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urine proteomics

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https://www.readbyqxmd.com/read/28717416/feasibility-of-urinary-extracellular-vesicle-proteome-profiling-using-a-robust-and-simple-clinically-applicable-isolation-method
#1
Irene V Bijnsdorp, Olga Maxouri, Aarzo Kardar, Tim Schelfhorst, Sander R Piersma, Thang V Pham, Andre Vis, R Jeroen van Moorselaar, Connie R Jimenez
Extracellular vesicles (EVs) secreted by prostate cancer (PCa) cells contain specific biomarkers and can be isolated from urine. Collection of urine is not invasive, and therefore urinary EVs represent a liquid biopsy for diagnostic and prognostic testing for PCa. In this study, we optimised urinary EV isolation using a method based on heat shock proteins and compared it to gold-standard ultracentrifugation. The urinary EV isolation protocol using the Vn96-peptide is easier, time convenient (≈1.5 h) and no special equipment is needed, in contrast to ultracentrifugation protocol (>3...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28711247/ratio-of-dietary-rumen-degradable-protein-to-rumen-undegradable-protein-affects-nitrogen-partitioning-but-does-not-affect-the-bovine-milk-proteome-produced-by-mid-lactation-holstein-dairy-cows
#2
R Tacoma, J Fields, D B Ebenstein, Y-W Lam, S L Greenwood
Little is known about the bovine milk proteome or whether it can be affected by diet. The objective of this study was to determine if the dietary rumen degradable protein (RDP):rumen undegradable protein (RUP) ratio could alter the bovine milk proteome. Six Holstein cows (parity: 2.5 ± 0.8) in mid lactation were blocked by days in milk (80 ± 43 d in milk) and milk yield (57.5 ± 6.0 kg) and randomly assigned to treatment groups. The experiment was conducted as a double-crossover design consisting of three 21-d periods...
July 12, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28681595/assessment-of-the-therapeutic-potential-of-persimmon-leaf-extract-on-prediabetic-subjects
#3
Mohd M Khan, Bao Quoc Tran, Yoon-Jin Jang, Soo-Hyun Park, William E Fondrie, Khadiza Chowdhury, Sung Hwan Yoon, David R Goodlett, Soo-Wan Chae, Han-Jung Chae, Seung-Young Seo, Young Ah Goo
Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health...
July 6, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28674889/proteomics-analysis-of-circulating-serum-exosomes
#4
Antonius Koller, Purvi Patel, Jenny Kim Kim, Emily I Chen
Proteomics characterization of biofluids, such as urine and plasma, has been explored for the discovery of predictive, prognostic, and mechanistic biomarkers of diseases and tissue injury. Here we describe comprehensive characterization of protein cargos from cell-derived secreted vesicles (extracellular vesicles or exosome) for biomarker discovery using the mass spectrometry-based technology.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28669814/quick-96fasp-for-high-throughput-quantitative-proteome-analysis
#5
Yanbao Yu, Shiferaw Bekele, Rembert Pieper
Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter...
June 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28665768/identification-of-a-sensitive-urinary-biomarker-selenium-binding-protein-1-for-early-detection-of-acute-kidney-injury
#6
Kyeong Seok Kim, Hun Yong Yang, Hosup Song, Ye Rim Kang, JiHoon Kwon, JiHye An, Ji Yeon Son, Seung Jun Kwack, Young-Mi Kim, Ok-Nam Bae, Mee-Young Ahn, Jaewon Lee, Sungpil Yoon, Byung Mu Lee, Hyung Sik Kim
Acute kidney injury (AKI) is associated with increased mortality rate in patients but clinically available biomarkers for disease detection are currently not available. Recently, a new biomarker, selenium-binding protein 1 (SBP1), was identified for detection of nephrotoxicity using proteomic analysis. The aim of this study was to assess the sensitivity of urinary SBP1 levels as an early detection of AKI using animal models such as cisplatin or ischemia/reperfusion (I/R). Sprague-Dawley rats were injected with cisplatin (6 mg/kg, once i...
June 30, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28635333/molecular-biomarkers-to-guide-precision-medicine-in-localized-prostate-cancer
#7
Minke Smits, Niven Mehra, Michiel Sedelaar, Winald Gerritsen, Jack A Schalken
Major advances through tumor profiling technologies, that include next-generation sequencing, epigenetic, proteomic and transcriptomic methods, have been made in primary prostate cancer, providing novel biomarkers that may guide precision medicine in the near future. Areas covered: The authors provided an overview of novel molecular biomarkers in tissue, blood and urine that may be used as clinical tools to assess prognosis, improve selection criteria for active surveillance programs, and detect disease relapse early in localized prostate cancer...
August 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28631898/mass-spectrometry-based-protein-analytics-to-unravel-the-tissue-pathophysiology-in-duchenne-muscular-dystrophy
#8
Stephanie J Carr, René P Zahedi, Hanns Lochmüller, Andreas Roos
Duchenne muscular dystrophy (DMD) is a genetic muscle wasting condition with limited treatment options available and is caused by the lack of Dystrophin. However, pathophysiology of different tissues is variable showing different histological and molecular signatures. Recently, a number of studies have employed gel-free proteomic approaches to unveil the molecular pathophysiology in terms of tissue-specific proteome changes in dystrophin-deficiency. We analysed studies in models of dystrophin-deficiency and patients both from the published literature...
