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Shiv Nadar University

(SoNS) School of Natural Sciences

We consider four nontrivial ensembles involving Gaussian Wigner and Wishart matrices. These are relevant to problems ranging from multiantenna communication to random supergravity. We derive the matrix probability density, as well as the eigenvalue densities for these ensembles. In all cases the joint eigenvalue density exhibits a biorthogonal structure. A determinantal representation, based on a generalization of Andréief's integration formula, is used to compactly express the r-point correlation function of eigenvalues. This representation circumvents the complications encountered in the usual approaches, and the answer is obtained immediately by examining the joint density of eigenvalues. We validate our analytical results using Monte Carlo simulations. © 2015 American Physical Society.

Physics

Fulltext

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Random matrix ensembles involving Gaussian Wigner and Wishart matrices, and biorthogonal structure

Successful application of interfacial engineering for the preparation of cross-linked epoxy microspheres containing thermally polymerizable cardanol-based benzoxazine (Bz-C) monomer in the core is demonstrated. Bz-C is facilely synthesized by Mannich type condensation of cardanol (a by-product of cashew nut industry) and aniline with formaldehyde under solventless conditions. The encapsulation process relies on the preferential reaction of polydimethylsiloxane immiscible epoxy resin and amine-based hardener to form a cross-linked spherical shell at the interface. The microcapsule dimensions and core content could be tailored by modulating the operating parameters, particularly stirring speed and Bz-C: epoxy ratio. Spherical microcapsules with a core content of ∼37\% were obtained when the reaction was carried out at 600 rpm, while maintaining the reaction medium at 70°C with Bz-C: epoxy ratio of 2.3: 1. The simplicity and versatility of the present methodology are the forte of this technique, which widens the scope for large-scale application of benzoxazines in the field of temperature triggered healing. © 2015 Wiley Periodicals, Inc.

World University root node

Chemistry

Journal of Applied Polymer Science

Interfacial encapsulation of bio-based benzoxazines in epoxy shells for temperature triggered healing

Expression of synthetic proteins from intergenic regions of E. coli and their functional association was recently demonstrated (Dhar et al. in J Biol Eng 3:2, 2009. doi:10.1186/1754-1611-3-2). This gave birth to the question: if one can make ‘user-defined’ genes from non-coding genome—how big is the artificially translatable genome? (Dinger et al. in PLoS Comput Biol 4, 2008; Frith et al. in RNA Biol 3(1):40–48, 2006a; Frith et al. in PLoS Genet 2(4):e52, 2006b). To answer this question, we performed a bioinformatics study of all reported E. coli intergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500 E. coli intergenic sequences were computationally translated into ‘protein sequence equivalents’ and matched against all known proteins. Sequences that did not show any resemblance were used for building a comprehensive profile in terms of their structure, function, localization, interactions, stability so on. A total of 362 protein sequences showed evidence of stable tertiary conformations encoded by the intergenic sequences of E. coli genome. Experimental studies are underway to confirm some of the key predictions. This study points to a vast untapped repository of functional molecules lying undiscovered in the non-expressed genome of various organisms. © 2015, Springer Science+Business Media Dordrecht.

Life Sciences

Systems and Synthetic Biology

Predicting stable functional peptides from the intergenic space of E. coli

Metastasis is a major cause of mortality and remains a hurdle in the search for a cure for cancer. Not much is known about metastatic cancer cells and endothelial cross-talk, which occurs at multiple stages during metastasis. Here we report a dynamic regulation of the endothelium by cancer cells through the formation of nanoscale intercellular membrane bridges, which act as physical conduits for transfer of microRNAs. The communication between the tumour cell and the endothelium upregulates markers associated with pathological endothelium, which is reversed by pharmacological inhibition of these nanoscale conduits. These results lead us to define the notion of 'metastatic hijack': cancer cell-induced transformation of healthy endothelium into pathological endothelium via horizontal communication through the nanoscale conduits. Pharmacological perturbation of these nanoscale membrane bridges decreases metastatic foci in vivo. Targeting these nanoscale membrane bridges may potentially emerge as a new therapeutic opportunity in the management of metastatic cancer. © 2015 Macmillan Publishers Limited. All rights reserved.

