bluuebunny/crossref_metadata_2025 huggingface dataset:
Russia and the Baltic states: problematizing the Soviet legacy discourse
Authors: Nikitina Yulia
Published: January 2014

Most studies of the post-Soviet space often explicitly or implicitly analyze Russia not as a new independent state but as the political successor of the USSR, thereby almost automatically leading to conclusions about Russian neo-imperialism. This paper explains how distorted discourses on the Soviet legacy originated and how they obstruct equal relations between Russia and other former Soviet republics using the example of the Baltic states.
Comparison of home advantage in men's and women's football leagues in Europe
Authors: Pollard Richard , Gómez Miguel A.
Published: January 2014

Most research into home advantage is based on men's sports. This article analyses home advantage in the women's domestic football leagues of Europe and makes a comparison with the corresponding men's football leagues. A total of 47,042 games were included. From 2004 to 2010, home advantage existed in the domestic women's soccer leagues of all 26 European countries analysed, ranging from 51.0% to 58.8% and averaging 54.2%. In every country, this was less than the corresponding men's home advantage which averaged 60.0%. Crowd effects, both on players and referees, and different gender perceptions of territorial protection are plausible reasons for the differences found. Using a regression model that controlled for the competitive balance of each league, as well as for crowd size, the Gender Gap Index, which quantifies the status of women in each country, was a significant predictor of the difference between men's and women's home advantage. As the status of women becomes closer to that of men within a country, the difference in home advantage is less between the men's and women's football leagues.
Clonal expansion capacity defines two consecutive developmental stages of long-term hematopoietic stem cells
Authors: Grinenko Tatyana , Arndt Kathrin , Portz Melanie , Mende Nicole , Günther Marko , Cosgun Kadriye Nehir , Alexopoulou Dimitra , Lakshmanaperumal Naharajan , Henry Ian , Dahl Andreas , Waskow Claudia
Published: January 2014

Long-term hematopoietic stem cells (HSCs [LT-HSCs]) are well known to display unpredictable differences in their clonal expansion capacities after transplantation. Here, by analyzing the cellular output after transplantation of stem cells differing in surface expression levels of the Kit receptor, we show that LT-HSCs can be systematically subdivided into two subtypes with distinct reconstitution behavior. LT-HSCs expressing intermediate levels of Kit receptor (Kitint) are quiescent in situ but proliferate extensively after transplantation and therefore repopulate large parts of the recipient’s hematopoietic system. In contrast, metabolically active Kithi LT-HSCs display more limited expansion capacities and show reduced but robust levels of repopulation after transfer. Transplantation into secondary and tertiary recipient mice show maintenance of efficient repopulation capacities of Kitint but not of Kithi LT-HSCs. Initiation of differentiation is marked by the transit from Kitint to Kithi HSCs, both of which precede any other known stem cell population.
High c-Kit expression identifies hematopoietic stem cells with impaired self-renewal and megakaryocytic bias
Authors: Shin Joseph Y. , Hu Wenhuo , Naramura Mayumi , Park Christopher Y.
Published: January 2014

Hematopoietic stem cells (HSCs) are heterogeneous with respect to their self-renewal, lineage, and reconstitution potentials. Although c-Kit is required for HSC function, gain and loss-of-function c-Kit mutants suggest that even small changes in c-Kit signaling profoundly affect HSC function. Herein, we demonstrate that even the most rigorously defined HSCs can be separated into functionally distinct subsets based on c-Kit activity. Functional and transcriptome studies show HSCs with low levels of surface c-Kit expression (c-Kitlo) and signaling exhibit enhanced self-renewal and long-term reconstitution potential compared with c-Kithi HSCs. Furthermore, c-Kitlo and c-Kithi HSCs are hierarchically organized, with c-Kithi HSCs arising from c-Kitlo HSCs. In addition, whereas c-Kithi HSCs give rise to long-term lymphomyeloid grafts, they exhibit an intrinsic megakaryocytic lineage bias. These functional differences between c-Kitlo and c-Kithi HSCs persist even under conditions of stress hematopoiesis induced by 5-fluorouracil. Finally, our studies show that the transition from c-Kitlo to c-Kithi HSC is negatively regulated by c-Cbl. Overall, these studies demonstrate that HSCs exhibiting enhanced self-renewal potential can be isolated based on c-Kit expression during both steady state and stress hematopoiesis. Moreover, they provide further evidence that the intrinsic functional heterogeneity previously described for HSCs extends to the megakaryocytic lineage.
A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2
Authors: Gill Sukhvinder , Krupovic Mart , Desnoues Nicole , Béguin Pierre , Sezonov Guennadi , Forterre Patrick
Published: January 2014

