bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative NanoUPLC-MSE analysis between magainin I-susceptible and -resistant Escherichia coli strains
Authors: Cardoso Marlon H. , de Almeida Keyla C. , Cândido Elizabete de S. , Murad André M. , Dias Simoni C. , Franco Octávio L. 
Published: June 2017

AbstractIn recent years the antimicrobial peptides (AMPs) have been prospected and designed as new alternatives to conventional antibiotics. Indeed, AMPs have presented great potential toward pathogenic bacterial strains by means of complex mechanisms of action. However, reports have increasingly emerged regarding the mechanisms by which bacteria resist AMP administration. In this context, we performed a comparative proteomic study by using the total bacterial lysate of magainin I-susceptible and –resistant E. coli strains. After nanoUPLC-MSE analyses we identified 742 proteins distributed among the experimental groups, and 25 proteins were differentially expressed in the resistant strains. Among them 10 proteins involved in bacterial resistance, homeostasis, nutrition and protein transport were upregulated, while 15 proteins related to bacterial surface modifications, genetic information and β-lactams binding-protein were downregulated. Moreover, 60 exclusive proteins were identified in the resistant strains, among which biofilm and cell wall formation and multidrug efflux pump proteins could be observed. Thus, differentially from previous studies that could only associate single proteins to AMP bacterial resistance, data here reported show that several metabolic pathways may be related to E. coli resistance to AMPs, revealing the crucial role of multiple “omics” studies in order to elucidate the global molecular mechanisms involved in this resistance.
Effect of dietary advanced glycation end products on inflammation and cardiovascular risks in healthy overweight adults: a randomised crossover trial
Authors: Baye Estifanos , de Courten Maximilian PJ , Walker Karen , Ranasinha Sanjeeva , Earnest Arul , Forbes Josephine M , de Courten Barbora 
Published: June 2017

AbstractDiets high in advanced glycation end products (AGEs) are thought to be detrimental to cardiovascular health. However, there remains uncertainty about the beneficial effect of a low AGE diet on cardiovascular risk factors and inflammatory markers in overweight individuals. We thus performed a randomised, double blind, crossover trial to determine whether consumption of low AGE diets reduce inflammation and cardiovascular risks in overweight and obese otherwise healthy adults. All participants (n = 20) consumed low and high AGE diets alternately for two weeks and separated by a four week washout period. Low AGE diets did not change systolic (p = 0.2) and diastolic blood pressure (p = 0.3), mean arterial pressure (p = 0.8) and pulse pressure (p = 0.2) compared to high AGE diets. Change in total cholesterol (p = 0.3), low-density lipoprotein (p = 0.7), high-density lipoprotein (p = 0.2), and triglycerides (p = 0.4) also did not differ and there was no difference in inflammatory markers: interleukin-6 (p = 0.6), monocyte chemoattractant protein-1 (p = 0.9), tumour necrosis factor α (p = 0.2), C-reactive protein (p = 0.6) and nuclear factor kappa beta (p = 0.2). These findings indicate that consumption of low AGE diets for two weeks did not improve the inflammatory and cardiovascular profiles of overweight and obese adults.
Optical coherence microscopy as a novel, non-invasive method for the 4D live imaging of early mammalian embryos
Authors: Karnowski Karol , Ajduk Anna , Wieloch Bartosz , Tamborski Szymon , Krawiec Krzysztof , Wojtkowski Maciej , Szkulmowski Maciej 
Published: June 2017

