bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis
Authors: Lee Seong Hyuk , Kim Min-Sik , Lee Jae-Hak , Kim Tae Wan , Bae Seung Seob , Lee Sung-Mok , Jung Hae Chang , Yang Tae-Jun , Choi Ae Ran , Cho Yong-Jun , Lee Jung-Hyun , Kwon Kae Kyoung , Lee Hyun Sook , Kang Sung Gyun 
Published: March 2016

AbstractThe hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H2 productivity at high CO flow rates using synthesis gas produced from coal gasification.
Quasi two-dimensional astigmatic solitons in soft chiral metastructures
Authors: Laudyn Urszula A. , Jung Paweł S. , Karpierz Mirosław A. , Assanto Gaetano 
Published: March 2016

AbstractWe investigate a non-homogeneous layered structure encompassing dual spatial dispersion: continuous diffraction in one transverse dimension and discrete diffraction in the orthogonal one. Such dual diffraction can be balanced out by one and the same nonlinear response, giving rise to light self-confinement into astigmatic spatial solitons: self-focusing can compensate for the spreading of a bell-shaped beam, leading to quasi-2D solitary wavepackets which result from 1D transverse self-localization combined with a discrete soliton. We demonstrate such intensity-dependent beam trapping in chiral soft matter, exhibiting one-dimensional discrete diffraction along the helical axis and one-dimensional continuous diffraction in the orthogonal plane. In nematic liquid crystals with suitable birefringence and chiral arrangement, the reorientational nonlinearity is shown to support bell-shaped solitary waves with simple astigmatism dependent on the medium birefringence as well as on the dual diffraction of the input wavepacket. The observations are in agreement with a nonlinear nonlocal model for the all-optical response.
Targeted disruption of sp7 and myostatin with CRISPR-Cas9 results in severe bone defects and more muscular cells in common carp
Authors: Zhong Zhaomin , Niu Pengfei , Wang Mingyong , Huang Guodong , Xu Shuhao , Sun Yi , Xu Xiaona , Hou Yi , Sun Xiaowen , Yan Yilin , Wang Han 
Published: March 2016

AbstractThe common carp (Cyprinus carpio) as one of the most important aquaculture fishes produces over 3 million metric tones annually, approximately 10% the annual production of the all farmed freshwater fish worldwide. However, the tetraploidy genome and long generation-time of the common carp have made its breeding and genetic studies extremely difficult. Here, TALEN and CRISPR-Cas9, two versatile genome-editing tools, are employed to target common carp bone-related genes sp7, runx2, bmp2a, spp1, opg and muscle suppressor gene mstn. TALEN were shown to induce mutations in the target coding sites of sp7, runx2, spp1 and mstn. With CRISPR-Cas9, the two common carp sp7 genes, sp7a and sp7b, were mutated individually, all resulting in severe bone defects; while mstnba mutated fish have grown significantly more muscle cells. We also employed CRISPR-Cas9 to generate double mutant fish of sp7a;mstnba with high efficiencies in a single step. These results demonstrate that both TALEN and CRISPR-Cas9 are highly efficient tools for modifying the common carp genome and open avenues for facilitating common carp genetic studies and breeding.
Resistance of Feather-Associated Bacteria to Intermediate Levels of Ionizing Radiation near Chernobyl
Authors: Ruiz-González Mario Xavier , Czirják Gábor Árpád , Genevaux Pierre , Møller Anders Pape , Mousseau Timothy Alexander , Heeb Philipp 
Published: March 2016

AbstractIonizing radiation has been shown to produce negative effects on organisms, although little is known about its ecological and evolutionary effects. As a study model, we isolated bacteria associated with feathers from barn swallows Hirundo rustica from three study areas around Chernobyl differing in background ionizing radiation levels and one control study site in Denmark. Each bacterial community was exposed to four different γ radiation doses ranging from 0.46 to 3.96 kGy to test whether chronic exposure to radiation had selected for resistant bacterial strains. Experimental radiation duration had an increasingly overall negative effect on the survival of all bacterial communities. After exposure to γ radiation, bacteria isolated from the site with intermediate background radiation levels survived better and produced more colonies than the bacterial communities from other study sites with higher or lower background radiation levels. Long-term effects of radiation in natural populations might be an important selective pressure on traits of bacteria that facilitate survival in certain environments. Our findings indicate the importance of further studies to understand the proximate mechanisms acting to buffer the negative effects of ionizing radiation in natural populations.
Oxidative stress generated during monensin treatment contributes to altered Toxoplasma gondii mitochondrial function
Authors: Charvat Robert A. , Arrizabalaga Gustavo 
Published: March 2016

