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https://www.readbyqxmd.com/read/28227691/understanding-the-cochlear-implant-environment-by-mapping-perilymph-proteomes-from-different-species
#1
Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Ya Lang Enke, Rylie A Green, Jonathan C Palmer, Nigel H Lovell, Paul M Carter, Jeremy L Pinyon, Gary D Housley, Andrew K Wise, Megan S Lord
Cochlear implants operate within a bony channel of the cochlea, bathed in a fluid known as the perilymph. The perilymph is a complex fluid containing ions and proteins, which are known to actively interact with metallic electrodes. To improve our understanding of how cochlear implant performance varies in preclinical in vivo studies in comparison to human trials and patient outcomes, the protein composition (or perilymph proteome) is needed. Samples of perilymph were gathered from feline and guinea pig subjects and analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) to produce proteomes and compare against the recently published human proteome...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226337/immunoassay-based-drug-tests-are-inadequately-sensitive-for-medication-compliance-monitoring-in-patients-treated-for-chronic-pain
#2
Marion L Snyder, Corrine R Fantz, Stacy Melanson
BACKGROUND: Enzyme immunoassays (EIA) have notable limitations for monitoring therapeutic compliance in pain management. Chromatography coupled with mass spectrometry provides definitive results and superior sensitivity and specificity over traditional EIA testing. OBJECTIVE: To analyze and compare the sensitivity of EIA results together with known prescriptions to liquid chromatography-tandem mass spectrometry (LC-MS/MS) for monitoring drug use (and abuse) in patients treated for chronic pain...
February 2017: Pain Physician
https://www.readbyqxmd.com/read/28226267/a-simple-lc-ms-ms-method-for-the-simultaneous-quantification-of-resveratrol-and-its-major-phase-ii-metabolites-assessment-of-their-urinary-and-biliary-excretions-in-rats
#3
Zhixia Qiu, Jiaojiao Yu, Yu Dai, Xijing Chen, Fang Huang, Ning Li
Trans-resveratrol (Res) is rapidly metabolized, extensively distributed into various tissues and mainly excreted by urine. The present study aimed to establish a simple LC-MS/MS method to simultaneously quantify Res and its major phase II metabolites (Res-3-O-β-d-glucuronide, R3G; Res-4'-O-β-d-glucuronide, R4'G; Res-resveratrol 3-sulfate, R3S; and Res-4'-sulfate, R4'S), and apply this method to assess their urinary and biliary excretions in rats. A simplified salting-out assisted liquid-liquid extraction (SALLE) strategy was developed to prepare samples with acetonitrile-methanol mixture (8:2, v/v) as extractant and ammonium acetate solution (10M) as salting-out reagent...
February 14, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28225907/characterisation-of-iunh-gene-knockout-strain-from-mycobacterium-tuberculosis
#4
Anne Drumond Villela, Valnês da Silva Rodrigues, Antônio Frederico Michel Pinto, Priscila Lamb Wink, Zilpa Adriana Sánchez-Quitian, Guilherme Oliveira Petersen, Maria Martha Campos, Luiz Augusto Basso, Diógenes Santiago Santos
BACKGROUND: Tuberculosis (TB) is an infectious disease caused mainly by the bacillus Mycobacterium tuberculosis. The better understanding of important metabolic pathways from M. tuberculosis can contribute to the development of novel therapeutic and prophylactic strategies to combat TB. Nucleoside hydrolase (MtIAGU-NH), encoded by iunH gene (Rv3393), is an enzyme from purine salvage pathway in M. tuberculosis. MtIAGU-NH accepts inosine, adenosine, guanosine, and uridine as substrates, which may point to a pivotal metabolic role...
