bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment
Authors: Yang Fu-Chun , Chen Yi-Lung , Tang Sen-Lin , Yu Chang-Ping , Wang Po-Hsiang , Ismail Wael , Wang Chia-Hsiang , Ding Jiun-Yan , Yang Cheng-Yu , Yang Chia-Ying , Chiang Yin-Ru 
Published: February 2016

Abstract
Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative ‘omics’ approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available.
Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments
Authors: Dyksma Stefan , Bischof Kerstin , Fuchs Bernhard M , Hoffmann Katy , Meier Dimitri , Meyerdierks Anke , Pjevac Petra , Probandt David , Richter Michael , Stepanauskas Ramunas , Mußmann Marc 
Published: February 2016

Abstract
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with 14C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with 14C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up &gt;50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
Interferon-inducible protein SCOTIN interferes with HCV replication through the autolysosomal degradation of NS5A
Authors: Kim Nari , Kim Min-Jung , Sung Pil Soo , Bae Yong Chul , Shin Eui-Cheol , Yoo Joo-Yeon 
Published: February 2016

AbstractHepatitis C virus (HCV) utilizes autophagy to promote its propagation. Here we show the autophagy-mediated suppression of HCV replication via the endoplasmic reticulum (ER) protein SCOTIN. SCOTIN overexpression inhibits HCV replication and infectious virion production in cells infected with cell culture-derived HCV. HCV nonstructural 5A (NS5A) protein, which is a critical factor for HCV RNA replication, interacts with the IFN-β-inducible protein SCOTIN, which transports NS5A to autophagosomes for degradation. Furthermore, the suppressive effect of SCOTIN on HCV replication is impaired in both ATG7-silenced cells and cells treated with autophagy or lysosomal inhibitors. SCOTIN does not affect the overall flow of autophagy; however, it is a substrate for autophagic degradation. The physical association between the transmembrane/proline-rich domain (TMPRD) of SCOTIN and Domain-II of NS5A is essential for autophagosomal trafficking and NS5A degradation. Altogether, our findings suggest that IFN-β-induced SCOTIN recruits the HCV NS5A protein to autophagosomes for degradation, thereby restricting HCV replication.
Lysosomal recruitment of TSC2 is a universal response to cellular stress
Authors: Demetriades Constantinos , Plescher Monika , Teleman Aurelio A. 
Published: February 2016

AbstractmTORC1 promotes cell growth and is therefore inactivated upon unfavourable growth conditions. Signalling pathways downstream of most cellular stresses converge on TSC1/2, which serves as an integration point that inhibits mTORC1. The TSC1/2 complex was shown to translocate to lysosomes to inactivate mTORC1 in response to two stresses: amino-acid starvation and growth factor removal. Whether other stresses also regulate TSC2 localization is not known. How TSC2 localization responds to combinations of stresses and other stimuli is also unknown. We show that both amino acids and growth factors are required simultaneously to maintain TSC2 cytoplasmic; when one of the two is missing, TSC2 relocalizes to lysosomes. Furthermore, multiple different stresses that inhibit mTORC1 also drive TSC2 lysosomal accumulation. Our findings indicate that lysosomal recruitment of TSC2 is a universal response to stimuli that inactivate mTORC1, and that the presence of any single stress is sufficient to cause TSC2 lysosomal localization.
Tripartite assembly of RND multidrug efflux pumps
Authors: Daury Laetitia , Orange François , Taveau Jean-Christophe , Verchère Alice , Monlezun Laura , Gounou Céline , Marreddy Ravi K. R. , Picard Martin , Broutin Isabelle , Pos Klaas M. , Lambert Olivier 
Published: February 2016

AbstractTripartite multidrug efflux systems of Gram-negative bacteria are composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein. They are assumed to form ducts inside the periplasm facilitating drug exit across the outer membrane. Here we present the reconstitution of native Pseudomonas aeruginosa MexAB–OprM and Escherichia coli AcrAB–TolC tripartite Resistance Nodulation and cell Division (RND) efflux systems in a lipid nanodisc system. Single-particle analysis by electron microscopy reveals the inner and outer membrane protein components linked together via the periplasmic adaptor protein. This intrinsic ability of the native components to self-assemble also leads to the formation of a stable interspecies AcrA–MexB–TolC complex suggesting a common mechanism of tripartite assembly. Projection structures of all three complexes emphasize the role of the periplasmic adaptor protein as part of the exit duct with no physical interaction between the inner and outer membrane components.
Anthropogenic effects are associated with a lower persistence of marine food webs
Authors: Gilarranz Luis J. , Mora Camilo , Bascompte Jordi 
Published: February 2016

