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https://www.readbyqxmd.com/read/28642494/proteome-profiling-reveals-novel-biomarkers-to-identify-complicated-parapneumonic-effusions
#1
Kuo-An Wu, Chih-Ching Wu, Chi-De Chen, Chi-Ming Chu, Li-Jane Shih, Yu-Ching Liu, Chih-Liang Wang, Hsi-Hsien Lin, Chia-Yu Yang
Patients with pneumonia and parapneumonic effusion (PPE) have elevated mortality and a poor prognosis. The aim of this study was to discover novel biomarkers to help distinguish between uncomplicated PPE (UPPE) and complicated PPE (CPPE). Using an iTRAQ-based quantitative proteomics, we identified 766 proteins in pleural effusions from PPE patients. In total, 45 of these proteins were quantified as upregulated proteins in CPPE. Four novel upregulated candidates (BPI, NGAL, AZU1, and calprotectin) were selected and further verified using enzyme-linked immunosorbent assays (ELISAs) on 220 patients with pleural effusions due to different causes...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634081/quantitative-proteomic-reveals-the-dynamic-of-protein-profile-during-zebrafish-final-oocyte-maturation
#2
Chunmei Ge, Weiqun Lu, Aqin Chen
The molecular mechanisms underlying final oocyte maturation zebrafish (Danio rerio) remain poorly understood. The present study aimed to employ iTRAQ approach for a comprehensive characterization of during zebrafish oocyte maturation proteome and for comparison between fully-grow immature and mature oocytes prior to ovulation. A total of 1568 proteins were identified, which was representing the largest zebrafish isolated oocytes proteome dataset to date. Differential expression analysis revealed 190 proteins significantly changes between immature and mature oocytes, which 136 proteins were up-regulated and 54 proteins were down-regulated in mature oocytes comparison with immature oocytes...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28632510/itraq-based-quantitative-proteomic-analysis-of-lungs-in-murine-polymicrobial-sepsis-with-hydrogen-gas-treatment
#3
Yingxue Bian, Chao Qin, Yuchang Xin, Yang Yu, Hongguang Chen, Guolin Wang, Keliang Xie, Yonghao Yu
Sepsis-associated acute lung injury (ALI), which carries a high morbidity and mortality in patients, has no effective therapeutic strategies to date. Our group have already reported that hydrogen gas (H2) exerts a protective effect against sepsis in mice. However, the molecular mechanisms underlying H2 treatment are not fully understood. This study investigated the effects of H2 on lung injuries in septic mice through the iTRAQ-based quantitative proteomic analysis. Male ICR mice used in this study were subjected to cecal ligation and puncture (CLP) or sham operation...
June 19, 2017: Shock
https://www.readbyqxmd.com/read/28626452/proteomic-differences-between-developmental-stages-of-toxoplasma-gondii-revealed-by-itraq-based-quantitative-proteomics
#4
Ze-Xiang Wang, Chun-Xue Zhou, Hany M Elsheikha, Shuai He, Dong-Hui Zhou, Xing-Quan Zhu
Toxoplasma gondii has a complex two-host life-cycle between intermediate host and definitive host. Understanding proteomic variations across the life-cycle stages of T. gondii may improve the understanding of molecular adaption mechanism of T. gondii across life-cycle stages, and should have implications for the development of new treatment and prevention interventions against T. gondii infection. Here, we utilized LC-MS/MS coupled with iTRAQ labeling technology to identify differentially expressed proteins (DEPs) specific to tachyzoite (T), bradyzoites-containing cyst (C) and sporulated oocyst (O) stages of the cyst-forming T...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28624519/itraq-based-quantitative-proteomics-analysis-of-molecular-mechanisms-associated-with-bombyx-mori-lepidoptera-larval-midgut-response-to-bmnpv-in-susceptible-and-near-isogenic-strains
#5
Haizhong Yu, Xueyang Wang, Jiaping Xu, Yan Ma, Shangzhi Zhang, Dong Yu, Dongqiong Fei, Azharuddin Muhammad
Bombyx mori nucleopolyhedrovirus (BmNPV) has been identified as a major pathogen responsible for severe economic loss. Most silkworm strains are susceptible to BmNPV, with only a few highly resistant strains thus far identified. Here we investigated the molecular basis of silkworm resistance to BmNPV using susceptible (the recurrent parent P50) and resistant (near-isogenic line BC9) strains and a combination of iTRAQ-based quantitative proteomics, reverse-transcription quantitative PCR and Western blotting...