March 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225766/marine-actinobacteria-as-a-source-of-compounds-for-phytopathogen-control-an-integrative-metabolic-profiling-bioactivity-and-taxonomical-approach
#5
Luz A Betancur, Sandra J Naranjo-Gaybor, Diana M Vinchira-Villarraga, Nubia C Moreno-Sarmiento, Luis A Maldonado, Zulma R Suarez-Moreno, Alejandro Acosta-González, Gillermo F Padilla-Gonzalez, Mónica Puyana, Leonardo Castellanos, Freddy A Ramos
Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia...
2017: PloS One
https://www.readbyqxmd.com/read/28225596/top-down-metabolomic-approaches-for-nitrogen-containing-metabolites
#6
Ryo Nakabayashi, Kei Hashimoto, Kiminori Toyooka, Kazuki Saito
Streamlining the processes that reveal heteroatom-containing metabolites and their biosynthetic genes is essential in integrated metabolomics studies. These metabolites are especially targeted for their potential pharmaceutical activities. By using a Fourier-transform ion cyclotron resonance-mass spectrometry (FTICR-MS) instrument, we provide top-down targeted metabolomic analyses using ultrahigh-resolution liquid chromatography-mass spectrometry (LC-MS), high-resolution matrix-assisted laser desorption/ionization (MALDI), and high-resolution imaging mass spectrometry (IMS) with (15)N labeling of nitrogen-containing metabolites...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28225594/mass-spectral-feature-list-optimizer-ms-flo-a-tool-to-minimize-false-positive-peak-reports-in-untargeted-lc-ms-data-processing
#7
Brian C Defelice, Sajjan Singh Mehta, Stephanie Samra, Tomas Cajka, Benjamin Wancewicz, Johannes F Fahrmann, Oliver Fiehn
Untargeted metabolomics by liquid chromatography-mass spectrometry generates data rich chromatograms in form of m/z-retention time features. Managing such datasets is a bottleneck. Many popular data processing tools, including XCMS-online and MZmine2, yield numerous false positive peak detections. Flagging and removing such false peaks manually is a time consuming task and prone to human error. We present a web application, MS Feature List Optimizer (MS-FLO), to improve the quality of feature lists after initial processing to expedite the process of data curation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28225587/compms2miner-an-automatable-metabolite-identification-visualization-and-data-sharing-r-package-for-high-resolution-lc-ms-datasets
#8
William Matthew Bell Edmands, Lauren M Petrick, Dinesh Kumar Barupal, Augustin Scalbert, Mark Wilson, Jeffrey Wickliffe, Stephen M Rappaport
A long-standing challenge of untargeted metabolomic profiling by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation, therefore a degree of software workflow autonomy is required for broad-scale metabolite annotation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28225296/development-and-validation-of-an-lc-ms-ms-method-for-simultaneously-determining-doxapram-and-keto-doxapram-in-human-serum
#9
Yuki Suzuki, Noboru Kamada, Hitoshi Ohno, Yoshikazu Abe, Takuro Endo, Mamoru Kobayashi
AIM: Doxapram, a respiratory stimulant, is used to treat apnea. A reliable method of determining doxapram in blood is required for monitoring purposes. RESULTS: Doxapram, keto-doxapram (active metabolite) and propranolol (internal standard) were extracted from human serum by protein precipitation and plate filtration. Molecular ions were generated by electrospray ionization in positive ion mode, and the ions were analyzed using a triple-quadrupole mass spectrometer...
February 22, 2017: Bioanalysis
https://www.readbyqxmd.com/read/28225217/proteomic-analysis-of-the-cullin4b-interactome-using-proximity-dependent-biotinylation-in-living-cells
#10
Hailong Zhang, Shupeng Li, Pingting Liu, Frankie H F Lee, Albert H C Wong, Fang Liu
Cullin 4B (CUL4B) mutations have been implicated in mental retardation and dopamine-related behaviors due to disruptions in their interaction with Cullin-RING E3 ligases (CRLs). Thus, further identification of CUL4B substrates can increase the knowledge of protein homeostasis and illuminate the role of CUL4B in neuropsychiatric disease. However, the transient nature of the coupling between CUL4B and its substrates is difficult to detect in vivo using current approaches, thus hampers efforts to investigate functions of CRLs within unperturbed living systems...
