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https://www.readbyqxmd.com/read/28937906/protein-activation-in-periapical-reaction-to-iodoform-containing-root-canal-sealer
#1
Nili Tickotsky, Moti Moskovitz
OBJECTIVES: An association between root canal sealers and periapical lesions in primary dentition has been suggested, yet the chemical-protein interactions that may be involved in it have not been studied. The present study explored root sealer components' effect on periapical tissue proteins using bioinformatics tools. STUDY DESIGN: For each chemical component of Endoflas F.S. root sealing material we identified the known and predicted target proteins, using STITCH (search tool for interactions of chemicals http://stitch...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28933415/integrative-systems-biology-investigation-of-fabry-disease
#2
Marco Fernandes, Holger Husi
Fabry disease (FD) is a rare X-linked recessive genetic disorder caused by a deficient activity of the lysosomal enzyme alpha-galactosidase A (GLA) and is characterised by intra-lysosomal accumulation of globotriaosylceramide (Gb3). We performed a meta-analysis of peer-reviewed publications including high-throughput omics technologies including naïve patients and those undergoing enzyme replacement therapy (ERT). This study describes FD on a systems level using a systems biology approach, in which molecular data sourced from multi-omics studies is extracted from the literature and integrated as a whole in order to reveal the biochemical processes and molecular pathways potentially affected by the dysregulation of differentially expressed molecules...
November 15, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28928672/micrornas-clustered-within-the-14q32-locus-are-associated-with-endothelial-damage-and-microparticle-secretion-in-bicuspid-aortic-valve-disease
#3
Neus Martínez-Micaelo, Raúl Beltrán-Debón, Gerard Aragonés, Marta Faiges, Josep M Alegret
Background: We previously described that PECAM(+) circulating endothelial microparticles (EMPs) are elevated in bicuspid aortic valve (BAV) disease as a manifestation of endothelial damage. In this study, we hypothesized that this endothelial damage, is functionally related to the secretion of a specific pattern of EMP-associated miRNAs. Methods: We used a bioinformatics approach to correlate the PECAM(+) EMP levels with the miRNA expression profile in plasma in healthy individuals and BAV patients (n = 36)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28926933/itraq-based-quantitative-proteomic-analysis-reveals-cold-responsive-proteins-involved-in-leaf-senescence-in-upland-cotton-gossypium-hirsutum-l
#4
Xuewei Zheng, Shuli Fan, Hengling Wei, Chengcheng Tao, Qiang Ma, Qifeng Ma, Siping Zhang, Hongbin Li, Chaoyou Pang, Shuxun Yu
Premature leaf senescence occurs in the ultimate phase of the plant, and it occurs through a complex series of actions regulated by stress, hormones and genes. In this study, a proteomic analysis was performed to analyze the factors that could induce premature leaf senescence in two cotton cultivars. We successfully identified 443 differential abundant proteins (DAPs) from 7388 high-confidence proteins at four stages between non-premature senescence (NS) and premature senescence (PS), among which 158 proteins were over-accumulated, 238 proteins were down-accumulated at four stages, and 47 proteins displayed overlapped accumulation...
September 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28918527/alterations-in-epididymal-proteomics-and-antioxidant-activity-of-mice-exposed-to-fluoride
#5
Zilong Sun, Sujuan Li, Yuxiang Yu, Hongyu Chen, Mohammad Mehdi Ommati, Ram Kumar Manthari, Ruiyan Niu, Jundong Wang
It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique...
September 16, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28910977/bisphenol-a-induced-apoptosis-and-transcriptome-differences-of-spermatogonial-stem-cells-in-vitro
#6
Xiaowen Gong, Hui Xie, Xiaoyong Li, Ji Wu, Yi Lin
Bisphenol A (BPA) is widely used as an industrial plasticizer, which is also an endocrine disruptor and considered to have adverse effects on reproduction. In male mammals, the long-term production of billions of spermatozoa relies on the regulated proliferation and differentiation of spermatogonial stem cells (SSCs). However, little is known about the effects of BPA on the viability of SSCs. To investigate the influence of BPA exposure on SSCs in vitro, we isolated SSCs from mouse and successfully established in vitro propagation of SSCs...
September 1, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28910747/transcriptome-analysis-of-rana-chensinensis-liver-under-trichlorfon-stress
#7
Yu Ma, Bo Li, Yang Ke, Yongan Zhang, Yuhui Zhang
Trichlorfon is a selective organophosphate insecticide that is widely applied in aquaculture and agriculture for control of various parasites. However, repeated and excess applications of trichlorfon often lead to water pollution and threaten non-targeted species. Our previous studies showed that trichlorfon could cause oxidative stress, lipid peroxidation and hepatic lesions in the liver of Rana chensinensis, but the related molecular mechanisms remain unclear. To explore the interference of trichlorfon in gene transcription, the differentially expressed genes in the liver of R...