We report the characterization of a DNA primase/polymerase protein (PolpTN2) encoded by the pTN2 plasmid from Thermococcus nautilus. Sequence analysis revealed that this protein corresponds to a fusion between an N-terminal domain homologous to the small catalytic subunit PriS of heterodimeric archaeal and eukaryotic primases (AEP) and a C-terminal domain related to their large regulatory subunit PriL. This unique domain configuration is not found in other virus- and plasmid-encoded primases in which PriS-like domains are typically fused to different types of helicases. PolpTN2 exhibited primase, polymerase and nucleotidyl transferase activities and specifically incorporates dNTPs, to the exclusion of rNTPs. PolpTN2 could efficiently prime DNA synthesis by the T. nautilus PolB DNA polymerase, suggesting that it is used in vivo as a primase for pTN2 plasmid replication. The N-terminal PriS-like domain of PolpTN2 exhibited all activities of the full-length enzyme but was much less efficient in priming cellular DNA polymerases. Surprisingly, the N-terminal domain possesses reverse transcriptase activity. We speculate that this activity could reflect an ancestral function of AEP proteins in the transition from the RNA to the DNA world.
Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast
Authors: Hirschmann Wolf D. , Westendorf Heidrun , Mayer Andreas , Cannarozzi Gina , Cramer Patrick , Jansen Ralf-Peter
Published: January 2014

The budding yeast multi-K homology domain RNA-binding protein Scp160p binds to >1000 messenger RNAs (mRNAs) and polyribosomes, and its mammalian homolog vigilin binds transfer RNAs (tRNAs) and translation elongation factor EF1alpha. Despite its implication in translation, studies on Scp160p's molecular function are lacking to date. We applied translational profiling approaches and demonstrate that the association of a specific subset of mRNAs with ribosomes or heavy polysomes depends on Scp160p. Interaction of Scp160p with these mRNAs requires the conserved K homology domains 13 and 14. Transfer RNA pairing index analysis of Scp160p target mRNAs indicates a high degree of consecutive use of iso-decoding codons. As shown for one target mRNA encoding the glycoprotein Pry3p, Scp160p depletion results in translational downregulation but increased association with polysomes, suggesting that it is required for efficient translation elongation. Depletion of Scp160p also decreased the relative abundance of ribosome-associated tRNAs whose codons show low potential for autocorrelation on mRNAs. Conversely, tRNAs with highly autocorrelated codons in mRNAs are less impaired. Our data indicate that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of tRNA pairing.
The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation
Authors: Posse Viktor , Hoberg Emily , Dierckx Anke , Shahzad Saba , Koolmeister Camilla , Larsson Nils-Göran , Wilhelmsson L. Marcus , Hällberg B. Martin , Gustafsson Claes M.
Published: January 2014

Mammalian mitochondrial transcription is executed by a single subunit mitochondrial RNA polymerase (Polrmt) and its two accessory factors, mitochondrial transcription factors A and B2 (Tfam and Tfb2m). Polrmt is structurally related to single-subunit phage RNA polymerases, but it also contains a unique N-terminal extension (NTE) of unknown function. We here demonstrate that the NTE functions together with Tfam to ensure promoter-specific transcription. When the NTE is deleted, Polrmt can initiate transcription in the absence of Tfam, both from promoters and non-specific DNA sequences. Additionally, when in presence of Tfam and a mitochondrial promoter, the NTE-deleted mutant has an even higher transcription activity than wild-type polymerase, indicating that the NTE functions as an inhibitory domain. Our studies lead to a model according to which Tfam specifically recruits wild-type Polrmt to promoter sequences, relieving the inhibitory effect of the NTE, as a first step in transcription initiation. In the second step, Tfb2m is recruited into the complex and transcription is initiated.
Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae
Authors: McIsaac R. Scott , Gibney Patrick A. , Chandran Sunil S. , Benjamin Kirsten R. , Botstein David
Published: January 2014

A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z3EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z3EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input–output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z3EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications.
Timing as an intrinsic property of neural networks: evidence from
in vivo
and
in vitro
experiments
Authors: Goel Anubhuti , Buonomano Dean V.
Published: January 2014

