bluuebunny/crossref_metadata_2025 huggingface dataset:
Gated rotation mechanism of site-specific recombination by ϕC31 integrase
Authors: Olorunniji Femi J. , Buck Dorothy E. , Colloms Sean D. , McEwan Andrew R. , Smith Margaret C. M. , Stark W. Marshall , Rosser Susan J.
Published: November 2012

Integrases, such as that of theStreptomycestemperate bacteriophage ϕC31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ϕC31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a “subunit rotation” mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombiningattsites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ϕC31 integrase-mediated recombination in a topologically constrained experimental system using hybrid “phes” recombination sites, each of which comprises a ϕC31attsite positioned adjacent to a regulatory sequence recognized by Tn3resolvase. The topologies of reaction products from circular substrates containing twophessites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive “360° rotation” rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory “gating” mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round.
Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding
Authors: Fenley Andrew T. , Muddana Hari S. , Gilson Michael K.
Published: November 2012

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy–enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy–enthalpy compensation.
Proteasome allostery as a population shift between interchanging conformers
Authors: Ruschak Amy M. , Kay Lewis E.
Published: November 2012

Protein degradation plays a critical role in cellular homeostasis, in regulating the cell cycle, and in the generation of peptides that are used in the immune response. The 20S proteasome core particle (CP), a barrel-like structure consisting of four heptameric protein rings stacked axially on top of each other, is central to this process. CP function is controlled by activator complexes that bind 75 Å away from sites catalyzing proteolysis, and biochemical data are consistent with an allosteric mechanism by which binding is communicated to distal active sites. However, little structural evidence has emerged from the high-resolution images of the CP. Using methyl TROSY NMR spectroscopy, we demonstrate that in solution, the CP interconverts between multiple conformations whose relative populations are shifted on binding of the 11S activator or mutation of residues that contact activators. These conformers differ in contiguous regions of structure that connect activator binding to the CP active sites, and changes in their populations lead to differences in substrate proteolysis patterns. Moreover, various active site modifications result in conformational changes to the activator binding site by modulating the relative populations of these same CP conformers. This distribution is also affected by the binding of a small-molecule allosteric inhibitor of proteolysis, chloroquine, suggesting an important avenue in the development of therapeutics for proteasome inhibition.
Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword
Authors: LeRoux Michele , De Leon Justin A. , Kuwada Nathan J. , Russell Alistair B. , Pinto-Santini Delia , Hood Rachel D. , Agnello Danielle M. , Robertson Stephen M. , Wiggins Paul A. , Mougous Joseph D.
Published: November 2012

Interbacterial interaction pathways play an important role in defining the structure and complexity of bacterial associations. A quantitative description of such pathways offers promise for understanding the forces that contribute to community composition. We developed time-lapse fluorescence microscopy methods for quantitation of interbacterial interactions and applied these to the characterization of type VI secretion (T6S) in
Pseudomonas aeruginosa
. Our analyses allowed a direct determination of the efficiency of recipient cell lysis catalyzed by this intercellular toxin delivery pathway and provided evidence that its arsenal extends beyond known effector proteins. Measurement of T6S apparatus localization revealed correlated activation among neighboring cells, which, taken together with genetic data, implicate the elaboration of a functional T6S apparatus with a marked increase in susceptibility to intoxication. This possibility was supported by the identification of T6S-inactivating mutations in a genome-wide screen for resistance to T6S-mediated intoxication and by time-lapse fluorescence microscopy analyses showing a decreased lysis rate of recipient cells lacking T6S function. Our discoveries highlight the utility of single-cell approaches for measuring interbacterial phenomena and provide a foundation for studying the contribution of a widespread bacterial interaction pathway to community structure.
Neural basis of contagious itch and why some people are more prone to it
Authors: Holle Henning , Warne Kimberley , Seth Anil K. , Critchley Hugo D. , Ward Jamie
Published: November 2012

Watching someone scratch himself can induce feelings of itchiness in the perceiver. This provides a unique opportunity to characterize the neural basis of subjective experiences of itch, independent of changes in peripheral inputs. In this study, we first established that the social contagion of itch is essentially a normative response (experienced by most people), and that the degree of contagion is related to trait differences in neuroticism (i.e., the tendency to experience negative emotions), but not to empathy. Watching video clips of someone scratching (relative to control videos of tapping) activated, as indicated by functional neuroimaging, many of the neural regions linked to the physical perception of itch, including anterior insular, primary somatosensory, and prefrontal (BA44) and premotor cortices. Moreover, activity in the left BA44, BA6, and primary somatosensory cortex was correlated with subjective ratings of itchiness, and the responsivity of the left BA44 reflected individual differences in neuroticism. Our findings highlight the central neural generation of the subjective experience of somatosensory perception in the absence of somatosensory stimulation. We speculate that the habitual activation of this central “itch matrix” may give rise to psychogenic itch disorders.
Generalized reproduction numbers and the prediction of patterns in waterborne disease
Authors: Gatto Marino , Mari Lorenzo , Bertuzzo Enrico , Casagrandi Renato , Righetto Lorenzo , Rodriguez-Iturbe Ignacio , Rinaldo Andrea
Published: November 2012

