bluuebunny/crossref_metadata_2025 huggingface dataset:
Zur Psychotherapie sozialer Ängste
Authors: Willutzki Ulrike , Teismann Tobias , Schulte Dietmar
Published: January 2011

Zusammenfassung. Theoretischer Hintergrund: Obwohl bekannt ist, dass Soziale Angststörungen mit geringem Wohlbefinden assoziiert sind, gibt es nur wenige Studien zur Auswirkung symptombezogener Behandlungen auf die Verbesserung des Wohlbefindens. Fragestellung: Inwieweit verbessert sich durch eine Psychotherapie das Wohlbefinden von Patienten mit sozialen Ängsten? Trägt ein kombiniert ressourcenorientiertes therapeutisches Vorgehen (KROT) stärker zur Verbesserung des Wohlbefindens bei als ein fokal kognitiv-verhaltenstherapeutisches Therapieangebot (KVT)? Methode: In einer randomisiert-kontrollierten Studie zur Psychotherapie sozialer Ängste (N = 62) wurde mittels abhängiger Varianzanalysen die Auswirkung einer KVT- und einer KROT-Behandlung auf Optimismus, Kohärenzgefühl, Selbstakzeptierung und Lebenszufriedenheit untersucht. Ergebnisse: Insgesamt kam es in beiden Behandlungsbedingungen zu einer signifikanten Zunahme von Optimismus, Selbstakzeptanz und Kohärenzempfinden sowie einer Abnahme von Pessimismus. Die Lebenszufriedenheit wurde durch die KROT-Behandlung in stärkerem Maße gefördert als durch die KVT-Behandlung. Schlussfolgerungen: Störungsspezifische Behandlungskonzepte scheinen nicht ausschließlich symptombezogene Verbesserungen zu erzielen, sondern darüber hinaus Wohlbefinden zu fördern.
Petrotectonics of lawsonite eclogite exhumation: Insights from the Sivrihisar massif, Turkey
Authors: Davis Peter B.
Published: January 2011

The Sivrihisar massif of the Tavşanlı Zone of Turkey is 1 of less than 10 known lawsonite eclogite localities worldwide. Rocks of the Sivrihisar massif consist of eclogite and blueschist in contact with metasedimentary host rocks and record decreasing maximum pressure conditions across three WNW‐ESE striking belts from 16–24 kbar in the northern Halilbağı belt to 14–16 kbar in the Karacaören belt and 8–10 kbar in the Kertek belt. Where present, sodic‐amphibole, phengite, chlorite, and quartz define a pervasive S0/S1 foliation; garnet, omphacite, and lawsonite define stretching lineations and kinematic indicators. D1 and D2 structures are similar in the Halilbağı and Karacaören belts but differ to those in the Kertek belt. D3 structures are uniform across the massif including fibrous calcite that occurs parallel to F3 fold axes. Shear sense indicators from field observations and asymmetric type‐I cross girdle of quartz c axes obtained from electron backscatter diffraction (EBSD) show top to the south thrusting throughout much of the massif. D1 and D2 structures are interpreted to have formed during exhumation by extrusion along a ∼5°C/km gradient. The Halilbağı and Karacaören belts were juxtaposed possibly as deep as 45 km within the subduction channel and exhumed by the arrival of the Anatolide microcontinent at approximately 70 Ma. Homogeneity of F3 axes and calcite fibers across the massif suggests that assembly occurred at blueschist conditions before exhumation through the aragonite‐calcite transition (∼350°C) above 8 kbar.
Neuroprotection by glutamate oxaloacetate transaminase in ischemic stroke: An experimental study
Authors: Campos Francisco , Sobrino Tomás , Ramos-Cabrer Pedro , Argibay Bárbara , Agulla Jesús , Pérez-Mato María , Rodríguez-González Raquel , Brea David , Castillo José
Published: January 2011

As ischemic stroke is associated with an excessive release of glutamate into the neuronal extracellular space, a decrease in blood glutamate levels could provide a mechanism to remove it from the brain tissue, by increasing the brain-blood gradient. In this regard, the ability of glutamate oxaloacetate transaminase (GOT) to metabolize glutamate in blood could represent a potential neuroprotective tool for ischemic stroke. This study aimed to determine the neuroprotective effects of GOT in an animal model of cerebral ischemia by means of a middle cerebral arterial occlusion (MCAO) following the Stroke Therapy Academic Industry Roundtable (STAIR) group guidelines. In this animal model, oxaloacetate-mediated GOT activation inhibited the increase of blood and cerebral glutamate after MCAO. This effect is reflected in a reduction of infarct size, smaller edema volume, and lower sensorimotor deficits with respect to controls. Magnetic resonance spectroscopy confirmed that the increase of glutamate levels in the brain parenchyma after MCAO is inhibited after oxaloacetate-mediated GOT activation. These findings show the capacity of the GOT to remove glutamate from the brain by means of blood glutamate degradation, and suggest the applicability of this enzyme as an efficient and novel neuroprotective tool against ischemic stroke.
Subtyping of Dengue Viruses using Return Time Distribution based Appproach
Authors: Kolekar Pandurang , Kale Mohan , Kulkarni-Kale Urmila
Published: January 2011

Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind & severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for alternative efficient approaches for subtyping of viruses becomes apparent. Recently, the concept of Return time distribution (RTD) was proposed and validated for alignment-free clustering and molecular phylogeny. The RTD-based approach is extended here for the subtyping of DENVs.Subtyping methodology involves compilation of curated genomic data of known subtypes, computing RTD of these sequences at different levels of k-mers, derivation a distance matrix and clustering. The subtype of the unknown is predicted based on its clustering with known subtypes.Dataset consisting of 1359 DENV genomes with sequence identity (>92%) were clustered using the RTD based approach at k=5. Serotype specific clades, despite geographical and temporal variation in the dataset, were observed with 100% accuracy. The method was also found to be efficient in terms of time and implementation, apart from accuracy in the subtyping of DENV.
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit
Authors: Wojtas Magdalena , Peralta Bibiana , Ondiviela Marina , Mogni Maria , Bell Stephen D. , Abrescia Nicola G.A.
Published: January 2011

We review recent results on the complete structure of the archaeal RNAP (RNA polymerase) enzyme of Sulfolobus shibatae. We compare the three crystal forms in which this RNAP packs (space groups P212121, P21212 and P21) and provide a preliminary biophysical characterization of the newly identified 13-subunit Rpo13. The availability of different crystal forms for this RNAP allows the analysis of the packing degeneracy and the intermolecular interactions that determine this degeneracy. We observe the pivotal role played by the protruding stalk composed of subunits Rpo4 and Rpo7 in the lattice contacts. Aided by MALLS (multi-angle laser light scattering), we have initiated the biophysical characterization of the recombinantly expressed and purified subunit Rpo13, a necessary step towards the understanding of Rpo13's role in archaeal transcription.
Cation–π interactions induce kinking of a molecular hinge in the RNA polymerase bridge–helix domain
Authors: Heindl Hans , Greenwell Pamela , Weingarten Noam , Kiss Tamas , Terstyanszky Gabor , Weinzierl Robert O.J.
Published: January 2011

RNAPs (RNA polymerases) are complex molecular machines that contain a highly conserved catalytic site surrounded by conformationally flexible domains. High-throughput mutagenesis in the archaeal model system Methanocaldococcus jannaschii has demonstrated that the nanomechanical properties of one of these domains, the bridge–helix, exert a key regulatory role on the rate of the NAC (nucleotide-addition cycle). Mutations that increase the probability and/or half-life of kink formation in the BH-HC (bridge–helix C-terminal hinge) cause a substantial increase in specific activity (‘superactivity’). Fully atomistic molecular dynamics simulations show that kinking of the BH-HC appears to be driven by cation–π interactions and involve amino acid side chains that are exceptionally highly conserved in all prokaryotic and eukaryotic species.
Archaeal promoter architecture and mechanism of gene activation
Authors: Peng Nan , Ao Xiang , Liang Yun Xiang , She Qunxin
Published: January 2011

Sulfolobus solfataricus and Sulfolobus islandicus contain several genes exhibiting D-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. At sequence level, only two highly conserved cis elements are present on the promoters: a regulatory element named ara box directing arabinose-inducible expression and the basal promoter element TATA, serving as the binding site for the TATA-binding protein. Strikingly, these promoters possess a modular structure that allows an essentially inactive basal promoter to be strongly activated. The invoked mechanisms include TFB (transcription factor B) recruitment by the ara-box-binding factor to activate gene expression and modulation of TFB recruitment efficiency to yield differential gene expression.
Potential role of cellular ESCRT proteins in the STIV life cycle
Authors: Snyder Jamie C. , Young Mark J.
Published: January 2011

We are examining the archaeal virus STIV (Sulfolobus turreted icosahedral virus) in order to elucidate the details of its replication cycle and its interactions with its cellular host, Sulfolobus solfataricus. Infection of Sulfolobus by STIV initiates an unusual cell lysis pathway. One component of this pathway is the formation of pyramid-like structures on the surface of infected cells. Multiple seven-sided pyramid-like structures are formed on infected cells late in the STIV replication cycle. These pyramid-like structures are formed at sites where the Sulfolobus S-layer has been disrupted and through which the cellular membrane protrudes. It is through the pyramid-like structures that virus-induced cell lysis occurs in the final stages of the STIV replication cycle. The pathway and process by which these unusual lysis structures are produced appears to be novel to archaeal viruses and are not related to the well-characterized lysis mechanisms utilized by bacterial viruses. We are interested in elucidating both the viral and cellular components involved with STIV lysis of its infected cell. In particular, we are examining the potential role that Sulfolobus ESCRT (endosomal sorting complex required for transport)-like proteins play during viral infection and lysis. We hypothesize that STIV takes advantage of the Sulfolobus ESCRT machinery for virus assembly, transport and cellular lysis.
Bacterial and eukaryotic systems collide in the three Rs of Methanococcus
Authors: Parker Richard P. , Walters Alison D. , Chong James P.J.
Published: January 2011

