bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metatranscriptomic analysis of extremely halophilic viral communities
Authors: Santos Fernando , Moreno-Paz Mercedes , Meseguer Inmaculada , López Cristina , Rosselló-Mora Ramon , Parro Víctor , Antón Josefa 
Published: April 2011

Abstract
Hypersaline environments harbour the highest number of viruses reported for aquatic environments. In crystallizer ponds from solar salterns, haloviruses coexist with extremely halophilic Archaea and Bacteria and present a high diversity although little is known about their activity. In this work, we analyzed the viral expression in one crystallizer using a metatranscriptomic approach in which clones from a metaviromic library were immobilized in a microarray and used as probes against total mRNA extracted from the hypersaline community. This approach has two advantages: (i) it overcomes the fact that there is no straightforward, unambiguous way to extract viral mRNA from bulk mRNAs and (ii) it makes the sequencing of all mRNAs unnecessary. Transcriptomic data indicated that the halovirus assemblage was highly active at the time of sampling and the viral groups with the highest expression levels were those related to high GC content haloarchaea and Salinibacter representatives, which are minor components in the environment. Moreover, the changes in the viral expression pattern and in the numbers of free viral particles were analyzed after submitting the samples to two stress conditions: ultraviolet-radiation and dilution. Results showed that Archaea were more sensitive than Bacteria to these stress conditions. The overexpression in the predicted archaeal virus fraction raised and the total numbers of free viruses increased. Furthermore, we identified some very closely related viral clones, displaying single-nucleotide polymorphisms, which were expressed only under certain conditions. These clones could be part of very closely related virus genomes for which we propose the term ‘ecoviriotypes’.
Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane
Authors: Levine Uri Y , Teal Tracy K , Robertson G Philip , Schmidt Thomas M 
Published: April 2011

Abstract
Agriculture has marked impacts on the production of carbon dioxide (CO2) and consumption of methane (CH4) by microbial communities in upland soils—Earth's largest biological sink for atmospheric CH4. To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH4-oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH4 and CO2 at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH4 consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH4 consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH4 consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO2 emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH4 oxidation, as compared with processes driven by widely distributed metabolic processes, like CO2 production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.
Birth Control Does Not Significantly Alter Women’s Preferences for Variants of Men’s Voices
Authors: Whitaker Jason W. , Setten Ryan , Ankerstjerne Ulv 
Published: April 2011

AbstractResearch shows that women‘s preferences for masculine voices (low pitch) vary as a function of the menstrual cycle, becoming positively augmented around ovulation. The proximate cause catalyzing this effect is attributed to fluctuating estrogen levels. Thus, the introduction of hormonally based birth control has been to shown to have a dampening effect in experiments researching women‘s preference of dimorphic secondary sexual characteristics. However, this dampening effect has not yet been explored in respect to women‘s preferences for masculine voice types. This experiment sought, first, to investigate the effect of birth control on subjects off and on birth control; and, second, to replicate past findings: Women‘s preference for masculine voice types increases during ovulation.Six voice stimuli were created from voice recordings of two men speaking monopthong vowels. Each recording‘s pitch was increased or decreased 3%. Subjects rated the attractiveness of each stimulus using a five point Likert type scale. Results showed that women (n = 145; 85 off and 60 on birth control, average age = 23.1±4.57) preferred the naturally lower pitched voice; though, this preference could not be attributed to pitch, solely. Fourth order polynomial regression analysis revealed preference for deep voice pitch was not influenced by ovulation, though significant fluctuation in preference occurred over the cycle. Lastly, there were no significant differences in preference scores between the on and off birth control samples. The authors discuss multiple methodological and statistical methods in respect to these novel findings.
Sophistopolis as Cosmopolis: Reading Postclassical Greek Rhetoric
Authors: Jarratt Susan C. 
Published: April 2011