Understanding, predicting, and controlling outbreaks of waterborne diseases are crucial goals of public health policies, but pose challenging problems because infection patterns are influenced by spatial structure and temporal asynchrony. Although explicit spatial modeling is made possible by widespread data mapping of hydrology, transportation infrastructure, population distribution, and sanitation, the precise condition under which a waterborne disease epidemic can start in a spatially explicit setting is still lacking. Here we show that the requirement that all the local reproduction numbersbe larger than unity is neither necessary nor sufficient for outbreaks to occur when local settlements are connected by networks of primary and secondary infection mechanisms. To determine onset conditions, we derive general analytical expressions for a reproduction matrix, explicitly accounting for spatial distributions of human settlements and pathogen transmission via hydrological and human mobility networks. At disease onset, a generalized reproduction number(the dominant eigenvalue of) must be larger than unity. We also show that geographical outbreak patterns in complex environments are linked to the dominant eigenvector and to spectral properties of. Tests against data and computations for the 2010 Haiti and 2000 KwaZulu-Natal cholera outbreaks, as well as against computations for metapopulation networks, demonstrate that eigenvectors ofprovide a synthetic and effective tool for predicting the disease course in space and time. Networked connectivity models, describing the interplay between hydrology, epidemiology, and social behavior sustaining human mobility, thus prove to be key tools for emergency management of waterborne infections.
Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations
Authors: Amaral Cristiano , Carnevale Vincenzo , Klein Michael L. , Treptow Werner
Published: November 2012

The X-ray structure of the bacterial voltage-gated sodium channel NavAb has been reported in a conformation with a closed conduction pore. Comparison between this structure and the activated-open and resting-closed structures of the voltage-gated Kv1.2 potassium channel suggests that the voltage-sensor domains (VSDs) of the reported structure are not fully activated. Using the aforementioned structures of Kv1.2 as templates, molecular dynamics simulations are used to identify analogous functional conformations of NavAb. Specifically, starting from the NavAb crystal structure, conformations of the membrane-bound channel are sampled along likely pathways for activation of the VSD and opening of the pore domain. Gating charge computations suggest that a structural rearrangement comparable to that occurring between activated-open and resting-closed states is required to explain experimental values of the gating charge, thereby confirming that the reported VSD structure is likely an intermediate along the channel activation pathway. Our observation that the X-ray structure exhibits a low pore domain-opening propensity further supports this notion. The present molecular dynamics study also identifies conformations of NavAb that are seemingly related to the resting-closed and activated-open states. Our findings are consistent with recent structural and functional studies of the orthologous channels NavRh, NaChBac, and NavMs and offer possible structures for the functionally relevant conformations of NavAb.
Effect of using poles on foot–ground kinetics during stance phase in trail running
Authors: Daviaux Yannick , Hintzy Frédérique , Samozino Pierre , Horvais Nicolas
Published: November 2012

The aim of this study was to investigate the effect of using poles on foot–ground interaction during trail running with slopes of varying incline. Ten runners ran on a loop track representative of a trail running field situation with uphill (+9°), level and downhill (−6°) sections at fixed speed (3.2 m.s−1). Experimental conditions included running with (WP) and without (NP) the use of poles for each of the three slopes. Several quantitative and temporal foot–ground interaction parameters were calculated from plantar pressure data measured with a portable device. Using poles induced a decrease in plantar pressure intensity even when the running velocity stayed constant. However, the localisation and the magnitude of this decrease depended on the slope situations. During WP level running, regional analysis of the foot highlighted a decrease of the force time integral (FTI) for absolute (FTIabs; −12.6%; P<0.05) and relative values (FTIrel; −14.3%; P<0.05) in the medial forefoot region. FTIabs (−14.2%; P<0.05) and duration of force application (Δt; −13.5%; P<0.05) also decreased in the medial heel region when WP downhill running. These results support a facilitating effect of pole use for propulsion during level running and for the absorption phase during downhill running.
The impact of working memory load on task execution and online plan adjustment during multitasking in a virtual environment
Authors: Law Anna S. , Trawley Steven L. , Brown Louise A. , Stephens Amanda N. , Logie Robert H.
Published: November 2012

Three experiments investigated the impact of working memory load on online plan adjustment during a test of multitasking in young, nonexpert, adult participants. Multitasking was assessed using the Edinburgh Virtual Errands Test (EVET). Participants were asked to memorize either good or poor plans for performing multiple errands and were assessed both on task completion and on the extent to which they modified their plans during EVET performance. EVET was performed twice, with and without a secondary task loading a component of working memory. In Experiment 1, articulatory suppression was used to load the phonological loop. In Experiment 2, oral random generation was used to load executive functions. In Experiment 3, spatial working memory was loaded with an auditory spatial localization task. EVET performance for both good- and poor-planning groups was disrupted by random generation and sound localization, but not by articulatory suppression. Additionally, people given a poor plan were able to overcome this initial disadvantage by modifying their plans online. It was concluded that, in addition to executive functions, multiple errands performance draws heavily on spatial, but not verbal, working memory resources but can be successfully completed on the basis of modifying plans online, despite a secondary task load.
Nucleoside salvage pathway kinases regulate hematopoiesis by linking nucleotide metabolism with replication stress
Authors: Austin Wayne R. , Armijo Amanda L. , Campbell Dean O. , Singh Arun S. , Hsieh Terry , Nathanson David , Herschman Harvey R. , Phelps Michael E. , Witte Owen N. , Czernin Johannes , Radu Caius G.
Published: November 2012