The discrimination and production of temporal patterns on the scale of hundreds of milliseconds are critical to sensory and motor processing. Indeed, most complex behaviours, such as speech comprehension and production, would be impossible in the absence of sophisticated timing mechanisms. Despite the importance of timing to human learning and cognition, little is known about the underlying mechanisms, in particular whether timing relies on specialized dedicated circuits and mechanisms or on general and intrinsic properties of neurons and neural circuits. Here, we review experimental data describing timing and interval-selective neurons
in vivo
and
in vitro
. We also review theoretical models of timing, focusing primarily on the state-dependent network model, which proposes that timing in the subsecond range relies on the inherent time-dependent properties of neurons and the active neural dynamics within recurrent circuits. Within this framework, time is naturally encoded in populations of neurons whose pattern of activity is dynamically changing in time. Together, we argue that current experimental and theoretical studies provide sufficient evidence to conclude that at least some forms of temporal processing reflect intrinsic computations based on local neural network dynamics.
Comparison of interval timing behaviour in mice following dorsal or ventral hippocampal lesions with mice having
δ
-opioid receptor gene deletion
Authors: Yin Bin , Meck Warren H.
Published: January 2014

Mice with cytotoxic lesions of the dorsal hippocampus (DH) underestimated 15 s and 45 s target durations in a bi-peak procedure as evidenced by proportional leftward shifts of the peak functions that emerged during training as a result of decreases in both ‘start’ and ‘stop’ times. In contrast, mice with lesions of the ventral hippocampus (VH) displayed rightward shifts that were immediately present and were largely limited to increases in the ‘stop’ time for the 45 s target duration. Moreover, the effects of the DH lesions were congruent with the scalar property of interval timing in that the 15 s and 45 s functions superimposed when plotted on a relative timescale, whereas the effects of the VH lesions violated the scalar property. Mice with DH lesions also showed enhanced reversal learning in comparison to control and VH lesioned mice. These results are compared with the timing distortions observed in mice lacking
δ
-opioid receptors (Oprd1
−/−
) which were similar to mice with DH lesions. Taken together, these results suggest a balance between hippocampal–striatal interactions for interval timing and demonstrate possible functional dissociations along the septotemporal axis of the hippocampus in terms of motivation, timed response thresholds and encoding in temporal memory.
Reading spike timing without a clock: intrinsic decoding of spike trains
Authors: Panzeri Stefano , Ince Robin A. A. , Diamond Mathew E. , Kayser Christoph
Published: January 2014

The precise timing of action potentials of sensory neurons relative to the time of stimulus presentation carries substantial sensory information that is lost or degraded when these responses are summed over longer time windows. However, it is unclear whether and how downstream networks can access information in precise time-varying neural responses. Here, we review approaches to test the hypothesis that the activity of neural populations provides the temporal reference frames needed to decode temporal spike patterns. These approaches are based on comparing the single-trial stimulus discriminability obtained from neural codes defined with respect to network-intrinsic reference frames to the discriminability obtained from codes defined relative to the experimenter's computer clock. Application of this formalism to auditory, visual and somatosensory data shows that information carried by millisecond-scale spike times can be decoded robustly even with little or no independent external knowledge of stimulus time. In cortex, key components of such intrinsic temporal reference frames include dedicated neural populations that signal stimulus onset with reliable and precise latencies, and low-frequency oscillations that can serve as reference for partitioning extended neuronal responses into informative spike patterns.
Timing in reward and decision processes
Authors: Bermudez Maria A. , Schultz Wolfram
Published: January 2014

Sensitivity to time, including the time of reward, guides the behaviour of all organisms. Recent research suggests that all major reward structures of the brain process the time of reward occurrence, including midbrain dopamine neurons, striatum, frontal cortex and amygdala. Neuronal reward responses in dopamine neurons, striatum and frontal cortex show temporal discounting of reward value. The prediction error signal of dopamine neurons includes the predicted time of rewards. Neurons in the striatum, frontal cortex and amygdala show responses to reward delivery and activities anticipating rewards that are sensitive to the predicted time of reward and the instantaneous reward probability. Together these data suggest that internal timing processes have several well characterized effects on neuronal reward processing.
Characterization and antigenicity of recombinant Campylobacter jejuni flagellar capping protein FliD
Authors: Yeh Hung-Yueh , Hiett Kelli L. , Line John E. , Seal Bruce S.
Published: January 2014