Methanococcus maripaludis S2 is a methanogenic archaeon with a well-developed genetic system. Its mesophilic nature offers a simple system in which to perform complementation using bacterial and eukaryotic genes. Although information-processing systems in archaea are generally more similar to those in eukaryotes than those in bacteria, the order Methanococcales has a unique complement of DNA replication proteins, with multiple MCM (minichromosome maintenance) proteins and no obvious originbinding protein. A search for homologues of recombination and repair proteins in M. maripaludis has revealed a mixture of bacterial, eukaryotic and some archaeal-specific homologues. Some repair pathways appear to be completely absent, but it is possible that archaeal-specific proteins could carry out these functions. The replication, recombination and repair systems in M. maripaludis are an interesting mixture of eukaryotic and bacterial homologues and could provide a system for uncovering novel interactions between proteins from different domains of life.
FRET (fluorescence resonance energy transfer) sheds light on transcription
Authors: Grohmann Dina , Klose Daniel , Fielden Daniel , Werner Finn
Published: January 2011

The complex organization of the transcription machinery has been revealed mainly by biochemical and crystallographic studies. X-ray structures describe RNA polymerases and transcription complexes on an atomic level, but fail to portray their dynamic nature. The use of fluorescence techniques has made it possible to add a new layer of information to our understanding of transcription by providing details about the structural rearrangement of mobile elements and the network of interactions within transcription complexes in solution and in real-time.
Winged helix domains with unknown function in Hel308 and related helicases
Authors: Woodman Isabel L. , Bolt Edward L.
Published: January 2011

Hel308 is a superfamily 2 helicase/translocase that is conserved throughout archaea and in some eukaryotes for repair of genotoxic lesions such as ICLs (interstrand DNA cross-links). Atomic structures of archaeal Hel308 have allowed mechanistic insights into ATPase and helicase functions, but have also highlighted structures that currently lack a known function, such as an unexpected WH (winged helix) domain. This domain and similar overall protein structural organization was also identified in other superfamily 2 helicases that process RNA molecules in eukaryotes: Brr2, Mtr4 and Prp43p. We survey the structure of Hel308 with regard to its WH domain in particular and its function(s) in maintaining structural integrity of the overall Hel308 ring structure, and possibly during interactions of Hel308 with other proteins and/or forked DNA.
Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions
Authors: Barzel Adi , Naor Adit , Privman Eyal , Kupiec Martin , Gophna Uri
Published: January 2011

Inteins are selfish genetic elements that disrupt the sequence of protein-coding genes and are excised post-translationally. Most inteins also contain a HEN (homing endonuclease) domain, which is important for their horizontal transmission. The present review focuses on the evolution of inteins and their nested HENs, and highlights several unsolved questions that could benefit from molecular genetic approaches. Such approaches can be well carried out in halophilic archaea, which are naturally intein-rich and have highly developed genetic tools for their study. In particular, the fitness effects of habouring an intein/HEN can be tested in direct competition assays, providing additional insights that will improve current evolutionary models.
Denitrification regulatory phenotype, a new term for the characterization of denitrifying bacteria
Authors: Bergaust Linda , Bakken Lars R. , Frostegård Åsa
Published: January 2011

Current knowledge of denitrification is based on detailed studies of a limited number of organisms. In most cases the importance of these paradigm species in natural ecosystems is questionable. Detailed phenotypic studies of a wider range of prokaryotes, both type strains and dominant denitrifiers isolated from complex systems, will aid the generation of more sophisticated mathematical models for the prediction of NO and N2O emission to the environment. However, in order to facilitate the comparison of a vast range of prokaryotes, phenotypic experiments and functional characteristics included should be standardized. In the present paper, we discuss the term DRP (denitrification regulatory phenotype) for describing a set of phenotypic traits and experimental conditions for the characterization of denitrifying organisms. This is exemplified by the contrasting DRP characteristics of the two well-studied denitrifiers Paracoccus denitrificans and Agrobacterium tumefaciens.
Nitrosative stress in Escherichia coli: reduction of nitric oxide
Authors: Vine Claire E. , Cole Jeffrey A.
Published: January 2011

The ability of enteric bacteria to protect themselves against reactive nitrogen species generated by their own metabolism, or as part of the innate immune response, is critical to their survival. One important defence mechanism is their ability to reduce NO (nitric oxide) to harmless products. The highest rates of NO reduction by Escherichia coli K-12 were detected after anaerobic growth in the presence of nitrate. Four proteins have been implicated as catalysts of NO reduction: the cytoplasmic sirohaem-containing nitrite reductase, NirB; the periplasmic cytochrome c nitrite reductase, NrfA; the flavorubredoxin NorV and its associated oxidoreductase, NorW; and the flavohaemoglobin, Hmp. Single mutants defective in any one of these proteins and even the mutant defective in all four proteins reduced NO at the same rate as the parent. Clearly, therefore, there are mechanisms of NO reduction by enteric bacteria that remain to be characterized. Far from being minor pathways, the currently unknown pathways are adequate to sustain almost optimal rates of NO reduction, and hence potentially provide significant protection against nitrosative stress.
Gene expression study of the flavodi-iron proteins from the cyanobacterium Synechocystis sp. PCC6803
Authors: Gonçalves Vera L. , Saraiva Lígia M. , Teixeira Miguel
Published: January 2011

