bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community analysis of apple rhizosphere around Bohai Gulf
Authors: Jiang Jihang , Song Zhen , Yang Xiaotong , Mao Zhiquan , Nie Xiaohong , Guo Hui , Peng Xiawei 
Published: August 2017

AbstractBohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees’ rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.
PDGF-BB enhances collagen gel contraction through a PI3K-PLCγ-PKC-cofilin pathway
Authors: Reyhani Vahid , Tsioumpekou Maria , van Wieringen Tijs , Rask Lars , Lennartsson Johan , Rubin Kristofer 
Published: August 2017

AbstractCell-mediated contraction of collagenous matrices is modulated by various growth factors and cytokines, such as platelet-derived growth factor-BB (PDGF-BB). Here we used a genetic cell model to delineate defined signaling pathways that enhance collagen gel contraction downstream of ligand-stimulated platelet-derived growth factor receptor-β (PDGF-Rβ). Our data show that PDGF BB-enhanced activations of phosphatidylinositol 3′-kinase (PI3K) and phospholipase Cγ (PLCγ) were necessary for PDGF-enhanced collagen gel contraction. Importantly, other defined signaling pathways down-stream of PDGF-Rβ were, however, dispensable. The decisive roles for PI3K and PLCγ were corroborated by experiments using selective inhibitors. Furthermore, we show that de-phosphorylation and thereby activation of cofilin that is important for the turnover of actin filaments, is depended on PI3K and PLCγ down-stream of PDGF-Rβ. Moreover, inhibition of protein kinase C (PKC) by GÖ6976 and bisindolylmaleimide-II abolished cofilin de-phosphorylation, as well as PDGF-enhanced contraction. In contrast, activation of the PKC protein family by 4β-phorbol 12-myristate 13-acetate (PMA) did not accelerate collagen gel contraction although it induced long-term cofilin de-phosphorylation, showing the need of a dynamic control of cofilin de-phosphorylation for PDGF-enhanced collagen gel contraction. Taken together, our data point to the involvement of a PI3K/PLCγ-PKC-cofilin pathway in both PDGF-enhanced cofilin de-phosphorylation and PDGF-enhanced collagen gel contraction.
Muscle and adipose tissue morphology, insulin sensitivity and beta-cell function in diabetic and nondiabetic obese patients: effects of bariatric surgery
Authors: Camastra Stefania , Vitali Alessandra , Anselmino Marco , Gastaldelli Amalia , Bellini Rosario , Berta Rossana , Severi Ilenia , Baldi Simona , Astiarraga Brenno , Barbatelli Giorgio , Cinti Saverio , Ferrannini Ele 
Published: August 2017

AbstractObesity is characterized by insulin-resistance (IR), enhanced lipolysis, and ectopic, inflamed fat. We related the histology of subcutaneous (SAT), visceral fat (VAT), and skeletal muscle to the metabolic abnormalities, and tested their mutual changes after bariatric surgery in type 2 diabetic (T2D) and weight-matched non-diabetic (ND) patients. We measured IR (insulin clamp), lipolysis (2H5-glycerol infusion), ß-cell glucose-sensitivity (ß-GS, mathematical modeling), and VAT, SAT, and rectus abdominis histology (light and electron microscopy). Presurgery, SAT and VAT showed signs of fibrosis/necrosis, small mitochondria, free interstitial lipids, thickened capillary basement membrane. Compared to ND, T2D had impaired ß-GS, intracapillary neutrophils and higher intramyocellular fat, adipocyte area in VAT, crown-like structures (CLS) in VAT and SAT with rare structures (cyst-like) ~10-fold larger than CLS. Fat expansion was associated with enhanced lipolysis and IR. VAT histology and intramyocellular fat were related to impaired ß-GS. Postsurgery, IR and lipolysis improved in all, ß-GS improved in T2D. Muscle fat infiltration was reduced, adipocytes were smaller and richer in mitochondria, and CLS density in SAT was reduced. In conclusion, IR improves proportionally to weight loss but remains subnormal, whilst SAT and muscle changes disappear. In T2D postsurgery, some VAT pathology persists and beta-cell dysfunction improves but is not normalized.
An integrated method for cell isolation and migration on a chip
Authors: Lv Xiaoqing , Geng Zhaoxin , Fan Zhiyuan , Wang Shicai , Pei WeiHua , Chen Hongda 
Published: August 2017