Campylobacter jejuni, a flagellated, spiral-rod, Gram-negative bacterium, is the leading pathogen of human acute bacterial gastroenteritis worldwide, and chickens are regarded as a major reservoir of this micro-organism. Bacterial flagella, composed of more than 35 proteins, play important roles in colonization and adhesion to the mucosal surface of chicken caeca. In this study, the flagellar capping protein, FliD, encoded by thefliDgene, from theCampylobacter jenuniD1-39 isolate was expressed and characterized, and its antigenicity determined. ThefliDgene comprised 1929 nt, potentially encoding a 642 aa peptide with a calculated molecular mass of 69.6 kDa. This gene was PCR amplified and overexpressed inEscherichia coli. The recombinant FliD protein was purified by cobalt-chelating affinity chromatography and confirmed by nucleotide sequencing of the expression plasmid, SDS-PAGE analysis, His tag detection and matrix-assisted laser desorption/ionization time of flight mass spectrometry. The immunoblot data showed that the purified recombinant FliD protein reacted strongly to sera from broiler chickens older than 4 weeks, indicating that anti-FliD antibody may be prevalent in the poultry population. These results provide a rationale for further evaluation of the FliD protein as a vaccine candidate for broiler chickens to improve food safety for poultry.
Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase
Authors: Ogata Hideaki , Decaneto Elena , Grossman Moran , Havenith Martina , Sagi Irit , Lubitz Wolfgang , Knipp Markus
Published: January 2014

Membrane type 1 matrix metalloproteinase (MT1-MMP) belongs to the large family of zinc-dependent endopeptidases termed MMPs that are located in the extracellular matrix. MT1-MMP was crystallized at 277 K using the vapour-diffusion method with PEG as a precipitating agent. Data sets for MT1-MMP were collected to 2.24 Å resolution at 100 K. The crystals belonged to space group P43212, with unit-cell parameters a = 62.99, c = 122.60 Å. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (V
M) of 2.90 Å3 Da−1; the solvent content is estimated to be 57.6%.
Crystallization and preliminary X-ray crystallographic analysis of the extracellular domain of LePRK2 from Lycopersicon esculentum
Authors: Xu Anbi , Huang Laiqiang
Published: January 2014

The tomato (Lycopersicon esculentum) pollen-specific receptor kinase 2 (LePRK2) is a member of the large receptor-like kinase (RLK) family and is expressed specifically in mature pollen and pollen tubes in L. esculentum. Like other RLKs, LePRK2 contains a characteristic N-terminal leucine-rich repeat (LRR) extracellular domain, the primary function of which is in protein–protein interactions. The LePRK2 LRR is likely to bind candidate ligands from the external environment, leading to a signal transduction cascade required for successful pollination. LePRK2-LRR was purified using an insect-cell secretion expression system and was crystallized using the vapour-diffusion method. The crystals diffracted to a resolution of 2.50 Å and belonged to space group I4122, with unit-cell parameters a = b = 93.94, c = 134.44 Å and one molecule per asymmetric unit.
Expression, purification, crystallization and preliminary X-ray analysis of full-length human RIG-I
Authors: Kwok Jane , Hui Kenrie P. Y. , Lescar Julien , Kotaka Masayo
Published: January 2014

The human innate immune system can detect invasion by microbial pathogens through pattern-recognition receptors that recognize structurally conserved pathogen-associated molecular patterns. Retinoic acid-inducible gene I (RIG-I)-like helicases (RLHs) are one of the two major families of pattern-recognition receptors that can detect viral RNA. RIG-I, belonging to the RLH family, is capable of recognizing intracellular viral RNA from RNA viruses, including influenza virus and Ebola virus. Here, full-length human RIG-I (hRIG-I) was cloned in Escherichia coli and expressed in a recombinant form with a His-SUMO tag. The protein was purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.85 Å resolution; the crystal belonged to space group F23, with unit-cell parameters a = b = c = 216.43 Å, α = β = γ = 90°.
Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA
Authors: Redondo Pilar , Merino Nekane , Villate Maider , Blanco Francisco J. , Montoya Guillermo , Molina Rafael
Published: January 2014

Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of DNA. The engineering of these enzymes provides novel instruments for genome modification in a wide range of fields, including gene targeting, by inducing specific double-strand breaks. I-CvuI is a homing endonuclease from the green alga Chlorella vulgaris. This enzyme was purified after overexpression in Escherichia coli. Crystallization experiments of I-CvuI in complex with its DNA target in the presence of Mg2+ yielded crystals suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 62.83, b = 83.56, c = 94.40 Å. The self-rotation function and the Matthews coefficient suggested the presence of one protein–DNA complex per asymmetric unit. The crystals diffracted to a resolution limit of 1.9 Å using synchrotron radiation.
Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 fromStrongylocentrotus purpuratus
Authors: Juneja Puneet , Rao Ashit , Cölfen Helmut , Diederichs Kay , Welte Wolfram
Published: January 2014

