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proteomics pathway analysis

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https://www.readbyqxmd.com/read/28734827/multi-omics-analyses-of-starvation-responses-reveal-a-central-role-for-lipoprotein-metabolism-in-acute-starvation-survival-in-c-%C3%A2-elegans
#1
Eva Bang Harvald, Richard R Sprenger, Kathrine Brændgaard Dall, Christer S Ejsing, Ronni Nielsen, Susanne Mandrup, Alejandro Brenes Murillo, Mark Larance, Anton Gartner, Angus I Lamond, Nils J Færgeman
Starvation causes comprehensive metabolic changes, which are still not fully understood. Here, we used quantitative proteomics and RNA sequencing to examine the temporal starvation responses in wild-type Caenorhabditis elegans and animals lacking the transcription factor HLH-30. Our findings show that starvation alters the abundance of hundreds of proteins and mRNAs in a temporal manner, many of which are involved in central metabolic pathways, including lipoprotein metabolism. We demonstrate that premature death of hlh-30 animals under starvation can be prevented by knockdown of either vit-1 or vit-5, encoding two different lipoproteins...
July 12, 2017: Cell Systems
https://www.readbyqxmd.com/read/28733544/identification-of-lefty-as-a-molecular-marker-for-ovarian-clear-cell-carcinoma
#2
Masashi Akiya, Masaaki Yamazaki, Toshihide Matsumoto, Yusuke Kawashima, Yasuko Oguri, Sabine Kajita, Daiki Kijima, Risako Chiba, Ako Yokoi, Hiroyuki Takahashi, Yoshio Kodera, Makoto Saegusa
To identify proteins involved in ovarian clear cell carcinoma (OCCCa), shotgun proteomics analysis was applied using formalin-fixed and paraffin-embedded samples of ovarian carcinoma. Analysis of 1521 proteins revealed that 52 were differentially expressed between four OCCCa and 12 non-OCCCa samples. Of the highly expressed proteins in OCCCa, we focused on left-right determination factor (LEFTY), a novel member of the transforming growth factor-β superfamily. In 143 cases of ovarian epithelial carcinoma including 99 OCCCas and 44 non-OCCCas, LEFTY expression at both mRNA and protein levels was significantly higher in OCCCas compared with non-OCCCas, with the mRNA expression of LEFTY1 being predominant compared to that of LEFTY2...
June 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28733522/abi3-a-component-of-the-wave2-complex-is-potentially-regulated-by-pi3k-akt-pathway
#3
Lais Moraes, Nilson I T Zanchin, Janete M Cerutti
We previously reported that ABI3 expression is lost in follicular thyroid carcinomas and its restoration significantly inhibited cell growth, invasiveness, migration, and reduced tumor growth in vivo. The mechanistic basis by which ABI3 exerts its tumor suppressive effects is not fully understood. In this study, we show that ABI3 is a phosphoprotein. Using proteomic array analysis, we showed that ABI3 modulated distinct cancer-related pathways in thyroid cancer cells. The KEA analysis found that PI3K substrates were enriched and forced expression of ABI3 markedly decreased the phosphorylation of AKT and the downstream-targeted protein pGSK3β...
June 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28733104/comparative-shoot-proteome-analysis-of-two-potato-solanum-tuberosum-l-genotypes-contrasting-in-nitrogen-deficiency-responses-in-vitro
#4
Philipp Meise, Anna Maria Jozefowicz, Ralf Uptmoor, Hans-Peter Mock, Frank Ordon, Annegret Schum
Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19...
July 18, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28732263/proteomic-analysis-of-naturally-occurring-boron-tolerant-plant-gypsophila-sphaerocephala-l-in-response-to-high-boron-concentration
#5
Huseyin Tombuloglu, Guzin Tombuloglu, Mehmet Serdal Sakcali, Ali Turkan, Khalid Rehman Hakeem, Hesham F Alharby, Shah Fahd, Waseem Mohammed Abdul
Gypsophila sphaerocephala is a naturally Boron (B) tolerant species that can grow around the B mining areas in Turkey, where the B concentration in soil reaches a lethal dose for plants (up to ∼8900mgkg(-1) (∼140mM). While its interesting survival capacity in extremely B containing soils, any molecular research has been conducted to understand its high tolerance mechanism yet. In the present study, we have performed a proteomic analysis of this plant to understand its high tolerance towards B-stress. Seedlings of G...
July 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28732011/proteomics-analysis-reveals-a-dynamic-diurnal-pattern-of-photosynthesis-related-pathways-in-maize-leaves
#6
Dan Feng, Yanwei Wang, Tiegang Lu, Zhiguo Zhang, Xiao Han
Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions...
