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Proteomics. Clinical Applications

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https://www.readbyqxmd.com/read/28371361/-identification-of-salivary-protein-biomarkers-for-orthodontically-induced-inflammatory-root-resorption
#1
Karolina Elżbieta Kaczor-Urbanowicz, Omer Deutsch, Batia Zaks, Guy Krief, Stella Chaushu, Aaron Palmon
INTRODUCTION: Orthodontically induced inflammatory root resorption (OIIRR) is one of the most prevalent and unavoidable consequence of orthodontic tooth movement. The aim of this study was to discover potential diagnostic protein biomarkers for detection of OIIRR in whole saliva (WS). METHODS AND MATERIAL: Unstimulated WS was collected from 72 subjects: 48 OIIRR patients and 24 untreated, generally healthy, age and gender matched controls. Radiographic assessment of periapical X-Rays of 4 upper incisors taken before and 9 months after bonding was done...
March 29, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28371297/the-differential-plasma-proteome-of-obese-and-overweight-individuals-undergoing-a-nutritional-weight-loss-and-maintenance-intervention
#2
Sergio Oller Moreno, Ornella Cominetti, Antonio Núñez Galindo, Irina Irincheeva, John Corthésy, Arne Astrup, Wim H M Saris, Jörg Hager, Martin Kussmann, Loïc Dayon
PURPOSE: The nutritional intervention program "DiOGenes" focuses on how obesity can be prevented and treated from a dietary perspective. We generated differential plasma proteome profiles in the DiOGenes cohort to identify proteins associated with weight loss and maintenance and explore their relation to body mass index, fat mass, insulin resistance and sensitivity. EXPERIMENTAL DESIGN: Relative protein quantification was obtained at baseline and after combined weight loss/maintenance phases using isobaric tagging and MS/MS...
March 29, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28371386/complementary-proteomic-approaches-reveal-mitochondrial-dysfunction-immune-and-inflammatory-dysregulation-in-a-mouse-model-of-gulf-war-illness
#3
Zuchra Zakirova, Jon Reed, Gogce Crynen, Lauren Horne, Samira Hassan, Venkatarajan Mathura, Michael Mullan, Fiona Crawford, Ghania Ait-Ghezala
PURPOSE: Long term consequences of combined pyridostigmine bromide and permethrin exposure in C57BL6/J mice using a well characterized mouse model of exposure to these Gulf War (GW) agents were explored at the protein level. EXPERIMENTAL DESIGN: We used orthogonal proteomic approaches to identify pathways that are chronically impacted in the mouse CNS due to semi-acute GW agent exposure early in life. These analyses were performed on soluble and membrane-bound protein fractions from brain samples using two orthogonal isotopic labeling LC-MS/MS proteomic approaches - stable isotope dimethyl labeling and isobaric tags for relative and absolute quantitation...
March 28, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28319654/an-alpha-synuclein-mrm-assay-with-diagnostic-potential-for-parkinson-s-disease-and-monitoring-disease-progression
#4
Li Yang, Tessandra Stewart, Min Shi, Gwenael Pottiez, Romel Dator, Rui Wu, Patrick Aro, Robert J Schuster, Carmen Ginghina, Catherine Pan, Yuqian Gao, Weijun Qian, Cyrus P Zabetian, Shu-Ching Hu, Joseph F Quinn, Jing Zhang
AIM: The alpha-synuclein (α-syn) level in human cerebrospinal fluid (CSF), as measured by immunoassays, is promising as a Parkinson's disease (PD) biomarker. However, the levels of total α-syn are inconsistent among studies with large cohorts and different measurement platforms. Total α-syn level also does not correlate with disease severity or progression. Here, we developed a highly sensitive Multiple Reaction Monitoring (MRM) method to measure absolute CSF α-syn peptide concentrations without prior enrichment or fractionation, aiming to discover new candidate biomarkers...
March 20, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28314077/comparative-subproteomic-analysis-of-clinically-acquired-fluoroquinolone-resistance-and-ciprofloxacin-stress-in-salmonella-typhimurium-dt104b
#5
Susana Correia, Michel Hébraud, Ingrid Chafsey, Christophe Chambon, Didier Viala, Yolanda Sáenz, José Luis Capelo, Patrícia Poeta, Gilberto Igrejas
PURPOSE: Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between a S...
