bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nutrient and herbivore alterations cause uncoupled changes in producer diversity, biomass and ecosystem function, but not in overall multifunctionality
Authors: Alberti J. , Cebrian J. , Alvarez F. , Escapa M. , Esquius K. S. , Fanjul E. , Sparks E. L. , Mortazavi B. , Iribarne O. 
Published: May 2017

AbstractAltered nutrient cycles and consumer populations are among the top anthropogenic influences on ecosystems. However, studies on the simultaneous impacts of human-driven environmental alterations on ecosystem functions, and the overall change in system multifunctionality are scarce. We used estuarine tidal flats to study the effects of changes in herbivore density and nutrient availability on benthic microalgae (diversity, abundance and biomass) and ecosystem functions (N2-fixation, denitrification, extracellular polymeric substances -EPS- as a proxy for sediment cohesiveness, sediment water content as a proxy of water retention capacity and sediment organic matter). We found consistent strong impacts of modified herbivory and weak effects of increased nutrient availability on the abundance, biomass and diversity of benthic microalgae. However, the effects on specific ecosystem functions were disparate. Some functions were independently affected by nutrient addition (N2-fixation), modified herbivory (sediment organic matter and water content), or their interaction (denitrification), while others were not affected (EPS). Overall system multifunction remained invariant despite changes in specific functions. This study reveals that anthropogenic pressures can induce decoupled effects between community structure and specific ecosystem functions. Our results highlight the need to address several ecosystem functions simultaneously for better ecosystem characterization and management.
φBO1E, a newly discovered lytic bacteriophage targeting carbapenemase-producing Klebsiella pneumoniae of the pandemic Clonal Group 258 clade II lineage
Authors: D’Andrea Marco Maria , Marmo Pasquale , Henrici De Angelis Lucia , Palmieri Mattia , Ciacci Nagaia , Di Lallo Gustavo , Demattè Elisa , Vannuccini Elisa , Lupetti Pietro , Rossolini Gian Maria , Thaller Maria Cristina 
Published: May 2017

AbstractThe pandemic dissemination of KPC carbapenemase-producing Klebsiella pneumoniae (KPC-KP) represents a major public health problem, given their extensive multidrug resistance profiles and primary role in causing healthcare-associated infections. This phenomenon has largely been contributed by strains of Clonal Group (CG) 258, mostly of clade II, which in some areas represent the majority of KPC-KP isolates. Here we have characterized a newly discovered lytic Podoviridae, named φBO1E, targeting KPC-KP strains of clade II lineage of CG258. Genomic sequencing revealed that φBO1E belongs to the Kp34virus genus (87% nucleotide identity to vB_KpnP_SU552A). ΦBO1E was stable over a broad pH and temperature range, exhibited strict specificity for K. pneumoniae strains of clade II of CG258, and was unable to establish lysogeny. In a Galleria mellonella infection model, φBO1E was able to protect larvae from death following infection with KPC-KP strains of clade II of CG258, including one colistin resistant strain characterized by a hypermucoviscous phenotype. To our best knowledge φBO1E is the first characterized lytic phage targeting K. pneumoniae strains of this pandemic clonal lineage. As such, it could be of potential interest to develop new agents for treatment of KPC-KP infections and for decolonization of subjects chronically colonized by these resistant superbugs.
Electrically driven deep ultraviolet MgZnO lasers at room temperature
Authors: Suja Mohammad , Bashar Sunayna Binte , Debnath Bishwajit , Su Longxing , Shi Wenhao , Lake Roger , Liu Jianlin 
Published: May 2017

AbstractSemiconductor lasers in the deep ultraviolet (UV) range have numerous potential applications ranging from water purification and medical diagnosis to high-density data storage and flexible displays. Nevertheless, very little success was achieved in the realization of electrically driven deep UV semiconductor lasers to date. In this paper, we report the fabrication and characterization of deep UV MgZnO semiconductor lasers. These lasers are operated with continuous current mode at room temperature and the shortest wavelength reaches 284 nm. The wide bandgap MgZnO thin films with various Mg mole fractions were grown on c-sapphire substrate using radio-frequency plasma assisted molecular beam epitaxy. Metal-semiconductor-metal (MSM) random laser devices were fabricated using lithography and metallization processes. Besides the demonstration of scalable emission wavelength, very low threshold current densities of 29~33 A/cm2 are achieved. Numerical modeling reveals that impact ionization process is responsible for the generation of hole carriers in the MgZnO MSM devices. The interaction of electrons and holes leads to radiative excitonic recombination and subsequent coherent random lasing.
A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases
Authors: Buey Rubén M. , Fernández-Justel David , Marcos-Alcalde Íñigo , Winter Graeme , Gómez-Puertas Paulino , de Pereda José María , Luis Revuelta José 
Published: May 2017