AbstractThe ionophore monensin displays potent activities against several coccidian parasites of veterinary and medical importance including the opportunistic pathogen of humans,Toxoplasma gondii. While monensin is used widely in animals, toxicity impedes its use in humans. Nonetheless, given its potency, understanding its mode of action would reveal vulnerable aspects of the parasite that can be exploited for drug development. We previously established that monensin inducesToxoplasmato undergo cell cycle arrest and an autophagy-like cell death. Interestingly, these effects are dependent on the mitochondrion-localized TgMSH-1 protein, suggesting that monensin disrupts mitochondrial function. We demonstrate that monensin treatment results in decreased mitochondrial membrane potential and altered morphology. These effects are mitigated by the antioxidant compound N-acetyl-cysteine suggesting that monensin causes an oxidative stress, which was indeed the case based on direct detection of reactive oxygen species. Moreover, over-expression of the antioxidant proteins glutaredoxin and peroxiredoxin 2 protectToxoplasmafrom the deleterious effects of monensin. Thus, our studies show that the effects of monensin onToxoplasmaare due to a disruption of mitochondrial function caused by the induction of an oxidative stress and implicate parasite redox biology as a viable target for the development of drugs againstToxoplasmaand related pathogenic parasites.
Olfactory perception and behavioral effects of sex pheromone gland components in Helicoverpa armigera and Helicoverpa assulta
Authors: Xu Meng , Guo Hao , Hou Chao , Wu Han , Huang Ling-Qiao , Wang Chen-Zhu 
Published: March 2016

AbstractTwo sympatric species Helicoverpa armigera and Helicoverpa assulta use (Z)-11-hexadecenal and (Z)-9-hexadecenal as sex pheromone components in reverse ratio. They also share several other pheromone gland components (PGCs). We present a comparative study on the olfactory coding mechanism and behavioral effects of these additional PGCs in pheromone communication of the two species using single sensillum recording, in situ hybridization, calcium imaging, and wind tunnel. We classify antennal sensilla types A, B and C into A, B1, B2, C1, C2 and C3 based on the response profiles, and identify the glomeruli responsible for antagonist detection in both species. The abundance of these sensilla types when compared with the number of OSNs expressing each of six pheromone receptors suggests that HarmOR13 and HassOR13 are expressed in OSNs housed within A type sensilla, HarmOR14b within B and C type sensilla, while HassOR6 and HassOR16 within some of C type sensilla. We find that for H. armigera, (Z)-11-hexadecenol and (Z)-11-hexadecenyl acetate act as behavioral antagonists. For H. assulta, instead, (Z)-11-hexadecenyl acetate acts as an agonist, while (Z)-9-hexadecenol, (Z)-11-hexadecenol and (Z)-9-hexadecenyl acetate are antagonists. The results provide an overall picture of intra- and interspecific olfactory and behavioral responses to all PGCs in two sister species.
Galunisertib inhibits glioma vasculogenic mimicry formation induced by astrocytes
Authors: Zhang Chao , Chen Wenliang , Zhang Xin , Huang Bin , Chen Aanjing , He Ying , Wang Jian , Li Xingang 
Published: March 2016

AbstractGliomas are among the most lethal primary brain tumors found in humans. In high-grade gliomas, vasculogenic mimicry is often detected and has been correlated with prognosis, thus suggesting its potential as a therapeutic target. Vasculogenic mimicry mainly forms vascular-like channels independent of endothelial cells; however, little is known about the relationship between astrocytes and vasculogenic mimicry. In our study, we demonstrated that the presence of astrocytes promoted vasculogenic mimicry. With suspension microarray technology and in vitro tube formation assays, we identified that astrocytes relied on TGF-β1 to enhance vasculogenic mimicry. We also found that vasculogenic mimicry was inhibited by galunisertib, a promising TGF-β1 inhibitor currently being studied in an ongoing trial in glioma patients. The inhibition was partially attributed to a decrease in autophagy after galunisertib treatment. Moreover, we observed a decrease in VE-cadherin and smooth muscle actin-α expression, as well as down-regulation of Akt and Flk phosphorylation in galunisertib-treated glioma cells. By comparing tumor weight and volume in a xenograft model, we acquired promising results to support our theory. This study expands our understanding of the role of astrocytes in gliomas and demonstrates that galunisertib inhibits glioma vasculogenic mimicry induced by astrocytes.
Mitochondrial Thioredoxin System as a Modulator of Cyclophilin D Redox State
Authors: Folda Alessandra , Citta Anna , Scalcon Valeria , Calì Tito , Zonta Francesco , Scutari Guido , Bindoli Alberto , Rigobello Maria Pia 
Published: March 2016