Nucleotide deficiency causes replication stress (RS) and DNA damage in dividing cells. How nucleotide metabolism is regulated in vivo to prevent these deleterious effects remains unknown. In this study, we investigate a functional link between nucleotide deficiency, RS, and the nucleoside salvage pathway (NSP) enzymes deoxycytidine kinase (dCK) and thymidine kinase (TK1). We show that inactivation of dCK in mice depletes deoxycytidine triphosphate (dCTP) pools and induces RS, early S-phase arrest, and DNA damage in erythroid, B lymphoid, and T lymphoid lineages. TK1−/− erythroid and B lymphoid lineages also experience nucleotide deficiency but, unlike their dCK−/− counterparts, they still sustain DNA replication. Intriguingly, dCTP pool depletion, RS, and hematopoietic defects induced by dCK inactivation are almost completely reversed in a newly generated dCK/TK1 double-knockout (DKO) mouse model. Using NSP-deficient DKO hematopoietic cells, we identify a previously unrecognized biological activity of endogenous thymidine as a strong inducer of RS in vivo through TK1-mediated dCTP pool depletion. We propose a model that explains how TK1 and dCK “tune” dCTP pools to both trigger and resolve RS in vivo. This new model may be exploited therapeutically to induce synthetic sickness/lethality in hematological malignancies, and possibly in other cancers.
Preferential binding of K+ ions in the selectivity filter at equilibrium explains high selectivity of K+ channels
Authors: Liu Shian , Bian Xuelin , Lockless Steve W.
Published: November 2012

K+ channels exhibit strong selectivity for K+ ions over Na+ ions based on electrophysiology experiments that measure ions competing for passage through the channel. During this conduction process, multiple ions interact within the region of the channel called the selectivity filter. Ion selectivity may arise from an equilibrium preference for K+ ions within the selectivity filter or from a kinetic mechanism whereby Na+ ions are precluded from entering the selectivity filter. Here, we measure the equilibrium affinity and selectivity of K+ and Na+ ions binding to two different K+ channels, KcsA and MthK, using isothermal titration calorimetry. Both channels exhibit a large preference for K+ over Na+ ions at equilibrium, in line with electrophysiology recordings of reversal potentials and Ba2+ block experiments used to measure the selectivity of the external-most ion-binding sites. These results suggest that the high selectivity observed during ion conduction can originate from a strong equilibrium preference for K+ ions in the selectivity filter, and that K+ selectivity is an intrinsic property of the filter. We hypothesize that the equilibrium preference for K+ ions originates in part through the optimal spacing between sites to accommodate multiple K+ ions within the selectivity filter.
Dissecting a regulatory calcium-binding site of CLC-K kidney chloride channels
Authors: Gradogna Antonella , Fenollar-Ferrer Cristina , Forrest Lucy R. , Pusch Michael
Published: November 2012

The kidney and inner ear CLC-K chloride channels, which are involved in salt absorption and endolymph production, are regulated by extracellular Ca2+ in the millimolar concentration range. Recently, Gradogna et al. (2010. J. Gen. Physiol. http://dx.doi.org/10.1085/jgp.201010455) identified a pair of acidic residues (E261 and D278) located in the loop between helices I and J as forming a putative intersubunit Ca2+-binding site in hClC-Ka. In this study, we sought to explore the properties of the binding site in more detail. First, we verified that the site is conserved in hClC-Kb and rClC-K1. In addition, we could confer Ca2+ sensitivity to the Torpedo marmorata ClC-0 channel by exchanging its I–J loop with that from ClC-Ka, demonstrating a direct role of the loop in Ca2+ binding. Based on a structure of a bacterial CLC and a new sequence alignment, we built homology models of ClC-Ka. The models suggested additional amino acids involved in Ca2+ binding. Testing mutants of these residues, we could restrict the range of plausible models and positively identify two more residues (E259 and E281) involved in Ca2+ coordination. To investigate cation specificity, we applied extracellular Zn2+, Mg2+, Ba2+, Sr2+, and Mn2+. Zn2+ blocks ClC-Ka as well as its Ca2+-insensitive mutant, suggesting that Zn2+ binds to a different site. Mg2+ does not activate CLC-Ks, but the channels are activated by Ba2+, Sr2+, and Mn2+ with a rank order of potency of Ca2+ > Ba2+ > Sr2+ = Mn2+ for the human CLC-Ks. Dose–response analysis indicates that the less potent Ba2+ has a lower affinity rather than a lower efficacy. Interestingly, rClC-K1 shows an altered rank order (Ca2+ > Sr2+ >> Ba2+), but homology models suggest that residues outside the I–J loop are responsible for this difference. Our detailed characterization of the regulatory Ca2+-binding site provides a solid basis for the understanding of the physiological modulation of CLC-K channel function in the kidney and inner ear.
State Trading Enterprises as Non‐Tariff Measures: Theory, Evidence, and Future Research Directions
Authors: McCorriston Steve , MacLaren Donald
Published: November 2012

