bluuebunny/crossref_metadata_2025_split huggingface dataset:
H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Authors: Rowbotham S. P. , Li F. , Dost A. F. M. , Louie S. M. , Marsh B. P. , Pessina P. , Anbarasu C. R. , Brainson C. F. , Tuminello S. J. , Lieberman A. , Ryeom S. , Schlaeger T. M. , Aronow B. J. , Watanabe H. , Wong K. K. , Kim C. F. 
Published: October 2018

AbstractEpigenetic regulators are attractive anticancer targets, but the promise of therapeutic strategies inhibiting some of these factors has not been proven in vivo or taken into account tumor cell heterogeneity. Here we show that the histone methyltransferase G9a, reported to be a therapeutic target in many cancers, is a suppressor of aggressive lung tumor-propagating cells (TPCs). Inhibition of G9a drives lung adenocarcinoma cells towards the TPC phenotype by de-repressing genes which regulate the extracellular matrix. Depletion of G9a during tumorigenesis enriches tumors in TPCs and accelerates disease progression metastasis. Depleting histone demethylases represses G9a-regulated genes and TPC phenotypes. Demethylase inhibition impairs lung adenocarcinoma progression in vivo. Therefore, inhibition of G9a is dangerous in certain cancer contexts, and targeting the histone demethylases is a more suitable approach for lung cancer treatment. Understanding cellular context and specific tumor populations is critical when targeting epigenetic regulators in cancer for future therapeutic development.
Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation
Authors: Rivas María José , Saura María , Pérez-Figueroa Andrés , Panova Marina , Johansson Tomas , André Carl , Caballero Armando , Rolán-Alvarez Emilio , Johannesson Kerstin , Quesada Humberto 
Published: October 2018

AbstractNatural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
An integrated impedance biosensor platform for detection of pathogens in poultry products
Authors: Liu Jiayu , Jasim Ibrahem , Abdullah Amjed , Shen Zhenyu , Zhao Lu , El-Dweik Majed , Zhang Shuping , Almasri Mahmoud 
Published: October 2018

AbstractThis paper presents an impedance-based biosensor for rapid and simultaneous detection of Salmonella serotypes B, D, and E with very low concentration. The biosensor consists of a focusing region, and three detection regions. The cells focusing was achieved using a ramp down electroplated vertical electrode pair along with tilted thin film finger pairs that generate p-DEP forces to focus and concentrate the bacterial cells into the center of the microchannel, and direct them toward the detection region. The detection regions consist of three interdigitated electrode arrays (IDEA), each with 20 pairs of finger coated with a mixture of anti-Salmonella antibody and crosslinker to enhance the adhesion to IDEA. The impedance changes as the target Salmonella binds to the antibody. The biosensor has showed excellent performance as proven by the detection of a single Salmonella serotype B, and simultaneous detection of two Salmonella serotypes B and D with a limit of detection (LOD) of 8 Cells/ml in ready-to-eat turkey samples, the addition of focusing capability improved the measured signal by a factor of between 4–4.5, the total detection time of 45 minutes, selectivity of the sensor on different types of bacterial cells, and the ability to distinguish between dead and live cells.
Epigenetic enzymes influenced by oxidative stress and hypoxia mimetic in osteoblasts are differentially expressed in patients with osteoporosis and osteoarthritis
Authors: Vrtačnik Peter , Zupan Janja , Mlakar Vid , Kranjc Tilen , Marc Janja , Kern Barbara , Ostanek Barbara 
Published: October 2018

AbstractEpigenetic mechanisms including posttranslational histone modifications and DNA methylation are emerging as important determinants of bone homeostasis. With our case-control study we aimed to identify which chromatin-modifying enzymes could be involved in the pathology of postmenopausal osteoporosis and osteoarthritis while co-regulated by estrogens, oxidative stress and hypoxia. Gene expression of HAT1, KAT5, HDAC6, MBD1 and DNMT3A affected by oxidative stress and hypoxia in an in vitro qPCR screening step performed on an osteoblast cell line was analysed in trabecular bone tissue samples from 96 patients. Their expression was significantly reduced in patients with postmenopausal osteoporosis and osteoarthritis as compared to autopsy controls and significantly correlated with bone mineral density and several bone histomorphometry-derived parameters of bone quality and quantity as well as indicators of oxidative stress, RANK/RANKL/OPG system and angiogenesis. Furthermore, oxidative stress increased DNA methylation levels at the RANKL and OPG promoters while decreasing histone acetylation levels at these two genes. Our study is the first to show that higher expression of HAT1, HDAC6 and MBD1 is associated with superior quantity as well as quality of the bone tissue having a more favourable trabecular structure.
Preliminary report on Sichuan golden snub-nosed monkeys (Rhinopithecus roxellana roxellana) at Laohegou Nature Reserve, Sichuan, China
Authors: Fang Gu , Li Man , Liu Xiao-Jie , Guo Wei-Jia , Jiang Yu-Ting , Huang Zhi-Pang , Tang Shi-Yi , Li Da-Yong , Yu Ji , Jin Tong , Liu Xiao-Geng , Wang Ji-Mei , Li Sheng , Qi Xiao-Guang , Li Bao-Guo 
Published: October 2018