AbstractInosine-5′-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.
Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane
Authors: Zhang Mingzhen , Zheng Jie , Nussinov Ruth , Ma Buyong 
Published: May 2017

AbstractHow cytochrome C is released from the mitochondria to the cytosol via Bax oligomeric pores, a process which is required for apoptosis, is still a mystery. Based on experimentally measured residue-residue distances, we recently solved the first atomic model for Bax oligomeric pores at the membranes using computational approaches. Here, we investigate the mechanism at the microsecond time- and nanometer space- scale using MD simulations. Our free energy landscape depicts a low barrier for the permeation of cytochrome C into the Bax C-terminal mouth, with the pathway proceeding to the inner cavity and exiting via the N-terminal mouth. Release is guided by organized charged/hydrophilic surfaces. The hydrophilicity and negative charge of the pore surface gradually increase along the release pathway from the pore entry to the exit opening. Rather than inert passing of the cytochrome C through a rigid pore, the flexible pore may selectively aid the cytochrome C passage. Once the Bax pore is formed in the membrane, with a low energy barrier, the release of cytochrome C may be readily achieved through energy fluctuations. Collectively, our work provides mechanistic insight in atomic detail into the release of cytochrome C through Bax oligomeric pores.
Cognitive ability and physical health: a Mendelian randomization study
Authors: Hagenaars Saskia P. , Gale Catharine R. , Deary Ian J. , Harris Sarah E. 
Published: May 2017

AbstractCauses of the association between cognitive ability and health remain unknown, but may reflect a shared genetic aetiology. This study examines the causal genetic associations between cognitive ability and physical health. We carried out two-sample Mendelian randomization analyses using the inverse-variance weighted method to test for causality between later life cognitive ability, educational attainment (as a proxy for cognitive ability in youth), BMI, height, systolic blood pressure, coronary artery disease, and type 2 diabetes using data from six independent GWAS consortia and the UK Biobank sample (N = 112 151). BMI, systolic blood pressure, coronary artery disease and type 2 diabetes showed negative associations with cognitive ability; height was positively associated with cognitive ability. The analyses provided no evidence for casual associations from health to cognitive ability. In the other direction, higher educational attainment predicted lower BMI, systolic blood pressure, coronary artery disease, type 2 diabetes, and taller stature. The analyses indicated no causal association from educational attainment to physical health. The lack of evidence for causal associations between cognitive ability, educational attainment, and physical health could be explained by weak instrumental variables, poorly measured outcomes, or the small number of disease cases.
Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions
Authors: Guo Cheng , Spinelli Matthew , Ye Congting , Li Qingshun Q. , Liang Chun 
Published: May 2017

AbstractMiniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes. They are known to critically influence the process of genome evolution and play a role in gene regulation. As the first study concentrated in the transposition activities of MITEs among different ecotype accessions within a species, we conducted a genome-wide comparative analysis by characterizing and comparing MITEs in 19Arabidopsis thalianaaccessions. A total of 343485 MITE putative sequences, including canonical, diverse and partial ones, were delineated from all 19 accessions. Within the entire population of MITEs sequences, 80.7% of them were previously unclassified MITEs, demonstrating a different genomic distribution and functionality compared to the classified MITEs. The interactions between MITEs and homologous genes across 19 accessions provided a fine source for analyzing MITE transposition activities and their impacts on genome evolution. Moreover, a significant proportion of MITEs were found located in the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of genes. Finally, analysis of the impact of MITEs on gene expression suggests that migrations of MITEs have no detectable effect on the expression level for host genes across accessions.
Gene-body CG methylation and divergent expression of duplicate genes in rice
Authors: Wang Xutong , Zhang Zhibin , Fu Tiansi , Hu Lanjuan , Xu Chunming , Gong Lei , Wendel Jonathan F. , Liu Bao 
Published: May 2017