We review issues concerning the use of state trading enterprises (STEs) as a non‐tariff measure in importing countries. We focus on a tariff equivalent measure that captures the main features of markets where STEs are used, and we identify the factors that influence tariff equivalent effect. We supplement this discussion with case studies highlighting the potential to improve the transparency of trade‐distorting enterprises as employed across importing countries. These studies also highlight that, as the role of the STE changes, so too does the size of the tariff equivalent. Increasing the transparency of STEs can aid the treatment of them in trade negotiations.
A Métier-Sustainability-Index (MSI25) to evaluate fisheries components: assessment of cases from data-poor fisheries from southern Europe
Authors: Tzanatos Evangelos , Castro Jose , Forcada Aitor , Matić-Skoko Sanja , Gaspar Miguel , Koutsikopoulos Constantin
Published: November 2012

Tzanatos, E., Castro, J., Forcada, A., Matić-Skoko, S., Gaspar, M., and Koutsikopoulos, C. 2013. A Métier-Sustainability-Index (MSI25) to evaluate fisheries components: assessment of cases from data-poor fisheries from southern Europe. – ICES Journal of Marine Science, 70:78–98.

The present work presents an integrated comparative assessment of the sustainability of fishing tactics or métiers (combinations of area, season, fishing gear, and target species). An index, which includes biological, conservation, socioeconomic, and management criteria, was created for this purpose: the “Métier Sustainability Index” (MSI25). It was designed using the traffic lights approach and comprises 25 indicators that refer to the “health” of the fisheries. Additionally, the MSI25 provides an indication of the “certainty” of that information with regard to the data type/heterogeneity. Subsequently, the index was tested using data from six case studies (81 métiers) from the Mediterranean and the Atlantic. The index showed that 63.0% of the métiers were “sustainable”, 21.0% were “unsustainable” and 16.0% were “under pressure”; 59.3% of characterizations were considered as “certain”. The index evaluation showed significant differences between areas and gears. This paper considers the characteristics of the datasets used, the case management status, and the applicability of the index in improving the management of specific fisheries. Overall, the MSI25 was found to be a useful tool for the evaluation and management of highly heterogeneous fisheries and data from various sources and types.
Modestobacter roseus sp. nov., an endophytic actinomycete isolated from the coastal halophyte Salicornia europaea Linn., and emended description of the genus

Modestobacter
Authors: Qin Sheng , Bian Guang-Kai , Zhang Yue-Ji , Xing Ke , Cao Cheng-Liang , Liu Chang-Hong , Dai Chuan-Chao , Li Wen-Jun , Jiang Ji-Hong
Published: November 2012

A novel actinomycete, designated strain KLBMP 1279T, was isolated from surface-sterilized roots of a coastal halophyte, Salicornia europaea Linn., collected from Jiangsu Province, in the east of China. The taxonomic status of this organism was established using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KLBMP 1279T was closely related to

Modestobacter marinus

42H12-1T (99.5 % 16S rRNA gene sequence similarity),

Modestobacter versicolor

CP153-2T (98.4 %) and

Modestobacter multiseptatus

AA-826T (97.5 %). Chemotaxonomic characteristics were consistent with its assignment to the genus

Modestobacter

in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, MK-9(H4) as major menaquinone and a polar lipid profile containing diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown aminophospholipids and an unknown phospholipid. The predominant fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c. The DNA G+C content was 71.7 mol%. However, DNA–DNA hybridization assays as well as physiological and biochemical analyses differentiated strain KLBMP 1279T from its closest phylogenetic relatives. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate KLBMP 1279T represents a novel species of the genus

Modestobacter

, for which the name Modestobacter roseus sp. nov. is proposed; the type strain is KLBMP 1279T ( = KCTC 19887T = NBRC 108673T = DSM 45764T). An emended description of the genus Modestobacter is also proposed.
Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae
Authors: Vaneechoutte Mario , Janssens Michèle , Avesani Véronique , Delmée Michel , Deschaght Pieter
Published: November 2012

Three Gram-negative strains, NF 1078T, NF 1598 and NF 1715, were isolated from clinical (two) and environmental (one) samples, respectively. Sequence analysis of the 16S rRNA genes revealed similarity of 100 % among the three strains and next highest similarity to the type strain ofAcidovorax avenae(98.16 %). The three strains were able to acidify lactose and rhamnose on low peptone phenol red agar and to alkalinize citrate on Simmons’ agar and were negative for nitrate reduction. The DNA G+C content of strain NF 1078Twas 67.1 mol%. The level of DNA–DNA relatedness between this strain and the type strains ofA. avenae(ATCC 19860T, LMG 2117T) was 29 %. Based on these phylogenetic, phenotypic and genotypic analyses, the three strains could be distinguished clearly from all other recognizedAcidovoraxspecies and should be classified as representatives of a novel species of the genusAcidovorax, for which the nameAcidovorax wautersiisp. nov. is proposed. The type strain is NF 1078T( = LMG 26971T = CCUG 62584T).
Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater
Authors: Park Sanghwa , Song Jaeho , Yoshizawa Susumu , Choi Ahyoung , Cho Jang-Cheon , Kogure Kazuhiro
Published: November 2012