AbstractTumour cell migration has an important impact on tumour metastasis. Magnetic manipulation is an ascendant method for guiding and patterning cells. Here, a unique miniaturized microfluidic chip integrating cell isolation and migration assay was designed to isolate and investigate cell migration. The chip was fabricated and composed of a magnet adapter, a polytetrafluoroethylene(PDMS) microfluidic chip and six magnetic rings. This device was used to isolate MCF-7 cells from MDA-MB-231-RFP cells and evaluate the effects of TGF-β on MCF-7 cells. First, the two cell types were mixed and incubated with magnetic beads modified with an anti-EpCAM antibody. Then, they were slowly introduced into the chip. MCF-7 cells bond to the magnetic beads in a ring-shaped pattern, while MDA-MB-231-RFP cells were washed away by PBS. Cell viability was examined during culturing in the micro-channel. The effects of TGF-β on MCF-7 cells were evaluated by migration distance and protein expression. The integrated method presented here is novel, low-cost and easy for performing cell isolation and migration assay. The method could be beneficial for developing microfluidic device applications for cancer metastasis research and could provide a new method for biological experimentation.
SIRT1 reduction is associated with sex-specific dysregulation of renal lipid metabolism and stress responses in offspring by maternal high-fat diet
Authors: Nguyen Long The , Chen Hui , Pollock Carol , Saad Sonia 
Published: August 2017

AbstractRodent models of maternal obesity have been associated with kidney damage and dysfunction in offspring. However, the underlying mechanisms are yet to be elucidated. In this study, female rats were fed a high-fat diet (HFD) for 6 weeks prior to mating, throughout gestation and lactation; both male and female offspring were examined at weaning. Our results demonstrate that renal lipid deposition was increased in male offspring only, which is associated with reduced protein expression of Sirtuin (SIRT) 1, an essential regulator of lipid metabolism and stress response. Other components in its signalling network including phosphorylated 5′-AMP-activated protein kinase (pAMPKα), Forkhead box FOXO3a and Peroxisome proliferator-activated receptor (PPAR)γ coactivator 1-alpha (PGC-1α) were also downregulated. By contrast, in female offspring, renal fat/lipid distribution was unchanged in coupling with normal SIRT1 regulation. Specific autophagy and antioxidant markers were suppressed in both sexes. On the other hand, fibronectin and Collagen type IV protein expression was significantly higher in the offspring born HFD-fed dams, particularly in the males. Collectively, these findings suggest that maternal HFD consumption can induce sex-specific changes in offspring kidney lipid metabolism and stress responses at early ages, which may underpin the risk of kidney diseases later in life.
Molecular dynamics for linear polymer melts in bulk and confined systems under shear flow
Authors: Cho Soowon , Jeong Sohdam , Kim Jun Mo , Baig Chunggi 
Published: August 2017

AbstractIn this work, we analyzed the individual chain dynamics for linear polymer melts under shear flow for bulk and confined systems using atomistic nonequilibrium molecular dynamics simulations of unentangled (C50H102) and slightly entangled (C178H358) polyethylene melts. While a certain similarity appears for the bulk and confined systems for the dynamic mechanisms of polymer chains in response to the imposed flow field, the interfacial chain dynamics near the boundary solid walls in the confined system are significantly different from the corresponding bulk chain dynamics. Detailed molecular-level analysis of the individual chain motions in a wide range of flow strengths are carried out to characterize the intrinsic molecular mechanisms of the bulk and interfacial chains in three flow regimes (weak, intermediate, and strong). These mechanisms essentially underlie various macroscopic structural and rheological properties of polymer systems, such as the mean-square chain end-to-end distance, probability distribution of the chain end-to-end distance, viscosity, and the first normal stress coefficient. Further analysis based on the mesoscopic Brightness method provides additional structural information about the polymer chains in association with their molecular mechanisms.
Cellular internalization of alpha-synuclein aggregates by cell surface heparan sulfate depends on aggregate conformation and cell type
Authors: Ihse Elisabet , Yamakado Hodaka , van Wijk Xander M. , Lawrence Roger , Esko Jeffrey D. , Masliah Eliezer 
Published: August 2017