Sea urchin spicules have a calcitic mesocrystalline architecture that is closely associated with a matrix of proteins and amorphous minerals. The mechanism underlying spicule formation involves complex processes encompassing spatio-temporally regulated organic–inorganic interactions. C-type lectin domains are present in several spicule matrix proteins inStrongylocentrotus purpuratus, implying their role in spiculogenesis. In this study, the C-type lectin domain of SM50 was overexpressed, purified and crystallized using a vapour-diffusion method. The crystal diffracted to a resolution of 2.85 Å and belonged to space groupP212121, with unit-cell parametersa= 100.6,b= 115.4,c= 130.6 Å, α = β = γ = 90°. Assuming 50% solvent content, six chains are expected to be present in the asymmetric unit.
Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods
Authors: Santoferrara Luciana F. , Grattepanche Jean‐David , Katz Laura A. , McManus George B.
Published: January 2014

Assessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger‐sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error‐correcting algorithms for pyrosequences (‘denoising’) reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced operational taxonomic units (OTUs) were distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.
Pathway of nitrous oxide consumption in isolated Pseudomonas stutzeri strains under anoxic and oxic conditions
Authors: Desloover Joachim , Roobroeck Dries , Heylen Kim , Puig Sebastià , Boeckx Pascal , Verstraete Willy , Boon Nico
Published: January 2014

The microbial consumption of nitrous oxide (N2O) has gained great interest since it was revealed that this process could mitigate the greenhouse effect of N2O. The consumption of N2O results from its reduction to dinitrogen gas (N2) as part of the denitrification process. However, there is ongoing debate regarding an alternative pathway, namely reduction of N2O to NH4+, or assimilatory N2O consumption. To date, this pathway is poorly investigated and lacks unambiguous evidence. Enrichment of denitrifying activated sludge using a mineral nitrogen‐free medium rendered a mixed culture capable of anoxic and oxic N2O consumption. Dilution plating, isolation and deoxyribonucleic acid fingerprinting identified a collection of Pseudomonas stutzeri strains as dominant N2O consumers in both anaerobic and aerobic enrichments. A detailed isotope tracing experiment with a Pseudomonas stutzeri isolate showed that consumption of N2O via assimilatory reduction to NH4+ was absent. Conversely, respiratory N2O reduction was directly coupled to N2 fixation.
The energy‐conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane‐bound complexes, Hdr‐Flox and Rnf
Authors: Meyer Birte , Kuehl Jennifer V. , Price Morgan N. , Ray Jayashree , Deutschbauer Adam M. , Arkin Adam P. , Stahl David A.
Published: January 2014

The adaptation capability of Desulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying Desulfovibrio alaskensis strain G20 under varying respiratory, fermentative and methanogenic coculture conditions in chemostats. Transition from lactate to pyruvate in coculture resulted in a dramatic shift in the population structure and closer interspecies cell‐to‐cell interactions. Lower methane production rates in coculture than predicted from pyruvate input was attributed to redirection of electron flow to fumarate reduction. Without a methanogenic partner, accumulation of H2 and formate resulted in greater succinate production. Comparative transcript and gene fitness analysis in concert with physiological data of G20 wildtype and mutants demonstrated that pyruvate fermentation involves respiration of cytoplasmically formed fumarate using cytoplasmic and membrane‐bound energy‐conserving complexes, Rnf, Hdr‐Flox‐1 and Hmc. At the low H2/formate levels maintained in coculture, Rnf likely functions as proton‐pumping ferredoxin (Fd) : type‐I cytochrome c oxidoreductase, which transitions to a proton‐pumping Fdred : nicotinamide adenine dinucleotide (NAD+) oxidoreductase at high H2/formate levels during fermentation in monoculture. Hdr‐Flox‐1 is postulated to recycle Fdred via a flavin‐based electron bifurcation involving NADH, Fdox and the thiol/disulphide‐containing DsrC. In a menaquinone (MQ)‐based electron confurcation reaction, the high‐molecular‐weight cytochrome‐c3 complex, Hmc, is proposed to then couple DsrCred and periplasmic H2/formate oxidation using the MQ pool to fuel a membrane‐bound fumarate reductase.
The gill chamber epibiosis of deep‐sea shrimp Rimicaris exoculata: an in‐depth metagenomic investigation and discovery of Zetaproteobacteria
Authors: Jan Cyrielle , Petersen Jillian M. , Werner Johannes , Teeling Hanno , Huang Sixing , Glöckner Frank Oliver , Golyshina Olga V. , Dubilier Nicole , Golyshin Peter N. , Jebbar Mohamed , Cambon‐Bonavita Marie‐Anne
Published: January 2014