2017: PloS One
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#7
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730483/characterization-of-the-phospho-adhesome-by-mass-spectrometry-based-proteomics
#8
Joseph Robertson, Jonathan D Humphries, Nikki R Paul, Stacey Warwood, David Knight, Adam Byron, Martin J Humphries
Integrin adhesion receptors engage with their extracellular matrix (ECM) ligands, initiating intracellular signaling pathways that regulate a range of fundamental cell functions. Protein kinases and phosphatases play an integral role in integrin adhesion-mediated signaling. However, until recently, knowledge of the phosphorylation sites regulated downstream of integrin ligation was limited to candidate-based approaches and did not support a system-level understanding of the molecular mechanisms through which ECM engagement influences cell behavior...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730077/proteomic-profiling-of-early-degenerative-retina-of-rcs-rats
#9
Zhi-Hong Zhu, Yan Fu, Chuan-Huang Weng, Cong-Jian Zhao, Zheng-Qin Yin
AIM: To identify the underlying cellular and molecular changes in retinitis pigmentosa (RP). METHODS: Label-free quantification-based proteomics analysis, with its advantages of being more economic and consisting of simpler procedures, has been used with increasing frequency in modern biological research. Dystrophic RCS rats, the first laboratory animal model for the study of RP, possess a similar pathological course as human beings with the diseases. Thus, we employed a comparative proteomics analysis approach for in-depth proteome profiling of retinas from dystrophic RCS rats and non-dystrophic congenic controls through Linear Trap Quadrupole - orbitrap MS/MS, to identify the significant differentially expressed proteins (DEPs)...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28729074/proteomic-analysis-of-the-effects-of-nur77-on-lipopolysaccharide-induced-microglial-activation
#10
Yan Chen, Yuexinzi Jin, Hui Zhan, Jian Chen, Yanting Chen, Hailan Meng, Jiali Jin, Linjie Yu, Xiang Cao, Yun Xu
Microglia are critical components of the immune response in the central nervous system. Our study aims to explore potential role of Nur77 in lipopolysaccharide (LPS)-induced microglial activation. Primary wild-type and Nur77(-/-) microglia were stimulated with LPS and protein extracts were detected via mass spectrometry. Q-PCR and western blotting were performed to validate candidate proteins. A total of 2004 proteins were identified, with 749 and 677 significantly differentially expressed proteins in wild-type and Nur77(-/-) microglia in resting and activated states, respectively...
July 17, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28728878/a-mass-spectrometry-based-proteomic-analysis-of-homer2-interacting-proteins-in-the-mouse-brain
#11
Scott P Goulding, Karen K Szumlinski, Candice Contet, Michael J MacCoss, Christine C Wu
In the brain, the Homer protein family modulates excitatory signal transduction and receptor plasticity through interactions with other proteins in dendritic spines. Homer proteins are implicated in a variety of psychiatric disorders such as schizophrenia and addiction. Since Homers serve as scaffolding proteins, identifying their interaction partners is an important first step in understanding their biological function and could help design novel therapeutic strategies. The present study set out to document Homer2-interacting proteins in the mouse brain using a co-immunoprecipitation-based mass spectrometry approach...
July 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28727291/proteomic-analysis-and-bioluminescent-reporter-gene-assays-to-investigate-effects-of-simulated-microgravity-on-caco-2-cells
#12
Giorgia La Barbera, Anna Laura Capriotti, Elisa Michelini, Susy Piovesana, Maria Maddalena Calabretta, Riccardo Zenezini Chiozzi, Aldo Roda, Aldo Laganà
Microgravity is one of the most important features in spaceflight. Previous evidence from in-vitro studies has shown that significant changes occur under simulated microgravity. For this reason, human colon adenocarcinoma Caco-2 cells were selected as cell model of intestinal epithelial barrier and their response to altered gravity conditions was investigated, especially on the protein level. In this study, we combined label-free shotgun proteomics and bioluminescent reporter gene assays to identify key proteins and pathways involved in the response of Caco-2 cells under reference and microgravity conditions...
July 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28727099/identification-of-differentially-expressed-proteins-in-testicular-semen-of-sex-reversed-female-xx-and-normal-male-xy-rainbow-trout
#13
J Nynca, M Adamek, A Ciereszko
Masculinized females, named sex-reversed females (SRF), have a male phenotype but retain the female genotype (XX) and all spermatozoa produced in their testes carry the X chromosome. Masculinization of females leads to incomplete testicular development and the production of lower-quality semen. The mechanism of masculinization is unknown at present. Therefore, the aim of our study was to identify differentially abundant proteins in testicular semen of normal males and SRF using a difference in-gel electrophoresis approach...
July 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726736/protozoadb-2-0-a-trypanosoma-brucei-case-study
#14
Rodrigo Jardim, Diogo Tschoeke, Alberto M R Da Vila
Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2...
July 20, 2017: Pathogens
https://www.readbyqxmd.com/read/28722676/comparative-proteomic-analysis-of-virulent-and-avirulent-strains-of-toxoplasma-gondii-reveals-strain-specific-patterns
#15
Dong-Hui Zhou, Ze-Xiang Wang, Chun-Xue Zhou, Shuai He, Hany M Elsheikha, Xing-Quan Zhu
Research exploring the proteome of Toxoplasma gondii oocysts has gained momentum over the past few years. However, little is known about the oocyst's protein repertoires that contribute to differential virulence among T. gondii strains. Here, we used isobaric tag for relative and absolute quantitation-based proteomic analysis of oocysts of two T. gondii strains exhibiting the virulent PYS (ToxoDB#9) phenotype versus the less virulent PRU (Type II, ToxoDB#1) phenotype. Our aim was to determine protein expression patterns that contribute to the virulence of a particular phenotype...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722160/placental-proteomics-reveal-insights-into-fetal-alcohol-spectrum-disorders
#16
Katie L Davis-Anderson, Sebastian Berger, Emilie R Lunde-Young, Vishal D Naik, Heewon Seo, Greg A Johnson, Hanno Steen, Jayanth Ramadoss
Fetal alcohol spectrum disorders (FASD) describe many of the well-known neurodevelopmental deficits afflicting children exposed to alcohol in utero. The effects of alcohol on the maternal-fetal interface, especially the placenta, have been less explored. We herein hypothesized that chronic binge alcohol exposure during pregnancy significantly alters the placental protein profile in a rat FASD model METHODS: Pregnant rats were orogastrically treated daily with alcohol (4.5 g/kg, gestational day (GD) 5-10; 6...
July 19, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28720800/itraq-based-quantitative-proteomic-analysis-reveals-alterations-in-the-metabolism-of-actinidia-arguta
#17
Miaomiao Lin, Jinbao Fang, Xiujuan Qi, Yukuo Li, Jinyong Chen, Leiming Sun, Yunpeng Zhong
Actinidia arguta 'Tianyuanhong' is a new kiwifruit variety with an all-red pericarp and pulp, in contrast to the all-green pulp of A. arguta 'Yongfengyihao'. Transcriptome profile analysis of fruit color has been reported, however, the metabolic mechanisms producing red flesh remain unknown, and it is unclear why the pulp of 'Tianyuanhong' is red rather than green. Herein, we identified differences between the proteomes of two A. arguta cultivars with different fruit color by using iTRAQ-based quantitative proteomic methods during the stage of color change...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28719341/label-free-quantitative-proteomics-analysis-on-the-cisplatin-resistance-in-ovarian-cancer-cells
#18
F Wang, Y Zhu, S Fang, S Li, S Liu
Quantitative proteomics has been made great progress in recent years. Label free quantitative proteomics analysis based on the mass spectrometry is widely used. Using this technique, we determined the differentially expressed proteins in the cisplatin-sensitive ovarian cancer cells COC1 and cisplatin-resistant cells COC1/DDP before and after the application of cisplatin. Using the GO analysis, we classified those proteins into different subgroups bases on their cellular component, biological process, and molecular function...
May 20, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28718674/design-and-synthesis-of-a-novel-photoaffinity-probe-for-labelling-egf-receptor-tyrosine-kinases
#19
You-Guang Zheng, Xiao-Qing Wu, Jun Su, Ping Jiang, Liang Xu, Jian Gao, Bin Cai, Min Ji
The epidermal growth factor receptor (EGFR) and HER2 are two important tyrosine kinases that play crucial roles in signal transduction pathways that regulate numerous cellular functions including proliferation, differentiation, migration, and angiogenesis. In the past 20 years, many proteomic methods have emerged as powerful methods to evaluate proteins in biological processes and human disease states. Among them, activity-based protein profiling (ABPP) is one useful approach for the functional analysis of proteins...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28715131/transcriptome-analysis-suggests-a-role-for-the-differential-expression-of-cerebral-aquaporins-and-the-mapk-signalling-pathway-in-human-temporal-lobe-epilepsy
#20
Mootaz M Salman, Mariam A Sheilabi, Dev Bhattacharyya, Philip Kitchen, Alex C Conner, Roslyn M Bill, M Nicola Woodroofe, Matthew T Conner, Alessandra P Princivalle
Epilepsies are common disorders of the central nervous system (CNS), affecting up to 2% of the global population. Pharmaco-resistance is a major clinical challenge affecting about 30% of temporal lobe epilepsy (TLE) patients. Water homeostasis has been shown crucial for regulation of neuronal excitability. The control of water movement is achieved through a family of small integral membrane channel proteins called aquaporins (AQPs). Despite the fact that changes in water homeostasis occur in sclerotic hippocampi of people with TLE, the expression of AQPs in the epileptic brain is not fully characterised...
July 17, 2017: European Journal of Neuroscience
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