AbstractImaging of living cells based on traditional fluorescence and confocal laser scanning microscopy has delivered an enormous amount of information critical for understanding biological processes in single cells. However, the requirement for a high numerical aperture and fluorescent markers still limits researchers’ ability to visualize the cellular architecture without causing short- and long-term photodamage. Optical coherence microscopy (OCM) is a promising alternative that circumvents the technical limitations of fluorescence imaging techniques and provides unique access to fundamental aspects of early embryonic development, without the requirement for sample pre-processing or labeling. In the present paper, we utilized the internal motion of cytoplasm, as well as custom scanning and signal processing protocols, to effectively reduce the speckle noise typical for standard OCM and enable high-resolution intracellular time-lapse imaging. To test our imaging system we used mouse and pig oocytes and embryos and visualized them through fertilization and the first embryonic division, as well as at selected stages of oogenesis and preimplantation development. Because all morphological and morphokinetic properties recorded by OCM are believed to be biomarkers of oocyte/embryo quality, OCM may represent a new chapter in imaging-based preimplantation embryo diagnostics.
Deformation pattern in vibrating microtubule: Structural mechanics study based on an atomistic approach
Authors: Havelka Daniel , Deriu Marco A. , Cifra Michal , Kučera Ondřej 
Published: June 2017

AbstractThe mechanical properties of microtubules are of great importance for understanding their biological function and for applications in artificial devices. Although microtubule mechanics has been extensively studied both theoretically and experimentally, the relation to its molecular structure is understood only partially. Here, we report on the structural analysis of microtubule vibration modes calculated by an atomistic approach. Molecular dynamics was applied to refine the atomic structure of a microtubule and a C
α
elastic network model was analyzed for its normal modes. We mapped fluctuations and local deformations up to the level of individual aminoacid residues. The deformation is mode-shape dependent and principally different in α-tubulins and β-tubulins. Parts of the tubulin dimer sequence responding specifically to longitudinal and radial stress are identified. We show that substantial strain within a microtubule is located both in the regions of contact between adjacent dimers and in the body of tubulins. Our results provide supportive evidence for the generally accepted assumption that the mechanics of microtubules, including its anisotropy, is determined by the bonds between tubulins.
Ribosome RNA Profiling to Quantify Ovarian Development and Identify Sex in Fish
Authors: Shen Zhi-Gang , Yao Hong , Guo Liang , Li Xiao-Xia , Wang Han-Ping 
Published: June 2017

AbstractTerminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S–18S rRNA ratio, using close relationship between volume percent of primary growth stage oocytes or gonadosomatic index and rRNA content, demonstrating species-specific quantification of ovary development can be established in species with either synchronous and asynchronous oogenesis. This approach may be extended to any species with primary growth oocytes, e.g. anurans and reptiles, to predict maturity stages in females. We further confirmed that 5S rRNA percent and 5S/18S rRNA ratio can serve as markers to distinguish sexes unambiguously. A micro-invasive sampling method may be invented for non-lethal prediction of ovary development and sex because only a small amount of ovary sample (<50 mg) is needed for the approach established in the current work. Researchers who work with ovary RNA-seq in these taxa should realize that insufficient depletion of rRNA will probably lead to incorrect quantification of gene expression and inaccurate conclusions.
MicroRNA-148 as a negative regulator of the common TLR adaptor mediates inflammatory response in teleost fish
Authors: Chu Qing , Gao Yunhang , Bi Dekun , Xu Tianjun 
Published: June 2017

AbstractMicroRNAs are small endogenous noncoding RNAs implicating in the regulation of diverse biological processes, including proliferation, differentiation, cancer, apoptosis, and viral infections. MicroRNAs regulate gene expression by either mRNA degradation or inhibition of protein translation. Although microRNAs have emerged as important controller involved in regulation of inflammatory response, the microRNA-mediated regulatory mechanism remains less clear in teleost. Here, we report that miR-148 targets MyD88 and down-regulates its expression by inhibition protein translation rather than degradation mRNA in miiuy croaker. Additionally, we found that miR-148 was significantly upregulated in miiuy croaker after treated with Vibro harveyi, as well as LPS. Overexpression of miR-148 inhibited LPS-induced inflammatory cytokines production, such as IL-6 and IL-1β, which then avoid excessive inflammation response. miR-148 has also been identified to suppress NF-κB pathway through targeting and repressing MyD88 expression. Taken together, our findings indicate that miR-148 participates in bacteria-induced inflammatory response and act as a negative regulator for MyD88-mediated NF-κB signaling, which may clarify the mechanism of microRNAs for avoiding excessive inflammation in teleost fish.
Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains
Authors: Yu Qianhui , He Zhisong 
Published: June 2017