February 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28225203/identification-of-interacting-proteins-of-the-tafve-protein-involved-in-spike-development-in-bread-wheat
#11
Yong-Sheng Zheng, Yu-Qing Lu, Ying-Ying Meng, Rong-Zhi Zhang, Han Zhang, Jia-Mei Sun, Mu-Mu Wang, Li-Hui Li, Ru-Yu Li
FVE/MSI4 plays important roles in determining flowering time in Arabidopsis. However, its function is unexplored in wheat. In the present study, Co-IP and nano-LC-MS/MS were used to identify TaFVE-interacting or associated proteins. Altogether 89 differentially expressed proteins showed the same down-regulated expression trends as TaFVE in wheat line 5660M. Among them, 62 proteins were further predicted to be involved in the interaction network of TaFVE and 11 proteins have been shown to be potential TaFVE interactors based on curated databases and experimentally determined in other species by the STRING...
February 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28225098/urinary-metabolic-signatures-and-early-triage-of-acute-radiation-exposure-in-rat-model
#12
Mingxiao Zhao, Kim Kt Lau, Xian Zhou, Jianfang Wu, Jun Yang, Chang Wang
After a large-scale radiological accident, early-response biomarkers to assess radiation exposure over a broad dose range are not only the basis of rapid radiation triage, but are also the key to the rational use of limited medical resources and to the improvement of treatment efficiency. Because of its high throughput, rapid assays and minimally invasive sample collection, metabolomics has been applied to research into radiation exposure biomarkers in recent years. Due to the complexity of radiobiological effects, most of the potential biomarkers are both dose-dependent and time-dependent...
February 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28225015/identification-of-protein-biomarkers-and-signaling-pathways-associated-with-prostate-cancer-radioresistance-using-label-free-lc-ms-ms-proteomic-approach
#13
Lei Chang, Jie Ni, Julia Beretov, Valerie C Wasinger, Jingli Hao, Joseph Bucci, David Malouf, David Gillatt, Peter H Graham, Yong Li
Identifying biomarkers and signaling pathways are important for the management of prostate cancer (CaP) radioresistance. In this study, we identified differential proteins and signaling pathways from parental CaP cell lines and CaP radioresistant (RR) sublines using a label-free LC-MS/MS proteomics approach. A total of 309 signaling pathway proteins were identified to be significantly altered between CaP and CaP-RR cells (p ≤ 0.05, fold differences >1.5, ≥80% power). Among these proteins, nineteen are common among three paired CaP cell lines and associated with metastasis, progression and radioresistance...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224913/parent-heparin-and-daughter-lmw-heparin-correlation-analysis-using-lc-ms-and-nmr
#14
Xinyue Liu, Kalib St Ange, Xiaohua Wang, Lei Lin, Fuming Zhang, Lianli Chi, Robert J Linhardt
Heparin is a structurally complex, polysaccharide anticoagulant derived from livestock, primarily porcine intestinal tissues. Low molecular weight (LMW) heparins are derived through the controlled partial depolymerization of heparin. Increased manufacturing and regulatory concerns have provided the motivation for the development of more sophisticated analytical methods for determining both their structure and pedigree. A strategy, for the comprehensive comparison of parent heparins and their LMW heparin daughters, is described that relies on the analysis of monosaccharide composition, disaccharide composition, and oligosaccharide composition...
