bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper amine oxidases catalyze the oxidative deamination and hydrolysis of cyclic imines
Authors: Nagakubo Toshiki , Kumano Takuto , Ohta Takehiro , Hashimoto Yoshiteru , Kobayashi Michihiko 
Published: January 2019

AbstractAlthough cyclic imines are present in various bioactive secondary metabolites, their degradative metabolism remains unknown. Here, we report that copper amine oxidases, which are important in metabolism of primary amines, catalyze a cyclic imine cleavage reaction. We isolate a microorganism (Arthrobacter sp. C-4A) which metabolizes a β-carboline alkaloid, harmaline. The harmaline-metabolizing enzyme (HarA) purified from strain C-4A is found to be copper amine oxidase and catalyze a ring-opening reaction of cyclic imine within harmaline, besides oxidative deamination of amines. Growth experiments on strain C-4A and Western blot analysis indicate that the HarA expression is induced by harmaline. We propose a reaction mechanism of the cyclic imine cleavage by HarA containing a post-translationally-synthesized cofactor, topaquinone. Together with the above results, the finding of the same activity of copper amine oxidase from E. coli suggests that, in many living organisms, these enzymes may play crucial roles in metabolism of ubiquitous cyclic imines.
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer
Authors: Du Qian , Bert Saul A. , Armstrong Nicola J. , Caldon C. Elizabeth , Song Jenny Z. , Nair Shalima S. , Gould Cathryn M. , Luu Phuc-Loi , Peters Timothy , Khoury Amanda , Qu Wenjia , Zotenko Elena , Stirzaker Clare , Clark Susan J. 
Published: January 2019

AbstractDNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
Membrane reshaping by micrometric curvature sensitive septin filaments
Authors: Beber Alexandre , Taveneau Cyntia , Nania Manuela , Tsai Feng-Ching , Di Cicco Aurelie , Bassereau Patricia , Lévy Daniel , Cabral João T. , Isambert Hervé , Mangenot Stéphanie , Bertin Aurélie 
Published: January 2019

AbstractSeptins are cytoskeletal filaments that assemble at the inner face of the plasma membrane. They are localized at constriction sites and impact membrane remodeling. We report in vitro tools to examine how yeast septins behave on curved and deformable membranes. Septins reshape the membranes of Giant Unilamellar Vesicles with the formation of periodic spikes, while flattening smaller vesicles. We show that membrane deformations are associated to preferential arrangement of septin filaments on specific curvatures. When binding to bilayers supported on custom-designed periodic wavy patterns displaying positive and negative micrometric radii of curvatures, septin filaments remain straight and perpendicular to the curvature of the convex parts, while bending negatively to follow concave geometries. Based on these results, we propose a theoretical model that describes the deformations and micrometric curvature sensitivity observed in vitro. The model captures the reorganizations of septin filaments throughout cytokinesis in vivo, providing mechanistic insights into cell division.
High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry
Authors: Fregin Bob , Czerwinski Fabian , Biedenweg Doreen , Girardo Salvatore , Gross Stefan , Aurich Konstanze , Otto Oliver 
Published: January 2019

AbstractIn life sciences, the material properties of suspended cells have attained significance close to that of fluorescent markers but with the advantage of label-free and unbiased sample characterization. Until recently, cell rheological measurements were either limited by acquisition throughput, excessive post processing, or low-throughput real-time analysis. Real-time deformability cytometry expanded the application of mechanical cell assays to fast on-the-fly phenotyping of large sample sizes, but has been restricted to single material parameters as the Young’s modulus. Here, we introduce dynamic real-time deformability cytometry for comprehensive cell rheological measurements at up to 100 cells per second. Utilizing Fourier decomposition, our microfluidic method is able to disentangle cell response to complex hydrodynamic stress distributions and to determine viscoelastic parameters independent of cell shape. We demonstrate the application of our technology for peripheral blood cells in whole blood samples including the discrimination of B- and CD4+ T-lymphocytes by cell rheological properties.
Binder-free graphene oxide doughs
Authors: Yeh Che-Ning , Huang Haiyue , Lim Alane Tarianna O. , Jhang Ren-Huai , Chen Chun-Hu , Huang Jiaxing 
Published: January 2019

