroupitine, indirubin, isatin, and phenolic substances. We report here the synthesis of silver nanoparticles (AgNPs) using cannonball leaves. Green synthesized nanoparticles have been characterized by UV-Vis spectroscopy, SEM, TEM, and FTIR. Cannonball leaf broth as a reducing agent converts silver ions to AgNPs in a rapid and ecofriendly manner. The UV-Vis spectra gave surface plasmon resonance peak at 434 nm. TEM image shows well-dispersed silver nanoparticles with an average particle size of 28.4 nm. FTIR showed the structure and respective bands of the synthesized nanoparticles and the stretch of bonds. Green synthesized silver nanoparticles by cannonball leaf extract show cytotoxicity to human breast cancer cell line (MCF-7). Overall, this environmentally friendly method of biological silver nanoparticles production provides rates of synthesis faster than or comparable to those of chemical methods and can potentially be used in various human contacting areas such as cosmetics, foods, and medical applications.

Abstract Optical absorption of tris thiourea zinc sulphate (ZTS) single crystals has been measured and its direct band gap was found to be 3.6 eV. Theoretical calculations were carried out to determine the linear optical constants such as extinction coefficient and refractive index. Further the optical nonlinearties of ZTS have been investigated by Z‐scan technique with He‐Ne laser at 632.8 nm. The nonlinear refractive index, absorption coefficient and third order susceptibility is found to be in the order of –5.36 ± 0.26 × 10 –12 cm 2 /W, 4.24 ± 0.21 × 10 –4 cm/W, 3.5 ± 0.17 × 10 –4 esu respectively. Thus optical characterization of ZTS reveals the various industrial application oriented properties of the material. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Indium tin oxide (ITO) thin films have been prepared by jet nebulizer spray pyrolysis technique for different Sn concentrations on glass substrates. X-ray diffraction patterns reveal that all the films are polycrystalline of cubic structure with preferentially oriented along (222) plane. SEM images show that films exhibit uniform surface morphology with well-defined spherical particles. The EDX spectrum confirms the presence of In, Sn and O elements in prepared films. AFM result indicates that the surface roughness of the films is reduced as Sn doping. The optical transmittance of ITO thin films is improved from 77% to 87% in visible region and optical band gap is increased from 3.59 to 4.07 eV. Photoluminescence spectra show mainly three emissions peaks (UV, blue and green) and a shift observed in UV emission peak. The presence of functional groups and chemical bonding was analyzed by FTIR. Hall effect measurements show prepared films having n-type conductivity with low resistivity (3.9 × 10−4 Ω-cm) and high carrier concentrations (6.1 × 1020 cm−3).

AIMS: Assessment of high-density polyethylene (HDPE)-degrading bacteria isolated from plastic waste dumpsites of Gulf of Mannar. METHODS AND RESULTS: Rationally, 15 bacteria (GMB1-GMB15) were isolated by enrichment technique. GMB5 and GMB7 were selected for further studies based on their efficiency to degrade the HDPE and identified as Arthrobacter sp. and Pseudomonas sp., respectively. Assessed weight loss of HDPE after 30 days of incubation was nearly 12% for Arthrobacter sp. and 15% for Pseudomonas sp. The bacterial adhesion to hydrocarbon (BATH) assay showed that the cell surface hydrophobicity of Pseudomonas sp. was higher than Arthrobacter sp. Both fluorescein diacetate hydrolysis and protein content of the biofilm were used to test the viability and protein density of the biomass. Acute peak elevation was observed between 2 and 5 days of inoculation for both bacteria. Fourier transform infrared (FT-IR) spectrum showed that keto carbonyl bond index (KCBI), Ester carbonyl bond index (ECBI) and Vinyl bond index (VBI) were increased indicating changes in functional group(s) and/or side chain modification confirming the biodegradation. CONCLUSION: The results pose us to suggest that both Pseudomonas sp. and Arthrobacter sp. were proven efficient to degrade HDPE, albeit the former was more efficacious, yet the ability of latter cannot be neglected. SIGNIFICANCE AND IMPACT OF THE STUDY: Recent alarm on ecological threats to marine system is dumping plastic waste in the marine ecosystem and coastal arena by anthropogenic activity. In maintenance phase of the plastic-derived polyethylene waste, the microbial degradation plays a major role; the information accomplished in this work will be the initiating point for the degradation of polyethylene by indigenous bacterial population in the marine ecosystem and provides a novel eco-friendly solution in eco-management.

Journal Scalable Computing: Practice and Experience. In this special issue on

Generally, silver is considered as a noble metal used for treating burn wound infections, open wounds and cuts. However, the emerging nanotechnology has made a remarkable impact by converting metallic silver into silver nanoparticles (AgNPs) for better applications. The advancement in technology has improved the synthesis of NPs using biological method instead of physical and chemical methods. Nonetheless, synthesizing AgNPs using biological sources is ecofriendly and cost effective. Till date, AgNPs are widely used as antibacterial agents; therefore, a novel idea is needed for the successful use of AgNPs as therapeutic agents to uncertain diseases and infections. In biomedicine, AgNPs possess significant advantages due to their physical and chemical versatility. Indeed, the toxicity concerns regarding AgNPs have created the need for non-toxic and ecofriendly approaches to produce AgNPs. The applications of AgNPs in nanogels, nanosolutions, silver based dressings and coating over medical devices are under progress. Still, an improvised version of AgNPs for extended applications in an ecofriendly manner is the need of the hour. Therefore, the present review emphasizes the synthesis methods, modes of action under dissipative conditions and the various biomedical applications of AgNPs in detail.