AbstractGene and genome duplication fosters genetic novelty, but redundant gene copies would undergo mutational decay unless preserved via selective or neutral forces. Molecular mechanisms mediating duplicate preservation remain incompletely understood. Several recent studies showed an association between DNA methylation and expression divergence of duplicated genes and suggested a role of epigenetic mechanism in duplicate retention. Here, we compare genome-wide gene-body CG methylation (BCGM) and duplicate gene expression between a rice mutant null for OsMet1-2(a major CG methytransferase in rice) and its isogenic wild-type. We demonstrate a causal link between BCGM divergence and expression difference of duplicate copies. Interestingly, the higher- and lower-expressing copies of duplicates as separate groups show broadly different responses with respect to direction of expression alteration upon loss of BCGM. A role for BCGM in conditioning expression divergence between copies of duplicates generally holds for duplicates generated by whole genome duplication (WGD) or by small-scale duplication processes. However, differences are evident among these categories, including a higher proportion of WGD duplicates manifesting expression alteration, and differential propensities to lose BCGM by the higher- and lower-expression copies in the mutant. Together, our results support the notion that differential epigenetic marking may facilitate long-term retention of duplicate genes.
Functional analysis of the role of hydrogen sulfide in the regulation of dark-induced leaf senescence in Arabidopsis
Authors: Wei Bo , Zhang Wei , Chao Jin , Zhang Tianru , Zhao Tingting , Noctor Graham , Liu Yongsheng , Han Yi 
Published: May 2017

AbstractThere is growing evidence that hydrogen sulfide (H2S) is involved in many physiological processes in plants, but the role of H2S in dark-induced leaf senescence remains unknown. In this work, we found that H2S not only inhibited chlorophyll degradation but also caused the accumulation of photoreactive pheide a in detached leaves under extended darkness. Despite this, transcript levels of senescence-associated genes (SAGs) were less affected in H2S-treated detached leaves compared with those in H2S-untreated detached leaves. Furthermore, cell death/rapid bleaching occurred in both H2S-treated detached and attached leaves after transfer from extended darkness to light. Unlike the lack of effect of H2S on SAG transcripts in darkened detached leaves, exogenous H2S induced higher SAG transcript levels in attached leaves than untreated attached leaves. Genetic evidence further underlined the positive correlation between SAG expression in attached leaves and H2S. In addition, effects of H2S on SAG expression in attached leaves were compromised in the S-nitrosoglutathione reductase-deficient mutant, gsnor1. Taken together, our results suggest that H2S suppresses chlorophyll degradation of detached leaves by regulating a dark-dependent reaction, and that this gas positively modulates SAG expression in attached leaves under prolonged darkness in a GSNOR1-dependent manner.
Expression and integrated network analyses revealed functional divergence of NHX-type Na+/H+ exchanger genes in poplar
Authors: Tian Fengxia , Chang Ermei , Li Yu , Sun Pei , Hu Jianjun , Zhang Jin 
Published: May 2017

AbstractThe Na+/H+ antiporters (NHXs) are secondary ion transporters to exchange H+ and transfer the Na+ or K+ across membrane, they play crucial roles during plant development and stress responses. To gain insight into the functional divergence of NHX genes in poplar, eight PtNHX were identified from Populus trichocarpa genome. PtNHXs containing 10 transmembrane helices (TMH) and a hydrophilic C-terminal domain, the TMH compose a hollow cylinder to provide the channel for Na+ and H+ transport. The expression patterns and cis-acting elements showed that all the PtNHXs were response to single or multiple stresses including drought, heat, cold, salinity, MV, and ABA. Both the co-expression network and protein-protein interaction network of PtNHXs implying their functional divergence. Interestingly, although PtNHX7 and PtNHX8 were generated by whole genome duplication event, they showed significant differences in expression pattern, protein structure, co-expressed genes, and interacted proteins. Only PtNHX7 interact with CBL and CIPK, indicating PtNHX7 is the primary NHX involved in CBL-CIPK pathway during salt stress responses. Natural variation analysis based on 549 P. trichocarpa individuals indicated the frequency of SNPs in PtNHX7 was significantly higher than other PtNHXs. Our findings provide new insights into the functional divergence of NHX genes in poplar.
Application of nuclear magnetic resonance spectroscopy in food adulteration determination: the example of Sudan dye I in paprika powder
Authors: Hu Yaxi , Wang Shuo , Wang Shenlin , Lu Xiaonan 
Published: May 2017