ABSTRACTThis article examines the interplay between the Stoic concept of cosmopolis and Greek rhetorical discourses of the polis in the Roman imperial period. D. A. Russell's “Sophistopolis” (from Greek Declamation, 1983) and Doyne Dawson's work on utopian political theory (1992) serve as points of departure for developing a method of reading the political in Second Sophistic rhetoric. The text under examination is a major first-century oration: Dio Chrysostom's Euboean Discourse. Composed around 96 CE, after Dio's return from exile by Domitian, the Euboicus combines a castaway's rural fable with didactic commentary, forcing the utopian pastoral hard up against a lecture on economic and social distress in the imperial city. Dio creates disjunctive moods, city-visions, and speaking personae, performing a rhetorical tour de force while simultaneously constructing a political subject at the limit of creaturely need. A “cosmopolitical” analysis of Second Sophistic rhetoric finds the consummate artistry of the paideia addressed to imperial power and provincial realities, revealing civic breakdown and human suffering in the city-spaces of empire.
Nietzsche's Sophist: Rhêtôr, Musician, Stoic
Authors: Crick Nathan 
Published: April 2011

ABSTRACT
Traditional readings of Nietzsche's essay “On Truth and Lying in a Non-Moral Sense” tend to emphasize the clash between philosophy and rhetoric in the form of two distinct personae—the intuitive, Sophistical artist who embraces the rhetorical power of language to create and destroy on the one hand, and the rational, Stoic philosopher who uses concepts to order the world into a block universe on the other. However, I argue that his essay presents us with not two characters but three—the Stoic philosopher, political rhêtôr, and the Dionysian artist. Furthermore, none of these three characters can be said to be representative of Nietzsche's attitude toward the Sophists. This article thus proposes a model of the Sophistical artist which combines aspects from each of these personae in a way that brings together the power of tragic suffering, persuasive word, and passionate music, respectively. This reading of Nietzsche's work discloses an ideal image of a “new” Sophist as an unfettered spirit for whom Dionysian music and philosophical word cooperate to produce a complex rhetorical discourse capable of overcoming the nihilism of the modern age in order to produce a higher culture. This attitude would therefore make the new Sophist capable of grand aspirations and opportune actions while always remaining cognizant of the sublime and terrible nature that underlies his fragile dreams of beauty.
Anesthetic Ketamine Impairs Rats' Recall of Previous Information
Authors: Boultadakis Antonios , Pitsikas Nikolaos 
Published: April 2011

Background
There is poor experimental evidence concerning the effects of anesthetic doses of the noncompetitive N-methyl-D-aspartate receptor antagonist ketamine on rodents' memory abilities. The current study was designed (1) to investigate the consequences of posttraining administration of anesthetic ketamine (100 mg/kg intraperitoneally) on rats' recognition memory and (2) to evaluate the ability of the nitric oxide synthase inhibitor N-nitro-L-arginine methylester (L-NAME; 1, 3, and 10 mg/kg intraperitoneally) to counteract the expected behavioral deficits produced by anesthetic ketamine. Finally, in an attempt to clarify if the expected memory impairments produced by anesthetic ketamine were related to the anesthesia, we also tested the effects of a subanesthetic dose of it (3 mg/kg intraperitoneally) on rats' recognition memory.

Methods
The novel object recognition test, a procedure assessing recognition memory in rats, was selected.

Results
Posttraining administration of anesthetic (but not of subanesthetic) ketamine disrupted rats' performance in the novel object recognition paradigm. The discrimination index (D) was decreased by ketamine from 0.415 (using saline) to 0.128, thus indicating that the anesthetic dose of ketamine impaired recognition memory. L-NAME (1-3, but not 10, mg/kg) reversed this memory deficit produced by ketamine; the D index of 0.128 using ketamine treatment was increased by 1 and 3 mg/kg L-NAME to 0.427 and 0.478, respectively.