AbstractComparative studies of subspecies under different ecological environments offer insights into intraspecies evolutionary adaptive mechanisms. Golden snub-nosed monkeys (Rhinopithecus roxellana) include three subspecies in China classified mainly by their morphological variations: R. r. roxellana (Sichuan and Gansu province), R. r. qinlingensis (Shaanxi province) and R. r. hubeiensis (Hubei province). These three subspecies live in three isolated area with different environments. Past works focused on the last two subspecies, but little information of habitat and behaviors of the nominated subspecies (R. r. roxellana) is available to date. We conducted a two-year study on the diet, activity budget, home range and social organization of 4 herds of R. r. roxellana, based on a total of 106 days’ observation in Laohegou (LHG) Nature Reserve, Sichuan province. By using scan sampling method, our results suggest that the R. r roxellana feeds predominantly on leaves (77.5%), and spends more time feeding (40.0%) and resting (27.0%) while compared to the other two subspecies. Kernel Density Estimation Method based on GPS technology confirms that R. r roxellana has relatively larger home ranges (49.1 km2). The unit size (8.3 ± 3.5 individuals) of R. r roxellana is also smaller. Therefore, it is possible that differences in food availability in relation to habitats have important impacts on the feeding strategy and social system of the golden snub-nosed monkey. These results provide data to further explore intraspecific adaptations of living primates.
TRPM7 and MagT1 in the osteogenic differentiation of human mesenchymal stem cells in vitro
Authors: Castiglioni Sara , Romeo Valentina , Locatelli Laura , Cazzaniga Alessandra , Maier Jeanette A. M. 
Published: October 2018

AbstractMesenchymal stem cells are fundamental for bone formation and repair since they respond to microenvironmental stimuli by undergoing osteogenic differentiation. We show that the kinase and cation channel TRPM7 and the magnesium transporter MagT1 have a role in harmonizing the osteogenic differentiation of human mesenchymal stem cells. TRPM7 and MagT1 are upregulated in osteogenic differentiation and silencing either one accelerates osteogenic differentiation, partly through the activation of autophagy. Intriguingly, similar results were obtained when the cells were cultured under magnesium deficient conditions. These results underpin the contribution of magnesium, TRPM7 and MagT1 to autophagy and osteoblastogenesis.
Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction
Authors: Thomaseth Caterina , Fey Dirk , Santra Tapesh , Rukhlenko Oleksii S. , Radde Nicole E. , Kholodenko Boris N. 
Published: October 2018

AbstractModular Response Analysis (MRA) is a method to reconstruct signalling networks from steady-state perturbation data which has frequently been used in different settings. Since these data are usually noisy due to multi-step measurement procedures and biological variability, it is important to investigate the effect of this noise onto network reconstruction. Here we present a systematic study to investigate propagation of noise from concentration measurements to network structures. Therefore, we design an in silico study of the MAPK and the p53 signalling pathways with realistic noise settings. We make use of statistical concepts and measures to evaluate accuracy and precision of individual inferred interactions and resulting network structures. Our results allow to derive clear recommendations to optimize the performance of MRA based network reconstruction: First, large perturbations are favorable in terms of accuracy even for models with non-linear steady-state response curves. Second, a single control measurement for different perturbation experiments seems to be sufficient for network reconstruction, and third, we recommend to execute the MRA workflow with the mean of different replicates for concentration measurements rather than using computationally more involved regression strategies.
Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken
Authors: Moreira Gabriel Costa Monteiro , Boschiero Clarissa , Cesar Aline Silva Mello , Reecy James M. , Godoy Thaís Fernanda , Pértille Fábio , Ledur Mônica Corrêa , Moura Ana Silvia Alves Meira Tavares , Garrick Dorian J. , Coutinho Luiz Lehmann 
Published: October 2018

AbstractExcessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43–0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.
Penetration of an antimicrobial zinc-sugar alcohol complex into Streptococcus mutans biofilms
Authors: Lim Jong Hyun , Jeong Yongbeom , Song Sang-Hun , Ahn Jae-Hyun , Lee Jeong Rae , Lee Sang-Min 
Published: October 2018