Two aerobic, Gram-stain-negative, pale-red-pigmented and rod-shaped bacterial strains, designated SAORIC-26 and SAORIC-28T, were isolated from seawater (3000 m depth) from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the familyRhodothermaceaeof the classCytophagia.Strains SAORIC-26 and SAORIC-28Tshared 99.7 % pairwise sequence similarity with each other and showed less than 92.6 % similarity with other cultivated members of the classCytophagia.The strains were found to be non-motile, oxidase-positive, catalase-negative and able to hydrolyse gelatin and aesculin. The DNA G+C contents were determined to be 64.8–65.8 mol% and MK-7 was the predominant menaquinone. Summed feature 9 (iso-C17 : 1ω9cand/or C16 : 010-methyl), summed feature 3 (C16 : 1ω6cand/or C16 : 1ω7c) and iso-C15 : 0were found to be the major cellular fatty acids. On the basis of this taxonomic study using a polyphasic approach, it was concluded that strains SAORIC-26 and SAORIC-28Trepresent a novel species of a new genus in the familyRhodothermaceae, for which the nameRubrivirga marinagen. nov., sp. nov. is proposed. The type strain of the type species of is SAORIC-28T( = KCTC 23867T = NBRC 108816T). An additional strain of the species is SAORIC-26.
Thalassolituus marinus sp. nov., a hydrocarbon-utilizing marine bacterium
Authors: Choi Ahyoung , Cho Jang-Cheon
Published: November 2012

Gram-negative strains, motile by a single polar flagellum, non-pigmented and with a curved rod-shaped morphology, designated IMCC1826T and IMCC1883, were isolated from a surface seawater sample from the Yellow Sea. The two strains shared 99.9 % 16S rRNA gene sequence similarity and showed 92 % DNA–DNA relatedness, suggesting that they belonged to the same genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were related most closely to the type strain of

Thalassolituus oleivorans

with a sequence similarity of 96.4 % and formed a robust phyletic lineage with

T. oleivorans

. DNA–DNA relatedness between the two strains and

T. oleivorans

DSM 14913T was 8.7–11.6 %. A putative alkane hydroxylase (alkB) gene was detected in strain IMCC1826T by PCR, but the amino acid sequence of the gene was distantly related to that of the AlkB homologue of

T. oleivorans

DSM 14913T. As expected from the presence of the alkB gene, the new strains utilized n-tetradecane and n-hexadecane as a carbon source. The DNA G+C content was 54.6–56.0 mol% and the main isoprenoid quinone detected was Q-9. Polar lipids of strain IMCC1826T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and amino-group-containing lipids. On the basis of taxonomic data obtained in this study, strains IMCC1826T and IMCC1883 represent a novel species of the genus

Thalassolituus

, for which the name Thalassolituus marinus sp. nov. is proposed, with IMCC1826T ( = KCTC 23084T = NBRC 107590T) as the type strain.
Aspergillus waksmanii sp. nov. and Aspergillus marvanovae sp. nov., two closely related species in section Fumigati
Authors: Hubka Vit , Peterson Stephen W. , Frisvad Jens C. , Yaguchi Takashi , Kubátová Alena , Kolařík Miroslav
Published: November 2012

Two new and phylogenetically closely related species in Aspergillus section Fumigati are described and illustrated. Homothallic Aspergillus waksmanii sp. nov. was isolated from New Jersey soil (USA) and is represented by the ex-type isolate NRRL 179T ( = CCF 4266T = Thom 4138.HS2T = IBT 31900T). Aspergillus marvanovae sp. nov. was isolated from water with high boracic acid anions content in Dukovany nuclear power station (Czech Republic). The sexual stage of this species is unknown, but the MAT1-1 locus was successfully amplified suggesting that the species is probably heterothallic and teleomorphic but is represented by only the ex-type isolate CCM 8003T ( = CCF 4037T = NRRL 62486T = IBT 31279T = IFM 60873T). Both species can be distinguished from all previously described species in section Fumigati based on morphology, maximum growth temperature, sequence data from five unlinked loci and unique secondary metabolites profiles.
Cauliform bacteria lacking phospholipids from an abyssal hydrothermal vent: proposal of Glycocaulis abyssi gen. nov., sp. nov., belonging to the family

Hyphomonadaceae
Authors: Abraham Wolf-Rainer , Lünsdorf Heinrich , Vancanneyt Marc , Smit John
Published: November 2012

Cauliform bacteria are prosthecate bacteria often specialized for oligotrophic environments. A polyphasic approach, comprising 16S rRNA gene sequencing, lipid analysis and salt tolerance characterizations, was used to clarify the taxonomy of one isolate, strain MCS 33T, obtained from above the hot water plume of a deep-sea hydrothermal vent near Vancouver island, Canada. Cells contained no detectable phospholipids or sulpholipids, but did contain 1,2-di-O-acyl-3-O-α-d-glucopyranosylglycerol, 1,2-di-O-acyl-3-O-α-d-glucopyranuronosylglycerol and the novel lipid 1,2-di-O-acyl-3-[O-α-d-glucopyranuronosyl]glycerol-6′-N-glycine. It is assumed that the various glucoronosyl lipids are replacing, at least partially, the phospholipids in their various tasks in the cell cycle. The G+C content of the genomic DNA of strain MCS 33T was 62.8 mol%, and Q10 was the predominant respiratory ubiquinone. The 16S rRNA gene sequence of this chemoheterotrophic, aerobic, moderately halophilic strain showed only a low similarity of 94.4 % to that of