March 17, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28296203/high-throughput-quantification-of-apolipoproteins-a-i-and-b-100-by-isotope-dilution-ms-targeting-fast-trypsin-releasable-peptides-without-reduction-and-alkylation
#6
Bryan A Parks, David M Schieltz, Michael L Andrews, Michael S Gardner, Jon C Rees, Christopher A Toth, Jeffrey I Jones, Lisa G McWilliams, Zsuzsanna Kuklenyik, James L Pirkle, John R Barr
PURPOSE: Apolipoprotein A-I (ApoA-I) and apolipoprotein B-100 (ApoB-100) are amphipathic proteins that are strong predictors of cardiovascular disease risk. The traceable calibration of apolipoprotein assays is a persistent challenge, especially for ApoB-100, which cannot be solubilized in purified form. EXPERIMENTAL DESIGN: A simultaneous quantitation method for ApoA-I and ApoB-100 was developed using tryptic digestion without predigestion reduction and alkylation, followed by LC separation coupled with isotope dilution MS analysis...
March 10, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28276159/comparative-proteome-analysis-of-wild-type-and-klotho-knockout-mouse-kidneys-using-a-combination-of-maldi-ims-and-lc-ms-ms
#7
Yoko Fujino, Tomoko Minamizaki, Ikue Hayashi, Asako Kawakami, Takaaki Miyaji, Kaoru Sakurai, Hirotaka Yoshioka, Katsuyuki Kozai, Mitsugi Okada, Yuji Yoshiko
PURPOSE: Mutation of the klotho gene in mice elicits a syndrome resembling accelerated human aging. However, there is limited evidence for the role of Klotho in the kidney. We conducted a comparative proteome analysis of wild-type (WT) and Klotho-knockout (kl(-/-) ) mouse kidneys to identify proteins involved in Klotho deficiency. EXPERIMENTAL DESIGN: MALDI-IMS of frozen kidney sections from 7-week-old male WT and kl(-/-) mice was used to determine genotype-specific differences in the MS distribution...
March 8, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28261998/use-of-a-targeted-urine-proteome-assay-tupa-to-identify-protein-biomarkers-of-delayed-recovery-after-kidney-transplant
#8
Kenneth R Williams, Christopher M Colangelo, Lin Hou, Lisa Chung, Justin M Belcher, Thomas Abbott, Isaac E Hall, Hongyu Zhao, Lloyd G Cantley, Chirag R Parikh
PURPOSE: Development of delayed graft function (DGF) following kidney transplant is associated with poor outcomes. An ability to rapidly identify patients with DGF versus those with immediate graft function (IGF) may facilitate the treatment of DGF and the research needed to improve prognosis. The purpose of this study was to use a Targeted Urine Proteome Assay to identify protein biomarkers of delayed recovery from kidney transplant. EXPERIMENTAL DESIGN: Potential biomarkers were identified using the Targeted Urine Proteome (MRM) Assay to interrogate the relative DGF/IGF levels of expression of 167 proteins in urine taken 12-18 h after kidney implantation from 21 DGF, 15 SGF (slow graft function), and 16 IGF patients...
March 6, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28261971/proteomics-a-new-perspective-for-the-understanding-of-pterygia
#9
Yi-Fan Feng, Fei Yuan
Pterygia is a common ocular surface disease bothering both the patient because of its unsightly appearance and the surgeon because of its tendency to recur. The pathogenesis of pterygia is complex and the exact mechanism(s), especially at the molecular level, remains unknown. The use of modern proteomic techniques such as isobaric tags for relative and absolute quantification (iTRAQ) may yield new knowledge on the underlying pathogenesis of pterygia. In this issue of Proteomics Clinical Applications, Linghu et al...
March 6, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28220636/identification-of-candidate-biomarkers-for-the-prediction-of-gestational-diabetes-mellitus-in-the-early-stages-of-pregnancy-using-itraq-quantitative-proteomics
#10
Danqing Zhao, Liming Shen, Yan Wei, Jiaming Xie, Shuqiang Chen, Yi Liang, Youjiao Chen, Haorong Wu
PURPOSE: Gestational diabetes mellitus (GDM) is one of the most common medical problems of pregnancy. This study is designed to identify serum biomarkers which can predict the subsequent development of GDM at early stages. EXPERIMENTAL DESIGN: Maternal blood was obtained prospectively from pregnant women at 12-16 weeks of pregnancy. Among these, 30 women were subsequently diagnosed with GDM at 24 to 28 weeks and were selected as case studies along with 30 normoglycemic women as controls...