June 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28623314/comparative-transcriptomic-and-proteomic-analyses-provide-insights-into-the-key-genes-involved-in-high-altitude-adaptation-in-the-tibetan-pig
#6
Bo Zhang, Yangzom Chamba, Peng Shang, Zhixiu Wang, Jun Ma, Liyuang Wang, Hao Zhang
Tibetan pigs that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from lowland pigs, and have adapted well to extreme conditions. However, the mechanisms involved in regulating gene expression at high altitude in these animals are not fully understood. In this study, we obtained transcriptomic and proteomic data from the heart tissues of Tibetan and Yorkshire pigs raised in the highlands (TH and YH) and lowlands (TL and YL) via RNA-seq and iTRAQ (isobaric tags for relative and absolute quantitation) analyses, respectively...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622966/immunohistochemical-expression-analysis-of-leucine-rich-ppr-motif-containing-protein-lrpprc-a-candidate-colorectal-cancer-biomarker-identified-by-shotgun-proteomics-using-itraq
#7
Tomohisa Nishio, Nobuya Kurabe, Naoko Goto-Inoue, Toshio Nakamura, Haruhiko Sugimura, Mitsutoshi Setou, Masato Maekawa
BACKGROUND: Colorectal cancer (CRC) is the fourth most frequent cause of cancer deaths in the world. Novel biomarkers for the diagnosis, prognosis, and treatment of CRC are required to improve the clinical strategy. METHODS: We applied shotgun proteomics using isobaric tags for relative and absolute quantitation (iTRAQ) to identify novel biomarkers of CRC, and then we detected leucine-rich PPR-motif-containing protein (LRPPRC) expression in 83 normal colorectal tissues and 133 CRC tissues by immunohistochemistry...
June 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28618117/itraq-based-proteomics-of-sunflower-cultivars-differing-in-resistance-to-parasitic-weed-orobanche-cumana
#8
Chong Yang, Ling Xu, Na Zhang, Faisal Islam, Wenjian Song, Luyang Hu, Dan Liu, Xiaonan Xie, Weijun Zhou
Orobanche cumana is an obligate root parasite causing severe damage to many economically important crops, including sunflowers worldwide. For efficient control measures, it is necessary to understand the resistant mechanism during interaction at molecular level. The present study emphasizes on comparative proteomics to investigate the mechanistic basis of compatible and incompatible interaction of O. cumana with resistant (JY207) and susceptible (TK0409) sunflowers. More than 3500 proteins were identified from two cultivars by iTRAQ analysis...
June 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28615669/differential-effects-of-a-post-anthesis-heat-stress-on-wheat-triticum-aestivum-l-grain-proteome-determined-by-itraq
#9
Yufeng Zhang, Jiajia Pan, Xiuwen Huang, Dandan Guo, Hongyao Lou, Zhenghong Hou, Meng Su, Rongqi Liang, Chaojie Xie, Mingshan You, Baoyun Li
Heat stress, a major abiotic stressor of wheat (Triticum aestivum L.), often results in reduced yield and decreased quality. In this study, a proteomic method, Tags for Relative and Absolute Quantitation Isobaric (iTRAQ), was adopted to analyze the protein expression profile changes among wheat cultivar Jing411 under heat stress. Results indicated that there were 256 different proteins expressed in Jing411 under heat stress. According to the result of gene annotation and functional classification, 239 proteins were annotated by 856 GO function entries, including growth and metabolism proteins, energy metabolism proteins, processing and storage proteins, defense-related proteins, signal transduction, unknown function proteins and hypothetical proteins...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607388/aerobic-biogenesis-of-selenium-nanoparticles-by-enterobacter-cloacae-z0206-as-a-consequence-of-fumarate-reductase-mediated-selenite-reduction
#10
Deguang Song, Xiaoxiao Li, Yuanzhi Cheng, Xiao Xiao, Zeqing Lu, Yizhen Wang, Fengqin Wang
In the present study, we examined the ability of Enterobacter cloacae Z0206 to reduce toxic sodium selenite and mechanism of this process. E. cloacae Z0206 was found to completely reduce up to 10 mM selenite to elemental selenium (Se°) and form selenium nanoparticles (SeNPs) under aerobic conditions. The selenite reducing effector of E. cloacae Z0206 cell was to be a membrane-localized enzyme. iTRAQ proteomic analysis revealed that selenite induced a significant increase in the expression of fumarate reductase...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28592253/itraq-based-proteome-profile-analysis-of-superior-and-inferior-spikelets-at-early-grain-filling-stage-in-japonica-rice
#11
Cuicui You, Lin Chen, Haibing He, Liquan Wu, Shaohua Wang, Yanfeng Ding, Chuanxi Ma
BACKGROUND: Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS: A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0)...