AbstractThe functions of human brains highly depend on the precise temporal regulation of gene expression, and the temporal brain transcriptome profile across lifespan has been observed. The substantial transcriptome alteration in neural disorders like autism has also been observed and is thought to be important for the pathology. While the cell type composition is known to be variable in brains, it remains unclear how it contributes to the temporal and pathological transcriptome changes in brains. Here, we applied a transcriptome deconvolution procedure to an age series RNA-seq dataset of healthy and autism samples, to quantify the contribution of cell type composition in shaping the temporal and autism pathological transcriptome in human brains. We estimated that composition change was the primary factor of both types of transcriptome changes. On the other hand, genes with substantial composition-independent expression changes were also observed in both cases. Those temporal and autism pathological composition-independent changes, many of which are related to synaptic functions, indicate the important intracellular regulatory changes in human brains in both processes.
Surface bioactivation through the nanostructured layer on titanium modified by facile HPT treatment
Authors: Guo Zhijun , Jiang Nan , Chen Chen , Zhu Songsong , Zhang Li , Li Yubao 
Published: June 2017

AbstractFacile fabrication of nanostructured surface is of great importance for the use of titanium (Ti) implants in biomedical field. In this study, a low-cost and easy-to-operate method called HPT (hydrothermal & pressure) here has been developed and used to fabricate the expected nanostructured surface on Ti substrates. The effects of experimental parameters on the morphology of Ti surface were investigated and characterized. The results indicated that by altering the hydrothermal pressure, NaOH concentration and treating time, surface nanostructure like nanopetals or nanoflakes could be formed on the surface of Ti substrates. The orthogonal experiments were conducted to demonstrate the optimized operation conditions. A formation mechanism of the nanostructured titanate layer was proposed, revealing that the nanostructured layer could be formed via a special upward and downward co-growth manner. In vitro cell culture showed that the HPT treated Ti substrates, especially the T-10 sample, could greatly enhance the cell-material interactions, i.e. the cell proliferation and differentiation, focal protein adhesion, and osteogenic factor expression. The HPT method paves a new way to modify the surface of Ti implants with better bioactivity and promising prospect for future biomedical applications.
Angiotensin II synergizes with BAFF to promote atheroprotective regulatory B cells
Authors: Ponnuswamy Padmapriya , Joffre Jeremie , Herbin Olivier , Esposito Bruno , Laurans Ludivine , Binder Christoph J. , Tedder Thomas F. , Zeboudj Lynda , Loyer Xavier , Giraud Andreas , Zhang Yujiao , Tedgui Alain , Mallat Ziad , Ait-Oufella Hafid 
Published: June 2017

AbstractAngiotensin II (AngII) promotes hypertension, atherogenesis, vascular aneurysm and impairs post-ischemic cardiac remodeling through concerted roles on vascular cells, monocytes and T lymphocytes. However, the role of AngII in B lymphocyte responses is largely unexplored. Here, we show that chronic B cell depletion (Baffr deficiency) significantly reduces atherosclerosis in Apoe−/− mice infused with AngII. While adoptive transfer of B cells in Apoe−/−/Baffr−/− mice reversed atheroprotection in the absence of AngII, infusion of AngII in B cell replenished Apoe−/−/Baffr−/− mice unexpectedly prevented the progression of atherosclerosis. Atheroprotection observed in these mice was associated with a significant increase in regulatory CD1dhiCD5+ B cells, which produced high levels of interleukin (IL)-10 (B10 cells). Replenishment of Apoe−/−/Baffr−/− mice with Il10−/− B cells reversed AngII-induced B cell-dependent atheroprotection, thus highlighting a protective role of IL-10+ regulatory B cells in this setting. Transfer of AngII type 1A receptor deficient (Agtr1a−/−) B cells into Apoe−/−/Baffr−/− mice substantially reduced the production of IL-10 by B cells and prevented the AngII-dependent atheroprotective B cell phenotype. Consistent with the in vivo data, AngII synergized with BAFF to induce IL-10 production by B cells in vitro via AngII type 1A receptor. Our data demonstrate a previously unknown synergy between AngII and BAFF in inducing IL-10 production by B cells, resulting in atheroprotection.
Size Dependent Uptake and Hemolytic Effect of Zinc Oxide Nanoparticles on Erythrocytes and Biomedical Potential of ZnO-Ferulic acid Conjugates
Authors: Preedia Babu E. , Subastri A. , Suyavaran A. , Premkumar K. , Sujatha V. , Aristatile B. , Alshammari Ghedeir M. , Dharuman V. , Thirunavukkarasu C. 
Published: June 2017