AbstractMature biofilms are highly resistant to antimicrobial agents due to the presence of extracellular polymeric substances (EPS), which inhibit the penetration of external molecules. In this study, we developed a coordination compound consisting of zinc chloride and erythritol that exhibits penetrating and bactericidal activity againstStreptococcus mutansbiofilms. Anin vitrobiofilm model was established in microplates, and bactericidal activity against biofilms was evaluated using an Alamar blue assay. The cause of the antimicrobial activity of the zinc-erythritol mixture on mature biofilms was demonstrated using fast atom bombardment-mass spectrometry, confocal laser scanning microscopy and atomic force microscopy. We demonstrated that zinc chloride spontaneously formed cationic complexes with erythritol in water. The zinc-erythritol complexes reduced intra- and inter-molecular interactions between bacterial exopolysaccharides, a major component of EPS. This activity was confirmed by measuring the attenuation of the hardness of dried polysaccharides isolated fromS. mutansbiofilms. The reduction in the interactions between polysaccharides allowed the complexes to penetrate into biofilms and kill the embedded bacteria. While approximately 13% of biofilm-associated microbes were killed by a 10 min treatment with 6.6 mM zinc chloride, 45% were killed when a solution containing 19.8 mM erythritol and 6.6 mM zinc chloride was used. This strategy of leveraging the coordination properties of metal ions with sugar alcohols provides a simple way to effectively remove mature biofilms using only conventional substances without the need for intricate chemical synthesis processes.
Pattern invariance for reaction-diffusion systems on complex networks
Authors: Cencetti Giulia , Clusella Pau , Fanelli Duccio 
Published: October 2018

AbstractGiven a reaction-diffusion system interacting via a complex network, we propose two different techniques to modify the network topology while preserving its dynamical behaviour. In the region of parameters where the homogeneous solution gets spontaneously destabilized, perturbations grow along the unstable directions made available across the networks of connections, yielding irregular spatio-temporal patterns. We exploit the spectral properties of the Laplacian operator associated to the graph in order to modify its topology, while preserving the unstable manifold of the underlying equilibrium. The new network is isodynamic to the former, meaning that it reproduces the dynamical response (pattern) to a perturbation, as displayed by the original system. The first method acts directly on the eigenmodes, thus resulting in a general redistribution of link weights which, in some cases, can completely change the structure of the original network. The second method uses localization properties of the eigenvectors to identify and randomize a subnetwork that is mostly embedded only into the stable manifold. We test both techniques on different network topologies using the Ginzburg-Landau system as a reference model. Whereas the correlation between patterns on isodynamic networks generated via the first recipe is larger, the second method allows for a finer control at the level of single nodes. This work opens up a new perspective on the multiple possibilities for identifying the family of discrete supports that instigate equivalent dynamical responses on a multispecies reaction-diffusion system.
Rapid selection of environmentally friendly layered alkaline-earth metal phosphates as solid lubricants using crystallographic data
Authors: Zhang Xiaosheng , Niu Wenxing , Dai Yingjing , Xu Hong , Dong Jinxiang 
Published: October 2018

AbstractLubricating technologies are essential for saving energy and identifying effective, environmentally friendly layered materials that meet the demands of solid lubricants is an important direction. Herein, we probed the relationships between load-carrying capacity and crystal structure. The results showed that increasing the sliding resistance of interlayers using corrugated layers increased the load-carrying capacity of layered solid lubricants. This finding expands on the traditional lubrication mechanism of layered materials. Following the rules, rapid selection of layered potassium magnesium and calcium phosphates (K-LMP and K-LCP) as effective solid lubricants was achieved using crystallographic data and strict filtering criteria. In order to prepare materials suitable for lubrication, the synthesis of K-LMP and K-LCP was optimised. These materials could be utilised in the food, textile or marine machinery industries in the future. The developed method could successfully guide the synthesis of application-oriented materials.
Photodiodes embedded within electronic textiles
Authors: Satharasinghe Achala , Hughes-Riley Theodore , Dias Tilak 
Published: October 2018