The flavodi-iron proteins, also named FDPs, are an extensive family of enzymes able to reduce dioxygen to water and/or nitric oxide to nitrous oxide. These proteins are formed by a metallo-β-lactamase-like module with a di-iron catalytic site fused to a flavodoxin-like module bearing an FMN. However, in cyanobacteria, which are oxygenic photosynthetic organisms widespread in Nature, FDPs have an extra NAD(P)H:flavin reductase-like domain as a C-terminal extension. Interestingly, cyanobacteria contain more than one gene encoding FDP-like proteins, with the genome of Synechocystis sp. PCC6803 containing four genes coding for putative FDPs. However, the function of those proteins remains unclear. In the present study, we have analysed the expression profile of these genes under oxidative and nitrosative stress conditions. The results indicate that one of the flavodi-iron genes, the so-called flv1, is induced in cells exposed to nitrosative stress. By conducting a broad analysis on the primary sequences of FDPs, we have identified that the FDPs of cyanobacteria and oxygenic photosynthetic eukaryotes may be divided into multiple types (1–12), according to the amino acid residues of the di-iron catalytic site.
Nitric oxide and nitrosative stress tolerance in yeast
Authors: Tillmann Anna , Gow Neil A.R. , Brown Alistair J.P.
Published: January 2011

The opportunistic human fungal pathogen Candida albicans encounters diverse environmental stresses when it is in contact with its host. When colonizing and invading human tissues, C. albicans is exposed to ROS (reactive oxygen species) and RNIs (reactive nitrogen intermediates). ROS and RNIs are generated in the first line of host defence by phagocytic cells such as macrophages and neutrophils. In order to escape these host-induced oxidative and nitrosative stresses, C. albicans has developed various detoxification mechanisms. One such mechanism is the detoxification of NO (nitric oxide) to nitrate by the flavohaemoglobin enzyme CaYhb1. Members of the haemoglobin superfamily are highly conserved and are found in archaea, eukaryotes and bacteria. Flavohaemoglobins have a dioxygenase activity [NOD (NO dioxygenase domain)] and contain three domains: a globin domain, an FAD-binding domain and an NAD(P)-binding domain. In the present paper, we examine the nitrosative stress response in three fungal models: the pathogenic yeast C. albicans, the benign budding yeast Saccharomyces cerevisiae and the benign fission yeast Schizosaccharomyces pombe. We compare their enzymatic and non-enzymatic NO and RNI detoxification mechanisms and summarize fungal responses to nitrosative stress.
An HcpR homologue from Desulfovibrio desulfuricans and its possible role in nitrate reduction and nitrosative stress
Authors: Cadby Ian T. , Busby Steve J.W. , Cole Jeffrey A.
Published: January 2011

The Escherichia coli CRP (cAMP receptor protein), is a global regulator of transcription that modulates gene expression by activation or repression at a range of promoters in E. coli. A major function is to regulate the selection of nutrients required for growth. The anaerobic sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC27774 is capable of utilizing sulfate, nitrite and nitrate as terminal electron acceptors. In the presence of both sulfate and nitrate, sulfate is reduced preferentially despite nitrate being the thermodynamically more favourable electron acceptor. Three inverted repeat sequences upstream of the D. desulfuricans ATCC27774 nap (nitrate reduction in the periplasm) operon have high levels of similarity to the consensus sequence for the E. coli CRP DNA-binding site. In other Desulfovibrio species a putative CRP homologue, HcpR [regulator of hcp (hybrid cluster protein) transcription], has a predicted regulon comprising genes involved in sulfate reduction and nitrosative stress. The presence of CRP consensus sites within the D. desulfuricans ATCC27774 nap promoter prompted a search for CRP homologues in the genomes of sulfate-reducing bacteria. This revealed the presence of a potential CRP homologue that we predict binds to CRP consensus sites such as those of the nap operon. Furthermore, we predict that much of the core HcpR regulon predicted in other Desulfovibrio species is conserved in D. desulfuricans.
Nitrate and (per)chlorate reduction pathways in (per)chlorate-reducing bacteria
Authors: Oosterkamp Margreet J. , Mehboob Farrakh , Schraa Gosse , Plugge Caroline M. , Stams Alfons J.M.
Published: January 2011

The reduction of (per)chlorate and nitrate in (per)chlorate-reducing bacteria shows similarities and differences. (Per)chlorate reductase and nitrate reductase both belong to the type II DMSO family of enzymes and have a common bis(molybdopterin guanine dinucleotide)molybdenum cofactor. There are two types of dissimilatory nitrate reductases. With respect to their localization, (per)chlorate reductase is more similar to the dissimilatory periplasmic nitrate reductase. However, the periplasmic, unlike the membrane-bound, respiratory nitrate reductase, is not able to use chlorate. Structurally, (per)chlorate reductase is more similar to respiratory nitrate reductase, since these reductases have analogous subunits encoded by analogous genes. Both periplasmic (per)chlorate reductase and membrane-bound nitrate reductase activities are induced under anoxic conditions in the presence of (per)chlorate and nitrate respectively. During microbial (per)chlorate reduction, molecular oxygen is generated. This is not the case for nitrate reduction, although an atypical reaction in nitrite reduction linked to oxygen formation has been described recently. Microbial oxygen production during reduction of oxyanions may enhance biodegradation of pollutants under anoxic conditions.
Electrocatalytic reduction of nitrate and selenate by NapAB
Authors: Gates Andrew J. , Butler Clive S. , Richardson David J. , Butt Julea N.
Published: January 2011