The gill chamber of deep‐sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin–Benson–Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp–epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at Rainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16S rRNA sequences and functional genes affiliated with iron‐oxidizing Zetaproteobacteria, which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Zetaproteobacteria in the R. exoculata gill chamber, thus providing the first evidence for a Zetaproteobacteria–invertebrate association.
Interplay between intrinsic and acquired resistance to quinolones in Stenotrophomonas maltophilia
Authors: García‐León Guillermo , Salgado Fabiola , Oliveros Juan Carlos , Sánchez María Blanca , Martínez José Luis
Published: January 2014

To analyse whether the mutation‐driven resistance‐acquisition potential of a given bacterium might be a function of its intrinsic resistome, quinolones were used as selective agents and Stenotrophomonas maltophilia was chosen as a bacterial model. S. maltophilia has two elements – SmQnr and SmeDEF – that are important in intrinsic resistance to quinolones. Using a battery of mutants in which either or both of these elements had been removed, the apparent mutation frequency for quinolone resistance and the phenotype of the selected mutants were found to be related to the intrinsic resistome and also depended on the concentration of the selector. Most mutants had phenotypes compatible with the overexpression of multidrug efflux pump(s); SmeDEF overexpression was the most common cause of quinolone resistance. Whole genome sequencing showed that mutations of the SmeRv regulator, which result in the overexpression of the efflux pump SmeVWX, are the cause of quinolone resistance in mutants not overexpressing SmeDEF. These results indicate that the development of mutation‐driven antibiotic resistance is highly dependent on the intrinsic resistome, which, at least for synthetic antibiotics such as quinolones, did not develop as a response to the presence of antibiotics in the natural ecosystems in which S. maltophilia evolved.
Sustained multiplicity in everyday cholesterol reduction: repertoires and practices in talk about ‘healthy living’
Authors: Will Catherine M. , Weiner Kate
Published: January 2014

This article is concerned with talk about and the practices of healthy living in relation to cholesterol reduction. It draws on qualitative interviews with 89 people who are current or former users of either cholesterol‐lowering functional foods or statins for cardiovascular risk reduction. Focusing on data about everyday activities including food preparation, shopping and exercise, we illustrate four repertoires that feature in talk about cholesterol reduction (health, pleasure, sociality and pragmatism). Using Gilbert and Mulkay's notion of a ‘reconciliation device’, we suggest ways in which apparently contradictory repertoires are combined (for example, through talk about moderation) or kept apart. We suggest that, in contrast to the interactiveness of the repertoires of health and pleasure, a pragmatic repertoire concerning food provisioning, storage and cooking as well as the realities of exercise, appears distinct from talk about health and is relatively inert. Finally we consider the implications of these discursive patterns for daily practices. Our data suggest there is little emphasis on coherence in people's practices and illustrate the significance of temporal, spatial and social distribution in allowing people to pursue different priorities in their everyday lives. Rather than the calculated trade‐offs of earlier medical sociology we draw on Mol to foreground the possibility of sustained multiplicity in daily practices.
How do values shape technology design? An exploration of what makes the pursuit of health and wealth legitimate in academic spin‐offs
Authors: Lehoux Pascale , Daudelin Geneviève , Hivon Myriam , Miller Fiona Alice , Denis Jean‐Louis
Published: January 2014

By actively supporting cooperation between academia, clinical settings and industry, several policy initiatives assume that the two policy agendas of health and wealth can be reconciled through the development of health technology. Our goal in this article is to shed light on the way the concurrent pursuit of health and wealth operates in practice by examining the valuation schemes, actions and decisions that shaped technology development in three Canadian spin‐offs. Drawing on the sociology of judgement, our analytical framework conceives of technology development as a purposive collective action that unfolds in a normatively heterogeneous context (one pervaded with both corporate and public service mission values and norms). Our qualitative empirical analyses explore four valuation schemes and their corresponding regimes of engagement that characterise why and how technology developers commit themselves to addressing certain clinical, interactional, organisational and economic concerns throughout the development process. Our discussion suggests that the ability to reconcile health and wealth goals is to be found in the moral repertoires that provide meaning to, and render coherent technology developers' participation in corporate activities driven by economic growth.
A relational approach to health practices: towards transcending the agency‐structure divide
Authors: Veenstra Gerry , Burnett Patrick John
Published: January 2014

Many health scholars find that Pierre Bourdieu's theory of practice leaves too little room for individual agency. We contend that, by virtue of its relational, field‐theoretic underpinnings, the idea of leaving room for agency in Bourdieu's theory of practice is misguided. With agency manifested in interactions and social structures consisting of relations built upon relations, the stark distinction between agency and structure inherent to substantialist thinking is undermined, even dissolved, in a relational field‐theoretic context. We also contend that, when treated as relationally bound phenomena, Bourdieu's notions of habitus, doxa, capital and field illuminate creative, adaptive and future‐looking practices. We conclude by discussing difficulties inherent to implementing a relational theory of practice in health promotion and public health.
Maternal and newborn outcomes among women with schizophrenia: a retrospective population‐based cohort study
Authors: Vigod SN , Kurdyak PA , Dennis CL , Gruneir A , Newman A , Seeman MV , Rochon PA , Anderson GM , Grigoriadis S , Ray JG
Published: January 2014

Objective

More women with schizophrenia are becoming pregnant, such that contemporary data are needed about maternal and newborn outcomes in this potentially vulnerable group. We aimed to quantify maternal and newborn health outcomes among women with schizophrenia.

