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https://www.readbyqxmd.com/read/28239986/molecular-analysis-of-the-early-interaction-between-the-grapevine-flower-and-botrytis-cinerea-reveals-that-prompt-activation-of-specific-host-pathways-leads-to-fungus-quiescence
#1
Zeraye H Mehari, Stefania Pilati, Paolo Sonego, Giulia Malacarne, Urska Vrhovsek, Kristof Engelen, Paul Tudzynski, Michela Zottini, Elena Baraldi, Claudio Moser
Grapes quality and yield can be impaired by bunch rot, caused by the necrotrophic fungus Botrytis cinerea. Infection often occurs at flowering and the pathogen stays quiescent until fruit maturity. Here, we report a molecular analysis of the early interaction between B. cinerea and Vitis vinifera flowers, using a controlled infection system, confocal microscopy and integrated transcriptomic and metabolic analysis of the host and the pathogen. Flowers from fruiting cuttings of the cv. Pinot Noir were infected with GFP-labeled B...
February 27, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28239968/training-in-metabolomics-research-ii-processing-and-statistical-analysis-of-metabolomics-data-metabolite-identification-pathway-analysis-applications-of-metabolomics-and-its-future
#2
Stephen Barnes, H Paul Benton, Krista Casazza, Sara J Cooper, Xiangqin Cui, Xiuxia Du, Jeffrey Engler, Janusz H Kabarowski, Shuzhao Li, Wimal Pathmasiri, Jeevan K Prasain, Matthew B Renfrow, Hemant K Tiwari
Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes...
August 2016: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28239964/training-in-metabolomics-research-ii-processing-and-statistical-analysis-of-metabolomics-data-metabolite-identification-pathway-analysis-applications-of-metabolomics-and-its-future
#3
S Barnes, H P Benton, K Casazza, S J Cooper, X Cui, X Du, J Engler, J H Kabarowski, S Li, W Pathmasiri, J K Prasain, M B Renfrow, H K Tiwari
Metabolomics is perhaps the most challenging of the -omics fields, given the complexity of an organism's metabolome and the rapid rate at which it changes. When one sets out to study metabolism there are numerous dynamic variables that can influence metabolism that must be considered. Recognizing the experimental challenges confronting researchers who undertake metabolism studies, workshops like the one at University of Alabama at Birmingham have been established to offer instructional guidance. A summary of the UAB course training materials is being published as a two-part Special Feature Tutorial...
August 2016: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28239646/mammary-adipocytes-stimulate-breast-cancer-invasion-through-metabolic-remodeling-of-tumor-cells
#4
Yuan Yuan Wang, Camille Attané, Delphine Milhas, Béatrice Dirat, Stéphanie Dauvillier, Adrien Guerard, Julia Gilhodes, Ikrame Lazar, Nathalie Alet, Victor Laurent, Sophie Le Gonidec, Denis Biard, Caroline Hervé, Frédéric Bost, Guo Sheng Ren, Françoise Bono, Ghislaine Escourrou, Marc Prentki, Laurence Nieto, Philippe Valet, Catherine Muller
In breast cancer, a key feature of peritumoral adipocytes is their loss of lipid content observed both in vitro and in human tumors. The free fatty acids (FFAs), released by adipocytes after lipolysis induced by tumor secretions, are transferred and stored in tumor cells as triglycerides in lipid droplets. In tumor cell lines, we demonstrate that FFAs can be released over time from lipid droplets through an adipose triglyceride lipase-dependent (ATGL-dependent) lipolytic pathway. In vivo, ATGL is expressed in human tumors where its expression correlates with tumor aggressiveness and is upregulated by contact with adipocytes...
February 23, 2017: JCI Insight
https://www.readbyqxmd.com/read/28239416/biodegradation-of-alkaline-lignin-by-bacillus-ligniniphilus-l1
#5
Daochen Zhu, Peipei Zhang, Changxiao Xie, Weimin Zhang, Jianzhong Sun, Wei-Jun Qian, Bin Yang
BACKGROUND: Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28239415/coupling-gene-regulatory-patterns-to-bioprocess-conditions-to-optimize-synthetic-metabolic-modules-for-improved-sesquiterpene-production-in-yeast
#6
Bingyin Peng, Manuel R Plan, Alexander Carpenter, Lars K Nielsen, Claudia E Vickers
BACKGROUND: Assembly of heterologous metabolic pathways is commonly required to generate microbial cell factories for industrial production of both commodity chemicals (including biofuels) and high-value chemicals. Promoter-mediated transcriptional regulation coordinates the expression of the individual components of these heterologous pathways. Expression patterns vary during culture as conditions change, and this can influence yeast physiology and productivity in both positive and negative ways...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28239414/a-novel-small-rna-coar-regulates-coenzyme-a-biosynthesis-and-tolerance-of-synechocystis-sp-pcc6803-to-1-butanol-possibly-via-promoter-directed-transcriptional-silencing
#7
Tao Sun, Guangsheng Pei, Jiangxin Wang, Lei Chen, Weiwen Zhang
BACKGROUND: Microbial small RNAs (sRNAs) have been proposed as valuable regulatory elements for optimizing cellular metabolism for industrial purposes. However, little information is currently available on functional relevance of sRNAs to biofuels tolerance in cyanobacteria. RESULTS: Here, we described the identification and functional characterization of a novel 124 nt sRNA Ncl1460 involved in tolerance to biofuel 1-butanol in Synechocystis sp. PCC 6803. The expression of Ncl1460 was verified by blotting assay and its length was determined through 3' RACE...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28239348/genetic-determinants-of-parkinson-s-disease-can-they-help-to-stratify-the-patients-based-on-the-underlying-molecular-defect
#8
REVIEW
Sara Redenšek, Maja Trošt, Vita Dolžan
Parkinson's disease (PD) is a sporadic progressive neurodegenerative brain disorder with a relatively strong genetic background. We have reviewed the current literature about the genetic factors that could be indicative of pathophysiological pathways of PD and their applications in everyday clinical practice. Information on novel risk genes is coming from several genome-wide association studies (GWASs) and their meta-analyses. GWASs that have been performed so far enabled the identification of 24 loci as PD risk factors...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28239160/insights-into-the-molecular-mechanisms-of-polygonum-multiflorum-thunb-induced-liver-injury-a-computational-systems-toxicology-approach
#9
Yin-Yin Wang, Jie Li, Zeng-Rui Wu, Bo Zhang, Hong-Bin Yang, Qin Wang, Ying-Chun Cai, Gui-Xia Liu, Wei-Hua Li, Yun Tang
An increasing number of cases of herb-induced liver injury (HILI) have been reported, presenting new clinical challenges. In this study, taking Polygonum multiflorum Thunb (PmT) as an example, we proposed a computational systems toxicology approach to explore the molecular mechanisms of HILI. First, the chemical components of PmT were extracted from 3 main TCM databases as well as the literature related to natural products. Then, the known targets were collected through data integration, and the potential compound-target interactions (CTIs) were predicted using our substructure-drug-target network-based inference (SDTNBI) method...
February 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28239031/cd44-variant-9-expression-as-a-predictor-for-gastric-cancer-recurrence-immunohistochemical-and-metabolomic-analysis-of-surgically-resected-tissues
#10
Yushi Yamakawa, Masatoshi Kusuhara, Masanori Terashima, Yusuke Kinugasa, Takashi Sugino, Masato Abe, Toru Mochizuki, Keiichi Hatakeyama, Kenjiro Kami, Ken Yamaguchi
CD44 variant 9 (CD44v9) and the heavy chain of 4F2 cell-surface antigen (CD98hc) appear important for regulation of reactive oxygen species defence and tumor growth in gastric cancer. This study examined the roles of CD44v9 and CD98hc as markers of gastric cancer recurrence, and investigated associations with energy metabolism. We applied capillary electrophoresis time-of-flight mass spectrometry to metabolome profiling of gastric cancer specimens from 103 patients who underwent resection with no residual tumor or microscopic residual tumor, and compared metabolite levels to immunohistochemical staining for CD44v9 and CD98hc...
2017: Biomedical Research
https://www.readbyqxmd.com/read/28239030/metabolic-profiling-of-gemcitabine-and-paclitaxel-treated-immortalized-human-pancreatic-cell-lines-with-k-ras-g12d
#11
Akiko Todaka, Rina Umehara, Keiko Sasaki, Masakuni Serizawa, Kenichi Urakami, Masatoshi Kusuhara, Ken Yamaguchi, Hirofumi Yasui
The mechanisms of action of gemcitabine (GEM) and paclitaxel (PTX) have been well investigated, and shown to be the inhibition of DNA polymerase and polymerization of tubulin, respectively. Meanwhile, genomic research has revealed that mutations in the K-RAS oncogene occur in over 90% of pancreatic cancer. Oncogenic alteration rewires alternative metabolic pathways to satisfy the demands of growth. The K-RAS oncogene also has been shown to upregulate glycolysis and glutaminolysis. However, it is still unclear whether K-RAS independently plays a central role in controlling tumor metabolism...
2017: Biomedical Research
https://www.readbyqxmd.com/read/28238949/defective-axonal-transport-a-common-pathological-mechanism-in-inherited-and-acquired-peripheral-neuropathies
#12
Robert Prior, Lawrence Van Helleputte, Veronick Benoy, Ludo Van Den Bosch
Peripheral neuropathies are characterized by a progressive and length-dependent loss of peripheral nerve function. This can be caused either by genetic defects, classified as 'inherited peripheral neuropathies', or they can be acquired throughout life. In that case, the disease is caused by various insults such as toxins and mechanical injuries, or it can arise secondary to medical conditions such as metabolic disorders, nutritional deficiencies, inflammation and infections. Peripheral neuropathies are not only very heterogeneous in etiology, but also in their pathology and clinical presentation...
February 23, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28238946/involvement-of-pregnane-x-receptor-in-the-suppression-of-carboxylesterases-by-metformin-in-vivo-and-in-vitro-mediated-by-the-activation-of-ampk-and-jnk-signaling-pathway
#13
Enfang Shan, Zhu Zhu, Shuangcheng He, Dongbao Chu, Dinghao Ge, Yunran Zhan, Wei Liu, Jian Yang, Jing Xiong
Type 2 diabetes mellitus (T2D) is a complex metabolic disorder requiring polypharmacy treatment in clinic, with metformin being widely used antihyperglycemic drug. However, the mechanisms of metformin as a perpetrator inducing potential drug-drug interactions and adverse drug reactions are scarcely known to date. Carboxylesterases (CESs) are major hydrolytic enzymes highly expressed in the liver, including mouse carboxylesterase 1d (Ces1d) and Ces1e. In the present study, experiments are designed to investigate the effects and mechanisms of metformin on Ces1d and Ces1e in vivo and in vitro...
February 23, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28238935/tryptophan-and-purine-metabolites-are-consistently-upregulated-in-the-urinary-metabolome-of-patients-diagnosed-with-gestational-diabetes-mellitus-throughout-pregnancy-a-longitudinal-metabolomics-study-of-chinese-pregnant-women-part-2
#14
Kai P Law, Ting-Li Han, Xun Mao, Hua Zhang
BACKGROUND: Gestational diabetes mellitus (GDM) is a pathological state of glucose intolerance associated with adverse pregnancy outcomes and an increased risk of developing maternal type 2 diabetes later in life. The mechanisms underlying GDM development are not fully understood. We examined the pathophysiology of GDM through comprehensive metabolic profiling of maternal urine, using participants from a longitudinal cohort of normal pregnancies and pregnancies complicated by GDM. METHODS: Based on ultra-performance liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry, an untargeted metabolomics study was performed to explore the differences in the urinary metabolome of GDM cases and healthy controls over the course of pregnancy...
February 23, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28238905/seasonal-heat-stress-affects-adipose-tissue-proteome-toward-enrichment-of-the-nrf2-mediated-oxidative-stress-response-in-late-pregnant-dairy-cows
#15
M Zachut, G Kra, L Livshitz, Y Portnick, S Yakoby, G Friedlander, Y Levin
: Environmental heat stress and metabolic stress during transition from late gestation to lactation are main factors limiting production in dairy cattle, and there is a complex interaction between them. Many proteins expressed in adipose tissue are involved in metabolic responses to stress. We aimed to investigate the effects of seasonal heat stress on adipose proteome in late-pregnant cows, and to identify biomarkers of heat stress. Late pregnant cows during summer heat stress (S, n=18), or during the winter season (W, n=12) were used...
February 23, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28238848/resveratrol-protects-against-spinal-cord-injury-by-activating-autophagy-and-inhibiting-apoptosis-mediated-by-the-sirt1-ampk-signaling-pathway
#16
Haosen Zhao, Shurui Chen, Kai Gao, Zipeng Zhou, Chen Wang, Zhaoliang Shen, Yue Guo, Zhuo Li, Zhanghui Wan, Chang Liu, Xifan Mei
Spinal cord injury (SCI) is a devastating condition with few effective treatments. Resveratrol, a polyphenolic compound, has exhibited neuroprotective effects in many neurodegenerative diseases. However, the explicit effect and mechanism of resveratrol on SCI is still unclear. Adenosine 5' monophosphate-activated protein kinase (AMPK) and Sirtuin 1 (SIRT1),the downstream protein, play key roles in metabolizing of energy, resisting of resistance, and cellularprotein homeostasis. In this study, we determined the effects of resveratrol on SCI and their potential relationship with SIRT1/AMPK signaling pathway, autophagy and apoptosis...
February 23, 2017: Neuroscience
https://www.readbyqxmd.com/read/28238819/alkylphospholipids-an-update-on-molecular-mechanisms-and-clinical-relevance
#17
REVIEW
Pablo Ríos-Marco, Carmen Marco, Xiomara Gálvez, Jose M Jiménez-López, María P Carrasco
Alkylphospholipid (APL) represent a new class of drugs which do not interact directly with DNA but act on the cell membrane where they accumulate and interfere with lipid metabolism and signalling pathways. This review summarizes the mode of action at the molecular level of these compounds. In this sense, a diversity of mechanisms has been suggested to explain the actions of clinically-relevant APLs, in particular, in cancer treatment. One consistently reported finding is that APLs reduce the biosynthesis of phosphatidylcholine (PC) by inhibiting the rate-limiting enzyme CTP:phosphocholine cytidylyltransferase (CT)...
February 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28238759/in-vitro-metabolic-engineering-for-the-production-of-%C3%AE-ketoglutarate
#18
Barbara Beer, André Pick, Volker Sieber
α-Ketoglutarate (aKG) represents a central intermediate of cell metabolism. It is used for medical treatments and as a chemical building block. Enzymatic cascade reactions have the potential to sustainably synthesize this natural product. Here we report a systems biocatalysis approach for an in vitro reaction set-up to produce aKG from glucuronate using the oxidative pathway of uronic acids. Because of two dehydrations, a decarboxylation, and reaction conditions favoring oxidation, the pathway is driven thermodynamically towards complete product formation...
February 22, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28238542/aberrant-expression-of-cell-cycle-and-material-metabolism-related-genes-contributes-to-hepatocellular-carcinoma-occurrence
#19
Hongxian Yan, Zhaohui Li, Quan Shen, Qian Wang, Jianguo Tian, Qingfeng Jiang, Linbo Gao
This study aims to deepen our understanding of the molecular mechanism underlying the occurrence of hepatocellular carcinoma (HCC). We first downloaded a gene expression profile dataset GSE29721 (10 HCC and 10 control samples) from Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/). Differentially expressed genes (DEGs) were identified by the paired t-test using limma package. Pathway and functional enrichment analyses were performed with DAVID tools. Transcription factors were annotated with TRANSFAC database and tumor associated genes (TAGs) were annotated with TAG and TSGene databases...
January 25, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28238530/a-membrane-associated-adenylate-cyclase-modulates-lactate-dehydrogenase-and-creatine-kinase-activities-required-for-bull-sperm-capacitation-induced-by-hyaluronic-acid
#20
Silvina Fernández, Mariana Córdoba
Hyaluronic acid, as well as heparin, is a glycosaminoglycan present in the female genital tract of cattle. The aim of this study was to evaluate oxidative metabolism and intracellular signals mediated by a membrane-associated adenylate cyclase (mAC), in sperm capacitation with hyaluronic acid and heparin, in cryopreserved bull sperm. The mAC inhibitor, 2',5'-dideoxyadenosine, was used in the present study. Lactate dehydrogenase (LDH) and creatine kinase (CK) activities and lactate concentration were determined spectrophotometrically in the incubation medium...
February 20, 2017: Animal Reproduction Science
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