Violation of Wiedemann-Franz Law for Hot Hadronic Matter created at NICA, FAIR and RHIC Energies using Non-extensive Statistics

We present here the computation of electrical and thermal conductivity by solving the Boltzmann transport equation in relaxation time approximation. We use the $q$-generalized Boltzmann distribution function to incorporate the effects of non-extensivity. The behaviour of these quantities with changing temperature and baryochemical potential has been studied as the system slowly moves towards thermodynamic equilibrium. We have estimated the Lorenz number at NICA, FAIR and the top RHIC energies and studied as a function of temperature, baryochemical potential and the non-extensive parameter, $q$. We have observed that Wiedemann-Franz law is violated for a non-extensive hadronic phase as well as for an equilibrated hadron gas at high temperatures.Comment: Same as the published versio

Combinatorial Recruitment of CREB, C/EBPβ and c-Jun Determines Activation of Promoters upon Keratinocyte Differentiation

Background: Transcription factors CREB, C/EBPβ and Jun regulate genes involved in keratinocyte proliferation and differentiation. We questioned if specific combinations of CREB, C/EBPβ and c-Jun bound to promoters correlate with RNA polymerase II binding, mRNA transcript levels and methylation of promoters in proliferating and differentiating keratinocytes. Results: Induction of mRNA and RNA polymerase II by differentiation is highest when promoters are bound by C/EBP β alone, C/EBPβ together with c-Jun, or by CREB, C/EBPβ and c-Jun, although in this case CREB binds with low affinity. In contrast, RNA polymerase II binding and mRNA levels change the least upon differentiation when promoters are bound by CREB either alone or in combination with C/EBPβ or c-Jun. Notably, promoters bound by CREB have relatively high levels of RNA polymerase II binding irrespective of differentiation. Inhibition of C/EBPβ or c-Jun preferentially represses mRNA when gene promoters are bound by corresponding transcription factors and not CREB. Methylated promoters have relatively low CREB binding and, accordingly, those which are bound by C/EBPβ are induced by differentiation irrespective of CREB. Composite “Half and Half” consensus motifs and co localizing consensus DNA binding motifs are overrepresented in promoters bound by the combination of corresponding transcription factors. Conclusion: Correlational and functional data describes combinatorial mechanisms regulating the activation of promoters. Colocalization of C/EBPβ and c-Jun on promoters without strong CREB binding determines high probability of activation upon keratinocyte differentiation

Distinct repeat motifs at the C-terminal region of CagA of Helicobacter pylori strains isolated from diseased patients and asymptomatic individuals in West Bengal, India

Background: Infection with Helicobacter pylori strains that express CagA is associated with gastritis, peptic ulcer disease, and gastric adenocarcinoma. The biological function of CagA depends on tyrosine phosphorylation by a cellular kinase. The phosphate acceptor tyrosine moiety is present within the EPIYA motif at the C-terminal region of the protein. This region is highly polymorphic due to variations in the number of EPIYA motifs and the polymorphism found in spacer regions among EPIYA motifs. The aim of this study was to analyze the polymorphism at the C-terminal end of CagA and to evaluate its association with the clinical status of the host in West Bengal, India. Results: Seventy-seven H. pylori strains isolated from patients with various clinical statuses were used to characterize the C-ternimal polymorphic region of CagA. Our analysis showed that there is no correlation between the previously described CagA types and various disease outcomes in Indian context. Further analyses of different CagA structures revealed that the repeat units in the spacer sequences within the EPIYA motifs are actually more discrete than the previously proposed models of CagA variants. Conclusion: Our analyses suggest that EPIYA motifs as well as the spacer sequence units are present as distinct insertions and deletions, which possibly have arisen from extensive recombination events. Moreover, we have identified several new CagA types, which could not be typed by the existing systems and therefore, we have proposed a new typing system. We hypothesize that a cagA gene encoding higher number EPIYA motifs may perhaps have arisen from cagA genes that encode lesser EPIYA motifs by acquisition of DNA segments through recombination events

Centrality dependence of Electrical and Hall conductivity at RHIC and LHC energies for a Conformal System

In this work, we study electrical conductivity and Hall conductivity in the presence of electromagnetic field using Relativistic Boltzmann Transport Equation with Relaxation Time Approximation. We evaluate these transport coefficients for a strongly interacting system consisting of nearly massless particles which is similar to Quark-Gluon Plasma and is likely to be formed in heavy-ion collision experiments. We explicitly include the effects of magnetic field in the calculation of relaxation time. The values of magnetic field are obtained for all the centrality classes of Au+Au collisions at $\sqrt {s_{\rm NN}} =$ 200 GeV and Pb+Pb collisions at $\sqrt {s_{\rm NN}} =$ 2.76 TeV. We consider the three lightest quark flavors and their corresponding antiparticles in this study. We estimate the temperature dependence of the electrical conductivity and Hall conductivity for different strengths of magnetic field. We observe a significant dependence of temperature on electrical and Hall conductivity in the presence of magnetic field.Comment: Same as the published version in EPJ

Studying Cosmic Dawn using redshifted HI 21-cm signal: A brief review

In this review article, we briefly outline our current understanding of the physics associated with the HI 21-cm signal from cosmic dawn. We discuss different phases of cosmic dawn as the ambient gas and the background radiations evolve with the redshift. We address the consequences of several possible heating sources and radiation background on the global 21-cm signal. We further review our present perspective of other important aspects of the HI 21-cm signal such as the power spectrum and imaging. Finally, we highlight the future key measurements of the Square Kilometre Array and other ongoing/upcoming experiments that will enlighten our understanding of the early Universe.Comment: 22 pages, 9 figures, Accepted for publication in Journal of Astrophysics and Astronomy(JoAA

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

Abstract Background Chromatin plays a critical role in regulating transcription factors (TFs) binding to their canonical transcription factor binding sites (TFBS). Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS. Results We used a logistic regression to evaluate how well the propensity for nucleosome binding and co-occurrence of a secondary motif identify which canonical motifs are bound in vivo. We used ChIP-seq data for three transcription factors binding to their canonical motifs: c-Jun binding the AP-1 motif (TGAC/GTCA), GR (glucocorticoid receptor) binding the GR motif (G-ACA---T/CGT-C), and Hoxa2 (homeobox a2) binding the Pbx (Pre-B-cell leukemia homeobox) motif (TGATTGAT). For all canonical TFBS in the mouse genome, we calculated intrinsic nucleosome occupancy scores (INOS) for its surrounding 150-bps DNA and examined the relationship with in vivo TF binding. In mouse mammary 3134 cells, c-Jun and GR proteins preferentially bound regions calculated to be well-bound by nucleosomes in vitro with the canonical AP-1 and GR motifs themselves contributing to the high INOS. Functional GR motifs are enriched for AP-1 motifs if they are within a nucleosome-sized 150-bps region. GR and Hoxa2 also bind motifs with low INOS, perhaps indicating a different mechanism of action. Conclusion Our analysis quantified the contribution of INOS and co-occurring sequence to the identification of functional canonical motifs in the genome. This analysis revealed an inherent competition between some TFs and nucleosomes for binding canonical TFBS. GR and c-Jun cooperate if they are within 150-bps. Binding of Hoxa2 and a fraction of GR to motifs with low INOS values suggesting they are not in competition with nucleosomes and may function using different mechanisms. </jats:sec

Human protein reference database—2006 update

Human Protein Reference Database (HPRD) () was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein–protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein–protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data