Design

Retrospective cohort study.

Setting

Population based in Ontario, Canada, from 2002 to 2011.

Population

Ontario women aged 15–49 years who gave birth to a liveborn or stillborn singleton infant.

Methods

Women with schizophrenia (n = 1391) were identified based on either an inpatient diagnosis or two or more outpatient physician service claims for schizophrenia within 5 years prior to conception. The reference group comprised 432 358 women without diagnosed mental illness within the 5 years preceding conception in the index pregnancy.

Main outcome measures

The primary maternal outcomes were gestational diabetes mellitus, gestational hypertension, pre‐eclampsia/eclampsia, and venous thromboembolism. The primary neonatal outcomes were preterm birth, and small and large birthweight for gestational age (SGA and LGA). Secondary outcomes included additional key perinatal health indicators.

Results

Schizophrenia was associated with a higher risk of pre‐eclampsia (adjusted odds ratio, aOR 1.84; 95% confidence interval, 95% CI 1.28–2.66), venous thromboembolism (aOR 1.72, 95% CI 1.04–2.85), preterm birth (aOR 1.75, 95% CI 1.46–2.08), SGA (aOR 1.49, 95% CI 1.19–1.86), and LGA (aOR 1.53, 95% CI 1.17–1.99). Women with schizophrenia also required more intensive hospital resources, including operative delivery and admission to a maternal intensive care unit, paralleled by higher neonatal morbidity.

Conclusions

Women with schizophrenia are at higher risk of multiple adverse pregnancy outcomes, paralleled by higher neonatal morbidity. Attention should focus on interventions to reduce the identified health disparities.
Public Equity and Audit Pricing in the United States
Authors: BADERTSCHER BRAD , JORGENSEN BJORN , KATZ SHARON , KINNEY WILLIAM
Published: January 2014

To what degree are audit fees for U.S. firms with publicly traded equity higher than fees for otherwise similar firms with private equity? The answer is potentially important for evaluating regulatory regime design efficiency and for understanding audit demand and production economics. For U.S. firms with publicly traded debt, we hold constant the regulatory regime, including mandated issuer reporting and auditor responsibilities. We vary equity ownership and thus public securities market contextual factors, including any related public firm audit fees from increased audit effort to reduce audit litigation risk and/or pure litigation risk premium (litigation channel effects). In cross‐section, we find that audit fees for public equity firms are 20–22% higher than fees for otherwise similar private equity firms. Time‐series comparisons for firms that change ownership status yield larger percentage fee increases (decreases) for those going public (private). Results are consistent with litigation channel effects giving rise to substantial incremental audit fees for U.S. firms with public equity ownership.
Preparation and Characterization of Novel Lipid Carriers Containing Microalgae Oil for Food Applications
Authors: Wang Jia‐Li , Dong Xu‐Yan , Wei Fang , Zhong Juan , Liu Bo , Yao Ming‐Hao , Yang Mei , Zheng Chang , Quek Siew‐Young , Chen Hong
Published: January 2014

This work investigated the suitability of lipid carriers as potential encapsulation method to improve the physical and chemical stability of microalgae oil high in docosahexaenoic acid (DHA). Lipid carriers with various oil contents were successfully prepared by a microfluidization method using stearic acid as solid lipid, microalgae oil as liquid lipid, and poloxamer 188 as surfactant. Results show that the mean particle diameter of the lipid carriers was in the range of 300 to 350 nm with the polydispersity index below 0.2. The lipid carriers were found to have spherical shape when examined under the transmission electron microscope. Data from the encapsulation efficiency and loading capacity indicate high distribution of microalgae oil throughout the lipid carriers and good physical stability as reflected by the particle size and size distribution during storage. Furthermore, the lower DPPH scavenging activity of lipid carriers compared with that of free microalgae oil suggests better chemical stability of microalgae oil encapsulated in lipid carriers. The addition of microalgae oil into lipid phase could disturb the crystalline order and form lattice defects to enable encapsulation of DHA as revealed by the results from differential scanning calorimetery. Current results suggest that this type of novel lipid carriers could be an efficient and promising carrier system for delivery of microalgae oil.
Determination of Caffeine, Myosmine, and Nicotine in Chocolate by Headspace Solid‑Phase Microextraction Coupled with Gas Chromatography‑Tandem Mass Spectrometry
Authors: Müller Christoph , Vetter Florian , Richter Elmar , Bracher Franz
Published: January 2014

