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https://www.readbyqxmd.com/read/29156766/isobaric-tags-for-relative-and-absolute-quantification-based-proteomic-analysis-of-testis-biopsies-in-rhesus-monkeys-treated-with-transient-scrotal-hyperthermia
#1
Meng Rao, Sha Ma, Shifu Hu, Hui Lei, Yanqing Wu, Yanfei Zhou, Wei Xia, Changhong Zhu
This study aimed to examine the cellular and molecular events that occur in rhesus monkey testes after scrotal hyperthermia. Eight male adult rhesus monkeys were subjected to scrotal hyperthermia at 43°C for 30 min daily for 6 consecutive days. Sperm concentration, reproductive hormones, and testis histology were examined before hyperthermia (day 0), and at 8, 15, 30, 45, 60, 75, and 90 days after the initiation of hyperthermia. iTRAQ-based proteomic analysis was conducted on testicular tissues collected on days 0, 8, and 60 to identify differentially expressed proteins at the early and recovery stages of testicular damage...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151355/matrix-effects-originating-from-coexisting-minerals-and-accurate-determination-of-stable-silver-isotopes-in-silver-deposits
#2
Qi Guo, Haizhen Wei, Shao-Yong Jiang, Simon Hohl, Yibo Lin, Yi-Jing Wang, Yin-Chuan Li
Except for extensive studies in core formation and volatile-element depletion processes using radiogenic Ag isotopes (i.e. the Pd-Ag chronometer), recent research has revealed that the mass fractionation of silver isotopes is in principle controlled by physico-chemical processes (e.g. evaporation, diffusion, chemical exchange etc.) during magmatic emplacement and hydrothermal alteration. As these geologic processes only produce very minor variations of δ109Ag from -0.5 ‰ to +1.1‰, more accurate and precise measurements are required...
November 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29149484/comparative-analysis-of-proteomes-between-diabetic-and-normal-human-sperm-insights-into-the-effects-of-diabetes-on-male-reproduction-based-on-the-regulation-of-mitochondria-related-proteins
#3
Tian An, Yue-Fen Wang, Jia-Xian Liu, Yan-Yun Pan, Yu-Fei Liu, Zhong-Chen He, Fang-Fang Mo, Jun Li, Li-Hua Kang, Yu-Jie Gu, Bo-Han Lv, Si-Huan Gao, Guang-Jian Jiang
This study sought to identify sources of the reduced fertility of men with type 2 diabetes mellitus. Significant reductions in semen volume, sperm concentration, and total sperm count were observed in diabetic individuals, while transmission electron microscopy revealed that the structure of mitochondria in the tail of sperm from diabetic patients was damaged. Proteins potentially associated with these sperm defects were identified using proteomics. Isobaric tagging for relative and absolute quantitation labeling and high-performance liquid chromatography-tandem mass spectrometry allowed us to identify 357 proteins significantly differentially expressed in diabetic versus control semen (>1...
November 17, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29145156/the-potential-of-ion-mobility-mass-spectrometry-for-high-throughput-and-high-resolution-lipidomics
#4
REVIEW
Christine Hinz, Sonia Liggi, Julian L Griffin
Lipids are a large and highly diverse family of biomolecules, which play essential structural, storage and signalling roles in cells and tissues. Although traditional mass spectrometry (MS) approaches used in lipidomics are highly sensitive and selective, lipid analysis remains challenging due to the chemical diversity of lipid structures, multiple isobaric species and incomplete separation using many forms of chromatography. Ion mobility (IM) separates ions in the gas phase based on their physicochemical properties...
November 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29141440/explaining-the-t-v-dependent-dynamics-of-glass-forming-liquids-the-cooperative-free-volume-model-tested-against-new-simulation-results
#5
Ronald P White, Jane E G Lipson
In this article, we derive a rate model, the "cooperative free volume" (CFV) model, to explain relaxation dynamics in terms of a system's free volume, Vfree, and its temperature, T, over widely varied pressure dependent conditions. In the CFV model, the rate a molecule moves a distance on the order of its own size is dependent on the cooperation of surrounding molecules to open up enough free space. To test CFV, we have generated extensive T,V dependent simulation data for structural relaxation times, τ, on a Kob and Andersen type Lennard-Jones (KA-LJ) fluid...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29141431/development-of-isothermal-isobaric-replica-permutation-method-for-molecular-dynamics-and-monte-carlo-simulations-and-its-application-to-reveal-temperature-and-pressure-dependence-of-folded-misfolded-and-unfolded-states-of-chignolin
#6
Masataka Yamauchi, Hisashi Okumura
We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29141195/determination-of-the-effect-of-pinellia-ternata-thunb-breit-on-nervous-system-development-by-proteomics
#7
Jian-Ya Xu, Chen Dai, Jin-Jun Shan, Tong Xie, Hui-Hui Xie, Ming-Ming Wang, Guang Yang
ETHNOPHARMACOLOGICAL RELEVANCE: Banxia (BX) is the dried tuber of Pinellia ternata (Thunb.) Breit., a commonly prescribed Chinese medicinal herb for the treatment of cough, phlegm, and vomiting in pregnant women. However, raw BX has been demonstrated to exert toxic effects on reproduction and the precise and comprehensive mechanisms remain elusive. AIM OF THE STUDY: We applied an iTRAQ (isobaric tags for relative and absolute quantitation, iTRAQ)-based proteomic method to explore the mechanisms of raw BX-induced fetal toxicity in mice...