AbstractThe mitochondrial thioredoxin system (NADPH, thioredoxin reductase, thioredoxin) is a major redox regulator. Here we have investigated the redox correlation between this system and the mitochondrial enzyme cyclophilin D. The peptidyl prolyl cis-trans isomerase activity of cyclophilin D was stimulated by the thioredoxin system, while it was decreased by cyclosporin A and the thioredoxin reductase inhibitor auranofin. The redox state of cyclophilin D, thioredoxin 1 and 2 and peroxiredoxin 3 was measured in isolated rat heart mitochondria and in tumor cell lines (CEM-R and HeLa) by redox Western blot analysis upon inhibition of thioredoxin reductase with auranofin, arsenic trioxide, 1-chloro-2,4-dinitrobenzene or after treatment with hydrogen peroxide. A concomitant oxidation of thioredoxin, peroxiredoxin and cyclophilin D was observed, suggesting a redox communication between the thioredoxin system and cyclophilin. This correlation was further confirmed by i) co-immunoprecipitation assay of cyclophilin D with thioredoxin 2 and peroxiredoxin 3, ii) molecular modeling and iii) depleting thioredoxin reductase by siRNA. We conclude that the mitochondrial thioredoxin system controls the redox state of cyclophilin D which, in turn, may act as a regulator of several processes including ROS production and pro-apoptotic factors release.
Hemodynamic (fNIRS) and EEG (N200) correlates of emotional inter-species interactions modulated by visual and auditory stimulation
Authors: Balconi Michela , Vanutelli Maria Elide 
Published: March 2016

AbstractThe brain activity, considered in its hemodynamic (optical imaging: functional Near-Infrared Spectroscopy, fNIRS) and electrophysiological components (event-related potentials, ERPs, N200) was monitored when subjects observed (visual stimulation, V) or observed and heard (visual + auditory stimulation, VU) situations which represented inter-species (human-animal) interactions, with an emotional positive (cooperative) or negative (uncooperative) content. In addition, the cortical lateralization effect (more left or right dorsolateral prefrontal cortex, DLPFC) was explored. Both ERP and fNIRS showed significant effects due to emotional interactions which were discussed at light of cross-modal integration effects. The significance of inter-species effect for the emotional behavior was considered. In addition, hemodynamic and EEG consonant results and their value as integrated measures were discussed at light of valence effect.
Online Measurement of Exhaled NO Concentration and Its Production Sites by Fast Non-equilibrium Dilution Ion Mobility Spectrometry
Authors: Peng Liying , Jiang Dandan , Wang Zhenxin , Liu Jiwei , Li Haiyang 
Published: March 2016

AbstractExhaled nitric oxide (NO) is one of the most promising breath markers for respiratory diseases. Its profile for exhalation and the respiratory NO production sites can provide useful information for medical disease diagnosis and therapeutic procedures. However, the high-level moisture in exhaled gas always leads to the poor selectivity and sensitivity for ion spectrometric techniques. Herein, a method based on fast non-equilibrium dilution ion mobility spectrometry (NED-IMS) was firstly proposed to directly monitor the exhaled NO profile on line. The moisture interference was eliminated by turbulently diluting the original moisture to 21% of the original with the drift gas and dilution gas. Weak enhancement was observed for humid NO response and its limit of detection at 100% relative humidity was down to 0.58 ppb. The NO concentrations at multiple exhalation flow rates were measured, while its respiratory production sites were determined by using two-compartment model (2CM) and Högman and Meriläinen algorithm (HMA). Last but not the least, the NO production sites were analyzed hourly to tentatively investigate the daily physiological process of NO. The results demonstrated the capacity of NED-IMS in the real-time analysis of exhaled NO and its production sites for clinical diagnosis and assessment.
Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Authors: Schweitzer Mary Higby , Zheng Wenxia , Zanno Lindsay , Werning Sarah , Sugiyama Toshie 
Published: March 2016

AbstractMedullary bone (MB), an estrogen-dependent reproductive tissue present in extant gravid birds, is texturally, histologically and compositionally distinct from other bone types. Phylogenetic proximity led to the proposal that MB would be present in non-avian dinosaurs and recent studies have used microscopic, morphological and regional homologies to identify this reproductive tissue in both theropod and ornithischian dinosaurs. Here, we capitalize on the unique chemical and histological fingerprint of MB in birds to characterize, at the molecular level, MB in the non-avian theropod Tyrannosaurus rex (MOR 1125) and show that the retention of original molecular components in fossils allows deeper physiological and evolutionary questions to be addressed.
Ultra-high dynamic range electro-optic sampling for detecting millimeter and sub-millimeter radiation
Authors: Ibrahim Akram , Férachou Denis , Sharma Gargi , Singh Kanwarpal , Kirouac-Turmel Marie , Ozaki Tsuneyuki 
Published: March 2016