The occurrence of the bioactive components caffeine (xanthine alkaloid), myosmine and nicotine (pyridine alkaloids) in different edibles and plants is well known, but the content of myosmine and nicotine is still ambiguous in milk/dark chocolate. Therefore, a sensitive method for determination of these components was established, a simple separation of the dissolved analytes from the matrix, followed by headspace solid‑phase microextraction coupled with gas chromatography‐tandem mass spectrometry (HS‑SPME‑GC‑MS/MS). This is the first approach for simultaneous determination of caffeine, myosmine, and nicotine with a convenient SPME technique. Calibration curves were linear for the xanthine alkaloid (250 to 3000 mg/kg) and the pyridine alkaloids (0.000125 to 0.003000 mg/kg). Residuals of the calibration curves were lower than 15%, hence the limits of detection were set as the lowest points of the calibration curves. The limits of detection calculated from linearity data were for caffeine 216 mg/kg, for myosmine 0.000110 mg/kg, and for nicotine 0.000120 mg/kg. Thirty samples of 5 chocolate brands with varying cocoa contents (30% to 99%) were analyzed in triplicate. Caffeine and nicotine were detected in all samples of chocolate, whereas myosmine was not present in any sample. The caffeine content ranged from 420 to 2780 mg/kg (relative standard deviation 0.1 to 11.5%) and nicotine from 0.000230 to 0.001590 mg/kg (RSD 2.0 to 22.1%).
Potential of Medicinal Plants as Antimicrobial and Antioxidant Agents in Food Industry: A Hypothesis
Authors: Ortega‐Ramirez Luis Alberto , Rodriguez‐Garcia Isela , Leyva Juan Manuel , Cruz‐Valenzuela Manuel Reynaldo , Silva‐Espinoza Brenda Adriana , Gonzalez‐Aguilar Gustavo A. , Siddiqui Md Wasim , Ayala‐Zavala Jesus Fernando
Published: January 2014

Many food preservation strategies can be used for the control of microbial spoilage and oxidation; however, these quality problems are not yet controlled adequately. Although synthetic antimicrobial and antioxidant agents are approved in many countries, the use of natural safe and effective preservatives is a demand of food consumers and producers. This paper proposes medicinal plants, traditionally used to treat health disorders and prevent diseases, as a source of bioactive compounds having food additive properties. Medicinal plants are rich in terpenes and phenolic compounds that present antimicrobial and antioxidant properties; in addition, the literature revealed that these bioactive compounds extracted from other plants have been effective in food systems. In this context, the present hypothesis paper states that bioactive molecules extracted from medicinal plants can be used as antimicrobial and antioxidant additives in the food industry.
Development of SNP‐genotyping arrays in two shellfish species
Authors: Lapègue S. , Harrang E. , Heurtebise S. , Flahauw E. , Donnadieu C. , Gayral P. , Ballenghien M. , Genestout L. , Barbotte L. , Mahla R. , Haffray P. , Klopp C.
Published: January 2014

Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium‐throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three‐generation families segregating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analysed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) populations and could contribute to future selective breeding programmes.
An American mink (Neovison vison) transcriptome
Authors: Christensen Knud , Anistoroaei Razvan
Published: January 2014

HiSeq2000 Illumina pair‐end sequenced transcript data originating from a pool of four different tissues of a wild‐type American mink yielded approximately 90 Gb of raw data. Subsequently, unique contigs were assembled by a combined approach using velvet and phrap. Of these assembled contigs, about 136 000 match the dog genome and nearly 30 000 contigs match the human transcriptome at more than 17 000 unique gene locations. Gene annotation for these contigs was performed employing custom‐made scripts run in combination with comparative sequence similarity search and alignment in the dog and human genome using blast algorithms. Transcripts representing five genes known to be associated with pigmentation were reliably aligned against large mink genomic contigs derived from BAC clones. Sequence comparison between transcript and genomic data revealed seven SNPs. In this study, we generated and annotated mink transcript sequences representing more than 16 000 known genes. This is the first comprehensive transcriptome for the American mink genome, which will facilitate further development in mink expression profiling studies and provide a good annotation basis in the perspectives of a whole genome sequencing project. The project was deposited at EMBL database with the accession number PRJEB1260.