June 7, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28587595/proteomic-analysis-by-itraq-mrm-of-soybean-resistance-to-lamprosema-indicate
#12
Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang, Xiangmin Tang
BACKGROUND: Lamprosema indicate is a major leaf feeding insect pest to soybean, which has caused serious yield losses in central and southern China. To explore the defense mechanisms of soybean resistance to Lamprosema indicate, a highly resistant line (Gantai-2-2) and a highly susceptible line (Wan 82-178) were exposed to Lamprosema indicate larval feedings for 0 h and 48 h, and the differential proteomic analyses of these two lines were carried out. RESULTS: The results showed that 31 differentially expressed proteins (DEPs) were identified in the Gantai-2-2 when comparing 48 h feeding with 0 h feeding, and 53 DEPs were identified in the Wan 82-178...
June 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28586360/comparative-proteomic-analysis-of-eggplant-solanum-melongena-l-heterostylous-pistil-development
#13
Yikui Wang, Ake Liu, Wenjia Li, Yaqing Jiang, Shiwei Song, Yan Li, Riyuan Chen
Heterostyly is a common floral polymorphism, but the proteomic basis of this trait is still largely unexplored. In this study, self- and cross-pollination of L-morph and S-morph flowers and comparison of embryo sac development in eggplant (Solanum melongena L.) suggested that lower fruit set from S-morph flowers results from stigma-pollen incompatibility. To explore the molecular mechanism underlying heterostyly development, we conducted isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis of eggplant pistils for L- and S-morph flowers...
2017: PloS One
https://www.readbyqxmd.com/read/28580786/quantitative-performance-evaluator-for-proteomics-qpep-web-based-application-for-reproducible-evaluation-of-proteomics-preprocessing-methods
#14
Dario Strbenac, Ling Zhong, Mark J Raftery, Penghao Wang, Susan R Wilson, Nicola J Armstrong, Jean Y H Yang
Tandem mass spectrometry is one of the most popular techniques for quantitation of proteomes. There exists a large variety of options in each stage of data preprocessing that impact the bias and variance of the summarized protein-level values. Using a newly released data set satisfying a replicated Latin squares design, a diverse set of performance metrics has been developed and implemented in a web-based application, Quantitative Performance Evaluator for Proteomics (QPEP). QPEP has the flexibility to allow users to apply their own method to preprocess this data set and share the results, allowing direct and straightforward comparison of new methodologies...
June 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28578006/increased-sat2-expression-is-associated-with-busulfan-induced-testicular-sertoli-cell-injury
#15
Yi Xian, Mingjun Wu, Yaping Liu, Jie Hao, Yu Wu, Xiaogang Liao, Gang Li
Busulfan is a chemotherapeutic agent used to treat chronic myelogenous leukemia and other myeloproliferative disorders. Increasing evidence has demonstrated that busulfan may induce testicular dysfunction by targeting genes that are expressed in the testis. Here, we showed that spermidine/spermine N1-acetyltransferase 2 (Sat2) was present in testicular Sertoli cells, and its expression was significantly increased by busulfan treatment. To investigate the implications of Sat2 upregulation for cell growth and function, a Sat2-overexpressing TM4 Sertoli cell model was established...
June 1, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28575129/the-involvement-and-possible-mechanism-of-pro-inflammatory-tumor-necrosis-factor-alpha-tnf-%C3%AE-in-thoracic-ossification-of-the-ligamentum-flavum
#16
Chi Zhang, Zhongqiang Chen, Xiangyu Meng, Mengtao Li, Li Zhang, Ann Huang
Thoracic ossification of the ligamentum flavum (TOLF) is characterized by ectopic bone formation in the ligamentum flavum and is considered to be a leading cause of thoracic spinal canal stenosis and myelopathy. However, the underlying etiology is not well understood. An iTRAQ proteomics was used to reveal the involvement of inflammation factors in TOLF. TNF-α is a pro-inflammatory cytokine implicated in the pathogenesis of many human diseases. Protein profiling analysis showed that the protein level of TNF-α increased in the ossified ligamentum flavum of TOLF, which was confirmed by western blot...
2017: PloS One
https://www.readbyqxmd.com/read/28574228/apkc-%C3%AE-p-sp1-snail-signaling-induces-epithelial-mesenchymal-transition-and-immunosuppression-in-cholangiocarcinoma
#17
Yawei Qian, Wei Yao, Tao Yang, Yan Yang, Yan Liu, Qi Shen, Jian Zhang, Weipeng Qi, Jianming Wang
Cholangiocarcinoma (CCA) is a highly malignant bile duct cancer that tends to invade and metastasize early. The epithelial-mesenchymal transition (EMT) has been implicated in cancer cell invasion and metastasis, as well as in cancer cell evasion of host immunity. In this study, we investigated the interaction between atypical protein kinase C-iota (aPKC-ι) and Snail in the regulation of EMT and its relationship to CCA immunosuppression. Our results demonstrated that aPKC-ι, Snail, and infiltrated immunosuppressive cells were significantly up-regulated in CCA tumor tissues and were linked to poor prognosis...
June 2, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28571968/determination-of-the-protein-expression-profiles-of-propsilocerus-akamusi-tokunaga-malpighian-tubules-response-to-cadmium-stress-by-itraq-coupled-lc-ms-ms
#18
Xianyun Zheng, Zhiying Xie, Shu Wang, Pipeng Lin
Propsilocerus akamusi (Tokunaga) is an important prey species for fish and aquatic birds, which represent an important link in the aquatic food chain as other species of Chironomidae. Malpighian tubules (MT) play an important role in metabolism and detoxification of harmful compounds and metal accumulation. Our previous studies have reported that P. akamusi have an extraordinary resistance to Cd. In this paper, iTRAQ-based proteomics technology was first used to study the differential proteomics of MT of Propsilocerus akamusi under sublethal Cd stress for different time courses...
May 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28570075/comparative-proteome-reveals-metabolic-changes-during-the-fruiting-process-in-flammulina-velutipes
#19
Jing-Yu Liu, Ming-Chang Chang, Jun-Long Meng, Cui-Ping Feng, Hui Zhao, Ming-Liang Zhang
Understanding the molecular mechanisms regulating the fruiting process in macro-fungi, especially industrially cultivated mushrooms, has long been a goal in mycological research. To gain insights into the events accompanying the transformation of mycelia into fruit-bodies in Flammulina velutipes, proteins expressed characteristically and abundantly at primordium and fruit-body stages were investigated by using the iTRAQ labeling technique. Among the 171 differentially expressed proteins, a total of 68 displayed up-regulated expression levels that were associated with 84 specific KEGG pathways...
June 21, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28562641/pgca-an-algorithm-to-link-protein-groups-created-from-ms-ms-data
#20
David Kepplinger, Mandeep Takhar, Mayu Sasaki, Zsuzsanna Hollander, Derek Smith, Bruce McManus, W Robert McMaster, Raymond T Ng, Gabriela V Cohen Freue
The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra...
2017: PloS One
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