February 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28198151/comparative-proteomic-analysis-of-the-influence-of-gender-and-acid-stimulation-on-normal-human-saliva-using-lc-ms-ms
#11
Xiaoping Xiao, Yaoran Liu, Zhengguang Guo, Xiaoyan Liu, Haidan Sun, Qian Li, Wei Sun
Human saliva is an important source for disease biomarker discovery. In this work, we investigate the influence of gender and acid stimulation on the normal human salivary proteome. Un-stimulated and acid-stimulated saliva samples from 5 males and 5 females were labeled with 4-plex iTRAQ and analyzed by 2-DLC MS/MS. A total of 1,770 proteins were identified, and 82 proteins in un-stimulated saliva were found to be gender-specific. These proteins were mainly associated with immune function, metabolism and inflammation...
February 15, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28195677/plasma-prefractionation-methods-for-proteomic-analysis-and-perspectives-in-clinical-applications
#12
Somchai Chutipongtanate, Supawat Chatchen, Jisnuson Svasti
Plasma is a rich source of biomarkers with clinical relevance. However, the wide dynamic range of protein concentration hinders the detection of low abundance proteins. Plasma prefractionation methods serve as indispensable tools to reduce plasma complexity, allowing the opportunity to explore tissue-derived proteins which leak into the circulation. This review summarizes common approaches in plasma prefractionation methods for proteomic analysis and then discusses some considerations in plasma prefractionation for clinical applications, reviewing some examples of its use in clinical situations...
February 14, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28176468/correlation-of-pre-operative-plasma-protein-concentrations-in-cardiac-surgery-patients-with-bleeding-outcomes-using-a-targeted-quantitative-proteomics-approach
#13
Nathan Clendenen, Ashley Tollefson, Monika Dzieciatkowska, Alice Cambiaghi, Manuela Ferrario, Miranda Kroehl, Anirban Banerjee, Angelo D'Alessandro, Kirk C Hansen, Nathaen Weitzel
PURPOSE: Despite recent advancements in the use of thrombelastography (TEG) in the surgical setting, adequate technology to accurately predict bleeding phenotypes for patients undergoing cardiopulmonary bypass on the basis of non-mechanical parameters is lacking. While basic science and translational studies have provided key mechanistic insights about the protein components of coagulation cascades and regulatory mediators of hemostasis and fibrinolysis, targeted protein assays are still missing and the association of protein profiles to bleeding phenotypes and TEG readouts have yet to be discovered...
February 8, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28164444/proteomic-analysis-of-cell-cycle-arrest-and-differentiation-induction-caused-by-atpr-a-derivative-of-all-trans-retinoic-acid-in-human-gastric-cancer-sgc-7901-cells
#14
Quan Xia, Yingli Zhao, Jiali Wang, Wenhao Qiao, Dongling Zhang, Hao Yin, Dujuan Xu, Feihu Chen
PURPOSE: 4-amino-2-trifluoromethyl-phenyl retinate (ATPR) was reported to potentially inhibit proliferation and induce differentiation activity in some tumor cells. In this study, a proteomics approach was used to investigate the possible mechanism by screening the differentially expressed protein profiles of SGC-7901 cells before and after ATPR-treatment in vitro. EXPERIMENTAL DESIGN: Peptides digested from the total cellular proteins were analyzed by reverse phase LC-MS/MS followed by a label-free quantification analysis...
February 6, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28155252/the-meta-analytical-paradigm-in-an-in-silico-hybrid-pathways-and-networks-perturbed-during-exposure-to-varying-degrees-of-hypobaric-hypoxia
#15
Subhojit Paul, Kalpana Bhargava, Yasmin Ahmad
PURPOSE: Computational biology has opened a gateway to omics data analysis and shifted the focus from molecules to systemic molecular networks in the domain of hypobaric hypoxia (HH). Yet there are no meta-analytical investigations circum-venting constraints like organism (rat/human), HH exposure conditions (acute/chronic) and the tissues that can be investigated simultaneously in the realm of wet-lab experiments. EXPERIMENTAL DESIGN: We analyzed 154 DE proteins upon HH exposure using IPA tool, without the constraint of using a single organism or tissue type, to determine the most significant pathways and networks that are perturbed across a range of HH conditions RESULTS: : We found Acute phase Response Signaling, FXR/RXR Activation, LXR/RXR Activation, Clathrin-mediated endocytosis signaling, Mitochondrial Dysfunction, Production of Nitric Oxide & ROS in Macrophages and Integrin Signaling to be the most significant universally perturbed pathways...