AbstractTime-domain spectroscopy using coherent millimeter and sub-millimeter radiation (also known as terahertz radiation) is rapidly expanding its application, owing greatly to the remarkable advances in generating and detecting such radiation. However, many current techniques for coherent terahertz detection have limited dynamic range, thus making it difficult to perform some basic experiments that need to directly compare strong and weak terahertz signals. Here, we propose and demonstrate a novel technique based on cross-polarized spectral-domain interferometry to achieve ultra-high dynamic range electro-optic sampling measurement of coherent millimeter and sub-millimeter radiation. In our scheme, we exploit the birefringence in a single-mode polarization maintaining fiber in order to measure the phase change induced by the electric field of terahertz radiation in the detection crystal. With our new technique, we have achieved a dynamic range of 7 × 106, which is 4 orders of magnitude higher than conventional electro-optic sampling techniques, while maintaining comparable signal-to-noise ratio. The present technique is foreseen to have great impact on experiments such as linear terahertz spectroscopy of optically thick materials (such as aqueous samples) and nonlinear terahertz spectroscopy, where the higher dynamic range is crucial for proper interpretation of experimentally obtained results.
The importance of interacting climate modes on Australia’s contribution to global carbon cycle extremes
Authors: Cleverly James , Eamus Derek , Luo Qunying , Restrepo Coupe Natalia , Kljun Natascha , Ma Xuanlong , Ewenz Cacilia , Li Longhui , Yu Qiang , Huete Alfredo 
Published: March 2016

AbstractThe global carbon cycle is highly sensitive to climate-driven fluctuations of precipitation, especially in the Southern Hemisphere. This was clearly manifested by a 20% increase of the global terrestrial C sink in 2011 during the strongest sustained La Niña since 1917. However, inconsistencies exist between El Niño/La Niña (ENSO) cycles and precipitation in the historical record; for example, significant ENSO–precipitation correlations were present in only 31% of the last 100 years, and often absent in wet years. To resolve these inconsistencies, we used an advanced temporal scaling method for identifying interactions amongst three key climate modes (El Niño, the Indian Ocean dipole, and the southern annular mode). When these climate modes synchronised (1999–2012), drought and extreme precipitation were observed across Australia. The interaction amongst these climate modes, more than the effect of any single mode, was associated with large fluctuations in precipitation and productivity. The long-term exposure of vegetation to this arid environment has favoured a resilient flora capable of large fluctuations in photosynthetic productivity and explains why Australia was a major contributor not only to the 2011 global C sink anomaly but also to global reductions in photosynthetic C uptake during the previous decade of drought.
Suppression of Structural Phase Transition in VO2 by Epitaxial Strain in Vicinity of Metal-insulator Transition
Authors: Yang Mengmeng , Yang Yuanjun , Bin Hong  , Wang Liangxin , Hu Kai , Dong Yongqi , Xu Han , Huang Haoliang , Zhao Jiangtao , Chen Haiping , Song Li , Ju Huanxin , Zhu Junfa , Bao Jun , Li Xiaoguang , Gu Yueliang , Yang Tieying , Gao Xingyu , Luo Zhenlin , Gao Chen 
Published: March 2016

AbstractMechanism of metal-insulator transition (MIT) in strained VO2 thin films is very complicated and incompletely understood despite three scenarios with potential explanations including electronic correlation (Mott mechanism), structural transformation (Peierls theory) and collaborative Mott-Peierls transition. Herein, we have decoupled coactions of structural and electronic phase transitions across the MIT by implementing epitaxial strain on 13-nm-thick (001)-VO2 films in comparison to thicker films. The structural evolution during MIT characterized by temperature-dependent synchrotron radiation high-resolution X-ray diffraction reciprocal space mapping and Raman spectroscopy suggested that the structural phase transition in the temperature range of vicinity of the MIT is suppressed by epitaxial strain. Furthermore, temperature-dependent Ultraviolet Photoelectron Spectroscopy (UPS) revealed the changes in electron occupancy near the Fermi energy EF of V 3d orbital, implying that the electronic transition triggers the MIT in the strained films. Thus the MIT in the bi-axially strained VO2 thin films should be only driven by electronic transition without assistance of structural phase transition. Density functional theoretical calculations further confirmed that the tetragonal phase across the MIT can be both in insulating and metallic states in the strained (001)-VO2/TiO2 thin films. This work offers a better understanding of the mechanism of MIT in the strained VO2 films.
Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora
Authors: Zhang Liwen , Zhou Zhengfu , Guo Qiannan , Fokkens Like , Miskei Márton , Pócsi István , Zhang Wei , Chen Ming , Wang Lei , Sun Yamin , Donzelli Bruno G. G. , Gibson Donna M. , Nelson David R. , Luo Jian-Guang , Rep Martijn , Liu Hang , Yang Shengnan , Wang Jing , Krasnoff Stuart B. , Xu Yuquan , Molnár István , Lin Min 
Published: March 2016

AbstractNematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle.