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proteomics pathway analysis

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https://www.readbyqxmd.com/read/29785723/decreased-e-cadherin-in-mcf7-human-breast-cancer-cells-forming-multicellular-spheroids-exposed-to-simulated-microgravity
#1
Jayashree Sahana, Mohamed Zakaria Nassef, Markus Wehland, Sascha Kopp, Marcus Krüger, Thomas J Corydon, Manfred Infanger, Johann Bauer, Daniela Grimm
MCF7 human breast cancer cells were cultured under normal gravity (1g) and on a random positioning machine (RPM) preventing sedimentation. After two weeks, adherent 1g-control and adherent RPM cells (AD) as well as multicellular spheroids (MCS) were harvested. AD and MCS had been exposed to the RPM in the same culture flask. In a subsequent proteome analysis, the majority of the proteins detected showed similar label-free quantification scores (LFQ) in each of the respective subpopulations, but in both AD or MCS cultures, proteins were also found whose LFQs deviated at least twofold from their counterparts in the 1g-control cells...
May 21, 2018: Proteomics
https://www.readbyqxmd.com/read/29784711/quantitative-proteome-and-phosphoproteome-analyses-of-streptomyces-coelicolor-reveal-proteins-and-phosphoproteins-modulating-differentiation-and-secondary-metabolism
#2
Beatriz Rioseras, Pavel V Sliaha, Vladimir Gorshkov, Paula Yagüe, Maria T López-García, Nathaly González-Quiñónez, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Ole N Jensen, Angel Manteca
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode a large number of Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor...
May 21, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29783952/differences-between-fast-and-slow-muscles-in-scallops-revealed-through-proteomics-and-transcriptomics
#3
Xiujun Sun, Zhihong Liu, Biao Wu, Liqing Zhou, Qi Wang, Wei Wu, Aiguo Yang
BACKGROUND: Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis. RESULTS: Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29782274/-dysfunctional-high-density-lipoproteins-role-in-atherogenesis-and-potential-targets-for-phospholipid-therapy
#4
T I Torchovskaya, V A Kudinov, T S Zakharova, S S Markin
In recent years the number of articles on damages of high-density lipoproteins (HDL) properties in patients with atherosclerosis has sharply increased. First, it concerns their ability to accept cholesterol (CH) from macrophages - the basis of antiatherogenic action of HDL. This ability was assessed ex vivo - by activity of cell cholesterol (CH) efflux to HDL or into patient's serum. In many works inverse relationship was shown between CH acceptor capacity of HDL and severity of atherosclerotic disease or frequency of its exacerbations during long-term observation, independent from HDL CH concentration...
March 2018: Kardiologiia
https://www.readbyqxmd.com/read/29780857/multi-omic-network-based-interrogation-of-rat-liver-metabolism-following-gastric-bypass-surgery-featuring-swath-proteomics
#5
Gautham Vivek Sridharan, Matthew D'Alessandro, Shyam Sundhar Bale, Vicky Bhagat, Hugo Gagnon, John M Asara, Korkut Uygun, Martin L Yarmush, Nima Saeidi
Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH)...
September 2017: Technology
https://www.readbyqxmd.com/read/29778837/defining-host-responses-during-systemic-bacterial-infection-through-construction-of-a-murine-organ-proteome-atlas
#6
John D Lapek, Robert H Mills, Jacob M Wozniak, Anaamika Campeau, Ronnie H Fang, Xiaoli Wei, Kirsten van de Groep, Araceli Perez-Lopez, Nina M van Sorge, Manuela Raffatellu, Rob Knight, Liangfang Zhang, David J Gonzalez
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues...
April 28, 2018: Cell Systems
https://www.readbyqxmd.com/read/29778478/quantitative-proteomics-of-lactococcus-lactis-f44-under-cross-stress-of-low-ph-and-lactate
#7
Hao Wu, Yue Zhao, Yuhui Du, Sen Miao, Jingui Liu, Yanni Li, Qinggele Caiyin, Jianjun Qiao
Lactococcus lactis encounters 3 environmental stimuli, H+ , lactate, and undissociated lactic acid, because of the accumulation of lactic acid-the predominant fermentation product. Few studies have examined how these stimuli synergistically affect the bacteria. Herein, we analyzed the dissociation degree of lactic acid at different pH and investigated the cellular response to cross-stress in L. lactis ssp. lactis F44 through quantitative proteomic analysis using isobaric tags for relative and absolute quantitation of 3 groups: 0% lactic acid with pH 4...
May 16, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29777486/physiological-and-quantitative-proteomic-analyses-unraveling-potassium-deficiency-stress-response-in-alligator-weed-alternanthera-philoxeroides-l-root
#8
Li-Qin Li, Lun Liu, Wei Zhuo, Qian Chen, Sheng Hu, Shuang Peng, Xi-Yao Wang, Yi-Fei Lu, Li-Ming Lu
Physiological and iTRAQ based proteomic analysis provided new insights into potassium deficiency stress response in alligator weed root. Alligator weed (Alternanthera philoxeroides) has a strong ability to adapt to potassium deficiency (LK) stress. Proteomic changes in response to this stress are largely unknown in alligator weed. In this study, we investigated physiological and molecular mechanisms under LK using isobaric tags for relative and absolute quantitation to characterize proteome-level changes in this plant...
May 18, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29776966/loss-of-tigar-induces-oxidative-stress-and-meiotic-defects-in-oocytes-from-obese-mice
#9
Haichao Wang, Qing Cheng, Xiaoyan Li, Feifei Hu, Longsen Han, Hao Zhang, Ling Li, Juan Ge, Xiaoyan Ying, Xuejiang Guo, Qiang Wang
Maternal obesity has been reported to impair oocyte quality in mice, however, the underlying mechanisms remain unclear. In the present study, by conducting a comparative proteomic analysis, we identified a reduced expression of TIGAR protein in ovulated oocytes from high-fat diet (HFD)-fed mice. Specific depletion of TIGAR in mouse oocytes results in the marked elevation of reactive oxygen species (ROS) levels and the failure of meiotic apparatus assembly. Importantly, forced expression of TIGAR in HFD oocytes not only attenuates ROS production, but also partly prevents spindle disorganization and chromosome misalignment during meiosis...
May 18, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29774542/accelerated-pre-senile-systemic-amyloidosis-in-pacap-knockout-mice-a-protective-role-of-pacap-in-age-related-degenerative-processes
#10
Dora Reglodi, Adel Jungling, Rémi Longuespée, Joerg Kriegsmann, Rita Casadonte, Mark Kriegsmann, Tamas Juhasz, Sebastian Bardosi, Andrea Tamas, Balazs Daniel Fulop, Krisztina Kovacs, Zsuzsanna Nagy, Jason Sparks, Attila Miseta, Gabriel Mazzucchelli, Hitoshi Hashimoto, Attila Bardosi
Dysregulation of neuropeptides may play an important role in aging-induced impairments. Among them, pituitary adenylate cyclase activating polypeptide (PACAP) is a potent cytoprotective peptide that provides an endogenous control against a variety of tissue-damaging stimuli. We hypothesized that the progressive decline of PACAP throughout life, and the well-known general cytoprotective effects of PACAP lead to age-related pathophysiological changes in PACAP deficiency, supported by the increased vulnerability to various stressors of animals partially or totally lacking PACAP...
May 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29774100/differential-proteomic-profile-of-leukemic-cd34-progenitor-cells-from-chronic-myeloid-leukemia-patients
#11
Maria Rosaria Ricciardi, Valentina Salvestrini, Roberto Licchetta, Simone Mirabilii, Mattia Forcato, Gabriele Gugliotta, Simona Salati, Fausto Castagnetti, Gianantonio Rosti, Massimo Breccia, Giuliana Alimena, Rossella Manfredini, Silvio Bicciato, Roberto Massimo Lemoli, Agostino Tafuri
Chronic Myeloid Leukemia (CML) is a stem cell disease sustained by a rare population of quiescent cells which are to some extent resistant to tyrosine kinase inhibitors (TKIs). BCR-ABL oncogene activates multiple cross-talking signal transduction pathways (STP), such as RAS/MEK/ERK, PI3K/Akt, Wnt and STAT5, contributing to abnormal proliferation of clonal cells. From this perspective, the aim of this study was to analyze the expression and activation profile of STP involved in the mechanisms of cell proliferation/quiescence and survival of the progenitor CD34+ cells from chronic phase (CP) CML...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29774096/gstm3-and-gstp1-novel-players-driving-tumor-progression-in-cervical-cancer
#12
Alberto Checa-Rojas, Luis Fernando Delgadillo-Silva, Martín Del Castillo Velasco-Herrera, Andrés Andrade-Domínguez, Jeovanis Gil, Orlando Santillán, Luis Lozano, Alfredo Toledo-Leyva, Alberto Ramírez-Torres, Patricia Talamas-Rohana, Sergio Encarnación-Guevara
The molecular processes and proteomic markers leading to tumor progression (TP) in cervical cancer (CC) are either unknown or only partially understood. TP affects metabolic and regulatory mechanisms that can be identified as proteomic changes. To identify which proteins are differentially expressed and to understand the mechanisms of cancer progression, we analyzed the dynamics of the tumor proteome in CC cell lines. This analysis revealed two proteins that are up-regulated during TP, GSTM3 and GSTP1. These proteins are involved in cell maintenance, cell survival and the cellular stress response via the NF-κB and MAP kinase pathways during TP...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29773844/identification-of-differentially-accumulated-proteins-involved-in-regulating-independent-and-combined-osmosis-and-cadmium-stress-response-in-brachypodium-seedling-roots
#13
Ziyan Chen, Dong Zhu, Jisu Wu, Zhiwei Cheng, Xing Yan, Xiong Deng, Yueming Yan
In this study, we aimed to identify differentially accumulated proteins (DAPs) involved in PEG mock osmotic stress, cadmium (Cd2+ ) stress, and their combined stress responses in Brachypodium distachyon seedling roots. The results showed that combined PEG and Cd2+ stresses had more significant effects on Brachypodium seedling root growth, physiological traits, and ultrastructures when compared with each individual stress. Totally, 106 DAPs were identified that are responsive to individual and combined stresses in roots...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773679/comparative-proteomic-analysis-reveals-the-regulatory-network-of-the-vea-gene-during-asexual-and-sexual-spore-development-of-aspergillus-cristatus
#14
Hui Liu, Shilei Sang, Hui Wang, Xiyi Ren, Yumei Tan, Wei Chen, Zuoyi Liu, Yongxiang Liu
Aspergillus cristatus belongs to the homothallic fungal group that undergoes a sexual stage without asexual conidiation under hypotonic conditions, while hypertonic medium induces initiation of the asexual stage and completely blocks sexual development. However, the veA deletion mutant only produces conidia in hypotonic medium after a 24 h culture, but both asexual and sexual spores are observed after 72 h. To elucidate the molecular mechanism of how VeA regulates asexual and sexual spore development in A. cristatus , two dimensional electrophoresis combined with matrix-assisted laser desorption/ionization-tandem time of flight mass spectrometry analysis were applied to identify 173 differentially expressed proteins (DEPs) by comparing the agamotype (24 h) and teleomorph (72 h) with wild-type A...
May 17, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29773673/lysosomal-proteome-and-secretome-analysis-identifies-missorted-enzymes-and-their-non-degraded-substrates-in-mucolipidosis-iii-mouse-cells
#15
Giorgia Di Lorenzo, Renata Voltolini Velho, Dominic Winter, Melanie Thelen, Shiva Ahmadi, Michaela Schweizer, Raffaella De Pace, Kerstin Cornils, Timur Alexander Yorgan, Saskia Grüb, Irm Hermans-Borgmeyer, Thorsten Schinke, Sven Müller-Loennies, Thomas Braulke, Sandra Pohl
Targeting of soluble lysosomal enzymes requires mannose 6-phosphate (M6P) signals whose formation is initiated by the hexameric N-acetylglucosamine (GlcNAc)-1-phosphotransferase complex (α2β2γ2). Upon proteolytic cleavage by site-1 protease, the α/β-subunit precursor is catalytically activated but the functions of γ-subunits (Gnptg) in M6P modification of lysosomal enzymes are unknown. To investigate this, we analyzed the Gnptg expression in mouse tissues, primary cultured cells, and in Gnptg reporter mice in vivo, and found high amounts in the brain, eye, kidney, femur, vertebra and fibroblasts...
May 17, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29770421/quantitative-proteomics-and-systems-analysis-of-cultured-h9c2-cardiomyoblasts-during-differentiation-over-time-supports-a-function-follows-form-model-of-differentiation
#16
Cynthia Kankeu, Kylie Clarke, Delphi Van Haver, Kris Gevaert, Francis Impens, Anna Dittrich, H Llewelyn Roderick, Egle Passante, Heinrich J Huber
The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis...
May 17, 2018: Molecular omics
https://www.readbyqxmd.com/read/29766243/a-proteomic-analysis-of-ferulic-acid-metabolism-in-amycolatopsis-sp-atcc-39116
#17
Florian Meyer, Julius Netzer, Christina Meinert, Birgit Voigt, Katharina Riedel, Alexander Steinbüchel
The pseudonocardiate Amycolatopsis sp. ATCC 39116 is used for the biotechnical production of natural vanillin from ferulic acid. Our laboratory has performed genetic modifications of this strain previously, but there are still many gaps in our knowledge regarding its vanillin tolerance and the general metabolism. We performed cultivations with this bacterium and compared the proteomes of stationary phase cells before ferulic acid feeding with those during ferulic acid feeding. Thereby, we identified 143 differently expressed proteins...
May 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29763921/peptidomic-analysis-of-endometrial-tissue-from-patients-with-ovarian-endometriosis
#18
Yunping Xue, Pengfei Xu, Sujuan Xu, Kai Xue, Lingling Xu, Jie Chen, Juan Xu, Xiaoyan Shi, Qian Li, Lin Gu
BACKGROUND/AIMS: Ovarian endometriosis (OvE) is ovarian cyst that is lined with endometrial tissue. They are found in 17-44% of women with endometriosis. Their clinical manifestations include pelvic pain, dysmenorrhea, dyspareunia, and infertility. Although the incidence of OvE has increased yearly, the exact pathogenesis of OvE is still unclear. We used peptidomics, an emerging branch of proteomics, to identify differentially expressed peptides in order to determine the possible roles of these peptides in the pathogenesis of OvE...
May 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29762640/mrmassaydb-an-integrated-resource-for-validated-targeted-proteomics-assays
#19
Pallab Bhowmick, Yassene Mohammed, Christoph H Borchers
Motivation: Multiple Reaction Monitoring (MRM)-based targeted proteomics is increasingly being used to study the molecular basis of disease. When combined with an internal standard, MRM allows absolute quantification of proteins in virtually any type of sample but the development and validation of an MRM assay for a specific protein is laborious. Therefore, several public repositories now host targeted proteomics MRM assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker, with all of which contain different levels of information...
May 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29762638/timexnet-web-identifying-cellular-response-networks-from-diverse-omics-time-course-data
#20
Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil
Summary: Condition-specific time-course omics profiles are frequently used to study cellular response to stimuli and identify associated signaling pathways. However, few online tools allow users to analyze multiple types of high-throughput time-course data. TimeXNet Web is a web server that extracts a time-dependent gene/protein response network from time-course transcriptomic, proteomic or phospho-proteomic data, and an input interaction network. It classifies the given genes/proteins into time-dependent groups based on the time of their highest activity and identifies the most probable paths connecting genes/proteins in consecutive groups...
May 14, 2018: Bioinformatics
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