AbstractAmyloid aggregates found in the brain of patients with neurodegenerative diseases, including Alzheimer’s and Parkinson’s disease, are thought to spread to increasingly larger areas of the brain through a prion-like seeding mechanism. Not much is known about which cell surface receptors may be involved in the cell-to-cell transfer, but proteoglycans are of interest due to their well-known propensity to interact with amyloid aggregates. In this study, we investigated the involvement of plasma membrane-bound heparan and chondroitin sulfate proteoglycans in cellular uptake of aggregates consisting of α-synuclein, a protein forming amyloid aggregates in Parkinson’s disease. We show, using a pH-sensitive probe, that internalization of α-synuclein amyloid fibrils in neuroblastoma cells is dependent on heparan sulfate, whereas internalization of smaller non-amyloid oligomers is not. We also show that α-synuclein fibril uptake in an oligodendrocyte-like cell line is equally dependent on heparan sulfate, while astrocyte- and microglia-like cell lines have other means to internalize the fibrils. In addition, we analyzed the interaction between the α-synuclein amyloid fibrils and heparan sulfate and show that overall sulfation of the heparan sulfate chains is more important than sulfation at particular sites along the chains.
MatCol: a tool to measure fluorescence signal colocalisation in biological systems
Authors: Khushi Matloob , Napier Christine E. , Smyth Christine M. , Reddel Roger R. , Arthur Jonathan W. 
Published: August 2017

AbstractProtein colocalisation is often studied using pixel intensity-based coefficients such as Pearson, Manders, Li or Costes. However, these methods cannot be used to study object-based colocalisations in biological systems. Therefore, a novel method is required to automatically identify regions of fluorescent signal in two channels, identify the co-located parts of these regions, and calculate the statistical significance of the colocalisation. We have developed MatCol to address these needs. MatCol can be used to visualise protein and/or DNA colocalisations and fine tune user-defined parameters for the colocalisation analysis, including the application of median or Wiener filtering to improve the signal to noise ratio. Command-line execution allows batch processing of multiple images. Users can also calculate the statistical significance of the observed object colocalisations compared to overlap by random chance using Student’s t-test. We validated MatCol in a biological setting. The colocalisations of telomeric DNA and TRF2 protein or TRF2 and PML proteins in >350 nuclei derived from three different cell lines revealed a highly significant correlation between manual and MatCol identification of colocalisations (linear regression R2 = 0.81, P < 0.0001). MatCol has the ability to replace manual colocalisation counting, and the potential to be applied to a wide range of biological areas.
RNA interference in the Asian Longhorned Beetle:Identification of Key RNAi Genes and Reference Genes for RT-qPCR
Authors: Rodrigues Thais B. , Dhandapani Ramesh Kumar , Duan Jian J. , Palli Subba Reddy 
Published: August 2017

