bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium‐oxidizing bacteria
Authors: Schmid Markus C. , Hooper Alan B. , Klotz Martin G. , Woebken Dagmar , Lam Phyllis , Kuypers Marcel M. M. , Pommerening‐Roeser Andreas , Op Den Camp Huub J. M. , Jetten Mike S. M. 
Published: September 2008

SummaryBacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium‐oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N2. While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus‘Kuenenia stuttgartiensis’ showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein‐encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium‐oxidizing bacteria.
Relative abundance and diversity of ammonia‐oxidizing archaea and bacteria in the San Francisco Bay estuary
Authors: Mosier Annika C. , Francis Christopher A. 
Published: September 2008

SummaryAmmonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia‐oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia‐oxidizing archaea (AOA) and betaproteobacteria (β‐AOB) across physicochemical gradients in San Francisco Bay – the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than β‐AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that β‐AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia‐oxidizing archaea were only more pervasive than β‐AOB in the low‐salinity region of the estuary. Both AOA and β‐AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low‐salinity phylogenetic group. The majority of the β‐AOB sequences were closely related to other marine/estuarine Nitrosomonas‐like and Nitrosospira‐like sequences. Both ammonia‐oxidizer community composition and abundance were strongly correlated with salinity. Ammonia‐oxidizing enrichment cultures contained AOA and β‐AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia‐oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and β‐AOB phylotypes may thrive.
The microbial nitrogen cycle
Authors: Jetten Mike S. M. 
Published: September 2008

SummaryThis special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen‐fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite‐dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.
COMMON STOCHASTIC TRENDS AMONG THE CYPRUS STOCK EXCHANGE AND THE ASE, LSE AND NYSE
Authors: Constantinou Eleni , Kazandjian Avo , Kouretas Georgios P. , Tahmazian Vera 
Published: September 2008

ABSTRACTCommon stochastic trends among major international stock price indices have been an intensively analysed issue mainly as a result of the 1987 stock market crash and the need for policy coordination in financial markets. This paper investigates the existence of common stochastic trends among an emerging equity market, the Cyprus Stock Exchange, and three mature equity markets, namely the Athens Stock Exchange (ASE), the London Stock Exchange (LSE) and the New York Stock Exchange (NYSE).
THE SOURCES OF AGGREGATE PRODUCTIVITY GROWTH: US MANUFACTURING INDUSTRIES, 1958–1996
Authors: Krüger Jens J. 
Published: September 2008

ABSTRACTThe sources of aggregate productivity growth are explored using detailed data for four‐digit US manufacturing industries during 1958–96 and a decomposition formula that allows us to quantify the contribution of structural change. Labour productivity as well as total factor productivity are considered with either value‐added or employment shares serving as aggregation weights. It is shown that structural change generally works in favour of industries with increasing productivity. This effect is particularly strong in the years since 1990, in high‐tech industries and in durable goods producing industries. The impact of the computer revolution can be clearly identified.
NORMEN HOCHSPRACHLICHEN SPRECHENS ZWISCHEN SCHRIFTSPRACHE UND PLURIZENTRISCHER SPRACHKULTUR
Authors: Eichinger Ludwig M. 
Published: September 2008

ABSTRACTErst seit dem 19. Jahrhundert gewinnt die deutsche Hochsprache in ihrer gesprochenen Form in großen Kreisen der Bevölkerung an Bedeutung. Bis dahin spricht der Großteil der Bevölkerung eine jener regionalen Varietäten des Deutschen, die unter dem Eindruck der Ausbreitung der Hochsprache und von sogenannten Umgangssprachen eine Verschiebung ihrer Funktion mitmachen, als der Hochsprache gegenüberstehender Pol verstanden, so als ‘Dialekt’ wissenschaftlich beschrieben und ideologisch integriert werden. Spätestens seit der Mitte des 20. Jahrhunderts verändert sich der Sprachgebrauch in eine Richtung, die eine solche dichotomische Einordnung als obsolet erscheinen lässt. In den letzten zwei Jahrzehnten beobachtet man eine beschleunigte weiträumige und tiefgreifende Annäherung an die Standardsprache auch beim Sprechen. Das hat Konsequenzen für die normativen Vorstellungen von solch einer Sprachform, für die das Bild vom plurizentrischen Charakter des Deutschen keine hinreichende Basis mehr abgibt. Eine andere Frage ist, wie sich diese Entwicklungen angemessen modellieren lassen und welche Rolle die Kategorie Regionalität dabei spielt.
THE GERMAN LANGUAGE AND THE FUTURE OF EUROPE: TOWARDS A RESEARCH AGENDA ON THE POLITICS OF LANGUAGE
Authors: Stevenson Patrick 
Published: September 2008

