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Shiv Nadar University

(SoNS) School of Natural Sciences

Background: MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30\% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function. We have analyzed expression profile of &gt;1000 human miRNAs in &gt;1400 samples representing seven different human tissue types obtained from cancer patients along with matched and unmatched controls.Results: We found 68\% of the miRNAs in this cluster to be significantly downregulated in glioblastoma multiforme (GBM), 61\% downregulated in kidney renal clear cell carcinoma (KIRC), 46\% in breast invasive carcinoma (BRCA) and 14\% in ovarian serous cystadenocarcinoma (OV). On a genome-wide scale C14 miRNAs accounted for 12-30\% of the total downregulated miRNAs in different cancers. Pathway enrichment for the predicted targets of C14 miRNA was significant for cancer pathways, especially Glioma (p&lt; 3.77x10-6, FDR&lt;0.005). The observed downregulation was confirmed in GBM patients by real-time PCR, where 79\% of C14 miRNAs (34/43) showed downregulation. In GBM samples, hypermethylation at C14 locus (p&lt;0.003) and downregulation of MEF2, a crucial transcription factor for the cluster was observed which likely contribute to the observed downregulation of the entire miRNA cluster.Conclusion: We provide compelling evidence that the entire C14 miRNA cluster is a tumor suppressor locus involved in multiple cancers, especially in GBM, and points toward a general mechanism of coordinated function for clustered miRNAs.Reviewers: Reviewed by: Prof. Gregory J Goodall and Dr. Alexander Max Burroughs. © 2013 Laddha et al.; licensee BioMed Central Ltd.

World University root node

Mathematics

Fulltext

Biology Direct

Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers

We study the role of predation dynamics in oscillation of pest population in insect ecology. A two-dimensional pest control model (under the use of insecticides) with time delay in predation is considered in this paper. By the Hopf bifurcation theory, we prove the existence of the stable oscillation of the system. We also consider the economic viability of the control process. First we improve the Pontryagin maximum principle (PMP) where the delay in the system is sufficiently small and control function is linear, and then we apply the improved version of PMP to perform the optimal analysis of the pest control model as a special case. © 2013 Samit Bhattacharyya and Suma Ghosh.

International Journal of Mathematics and Mathematical Sciences

Oscillation in pest population and its management: A mathematical study

Summary Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27 571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Life Sciences

Plant Journal

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

Facile synthesis of ultrasmall gold nanoclusters of size <2 nm dispersible in water using a novel quaternary ammonium ligand is reported. Further, arrays of these nanoclusters are encapsulated in monodisperse silica nanospheres of size 25-30 nm. The photophysical characteristics of the clusters are found to be intact upon encapsulation, rendering the resulting composite material ideal for fluorescence imaging applications. We have further shown the utilization of these materials in catalysis as precursors for Au nanoparticles encapsulated in porous silica. © 2011 American Chemical Society.

Chemistry

Journal of Physical Chemistry C

Ultrasmall gold cluster arrays encapsulated in silica nanospheres: Applications in fluorescence imaging and catalysis

The interface between the polar LaAlO 3 and nonpolar SrTiO 3 layers has been shown to exhibit various electronic and magnetic phases such as two-dimensional electron gas (2DEG), superconductivity, magnetism, and electronic phase separation. These rich phases are expected due to the strong interplay between charge, spin, and orbital degree of freedom at the interface between these complex oxides, leading to the electronic reconstruction in this system. However, until now all of these new properties have been studied extensively based on the interfaces which involve a polar LaAlO 3 layer. To investigate the role of the ABO 3 polar layer, here we study various combinations of polar/nonpolar oxide (NdAlO 3/SrTiO 3, PrAlO 3/SrTiO 3, and NdGaO 3/SrTiO 3) interfaces which are similar in nature to the LaAlO 3/SrTiO 3 interface. Our results show that all of these new interfaces can also produce 2DEG at their interfaces, supporting the idea that the electronic reconstruction could be the driving mechanism for the creation of the 2DEG at these oxide interfaces. Furthermore, the electrical properties of these interfaces are shown to be governed by the interface strain and the type of cations in the polar overlayers. Our observations may provide an approach to further tune the properties of the 2DEG at the selected polar/nonpolar oxide interfaces. © 2012 American Physical Society.

Physics

Physical Review B - Condensed Matter and Materials Physics

Electronic correlation and strain effects at the interfaces between polar and nonpolar complex oxides

Solution processable diketopyrrolopyrrole (DPP)-bithiophene polymers (PDBT) with long branched alkyl side chains on the DPP unit are synthesized. These polymers have favourable highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels for the injection and transport of both holes and electrons. Organic thin film transistors (OTFTs) using these polymers as semiconductors and gold as source/drain electrodes show typical ambipolar characteristics with very well balanced high hole and electron mobilities (μh = 0.024 cm2 V-1 s -1 and μe = 0.056 cm2 V-1 s -1). These simple and high-performing polymers are promising materials for ambipolar organic thin film transistors for low-cost CMOS-like logic circuits. © 2012 Elsevier B.V. All rights reserved.