AbstractDespite zinc oxide nanoparticles (ZnONPs) being increasingly used as carriers in biomedical fields due to their multifaceted properties and therapeutic importance, better understanding of the mechanisms and cellular consequences resulting from their interaction with cells and cellular components has been warranted. In the present study, we investigate the size-dependent interaction of ZnONPs on RBCs, and its impact on cell viability, DNA damage, ROS generation and morphological changes, employing cellular and analytical methods. Size, charge, stability and solubility were confirmed by DLS, zeta potential, ICP-AES and TEM analysis. Further ICP-AES, TEM, spectroscopic observations and cell based assays showed that ZnONPs exhibited a size dependent impact on RBCs and haemoglobin (Hb), particularly size <50 nm. Conversely, ferulic acid (FA) conjugates and serum albumin significantly reduced the adverse effects exhibited by ZnONPs. The extent of DNA damage and ROS generation is comparatively low in ZnONPs-FA than in ZnONPs alone treated cells. Thus our study documents a novel conceptualization delineating the influence of size on the material properties and therapeutic potential of nanoparticle.
Regular exercise participation improves genomic stability in diabetic patients: an exploratory study to analyse telomere length and DNA damage
Authors: Dimauro Ivan , Sgura Antonella , Pittaluga Monica , Magi Fiorenza , Fantini Cristina , Mancinelli Rosa , Sgadari Antonio , Fulle Stefania , Caporossi Daniela 
Published: June 2017

AbstractPhysical activity has been demonstrated to be effective in the prevention and treatment of different chronic conditions, including type 2 diabetes (T2D). In particular, several studies highlighted how the beneficial effects of physical activity may be related to the stability of the DNA molecule, such as longer telomeric ends. Here we analyze the effect of exercise training on telomere length, spontaneous and H2O2-induced DNA damage, as well as the apoptosis level in leukocytes from untrained or trained T2D patients vs. age-matched control subjects (CS) (57–66 years). Moreover, expression analysis of selected genes belonging to DNA repair systems, cell cycle control, antioxidant and defence systems was performed. Subjects that participated in a regular exercise program showed a longer telomere sequence than untrained counterparts. Moreover, ex vivo treatment of leukocytes with H2O2 highlighted that: (1) oxidative DNA damage induced similar telomere attrition in all groups; (2) in T2D subjects, physical activity seemed to prevent a significant increase of genomic oxidative DNA damage induced by chronic exposure to pro-oxidant stimulus, and (3) decreased the sensitivity of leukocytes to apoptosis. Finally, the gene expression analysis in T2D subjects suggested an adaptive response to prolonged exercise training that improved the response of specific genes.
Universal framework for edge controllability of complex networks
Authors: Pang Shao-Peng , Wang Wen-Xu , Hao Fei , Lai Ying-Cheng 
Published: June 2017