September 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28902884/development-of-est-ssr-markers-in-flowering-chinese-cabbage-brassica-campestris-l-ssp-chinensis-var-utilis-tsen-et-lee-based-on-de-novo-transcriptomic-assemblies
#8
Jingfang Chen, Ronghua Li, Yanshi Xia, Guihua Bai, Peiguo Guo, Zhiliang Wang, Hua Zhang, Kadambot H M Siddique
Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs)...
2017: PloS One
https://www.readbyqxmd.com/read/28900139/gene-expression-profiling-of-calcifications-in-breast-cancer
#9
Sung Ui Shin, Jeonghoon Lee, Ju Han Kim, Won Hwa Kim, Sung Eun Song, Ajung Chu, Hoe Suk Kim, Wonshik Han, Han Suk Ryu, Woo Kyung Moon
We investigated the gene expression profiles of calcifications in breast cancer. Gene expression analysis of surgical specimen was performed using Affymetrix GeneChip® Human Gene 2.0 ST arrays in 168 breast cancer patients. The mammographic calcifications were reviewed by three radiologists and classified into three groups according to malignancy probability: breast cancers without suspicious calcifications; breast cancers with low-to-intermediate suspicious calcifications; and breast cancers with highly suspicious calcifications...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28899644/transcriptomics-reveals-tissue-organ-specific-differences-in-gene-expression-in-the-starfish-patiria-pectinifera
#10
Chan-Hee Kim, Hye-Jin Go, Hye Young Oh, Yong Hun Jo, Maurice R Elphick, Nam Gyu Park
Starfish (Phylum Echinodermata) are of interest from an evolutionary perspective because as deuterostomian invertebrates they occupy an "intermediate" phylogenetic position with respect to chordates (e.g. vertebrates) and protostomian invertebrates (e.g. Drosophila). Furthermore, starfish are model organisms for research on fertilization, embryonic development, innate immunity and tissue regeneration. However, large-scale molecular data for starfish tissues/organs are limited. To provide a comprehensive genetic resource for the starfish Patiria pectinifera, we report de novo transcriptome assemblies and global gene expression analysis for six P...
September 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28892663/hepatic-transcriptome-analysis-of-juvenile-gift-tilapia-oreochromis-niloticus-fed-diets-supplemented-with-different-concentrations-of-resveratrol
#11
Yao Zheng, Wei Wu, Gengdong Hu, Zhixiang Zhao, Shunlong Meng, Limin Fan, Chao Song, Liping Qiu, Jiazhang Chen
The GIFT (Genetically Improved Farmed Tilapia) tilapia, Oreochromis niloticus, is cultured widely for the production of freshwater fish in China. Streptococcosis, which is related to pathogenic infections, occurs frequently in juvenile and adult female GIFT individuals. Resveratrol (RES) has been used in feed to control these infections in freshwater tilapia. To address the effects of RES on tilapia, we used high-throughput RNA sequencing technology (RNA-Seq, HiSeq. 2500) to explore the global transcriptomic response and specific involvement of hepatic mRNA of juvenile O...
September 8, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28888603/potential-factors-involved-in-virulence-of-cronobacter-sakazakii-isolates-by-comparative-transcriptome-analysis
#12
Yingwang Ye, Xiyan Zhang, Maofeng Zhang, Na Ling, Haiyan Zeng, Jina Gao, Rui Jiao, Qingping Wu, Jumei Zhang
Cronobacter species are important foodborne pathogens causing severe infections in neonates through consumption of contaminated powdered infant formula. However, the virulence-associated factors in Cronobacter are largely unknown. In this study, the transcriptome analysis between highly virulent Cronobacter sakazakii G362 and attenuated L3101 strains was used to reveal the potential factors involved in virulence. The total transcripts were grouped into 20 clusters of orthologous group categories and summarized in 3 gene ontology categories (biological process, cellular component, and molecular function)...
September 6, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28886561/zinc-protects-against-cadmium-induced-toxicity-by-regulating-oxidative-stress-ions-homeostasis-and-protein-synthesis
#13
Jingmei Pan, Xinhe Huang, Yuxing Li, Ming Li, Ning Yao, Zhengdong Zhou, Xueru Li
The widespread environmental toxin cadmium (Cd) is associated with numerous human diseases. The essential trace element zinc (Zn) strongly counteracts Cd-induced toxicity; however, the mechanism is incompletely understood. Here, we conducted RNA sequencing and bioinformatics analyses to determine the global gene expression profiles of yeast cells exposed to Cd or Cd plus Zn. We identified 912 Cd-induced and 627 Cd plus Zn-induced differentially expressed genes (DEGs). Adding Zn during Cd exposure efficiently reversed the expression of 92...
August 21, 2017: Chemosphere
https://www.readbyqxmd.com/read/28885159/identification-of-protein-complexes-by-using-a-spatial-and-temporal-active-protein-interaction-network
#14
Min Li, Xiangmao Meng, Ruiqing Zheng, Fang-Xiang Wu, Yaohang Li, Yi Pan, Jianxin Wang
The rapid development of proteomics and high-throughput technologies has produced a large amount of Protein-Protein Interaction (PPI) data, which makes it possible for considering dynamic properties of protein interaction networks (PINs) instead of static properties. Identification of protein complexes from dynamic PINs becomes a vital scientific problem for understanding cellular life in the post genome era. Up to now, a plenty of models or methods have been proposed for the construction of dynamic PINs to identify protein complexes...