November 12, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29140297/a-proteomic-approach-to-investigate-the-drought-response-in-the-orphan-crop-eragrostis-tef
#8
Rizqah Kamies, Jill M Farrant, Zerihun Tadele, Gina Cannarozzi, Mohammed Suhail Rafudeen
The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions...
November 15, 2017: Proteomes
https://www.readbyqxmd.com/read/29136864/suspect-screening-of-halogenated-carboxylic-acids-in-drinking-water-using-ion-exchange-chromatography-high-resolution-orbitrap-mass-spectrometry-ic-hrms
#9
Matteo D Gallidabino, Laurence Hamdan, Bronagh Murphy, Leon P Barron
Retrospective in silico screening of analytical data for the identification of new or emerging disinfection by-products in drinking waters could be useful to assess quality and potential hazards, as well as help implement mitigation procedures more rapidly. Herein, the first study coupling ion exchange chromatography (IC) with high resolution mass spectrometry (HRMS) for the determination of halogenated carboxylic acid disinfectant by-products is reported. Separation was achieved using a Metrohm A Supp 5 column and a Na2CO3/NaHCO3 gradient eluent from 1/0...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29131595/variability-in-toxin-profiles-of-the-mediterranean-ostreopsis-cf-ovata-and-in-structural-features-of-the-produced-ovatoxins
#10
Luciana Tartaglione, Emma Dello Iacovo, Antonia Mazzeo, Silvia Casabianca, Patrizia Ciminiello, Antonella Penna, Carmela Dell'Aversano
Fifty-five strains of Ostreopsis were collected in the Mediterranean Sea and analysed to characterize their toxin profiles. All the strains were grown in culture under the same experimental conditions and identified by molecular PCR assay based on the ITS-5.8S rDNA. A liquid chromatography-high resolution multiple stage mass spectrometry (LC-HRMSn) approach was used to analyze toxin profiles and to structurally characterize the detected toxins. Despite morphological and molecular characterization being consistent with the species O...
November 13, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29130966/itraq-based-proteomic-analysis-of-neonatal-kidney-from-offspring-of-protein-restricted-rats-reveals-abnormalities-in-intraflagellar-transport-proteins
#11
Xiaomei Liu, Jun Wang, Linlin Gao, Hao Liu, Caixia Liu
BACKGROUND: It is well recognized that adverse events in utero can impair fetal development and lead to the development of kidney injury and hypertension in adulthood. We previously reported a lower kidney index, glomeruli number, and decreased glomerular filtration rate in intrauterine growth restriction (IUGR) offspring induced by maternal protein malnutrition. To explore the molecular mechanisms linking impaired fetal growth to renal diseases, we investigated differentially expressed proteins (DEPs) in the IUGR neonatal kidneys by isobaric tags for relative and absolute quantitation (iTRAQ) analysis...
November 6, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29129749/quantitative-proteomic-analysis-of-deciduous-molars-during-cap-to-bell-transition-in-miniature-pig
#12
Yang Li, Yiyi Gong, Xiaoshan Wu, Fu Wang, Yilin Xie, Zhao Zhu, Yingying Su, Jinsong Wang, Chunmei Zhang, Junqi He, Haiteng Deng, Songlin Wang
Taking advantage of genetic manipulation tools and accessibility, almost all molecular knowledge on vertebrate tooth development was obtained from rodent models that only have one dentition in their entire lives. Whether the tooth development in other vertebrates such as swine or human follows the same rules remains elusive. Rodent dentitions differ considerably from human dentitions, therefore limiting the application of knowledge from rodent tooth to human tooth. Signal-mediated communication between cells and complex gene and protein regulatory networks are key components of tooth development...
November 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29126587/dispersive-magnetic-immunoaffinity-extraction-anatoxin-a-determination
#13
Tinh Le, Francesc A Esteve-Turrillas, Sergio Armenta, Miguel de la Guardia, Guillermo Quiñones-Reyes, Antonio Abad-Fuentes, Antonio Abad-Somovilla
Specific monoclonal antibodies were coupled with magnetic Sepharose-based beads and used, for the first time. The methodology was applied to preconcentrate anatoxin-a from water and the later determination by ion mobility spectrometry (IMS). Dispersive magnetic immunoaffinity (d-MagIA) extraction methodology provided a limit of detection of 0.02μgL(-1) and a satisfactory precision with a relative standard deviation lower than 15%. Recoveries were evaluated at 0.5, 1.0 and 5.0μgL(-1) anatoxin-a with quantitative values from 91 to 115%...