Oceanicaulis alexandrii

C116-18T, and both strains also differed based on their lipids. Although the novel strain was isolated from seawater sampled near a hydrothermal vent, its optimum temperature for growth was 30 °C. The main cellular fatty acids were C18 : 1ω7c, C18 : 0 and the unknown fatty acid ECL 11.798, and the main hydroxy fatty acid was C12 : 0 3-OH. The strain is proposed to represent a novel species of a new genus, Glycocaulis abyssi gen. nov., sp. nov. The type strain of the type species is MCS 33T ( = LMG 27140T = CCUG 62981T).
Differential Mobility of Pigment-Protein Complexes in Granal and Agranal Thylakoid Membranes of C3 and C4 Plants
Authors: Kirchhoff Helmut , Sharpe Richard M. , Herbstova Miroslava , Yarbrough Robert , Edwards Gerald E.
Published: November 2012

The photosynthetic performance of plants is crucially dependent on the mobility of the molecular complexes that catalyze the conversion of sunlight to metabolic energy equivalents in the thylakoid membrane network inside chloroplasts. The role of the extensive folding of thylakoid membranes leading to structural differentiation into stacked grana regions and unstacked stroma lamellae for diffusion-based processes of the photosynthetic machinery is poorly understood. This study examines, to our knowledge for the first time, the mobility of photosynthetic pigment-protein complexes in unstacked thylakoid regions in the C3 plant Arabidopsis (Arabidopsis thaliana) and agranal bundle sheath chloroplasts of the C4 plants sorghum (Sorghum bicolor) and maize (Zea mays) by the fluorescence recovery after photobleaching technique. In unstacked thylakoid membranes, more than 50% of the protein complexes are mobile, whereas this number drops to about 20% in stacked grana regions. The higher molecular mobility in unstacked thylakoid regions is explained by a lower protein-packing density compared with stacked grana regions. It is postulated that thylakoid membrane stacking to form grana leads to protein crowding that impedes lateral diffusion processes but is required for efficient light harvesting of the modularly organized photosystem II and its light-harvesting antenna system. In contrast, the arrangement of the photosystem I light-harvesting complex I in separate units in unstacked thylakoid membranes does not require dense protein packing, which is advantageous for protein diffusion.
An Essential Role for Tomato Sulfite Oxidase and Enzymes of the Sulfite Network in Maintaining Leaf Sulfite Homeostasis
Authors: Brychkova Galina , Grishkevich Vladislav , Fluhr Robert , Sagi Moshe
Published: November 2012

Little is known about the homeostasis of sulfite levels, a cytotoxic by-product of plant sulfur turnover. By employing extended dark to induce catabolic pathways, we followed key elements of the sulfite network enzymes that include adenosine-5′-phosphosulfate reductase and the sulfite scavengers sulfite oxidase (SO), sulfite reductase, UDP-sulfoquinovose synthase, and β-mercaptopyruvate sulfurtransferases. During extended dark, SO was enhanced in tomato (Solanum lycopersicum) wild-type leaves, while the other sulfite network components were down-regulated. SO RNA interference plants lacking SO activity accumulated sulfite, resulting in leaf damage and mortality. Exogenous sulfite application induced up-regulation of the sulfite scavenger activities in dark-stressed or unstressed wild-type plants, while expression of the sulfite producer, adenosine-5′-phosphosulfate reductase, was down-regulated. Unstressed or dark-stressed wild-type plants were resistant to sulfite applications, but SO RNA interference plants showed sensitivity and overaccumulation of sulfite. Hence, under extended dark stress, SO activity is necessary to cope with rising endogenous sulfite levels. However, under nonstressed conditions, the sulfite network can control sulfite levels in the absence of SO activity. The novel evidence provided by the synchronous dark-induced turnover of sulfur-containing compounds, augmented by exogenous sulfite applications, underlines the role of SO and other sulfite network components in maintaining sulfite homeostasis, where sulfite appears to act as an orchestrating signal molecule.
A new ring-like arrangement of vanadyl(IV) groups bridged by monodentate alkoxides:cyclo-decakis(μ-cyclohexylmethanolato)pentakis[oxidovanadium(IV)]
Authors: Stinghen Danilo , Ferreira Janaina G. , Nunes Giovana G. , Soares Jaísa F.
Published: November 2012