Bacterial cellular metabolism is renowned for its metabolic diversity and adaptability. However, certain environments present particular challenges. Aerobic metabolism of highly reduced carbon substrates by soil bacteria such as Paracoccus pantotrophus presents one such challenge since it may result in excessive electron delivery to the respiratory redox chain when compared with the availability of terminal oxidant, O2. The level of a periplasmic ubiquinol-dependent nitrate reductase, NAP, is up-regulated in the presence of highly reduced carbon substrates. NAP oxidizes ubiquinol at the periplasmic face of the cytoplasmic membrane and reduces nitrate in the periplasm. Thus its activity counteracts the accumulation of excess reducing equivalents in ubiquinol, thereby maintaining the redox poise of the ubiquinone/ubiquinol pool without contributing to the protonmotive force across the cytoplasmic membrane. Although P. pantotrophus NapAB shows a high level of substrate specificity towards nitrate, the enzyme has also been reported to reduce selenate in spectrophotometric solution assays. This transaction draws on our current knowledge concerning the bacterial respiratory nitrate reductases and extends the application of PFE (protein film electrochemistry) to resolve and quantify the selenate reductase activity of NapAB.
Molecular interactions between multihaem cytochromes: probing the protein–protein interactions between pentahaem cytochromes of a nitrite reductase complex
Authors: Lockwood Colin , Butt Julea N. , Clarke Thomas A. , Richardson David J.
Published: January 2011

The cytochrome c nitrite reductase NrfA is a 53 kDa pentahaem enzyme that crystallizes as a decahaem homodimer. NrfA catalyses the reduction of NO2− to NH4+ through a six electron reduction pathway that is of major physiological significance to the anaerobic metabolism of enteric and sulfate reducing bacteria. NrfA receives electrons from the 21 kDa pentahaem NrfB donor protein. This requires that redox complexes form between the NrfA and NrfB pentahaem cytochromes. The formation of these complexes can be monitored using a range of methodologies for studying protein–protein interactions, including dynamic light scattering, gel filtration, analytical ultracentrifugation and visible spectroscopy. These methods have been used to show that oxidized NrfA exists in dynamic monomer–dimer equilibrium with a Kd (dissociation constant) of 4 μM. Significantly, the monomeric and dimeric forms of NrfA are equally active for either the six electron reduction of NO2− or HSO3−. When mixed together, NrfA and NrfB exist in equilibrium with NrfAB, which is described by a Kd of 50 nM. Thus, since NrfA and NrfB are present in micromolar concentrations in the periplasmic compartment, it is likely that NrfB remains tightly associated with its NrfA redox partner under physiological conditions.
Plant influence on nitrification
Authors: Skiba Marcin W. , George Timothy S. , Baggs Elizabeth M. , Daniell Tim J.
Published: January 2011

Modern agriculture has promoted the development of high-nitrification systems that are susceptible to major losses of nitrogen through leaching of nitrate and gaseous emissions of nitrogen oxide (NO and N2O), contributing to global warming and depletion of the ozone layer. Leakage of nitrogen from agricultural systems forces increased use of nitrogen fertilizers and causes water pollution and elevated costs of food production. Possible strategies for prevention of these processes involve various agricultural management approaches and use of synthetic inhibitors. Growing plants capable of producing nitrification suppressors could become a potentially superior method of controlling nitrification in the soil. There is a need to investigate the phenomenon of biological nitrification inhibition in arable crop species.
Advances in 15N-tracing experiments: new labelling and data analysis approaches
Authors: Rütting Tobias , Huygens Dries , Staelens Jeroen , Müller Christoph , Boeckx Pascal
Published: January 2011

To obtain an in-depth understanding of soil nitrogen dynamics, it is necessary to quantify a variety of simultaneously occurring gross nitrogen transformation processes. In order to do so, most studies apply 15N in a disturbed soil–microbial–root system and quantify gross rates based on the principles of 15N isotope dilution. However, this approach has several shortcomings. First, studying disturbed soil provides only limited information on in situ soil nitrogen dynamics. Secondly, the analytical data analysis allows the quantification of total production and consumption rates of the labelled pool, but does not provide information on process-specific transformation rates. Combining in situ15N isotope labelling over 1–2 weeks with numerical data analysis allows determining process-specific gross nitrogen transformations in undisturbed soils under field conditions in the presence of live roots and their associated microbial communities. This has the potential to increase our understanding of nitrogen dynamics in the soil environment.
Respiratory nitrogen metabolism and nitrosative stress defence in ϵ-proteobacteria: the role of NssR-type transcription regulators
Authors: Kern Melanie , Winkler Christine , Simon Jörg
Published: January 2011

ϵ-Proteobacteria form a globally ubiquitous group of ecologically significant organisms and comprise a diverse range of host-associated and free-living species. To grow by anaerobic respiration, many ϵ-proteobacteria reduce nitrate to nitrite followed by either nitrite ammonification or denitrification. Using the ammonifying model organisms Wolinella succinogenes and Campylobacter jejuni, the electron transport chains of nitrate respiration, respiratory nitrite ammonification and even N2O (nitrous oxide) respiration have been characterized in recent years, but knowledge on nitrosative stress defence, nitrogen compound-sensing and corresponding signal transduction pathways is limited. The potentially dominant role of NssR (nitrosative stress-sensing regulator)-type transcription regulators in ϵ-proteobacterial nitrogen metabolism is discussed.
Proteins and protein complexes involved in the biochemical reactions of anaerobic ammonium-oxidizing bacteria
Authors: de Almeida Naomi M. , Maalcke Wouter J. , Keltjens Jan T. , Jetten Mike S.M. , Kartal Boran
Published: January 2011