Nature Communications

Physical nanoscale conduit-mediated communication between tumour cells and the endothelium modulates endothelial phenotype

The present climatic deterioration including the much debated anthropogenic acceleration to the global warming phenomenon has drawn the attention of scientific community, policy makers as well as the general public to the problem of climate change. Chemostratigraphic techniques have proven to be very useful to understand the past climate of the earth that has been changing naturally on timescales ranging from decades to millions of years. Therefore, it is important to filter out the natural signal to correctly gauge the effects induced by humans. This is where the science of paleoclimatology becomes very important. It helps us to understand the pattern of evolution of the earth's climate system, its rhythm, and pulse using various natural archives such as marine and lacustrine sediments, speleothems, ice cores, corals, trees, etc., that hold the clue to the past climate variability. Several proxies are studied from such natural archives to reconstruct the past climatic changes. Out of these, the stable isotopes are one of the most useful and widely employed. In this present study, we explain the methodology behind the application of the stable isotopes as a proxy to reconstruct past climatic changes. We present here a few examples of the stable isotopes of the most widely used elements viz oxygen, carbon, and nitrogen from the marine realm and their systematics. The use of chemostratigraphic techniques like application of oxygen isotopes in stratigraphy, temperature, salinity, and ice-volume reconstruction; Cenozoic oxygen and carbon isotope curves; the limitations in the form of vital effect and diagenesis in the case of foraminifera; use of nitrogen and carbon isotopes as productivity and provenance indicator, respectively, are presented in this paper. © 2015 Elsevier Inc. All rights reserved.

Chemostratigraphy: Concepts, Techniques, and Applications

Stable Isotopes: Tools for Understanding Past Climatic Conditions and Their Applications in Chemostratigraphy

1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N2-yl)-1-aminopyrene (dG1,8), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG1,8 bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG1,8, we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG1,8 lesion in the absence or presence of dCTP. The Dpo4{\textperiodcentered}DNA-dG1,8 binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4{\textperiodcentered}DNA-dG1,8{\textperiodcentered}dCTP ternary structure, the aminopyrene moiety of the dG1,8 lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson-Crick base pair with dG, two nucleotides upstream from the dG1,8 site, creating a complex for "-2" frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism.

Journal of the American Chemical Society

Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase

The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins. © Banerjee et al.

eLife

Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein

We investigate the photoexcited state dynamics in a donor-acceptor copolymer, poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]- pyrrole-1,4-dione-alt-naphthalene} (pDPP-TNT), by picosecond fluorescence and femtosecond transient absorption spectroscopies. Timeresolved fluorescence lifetime measurements of pDPP-TNT thin films reveal that the lifetime of the singlet excited state is 185 ± 5 ps and that singlet-singlet annihilation occurs at excitation photon densities above 6 × 1017 photons/cm3. From the results of singlet-singlet annihilation analysis, we estimate that the single-singlet annihilation rate constant is (6.0 ± 0.2) × 109cm3 s-1 and the singlet diffusion length is -7 nm. From the comparison of femtosecond transient absorption measurements and picosecond fluorescence measurements, it is found that the time profile of the photobleaching signal in the charge-transfer (CT) absorption band coincides with that of the fluorescence intensity and there is no indication of long-lived species, which clearly suggests that charged species, such as polaron pairs and triplet excitons, are not effectively photogenerated in the neat pDPP-TNT polymer. © 2014 The Japan Society of Applied Physics.

Japanese Journal of Applied Physics

Excited-state dynamics in diketopyrrolopyrrole-based copolymer for organic photovoltaics investigated by transient optical spectroscopy

We obtain a necessary and sufficient condition for a matrix A to be Birkhoff-James orthogonal to any subspace W of Mn(C). Using this we obtain an expression for the distance of A from any unital C*- subalgebra of Mn(C). © 2013 Elsevier Inc. All rights reserved.

Mathematics

Linear Algebra and Its Applications

Orthogonality to matrix subspaces, and a distance formula

In the minimal supersymmetric standard model (MSSM) the lightest superpartner of the left-handed neutrinos is ruled out as a candidate for dark matter because of its large elastic cross section with the nucleus mediated via the Z boson. We resurrect this candidate by extending the MSSM with two triplets with opposite hypercharge. The addition of the triplets not only plays the role of generating small Majorana masses for the left-handed active neutrinos, but it also makes the lightest sneutrino a viable candidate for dark matter. We then discuss the relevant parameter space that can give rise to the right amount of (thermal) relic abundance as well as satisfy the current direct-detection constraints from XENON100 and LUX. We find that sneutrino dark matter with mass 370-550 GeV can give rise to the correct thermal relic abundance while coannihilating with the bino-like neutralino.