AbstractAsian Longhorned Beetle (ALB) Anoplophora glabripennis is a serious invasive forest pest in several countries including the United States, Canada, and Europe. RNA interference (RNAi) technology is being developed as a novel method for pest management. Here, we identified the ALB core RNAi genes including those coding for Dicer, Argonaute, and double-stranded RNA-binding proteins (dsRBP) as well as for proteins involved in dsRNA transport and the systemic RNAi. We also compared expression of six potential reference genes that could be used to normalize gene expression and selected gapdh and rpl32 as the most reliable genes among different tissues and stages of ALB. Injection of double-stranded RNA (dsRNA) targeting gene coding for inhibitor of apoptosis (IAP) into larvae and adults resulted in a significant knockdown of this gene and caused the death of 90% of the larvae and 100% of adults. No mortality of both larvae and adults injected with dsRNA targeting gene coding for green fluorescence protein (GFP, as a negative control) was observed. These data suggest that functional RNAi machinery exists in ALB and a potential RNAi-based method could be developed for controlling this insect.
Cognitive fatigue in individuals with traumatic brain injury is associated with caudate activation
Authors: Wylie G. R. , Dobryakova E. , DeLuca J. , Chiaravalloti N. , Essad K. , Genova H. 
Published: August 2017

AbstractWe investigated differences in brain activation associated with cognitive fatigue between persons with traumatic brain injury (TBI) and healthy controls (HCs). Twenty-two participants with moderate-severe TBI and 20 HCs performed four blocks of a difficult working memory task and four blocks of a control task during fMRI imaging. Cognitive fatigue, assessed before and after each block, was used as a covariate to assess fatigue-related brain activation. The TBI group reported more fatigue than the HCs, though their performance was comparable. Regarding brain activation, the TBI group showed a Task X Fatigue interaction in the caudate tail resulting from a positive correlation between fatigue and brain activation for the difficult task and a negative relationship for the control task. The HC group showed the same Task X Fatigue interaction in the caudate head. Because we had prior hypotheses about the caudate, we performed a confirmatory analysis of a separate dataset in which the same subjects performed a processing speed task. A relationship between Fatigue and brain activation was evident in the caudate for this task as well. These results underscore the importance of the caudate nucleus in relation to cognitive fatigue.
Ecological effects of full and partial protection in the crowded Mediterranean Sea: a regional meta-analysis
Authors: Giakoumi Sylvaine , Scianna Claudia , Plass-Johnson Jeremiah , Micheli Fiorenza , Grorud-Colvert Kirsten , Thiriet Pierre , Claudet Joachim , Di Carlo Giuseppe , Di Franco Antonio , Gaines Steven D. , García-Charton José A. , Lubchenco Jane , Reimer Jessica , Sala Enric , Guidetti Paolo 
Published: August 2017

AbstractMarine protected areas (MPAs) are a cornerstone of marine conservation. Globally, the number and coverage of MPAs are increasing, but MPA implementation lags in many human-dominated regions. In areas with intense competition for space and resources, evaluation of the effects of MPAs is crucial to inform decisions. In the human-dominated Mediterranean Sea, fully protected areas occupy only 0.04% of its surface. We evaluated the impacts of full and partial protection on biomass and density of fish assemblages, some commercially important fishes, and sea urchins in 24 Mediterranean MPAs. We explored the relationships between the level of protection and MPA size, age, and enforcement. Results revealed significant positive effects of protection for fisheries target species and negative effects for urchins as their predators benefited from protection. Full protection provided stronger effects than partial protection. Benefits of full protection for fish biomass were only correlated with the level of MPA enforcement; fish density was higher in older, better enforced, and —interestingly— smaller MPAs. Our finding that even small, well-enforced, fully protected areas can have significant ecological effects is encouraging for “crowded” marine environments. However, more data are needed to evaluate sufficient MPA sizes for protecting populations of species with varying mobility levels.
Expansion of C9ORF72 in amyotrophic lateral sclerosis correlates with brain-computer interface performance
Authors: Geronimo Andrew , Sheldon Kathryn E. , Broach James R. , Simmons Zachary , Schiff Steven J. 
Published: August 2017