AbstractDynamical processes occurring on the edges in complex networks are relevant to a variety of real-world situations. Despite recent advances, a framework for edge controllability is still required for complex networks of arbitrary structure and interaction strength. Generalizing a previously introduced class of processes for edge dynamics, the switchboard dynamics, and exploit- ing the exact controllability theory, we develop a universal framework in which the controllability of any node is exclusively determined by its local weighted structure. This framework enables us to identify a unique set of critical nodes for control, to derive analytic formulas and articulate efficient algorithms to determine the exact upper and lower controllability bounds, and to evaluate strongly structural controllability of any given network. Applying our framework to a large number of model and real-world networks, we find that the interaction strength plays a more significant role in edge controllability than the network structure does, due to a vast range between the bounds determined mainly by the interaction strength. Moreover, transcriptional regulatory networks and electronic circuits are much more strongly structurally controllable (SSC) than other types of real-world networks, directed networks are more SSC than undirected networks, and sparse networks are typically more SSC than dense networks.
Human Sialidase Neu3 is S-Acylated and Behaves Like an Integral Membrane Protein
Authors: Rodriguez-Walker Macarena , Daniotti Jose L. 
Published: June 2017

AbstractMembrane-bound sialidase Neu3 is involved in the catabolism of glycoconjugates, and plays crucial roles in numerous biological processes. Since the mechanism of its association with membranes is still not completely understood, the aim of this work was to provide further information regarding this aspect. Human Neu3 was found to be associated with the plasma membrane and endomembranes, and it was not released from the lipid bilayer under conditions that typically release peripheral membrane proteins. By different experimental approaches, we demonstrated that its C-terminus is exposed to the cytosol while another portion of the protein is exposed to the extracellular space, suggesting that Neu3 possesses the features of a transmembrane protein. However, in silico analysis and homology modeling predicted that the sialidase does not contain any α-helical transmembrane segment and shares the same β-propeller fold typical of viral and bacterial sialidases. Additionally, we found that Neu3 is S-acylated. Since this post-translational modification is restricted to the cytosolic side of membranes, this finding strongly supports the idea that Neu3 may contain a cytosolic-exposed domain. Although it remains to be determined exactly how this sialidase crosses the lipid bilayer, this study provides new insights about membrane association and topology of Neu3.
Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura
Authors: Xin Zhao-Zhe , Liu Yu , Zhang Dai-Zhen , Chai Xin-Yue , Wang Zheng-Fei , Zhang Hua-Bin , Zhou Chun-Lin , Tang Bo-Ping , Liu Qiu-Ning 
Published: June 2017

AbstractDeciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.
Hyperspectral Imaging for Presymptomatic Detection of Tobacco Disease with Successive Projections Algorithm and Machine-learning Classifiers
Authors: Zhu Hongyan , Chu Bingquan , Zhang Chu , Liu Fei , Jiang Linjun , He Yong 
Published: June 2017

AbstractWe investigated the feasibility and potentiality of presymptomatic detection of tobacco disease using hyperspectral imaging, combined with the variable selection method and machine-learning classifiers. Images from healthy and TMV-infected leaves with 2, 4, and 6 days post infection were acquired by a pushbroom hyperspectral reflectance imaging system covering the spectral range of 380–1023 nm. Successive projections algorithm was evaluated for effective wavelengths (EWs) selection. Four texture features, including contrast, correlation, entropy, and homogeneity were extracted according to grey-level co-occurrence matrix (GLCM). Additionally, different machine-learning algorithms were developed and compared to detect and classify disease stages with EWs, texture features and data fusion respectively. The performance of chemometric models with data fusion manifested better results with classification accuracies of calibration and prediction all above 80% than those only using EWs or texture features; the accuracies were up to 95% employing back propagation neural network (BPNN), extreme learning machine (ELM), and least squares support vector machine (LS-SVM) models. Hence, hyperspectral imaging has the potential as a fast and non-invasive method to identify infected leaves in a short period of time (i.e. 48 h) in comparison to the reference images (5 days for visible symptoms of infection, 11 days for typical symptoms).