Conclusions
The current results indicate that anesthetic ketamine impaired rats' posttraining memory components (storage and/or retrieval of information) and that a nitric oxide component modulates its behavioral effects.
High-Resolution Secondary Ion Mass Spectrometry Reveals the Contrasting Subcellular Distribution of Arsenic and Silicon in Rice Roots
Authors: Moore Katie L. , Schröder Markus , Wu Zhongchang , Martin Barry G.H. , Hawes Chris R. , McGrath Steve P. , Hawkesford Malcolm J. , Feng Ma Jian , Zhao Fang-Jie , Grovenor Chris R.M. 
Published: April 2011

AbstractRice (Oryza sativa) takes up arsenite mainly through the silicic acid transport pathway. Understanding the uptake and sequestration of arsenic (As) into the rice plant is important for developing strategies to reduce As concentration in rice grain. In this study, the cellular and subcellular distributions of As and silicon (Si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy. Rice plants, both the lsi2 mutant lacking the Si/arsenite efflux transporter Lsi2 and its wild-type cultivar, with or without an iron plaque, were treated with arsenate or arsenite. The formation of iron plaque on the root surface resulted in strong accumulation of As and phosphorous on the epidermis. The lsi2 mutant showed stronger As accumulation in the endodermal vacuoles, where the Lsi2 transporter is located in the plasma membranes, than the wild-type line. As also accumulated in the vacuoles of some xylem parenchyma cells and in some pericycle cells, particularly in the wild-type mature root zone. Vacuolar accumulation of As is associated with sulfur, suggesting that As may be stored as arsenite-phytochelatin complexes. Si was localized in the cell walls of the endodermal cells with little apparent effect of the Lsi2 mutation on its distribution. This study reveals the vacuolar sequestration of As in rice roots and contrasting patterns of As and Si subcellular localization, despite both being transported across the plasma membranes by the same transporters.
Physical and mental health in severe opioid‐dependent patients within a randomized controlled maintenance treatment trial
Authors: Reimer Jens , Verthein Uwe , Karow Anne , Schäfer Ingo , Naber Dieter , Haasen Christian 
Published: April 2011

ABSTRACTAims  To evaluate physical and mental health and compare treatment outcomes in opiate‐dependent patients substituted either with heroin or methadone.Design  Twelve‐month open‐label randomized controlled trial.Setting  Out‐patient substitution clinics in seven German cities.Participants  A total of 1015 opiate‐dependent individuals.Measurements  Opiate Treatment Index–Health Scale Score (OTI), Body Mass Index (BMI), serology for infectious diseases such as hepatitis B, C and human immunodeficiency virus as well as tuberculosis, Karnofsky Performance Scale (KPS), electrocardiogram (ECG), echocardiogram, Symptom Checklist 90‐R (SCL‐90‐R), Global Assessment of Functioning (GAF), Modular System for Quality of Life and study medication‐related serious adverse events (SAE).Findings  Improvements were found in both heroin and methadone substituted patients regarding OTI, BMI, KPS, SCL‐90‐R, and GAF, but they were more pronounced for the heroin group (analysis of variance, all P = 0.000). The frequency of pathological echocardiograms decreased in the heroin group and increased in the methadone group (χ2 test, <0.05). Markers for infectious diseases and frequencies of pathological ECGs did not differ between baseline and 12 months, or between treatment groups. Study medication‐related serious adverse events, all of which were treated successfully, occurred 2.5 times more often in the heroin group. The majority of heroin‐related SAEs (41 of 58) occurred within a few minutes of the injections.Conclusions  The integration of severe injection drug users either in methadone or heroin‐assisted maintenance treatment has positive effects on most physical and mental change‐sensitive variables, with heroin showing superior results. Due to medication‐related adverse events, patients should be observed for 15 minutes after a heroin injection.
Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites
Authors: Zhong T. , Han J. L. , Guo J. , Zhao Q. J. , Fu B. L. , Pu Y. B. , He X. H. , Jeon J. T. , Guan W. J. , Ma Y.‐H. 
Published: April 2011