June 20, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28618237/effect-of-sweetened-dried-cranberry-consumption-on-urinary-proteome-and-fecal-microbiome-in-healthy-human-subjects
#9
Nell Bekiares, Christian G Krueger, Jennifer J Meudt, Dhanansayan Shanmuganayagam, Jess D Reed
The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28596590/a-comprehensive-analysis-and-annotation-of-human-normal-urinary-proteome
#10
Mindi Zhao, Menglin Li, Yehong Yang, Zhengguang Guo, Ying Sun, Chen Shao, Mingxi Li, Wei Sun, Youhe Gao
Biomarkers are measurable changes associated with the disease. Urine can reflect the changes of the body while blood is under control of the homeostatic mechanisms; thus, urine is considered an important source for early and sensitive disease biomarker discovery. A comprehensive profile of the urinary proteome will provide a basic understanding of urinary proteins. In this paper, we present an in-depth analysis of the urinary proteome based on different separation strategies, including direct one dimensional liquid chromatography-tandem mass spectrometry (LC/MS/MS), two dimensional LC/MS/MS, and gel-eluted liquid fraction entrapment electrophoresis/liquid-phase isoelectric focusing followed by two dimensional LC/MS/MS...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28595723/stable-isotope-n-phosphoryl-amino-acids-labeling-for-quantitative-profiling-of-amine-containing-metabolites-using-liquid-chromatography-mass-spectrometry
#11
Shanshan Zhang, Jinwen Shi, Changkai Shan, Chengting Huang, Yile Wu, Rong Ding, Yuhua Xue, Wen Liu, Qiang Zhou, Yufen Zhao, Pengxiang Xu, Xiang Gao
Stable isotope chemical labeling liquid chromatography-mass spectrometry (LC-MS) is a powerful strategy for comprehensive metabolomics profiling, which can improve metabolites coverage and quantitative information for exploration of metabolic regulation in complex biological systems. In the current work, a novel stable isotope N-phosphoryl amino acids labeling strategy (SIPAL) has been successful developed for quantitative profiling of amine-containing metabolites in urine based on organic phosphorus chemistry...
July 25, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28592876/elongation-factor-tu-on-escherichia-coli-isolated-from-urine-of-kidney-stone-patients-promotes-calcium-oxalate-crystal-growth-and-aggregation
#12
Piyawan Amimanan, Ratree Tavichakorntrakool, Kedsarin Fong-Ngern, Pipat Sribenjalux, Aroonlug Lulitanond, Vitoon Prasongwatana, Chaisiri Wongkham, Patcharee Boonsiri, Jariya Umka Welbat, Visith Thongboonkerd
Escherichia coli is the most common bacterium isolated from urine and stone matrix of calcium oxalate (CaOx) stone formers. Whether it has pathogenic role(s) in kidney stone formation or is only entrapped inside the stone remains unclear. We thus evaluated differences between E. coli isolated from urine of patients with kidney stone (EUK) and that from patients with urinary tract infection (UTI) without stone (EUU). From 100 stone formers and 200 UTI patients, only four pairs of EUK/EUU isolates had identical antimicrobial susceptibility patterns...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28585182/lime-powder-treatment-reduces-urinary-excretion-of-total-protein-and-transferrin-but-increases-uromodulin-excretion-in-patients-with-urolithiasis
#13
Piyaratana Tosukhowong, Pimsuda Kulpradit, Sakdithep Chaiyarit, Wattanachai Ungjareonwattana, Nuttiya Kalpongnukul, Supoj Ratchanon, Visith Thongboonkerd
Our previous study has shown that lime powder (LP) had an inhibitory effect against calcium oxalate stone formation. However, the precise mechanisms underlying such beneficial effect remained unclear. Our present study thus aimed to address the effect of LP on excretory level and compositions of urinary proteins using a proteomics approach. From a total of 80 calcium oxalate stone formers recruited into our 2-year randomized clinical trial of LP effect, 10 patients with comparable age and clinical parameters were selected for this proteomic study...
June 5, 2017: Urolithiasis
https://www.readbyqxmd.com/read/28560103/effects-of-arginine-vasopressin-on-the-urine-proteome-in-rats
#14
Manxia An, Yanying Ni, Xundou Li, Youhe Gao
Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats' urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett's T3 test...