The pentanuclear title compound, [V5(C7H13O)10O5], has a metal–oxygen core that consists of five vanadyl(IV) centres bridged by the O atoms of cyclohexylmethanolate ligands. This particular ring topology is new to oxovanadium(IV) chemistry and resembles the structure proposed for [V5O15]5−on the basis of51V NMR studies in aqueous solution. The bulky cyclohexylmethanolate ligands adopt chair-like conformations and project outwards from the central cyclic core. The title compound crystallizes in a centrosymmetric triclinic unit cell, which contains four independent but chemically identical molecules in the asymmetric unit. The crystal structure is devoid of any significant intermolecular interactions.
Distinct lipopeptide production systems for WLIP (white line‐inducing principle) in Pseudomonas fluorescens and Pseudomonas putida
Authors: Rokni‐Zadeh Hassan , Li Wen , Yilma Eshetu , Sanchez‐Rodriguez Aminael , De Mot René
Published: November 2012

The interaction of WLIP (white line‐inducing principle), a member of the viscosin group of Pseudomonas lipopeptides, with tolaasin, a lipopeptide mycotoxin secreted by Pseudomonas tolaasii, enables identification of the mushroom pathogen relying on formation of a lipopeptide coprecipitate between confronted colonies of an indicator strain (designated Pseudomonas ‘reactans’) and P. tolaasii. The WLIP non‐ribosomal lipopeptide synthesis system of the mushroom isolate P. ‘reactans’ LMG 5329 (Wip) was identified and shown to be most similar to the Pseudomonas fluorescens SBW25 viscosin system (Visc), but remarkably different from the WLIP‐generating Wlp system previously identified in the rice rhizosphere isolate Pseudomonas putida RW10S2. The Wlp machinery is composed of modules most similar to those recruited for biosynthesis of the non‐viscosin‐type lipopeptides putisolvin and entolysin by strains from the P. putida clade. In line with the pronounced synteny between the wip and visc flanking regions, strain LMG 5329 was identified as an authentic P. fluorescens closely related to strain SBW25. In both P. putida and P. fluorescens, WLIP production confers similar phenotypes of microbial antagonism and surface colonization. Genotypes other than wlp or wip were not identified among WLIP producers isolated from mushroom, maize rhizosphere or water.
A metapopulation model forCanadian andWestGreenland narwhals
Authors: Heide‐Jørgensen M. P. , Richard P. R. , Dietz R. , Laidre K. L.
Published: November 2012

A model of the metapopulation structure of narwhalsMonodon monocerosinBaffinBay,HudsonBay and adjacent waters is proposed based on satellite telemetry data collected over two decades from six coastal aggregations of narwhals in the easternCanadian highArctic,HudsonBay andWestGreenland. In addition, data on seasonal catches of narwhals in 11Inuit communities are used to provide information on the occurrence of narwhals. The tracking data suggest that disjunct summer aggregations of narwhals are, to some extent, demographically independent subpopulations, with minimal or no exchange with other summering aggregations. We propose that these should be considered separate stocks for management purposes. Year‐round satellite tracking of individuals demonstrates that whales return to the same summering areas the following year, suggesting inter‐annual site fidelity. We propose that the narwhals inCanada constitute five separate stocks, with limited exchange between three of the stocks.Coastal summer aggregations inGreenland constitute two stocks in addition to two fall and winter aggregations supplied by narwhals from several summering areas. Several narwhal stocks mix on the wintering areas inBaffinBay, but the metapopulation structure is likely maintained through a combination of life‐history traits and migratory routes, as mating most likely occurs after the initiation of the return migration toward summering areas. The metapopulation structure inBaffinBay narwhals will be impacted differentially byInuit subsistence hunting, depending on the migratory schedule of narwhals and dates at which whales occur in different seasonal hunting areas. It is therefore important to identify which narwhal stocks contribute to which subsistence hunts in order to assess the sustainability of those hunts. This paper proposes a preliminary stock model for this purpose.
Long term outcomes of pharmacological treatments for opioid dependence: does methadone still lead the pack?
Authors: Garcia‐Portilla Maria Paz , Bobes‐Bascaran Maria Teresa , Bascaran Maria Teresa , Saiz Pilar Alejandra , Bobes Julio
Published: November 2012

The aim of this review was to update and summarize the scientific knowledge on the long term outcomes of the different pharmacological treatment options for opioid dependence currently available and to provide a critical discussion on the different treatment options based on these results. We performed a literature search using the PubMed databases and the reference lists of the identified articles. Data from research show that the three pharmacological options reviewed are effective treatments for opioid dependence with positive long term outcomes. However, each one has its specific target population and setting. While methadone and buprenorphine are first line options, heroin‐assisted treatment is a second line option for those patients refractory to treatment with methadone with concomitant severe physical, mental, social and/or functional problems. Buprenorphine seems to be the best option for use in primary care offices. The field of opioid dependence treatment is poised to undergo a process of reinforcement and transformation. Further efforts from researchers, clinicians and authorities should be made to turn new pharmacological options into clinical reality and to overcome the structural and functional obstacles that maintenance programmes face in combatting opioid dependence.
A systematic review of the effect of paracetamol on blood pressure in hypertensive and non‐hypertensive subjects
Authors: Turtle Emma J. , Dear James W. , Webb David J.
Published: November 2012

Aim

To review current evidence on the effect of paracetamol on blood pressure (BP), the quality of the previous studies and the validity of the results, and to summarize these findings.

Methods

A systematic literature review was performed by searching PubMed, the Cochrane library and EMBASE for publications between the years 1963 and 2012.