It has been less than two decades since anammox (anaerobic ammonium oxidation) coupled to nitrite reduction has been discovered. Already, this process has been recognized as an important sink for fixed nitrogen in the natural environment and has been implemented as a cost-effective ammonium removal technology. Still, little is known about the molecular mechanism of this remarkable reaction. In this mini review, we present an insight into how ammonium and nitrite are combined to form dinitrogen gas.
Glycoconjugates in the detection of alcohol abuse
Authors: Waszkiewicz Napoleon , Szajda Sławomir Dariusz , Kępka Alina , Szulc Agata , Zwierz Krzysztof
Published: January 2011

Up to 30% of all hospital admissions and health-care costs may be attributable to alcohol abuse. Ethanol, its oxidative metabolites, acetaldehyde and ROS (reactive oxygen species), non-oxidative metabolites of alcohol [e.g. FAEEs (fatty acid ethyl esters)] and the ethanol–water competition mechanism are all involved in the deregulation of glycoconjugate (glycoprotein, glycolipid and proteoglycan) metabolic processes including biosynthesis, modification, transport, secretion, elimination and catabolism. An increasing number of new alcohol biomarkers that are the result of alcohol-induced glycoconjugate metabolic errors have appeared in the literature. Glycoconjugate-related alcohol markers are involved in, or are a product of, altered glycoconjugate metabolism, e.g. CDT (carbohydrate-deficient transferrin), SA (sialic acid), plasma SIJ (SA index of apolipoprotein J), CETP (cholesteryl ester transfer protein), β-HEX (β-hexosaminidase), dolichol, EtG (ethyl glucuronide) etc. Laboratory tests based on changes in glycoconjugate metabolism are useful in settings where the co-operativeness of the patient is impaired (e.g. driving while intoxicated) or when a history of alcohol use is not available (e.g. after trauma). In clinical practice, glycoconjugate markers of alcohol use/abuse let us distinguish alcoholic from non-alcoholic tissue damage, having important implications for the treatment and management of diseases.
Glycans in melanoma screening. Part 2. Towards the understanding of integrin N-glycosylation in melanoma
Authors: Link-Lenczowski Paweł , Lityńska Anna
Published: January 2011

Although melanoma is one of the most studied malignancies, it still remains challenging for biomedicine. Since aberrant glycosylation has been considered as an important hallmark of cancer for many years, melanoma glycomic studies give a chance of better understanding the biology of the disease. The multistage nature of melanoma development, which is accompanied by changes in the expression of adhesion receptors from the integrin family, provides a chance for searching for neoglycoforms of proteins that can be considered as future sensitive melanoma biomarkers. The β1,6-branching, sialylation and fucosylation seem to be important modifications of integrin N-glycans in the case of malignant melanoma progression.
The cellular microenvironment and cell adhesion: a role for O-glycosylation
Authors: Zhang Liping , Ten Hagen Kelly G.
Published: January 2011

Glycosylation is one of the most abundant protein modifications in Nature, having roles in protein stability, secretion and function. Alterations in mucin-type O-glycosylation are responsible for a number of human diseases and developmental defects, as well as associated with certain types of cancer. However, the mechanistic role of this form of glycosylation in many of these instances is unclear. Here we describe how one glycosyltransferase responsible for initiating mucin-type O-glycosylation (PGANT3), specifically modulates integrin-mediated cell adhesion by influencing the secretion and localization of an integrin ligand. The integrin ligand Tiggrin, is normally O-glycosylated and localized to the basal matrix, where adhesion of two opposing cell layers takes place. In pgant3 mutants, Tiggrin is no longer O-glycosylated and fails to be properly secreted to the basal cell layer interface, resulting in disruption of proper cell adhesion. pgant3-mediated effects are dependent on the enzymatic activity of PGANT3 and cannot be rescued by another pgant family member, indicating a unique role for this glycosyltransferase. These results provide in vivo evidence for the role of O-glycosylation in the secretion of specific extracellular matrix proteins, which thereby influences the composition of the cellular ‘microenvironment’ and modulates cell adhesion events. The studies described in this review provide insight into the long-standing association between aberrant O-glycosylation and tumorigenesis, as changes in tumour environment and cell adhesion are hallmarks of cancer progression.
Glycosaminoglycans as regulators of stem cell differentiation
Authors: Smith Raymond A.A. , Meade Kate , Pickford Claire E. , Holley Rebecca J. , Merry Catherine L.R.
Published: January 2011