November 1, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29125736/pdeep-predicting-ms-ms-spectra-of-peptides-with-deep-learning
#14
Xie-Xuan Zhou, Wen-Feng Zeng, Hao Chi, Chunjie Luo, Chao Liu, Jianfeng Zhan, Si-Min He, Zhifei Zhang
In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0...
November 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29124938/quality-assessments-of-long-term-quantitative-proteomic-analysis-of-breast-cancer-xenograft-tissues
#15
Jian-Ying Zhou, Lijun Chen, Bai Zhang, Yuan Tian, Tao Liu, Stefani N Thomas, Li Chen, Michael Schnaubelt, Emily Boja, Tara Hiltke, Christopher R Kinsinger, Henry Rodriguez, Sherri R Davies, Shunqiang Li, Jacqueline E Snider, Petra Erdmann-Gilmore, David L Tabb, R Reid Townsend, Matthew J Ellis, Karin D Rodland, Richard D Smith, Steven A Carr, Zhen Zhang, Daniel W Chan, Hui Zhang
Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. We evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating six 2D LC-MS/MS data sets for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes...
November 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29123261/a-new-panel-of-pancreatic-cancer-biomarkers-discovered-using-a-mass-spectrometry-based-pipeline
#16
Xiaohui Liu, Weimin Zheng, Wansheng Wang, Huali Shen, Linxiao Liu, Wenhui Lou, Xiaolin Wang, Pengyuan Yang
BACKGROUND: Pancreatic carcinoma (PC) is an aggressive malignancy that lacks strategies for early detection. This study aimed to develop a coherent, high-throughput and non-discriminatory pipeline for the novel clinical biomarker discovery of PC. METHODS: We combined mass spectrometry (MS)-intensive methods such as isobaric tags for relative and absolute quantitation with two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS), 1D-targeted LC-MS/MS, prime MRM (P-MRM) and stable isotope dilution-based MRM (SID-MRM) to analyse serum samples from healthy people (normal control, NC), patients with benign diseases (BD) and PC patients to identify novel biomarkers of PC...
November 9, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29121466/reaching-a-vapor-sensitivity-of-0-01-parts-per-quadrillion-in-the-screening-of-large-volume-freight
#17
Daoiz Zamora, Mario Amo-Gonzalez, Marta Lanza, Gonzalo Fernandez De La Mora, Juan Fernandez de la Mora
The feasibility of detecting explosives in the atmosphere at concentrations as low as 0.01 ppq hinges on the poorly known question of what interfering species exist at these or higher concentrations. To clarify the issue, hundreds of samples of ambient air, either clean or loaded with explosives (from lightly contaminated environments) have been collected in fiberglass/stainless steel filters coated with Tenax-GR, thermally desorbed at variable temperature, and ionized with Cl- via secondary electrospray (SESI)...
November 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29120501/analysis-of-the-plasma-proteome-using-itraq-and-tmt-based-isobaric-labeling
#18
REVIEW
Robert Moulder, Santosh D Bhosale, David R Goodlett, Riitta Lahesmaa
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches...
November 9, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/29118029/giapronto-a-one-click-graph-visualization-software-for-proteomics-datasets
#19
Amber Kathryn Weiner, Simone Sidoli, Sharon J Diskin, Ben Garcia
Here we present a free interactive web tool to process and visualize proteomics datasets with a single click. GiaPronto can process all proteomics quantification methods, i.e. label-free, SILAC and isobaric labeling, and analyze post-translational modifications (PTMs). The software performs normalization and statistics, assists determination of regulated proteins, biomarkers and Gene Ontology (GO) enrichment, and provides high resolution images and tables for further data analysis. We foresee that GiaPronto will become the most rapid and simple tool for assessing data quality and determining most relevant features of proteomic datasets...
November 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29115597/quantitative-proteomic-study-of-the-plasma-reveals-acute-phase-response-and-lxr-rxr-and-fxr-rxr-activation-in-the-chronic-unpredictable-mild-stress-mouse-model-of-depression
#20
Chuangchuang Yang, Chanjuan Zhou, Jie Li, Zhi Chen, Haiyang Shi, Wensong Yang, Yinhua Qin, Lin Lü, Libo Zhao, Liang Fang, Haiyang Wang, Zicheng Hu, Peng Xie
Major depressive disorder is a severe neuropsychiatric disease that negatively impacts the quality of life of a large portion of the population. However, the molecular mechanisms underlying depression are still unclear. The pathogenesis of depression involves several brain regions. However, most previous studies have focused only on one specific brain region. Plasma and brain tissues exchange numerous components through the blood‑brain barrier. Therefore, in the present study, plasma samples from control (CON) mice and mice subjected to chronic unpredictable mild stress (CUMS) were used to investigate the molecular pathogenesis of depression, and the association between the peripheral circulation and the central nervous system...
October 20, 2017: Molecular Medicine Reports
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