AbstractCarcinogenic Sudan I has been added illegally into spices for an apparent freshness. 1H solution and solid-state (SS) nuclear magnetic resonance (NMR) spectroscopies were applied and compared for determination of Sudan I in paprika powders (PPs). For solution NMR, PPs spiked with Sudan I were extracted with acetonitrile, centrifuged, rotor-evaporated, and re-dissolved in DMSO-d6 for spectral collection. For SSNMR, Sudan I contaminated PPs were mixed with DMSO-d6 solution and used for spectral collection. Linear regression models constructed for quantitative analyses resulted in the average accuracies for unknown samples as 98% and 105%, respectively. Limits of detection for the solution NMR and SSNMR spectrometers were 6.7 and 128.6 mg kg−1, while the limits of quantification were 22.5 and 313.7 mg kg−1. The overall analysis time required by both methods was similar (35 and 32 min). Both NMR techniques are feasible for rapid and accurate determination of Sudan I adulteration in PPs.
The Toxic Effects of Tetrachlorobisphenol A in Saccharomyces cerevisiae Cells via Metabolic Interference
Authors: Tian Juan , Ji Zhihua , Wang Fengbang , Song Maoyong , Li Hao 
Published: May 2017

AbstractTetrachlorobisphenol A (TCBPA) is a common flame retardant detected in different environments. However, its toxic effects on animals and humans are not fully understood. Here, the differential intracellular metabolites and associated gene expression were used to clarify the metabolic interference of TCBPA in Saccharomyces cerevisiae, a simple eukaryotic model organism. The results indicated that TCBPA treatment promoted the glycolysis pathway but inhibited the tricarboxylic acid (TCA) cycle, energy metabolism and the hexose monophosphate pathway (HMP) pathway. Thus, the HMP pathway produced less reducing power, leading to the accumulation of reactive oxygen species (ROS) and aggravation of oxidative damage. Accordingly, the carbon flux was channelled into the accumulation of fatty acids, amino acids and glycerol instead of biomass production and energy metabolism. The accumulation of these metabolites might serve a protective function against TCBPA stress by maintaining the cell membrane integrity or providing a stable intracellular environment in S. cerevisiae. These results enhance our knowledge of the toxic effects of TCBPA on S. cerevisiae via metabolic interference and pave the way for clarification of the mechanisms underlying TCBPA toxicity in animals and humans.
Isolated Congenital Anosmia and CNGA2 Mutation
Authors: Sailani M. Reza , Jingga Inlora , MirMazlomi Seyed Hashem , Bitarafan Fatemeh , Bernstein Jonathan A. , Snyder Michael P. , Garshasbi Masoud 
Published: May 2017

AbstractIsolated congenital anosmia (ICA) is a rare condition that is associated with life-long inability to smell. Here we report a genetic characterization of a large Iranian family segregating ICA. Whole exome sequencing in five affected family members and five healthy members revealed a stop gain mutation in CNGA2 (OMIM 300338) (chrX:150,911,102; CNGA2. c.577C > T; p.Arg193*). The mutation segregates in an X-linked pattern, as all the affected family members are hemizygotes, whereas healthy family members are either heterozygote or homozygote for the reference allele. cnga2 knockout mice are congenitally anosmic and have abnormal olfactory system physiology, additionally Karstensen et al. recently reported two anosmic brothers sharing a CNGA2 truncating variant. Our study in concert with these findings provides strong support for role of CNGA2 gene with pathogenicity of ICA in humans. Together, these results indicate that mutations in key olfactory signaling pathway genes are responsible for human disease.
Ultra-large non-volatile modulation of magnetic moments in PbZr0.2Ti0.8O3/MgO/La0.7Sr0.3MnO3 heterostructure at room temperature via interfacial polarization mediation
Authors: Liu Q. , Miao J. , Reeve Robert , Meng K. K. , Xu X. G. , Wu Y. , Jiang Y. 
Published: May 2017