AbstractGraphene oxide (GO) sheets have been used to construct various bulk forms of GO and graphene-based materials through solution-based processing techniques. Here, we report a highly cohesive dough state of GO with tens of weight percent loading in water without binder-like additives. The dough state can be diluted to obtain gels or dispersions, and dried to yield hard solids. It can be kneaded without leaving stains, readily reshaped, connected, and further processed to make bulk GO and graphene materials of arbitrary form factors and tunable microstructures. The doughs can be transformed to dense glassy solids of GO or graphene without long-range stacking order of the sheets, which exhibit isotropic and much enhanced mechanical properties due to hindered sliding between the sheets. GO dough is also found to be a good support material for electrocatalysts as it helps to form compliant interface to access the active particles.
Decrease in radiative forcing by organic aerosol nucleation, climate, and land use change
Authors: Zhu Jialei , Penner Joyce E. , Yu Fangqun , Sillman Sanford , Andreae Meinrat O. , Coe Hugh 
Published: January 2019

AbstractOrganic nucleation is an important source of atmospheric aerosol number concentration, especially in pristine continental regions and during the preindustrial period. Here, we improve on previous simulations that overestimate boundary layer nucleation in the tropics and add changes to climate and land use to evaluate climate forcing. Our model includes both pure organic nucleation and heteromolecular nucleation of sulfuric acid and organics and reproduces the profile of aerosol number concentration measured in the Amazon. Organic nucleation decreases the sum of the total aerosol direct and indirect radiative forcing by 12.5%. The addition of climate and land use change decreases the direct radiative forcing (−0.38 W m−2) by 6.3% and the indirect radiative forcing (−1.68 W m−2) by 3.5% due to the size distribution and number concentration change of secondary organic aerosol and sulfate. Overall, the total radiative forcing associated with anthropogenic aerosols is decreased by 16%.
Sperm-dependent asexual hybrids determine competition among sexual species
Authors: Janko Karel , Eisner Jan , Mikulíček Peter 
Published: January 2019

AbstractInterspecific competition is a fundamental process affecting community structure and evolution of interacting species. Besides direct competition, this process is also mediated by shared enemies, which can change the outcome of competition dramatically. However, previous studies investigating interactions between competing species and their parasites (parasite-mediated competition) completely overlooked the effect of ‘sperm’ parasites (i.e. sperm-dependent parthenogens or pseudogams) on competition. These organisms originate by interspecific hybridization, produce clonal gametes, but exploit parental species for their own reproduction, being therefore analogous to classical parasites. Here we use the reaction-diffusion model and show that pseudogams alter the outcome of interspecific competition significantly. They may either slow down competitive exclusion of the inferior competitor or even turn the outcome of competition between the species. Asexual organisms may thus have unexpectedly strong impact on community structure, and have more significant evolutionary potential than was previously thought.
Interaction strength promotes robustness against cascading effects in mutualistic networks
Authors: Gaiarsa Marília P. , Guimarães Paulo R. 
Published: January 2019

AbstractPerturbations, such as fluctuations in abundance, can ripple across species assemblages through ecological interactions. Furthermore, the way in which ecological interactions are organized into a network and the interaction strengths connecting species may be important for cascading effects. Previous work revealed that network structure determines how cascading effects spread across species assemblages. A next step is to understand how interaction strengths influence cascading effects. Here, we assume that perturbations have negative effects, and we evaluate whether interaction strength affects network robustness to cascading effects in mutualistic interactions, and examine the role of network structure in mediating perturbation cascades when interaction strength is incorporated. We combine empirical data on 18 mutualistic networks, two simulations scenarios, and network theory, to investigate how network structure affects perturbation spreading time, a proxy of network robustness to cascading effects. Simulations in which we included interaction strength presented higher mean spreading time, indicating that interaction strength increases network robustness. Richness, modularity, and nestedness had a strong, positive effect, on mean perturbation spreading time regardless of the interaction strengths. We found that network structure and the distribution of interaction strengths affected communities’ robustness to perturbation spreading. Our results contribute to the discussion on the danger that ecosystems face when species, and interactions alike, become extinct.
STAT3-induced upregulation of lncRNA MEG3 regulates the growth of cardiac hypertrophy through miR-361-5p/HDAC9 axis
Authors: Zhang Jingchang , Liang Yi , Huang Xuecheng , Guo Xiaoyan , Liu Yang , Zhong Jiming , Yuan Jielin 
Published: January 2019