AbstractAbnormal expansion of hexanucleotide GGGGCC (G4C2) in the C9ORF72 gene has been associated with multiple neurodegenerative disorders, with particularly high prevalence in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions of this type have been associated with altered pathology, symptom rate and severity, as well as psychological changes. In this study, we enrolled twenty-five patients with ALS and fifteen neurologically healthy controls in a P300 brain-computer interface (BCI) training procedure. Four of the patients were found to possess an expanded allele, which was associated with a reduction in the quality of evoked potentials that led to reduced performance on the BCI task. Our findings warrant further exploration of the relationship between brain function and G4C2 repeat length. Such a relationship suggests that personalized assessment of suitability of BCI as a communication device in patients with ALS may be feasible.
Octacosanol restores stress-affected sleep in mice by alleviating stress
Authors: Kaushik Mahesh K. , Aritake Kosuke , Takeuchi Atsuko , Yanagisawa Masashi , Urade Yoshihiro 
Published: August 2017

AbstractOctacosanol, a component of various food materials, possesses prominent biological activities and functions. It fights against cellular stress by increasing glutathione level and thus scavenging oxygen reactive species. However, its anti-stress activity and role in sleep induction remained elusive. We hypothesize that octacosanol can restore stress-affected sleep by mitigating stress. Cage change strategy was used to induce mild stress and sleep disturbance in mice, and effects of octacosanol administration on amount of sleep and stress were investigated. Results showed that octacosanol did not change rapid eye movement (REM) or non-REM (NREM) sleep compared to vehicle in normal mice. However, in cage change experiment, octacosanol induces significant increase in NREM sleep at doses of 100 and 200 mg/kg (75.7 ± 14.9 and 82.7 ± 9.3 min/5 h) compared to vehicle (21.2 ± 5.1 min/5 h), and decreased sleep latency. Octacosanol induced sleep by increasing number of sleep episodes and decreasing wake episode duration. Plasma corticosterone levels were significantly reduced after octacosanol (200 mg/kg) administration, suggesting a decrease in stress level. Octacosanol-induced changes in sleep-wake parameters in stressed-mice were comparable to the values in normal mice. Together, these data clearly showed that, though octacosanol does not alter normal sleep, it clearly alleviates stress and restore stress-affected sleep.
Polymer encapsulated microcavity optomechanical magnetometer
Authors: Zhu Jiangang , Zhao Guangming , Savukov Igor , Yang Lan 
Published: August 2017

AbstractWe demonstrate a magnetometer using polymer encapsulated whispering-gallery-mode microcavity actuated by a micro-magnet. The magnetic field induces force on the micro-magnet causing deformation in the polymer around the microcavity. Subsequently the microcavity detects the change in the refractive index of the polymer resulted from the deformation. This magnetometer works in the frequency range of hertz-to-kilohertz range and achieves a sensitivity of 880 pT/Hz1/2 at 200 Hz in a micro-scale sensor volume. Polymer encapsulation of the magnetometer and fiber optical connection ensures environmental robustness and practicality of the sensor.
Chilling temperature remodels phospholipidome of Zea mays seeds during imbibition
Authors: Noblet Agathe , Leymarie Juliette , Bailly Christophe 
Published: August 2017

AbstractGlobal warming is a major agricultural issue in the Northern hemisphere where higher temperatures are expected to be associated with restricted water availability. In Europe, for maize, earlier and further northward sowings are forecasted in order to avoid water deficit periods in the crop life cycle. However these conditions may compromise seed germination and stand establishment since they will take place at cold temperatures. It is urgent to better understand the molecular bases of response of germinating maize seeds to cold in order to design genotypes adapted to these novel agricultural practices. Here we have performed a global phospholipidomic study to profile changes in membrane reorganisation during seed imbibition at 10 °C of cold-tolerant and -sensitive maize hybrids. Using a Multiple Reaction Monitoring (MRM-MS/MS) method coupled with HPLC we have identified 80 distinct phospholipids. We show that seed sensitivity to cold temperatures during imbibition relies on the accumulation of saturated or poorly unsaturated fatty acids, whatever the phospholipid class. In contrast seeds of cold-tolerant hybrid accumulated polyunsaturated chains which was associated with lower electrolyte leakage during imbibition at 10 °C. The expression of fatty acid desaturase genes provides a molecular model of maize seed sensitivity to imbibitional chilling damage.