AbstractMultiferroic hybrid structures PbZr0.2Ti0.8O3 (PZT)/La0.7Sr0.3MnO3 (LSMO) and PZT/MgO/LSMO were epitaxially deposited on (001) Nb:SrTiO3 crystals. Crystallinity and ferroelectric domain structures were investigated for the PZT/LSMO heterostructure. Interestingly, relatively high non-volatile magnetoelectric coupling effects were observed in both heterostructures at room temperature. The change of chemical valence for Mn and Ti at the PZT/MgO/LSMO interface may play a dominant role rather than external strain or orbital reconstruction, which lead to a large modulation of the magnetization. Correspondingly, the transport behavior of the PZT/MgO/LSMO heterostructure is investigated to confirm the role of oxygen vacancies motion. Our result indicates that the PZT/MgO/LSMO heterostructure have a promising application for future high-density non-volatile memories.
Cytokine profiling in the sub-silicone oil fluid after vitrectomy surgeries for refractory retinal diseases
Authors: Kaneko Hiroki , Takayama Kei , Asami Tetsu , Ito Yasuki , Tsunekawa Taichi , Iwase Takeshi , Funahashi Yasuhito , Ueno Shinji , Nonobe Norie , Yasuda Shunsuke , Suzumura Ayana , Shimizu Hideyuki , Kimoto Reona , Hwang Shiang-Jyi , Terasaki Hiroko 
Published: May 2017

AbstractSilicone oil (SO) is an intraocular surgical adjuvant that reduces the surgical complications in refractory retinal diseases, although membrane and cellular proliferation is often seen even in SO-filled eyes. We hypothesised that the fluid in the space between the SO and the retina, named the “sub-silicone oil fluid (SOF)”, enhances these biological responses. We proposed a safe method for SOF extraction. We also analysed inflammatory cytokine expressions and SOF osmotic pressures from eyes with rhegmatogenous retinal detachment (RRD), proliferative diabetic retinopathy (PDR), proliferative vitreoretinopathy (PVR) and macular hole-associated retinal detachment (MHRD). Interleukin (IL)-10, IL-12p40, IL-6, monocyte chemotactic protein-1, and vascular endothelial growth factor (VEGF) in the SOF with PVR were significantly higher than in those with RRD or MHRD. Fibroblast growth factor-2, IL-10, IL-12p40, IL-8, VEGF, and transforming growth factor beta 1 levels in eyes with exacerbated PDR indicated a significantly higher expression than those with simple PDR. IL-6 and tumour necrosis factor alpha in eyes with exacerbated PVR demonstrated a significantly higher expression than in those with simple PVR. However, there was no difference in SOF osmotic pressure between group of each disease. These studies indicate that disease-specific SOF is a significant reflection of disease status.
60 GHz digitally controllable and sequentially rotated fed antenna array
Authors: Kim H. , Lee Y. , Kim B. , Baek K. , Ko S. , Yang T. , Lee J. , Nam S. 
Published: May 2017

Sixteen‐chain sequentially rotated fed antenna array on low‐temperature cofired ceramic substrate is presented. A 60 GHz broadband circular polarised (CP) stacked rectangular patch antenna is implemented as an element. All the feedlines have the same length which is differentiated from conventional T‐junction divider feeder. By this way, several drawbacks of conventional sequential rotated array can be overcome such as phase error occurrence, amplitude mismatch, and axial ratio bandwidth degradation. Moreover, digitally controlled by phase shifters, beamforming performance can be evaluated. The simulated and measured S11 shows broad bandwidth from 57 to 66 GHz. In addition, the radiation patterns show a peak gain of 17.2 dBi and a wide coverage of ±63°.
Spinal Neurocytoma: A Case Report and Review of Literature
Authors: Guedira Khalil , Matar Nidhal , Salem Maher , Chelly Ines , Zemmel Ihsen 
Published: May 2017

AbstractExtraventricular locations of neurocytoma are extremely rare, especially in the spinal cord, which has been reported in only sporadic cases. In this article, we report a new pediatric case of a spinal neurocytoma in a 12-year-old girl and briefly review the relevant literature.