February 2, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28112871/quantification-by-nano-liquid-chromatography-parallel-reaction-monitoring-mass-spectrometry-of-human-apolipoprotein-a-i-apolipoprotein-b-and-hemoglobin-a1c-in-dried-blood-spots
#16
Clark M Henderson, James G Bollinger, Jessica O Becker, Jennifer M Wallace, Thomas J Laha, Michael J MacCoss, Andrew N Hoofnagle
PURPOSE: Proteomic analysis of blood proteins in DBS is gaining attention as a possible replacement for measurements in plasma/serum collected by venipuncture. We aimed to develop and provisionally validate a nanoflow LC-PRM-MS method for clinical use. EXPERIMENTAL DESIGN: We used Skyline to develop a nanoflow LC-PRM-MS method to quantify glycated hemoglobin-β, apolipoprotein A-I, and apolipoprotein B in DBS. Precision, linearity, interferences, and stability and were determined and the method was used to analyze samples from 36 human volunteers...
January 23, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28087900/itraq-based-quantitative-proteomic-analysis-and-bioinformatics-study-of-proteins-in-pterygia
#17
Dandan Linghu, Lili Guo, Yinghua Zhao, Zhiming Liu, Mingwei Zhao, Lvzhen Huang, Xiaoxin Li
PURPOSE: To analysis proteins in the tissue of pterygia, and to investigate their potential roles in pterygia, using the comparative proteomic technique of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) coupled with offline 2DLC-MS/MS, Western-bolt. METHOD: The tissues of pterygia and healthy conjunctiva were collected from 10 pterygia patients (6 females, 4 males; average age was 52 years old; average course of disease was 6 years) in our hospital from September, 2015 to March, 2016...
January 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28084002/identification-of-potential-protein-quality-markers-in-pathogen-inactivated-and-gamma-irradiated-red-cell-concentrates
#18
Deborah Chen, Peter Schubert, Dana V Devine
PURPOSE: Post-collection manipulations (PCMs) aim to increase blood product safety. However, PCMs improve safety at a cost to quality, causing elevated hemolysis. As hemolysis is linked to red blood cell (RBC) membrane integrity, a quantitative proteomics approach was employed to assess membrane proteome alterations induced by PCMs. EXPERIMENTAL DESIGN: Three ABO-matched whole blood (WB) units were pooled-and-split into three identical units. One WB unit was treated with riboflavin/ultraviolet illumination prior to red cell concentrate (RCC) production (RCC(WB*) )...
January 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28083997/dysregulation-of-cell-cell-interactions-in-brain-arteriovenous-malformations-a-quantitative-proteomic-study
#19
Xia Wang, Qiang Hao, Yuanli Zhao, Yi Guo, Wei Ge
PURPOSE: Detailed and exact mechanisms underlying brain arteriovenous malformations (bAVM) are still clinically confusing. Understanding the quantitative changes in proteins and signaling pathways would provide useful information for clinicians to understand the formation and development of bAVM, guiding individualized treatment strategies. This study was performed to establish a large human bAVM proteome database using tandem mass tag (TMT)-labeling and to detect changes of protein expression and pathways in human bAVM...
January 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28066995/molecular-galactose-galectin-association-in-neuroblastoma-cells-an-unconventional-tool-for-qualitative-quantitative-screening
#20
Fabio Pastorino, Mirco Ponzoni, Giuseppina Simone
Galectin decorates the cell membrane and forms an extracellular molecular association with galactoside units. Here, galactoside probes have been used to study galectin expression in neuroblastoma cells. The hypothesis behind this investigation has been that the molecular mechanisms by which glycans modulate neural metastatic cells involve a protein-carbohydrate association, galectin-galactose. Preliminary screening to validate the hypothesis has been performed with galactose moieties anchored to beads. The molecular association has been studied by FACS...
January 9, 2017: Proteomics. Clinical Applications
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