SummaryThe genetic consequences of population differentiation and isolation have been the subject of conservation biology. In this study, we analysed the genetic diversity and structure of Mongolian sheep in China. These animals belong to a traditional local breed with high production, extensive adaption, early maturity and roughage resistance. For this purpose, 26 microsatellites were genotyped for five Mongolian sheep populations. The Bayesian clustering indicated five clusters as the most probable genetic structure of the populations investigated. In addition, a clear genetic structure was revealed in three populations distributed at large geographical scales, while the other cluster encompassed UQ and HLBR sheep that displayed no clear differentiation, probably due to their close and small geographical distributions. Overall, our results are helpful in understanding the interplay of population dynamics in these close genetic lineages of Mongolian sheep.
Cattle and chemokines: evidence for species‐specific evolution of the bovine chemokine system
Authors: Widdison S. , Coffey T. J. 
Published: April 2011

SummaryThe chemokine system comprises a family of small chemoattractant molecules that have roles in both the healthy and diseased organism. Chemokines act by binding specific receptors on the target cell surface and inducing chemotaxis. The human chemokine system is well characterized, with approximately fifty chemokines identified that fall into four families. The chemokines and their receptors are promiscuous in that one chemokine can often bind several receptors, and vice versa. Study of the bovine chemokine system has been restricted to date to a handful of chemokines, and the identification of bovine chemokines is largely based on the closest human homologue. This method of identification is prone to error and may result in the misassumption of function of a particular chemokine. Here, we review current knowledge of bovine chemokines and reassess the bovine chemokine system based on phylogenetic and syntenic approaches. The bovine chemokine system, for the most part, shows high similarity to the chemokine system of other mammals such as humans; however, differences have been identified. Cattle possess fewer chemokines than humans, yet also possess chemokines that have no obvious homologue in the human system. These ‘missing’ and ‘novel’ chemokines may represent functional differences between the bovine and human chemokine systems that may affect the way in which these species are able to respond to specific pathogen repertoires.
Dispersal in the course of an invasion
Authors: NOLTE ARNE W. 
Published: April 2011

Invasive species receive attention as manifestations of global ecological change and because of the effects that they may have on other organisms. They are commonly discussed in the context of the ecological perturbations or the human activities that permitted the invasion. There is also evidence, that there is an intrinsic component to biological invasions in that evolutionary changes of the invaders themselves can facilitate or limit invasions (Lee 2002; Urban et al. 2007; Van Bocxlaer et al. 2010). Hence, teasing apart whether environmental change or changes of the organism foster invasions is an interesting field of research. Ample evidence for plants and animals documents that ecological change and human activities trigger range expansions and invasions, but questions regarding evolutionary change of invaders remain less explored although there are several reasons to believe it matters. Firstly, rapid evolutionary change is possible in timeframes relevant for contemporary biological invasions (Hendry et al. 2007). Furthermore, population genetic modelling suggests that there are circumstances where the range expansion and colonization of empty spaces in the course of an invasion can induce evolutionary change in a way that is specific to invaders: the process of repeated founding out of marginal populations in the course of a range expansion can shift allele frequencies and has been referred to as allele surfing, which not only affects neutral genetic variance, but also fitness relevant traits (Klopfstein et al. 2006; Travis et al. 2007; Burton & Travis 2008). Importantly, this process poses a null model for evolutionary inference in invasive populations. It predicts conspicuous allele frequency changes in an expanding metapopulation unless migration homogenizes the gene pool. Despite this relevance, ideas about allele surfing rely heavily on modelling although some experimental evidence comes from studies that document the segregation of genetic variants in growing plaques of bacteria (Hallatschek et al. 2007). To date, little empirical data is available that would reveal the migration processes that affect the establishment of gene pools at invasion fronts in natural systems. This aspect sets the study of Bronnenhuber et al. (2011) apart. They quantify migration behind the expansion front of an invading fish and thus provide important baseline data for the interpretation of the emerging patterns of genetic differentiation.
Circuitry linking the Csr and stringent response global regulatory systems
Authors: Edwards Adrianne N. , Patterson‐Fortin Laura M. , Vakulskas Christopher A. , Mercante Jeffrey W. , Potrykus Katarzyna , Vinella Daniel , Camacho Martha I. , Fields Joshua A. , Thompson Stuart A. , Georgellis Dimitris , Cashel Michael , Babitzke Paul , Romeo Tony 
Published: April 2011

