<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

Shiv Nadar University

(SoNS) School of Natural Sciences

A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2-6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators. © 2011 Indian Academy of Sciences.

World University root node

Life Sciences

Journal of Genetics

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

Marker assisted backcross breeding (MABB) provides a great opportunity for precise transfer of desirable donor segment by minimizing the linkage drag into a recurrent parent. In our lab, MABB was used for incorporating bacterial blight (BB) resistance genes (xa13 and Xa21) into the genetic background of Pusa Basmati1, which led to development of Improved Pusa Basmati 1 (Pusa 1460) as one of the first products of molecular breeding. Further, the parental lines of superfine grain aromatic rice hybrid Pusa RH 10 namely, Pusa 6A, Pusa 6B and PRR78 were improved for resistance to BB and blast by transferring genes xa13+Xa21 and Pi54 +Piz5, respectively. Presently, the pyramiding of genes for resistance to BB (xa13 and Xa21), blast (Piz5 and Pi54) and brown plant hopper (BPH; Bph 3, Bph 17, Bph 18, Bph20 and Bph 21) into Basmati rice varieties viz., Pusa Basmati 1121 and Pusa Basmati 6 is under way. In addition, a major QTL for salt tolerance (Saltol) is being transferred to Pusa Basmati 1121, which is widely grown in Haryana, the state having problem of salinity owing to underground brackish water. In order to develop genetically enhanced donor sources for resistance to biotic (BB, blast and BPH) and abiotic (salt tolerance, and phosphorus uptake) stresses in Basmati background, isogenic lines are being developed for major resistance genes/QTLs for respective stresses in the background of Pusa Basmati 1. Molecular mapping of fertility restorer gene(s) in Basmati restorer line PRR78 led to identification of two Rf gene linked molecular markers, RM258 and RM6100. Of these, RM6100 on validation in a set of rice germplasm showed 97.4% efficacy in identifying restorer lines from germplasm.QTL mapping using RIL population has unveiled several novel QTLs for grain and cooking quality traits. Molecular markers are also being routinely used for establishing variety/hybrids identity and authentication of genetic purity of hybrid seed lots.

Indian Journal of Genetics and Plant Breeding

Marker assisted selection: A paradigm shift in Basmati breeding

Background &amp; Aims: Hepatitis C virus (HCV) infection is characterized by lack of immune-mediated liver injury despite a high level of HCV replication during the incubation phase, which lasts about 8 weeks. We investigated whether this results from delayed recruitment of HCV-specific T cells and whether it facilitates HCV persistence. Methods: Six chimpanzees were infected with HCV; blood and liver samples were collected for 28 weeks and analyzed for immune cells and chemokines. Results: Two chimpanzees developed self-limited infections, whereas the remaining 4 developed chronic infections. Levels of the chemokines CXCL10, CXCL11, CCL4, and CCL5 increased in blood and liver samples from all chimpanzees within 1 month of HCV infection. Chemokine induction correlated with intrahepatic type I interferon (IFN) responses in vivo and was blocked by neutralizing antibodies against IFN-β in vitro. Despite the early-stage induction of chemokines, the intrahepatic lymphocytic infiltrate started to increase no earlier than 8 weeks after HCV infection, when HCV-specific, tetramer-positive CD8+ T cells appeared in the circulation. The HCV-specific CD8+ T cells expressed chemokine receptors when they were initially detected in blood samples, so they could be recruited to the liver as soon as they entered the circulation. Conclusions: Chemokines are induced during early stages of HCV infection, which requires a type I IFNmediated response. The delayed onset of acute hepatitis does not result from delayed recruitment of HCV-specific T cells, but could instead be related to a primary delay in the induction of HCV-specific T cells. Divergent outcomes occur without evident differences in chemokine induction and T-cell recruitment. © 2011 AGA Institute.