2017: PeerJ
https://www.readbyqxmd.com/read/28522940/potential-urine-proteomics-biomarkers-for-primary-nephrotic-syndrome
#15
Young Wook Choi, Yang Gyun Kim, Min-Young Song, Ju-Young Moon, Kyung-Hwan Jeong, Tae-Won Lee, Chun-Gyoo Ihm, Kang-Sik Park, Sang-Ho Lee
BACKGROUND: Nephrotic syndrome (NS) is a nonspecific kidney disorder, commonly caused by minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), and membranous nephropathy (MN). Here we analyzed urinary protein profiles, aiming to discover disease-specific biomarkers of these three common diseases in NS. METHODS: Sixteen urine samples were collected from patients with biopsy-proven NS and healthy controls. After removal of high-abundance proteins, the urinary protein profile was analyzed by LC-MS/MS to generate a discovery set...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28522341/systemic-and-ocular-fluid-compounds-as-potential-biomarkers-in-age-related-macular-degeneration
#16
REVIEW
Eveline Kersten, Constantin C Paun, Rosa L Schellevis, Carel B Hoyng, Cécile Delcourt, Imre Lengyel, Tunde Peto, Marius Ueffing, Caroline C W Klaver, Sascha Dammeier, Anneke I den Hollander, Eiko K de Jong
Biomarkers can help unravel mechanisms of disease and identify new targets for therapy. They can also be useful in clinical practice for monitoring disease progression, evaluation of treatment efficacy and risk assessment in multifactorial diseases, such as age-related macular degeneration (AMD). AMD is a highly prevalent progressive retinal disorder for which multiple genetic and environmental risk factors have been described, but the exact etiology is not yet fully understood. Many compounds have been evaluated for their association with AMD...
May 15, 2017: Survey of Ophthalmology
https://www.readbyqxmd.com/read/28505128/a-proposal-for-a-study-on-treatment-selection-and-lifestyle-recommendations-in-chronic-inflammatory-diseases-a-danish-multidisciplinary-collaboration-on-prognostic-factors-and-personalised-medicine
#17
Vibeke Andersen, Uffe Holmskov, Signe Bek Sørensen, Mohamad Jawhara, Karina W Andersen, Anette Bygum, Lone Hvid, Jakob Grauslund, Jimmi Wied, Henning Glerup, Ulrich Fredberg, Jan Alexander Villadsen, Søren Geill Kjær, Jan Fallingborg, Seyed A G R Moghadd, Torben Knudsen, Jacob Brodersen, Jesper Frøjk, Jens F Dahlerup, Ole Haagen Nielsen, Robin Christensen, Anders Bo Bojesen, Grith Lykke Sorensen, Steffen Thiel, Nils J Færgeman, Ivan Brandslund, Allan Stensballe, Erik Berg Schmidt, Andre Franke, David Ellinghaus, Philip Rosenstiel, Jeroen Raes, Berit Heitmann, Mette Boye, Charlotte Lindgaard Nielsen, Lars Werner, Jens Kjeldsen, Torkell Ellingsen
Chronic inflammatory diseases (CIDs), including Crohn's disease and ulcerative colitis (inflammatory bowel diseases, IBD), rheumatoid arthritis, psoriasis, psoriatic arthritis, spondyloarthritides, hidradenitis suppurativa, and immune-mediated uveitis, are treated with biologics targeting the pro-inflammatory molecule tumour necrosis factor-α (TNF) (i.e., TNF inhibitors). Approximately one-third of the patients do not respond to the treatment. Genetics and lifestyle may affect the treatment results. The aims of this multidisciplinary collaboration are to identify (1) molecular signatures of prognostic value to help tailor treatment decisions to an individual likely to initiate TNF inhibitor therapy, followed by (2) lifestyle factors that support achievement of optimised treatment outcome...
May 15, 2017: Nutrients
https://www.readbyqxmd.com/read/28501217/edta-functionalized-magnetic-nanoparticles-a-suitable-platform-for-the-analysis-of-low-abundance-urinary-proteins
#18
Paulo Bastos, Fábio Trindade, Rita Ferreira, Adelino Leite-Moreira, Inês Falcão-Pires, Bruno Manadas, Ana L Daniel-da-Silva, Rui Vitorino
Urine is a highly attractive source of biological information and disease biomarkers, whose proteome characterization is ongoing. To that end, depletion/enrichment strategies for protein analysis can be of great convenience. We have thus developed a method based on the use of EDTA-functionalized magnetic nanoparticles (NPs@EDTA), to fractionate urine samples before liquid chromatography-mass spectrometry analysis and compared the identified proteins with those obtained from ultrafiltrated/unfractionated (UF) urine samples...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28469965/eight-plex-itraq-labeling-and-quantitative-proteomic-analysis-for-human-bladder-cancer
#19
Qimin Zhang, Shengsong Huang, Huarong Luo, Xin Zhao, Gang Wu, Denglong Wu
Bladder cancer is one of the most prevalent cancers worldwide, and increasing research has focused on new technologies for early detection of bladder cancer. For example, proteomic techniques for biomarker discovery have been implemented for the detection and analysis of protein changes in the tissues, blood, and urine from bladder cancer patients. In this present study, we evaluated the effectiveness of the eight-plex iTRAQ labeling and quantitative proteomic approaches for differentially analyzing proteins found in normal and bladder cancer tissues from individual patients...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28444712/the-urinary-microbiome-and-its-contribution-to-lower-urinary-tract-symptoms-ici-rs-2015
#20
REVIEW
Marcus J Drake, Nicola Morris, Apostolos Apostolidis, Mohammad S Rahnama'i, Julian R Marchesi
AIMS: The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. METHODS: The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities...
April 2017: Neurourology and Urodynamics
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