bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformations and Metal Ion Affinities of Glutamine Binding with Alkali and Alkaline Earth Metal Cations: an ab initio Study
Authors: Pang Rui , Lin Zi-jing
Published: May 2014

Conformations and reaction energetics are important for understanding the interactions between biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion affinities of glutamine (Gln) binding with alkali and alkaline earth metal ions. An efficient and reliable method of searching low energy conformations of metalated Gln is proposed and applied to the complexes of Gln·M+/++ (M+/++=Li+, Na+, K+, Rb+, Cs+, Be++, Mg++, Ca++, Sr++, and Ba++). In addition to all conformers known in literatures, many new important conformations are located, demonstrating the power of the new method and the necessity of the conformational search performed here. The metal coordination modes, relative energies, dipole moments, and equilibrium distributions of all important conformations of Gln·M+/++ are calculated by the methods of B3LYP, BHandHLYP, and MP2. IR spectra and metalation enthalpies and free energies are also presented and compared with the available experiments. The results form an extensive database for systematic examination of the metalation properties of Gln.
Production of Light Olefins from Biosyngas by Two-stage Catalytic Conversion Process via Dimethyl Ether
Authors: Li Yu-ping , Tu Jun-ling , Wang Tie-jun , Ma Long-long , Zhang Xing-hua , Zhang Qing , Cai Chi-liu
Published: May 2014

NiSAPO-34 and NiSAPO-34/HZSM-5 were prepared and evaluated for the performance of dimethyl ether (DME) conversion to light olefins (DTO). The processes of two-stage light olefin production, DME synthesis and the following DTO, were also investigated using biosyngas as feed gas over Cu/Zn/Al/HZSM-5 and the optimized 2%NiSAPO-34/HZSM-5. The results indicated that adding 2%Ni to SAPO-34 did not change its topology structure, but resulted in the forming of the moderately strong acidity with decreasing acid amounts, which slightly enhanced DME conversion activity and C2=-C3= selectivity. Mechanically mixing 2%NiSAPO-34 with HZSM-5 at the weight ratio of 3.0 further prolonged DME conversion activity to be more than 3 h, which was due to the stable acid sites from HZSM-5. The highest selectivity to light olefins of 90.8% was achieved at 2 h time on stream. The application of the optimized 2%NiSAPO-34/HZSM-5 in the second-stage reactor for DTO reaction showed that the catalytic activity was steady for more than 5 h and light olefin yield was as high as 84.6 g/m3syngas when the biosyngas (H2/CO/CO2/N2/CH4=41.5/26.9/14.2/14.6/2.89, vol%) with low H/C ratio of 1.0 was used as feed gas.
N2O Decomposition over K-Ce Promoted Co-M-Al Mixed Oxide Catalysts Prepared from Hydrotalcite-like Precursors
Authors: Zhang Jin-li , Wu Shuang , Hu Hui , Wu Gao-ming , Zeng Zhao-wei
Published: May 2014

A series of mixed oxide catalysts with different composition of Co-M-Al and Co-M-Ce-Al (M=Zn, Ni, Cu) were prepared by co-precipitation method from hydrotalcite-like compounds. The experimental results revealed the catalytic activity of Co-Ni-Al is slightly higher than that of Co-Zn-Al and much higher than that of Co-Cu-Al for direct decomposition of N2O. Moreover, addition of small amounts of CeO2 improved the catalytic activity significantly and made the decomposition temperatures at which the N2O conversion was 50% and 90% (T50 and T90) both decreased 80 °C than those of Co-M-Al catalysts without CeO2 added. Further, potassium-load also promoted the catalytic activity, and the decomposition temperatures of T50 and T90 both decreased approximately 50 °C. It is significant for decomposing N2O from industries and reducing carbon emission from atmosphere.
GT-Scan: identifying unique genomic targets
Authors: O’Brien Aidan , Bailey Timothy L.
Published: May 2014

Summary: A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome editing or regulatory interference. Specificity, however, is a major problem, and the targeted locus must be chosen with care to avoid inadvertently affecting other loci (‘off-targets’) in the genome. To address this we have created ‘Genome Target Scan’ (GT-Scan), a flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have. GT-Scan gives the user flexibility to define the desired characteristics of targets and off-targets via a simple ‘target rule’, and its interactive output allows detailed inspection of each of the most promising candidate targets. GT-Scan can be used to identify optimal targets for CRISPR/Cas systems, but its flexibility gives it potential to be adapted to other genome-targeting technologies as well.

Availability and implementation: GT-Scan can be run via the web at: http://gt-scan.braembl.org.au .

Contact:  t.bailey@uq.edu.au
Fish growth, reproduction, and tissue production on artificial reefs relative to natural reefs
Authors: Granneman Jennifer E. , Steele Mark A.
Published: May 2014

The extent to which artificial reefs may be useful for mitigation of environmental impacts, fisheries management, and conservation depends in part upon how well the organisms that live on them fare. We tested whether fish living on artificial reefs were in similar condition (weight-at-length), grew, foraged, reproduced, and produced tissue at rates similar to those on natural reefs. We studied five artificial–natural reef pairs spread over >200 km in the Southern California Bight. Underwater visual transects were used to quantify density and size structure of four target species (Paralabrax clathratus, Paralabrax nebulifer, Semicossyphus pulcher, and Embiotoca jacksoni), which were also collected to measure foraging success, condition, growth, reproductive output, and tissue production. Generally, fish living on artificial reefs fared as well or better than those on natural reefs, with some exceptions. Semicossyphus pulcher fared better on artificial reefs, having higher foraging success, fecundity, densities, and tissue production. Embiotoca jacksoni grew faster on natural reefs, and P. nebulifer was in slightly better condition on natural reefs. Total fish tissue production tended to be higher on artificial reefs than on natural reefs, though this pattern was not evident on all reef pairs. Tissue production was positively correlated with the abundance of large boulders, which was higher on artificial reefs than natural reefs. The similar or greater production of fish tissue per cubic metre on artificial reefs relative to natural reefs indicates that these artificial habitats are valuable in producing fish biomass. Fish living on artificial reefs fared as well as those living on natural reefs, indicating that well-designed artificial reefs can be useful tools for mitigation, conservation, and fisheries management.
TUPE: Ringing the (Wrong) Changes. The Collective Redundancies and Transfer of Undertakings (Protection of Employment) (Amendment) Regulations 2014
Authors: McMullen John
Published: May 2014

Following the review of the Transfer of Undertakings (Protection of Employment) (TUPE) Regulations 2006 by the Department for Business Innovation and Skills it was feared that a seismic change would be made to the TUPE regulations under the banner of cutting red tape and reducing gold plating of legislation perceived to exceed the minimal requirements of the Acquired Rights Directive. Key headlines in the review were the suggested repeal of the service provision change rules and the abolition of the duty on a transferring employer to provide to the transferee employer a statutory list of employee liability information. The 2014 regulations however reflect a compromise. The thrust of most responses to the Government consultation was to leave well alone and, as a result, the service provision change rules have been retained and the duty to provide employee liability information fortified rather than repealed. But this is a ‘curate's egg’ of a set of regulations. Some elements are followed through by clear thinking. Others reflect a purported compromise between business interests and employee rights that on occasion, we suggest, breaches European Union law.
Non-coding RNAs and DNA methylation in plants
Authors: Zhao Yuanyuan , Chen Xuemei
Published: May 2014

Cytosine DNA methylation is an epigenetic modification in eukaryotes that maintains genome integrity and regulates gene expression. The DNA methylation patterns in plants are more complex than those in animals, and plants and animals have common as well as distinct pathways in regulating DNA methylation. Recent studies involving genetic, molecular, biochemical and genomic approaches have greatly expanded our knowledge of DNA methylation in plants. The roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.
Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov.
Authors: Watanabe Miho , Kojima Hisaya , Fukui Manabu
Published: May 2014

A novel thermophilic, facultatively anaerobic bacterium, strain skLN1T, was isolated from the sediment of a freshwater lake in Japan. Cells of strain skLN1T were rod-shaped and Gram-stain-variable. A KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH was pH 7.25–7.50 and the optimum temperature was 50–52 °C. The G+C content of the genomic DNA was 50.8 mol%. Nitrate was reduced to nitrite. Alicyclic fatty acids were not detected, and branched-chain fatty acids were major components in the cellular fatty acid profile. MK-7 was the predominant respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strain was related most closely to

Alicyclobacillus consociatus

CCUG 53762T (95 % similarity). This analysis also showed that the monophyly of the genus

Alicyclobacillus

had been lost. On the basis of phylogenetic and phenotypic characterization, Effusibacillus lacus gen. nov., sp. nov. is proposed. The type strain of Effusibacillus lacus is skLN1T ( = NBRC 109614T = DSM 27172T). It is also proposed that

Alicyclobacillus pohliae

and

Alicyclobacillus consociatus

should be reclassified to the genus Effusibacillus as Effusibacillus pohliae comb. nov. and Effusibacillus consociatus comb. nov., respectively.
Halopolyspora
alba gen. nov., sp. nov., isolated from sediment
Authors: Lai Hangxian , Wei Xiaomin , Jiang Yingying , Chen Xiu , Li Qinyuan , Jiang Yi , Jiang Chenglin , Gillerman Leionid
Published: May 2014

A novel halophilic, filamentous actinomycete, designated strain AFM 10251T, was isolated from a sediment sample collected from the Dead Sea, Israel. The isolate grew with 10–35 % multi-salts, and did not grow without NaCl or MgCl2. The isolate formed a white aerial mycelium, and long chains of arthrospores with more than 10 spores per chain. The spores were spherical or oval with warty surfaces, and sterile mycelium was present between individual spores. The isolate contained meso-diaminopimelic acid and a small proportion of ll-diaminopimelic acid as cell-wall diamino acids, and galactose and arabinose as whole-cell sugars. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C17 : 0, iso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain AFM 10251T was 66.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10251T and the genus

Actinopolyspora

formed a distinct lineage. Analysis of the secondary structures of variable areas of the 16S rRNA gene showed that strain AFM 10251T was different from all recognized species of the genus

Actinopolyspora

and members of the family

Pseudonocardiaceae

. Analysis of the signature nucleotides of the 16S rRNA gene showed that strain AFM 10251T and

Actinopolyspora halophila

formed a single group, but with base pair differences at positions 127 : 234 and 183 : 194. On the basis of analysis of chemical and molecular characteristics, strain AFM 10251T is considered to represent a novel species of a new genus in the family

Actinopolysporaceae

, for which the name Halopolyspora alba gen. nov., sp. nov. is proposed. The type strain of Halopolyspora alba is AFM 10251T ( = DSM 45976T = CGMCC 4.7114T).
Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor
Authors: Hahnke Sarah , Striesow Jutta , Elvert Marcus , Mollar Xavier Prieto , Klocke Michael
Published: May 2014

A novel anaerobic, mesophilic, hydrogen-producing bacterium, designated strain M2/40T, was isolated from a mesophilic, two-phase, laboratory-scale biogas reactor fed continuously with maize silage supplemented with 5 % wheat straw. 16S rRNA gene sequence comparison revealed an affiliation to the genus

Clostridium

sensu stricto (cluster I of the clostridia), with

Clostridium cellulovorans

as the closest characterized species, showing 93.8 % sequence similarity to the type strain. Cells of strain M2/40T were rods to elongated filamentous rods that showed variable Gram staining. Optimal growth occurred at 35 °C and at pH 7. Grown on glucose, the main fermentation products were H2, CO2, formate, lactate and propionate. The DNA G+C content was 29.6 mol%. The major fatty acids (>10 %) were C16 : 0, summed feature 10 (C18 : 1ω11c/ω9t/ω6t and/or unknown ECL 17.834) and C18 : 1ω11c dimethylacetal. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain M2/40T represents a novel species within the genus

Clostridium

, for which we propose the name Clostridium bornimense sp. nov. The type strain is M2/40T ( = DSM 25664T = CECT 8097T).
The molecular biology of mycobacterial trehalose in the quest for advanced tuberculosis therapies
Authors: Nobre Ana , Alarico Susana , Maranha Ana , Mendes Vitor , Empadinhas Nuno
Published: May 2014

Trehalose is a natural glucose disaccharide identified in the 19th century in fungi and insect cocoons, and later across the three domains of life. In members of the genusMycobacterium, which includes the tuberculosis (TB) pathogen and over 160 species of nontuberculous mycobacteria (NTM), many of which are opportunistic pathogens, trehalose has been an important focus of research over the last 60 years. It is a crucial player in the assembly and architecture of the remarkable mycobacterial cell envelope as an element of unique highly antigenic glycolipids, namely trehalose dimycolate (‘cord factor’). Free trehalose has been detected in the mycobacterial cytoplasm and occasionally in oligosaccharides with unknown function. TB and NTM infection statistics and death toll, the decline in immune responses in the aging population, human immunodeficiency virus/AIDS or other debilitating conditions, and the proliferation of strains with different levels of resistance to the dated drugs in use, all merge into a serious public-health threat urging more effective vaccines, efficient diagnostic tools and new drugs. This review deals with the latest findings on mycobacterial trehalose biosynthesis, catabolism, processing and recycling, as well with the ongoing quest for novel trehalose-related mechanisms to be targeted by novel TB therapeutics. In this context, the drug-discovery pipeline has recently included new lead compounds directed toward trehalose-related targets highlighting the potential of these pathways to stem the tide of rising drug resistance.
SecA defects are accompanied by dysregulation of MukB, DNA gyrase, chromosome partitioning and DNA superhelicity in Escherichia coli
Authors: Adachi Shun , Murakawa Yasuhiro , Hiraga Sota
Published: May 2014

Spatial regulation of nucleoids and chromosome-partitioning proteins is important for proper chromosome partitioning inEscherichia coli. However, the underlying molecular mechanisms are unknown. In the present work, we showed that mutation or chemical perturbation of secretory A (SecA), an ATPase component of the membrane protein translocation machinery, SecY, a component of the membrane protein translocation channel and acyl carrier protein P (AcpP), which binds to SecA and MukB, a functional homologue of structural maintenance of chromosomes protein (SMC), resulted in a defect in chromosome partitioning. We further showed that SecA is essential for proper positioning of theoriCDNA region, decatenation and maintenance of superhelicity of DNA. Genetic interaction studies revealed that the topological abnormality observed in thesecAmutant was due to combined inhibitory effects of defects in MukB, DNA gyrase and Topo IV, suggesting a role for the membrane protein translocation machinery in chromosome partitioning and/or structural maintenance of chromosomes.
Observation of the time-course for peptidoglycan lipid intermediate II polymerization by Staphylococcus aureus monofunctional transglycosylase
Authors: Braddick Darren , Sandhu Sandeep , Roper David I. , Chappell Michael J. , Bugg Timothy D. H.
Published: May 2014

The polymerization of lipid intermediate II by the transglycosylase activity of penicillin-binding proteins (PBPs) represents an important target for antibacterial action, but limited methods are available for quantitative assay of this reaction, or screening potential inhibitors. A new labelling method for lipid II polymerization products using Sanger’s reagent (fluoro-2,4-dinitrobenzene), followed by gel permeation HPLC analysis, has permitted the observation of intermediate polymerization products for Staphylococcus aureus monofunctional transglycosylase MGT. Peak formation is inhibited by 6 µM ramoplanin or enduracidin. Characterization by mass spectrometry indicates the formation of tetrasaccharide and octasaccharide intermediates, but not a hexasaccharide intermediate, suggesting a dimerization of a lipid-linked tetrasaccharide. Numerical modelling of the time-course data supports a kinetic model involving addition to lipid-linked tetrasaccharide of either lipid II or lipid-linked tetrasaccharide. Observation of free octasaccharide suggests that hydrolysis of the undecaprenyl diphosphate lipid carrier occurs at this stage in peptidoglycan transglycosylation.
Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess
Authors: Pontel Lucas B. , Scampoli Nadia L. , Porwollik Steffen , Checa Susana K. , McClelland Michael , Soncini Fernando C.
Published: May 2014

Copper and zinc are essential metal ions, but toxic in excess. Bacteria have evolved different strategies to control their intracellular concentrations, ensuring proper supply while avoiding toxicity, including the induction of metal-specific as well as non-specific mechanisms. We compared the transcriptional profiles ofSalmonellaTyphimurium after exposure to either copper or zinc ions in both rich and minimal media. Besides metal-specific regulatory networks many global stress-response pathways react to an excess of either of these metal ions. Copper excess affects both zinc and iron homeostasis by inducing transcription of these metal-specific regulons. In addition to the control of zinc-specific regulons, zinc excess affects the Cpx regulon and the σEenvelope-stress responses. Finally, novel metal-specific upregulated genes were detected including a new copper-detoxification pathway that involves the siderophore enterobactin and the outer-membrane protein TolC. This work sheds light onto the transcriptional landscape ofSalmonellaafter copper or zinc overload, and discloses a new mechanism of copper detoxification.
Powerful tests for multi-marker association analysis using ensemble learning
Authors: Padhukasahasram Badri , Reddy Chandan K. , Williams L. Keoki
Published: May 2014

Multi-marker approaches are currently gaining a lot of interest in genome wide association studies and can enhance power to detect new associations under certain conditions. Gene and pathway based association tests are increasingly being viewed as useful complements to the more widely used single marker association analysis which have successfully uncovered numerous disease variants. A major drawback of single-marker based methods is that they do not consider pairwise and higher-order interactions between genetic variants. Here, we describe novel tests for multi-marker association analyses that are based on phenotype predictions obtained from machine learning algorithms. Instead of utilizing only a linear or logistic regression model, we propose the use of ensembles of diverse machine learning algorithms for constructing such association tests. As the true mathematical relationship between a phenotype and any group of genetic and clinical variables is unknown in advance and may be complex, such a strategy gives us a general and flexible framework to approximate this relationship across different sets of SNPs. We show how phenotype prediction obtained from ensemble learning algorithms can be used for constructing tests for the joint association of multiple variants. We first apply our method to simulated datasets to demonstrate its power and correctness. Then, we apply our method to previously studied asthma-related genes in two independent asthma cohorts to conduct association tests.
PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activity of CONSTITUTIVE PHOTOMORPHOGENIC1 to Synergistically Repress Photomorphogenesis in Arabidopsis
Authors: Xu Xiaosa , Paik Inyup , Zhu Ling , Bu Qingyun , Huang Xi , Deng Xing Wang , Huq Enamul
Published: May 2014

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is a RING/WD40 repeat–containing ubiquitin E3 ligase that is conserved from plants to humans. COP1 forms complexes with SUPPRESSOR OF PHYTOCHROME A (SPA) proteins, and these complexes degrade positively acting transcription factors in the dark to repress photomorphogenesis. Phytochrome-interacting basic helix-loop-helix transcription factors (PIFs) also repress photomorphogenesis in the dark. In response to light, the phytochrome family of sensory photoreceptors simultaneously inactivates COP1-SPA complexes and induces the rapid degradation of PIFs to promote photomorphogenesis. However, the functional relationship between PIFs and COP1-SPA complexes is still unknown. Here, we present genetic evidence that the pif and cop1/spa Arabidopsis thaliana mutants synergistically promote photomorphogenesis in the dark. LONG HYPOCOTYL5 (HY5) is stabilized in the cop1 pif1, spa123 pif1, and pif double, triple, and quadruple mutants in the dark. Moreover, the hy5 mutant suppresses the constitutive photomorphogenic phenotypes of the pifq mutant in the dark. PIF1 forms complexes with COP1, HY5, and SPA1 and enhances the substrate recruitment and autoubiquitylation and transubiquitylation activities of COP1. These data uncover a novel function of PIFs as the potential cofactors of COP1 and provide a genetic and biochemical model of how PIFs and COP1-SPA complexes synergistically repress photomorphogenesis in the dark.
Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+
Authors: Wan Qun , Kovalevsky Andrey Y. , Wilson Mark A. , Bennett Brad C. , Langan Paul , Dealwis Chris
Published: May 2014

A crystal ofEscherichia colidihydrofolate reductase (ecDHFR) complexed with folate and NADP+of 4 × 1.3 × 0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR–folate–NADP+ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.
Crystallization and preliminary X-ray characterization of the 2,4′-dihydroxyacetophenone dioxygenase fromAlcaligenessp. 4HAP
Authors: Beaven G. , Bowyer A. , Erskine P. , Wood S. P. , McCoy A. , Coates L. , Keegan R. , Lebedev A. , Hopper D. J. , Kaderbhai M. A. , Cooper J. B.
Published: May 2014

The enzyme 2,4′-dihydroxyacetophenone dioxygenase (or DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C—C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits each containing nonhaem iron and its sequence suggests that it belongs to the cupin family of dioxygenases. By the use of limited chymotrypsinolysis, the DAD enzyme fromAlcaligenessp. 4HAP has been crystallized in a form that diffracts synchrotron radiation to a resolution of 2.2 Å.
Trait‐based diet selection: prey behaviour and morphology predict vulnerability to predation in reef fish communities
Authors: Green Stephanie J. , Côté Isabelle M.
Published: May 2014

Understanding how predators select their prey can provide important insights into community structure and dynamics. However, the suite of prey species available to a predator is often spatially and temporally variable. As a result, species‐specific selectivity data are of limited use for predicting novel predator–prey interactions because they are assemblage specific.

We present a method for predicting diet selection that is applicable across prey assemblages, based on identifying general morphological and behavioural traits of prey that confer vulnerability to predation independent of species identity. We apply this trait‐based approach to examining prey selection by Indo‐Pacific lionfish (Pterois volitans and Pterois miles), invasive predators that prey upon species‐rich reef fish communities and are rapidly spreading across the western Atlantic.

We first generate hypotheses about morphological and behavioural traits recurring across fish species that could facilitate or deter predation by lionfish. Constructing generalized linear mixed‐effects models that account for relatedness among prey taxa, we test whether these traits predict patterns of diet selection by lionfish within two independent data sets collected at different spatial scales: (i) in situ visual observations of prey consumption and availability for individual lionfish and (ii) comparisons of prey abundance in lionfish stomach contents to availability on invaded reefs at large.

Both analyses reveal that a number of traits predicted to affect vulnerability to predation, including body size, body shape, position in the water column and aggregation behaviour, are important determinants of diet selection by lionfish. Small, shallow‐bodied, solitary fishes found resting on or just above reefs are the most vulnerable. Fishes that exhibit parasite cleaning behaviour experience a significantly lower risk of predation than non‐cleaning fishes, and fishes that are nocturnally active are at significantly greater risk. Together, vulnerable traits heighten the risk of predation by a factor of nearly 200.

Our study reveals that a trait‐based approach yields insights into predator–prey interactions that are robust across prey assemblages. Importantly, in situ observations of selection yield similar results to broadscale comparisons of prey use and availability, which are more typically gathered for predator species. A trait‐based approach could therefore be of use across predator species and ecosystems to predict the outcomes of changing predator–prey interactions on community dynamics.
Enhanced external counterpulsation improves endothelial function and exercise capacity in patients with ischaemic left ventricular dysfunction
Authors: Beck Darren T , Martin Jeffrey S , Casey Darren P , Avery Joseph C , Sardina Paloma D , Braith Randy W
Published: May 2014

Enhanced external counterpulsation (EECP) therapy decreases angina episodes and improves quality of life in patients with left ventricular (LV) dysfunction (LVD). However, studies have not elucidated the mechanisms of action and overall effects of EECP in patients with LVD. The purpose of the present study was to investigate the effects of EECP on endothelial function in peripheral conduit arteries and exercise capacity (peak Vo2) in patients with LVD. Patients with ischaemic LVD (ejection fraction (EF) 34.5 ± 4.2%; n = 9) and patients with symptomatic coronary artery disease (CAD) and preserved LV function (EF 53.5 ± 6.6%; n = 15) were studied before and after 35 sessions (1 h) of EECP. Brachial and femoral artery flow‐mediated dilation (bFMD and fFMD, respectively) were evaluated using high‐resolution ultrasound. Enhanced external counterpulsation elicited similar significant improvements in the following FMD parameters in the CAD and LVD groups (P ≥ 0.05 between groups for all): absolute bFMD (+53% and +70%, respectively), relative bFMD (+50% and +74%, respectively), bFMD normalized for shear rate (+70% and +61%, respectively), absolute fFMD (+33% and +21%, respectively) and relative fFMD (+32% and +17%, respectively). In addition, EECP significantly improved plasma levels of nitrate/nitrite (+55% and +28%) and prostacyclin (+50% and +70%), as well as peak Vo2 (+36% and +21%), similarly in both the CAD and LVD groups (P ≥ 0.05 between groups for all). Despite reduced LV function, EECP therapy significantly improves peripheral vascular function and functional capacity in CAD patients with ischaemic LVD to a similar degree to that seen in CAD patients with preserved LV function.
Higher systolic blood pressure with normal vascular function measurements in preterm‐born children
Authors: Edwards Martin O. , Watkins William John , Kotecha Sarah J. , Halcox Julian P. J. , Dunstan Frank D. , Henderson Alexander John , Kotecha Sailesh
Published: May 2014

Preterm birth, low birth weight and poor foetal nutrition have been linked to cardiovascular disease, but the underlying mechanisms remain unclear. We explored prematurity and vascular function by studying a UK cohort of 14 049 children and conducting a systematic review.

Conclusion

Systolic blood pressure was higher in subjects born preterm than term, but there were no differences in endothelial dysfunction or arterial stiffness. The systematic review revealed no clear association between prematurity and vascular function.
Oestrogen‐dependent satellite cell activation and proliferation following a running exercise occurs via the PI3K signalling pathway and not IGF‐1
Authors: Mangan G. , Bombardier E. , Mitchell A. S. , Quadrilatero J. , Tiidus P. M.
Published: May 2014

Aim

The purpose of this study was to determine whether 17β‐estradiol (E2) enhances the activation, proliferation and differentiation of muscle satellite cells (SC) following eccentric exercise either via insulin‐like growth factor‐1 (IGF‐1) or through phosphatidylinositol 3‐kinase (PI3K) signalling.

Methods

This study used 64, 9‐week‐old, ovariectomized Sprague–Dawley rats that were divided into eight treatments groups based on oestrogen status (0.25 mg oestrogen pellet or sham), exercise status (90 min run @ 17 m min−1, −13.5° or unexercised) and PI3K signalling inhibition (0.7 mg wortmannin kg−1 body weight or DMSO control).

Results

Significant increases in total SCs were found in both soleus and white gastrocnemius muscles (immunofluorescent co‐localization of Pax7+ nuclei) 72 h following eccentric exercise (P < 0.05). Oestrogen supplementation caused a further enhancement in total SCs in exercised rats (P < 0.05). In animals where the PI3K pathway was inhibited, regardless of oestrogen or exercise status, there was no significant enhancement of SC number in both the soleus or white gastrocnemius muscles. Interestingly, oestrogen supplementation lowered muscle levels of IGF‐1 with this effect being most prominent in the soleus muscle. While IGF‐1 was increased following exercise (P < 0.05), oestrogen supplementation abrogated this increase back to sedentary levels.

Conclusion

These data suggest that the increase in SC population following exercise in oestrogen‐supplemented females may be mediated via PI3K pathway signalling and not IGF‐1.
Clinical impact of c‐MET expression and genetic mutational status in colorectal cancer patients after liver resection
Authors: Shoji Hirokazu , Yamada Yasuhide , Taniguchi Hirokazu , Nagashima Kengo , Okita Natsuko , Takashima Atsuo , Honma Yoshitaka , Iwasa Satoru , Kato Ken , Hamaguchi Tetsuya , Shimada Yasuhiro
Published: May 2014

c‐MET is implicated in the pathogenesis and growth of a wide variety of human malignancies, including colorectal cancer (CRC). The aim of the present study was to clarify the association between c‐MET expression and tumor recurrence in CRC patients after curative liver resection, and to evaluate concordance in c‐MET expression and various mutations of KRAS, BRAF and PIK3CA between primary CRC and paired liver metastases. A cohort of patients was tested for c‐MET immunoreactivity (i.e. immunohistochemistry [IHC]) and KRAS, BRAF and PIK3CA mutations. Analyses were performed both on primary tumors and paired liver metastases, and the association between IHC and mutations results were assessed. A total of 108 patients were eligible. A total of 53% of patients underwent simultaneous resection of primary tumors and metastases, and the others underwent metachronous resection. Levels of concordance between primary tumors and metastases were 65.7%, 87.7%, 100% and 95.2% for c‐MET, KRAS, BRAF and PIK3CA, respectively. High levels of c‐MET expression (c‐MET‐high) in the primary tumors were observed in 52% of patients. Relapse‐free survival was significantly shorter for patients with c‐MET‐high primary tumors (9.7 months) than for those with c‐MET‐low primary tumors (21.1 months) (P = 0.013). These results suggest that a high level of genetic concordance in KRAS, BRAF and PIK3CA between primary tumors and liver metastases, and c‐MET‐high in the primary tumors were associated with shorter relapse‐free survival after hepatic metastasectomy.
Routine prophylactic central neck dissection for low‐risk papillary thyroid cancer is not cost‐effective
Authors: Garcia Arturo , Palmer Barnard J.A. , Parks Nancy A. , Liu Terrence H.
Published: May 2014

Background

The role of routine prophylactic central neck dissection (CND) in papillary thyroid cancer (PTC) remains controversial. The aim of this study was to evaluate the cost utility of the addition of routine CND in patients with low‐risk PTC compared with total thyroidectomy (TT) alone.

Methods

A Markov model for low‐risk PTC was constructed with a treatment algorithm based on the American Thyroid Association guidelines for well‐differentiated thyroid carcinoma. Utilities and outcome probabilities were derived from published medical literature. US 2010 costs were examined from a society perspective using Medicare reimbursement rates and opportunity loss based on published US government data. Monte Carlo simulation and sensitivity analysis were used to examine the uncertainty of probability, cost and utility estimates.

Results

Initial TT alone is more cost‐effective than TT with CND, resulting in a cost savings of US $5763 per patient with slightly higher effectiveness per patient (0·03 QALY) for a cost savings of $285 per QALY. Sensitivity analysis shows that TT alone offers no advantage when radioactive iodine (RAI) becomes more detrimental to a patient's state of health, when the incidence of non‐neck recurrence increases above 5% in patients undergoing TT alone or decreases below 3·9% in patients undergoing TT with CND or when the rate of permanent hypocalcaemia rises above 4%.

Conclusions

TT with CND is not a cost‐effective strategy in low‐risk PTC. Initial TT alone is favourable because of the low complication rates and low recurrence rates associated with the initial surgery. Alternative strategies such as unilateral prophylactic neck dissection require additional study to assess their cost‐effectiveness.
Cortical bone mineral density in patients with congenital adrenal hyperplasia due to 21‐hydroxylase deficiency
Authors: El‐Maouche Diala , Collier Suzanne , Prasad Mala , Reynolds James C. , Merke Deborah P.
Published: May 2014

Background

Prior studies reveal that bone mineral density (BMD) in congenital adrenal hyperplasia (CAH) is mostly in the osteopaenic range and is associated with lifetime glucocorticoid dose. The forearm, a measure of cortical bone density, has not been evaluated.

Objective

We aimed to evaluate BMD at various sites, including the forearm, and the factors associated with low BMD in CAH patients.

Methods

Eighty CAH adults (47 classic, 33 nonclassic) underwent dual‐energy‐x‐ray absorptiometry and laboratory and clinical evaluation. BMD Z‐scores at the AP spine, total hip, femoral neck, forearm and whole body were examined in relation to phenotype, body mass index, current glucocorticoid dose, average 5‐year glucocorticoid dose, vitamin D, 17‐hydroxyprogesterone, androstenedione, testosterone, dehydroepiandrosterone and dehydroepiandrosterone sulphate (DHEAS).

Results

Reduced BMD (T‐score <−1 at hip, spine, or forearm) was present in 52% and was more common in classic than nonclassic patients (P = 0·005), with the greatest difference observed at the forearm (P = 0·01). Patients with classic compared to nonclassic CAH, had higher 17‐hydroxyprogesterone (P = 0·005), lower DHEAS (P = 0·0002) and higher non‐traumatic fracture rate (P = 0·0005). In a multivariate analysis after adjusting for age, gender, height standard deviation, phenotype and cumulative glucocorticoid exposure, higher DHEAS was independently associated with higher BMD at the spine, radius and whole body.

Conclusion

Classic CAH patients have lower BMD than nonclassic patients, with the most affected area being the forearm. This first study of forearm BMD in CAH patients suggests that low DHEAS may be associated with weak cortical bone independent of glucocorticoid exposure.
Does omega‐3 fatty acids supplementation affect circulating leptin levels? A systematic review and meta‐analysis on randomized controlled clinical trials
Authors: Hariri Mitra , Ghiasvand Reza , Shiranian Afshin , Askari Gholamreza , Iraj Bijan , Salehi‐Abargouei Amin
Published: May 2014

Background

Omega‐3 fatty acids have attracted researchers for their effect on circulatory hormone‐like peptides affecting weight control.

Objective

Our objective was to conduct a systematic review and meta‐analysis on randomized controlled trials (RCTs) assessed the effects of omega‐3 supplementation on serum leptin concentration and to find the possible sources of heterogeneity in their results.

Methods

We searched PubMed/Medline, Google Scholar, Ovid, SCOPUS and ISI web of science up to April 2014. RCTs conducted among human adults, examined the effect of omega‐3 fatty acid supplements on serum leptin concentrations as an outcome variable were included. The mean difference and standard deviation (SD) of changes in serum leptin levels were used as effect size for the meta‐analysis. Summary mean estimates with their corresponding SDs were derived using random effects model.

Results

Totally 14 RCTs were eligible to be included in the systematic review, and the meta‐analysis was performed on 13 articles. Our analysis showed that omega‐3 supplementation significantly reduces leptin levels (mean difference (MD) = −1·71 ng/ml 95% confidence interval (CI): −3·17 to −0·24, P = 0·022). Subgroup analysis based on BMI status showed that the omega‐3 supplementation reduces leptin when used for nonobese subjects (MD = −3·60 ng/ml; 95% CI −6·23 to −0·90; P = 0·011); however, this was not true for obese participants (MD = −0·86 ng/ml; 95% CI: −2·63 to −0·90; P = 0·296). Subgroup analysis based on omega‐3 source also showed that omega‐3 from marine sources may significantly reduce leptin levels (MD = −1·73 ng/ml; 95% CI −3·25 to −0·2; P = 0·026), but plant sources do not significantly affect serum leptin levels (MD = −1·48 ng/ml; 95% CI −6·78 to 3·23; P = 0·585). Our results were highly sensitive to one study.

Conclusions

Omega‐3 supplementation might moderately decrease circulatory leptin levels only among nonobese adults. RCTs with longer follow‐up period, using higher doses for obese adults and exploring the effect in different genders, are needed to replicate our results.
Acute and chronic effects of kisspeptin‐54 administration on GH, prolactin and TSH secretion in healthy women
Authors: Jayasena Channa N. , Comninos Alexander N. , Narayanaswamy Shakunthala , Bhalla Sanjana , Abbara Ali , Ganiyu‐Dada Zainab , Busbridge Mark , Ghatei Mohammad A. , Bloom Stephen R. , Dhillo Waljit S.
Published: May 2014

Background

The peptide hormone kisspeptin is essential for human reproduction, acting on the hypothalamus to stimulate gonadotrophin‐releasing hormone (GnRH) secretion. Kisspeptin is currently being evaluated as a novel therapeutic for women with infertility. However, some animal studies suggest that kisspeptin may also stimulate growth hormone (GH), prolactin and thyroid‐stimulating hormone (TSH) secretion, with implications for its safety; no previous study has investigated whether kisspeptin stimulates these pituitary hormones in humans.

Aim

To determine whether kisspeptin‐54 modulates GH, prolactin and TSH secretion in healthy women.

Design and participants

Prospective, single‐blinded, placebo‐controlled, one‐way crossover study. Five healthy women received 7 days of twice‐daily subcutaneous bolus vehicle (month 1) or 6·4 nmol/kg kisspeptin‐54 (month 2).

Measurements

Serum samples were analysed post hoc for GH, prolactin and TSH.

Results

Mean serum GH, PRL and TSH did not change during the first 4 h following kisspeptin‐54 injection when compared with vehicle. The mean frequency or amplitude of GH pulses (which influence GH function) did not change acutely following kisspeptin‐54 injection when compared with vehicle. No chronic changes in serum GH, PRL or TSH were observed over the 7‐day period of twice‐daily kisspeptin‐54 injections when compared with vehicle.

Conclusion

While we cannot exclude any effect of kisspeptin‐54 on GH, prolactin or TSH secretion, we observed no significant changes in these hormones at a dose of kisspeptin‐54 administration known to stimulate gonadotrophin secretion in a small study of healthy women. These data have important implications for the potential of kisspeptin to treat patients with infertility.
Impact of unilateral vocal fold mobility impairment on laryngopulmonary physiology
Authors: Nouraei S.A.R. , Whitcroft K. , Patel A. , Chatrath P. , Sandhu G.S. , Kaddour H.
Published: May 2014

Objective

To examine the impact of unilateral vocal fold mobility impairment (UVFMI) on airway physiology.

Study design

Cross‐sectional observational study.

Participants

There were 21 patients with UVFMI and 53 controls.

Main outcome measures

All patients and patient controls underwent a maximum‐effort flow‐volume loop examination. Forced expiratory flow in one second (FEV1), forced expiratory volume (FVC), peak inspiratory flow rate and peak expiratory flow rate (PIFR and PEFR, respectively) and area under the inspiratory and expiratory flow‐volume loops (AUCInspiratory and AUCExpiratory, respectively) were measured. The ratio of PEFR to PIFR and AUCExpiratory to AUCInspiratory was derived.

Results

There were 48 males and 26 females. Mean age at measurement was 39 ± 11 years. Patients and controls were matched for age, sex, height and weight. None of the expiratory variables were significantly different between the groups. PIFR was significantly lower in UVFMI patients compared with controls (3.4 ± 1.2 versus 5.3 ± 1.8; P < 0.0001), as was AUCInspiratory (11.5 ± 6.3 versus 17.5 ± 8.5; P = 0.0002). PEFR/PIFR provided the best differentiation between patients with UVFMI and controls with an area under the Receiver Operating Characteristic (ROC) curve of 0.96 and at a threshold of 1.9, and PEFR/PIFR had sensitivity and specificity of 95.2% and 90.6%, respectively.

Conclusions

Flow‐volume loops are a non‐invasive method of studying vocal abduction and could compliment voice assessment and laryngoscopy in UVFMI. With further research, they could provide an outcome measure for laryngeal rehabilitative procedures, and a shared physiological language for screening and surgical quality assurance.
Cell proliferation in in vivo‐like three‐dimensional cell culture is regulated by sequestration of ERK1/2 to lipid rafts
Authors: Skrobanska R. , Evangelatov A. , Stefanova N. , Topouzova‐Hristova T. , Momchilova A. , Pankov R.
Published: May 2014

Objectives

Regulatory mechanisms of cell proliferation have been extensively studied as they represent major challenges when dealing with pathologies such as fibrosis, tumourigenesis or tissue regeneration. Numerous in vitro studies still exploit conventional, two‐dimensional cell cultures where cells are forced to adhere to unnaturally stiff and flat surfaces of culture dishes. In the living organism, however, each cell is in contact with components of the extracellular matrix and/or neighbouring cells, thus creating a complex three‐dimensional (3D) tissue structure. The current paper describes a native 3D culture of cells, based on the GD25β1 fibroblast cell line, and its use for investigating cell proliferation in in vivo‐like conditions.

Materials and methods

Four‐day post‐confluent culture of GD25β1 fibroblasts resulted in formation of a 3D system of cells embedded in naturally synthesized extracellular matrix. Morphological characterization of the culture was performed by histochemistry, immunohistochemistry and immunofluorescence. Viability/proliferation was assayed by MTT testing, FACS analysis and Western blotting for determination of expression levels and activation status of the relevant signalling molecules.

Results

GD25b1 fibroblasts, grown as 3D culture, gave rise to tissue‐like structures characterized by low level of apoptosis, low senescence and development of 3D matrix adhesions, typical of living tissues. Transition to three‐dimensionality led to a switch from exponential to linear culture growth, accompanied by accumulation of activated ERK1/2 into caveolin‐containing raft domains. Disruption of raft domains as well as reverse transition from 3D back to monolayer culture led to release of phosphorylated ERK1/2 from rafts, activation of cyclin D1 expression and increase in proliferation levels.

Conclusions

These results imply that under in vivo‐like conditions, cells might achieve reduction of their proliferation level by sequestering activated ERK1/2 to lipid rafts.
Research in practice: Substance P antagonism in chronic pruritus
Authors: Lotts Tobias , Ständer Sonja
Published: May 2014

Pruritus is an unpleasant sensation of the skin, which triggers a desire to scratch or rub. The chronic form (≥6 weeks’ duration) often occurs as a side effect of many diseases and is usually accompanied by a high loss in quality of life for patients, especially in cases in which the symptom is chronic without adequate treatment options. In recent years, the situation improved continuously, guidelines for chronic pruritus have been defined and standard medications have been proposed. For many reasons, there are still patients who are unable to obtain relief. New therapeutic approaches are therefore urgently needed. Blocking the neuropeptide substance P is a promising strategy; substance P mediates clinically relevant pro‐inflammatory effects by binding to the neurokinin 1 receptor (NK‐1R). This led us to hypothesize that NK‐1R antagonists are promising therapeutic options for chronic pruritus. Several international case series have meanwhile proven the antipruritic effect of the NK‐1R antagonist aprepitant for various forms of chronic pruritus. Initiation of clinical trials with new NK‐1R‐antagonists as a new therapeutic option continues this trend.