Fulltext

Gastroenterology

Delayed induction, not impaired recruitment, of specific CD8+ T cells causes the late onset of acute hepatitis C

Background & Aims: Several studies have reported hepatitis C virus (HCV) RNA sequences in the circulation after treatment-induced or spontaneous recovery. We investigated whether the HCV RNA represents persistence of HCV infection or reinfection. Methods: We studied 117 patients who recovered from HCV infection (98 following therapy and 19 spontaneously). A reverse-transcription polymerase chain reaction assay was used to detect the 5′-untranslated region of HCV. T-cell responses were studied by enzyme-linked immunospot for interferon-γ. Results: Plasma samples from 15% of treatment-recovered patients and no spontaneously recovered patient tested positive for HCV RNA. Lymphocytes from 3 patients who responded to therapy and 1 who recovered spontaneously tested positive. The frequency of HCV RNA detection in plasma correlated inversely with the time after the end of treatment. Post-treatment HCV 5′-untranslated region sequences matched pretreatment sequences in 85% of cases. T-cell responses were significantly greater at time points with detectable trace amounts of HCV RNA than at time points without detectable HCV RNA (P = .035) and were primarily against nonstructural HCV antigens. The immune hierarchy was preserved over 5 years in patients whose post-treatment HCV RNA sequences matched pretreatment sequences, indicating HCV RNA persistence. An altered immune hierarchy with dominant immune responses, shifting from nonstructural to structural antigens, was observed in a single patient whose post-treatment HCV genotype differed from that of the pretreatment genotype, indicating HCV reinfection. Conclusions: Trace amounts of HCV RNA of pretreatment sequence persisted and reappeared sporadically in the circulation within 8 years after recovery from hepatitis C but not thereafter, indicating that patients are cured of HCV infection. Reappearance of HCV RNA induced HCV-specific T-cell responses. © 2011 AGA Institute.

Sporadic reappearance of minute amounts of hepatitis C virus RNA after successful therapy stimulates cellular immune responses

Purpose: Phosphatase and tensin homolog (PTEN) loss or activating mutations of phosphoinositol-3 (PI3) kinase (PIK3CA) may be associated with trastuzumab resistance. Trastuzumab, the humanized human epidermal growth factor receptor 2 (HER2) monoclonal antibody, and lapatinib, an epidermal growth factor receptor/HER2 tyrosine kinase inhibitor, are both established treatments for HER2-overexpressing breast cancers. Understanding of the cellular response to HER2-targeted therapies is needed to tailor treatments and to identify patients less likely to benefit. Methods: We evaluated the effect of trastuzumab or lapatinib in three HER2-overexpressing cell lines. We confirmed the in vitro observations in two neoadjuvant clinical trials in patients with HER2 overexpression; 35 patients received trastuzumab as a single agent for the first 3 weeks, then docetaxel every 3 weeks for 12 weeks (trastuzumab regimen), whereas 49 patients received lapatinib as a single agent for 6 weeks, followed by trastuzumab/docetaxel for 12 weeks before primary surgery (lapatinib regimen). Apoptosis, Ki67, p-MAPK, p-AKT, and PTEN were assessed by immunohistochemistry. Genomic DNA was sequenced for PIK3CA mutations. Results: Under low PTEN conditions, in vitro data indicate that lapatinib alone and in combination with trastuzumab was effective in decreasing p-MAPK and p-AKT levels, whereas trastuzumab was ineffective. In the clinical trials, we confirmed that low PTEN or activating mutation in PIK3CA conferred resistance to the trastuzumab regimen (P = .015), whereas low PTEN tumors were associated with a high pathologic complete response rate (P = .007). Conclusion: Activation of PI3 kinase pathway is associated with trastuzumab resistance, whereas low PTEN predicted for response to lapatinib. These observations support clinical trials with the combination of both agents. © 2010 by American Society of Clinical Oncology.

Journal of Clinical Oncology

Loss of phosphatase and tensin homolog or phosphoinositol-3 kinase activation and response to trastuzumab or lapatinib in human epidermal growth factor receptor 2 - Overexpressing locally advanced breast cancers

The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade. {\textcopyright} 2011 Informa Healthcare USA, Inc.