Results

We identified three case reports, seven prospective observational trials, six randomized controlled trials, one commentary and two reviews. Some, but not all, of the observational studies, which included over 147 000 patients, showed an increased risk of hypertension with paracetamol use. The randomized studies were generally small and the results were inconsistent. Three studies, which included 104 patients, showed an increase of systolic BP by ∼4 mmHg, two studies, which included 27 patients, reported no change in BP and one study, which included 21 patients, reported a fall in BP although no placebo arm was included for comparison.

Conclusions

The overall effect of paracetamol on BP is unclear. Given that paracetamol is often suggested as a safer alternative to non‐steroidal anti‐inflammatory drugs (NSAIDs), it would seem that further prospective evidence is now needed to address the effect of paracetamol on BP. This would be best done with larger studies in relevant cohorts using BP measured by ambulatory BP monitoring as the primary endpoint.
An active metabolite of oltipraz (M2) increases mitochondrial fuel oxidation and inhibits lipogenesis in the liver by dually activating AMPK
Authors: Kim Tae Hyun , Eom Jeong Sik , Lee Chan Gyu , Yang Yoon Mee , Lee Yong Sup , Kim Sang Geon
Published: November 2012

Background and Purpose

Oltipraz, a cancer chemopreventive agent, has an anti‐steatotic effect via liver X receptor‐α (LXRα) inhibition. Here we have assessed the biological activity of a major metabolite of oltipraz (M2) against liver steatosis and steatohepatitis and the underlying mechanism(s).

Experimental Approach

Blood biochemistry and histopathology were assessed in high‐fat diet (HFD)‐fed mice treated with M2. An in vitro HepG2 cell model was used to study the mechanism of action. Immunoblotting, real‐time PCR and luciferase reporter assays were performed to measure target protein or gene expression levels.

Key Results

M2 treatment inhibited HFD‐induced steatohepatitis and diminished oxidative stress in liver. It increased expression of genes encoding proteins involved in mitochondrial fuel oxidation. Mitochondrial DNA content and oxygen consumption rate were enhanced. Moreover, M2 treatment repressed activity of LXRα and induction of its target genes, indicating anti‐lipogenic effects. M2 activated AMP‐activated protein kinase (AMPK). Inhibition of AMPK by over‐expression of dominant negative AMPK (DN‐AMPK) or by Compound C prevented M2 from inducing genes for fatty acid oxidation and repressed sterol regulatory element binding protein‐1c (SREBP‐1c) expression. M2 activated liver kinase B1 (LKB1) and increased the AMP/ATP ratio. LKB1 knockdown failed to reverse target protein modulations or AMPK activation by M2, supporting the proposal that both LKB1 and increased AMP/ATP ratio contribute to its anti‐steatotic effect.

Conclusion and Implications

M2 inhibited liver steatosis and steatohepatitis by enhancing mitochondrial fuel oxidation and inhibiting lipogenesis. These effects reflected activation of AMPK elicited by increases in LKB1 activity and AMP/ATP ratio.
Gene expression of glutamate metabolizing enzymes in the hippocampal formation in human temporal lobe epilepsy
Authors: Eid Tore , Lee Tih‐Shih W. , Wang Yue , Peréz Edgar , Drummond Jana , Lauritzen Fredrik , Bergersen Linda H. , Meador‐Woodruff James H. , Spencer Dennis D. , de Lanerolle Nihal C. , McCullumsmith Robert E.
Published: November 2012

Purpose:  Increased interictal concentrations of extracellular hippocampal glutamate have been implicated in the pathophysiology of temporal lobe epilepsy (TLE). Recent studies suggest that perturbations of the glutamate metabolizing enzymes glutamine synthetase (GS) and phosphate activated glutaminase (PAG) may underlie the glutamate excess in TLE. However, the molecular mechanism of the enzyme perturbations remains unclear. A better understanding of the regulatory mechanisms of GS and PAG could facilitate the discovery of novel therapeutics for TLE.

Methods:  We used in situ hybridization on histologic sections to assess the distribution and quantity of messenger RNA (mRNA) for GS and PAG in subfields of hippocampal formations from the following: (1) patients with TLE and concomitant hippocampal sclerosis, (2) patients with TLE and no hippocampal sclerosis, and (3) nonepilepsy autopsy subjects.

Key Findings:  GS mRNA was increased by ∼50% in the CA3 in TLE patients without hippocampal sclerosis versus in TLE patients with sclerosis and in nonepilepsy subjects. PAG mRNA was increased by >100% in the subiculum in both TLE patient categories versus in nonepilepsy subjects. PAG mRNA was also increased in the CA1, CA2, CA3, and dentate hilus in TLE without hippocampal sclerosis versus in TLE with sclerosis. Finally, PAG mRNA was increased in the dentate gyrus in TLE with sclerosis versus in nonepilepsy subjects, and also increased in the hilus in TLE without sclerosis versus in TLE with sclerosis.

Significance:  These findings demonstrate complex changes in the expression of mRNAs for GS and PAG in the hippocampal formation in TLE, and raise the possibility that both transcriptional and posttranscriptional mechanisms may underlie the regulation of GS and PAG proteins in the epileptic brain.