AbstractCardiac hypertrophy is closely correlated with diverse cardiovascular diseases, augmenting the risk of heart failure and sudden death. Long non-coding RNAs (lncRNAs) have been studied in cardiac hypertrophy for their regulatory function. LncRNA MEG3 has been reported in human cancers. Whereas, it is unknown whether MEG3 regulates the growth of cardiac hypertrophy. Therefore, this study aims to investigate the specific role of MEG3 in the progression of cardiac hypertrophy. Here, we found that MEG3 contributed to the pathogenesis of cardiac hypertrophy. MEG3 expression was remarkably strengthened in the mice heart which undergone the transverse aortic constriction (TAC). Moreover, qRT-PCR analysis revealed that MEG3 was upregulated in the cardiomyocytes which were treated with Ang-II. Silenced MEG3 inhibited the increasing size of hypertrophic cardiomyocytes and reversed other hypertrophic responses. Mechanically, MEG3 could affect cardiac hypertrophy by regulating gene expression. Mechanically, we found that MEG3 could be upregulated by the transcription factor STAT3 and could regulate miR-361-5p and HDAC9 by acting as a ceRNA. Finally, rescue assays were made to do further confirmation. All our findings revealed that STAT3-inducetd upregulation of lncRNA MEG3 controls cardiac hypertrophy by regulating miR-362-5p/HDAC9 axis.
Chinese lantern in Physalis is an advantageous morphological novelty and improves plant fitness
Authors: Li Jing , Song Chunjing , He Chaoying 
Published: January 2019

AbstractThe origin of morphological novelties is an important but neglected issue of evolutionary biology. The fruit of the genus Physalis, a berry, is encapsulated by a novel morphological feature of the post-floral, accrescent calyx that is referred to as a Chinese lantern. The evolutionary developmental genetics of the Chinese lantern have been investigated in the last decade; however, the selective values of the morphological novelty remain elusive. Here, we measured the photosynthetic parameters of the fruiting calyces, monitored microclimatic variation within the Chinese lanterns during fruit development, performed floral-calyx-removal experiments, and recorded the fitness-related traits in Physalis floridana. Ultimately, we show that the green-fruiting calyx of Physalis has photosynthetic capabilities, thus serving as an energy source for fruit development. Moreover, the developing Chinese lantern provides a microclimate that benefits the development and maturation of berry and seed, and it improves plant fitness in terms of fruit/seed weight and number, and fruit maturation under low-temperature environments. Furthermore, the lantern structure facilitates the dispersal of fruits and seeds by water and wind. Our results suggest that the Chinese lantern morphology of Physalis is an evolutionary adaptive trait and improves plant fitness, thus providing new insight into the origin of morphological novelties.
High-temperature operation of a silicon qubit
Authors: Ono Keiji , Mori Takahiro , Moriyama Satoshi 
Published: January 2019

AbstractThis study alleviates the low operating temperature constraint of Si qubits. A qubit is a key element for quantum sensors, memories, and computers. Electron spin in Si is a promising qubit, as it allows both long coherence times and potential compatibility with current silicon technology. Si qubits have been implemented using gate-defined quantum dots or shallow impurities. However, operation of Si qubits has been restricted to milli-Kelvin temperatures, thus limiting the application of the quantum technology. In this study, we addressed a single deep impurity, having strong electron confinement of up to 0.3 eV, using single-electron tunnelling transport. We also achieved qubit operation at 5–10 K through a spin-blockade effect based on the tunnelling transport via two impurities. The deep impurity was implemented by tunnel field-effect transistors (TFETs) instead of conventional FETs. With further improvement in fabrication and controllability, this work presents the possibility of operating silicon spin qubits at elevated temperatures.
The proteome of frozen-thawed pig spermatozoa is dependent on the ejaculate fraction source
Authors: Pérez-Patiño Cristina , Li Junwei , Barranco Isabel , Martínez Emilio A. , Rodriguez-Martínez Heriberto , Roca Jordi , Parrilla Inmaculada 
Published: January 2019

AbstractThe preservation of sperm functional parameters and fertility post-cryopreservation largely varies in the porcine, a species with a fractionated ejaculate. Although intrinsic individual differences have primarily been linked to this variation, differences in protein abundance among frozen-thawed (FT)-spermatozoa are far more relevant. This study, performed in two experiments, looked for proteomic quantitative differences between FT-sperm samples differing in post-thaw viability, motility, apoptosis, membrane lipid peroxidation and nuclear DNA fragmentation. The spermatozoa were either derived from the sperm-rich ejaculate fraction (SRF) or the entire ejaculate (Experiment 1) or from the first 10 mL of the SRF, the remaining SRF and the post-SRF (Experiment 2). Quantitative sperm proteomic differences were analysed using a LC-ESI-MS/MS-based SWATH approach. In Experiment 1, FT-spermatozoa from the SRF showed better preservation parameters than those from the entire ejaculate, with 26Sus scrofaproteins with functional sperm relevance showing relative quantitative differences (FC ≥ 1.5) between sperm sources. In Experiment 2, FT-spermatozoa from the first 10 mL of the SRF and the remaining SRF were qualitatively better than those from the post-SRF, and 187 proteins showed relative quantitative differences among the three ejaculate sources. The results indicate that quantitative proteome differences are linked to sperm cryosurvival.
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses
Authors: Amemiya Takayuki , Gromiha M. Michael , Horimoto Katsuhisa , Fukui Kazuhiko 
Published: January 2019