AbstractA novel photodiode-embedded yarn has been presented and characterized for the first time, offering new possibilities for applications including monitoring body vital signs (including heart rate, blood oxygen and skin temperature) and environmental conditions (light, humidity and ultraviolet radiation). To create an E-Textile integrated with electronic devices that is comfortable, conformal, aesthetically pleasing and washable, electronic components are best integrated within the structure of a textile fabric in yarn form. The device is first encapsulated within a protective clear resin micro-pod before being covered in a fibrous sheath. The resin micro-pod and covering fibres have a significant effect on the nature of light received by the photoactive region of the device. This work characterised the effects of both encapsulating photodiodes within resin micro-pods and covering the micro-pod with a fibrous sheath on the opto-electronic parameters. A theoretical model is presented to provide an estimate for these effects and validated experimentally using two photodiode types and a range of different resin micro-pods. This knowledge may have wider applications to other devices with small-scale opto-electronic components. Wash tests confirmed that the yarns could survive multiple machine wash and drying cycles without deterioration in performance.
Quantum probability in decision making from quantum information representation of neuronal states
Authors: Khrennikov Andrei , Basieva Irina , Pothos Emmanuel M. , Yamato Ichiro 
Published: October 2018

AbstractThe recent wave of interest to modeling the process of decision making with the aid of the quantum formalism gives rise to the following question: ‘How can neurons generate quantum-like statistical data?’ (There is a plenty of such data in cognitive psychology and social science). Our model is based on quantum-like representation of uncertainty in generation of action potentials. This uncertainty is a consequence of complexity of electrochemical processes in the brain; in particular, uncertainty of triggering an action potential by the membrane potential. Quantum information state spaces can be considered as extensions of classical information spaces corresponding to neural codes; e.g., 0/1, quiescent/firing neural code. The key point is that processing of information by the brain involves superpositions of such states. Another key point is that a neuronal group performing some psychological functionFis an open quantum system. It interacts with the surrounding electrochemical environment. The process of decision making is described as decoherence in the basis of eigenstates ofF. A decision state is a steady state. This is a linear representation of complex nonlinear dynamics of electrochemical states. Linearity guaranteesexponentially fast convergence to the decision state.
ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart
Authors: Yakubova Aziza , Thorrez Lieven , Svetlichnyy Dmitry , Zwarts Liesbeth , Vulsteke Veerle , Laenen Griet , Oosterlinck Wouter , Moreau Yves , Dehaspe Luc , Van Houdt Jeroen , Cortés-Calabuig Álvaro , De Moor Bart , Callaerts Patrick , Herijgers Paul 
Published: October 2018

AbstractCardiovascular disease associated with metabolic syndrome has a high prevalence, but the mechanistic basis of metabolic cardiomyopathy remains poorly understood. We characterised the cardiac transcriptome in a murine metabolic syndrome (MetS) model (LDLR−/−; ob/ob, DKO) relative to the healthy, control heart (C57BL/6, WT) and the transcriptional changes induced by ACE-inhibition in those hearts. RNA-Seq, differential gene expression and transcription factor analysis identified 288 genes differentially expressed between DKO and WT hearts implicating 72 pathways. Hallmarks of metabolic cardiomyopathy were increased activity in integrin-linked kinase signalling, Rho signalling, dendritic cell maturation, production of nitric oxide and reactive oxygen species in macrophages, atherosclerosis, LXR-RXR signalling, cardiac hypertrophy, and acute phase response pathways. ACE-inhibition had a limited effect on gene expression in WT (55 genes, 23 pathways), and a prominent effect in DKO hearts (1143 genes, 104 pathways). In DKO hearts, ACE-I appears to counteract some of the MetS-specific pathways, while also activating cardioprotective mechanisms. We conclude that MetS and control murine hearts have unique transcriptional profiles and exhibit a partially specific transcriptional response to ACE-inhibition.
Evolution of Chikungunya virus in mosquito cells
Authors: Mohamed Ali Souand , Amroun Abdennour , de Lamballerie Xavier , Nougairède Antoine 
Published: October 2018

AbstractIt has been observed that replication of Chikungunya virus (CHIKV) in C6/36 Aedes albopictus cells has little effect on virus evolution. To characterize evolutionary patterns associated with CHIKV replication in mosquito cells, we performed serial passages of the LR2006 strain in Ae. albopictus cells (75 and 30 passages in C6/36 and U4.4 respectively) and Ae. aegypti cells (100 passages in AA-A20 and in AE) and studied genotypic changes accompanying adaptation during this evolutionary process. Quantitative analysis revealed cell specific patterns: low mutation rates in C6/36 cells except when a CHIKV strain pre-adapted to mammalian was used and typical features of adaptation to cell culture conditions with a high number of fixed mutations in AE and AA-A20 cells probably due to the weak permissiveness of these latter cell lines. Altogether, these results suggested that both cell line and viral strain influence rates of viral evolution. In contrast, characteristics and distribution of mutations were qualitatively very similar in all mosquito cells with a high level of parallel evolution including 4 deletion mutations. Serial passage in mammalian cells of viruses pre-adapted to mosquito cells revealed disappearance of almost all shared mutations suggesting that many of these mutational patterns are vector-specific.