AbstractMarine coastal ecosystems are among the most exposed to global environmental change, with reported effects on species biomass, species richness and length of trophic chains. By combining a biologically informed food-web model with information on anthropogenic influences in 701 sites across the Caribbean region, we show that fishing effort, human density and thermal stress anomaly are associated with a decrease in local food-web persistence. The conservation status of the site, in turn, is associated with an increase in food-web persistence. Some of these associations are explained through effects on food-web structure and total community biomass. Our results unveil a hidden footprint of human activities. Even when food webs may seem healthy in terms of the presence and abundance of their constituent species, they may be losing the capacity to withstand further environmental degradation.
Fenestrated and Chimney Technique for Juxtarenal Aortic Aneurysm: A Systematic Review and Pooled Data Analysis
Authors: Li Yue , Hu Zhongzhou , Bai Chujie , Liu Jie , Zhang Tao , Ge Yangyang , Luan Shaoliang , Guo Wei 
Published: February 2016

AbstractJuxtarenal aortic aneurysms (JAA) account for approximately 15% of abdominal aortic aneurysms. Fenestrated endovascular aneurysm repair (FEVAR) and chimney endovascular aneurysm repair (CH-EVAR) are both effective methods to treat JAAs, but the comparative effectiveness of these treatment modalities is unclear. We searched the PubMed, Medline, Embase and Cochrane databases to identify English language articles published between January 2005 and September 2013 on management of JAA with fenestrated and chimney techniques to conduct a systematic review to compare outcomes of patients with juxtarenal aortic aneurysm (JAA) treated with the two techniques. We compared nine F-EVAR cohort studies including 542 JAA patients and 8 CH-EVAR cohorts with 158 JAA patients regarding techniques success rates, 30-day mortality, late mortality, endoleak events and secondary intervention rates. The results of this systematic review indicate that both fenestrated and chimney techniques are attractive options for JAAs treatment with encouraging early and mid-term outcomes.
On spatial pattern of concentration distribution for Taylor dispersion process
Authors: Wu Zi , Fu Xudong , Wang Guangqian 
Published: February 2016

AbstractTaylor dispersion is a key concept in many fields. In the present paper, we characterize the pattern of the complete spatial concentration distribution for laminar tube flow; the obtained simple description is shown to represent the nature of Taylor dispersion. Importantly, we find that during the approach to the longitudinal normality of the transverse mean concentration at the time scale of R2/D (R is the tube radius and D is the molecular diffusivity), the solute concentration becomes uniformly distributed across a family of invariant curved transverse surfaces instead of the flat cross-sections in the traditional view. The family of curved surfaces is analytically determined, and a transformation is devised for the previously obtained analytical solution to discuss the decay of the concentration difference across the curved surfaces. The approach to a uniform concentration across the flat cross-sections to the same degree (~3% by concentration difference percentage), achieved at a time-scale of 100 R2/D, is shown to be the natural consequence of the longitudinal separation of the concentration contours on the curved surfaces.
Sub-nanometre resolution of atomic motion during electronic excitation in phase-change materials
Authors: Mitrofanov Kirill V. , Fons Paul , Makino Kotaro , Terashima Ryo , Shimada Toru , Kolobov Alexander V. , Tominaga Junji , Bragaglia Valeria , Giussani Alessandro , Calarco Raffaella , Riechert Henning , Sato Takahiro , Katayama Tetsuo , Ogawa Kanade , Togashi Tadashi , Yabashi Makina , Wall Simon , Brewe Dale , Hase Muneaki 
Published: February 2016

AbstractPhase-change materials based on Ge-Sb-Te alloys are widely used in industrial applications such as nonvolatile memories, but reaction pathways for crystalline-to-amorphous phase-change on picosecond timescales remain unknown. Femtosecond laser excitation and an ultrashort x-ray probe is used to show the temporal separation of electronic and thermal effects in a long-lived (>100 ps) transient metastable state of Ge2Sb2Te5 with muted interatomic interaction induced by a weakening of resonant bonding. Due to a specific electronic state, the lattice undergoes a reversible nondestructive modification over a nanoscale region, remaining cold for 4 ps. An independent time-resolved x-ray absorption fine structure experiment confirms the existence of an intermediate state with disordered bonds. This newly unveiled effect allows the utilization of non-thermal ultra-fast pathways enabling artificial manipulation of the switching process, ultimately leading to a redefined speed limit and improved energy efficiency and reliability of phase-change memory technologies.
Electron work functions of ferrite and austenite phases in a duplex stainless steel and their adhesive forces with AFM silicon probe
Authors: Guo Liqiu , Hua Guomin , Yang Binjie , Lu Hao , Qiao Lijie , Yan Xianguo , Li Dongyang 
Published: February 2016