AbstractTo detect drug candidates for dengue haemorrhagic fever (DHF), we employed a computational drug repositioning method to perform an integrated multiple omics analysis based on transcriptomic, proteomic, and interactomic data. We identified 3,892 significant genes, 389 proteins, and 221 human proteins by transcriptomic analysis, proteomic analysis, and human–dengue virus protein–protein interactions, respectively. The drug candidates were selected using gene expression profiles for inverse drug–disease relationships compared with DHF patients and healthy controls as well as interactomic relationships between the signature proteins and chemical compounds. Integrating the results of the multiple omics analysis, we identified eight candidates for drug repositioning to treat DHF that targeted five proteins (ACTG1, CALR, ERC1, HSPA5, SYNE2) involved in human–dengue virus protein–protein interactions, and the signature proteins in the proteomic analysis mapped to significant pathways. Interestingly, five of these drug candidates, valparoic acid, sirolimus, resveratrol, vorinostat, and Y-27632, have been reported previously as effective treatments for flavivirus-induced diseases. The computational approach using multiple omics data for drug repositioning described in this study can be used effectively to identify novel drug candidates.
TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
Authors: Lagström Sonja , Umu Sinan Uğur , Lepistö Maija , Ellonen Pekka , Meisal Roger , Christiansen Irene Kraus , Ambur Ole Herman , Rounge Trine B. 
Published: January 2019

AbstractHPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
Optimization of Normal Human Bronchial Epithelial (NHBE) Cell 3D Cultures for in vitro Lung Model Studies
Authors: Rayner Rachael E. , Makena Patrudu , Prasad Gaddamanugu L. , Cormet-Boyaka Estelle 
Published: January 2019

AbstractRobust in vitro lung models are required for risk assessment to measure key events leading to respiratory diseases. Primary normal human bronchial epithelial cells (NHBE) represent a good lung model but obtaining well-differentiated 3D cultures can be challenging. Here, we evaluated the ability to expand primary NHBE cells in different culture conditions while maintaining their 3D culture characteristics such as ciliated and goblet cells, and ion channel function. Differentiated cultures were optimally obtained with PneumaCult-Ex Plus (expansion medium)/PneumaCult-ALI (differentiation medium). Primary cells passaged up to four times maintained airway epithelial characteristics as evidenced by ciliated pseudostratified columnar epithelium with goblet cells, trans-epithelial electrical resistance (TEER) (>400 Ohms.cm2), and cystic fibrosis transmembrane conductance regulator-mediated short-circuit currents (>3 µA/cm2). No change in ciliary beat frequency (CBF) or airway surface liquid (ASL) meniscus length was observed up to passage six. For the first time, this study demonstrates that CFTR ion channel function and normal epithelial phenotypic characteristics are maintained in passaged primary NHBE cells. Furthermore, this study highlights the criticality of evaluating expansion and differentiation conditions for achieving optimal phenotypic and functional endpoints (CBF, ASL, ion channel function, presence of differentiated cells, TEER) when developing in vitro lung models.
Sensitive Molybdenum Disulfide Based Field Effect Transistor Sensor for Real-time Monitoring of Hydrogen Peroxide
Authors: Zheng Chao , Jin Xin , Li Yutao , Mei Junchi , Sun Yujie , Xiao Mengmeng , Zhang Hong , Zhang Zhiyong , Zhang Guo-Jun 
Published: January 2019

AbstractA reliable and highly sensitive hydrogen peroxide (H2O2) field effect transistor (FET) sensor is reported, which was constructed by using molybdenum disulfide (MoS2)/reduced graphene oxide (RGO). In this work, we prepared MoS2 nanosheets by a simple liquid ultrasonication exfoliation method. After the RGO-based FET device was fabricated, MoS2 was assembled onto the RGO surface for constructing MoS2/RGO FET sensor. The as-prepared FET sensor showed an ultrahigh sensitivity and fast response toward H2O2 in a real-time monitoring manner with a limit of detection down to 1 pM. In addition, the constructed sensor also exhibited a high specificity toward H2O2 in complex biological matrix. More importantly, this novel biosensor was capable of monitoring of H2O2 released from HeLa cells in real-time. So far, this is the first report of MoS2/RGO based FET sensor for electrical detection of signal molecules directly from cancer cells. Hence it is promising as a new platform for the clinical diagnosis of H2O2-related diseases.