April 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28224912/high-throughput-screening-and-quantitation-of-guanidino-and-ureido-compounds-using-liquid-chromatography-drift-tube-ion-mobility-spectrometry-mass-spectrometry
#15
Ruo-Jing Fan, Fang Zhang, Xiu-Ping Chen, Wan-Shu Qi, Qing Guan, Tuan-Qi Sun, Yin-Long Guo
The present work focused on the high-throughput screening and quantitation of guanidino compounds (GCs) and ureido compounds (UCs) in human thyroid tissues. The strategy employed benzylic rearrangement stable isotope labeling (BRSIL) for the sample preparation and then detection using liquid chromatography-drift tube ion mobility spectrometry-quadrupole time of flight mass spectrometry (LC-DTIMS-QTOF MS). A short reversed-phase LC realized an on-line desalting and a measurement cycle of 5.0 min. DTIMS separation enhanced the better specificity and selectivity for the benzil labeled GCs and UCs...
April 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28224723/synthetic-extreme-environments-overlooked-sources-of-potential-biotechnologically-relevant-microorganisms
#16
Timothy Sibanda, Ramganesh Selvarajan, Memory Tekere
Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture- and molecular-based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp...
February 22, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28224688/liver-tissue-metabolic-profiling-and-pathways-of-nonalcoholic-steatohepatitis-in-rats
#17
Suwen Qi, Si Huang, Xin Chen, Qin Huo, Ni Xie, Jun Xia
AIM: The mechanisms of nonalcoholic steatohepatitis (NASH) in hepatocytes is unknown, and our aim is to study the tissue metabolic profiling and pathways of NASH. METHODS: We built rat models for simple steatosis and NASH and analyzed the liver extract using a liquid chromatograph-mass spectrometer (LC-MS). The acquired data were processed by multivariate principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) to obtain metabolic profiling...
February 22, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28224643/endophytic-phomopsis-sp-colonization-in-oryza-sativa-was-found-to-result-in-plant-growth-promotion-and-piperine-production
#18
Chithra S, Jasim B, Jyothis Mathew, Radhakrishnan E K
Endophytic fungi have been reported to have the acquired ability to synthesize host plant specific medicinal natural products. Many fungi with such properties have been characterized and optimized for the conditions which favor maximal production of desired products. However, the inherent plant colonization property of promising endophytic fungi is least studied. Exploiting the transgenome functioning of these fungi have immense applications to add beneficial features to non-host plants. In the present study, endophytic fungus Phomopsis sp...
February 22, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28224252/heat-shock-protein-70-in-lung-and-kidney-of-specific-pathogen-free-chickens-is-a-receptor-associated-protein-that-interacts-with-the-binding-domain-of-the-spike-protein-of-infectious-bronchitis-virus
#19
ZhiKun Zhang, Xin Yang, PengWei Xu, Xuan Wu, Long Zhou, HongNing Wang
Avian infectious bronchitis virus (IBV) is a member of the family Coronaviridae. A binding domain that mediates the attachment of the virus to its receptor has been identified in the S1 protein of prototype IBV strain M41. In this study, we identified this binding domain in a different strain, as well as the cellular proteins that interact with it. First, we expressed the S1N proteins (residues 19-270) of M41 and another isolate, SCZJ3, and compared the binding capacities of recombinant S1N-M41 and S1N-SCZJ3 to host tissues...
February 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28224249/signal-enhancement-in-the-hplc-esi-ms-ms-analysis-of-spironolactone-and-its-metabolites-using-hfip-and-nh4f-as-eluent-additives
#20
Kalev Takkis, Rudolf Aro, Lenne-Triin Kõrgvee, Heili Varendi, Jana Lass, Koit Herodes, Karin Kipper
This paper describes an LC-MS/MS method to determine the concentration of spironolactone and its metabolites 7-alpha-methylthiospironolactone and canrenone in blood plasma samples. The resulting assay is simple (using protein precipitation for sample preparation) and sensitive (the lower limit of quantification is close to 0.5 ng/ml) while requiring only 50 μl of plasma, making it especially suitable for analyzing samples obtained from pediatric and neonatal patients where sample sizes are limited. The sensitivity is achieved by using ammonium fluoride as an eluent additive, which in our case amplifies the signal from our analytes in the plasma solution on average about 70 times...
February 21, 2017: Analytical and Bioanalytical Chemistry
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