September 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28881804/altered-erythropoiesis-and-decreased-number-of-erythrocytes-in-children-with-neuroblastoma
#15
Fabio Morandi, Sebastiano Barco, Sara Stigliani, Michela Croce, Luca Persico, Corrado Lagazio, Francesca Scuderi, Maria Luisa Belli, Mariapina Montera, Giuliana Cangemi, Sarah Pozzi, Valentina Rigo, Paola Scaruffi, Loredana Amoroso, Giovanni Erminio, Vito Pistoia, Silvano Ferrini, Maria Valeria Corrias
Neuroblastoma (NB) is a pediatric tumor presenting at diagnosis either as localized or metastatic disease, which mainly involves the bone marrow (BM). The physical occupancy of BM space by metastatic NB cells has been held responsible for impairment of BM function. Here, we investigated whether localized or metastatic NB may alter hematopoietic lineages' maturation and release of mature cells in the periphery, through gene expression profiling, analysis of BM smears, cell blood count and flow cytometry analysis...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28869321/series-test-of-cluster-and-network-analysis-for-lupus-nephritis-before-and-after-ifn-k-immunosuppressive-therapy
#16
Sen Luan, Ping Li, Tingting Yi
AIM: The purpose was to screen potential targets of IFN-K-immunosuppressive therapy, which was used to offer effective information and resources for molecular targeted therapy. METHODS: The gene expression profile of GSE72747 was used to screen out significant differently expressed genes (DEGs). Series Test of Cluster (STC) analysis for DEGs was performed. For all DEGs, the Database for Annotation, Visualization, and Integrated Discovery was performed for Gene Ontology (GO) enrichment analysis...
September 4, 2017: Nephrology
https://www.readbyqxmd.com/read/28863455/characterization-of-2-novel-ependymoma-cell-lines-with-chromosome-1q-gain-derived-from-posterior-fossa-tumors-of-childhood
#17
Vladimir Amani, Andrew M Donson, Seth C Lummus, Eric W Prince, Andrea M Griesinger, Davis A Witt, Todd C Hankinson, Michael H Handler, Kathleen Dorris, Rajeev Vibhakar, Nicholas K Foreman, Lindsey M Hoffman
Ependymoma (EPN) is a common brain tumor of childhood that, despite standard surgery and radiation therapy, has a relapse rate of 50%. Clinical trials have been unsuccessful in improving outcome by addition of chemotherapy, and identification of novel therapeutics has been hampered by a lack of in vitro and in vivo models. We describe 2 unique EPN cell lines (811 and 928) derived from recurrent intracranial metastases. Both cell lines harbor the high-risk chromosome 1q gain (1q+) and a derivative chromosome 6, and both are classified as molecular group A according to transcriptomic analysis...
July 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28858211/cytocluster-a-cytoscape-plugin-for-cluster-analysis-and-visualization-of-biological-networks
#18
Min Li, Dongyan Li, Yu Tang, Fangxiang Wu, Jianxin Wang
Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function...
August 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28852045/analysis-of-temporal-expression-profiles-after-sciatic-nerve-injury-by-bioinformatic-method
#19
Yichong Zhang, Yuanbo Zhan, Na Han, Yuhui Kou, Xiaofeng Yin, Peixun Zhang
After Peripheral nerve injuries (PNI), many complicated pathophysiologic processes will happen. A global view of functional changes following PNI is essential for the looking for the adequate therapeutic approaches. In this study, we performed an in-depth analysis on the temporal expression profiles after sciatic nerve injury by bioinformatic methods, including (1) cluster analysis of the samples; (2) identification of gene co-expression modules(CEMs) correlated with the time points; (3) analysis of differentially expressed genes at each time point (DEGs-ET); (4) analysis of differentially expressed genes varying over time (DEGs-OT); (5) creating Pairwise Correlation Plot for the samples; (6) Time Series Regression Analysis; (7) Determining the pathway, GO (gene ontology) and drug by enrichment analysis...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28841668/differential-gene-expression-in-leaf-tissues-between-mutant-and-wild-type-genotypes-response-to-late-leaf-spot-in-peanut-arachis-hypogaea-l
#20
Suoyi Han, Hua Liu, Mei Yan, Feiyan Qi, Yaqi Wang, Ziqi Sun, Bingyan Huang, Wenzhao Dong, Fengshou Tang, Xinyou Zhang, Guohao He
Late leaf spot (LLS) is a major foliar disease in peanut (A. hypogaea L.) worldwide, causing significant losses of potential yield in the absence of fungicide applications. Mutants are important materials to study the function of disease-related genes. In this study, the mutant line M14 was derived from cultivar Yuanza 9102 treated with EMS. Yuanza 9102 was selected from an interspecific cross of cultivar Baisha 1016 with A. diogoi, and is resistant to several fungal diseases. By contrast, the M14 was highly susceptible to late leaf spot...
2017: PloS One
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