ABSTRACTMost accounts of nationalism and national identity include the idea of a ‘national language’ as a foundational element and key organising principle, yet even before the advent of new technologies of communication these defining codes were rarely, if ever, contained within national boundaries. The coexistence of what are perceived as distinct linguistic varieties (‘languages’) is therefore the normal condition of the nation‐state. This contradiction between the multilingual reality of individuals and communities and what Ingrid Gogolin calls the ‘monolingual habitus’ is fundamental to Susan Gal's (2006) discussion of the ironies of linguistic regimes in contemporary Europe that continue to be based on Herderian principles in spite of the pluralising rhetoric of European institutions.In this paper, I start from Gal's observations on migration, minorities, and multilingualism in Europe and consider their implications for a research agenda on the politics of language that takes account of the multiple layers of language policy on the one hand and the complexity of individual experiences with language on the other. I then illustrate this agenda with reference to a project on the present relationship between the German language and different forms of social identification in central Europe.
Disentangling Energy Policy from Environmental Policy*
Authors: Lowry William R. 
Published: September 2008

Objectives. I attempt to disentangle energy policy from environmental policy in order to explain the shifting politics surrounding the former. I can then explain why energy policies have historically provided distributive benefits but also the implications of the fact that energy proposals have in recent years become more regulatory in nature.Methods. I use a range of methods. These include qualitative accounts of the evolution of energy policy, graphic depictions of congressional activity, spending, and partisanship, and multivariate analyses of oversight activities.Results. I find that policymakers have historically treated energy issues as distributive policy, resulting in an emphasis on spending and oversight but not on substantial legislation. Over the last three decades, as policymakers push energy proposals that are more regulatory in nature, energy politics have become more divisive and partisan.Conclusion. Ultimately, I conclude that the enactment of strong energy policies will necessarily involve conditions that have been conducive to passage of other strong regulatory policies.
Environmental Policy Attitudes: Issues, Geographical Scale, and Political Trust*
Authors: Konisky David M. , Milyo Jeffrey , Richardson Lilliard E. 
Published: September 2008

Objectives. This article examines environmental policy attitudes, focusing on the differences in preferences across issue type (i.e., pollution, resource preservation) and geographical scale (i.e., local, national, global). In addition, we study whether an individual's trust in government influences environmental policy attitudes.Methods. Analyzing data from the 2007 Cooperative Congressional Election Study, we estimate a series of OLS regression models to examine the public's environmental policy attitudes.Results. We find stronger public support for government action to address pollution issues than resources issues, and stronger support for local and national pollution abatement than dealing with global problems. We also find that Republicans and ideological conservatives are less likely to support further government effort to address the environment, and that more trusting individuals are more favorable to government action to address pollution and global issues.Conclusion. Environmental policy attitudes vary by the nature of the issue; however, political ideology and partisan affiliation are consistent predictors of preferences across issues, even when controlling for an individual's level of trust in government.
Exploring the Social Roots of Smart Growth Policy Adoption by Cities*
Authors: O'Connell Lenahan 
Published: September 2008

Objective. This study identifies: (1) the smart growth policies adopted in a sample of U.S. cities; and (2) the relative impact of four social factors—education, local environmental activism, race, and homeownership on policy adoption.Method. A survey was sent to planning and development officials in a sample of 340 cities.Results. On average, the cities have 4.96 smart growth policies on their books. Adoption of such policies is more associated with two indicators of the new political culture (NPC)—the presence of environmental activist groups at the local level and the percent of college‐educated residents—than with the percent of residents who are white or the percent who are homeowners.Conclusion. The smart growth movement at the local level is a product of the environmental concerns associated with the NPC and is more likely to influence the adoption of land‐preserving policies than land‐use‐intensifying policies.
Expression of PLUNC family members in benign and malignant salivary gland tumours
Authors: Vargas PA , Speight PM , Bingle CD , Barrett AW , Bingle L 
Published: September 2008

Objectives:  The aim of this study was to determine the expression of PLUNC proteins in benign and malignant salivary gland tumours and thus their potential use as diagnostic and / or prognostic tools.Materials and methods:  A tissue microarray was assembled from 64 salivary gland tumours including adenoid cystic carcinoma, carcinoma ex‐pleomorphic adenoma, mucoepidermoid carcinoma, polymorphous low‐grade adenocarcinoma, pleomorphic adenoma, acinic cell carcinoma, myoepithelial carcinoma and papillary cystadenocarcinoma. Clinicopathological data were collected retrospectively and immunohistochemical analysis of three PLUNC proteins (SPLUNC1, SPLUNC2 and LPLUNC1) was performed. Immunoreactivity was assessed as positive or negative.Results:  PLUNC expression was only found in mucoepidermoid carcinomas and papillary cystadenocarcinoma; all other tumours studied were negative. Mucin plugs, mucous and intermediate cells of mucoepidermoid carcinomas were positive for LPLUNC1 and SPLUNC2, but areas composed of epidermoid and clear cells were negative for all PLUNCs. Papillary cystadenocarcinoma was positive for all PLUNCs. No correlation was found with tumour grade or outcome.Conclusions:  Intense expression of two PLUNC proteins in mucous cells and mucin plugs of mucoepidermoid carcinoma and papillary cystadenocarcinoma indicate that they could be used as additional diagnostic tools in some equivocal cases, but further studies are needed to understand the biological processes involved in PLUNC expression.
Activity Patterns of a Neotropical Ambush Predator: Spatial Ecology of the Fer‐de‐lance (Bothrops asper, Serpentes: Viperidae) in Costa Rica
Authors: Wasko Dennis K. , Sasa Mahmood 
Published: September 2008

