Regulation, sensory domains and roles of two Desulfovibrio desulfuricans ATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress

In silico analyses identified a Crp/Fnr family transcription factor (HcpR) in sulfate-reducing bacteria that controls expression of the hcp gene, which encodes the hybrid cluster protein and contributes to nitrosative stress responses. There is only one hcpR gene in the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, but two copies in D. desulfuricans 27774, which can use nitrate as an alternative electron acceptor to sulfate. Structures of the D. desulfuricans hcpR1, hcpR2 and hcp operons are reported. We present evidence that hcp expression is regulated by HcpR2, not by HcpR1, and that these two regulators differ in both their DNA-binding site specificity and their sensory domains. HcpR1 is predicted to be a b-type cytochrome. HcpR1 binds upstream of the hcpR1 operon and its synthesis is regulated coordinately with hcp in response to NO. In contrast, hcpR2 expression was not induced by nitrate, nitrite or NO. HcpR2 is an iron-sulfur protein that reacts with NO and O2 . We propose that HcpR1 and HcpR2 use different sensory mechanisms to regulate subsets of genes required for defense against NO-induced nitrosative stress, and that diversification of signal perception and DNA recognition by these two proteins is a product of D. desulfuricans adaptation to its particular environmental niche. This article is protected by copyright. All rights reserved

The beginnings of geography teaching and research in the University of Glasgow: the impact of J.W. Gregory

J.W. Gregory arrived in Glasgow from Melbourne in 1904 to take up the post of foundation Professor of Geology in the University of Glasgow. Soon after his arrival in Glasgow he began to push for the setting up of teaching in Geography in Glasgow, which came to pass in 1909 with the appointment of a Lecturer in Geography. This lecturer was based in the Department of Geology in the University's East Quad. Gregory's active promotion of Geography in the University was matched by his extensive writing in the area, in textbooks, journal articles and popular books. His prodigious output across a wide range of subject areas is variably accepted today, with much of his geomorphological work being judged as misguided to varying degrees. His 'social science' publications - in the areas of race, migration, colonisation and economic development of Africa and Australia - espouse a viewpoint that is unacceptable in the twenty-first century. Nonetheless, that viewpoint sits squarely within the social and economic traditions of Gregory's era, and he was clearly a key 'Establishment' figure in natural and social sciences research in the first half of the twentieth century. The establishment of Geography in the University of Glasgow remains enduring testimony of J.W. Gregory's energy, dedication and foresight

Free induction signal from biexcitons and bound excitons

A theory of the free induction signal from biexcitons and bound excitons is presented. The simultaneous existence of the exciton continuum and a bound state is shown to result in a new type of time dependence of the free induction. The optically detected signal increases in time and oscillates with increasing amplitude until damped by radiative or dephasing processes. Radiative decay is anomalously fast and can result in strong picosecond pulses. The expanding area of a coherent exciton polarization (inflating antenna), produced by the exciting pulse, is the underlying physical mechanism. The developed formalism can be applied to different biexciton transients.Comment: RevTeX, 20 p. + 2 ps fig. To appear in Phys. Rev. B1

Guidelines for the functional annotation of microRNAs using the Gene Ontology

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual)

Theory of exciton-exciton correlation in nonlinear optical response

We present a systematic theory of Coulomb interaction effects in the nonlinear optical processes in semiconductors using a perturbation series in the exciting laser field. The third-order dynamical response consists of phase-space filling correction, mean-field exciton-exciton interaction, and two-exciton correlation effects expressed as a force-force correlation function. The theory provides a unified description of effects of bound and unbound biexcitons, including memory-effects beyond the Markovian approximation. Approximations for the correlation function are presented.Comment: RevTex, 35 pages, 10 PostScript figs, shorter version submitted to Physical Review

Binding of biexcitons in GaAs/AlxGa1-xAs superlattices

Binding of the heavy-hole excitons and biexcitons in GaAs/Al0.3Ga0.7As superlattices is studied using linear and nonlinear optical techniques. High biexciton binding energies characteristic of quasi two-dimensional biexcitons are observed in superlattices with considerable miniband dispersion

Facile access to a heterocyclic, sp3-rich chemical scaffold via a tandem condensation/intramolecular nitrone–alkene [3+2] cycloaddition strategy

A heterocyclic, sp3-rich chemical scaffold was synthesised in just 6 steps via a highly regio- and diastereo-selective tandem nitrone formation/intramolecular nitrone–alkene [3+2] cycloaddition reaction. A library of 543 lead-like compounds based on the scaffold core has been produced

Security governance and the private military industry in Europe and North America

Even before Iraq the growing use of private military contractors has been widely discussed in the academic and public literature. However, the reasons for this proliferation of private military companies and its implications are frequently generalized due to a lack of suitable theoretical approaches for the analysis of private means of violence in contemporary security. As a consequence, this article contends, the analysis of the growth of the private military industry typically conflates two separate developments: the failure of some developing states to provide for their national security and the privatisation of military services in industrialized nations in Europe and North America. This article focuses on the latter and argues that the concept of security governance can be used as a theoretical framework for understanding the distinct development, problems and solutions for the governance of the private military industry in developed countries.The United States Institute of Peace and the German Academic Exchange Service

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology

BACKGROUND: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. METHODS AND RESULTS: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. CONCLUSIONS: We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects