bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus sciuri bacteriophages double-convert for staphylokinase and phospholipase, mediate interspecies plasmid transduction, and package mecA gene
Authors: Zeman M. , Mašlaňová I. , Indráková A. , Šiborová M. , Mikulášek K. , Bendíčková K. , Plevka P. , Vrbovská V. , Zdráhal Z. , Doškař J. , Pantůček R. 
Published: April 2017

AbstractStaphylococcus sciuri is a bacterial pathogen associated with infections in animals and humans, and represents a reservoir for the mecA gene encoding methicillin-resistance in staphylococci. No S. sciuri siphophages were known. Here the identification and characterization of two temperate S. sciuri phages from the Siphoviridae family designated ϕ575 and ϕ879 are presented. The phages have icosahedral heads and flexible noncontractile tails that end with a tail spike. The genomes of the phages are 42,160 and 41,448 bp long and encode 58 and 55 ORFs, respectively, arranged in functional modules. Their head-tail morphogenesis modules are similar to those of Staphylococcus aureus ϕ13-like serogroup F phages, suggesting their common evolutionary origin. The genome of phage ϕ575 harbours genes for staphylokinase and phospholipase that might enhance the virulence of the bacterial hosts. In addition both of the phages package a homologue of the mecA gene, which is a requirement for its lateral transfer. Phage ϕ879 transduces tetracycline and aminoglycoside pSTS7-like resistance plasmids from its host to other S. sciuri strains and to S. aureus. Furthermore, both of the phages efficiently adsorb to numerous staphylococcal species, indicating that they may contribute to interspecies horizontal gene transfer.
Actomyosin contractility provokes contact inhibition in E-cadherin-ligated keratinocytes
Authors: Hirata Hiroaki , Samsonov Mikhail , Sokabe Masahiro 
Published: April 2017

AbstractConfluence-dependent inhibition of epithelial cell proliferation, termed contact inhibition, is crucial for epithelial homeostasis and organ size control. Here we report that among epithelial cells, keratinocytes, which compose the stratified epithelium in the skin, possess a unique, actomyosin-dependent mechanism for contact inhibition. We have observed that under actomyosin-inhibited conditions, cell-cell contact itself through E-cadherin promotes proliferation of keratinocytes. Actomyosin activity in confluent keratinocytes, however, inhibits nuclear localization of β-catenin and YAP, and causes attenuation of β-catenin- and YAP-driven cell proliferation. Confluent keratinocytes develop E-cadherin-mediated punctate adhesion complexes, to which radial actin cables are connected. Eliminating the actin-to-E-cadherin linkage by depleting α-catenin increases proliferation of confluent keratinocytes. By contrast, enforced activation of RhoA-regulated actomyosin or external application of pulling force to ligated E-cadherin attenuates their proliferation, suggesting that tensile stress at E-cadherin-mediated adhesion complexes inhibits proliferation of confluent keratinocytes. Our results highlight actomyosin contractility as a crucial factor that provokes confluence-dependent inhibition of keratinocyte proliferation.
DNA methylation landscape of ocular tissue relative to matched peripheral blood
Authors: Hewitt Alex W , Januar Vania , Sexton-Oates Alexandra , Joo Jihoon E , Franchina Maria , Wang Jie Jin , Liang Helena , Craig Jamie E , Saffery Richard 
Published: April 2017

AbstractEpigenetic variation is implicated in a range of non-communicable diseases, including those of the eye. However, investigating the role of epigenetic variation in central tissues, such as eye or brain, remains problematic and peripheral tissues are often used as surrogates. In this study, matched human blood and eye tissue (n = 8) were obtained post-mortem and DNA methylation profiling performed on blood, neurosensory retina, retinal pigment epithelium (RPE)/choroid and optic nerve tissue using the Illumina Infinium HumanMethylation450 platform. Unsupervised clustering and principal components analysis revealed tissue of origin as the main driver of methylation variation. Despite this, there was a strong correlation of methylation profiles between tissues with >255,000 CpG sites found to have similar methylation levels. An additional ~16,000 show similarity across ocular tissues only. A small proportion of probes showing inter-individual variation in blood co-varied with eye tissues within individuals, however much of this variation may be genetically driven. An improved understanding of the epigenetic landscape of the eye will have important implications for understanding eye disease. Despite a generally high correlation irrespective of origin, tissue type is the major driver of methylation variation, with only limited covariation between blood and any specific ocular tissue.
Synthesis and Biological Evaluation of 2-Methyl-4,5-Disubstituted Oxazoles as a Novel Class of Highly Potent Antitubulin Agents
Authors: Romagnoli Romeo , Baraldi Pier Giovanni , Prencipe Filippo , Oliva Paola , Baraldi Stefania , Salvador Maria Kimatrai , Lopez-Cara Luisa Carlota , Brancale Andrea , Ferla Salvatore , Hamel Ernest , Ronca Roberto , Bortolozzi Roberta , Mariotto Elena , Porcù Elena , Basso Giuseppe , Viola Giampietro 
Published: April 2017

AbstractAntimitotic agents that interfere with microtubule formation are one of the major classes of cytotoxic drugs for cancer treatment. Multiple 2-methyl-4-(3′,4′,5′-trimethoxyphenyl)-5-substituted oxazoles and their related 4-substituted-5-(3′,4′,5′-trimethoxyphenyl) regioisomeric derivatives designed as cis-constrained combretastatin A-4 (CA-4) analogues were synthesized and evaluated for their antiproliferative activity in vitro against a panel of cancer cell lines and, for selected highly active compounds, interaction with tubulin, cell cycle effects and in vivo potency. Both these series of compounds were characterized by the presence of a common 3′,4′,5′-trimethoxyphenyl ring at either the C-4 or C-5 position of the 2-methyloxazole ring. Compounds 4g and 4i, bearing a m-fluoro-p-methoxyphenyl or p-ethoxyphenyl moiety at the 5-position of 2-methyloxazole nucleus, respectively, exhibited the greatest antiproliferative activity, with IC50 values of 0.35-4.6 nM (4g) and 0.5–20.2 nM (4i), which are similar to those obtained with CA-4. These compounds bound to the colchicine site of tubulin and inhibited tubulin polymerization at submicromolar concentrations. Furthermore, 4i strongly induced apoptosis that follows the mitochondrial pathway. In vivo, 4i in a mouse syngeneic model demonstrated high antitumor activity which significantly reduced the tumor mass at doses ten times lower than that required for CA-4P, suggesting that 4i warrants further evaluation as a potential anticancer drug.
Persistence of a sugar-rejecting cockroach genotype under various dietary regimes
Authors: Jensen Kim , Wada-Katsumata Ayako , Schal Coby , Silverman Jules 
Published: April 2017

AbstractGlucose-aversion is a heritable trait that evolved in a number of German cockroach (Blattella germanicaL.) populations in response to strong selection with glucose-containing insecticide baits. However, in the absence of glucose-containing bait, glucose-averse (GA) cockroaches have lower performance than wild-type (WT) cockroaches in several fitness-determining traits. We allocated 48 caged populations initiated with homozygous GA and WT adults to four dietary treatments consisting of either pure rodent chow, rodent chow mixed to yield a content of either 20% glucose or 20% fructose, or a treatment consisting of choice between the 20% glucose- and the 20% fructose-containing food. After 6 months we found significantly higher frequency of WT individuals in populations restricted to the 20% glucose food, and after 12 months all dietary treatments contained significantly more WT individuals than expected. In accompanying experiments, we found lower survival and longer development time of GA nymphs restricted to glucose-containing food. We furthermore found evidence for assortative mating of females with males from their own genotype, with significant differences within WT cockroaches. Our study shows experimental evidence that within heterogeneous populations, WT German cockroaches will over time prevail in abundance over GA individuals, even when glucose is not a dietary component.
Diamond-like carbon coating under oleic acid lubrication: Evidence for graphene oxide formation in superlow friction
Authors: De Barros Bouchet Maria Isabel , Martin Jean Michel , Avila José , Kano Makoto , Yoshida Kentaro , Tsuruda Takeshi , Bai Shandan , Higuchi Yuji , Ozawa Nobuki , Kubo Momoji , Asensio Maria C. 
Published: April 2017

AbstractThe achievement of the superlubricity regime, with a friction coefficient below 0.01, is the Holy Grail of many tribological applications, with the potential to have a remarkable impact on economic and environmental issues. Based on a combined high-resolution photoemission and soft X-ray absorption study, we report that superlubricity can be realized for engineering applications in bearing steel coated with ultra-smooth tetrahedral amorphous carbon (ta-C) under oleic acid lubrication. The results show that tribochemical reactions promoted by the oil lubrication generate strong structural changes in the carbon hybridization of the ta-C hydrogen-free carbon, with initially high sp3 content. Interestingly, the macroscopic superlow friction regime of moving mechanical assemblies coated with ta-C can be attributed to a few partially oxidized graphene-like sheets, with a thickness of not more than 1 nm, formed at the surface inside the wear scar. The sp2 planar carbon and oxygen-derived species are the hallmark of these mesoscopic surface structures created on top of colliding asperities as a result of the tribochemical reactions induced by the oleic acid lubrication. Atomistic simulations elucidate the tribo-formation of such graphene-like structures, providing the link between the overall atomistic mechanism and the macroscopic experimental observations of green superlubricity in the investigated ta-C/oleic acid tribological systems.
Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau
Authors: Li Yuntao , Adams Jonathan , Shi Yu , Wang Hao , He Jin-Sheng , Chu Haiyan 
Published: April 2017

AbstractGlobal change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem.
The Phosphatidylcholine Transfer Protein Stard7 is Required for Mitochondrial and Epithelial Cell Homeostasis
Authors: Yang Li , Na Cheng-Lun , Luo Shiyu , Wu David , Hogan Simon , Huang Taosheng , Weaver Timothy E. 
Published: April 2017

AbstractMitochondria synthesize select phospholipids but lack the machinery for synthesis of the most abundant mitochondrial phospholipid, phosphatidylcholine (PC). Although the phospholipid transfer protein Stard7 promotes uptake of PC by mitochondria, the importance of this pathway for mitochondrial and cellular homeostasis represents a significant knowledge gap. Haploinsufficiency for Stard7 is associated with significant exacerbation of allergic airway disease in mice, including an increase in epithelial barrier permeability. To test the hypothesis that Stard7 deficiency leads to altered barrier structure/function downstream of mitochondrial dysfunction, Stard7 expression was knocked down in a bronchiolar epithelial cell line (BEAS-2B) and specifically deleted in lung epithelial cells of mice (Stard7epi∆/∆). Stard7 deficiency was associated with altered mitochondrial size and membrane organization both in vitro and in vivo. Altered mitochondrial structure was accompanied by disruption of mitochondrial homeostasis, including decreased aerobic respiration, increased oxidant stress, and mitochondrial DNA damage that, in turn, was linked to altered barrier integrity and function. Both mitochondrial and barrier defects were largely corrected by targeting Stard7 to mitochondria or treating epithelial cells with a mitochondrial-targeted antioxidant. These studies suggest that Stard7-mediated transfer of PC is crucial for mitochondrial homeostasis and that mitochondrial dysfunction contributes to altered barrier permeability in Stard7-deficient mice.
Nkx2-5 and Sarcospan genetically interact in the development of the muscular ventricular septum of the heart
Authors: Panzer Adam A. , Regmi Suk D. , Cormier DePorres , Danzo Megan T. , Chen Iuan-bor D. , Winston Julia B. , Hutchinson Alayna K. , Salm Diana , Schulkey Claire E. , Cochran Rebecca S. , Wilson David B. , Jay Patrick Y. 
Published: April 2017

AbstractThe muscular ventricular septum separates the flow of oxygenated and de-oxygenated blood in air-breathing vertebrates. Defects within it, termed muscular ventricular septal defects (VSDs), are common, yet less is known about how they arise than rarer heart defects. Mutations of the cardiac transcription factor NKX2-5 cause cardiac malformations, including muscular VSDs. We describe here a genetic interaction between Nkx2-5 and Sarcospan (Sspn) that affects the risk of muscular VSD in mice. Sspn encodes a protein in the dystrophin-glycoprotein complex. Sspn knockout (SspnKO) mice do not have heart defects, but Nkx2-5+/−/SspnKO mutants have a higher incidence of muscular VSD than Nkx2-5+/− mice. Myofibers in the ventricular septum follow a stereotypical pattern that is disrupted around a muscular VSD. Subendocardial myofibers normally run in parallel along the left ventricular outflow tract, but in the Nkx2-5+/−/SspnKO mutant they commonly deviate into the septum even in the absence of a muscular VSD. Thus, Nkx2-5 and Sspn act in a pathway that affects the alignment of myofibers during the development of the ventricular septum. The malalignment may be a consequence of a defect in the coalescence of trabeculae into the developing ventricular septum, which has been hypothesized to be the mechanistic basis of muscular VSDs.
Anchored but not internalized: shape dependent endocytosis of nanodiamond
Authors: Zhang Bokai , Feng Xi , Yin Hang , Ge Zhenpeng , Wang Yanhuan , Chu Zhiqin , Raabova Helena , Vavra Jan , Cigler Petr , Liu Renbao , Wang Yi , Li Quan 
Published: April 2017

AbstractNanoparticle-cell interactions begin with the cellular uptake of the nanoparticles, a process that eventually determines their cellular fate. In the present work, we show that the morphological features of nanodiamonds (NDs) affect both the anchoring and internalization stages of their endocytosis. While a prickly ND (with sharp edges/corners) has no trouble of anchoring onto the plasma membrane, it suffers from difficult internalization afterwards. In comparison, the internalization of a round ND (obtained by selective etching of the prickly ND) is not limited by its lower anchoring amount and presents a much higher endocytosis amount. Molecular dynamics simulation and continuum modelling results suggest that the observed difference in the anchoring of round and prickly NDs likely results from the reduced contact surface area with the cell membrane of the former, while the energy penalty associated with membrane curvature generation, which is lower for a round ND, may explain its higher probability of the subsequent internalization.
Peptidoglycan O-acetylation increases in response to vancomycin treatment in vancomycin-resistant Enterococcus faecalis
Authors: Chang James D. , Foster Erin E. , Wallace Ashley G. , Kim Sung Joon 
Published: April 2017

AbstractVancomycin resistance is conferred upon vancomycin-resistant enterococci (VRE) through the replacement of peptidoglycan (PG) stem terminal d-Ala-d-Ala with d-Ala-d-Lac. The d-Ala-d-Lac incorporation can affect both the fitness and virulence of VRE. Here we comprehensively investigate the changes to PG composition in vancomycin-resistant Enterococcus faecalis following the growth in presence of vancomycin using liquid chromatography-mass spectrometry. Using high-resolution mass spectrometry, 104 unique muropeptides fragments were identified and the relative abundance of each fragment was accurately quantified by integrating the ion current of a selected ion using extracted-ion chromatogram. The analysis indicates reduced PG cross-linking, increased carboxypeptidase activities, increased N-deacetylation, and increased O-acetylation in VRE when grown in the presence of vancomycin. We found that O-acetylation preferentially occurred on muropeptides fragments with reduced cross-linking with a pentapeptide stem that terminated in d-Ala-d-Lac. These findings show that O-acetylation preferentially occurred in regions of the cell wall with reduced PG cross-linking on PG units that have stems terminating in d-Ala-d-Lac, serving as markers to prevent both the PG-stem modification by carboxypeptidases and the cell wall degradation by autolysins. Accurate quantitative PG composition analysis provided compositional insights into altered cell wall biosynthesis and modification processes in VRE that contribute to lysozyme resistance and enhanced virulence for VRE grown in the presence of vancomycin.
Renin-Angiotensin System Inhibitor is Associated with Lower Risk of Ensuing Chronic Kidney Disease after Functional Recovery from Acute Kidney Injury
Authors: Chou Yu-Hsiang , Huang Tao-Min , Pan Szu-Yu , Chang Chin-Hao , Lai Chun-Fu , Wu Vin-Cent , Wu Ming-Shiou , Wu Kwan-Dun , Chu Tzong-Shinn , Lin Shuei-Liong 
Published: April 2017

AbstractAcute kidney injury (AKI) is an independent risk factor for ensuing chronic kidney disease (CKD). Animal studies have demonstrated that renin-angiotensin system (RAS) inhibitor can reduce ensuing CKD after functional recovery from AKI. Here we study the association between ensuing CKD and use of RAS inhibitor including angiotensin converting enzyme inhibitor or angiotensin II type 1a receptor blocker starting after renal functional recovery in our prospectively collected observational AKI cohort. Adult patients who had cardiac surgery–associated AKI (CSA-AKI) are studied. Patients with CKD, unrecovered AKI, and use of RAS inhibitor before surgery are excluded. Among 587 eligible patients, 94 patients are users of RAS inhibitor which is started and continued after complete renal recovery during median follow-up period of 2.99 years. The users of RAS inhibitor show significantly lower rate of ensuing CKD (users vs. non-users, 26.6% vs. 42.2%) and longer median CKD-free survival time (users vs. non-users, 1079 days vs. 520 days). Multivariate Cox regression analyses further demonstrate that use of RAS inhibitor is independently associated with lower risk of ensuing CKD (hazard ratio = 0.46, P < 0.001). We conclude that use of RAS inhibitor in CSA-AKI patients after renal functional recovery is associated with lower risk of ensuing CKD development.
Scale model technology for floating offshore wind turbines
Authors: Bayati Ilmas , Belloli Marco , Bernini Luca , Giberti Hermes , Zasso Alberto 
Published: April 2017

This study illustrates the aerodynamic and mechatronic design of a 1/75 scaled model of the DTU 10 MW wind turbine to perform wind tunnel tests in floating offshore configuration. Due to the strong discrepancy of the Reynolds number between full and model scale (up to 150), a dedicated low‐Reynolds airfoil (SD7032) was chosen for the aerodynamic design of the blades, and the final shape was defined based on a dedicated optimisation algorithm which had as target the matching of the scaled thrust force and the first flap‐wise bending frequency, as it is thoroughly explained in the study. Furthermore, the mechatronic design is reported in terms of the design choices adopted to get the best target‐oriented functionalities to the model (i.e. individual pitch control, bandwidth) and to reduce as much as possible the weights, greatly affecting the aero‐elastic scaling. The results gathered during experimental campaigns at Politecnico di Milano wind tunnel, are reported confirming the validity of the design and manufacturing choices.
Flux rope, hyperbolic flux tube, and late extreme ultraviolet phases in a non-eruptive circular-ribbon flare
Authors: Masson Sophie , Pariat Étienne , Valori Gherardo , Deng Na , Liu Chang , Wang Haimin , Reid Hamish 
Published: April 2017

Context. The dynamics of ultraviolet (UV) emissions during solar flares provides constraints on the physical mechanisms involved in the trigger and the evolution of flares. In particular it provides some information on the location of the reconnection sites and the associated magnetic fluxes. In this respect, confined flares are far less understood than eruptive flares generating coronal mass ejections.
Aims. We present a detailed study of a confined circular flare dynamics associated with three UV late phases in order to understand more precisely which topological elements are present and how they constrain the dynamics of the flare.
Methods. We perform a non-linear force-free field extrapolation of the confined flare observed with the Helioseismic and Magnetic Imager (HMI) and Atmospheric Imaging Assembly (AIA) instruments on board Solar Dynamics Observatory (SDO). From the 3D magnetic field we compute the squashing factor and we analyse its distribution. Conjointly, we analyse the AIA extreme ultraviolet (EUV) light curves and images in order to identify the post-flare loops, and their temporal and thermal evolution. By combining the two analyses we are able to propose a detailed scenario that explains the dynamics of the flare.
Results. Our topological analysis shows that in addition to a null-point topology with the fan separatrix, the spine lines and its surrounding quasi-separatix layer (QSL) halo (typical for a circular flare), a flux rope and its hyperbolic flux tube (HFT) are enclosed below the null. By comparing the magnetic field topology and the EUV post-flare loops we obtain an almost perfect match between the footpoints of the separatrices and the EUV 1600 Å ribbons and between the HFT field line footpoints and bright spots observed inside the circular ribbons. We show, for the first time in a confined flare, that magnetic reconnection occurred initially at the HFT below the flux rope. Reconnection at the null point between the flux rope and the overlying field is only initiated in a second phase. In addition, we showed that the EUV late phase observed after the main flare episode is caused by the cooling loops of different length which have all reconnected at the null point during the impulsive phase.
Conclusions. Our analysis shows in one example that flux ropes are present in null-point topology not only for eruptive and jet events, but also for confined flares. This allows us to conjecture on the analogies between conditions that govern the generation of jets, confined flares or eruptive flares.