ABSTRACTPatterns of movement and space usage are important components of the ecology of any organism. Among snakes, this information is often lacking even for species that are abundant, ecologically important, and/or relevant to human health. We used radiotelemetry to examine the spatial ecology and behavior of the fer‐de‐lance (Bothrops asper), a highly venomous pit viper that is ubiquitous throughout much of Central America. Sixteen adult snakes were tracked over 2 yr in lowland rainforest of Costa Rica to determine home range, movement patterns, and foraging behavior. Consistent with previous descriptions, B. asper was found to be a highly nocturnal ambush predator, exhibiting virtually no activity during the day. Overall home range was determined using both minimum convex polygon (mean size = 5.95 ha) and 95 and 50 percent kernel density (mean size = 3.71 and 0.370 ha, respectively); home range size did not differ between males and females by any estimation method. Movement pattern was largely aseasonal and unrelated to any observed environmental conditions other than the daily low temperature. Most movements consisted of short (< 10 m) movements between daytime shelter and nocturnal ambush sites within a given area, interspersed with longer distance (> 50 m) movements to new foraging areas. Compositional analysis of habitat usage indicated an avoidance of developed areas and selection of swamp habitat. Most snakes had several activity cores (50% kernel density), the majority which were in or near swamps. These patterns suggest that space and habitat usage of fer‐de‐lance may be related to foraging strategy.
Complex Ciprofloxacin Resistome Revealed by Screening a
Pseudomonas aeruginosa
Mutant Library for Altered Susceptibility
Authors: Breidenstein Elena B. M. , Khaira Bhavjinder K. , Wiegand Irith , Overhage Joerg , Hancock Robert E. W. 
Published: September 2008

ABSTRACT

Pseudomonas aeruginosa
offers substantial therapeutic challenges due to its high intrinsic resistance to many antibiotics and its propensity to develop mutational and/or adaptive resistance. The PA14 comprehensive mutant library was screened for mutants exhibiting either two- to eightfold increased susceptibilities (revealing genes involved in intrinsic resistance) or decreased susceptibilities (mutational resistance) to the fluoroquinolone ciprofloxacin. Thirty-five and 79 mutants with increased and decreased susceptibilities, respectively, were identified, as confirmed by broth dilution.
Preclinical Characteristics of the Hepatitis C Virus NS3/4A Protease Inhibitor ITMN-191 (R7227)
Authors: Seiwert Scott D. , Andrews Steven W. , Jiang Yutong , Serebryany Vladimir , Tan Hua , Kossen Karl , Rajagopalan P. T. Ravi , Misialek Shawn , Stevens Sarah K. , Stoycheva Antitsa , Hong Jin , Lim Sharlene R. , Qin Xiaoli , Rieger Robert , Condroski Kevin R. , Zhang Hailong , Do Mary Geck , Lemieux Christine , Hingorani Gary P. , Hartley Dylan P. , Josey John A. , Pan Lin , Beigelman Leonid , Blatt Lawrence M. 
Published: September 2008

ABSTRACT
Future treatments for chronic hepatitis C virus (HCV) infection are likely to include agents that target viral components directly. Here, the preclinical characteristics of ITMN-191, a peptidomimetic inhibitor of the NS3/4A protease of HCV, are described. ITMN-191 inhibited a reference genotype 1 NS3/4A protein in a time-dependent fashion, a hallmark of an inhibitor with a two-step binding mechanism and a low dissociation rate. Under preequilibrium conditions, 290 pM ITMN-191 half-maximally inhibited the reference NS3/4A protease, but a 35,000-fold-higher concentration did not appreciably inhibit a panel of 79 proteases, ion channels, transporters, and cell surface receptors. Subnanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 4, 5, and 6, while single-digit nanomolar potency was observed against NS3/4A from genotypes 2b and 3a. Dilution of a preformed enzyme inhibitor complex indicated ITMN-191 remained bound to and inhibited NS3/4A for more than 5 h after its initial association. In cell-based potency assays, half-maximal reduction of genotype 1b HCV replicon RNA was afforded by 1.8 nM; 45 nM eliminated the HCV replicon from cells. Peginterferon alfa-2a displayed a significant degree of antiviral synergy with ITMN-191 and reduced the concentration of ITMN-191 required for HCV replicon elimination. A 30-mg/kg of body weight oral dose administered to rats or monkeys yielded liver concentrations 12 h after dosing that exceeded the ITMN-191 concentration required to eliminate replicon RNA from cells. These preclinical characteristics compare favorably to those of other inhibitors of NS3/4A in clinical development and therefore support the clinical investigation of ITMN-191 for the treatment of chronic hepatitis C.
Antimony Resistance and Trypanothione in Experimentally Selected and Clinical Strains of
Leishmania panamensis
Authors: Goyeneche-Patino Diego A. , Valderrama Liliana , Walker John , Saravia Nancy G. 
Published: September 2008