ES (embryonic stem) cell differentiation is dependent on the presence of HS (heparan sulfate). We have demonstrated that, during differentiation, the evolution of specific cell lineages is associated with particular patterns of GAG (glycosaminoglycan) expression. For example, different HS epitopes are synthesized during neural or mesodermal lineage formation. Cell lines mutant for various components of the HS biosynthetic pathway are selectively impaired in their differentiation, with lineage-specific effects observed for some lines. We have also observed that the addition of soluble GAG saccharides to cells, with or without cell-surface HS, can influence the pace and outcome of differentiation, again highlighting specific pattern requirements for particular lineages. We are combining this work with ongoing studies into the design of artificial cell environments where we have optimized three-dimensional scaffolds, generated by electrospinning or by the formation of hydrogels, for the culture of ES cells. By permeating these scaffolds with defined GAG oligosaccharides, we intend to control the mechanical environment of the cells (via the scaffold architecture) as well as their biological signalling environment (using the oligosaccharides). We predict that this will allow us to control ES cell pluripotency and differentiation in a three-dimensional setting, allowing the generation of differentiated cell types for use in drug discovery/testing or in therapeutics.
Urinary glycan markers for disease
Authors: Alonzi Dominic S. , Su Ying-Hsiu , Butters Terry D.
Published: January 2011

Robust assays for the isolation and characterization of urinary FOS (free oligosaccharides) have been developed to screen patients for altered protein and/or lipid glycosylation. A FOS analysis can therefore identify potential biomarkers for hepatocellular carcinoma, since variations in glycosylation as a result of tumorigenecity should be detectable in the FOS of patients. HCC (hepatocellular carcinoma) accounts for 80–90% of all liver cancers. It occurs more often in men than women and occurs mostly in people 50–60 years old. The disease is more common in parts of Africa and Asia than in North or South America and Europe. Using a combination of solid-phase extraction techniques and affinity chromatography, followed by separation of urinary FOS by NP (normal phase)-HPLC and HIAX (hydrophilic interaction and anion-exchange)-HPLC, more than 200 different species have been identified in patient samples. The high incidence of small sialylated oligosaccharides in HCC patients suggests that pro-inflammatory markers may be detected as early indicators of disease progression. In addition, the methods developed here to isolate and analyse excreted glycoprotein- and glycosphingolipid-bound oligosaccharides have been used to characterize changes in metabolic processes that underlie a number of human genetic disorders. The ability to predict disease status in microlitre amounts of readily available non-invasive urine samples indicates that rapid methods for screening can be developed.
Glycobiomarkers by glycoproteomics and glycan profiling (glycomics): emergence of functionality
Authors: Gabius Hans-Joachim
Published: January 2011

Glycans stand out from all classes of biomolecules because of their unsurpassed structural complexity. This is generated by variability in anomeric status of the glycosidic bond and its linkage points, ring size, potential for branching and introduction of diverse site-specific substitutions. What poses an enormous challenge for analytical processing is, at the same time, the basis for the fingerprint-like glycomic profiles of glycoconjugates and cells. What's more, the glycosylation machinery is sensitive to disease manifestations, earning glycan assembly a reputation as a promising candidate to identify new biomarkers. Backing this claim for a perspective in clinical practice are recent discoveries that even seemingly subtle changes in the glycan structure of glycoproteins, such as a N-glycan core substitution by a single sugar moiety, have far-reaching functional consequences. They are brought about by altering the interplay between the glycan and (i) its carrier protein and (ii) specific receptors (lectins). Glycan attachment thus endows the protein with a molecular switch and new recognition sites. Co-ordinated regulation of glycan display and presentation of the cognate lectin, e.g. in cancer growth regulation exerted by a tumour suppressor, further exemplifies the broad functional dimension inherent to the non-random shifts in glycosylation. Thus studies on glycobiomarkers converge with research on how distinct carbohydrate determinants are turned into bioactive signals.
Low noise constant current source for bias dependent noise measurements
Authors: Talukdar D. , Chakraborty R. K. , Bose Suvendu , Bardhan K. K.
Published: January 2011

A low noise constant current source used for measuring the 1/f noise in disordered systems in ohmic as well as nonohmic regime is described. The source can supply low noise constant current starting from as low as 1 μA to a few tens of milliampere with a high voltage compliance limit of around 20 V. The constant current source has several stages, which can work in a standalone manner or together to supply the desired value of load current. The noise contributed by the current source is very low in the entire current range. The fabrication of a low noise voltage preamplifier modified for bias dependent noise measurements and based on the existing design available in the MAT04 data sheet is also described.
Ultraviolet superfluorescence from oxygen vacancies in WO3−x nanowires at room temperature
Authors: Luo Jian Yi , Xu Ning Sheng , Zhao Fu Li , Deng Shao Zhi , Tao Yu Ting
Published: January 2011

We report the first observation of ultraviolet superfluorescence (SF) from oxygen vacancies in WO3−x nanowires at room temperature, and of picosecond-scale energy transfer between emission centers (oxygen vacancies) in a plane. A theoretical development from Dicke’s model leads to general formulation for a two-dimensional system, and is applied to explain the energy transfer process. The results demonstrate a possibility to generate ultrafast pulse of ultraviolet light through SF from a localized ensemble of defect states.
Magnetic field effects on tactoids of plate-like colloids
Authors: Verhoeff A. A. , Otten R. H. J. , van der Schoot Paul , Lekkerkerker H. N. W.
Published: January 2011