Critical Reviews in Biotechnology

Peptidoglycan biosynthesis machinery: A rich source of drug targets

The electroluminescence (EL) of Er-implanted SiO2 layers containing Ge nanocrystals (NCs) was investigated and correlated with microstructural results obtained by transmission electron microscopy, Raman spectroscopy and X-ray diffraction. In case of EL, and in contrast to the behaviour of Er-doped Si-rich SiO2 known from the literature it appears that there is an inverse energy transfer from Er to Ge-related oxygen deficiency centres which are located at the surface of the Ge NCs or in the transition region between the NC and the SiO2 matrix. This is indicated by the increase of the blue-violet, Ge-related EL in presence of Er, although the Ge-related photoluminescence, which was excited by UV wavelengths non-resonant to Er, decreases at the same time. The microstructural results reveal that the maximum increase of the Ge-related EL occurs when the Ge NCs are not amorphized and/or fragmented by the Er implantation but surrounded by an Er shell. Finally a qualitative model is given explaining the different behaviour of Er-implanted SiO2 containing Ge NCs compared to the case of Si NCs by the different quality of the NC interface to the SiO2 matrix. © 2010 Elsevier B.V. All rights reserved.

Physics

Optical Materials

The inverse energy transfer between Ge nanocrystals and erbium in SiO 2 and its dependence on microstructure

In insect ecosystem, the dynamics of prey and predator is regulated by complex interactions between them. Insect pests are spatially aggregated in patches forming a spatial pattern in the environment. An efficient predator dynamically changes its strategies and time for its random search movements to concentrate on higher resource patches based on the benefit of assessment. This food-gathering activity of both prey and predator plays a major role in stabilizing the system by influencing the per unit food consumption. Extending Holling time-budget argument by migration, here we formulate a two patch prey-predator model and show that how several foraging parameters such as handling time, dispersal rate can have important consequences in stability of prey-predator system. Specifically, the ratio between timings that a predator remains mobile in searching and handling their food, is the most important one and simulation on this suggests that the stabilizing effect continues to operate when the dispersal process is modeled more realistically. Thus we conclude that the migration submodel is an important constituent of a spatial predator-prey system. These results are shown to have important implications for possible biological control. © 2010 Korean Society for Computational and Applied Mathematics.

Mathematics

Journal of Applied Mathematics and Computing

A two-patch prey-predator model with food-gathering activity

We report on the electric-field-induced reversible metal-insulator transition (MIT) of the insulating LaAlO3 thin films observed in metal/LaAlO3/Nb-SrTiO3 heterostructures. The switching voltage depends strongly on the thickness of the LaAlO3 thin film which indicates that a minimum thickness is required for the MIT. A constant opposing voltage is required to deplete the charges from the defect states. Our experimental results exclude the possibility of diffusion of the metal electrodes or oxygen vacancies into the LaAlO3 layer. Instead, the phenomenon is attributed to the formation of a quasi-conduction band (QCB) in the defect states of LaAlO3 that forms a continuum state with the conduction band of the Nb-SrTiO3. Once this continuum (metallic) state is formed, the state remains stable even when the voltage bias is turned off. The thickness dependent reverse switch-on voltage and the constant forward switch-off voltage are consistent with our model. The viewpoint proposed here can provide an alternative mechanism for resistive switching in complex oxides. © 2011 American Physical Society.

Physical Review B - Condensed Matter and Materials Physics

Reversible metal-insulator transition in LaAlO3 thin films mediated by intragap defects: An alternative mechanism for resistive switching

Magnetoresistance (MR) anisotropy in LaAlO3/SrTiO3 interfaces is compared between samples prepared in high-oxygen partial-pressure (PO2) of 10-4 mbar exhibiting quasi-two-dimensional (quasi-2D) electron gas and low PO2 of 10-6 mbar exhibiting 3D conductivity. While the 3D interfaces show positive MR for all temperatures, the quasi-2D interfaces show negative MR below 30 K, suggesting the presence of magnetic centers in the quasi-2D system. Interestingly, a linear relation between MR and applied magnetic fields was observed in the 3D interfaces for an in-plane field, while in the quasi-2D interfaces for an out-of-plane field, demonstrating the dominant effect of the interface and substrate's vicinal step scattering, respectively. Furthermore, the MR with the out-of-plane field is always larger compared to the MR with in-plane field, suggesting lower dissipation of electrons from interface than defect scattering. Our study demonstrates that MR can be used to distinguish the dimensionality of the charge transport and various (defect, magnetic center, and interface boundary) scattering processes in this system. © 2011 American Physical Society.

Magnetoresistance of two-dimensional and three-dimensional electron gas in LaAlO3/SrTiO3 heterostructures: Influence of magnetic ordering, interface scattering, and dimensionality