Organic Electronics

Solution processable poly(2,5-dialkyl-2,5-dihydro-3,6-di-2-thienyl- pyrrolo[3,4-c]pyrrole-1,4-dione) for ambipolar organic thin film transistors

Immunization programs have often been impeded by vaccine scares, as evidenced by the measles-mumps-rubella (MMR) autism vaccine scare in Britain. A "free rider" effect may be partly responsible: vaccine-generated herd immunity can reduce disease incidence to such low levels that real or imagined vaccine risks appear large in comparison, causing individuals to cease vaccinating. This implies a feedback loop between disease prevalence and strategic individual vaccinating behavior. Here, we analyze a model based on evolutionary game theory that captures this feedback in the context of vaccine scares, and that also includes social learning. Vaccine risk perception evolves over time according to an exogenously imposed curve. We test the model against vaccine coverage data and disease incidence data from two vaccine scares in England & Wales: the whole cell pertussis vaccine scare and the MMR vaccine scare. The model fits vaccine coverage data from both vaccine scares relatively well. Moreover, the model can explain the vaccine coverage data more parsimoniously than most competing models without social learning and/or feedback (hence, adding social learning and feedback to a vaccine scare model improves model fit with little or no parsimony penalty). Under some circumstances, the model can predict future vaccine coverage and disease incidence-up to 10 years in advance in the case of pertussis-including specific qualitative features of the dynamics, such as future incidence peaks and undulations in vaccine coverage due to the population's response to changing disease incidence. Vaccine scares could become more common as eradication goals are approached for more vaccine-preventable diseases. Such models could help us predict how vaccine scares might unfold and assist mitigation efforts. © 2012 Bauch, Bhattacharyya.

PLoS Computational Biology

Evolutionary game theory and social learning can determine how vaccine scares unfold

We report room-temperature ferromagnetism (FM) in highly conducting, transparent anatase Ti1-xTaxO2 (x ∼0.05) thin films grown by pulsed laser deposition on LaAlO3 substrates. Rutherford backscattering spectrometry (RBS), X-ray diffraction, protoninduced X-ray emission, X-ray absorption spectroscopy (XAS) and time-of-flight secondary-ion mass spectrometry indicated negligible magnetic contaminants in the films. The presence of FM with concomitant large carrier densities was determined by a combination of superconducting quantum interference device magnetometry, electrical transport measurements, soft X-ray magnetic circular dichroism (SXMCD), XAS and optical magnetic circular dichroism, and was supported by first-principles calculations. SXMCD and XAS measurements revealed a 90 per cent contribution to FM from the Ti ions, and a 10 per cent contribution from the O ions. RBS/channelling measurements show complete Ta substitution in the Ti sites, though carrier activation was only 50 per cent at 5 per cent Ta concentration, implying compensation by cationic defects. The role of the Ti vacancy (VTi) and Ti3+ was studied via XAS and X-ray photoemission spectroscopy, respectively. It was found that, in films with strong FM, the VTi signal was strong while the Ti3+ signal was absent. We propose (in the absence of any obvious exchange mechanisms) that the localized magnetic moments, VTi sites, are ferromagnetically ordered by itinerant carriers. Cationic-defect-induced magnetism is an alternative route to FM in wide-band-gap semiconducting oxides without any magnetic elements. © 2012 The Royal Society.

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Cationic-vacancy-induced room-temperature ferromagnetism in transparent, conducting anatase Ti1-xTaxO2 (x ∼0.05) thin films

The kinetics of the irreversible photoinduced switch in polarisation (p) observed in single crystals of a fullerene derivative possessing hydrogen-bonding barbiturate units were investigated using confocal fluorescence microscopy. In the samples investigated, it was found that the maximum luminescence polarisation (p = 0.78) is obtained for an orientation of ca. 60°from the long axis of the crystal. Upon irradiation at 385 nm, the maximum luminescence polarisation undergoes a rotation of ca. 70°with respect to the initial orientation and reaches a new value of p = 0.40. The results indicate that the process is not dependent on the orientation of the incident polarised excitation beam and that it is not accompanied by a noticeable change in the photophysical properties of the crystal. Based on these observations, a mechanism is proposed in which photoinduced dimerisation occurs from the lowest energy emissive excimer-like state that acts as a sink for the excitation energy. © 2012 the Owner Societies.

Physical Chemistry Chemical Physics

Effect of hydrogen-bonding on the excited-state reactivity of fullerene derivatives and its impact on the control of the emission polarisation from photopolic single crystals