We investigate the effect of a magnetic field on the shape and director field of nematic droplets in dispersions of sterically stabilized and charge-stabilized colloidal gibbsite platelets with a negative diamagnetic anisotropy. Depending on the magnetic field strength and tactoid size, we observe with polarized light microscopy several interesting structures, with different shapes and director fields both with and without defects. In particular, our findings provide the first experimental evidence for the existence of the split-core defect structure predicted ten years ago by Mkaddem and Gartland [Phys. Rev. E 62, 6694 (2000)]. The split-core structure is a metastable director-field configuration that can be stabilized by a sufficiently strong externally applied magnetic field but only if the diamagnetic anisotropy of the particles is negative. To account for our observations, we present a calculation of the stability regions of different shapes and director-field structures as a function of tactoid size, anchoring conditions, surface tension, elastic constants, and magnetic field strength. By fitting the experimental data to the theoretically predicted structures, we are able to extract values for the splay elastic constant, interfacial tension, and anchoring strength. Remarkably, we find significant differences between the two systems studied: for sterically stabilized gibbsite in bromotoluene the anchoring strength is one order of magnitude larger than that of aqueous gibbsite, with the latter exhibiting weak and the former strong anchoring of the director field to the interface. The splay elastic constants that we obtain are in agreement with earlier experiments, simulations, and theory, while the interfacial tension and anchoring strength are considerably larger than what was found in earlier experiments.
A tight binding model for water
Authors: Paxton A. T. , Kohanoff J. J.
Published: January 2011

We demonstrate for the first time a tight binding model for water incorporating polarizable oxygen atoms. A novel aspect is that we adopt a “ground up” approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical Hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up toward the limit of bulk liquid. We concentrate on properties of liquid water, particularly dielectric constant and self diffusion coefficient, which are very well rendered in comparison with experiment. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond.
Magnetic properties of nanocrystallized nickel films on gold substrate deposited by cathodic voltammetry: Scan rate induced effects
Authors: Nzoghé-Mendome Lény , Ebothé Jean , Molinari Michael
Published: January 2011

Ni electrodeposits of thickness values ranged from 70 nm till about 1.20 μm and grown on gold substrate by cathodic voltammetry (C-V) technique are investigated varying the scan rate (r) of the related (C-V) curves in the interval 0.167<r<1.67 mV/s. The system engenders thinner films having rougher surfaces for higher r values while lower ones leads to thicker and smoother samples. Their magnetic reversal is ruled by the domain wall (DW) nucleation and motion. Their ferromagnetic-topography dependence reveals the existence of a critical thickness dc∼375 nm for both their microstructure and magnetic nanostructure. Their magnetic domain sizes (w) evolution with the sample roughness is typical of the Bloch domain type (MD)B below dc while the Néel type (MD)N appears beyond dc according to the topography-based model of Zhao et al. [J. Appl. Phys. 89, 1325 (2001)]. The magnetic anisotropy of the Ni samples exhibits a predominant parallel component for the thinnest sample while the perpendicular one grows with the thickness increase.
On the equilibrium structures of the complexes H2C3H+·Ar and c-${\rm C}_{\rm 3} {\rm H}_{\rm 3}^{\rm + }$C3H3+·Ar: Results of explicitly correlated coupled cluster calculations
Authors: Botschwina Peter , Oswald Rainer
Published: January 2011

Explicitly correlated coupled cluster theory at the CCSD(T)-F12x (x = a, b) level [T. B. Adler et al., J. Chem. Phys. 127, 221106 (2007)] has been employed in a study of the potential energy surfaces for the complexes H2C3H+·Ar and c-${\rm C}_{\rm 3} {\rm H}_{\rm 3}^{\rm + }$C3H3+·Ar. For the former complex, a pronounced minimum with Cs symmetry was found (De ≈ 780 cm−1), well below the local “H-bound” minimum with C2v symmetry (De ≈ 585 cm−1). The absorption at 3238 cm−1 found in the recent infrared photodissociation spectra [A. M. Ricks et al., J. Chem. Phys. 132, 051101 (2010)] is, thus, interpreted as an essentially free acetylenic CH stretching vibration of the propargyl cation. A global minimum of Cs symmetry was also obtained for c-${\rm C}_{\rm 3} {\rm H}_{\rm 3}^{\rm + }$C3H3+ (De ≈ 580 cm−1), but the energy difference with respect to the local C2v minimum is only 54 cm−1.
Effects of electrostatic potential and shape on diffusion-controlled reaction at an elliptic site
Authors: Strieder William
Published: January 2011

The calculation of the diffusion-controlled reaction rate of an ionic reactant on a charged elliptic site is performed in order to examine the interaction of the site charge and shape. In the absence of site charge, the reaction rate for a fixed site area is always enhanced with decrease in circularity (ratio of minor to major axis lengths), going to infinity as the circularity vanishes to zero. In the case of attractive ion-site charge forces for any finite circularity, but a very large site charge, the shape enhancement is suppressed. For repulsive ion-site forces with a very large site charge and the same finite circularity, the shape enhancement effect on the site reaction rate is increased. Away from these large site charge limits for more typical ion-site charge pairs and site circularities the same trends are observed. The results shed light on experimental and numerical simulation phenomena observed for both repulsive and attractive reactant ion-charged site pairs.