SummaryCsrA protein regulates important cellular processes by binding to target mRNAs and altering their translation and/or stability. In Escherichia coli, CsrA binds to sRNAs, CsrB and CsrC, which sequester CsrA and antagonize its activity. Here, mRNAs for relA, spoT and dksA of the stringent response system were found among 721 different transcripts that copurified with CsrA. Many of the transcripts that copurified with CsrA were previously determined to respond to ppGpp and/or DksA. We examined multiple regulatory interactions between the Csr and stringent response systems. Most importantly, DksA and ppGpp robustly activated csrB/C transcription (10‐fold), while they modestly activated csrA expression. We propose that CsrA‐mediated regulation is relieved during the stringent response. Gel shift assays confirmed high affinity binding of CsrA to relA mRNA leader and weaker interactions with dksA and spoT. Reporter fusions, qRT‐PCR and immunoblotting showed that CsrA repressed relA expression, and (p)ppGpp accumulation during stringent response was enhanced in a csrA mutant. CsrA had modest to negligible effects on dksA and spoT expression. Transcription of dksA was negatively autoregulated via a feedback loop that tended to mask CsrA effects. We propose that the Csr system fine‐tunes the stringent response and discuss biological implications of the composite circuitry.
Two gene clusters co‐ordinate for a functional N‐acetylglucosamine catabolic pathway in Vibrio cholerae
Authors: Ghosh Swagata , Rao K. Hanumantha , Sengupta Manjistha , Bhattacharya Sujit K. , Datta Asis 
Published: April 2011

SummaryPathogenic microorganisms like Vibrio cholerae are capable of adapting to diverse living conditions, especially when they transit from their environmental reservoirs to human host. V. cholerae attaches to N‐acetylglucosamine (GlcNAc) residues in glycoproteins and lipids present in the intestinal epithelium and chitinous surface of zoo‐phytoplanktons in the aquatic environment for its survival and colonization. GlcNAc utilization thus appears to be important for the pathogen to reach sufficient titres in the intestine for producing clinical symptoms of cholera. We report here the involvement of a second cluster of genes working in combination with the classical genes of GlcNAc catabolism, suggesting the occurrence of a novel variant of the process of biochemical conversion of GlcNAc to Fructose‐6‐phosphate as has been described in other organisms. Colonization was severely attenuated in mutants that were incapable of utilizing GlcNAc. It was also shown that N‐acetylglucosamine specific repressor (NagC) performs a dual role – while the classical GlcNAc catabolic genes are under its negative control, the genes belonging to the second cluster are positively regulated by it. Further application of tandem affinity purification to NagC revealed its interaction with a novel partner. Our results provide a genetic program that probably enables V. cholerae to successfully utilize amino – sugars and also highlights a new mode of transcriptional regulation, not described in this organism.
Tapping into the biofilm: insights into assembly and disassembly of a novel amyloid fibre in Bacillus subtilis
Authors: Driks Adam 
Published: April 2011

SummaryThe Bacillus subtilis biofilm matrix harbours a functionally important amyloid fibre network composed of the protein TasA. Previous studies showed that the protein TapA (formerly YqxM) plays roles in TasA fibre formation and disassembly. In this issue, Romero et al., 2011 show that TapA is a component of the fibre and links it to the peptidoglycan. Therefore, TapA directs TasA fibre formation, links it to the cell wall and, most likely, participates in fibre dispersal. These results provide important insights into the control of biofilm formation in B. subtilis and, potentially, the regulation of amyloid fibre formation in diverse species.