ABSTRACT

The participation of trypanothione in clinical and experimental antimony (Sb) resistance in
Leishmania panamensis
was examined by using specific inhibitors. Buthionine sulfoximine (BSO) significantly reversed the resistance to trivalent Sb (Sb
III
) of promastigotes of experimentally derived Sb-resistant lines, supporting the participation of a trypanothione-mediated mechanism of resistance. In contrast, promastigotes of strains isolated at the time of clinical treatment failure and resistant to pentavalent Sb (Sb
V
) as intracellular amastigotes were not cross resistant to Sb
III
, and BSO had little or no effect on susceptibility. Difluoromethylornithine did not alter the Sb
III
susceptibilities of experimentally selected lines or clinical strains. The mechanisms of acquired resistance emerging in clinical settings may differ from those selected by in vitro exposure to Sb.
A Type IV Secretion System Contributes to Intracellular Survival and Replication of
Burkholderia cenocepacia
Authors: Sajjan S. Umadevi , Carmody Lisa A. , Gonzalez Carlos F. , LiPuma John J. 
Published: September 2008

ABSTRACT

Burkholderia cenocepacia
is an important respiratory pathogen in persons with cystic fibrosis (CF). Recent studies indicate that
B. cenocepacia
survives within macrophages and airway epithelial cells in vitro by evading endosome-lysosome fusion. We investigated the role of a plasmid-encoded type IV secretion system in the intracellular survival, replication, and processing of
B. cenocepacia
. Both a wild-type strain (K56-2) and its type IV secretion system mutant (designated LC101) entered and replicated in CF airway epithelial cells and monocyte-derived macrophages. However, significantly more intracellular K56-2 than LC101 bacteria were found in both cell types at 24 h postinfection. Colocalization of bacteria with markers of the classical endocytic pathway indicated that although both K56-2 and LC101 reside transiently in early endosomes, a greater proportion of the mutant bacteria are targeted to lysosomal degradation. In contrast, wild-type bacteria escape from the classical endocytic pathway and traffic to the endoplasmic reticulum, where they replicate. Our results show that the intracellular processing of
B. cenocepacia
is similar in both professional and nonprofessional phagocytes and that a functional plasmid-encoded type IV secretion system contributes to the survival and replication of
B. cenocepacia
in eukaryotic cells.
Adenoviral Delivery of Interleukin-10 Fails To Attenuate Experimental Lyme Disease
Authors: Brown Charles R. , Lai Annie Y.-C. , Callen Steven T. , Blaho Victoria A. , Hughes Jennifer M. , Mitchell William J. 
Published: September 2008

ABSTRACTProduction of interleukin-10 (IL-10) by C57BL/6 mice following infection withBorrelia burgdorferihas been proposed as a mechanism whereby resistance to the development of experimental Lyme arthritis is maintained. In the current study, we sought to determine the role of IL-10 during infection of arthritis- and carditis-susceptible C3H mice. Infection of C3H IL-10−/−mice led to increased joint swelling and arthritis severity scores over those of wild-type C3H mice. Measurement ofB. burgdorferinumbers in joints or disseminated tissues indicated a more efficient clearance of spirochetes in the absence of IL-10, similar to that reported in C57BL/6 IL-10−/−mice. However, in contrast to previous in vitro work, infection of C3H IL-10−/−mice led to decreased in vivo expression of the cytokines KC, IL-1β, IL-4, and IL-12p70 in the infected joints. Finally, adenoviral expression of IL-10 in the infected joints of C3H mice was unable to modulate the development of severe Lyme arthritis and had no effect on spirochete clearance orBorrelia-specific antibody production. Development of Lyme carditis appeared to be independent of modulation by IL-10. These results suggest that IL-10 limits the development of joint inflammation in both arthritis-resistant and -susceptible mouse strains infected withB. burgdorferiand that increased IL-10 production cannot rescue genetic susceptibility to development of pathology in this model.