AbstractLocal electron work function, adhesive force, modulus and deformation of ferrite and austenite phases in a duplex stainless steel were analyzed by scanning force microscopy. It is demonstrated that the austenite has a higher electron work function than the ferrite, corresponding to higher modulus, smaller deformation and larger adhesive force. Relevant first-principles calculations were conducted to elucidate the mechanism behind. It is demonstrated that the difference in the properties between austenite and ferrite is intrinsically related to their electron work functions.
Clinicopathological correlation of psychosis and brain vascular changes in Alzheimer’s disease
Authors: Ting Simon Kang Seng , Hao Ying , Chia Pei Shi , Tan Eng-King , Hameed Shahul 
Published: February 2016

AbstractPsychosis is common in Alzheimer’s disease (AD). However, studies on neuropathology in vascular etiology contributing to psychosis in AD is lacking to date. The aim of this study was to investigate neuropathological vascular related changes in Alzheimer’s disease with psychosis. Data of patients with AD from the National Alzheimer’s Coordinating Center between 2005 to September 2013 was accessed and reviewed. Presence of psychosis was determined based on Neuropsychiatric Inventory Questionnaire taken from the last visit within one year prior to death and patients were divided into psychosis positive and negative group. Comparison of clinical details and neuropathological vascular changes between the groups was performed using Wilcoxon rank sum test and Chi-square/ Fisher’s exact test. Significant variables were further included in a multivariate logistic model. Overall, 145 patients was included. Of these, 50 patients were psychosis positive. Presence of one or more cortical microinfarcts and moderate to severe arteriosclerosis was found to be positively associated with psychosis. Our results suggest vascular changes correlate with psychosis in Alzheimer’s disease.
Selective inhibition of EZH2 by ZLD1039 blocks H3K27methylation and leads to potent anti-tumor activity in breast cancer
Authors: Song Xuejiao , Gao Tiantao , Wang Ningyu , Feng Qiang , You Xinyu , Ye Tinghong , Lei Qian , Zhu Yongxia , Xiong Menghua , Xia Yong , Yang Fangfang , Shi Yaojie , Wei Yuquan , Zhang Lidan , Yu Luoting 
Published: February 2016

AbstractEnhancer of zeste homolog 2 (EZH2) is a candidate oncogenic driver due to its prevalent overexpression and aberrant repression of tumor suppressor genes in diverse cancers. Therefore, blocking EZH2 enzyme activity may present a valid therapeutic strategy for the treatment of cancers with EZH2 overexpression including breast cancers. Here, we described ZLD1039 a potent, highly selective, and orally bioavailable small molecule inhibitor of EZH2, which inhibited breast tumor growth and metastasis. ZLD1039 considerably inhibited EZH2 methyltransferase activity with nanomolar potency, decreased global histone-3 lysine-27 (H3K27) methylation, and reactivated silenced tumor suppressors connected to increased survival of patients with breast cancer. Comparable to conditional silencing of EZH2, its inhibition by ZLD1039 decreased cell proliferation, cell cycle arrest, and induced apoptosis. Comparably, treatment of xenograft-bearing mice with ZLD1039 led to tumor growth regression and metastasis inhibition. These data confirmed the dependency of breast cancer progression on EZH2 activity and the usefulness of ZLD1039 as a promising treatment for breast cancer.
Quantitative profiling of sphingolipids in wild Cordyceps and its mycelia by using UHPLC-MS
Authors: Mi Jia-Ning , Wang Jing-Rong , Jiang Zhi-Hong 
Published: February 2016

AbstractIn the present study, 101 sphingolipids in wild Cordyceps and its five mycelia were quantitatively profiled by using a fully validated UHPLC-MS method. The results revealed that a general rank order for the abundance of different classes of sphingolipids in wild Cordyceps and its mycelia is sphingoid bases/ceramides > phosphosphingolipids > glycosphingolipids. However, remarkable sphingolipid differences between wild Cordyceps and its mycelia were observed. One is that sphingoid base is the dominant sphingolipid in wild Cordyceps, whereas ceramide is the major sphingolipid in mycelia. Another difference is that the abundance of sphingomyelins in wild Cordyceps is almost 10-folds higher than those in most mycelia. The third one is that mycelia contain more inositol phosphorylceramides and glycosphingolipids than wild Cordyceps. Multivariate analysis was further employed to visualize the difference among wild Cordyceps and different mycelia, leading to the identification of respective sphingolipids as potential chemical markers for the differentiation of wild Cordyceps and its related mycelia. This study represents the first report on the quantitative profiling of sphingolipids in wild Cordyceps and its related mycelia, which provided comprehensive chemical evidence for the quality control and rational utilization of wild Cordyceps and its mycelia.
Protecting the properties of monolayer MoS2 on silicon based substrates with an atomically thin buffer
Authors: Man Michael K. L. , Deckoff-Jones Skylar , Winchester Andrew , Shi Guangsha , Gupta Gautam , Mohite Aditya D. , Kar Swastik , Kioupakis Emmanouil , Talapatra Saikat , Dani Keshav M. 
Published: February 2016

AbstractSemiconducting 2D materials, like transition metal dichalcogenides (TMDs), have gained much attention for their potential in opto-electronic devices, valleytronic schemes and semi-conducting to metallic phase engineering. However, like graphene and other atomically thin materials, they lose key properties when placed on a substrate like silicon, including quenching of photoluminescence, distorted crystalline structure and rough surface morphology. The ability to protect these properties of monolayer TMDs, such as molybdenum disulfide (MoS2), on standard Si-based substrates, will enable their use in opto-electronic devices and scientific investigations. Here we show that an atomically thin buffer layer of hexagonal-boron nitride (hBN) protects the range of key opto-electronic, structural and morphological properties of monolayer MoS2 on Si-based substrates. The hBN buffer restores sharp diffraction patterns, improves monolayer flatness by nearly two-orders of magnitude and causes over an order of magnitude enhancement in photoluminescence, compared to bare Si and SiO2 substrates. Our demonstration provides a way of integrating MoS2 and other 2D monolayers onto standard Si-substrates, thus furthering their technological applications and scientific investigations.
Risk and contributing factors of ecosystem shifts over naturally vegetated land under climate change in China
Authors: Yin Yuanyuan , Tang Qiuhong , Wang Lixin , Liu Xingcai 
Published: February 2016

AbstractIdentifying the areas at risk of ecosystem transformation and the main contributing factors to the risk is essential to assist ecological adaptation to climate change. We assessed the risk of ecosystem shifts in China using the projections of four global gridded vegetation models (GGVMs) and an aggregate metric. The results show that half of naturally vegetated land surface could be under moderate or severe risk at the end of the 21st century under the middle and high emission scenarios. The areas with high risk are the Tibetan Plateau region and an area extended northeastward from the Tibetan Plateau to northeast China. With the three major factors considered, the change in carbon stocks is the main contributing factor to the high risk of ecosystem shifts. The change in carbon fluxes is another important contributing factor under the high emission scenario. The change in water fluxes is a less dominant factor except for the Tibetan Plateau region under the high emission scenario. Although there is considerable uncertainty in the risk assessment, the geographic patterns of the risk are generally consistent across different scenarios. The results could help develop regional strategies for ecosystem conservation to cope with climate change.
The language-related transcription factor FOXP2 is post-translationally modified with small ubiquitin-like modifiers
Authors: Estruch Sara B. , Graham Sarah A. , Deriziotis Pelagia , Fisher Simon E. 
Published: February 2016

AbstractMutations affecting the transcription factor FOXP2 cause a rare form of severe speech and language disorder. Although it is clear that sufficient FOXP2 expression is crucial for normal brain development, little is known about how this transcription factor is regulated. To investigate post-translational mechanisms for FOXP2 regulation, we searched for protein interaction partners of FOXP2 and identified members of the PIAS family as novel FOXP2 interactors. PIAS proteins mediate post-translational modification of a range of target proteins with small ubiquitin-like modifiers (SUMOs). We found that FOXP2 can be modified with all three human SUMO proteins and that PIAS1 promotes this process. An aetiological FOXP2 mutation found in a family with speech and language disorder markedly reduced FOXP2 SUMOylation. We demonstrate that FOXP2 is SUMOylated at a single major site, which is conserved in all FOXP2 vertebrate orthologues and in the paralogues FOXP1 and FOXP4. Abolishing this site did not lead to detectable changes in FOXP2 subcellular localization, stability, dimerization or transcriptional repression in cellular assays, but the conservation of this site suggests a potential role for SUMOylation in regulating FOXP2 activity in vivo.