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https://www.readbyqxmd.com/read/28646744/systematic-biobanking-novel-imaging-techniques-and-advanced-molecular-analysis-for-precise-tumor-diagnosis-and-therapy-the-polish-mobit-project
#1
Jacek Niklinski, Adam Kretowski, Marcin Moniuszko, Joanna Reszec, Anna Michalska-Falkowska, Magdalena Niemira, Michal Ciborowski, Radoslaw Charkiewicz, Dorota Jurgilewicz, Miroslaw Kozlowski, Rodryg Ramlau, Cezary Piwkowski, Miroslaw Kwasniewski, Monika Kaczmarek, Andrzej Ciereszko, Tomasz Wasniewski, Robert Mroz, Wojciech Naumnik, Ewa Sierko, Magdalena Paczkowska, Joanna Kisluk, Anetta Sulewska, Adam Cybulski, Zenon Mariak, Boguslaw Kedra, Jacek Szamatowicz, Paweł Kurzawa, Lukasz Minarowski, Angelika Edyta Charkiewicz, Barbara Mroczko, Jolanta Malyszko, Christian Manegold, Lothar Pilz, Heike Allgayer, Mohammed L Abba, Hartmut Juhl, Frauke Koch
Personalized and precision medicine is gaining recognition due to the limitations by standard diagnosis and treatment; many areas of medicine, from cancer to psychiatry, are moving towards tailored and individualized treatment for patients based on their clinical characteristics and genetic signatures as well as novel imaging techniques. Advances in whole genome sequencing have led to identification of genes involved in a variety of diseases. Moreover, biomarkers indicating severity of disease or susceptibility to treatment are increasingly being characterized...
June 21, 2017: Advances in Medical Sciences
https://www.readbyqxmd.com/read/28646358/metabolomics-of-diabetes-in-pregnancy
#2
REVIEW
Carolyn F McCabe, Wei Perng
PURPOSE OF REVIEW: The purpose of this review is to describe ways in which metabolomics may enhance understanding of gestational diabetes mellitus (GDM) etiology and refine current diagnostic criteria. RECENT FINDINGS: Current clinical recommendations suggest screening for GDM between 24 and 28 of gestational weeks using an oral glucose tolerance test. Despite this consensus, there are discrepancies regarding the exact criteria for GDM diagnosis. Further, emerging evidence has unveiled heterogeneous physiological pathways underlying GDM-specifically, GDM with defective insulin secretion vs...
August 2017: Current Diabetes Reports
https://www.readbyqxmd.com/read/28646338/chemotherapy-induced-gastrointestinal-toxicity-is-associated-with-changes-in-serum-and-urine-metabolome-and-fecal-microbiota-in-male-sprague-dawley-rats
#3
Richard A Forsgård, Vannina G Marrachelli, Katri Korpela, Rafael Frias, Maria Carmen Collado, Riitta Korpela, Daniel Monleon, Thomas Spillmann, Pia Österlund
PURPOSE: Chemotherapy-induced gastrointestinal toxicity (CIGT) is a complex process that involves multiple pathophysiological mechanisms. We have previously shown that commonly used chemotherapeutics 5-fluorouracil, oxaliplatin, and irinotecan damage the intestinal mucosa and increase intestinal permeability to iohexol. We hypothesized that CIGT is associated with alterations in fecal microbiota and metabolome. Our aim was to characterize these changes and examine how they relate to the severity of CIGT...
June 23, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28646024/metabolic-reprogramming-via-ppar%C3%AE-signaling-in-cardiac-hypertrophy-and-failure-from-metabolomics-to-epigenetics
#4
Junco Shibayama Warren, Shin-Ichi Oka, Daniela Zablocki, Junichi Sadoshima
Studies using -omics-based approaches have advanced our knowledge of metabolic remodeling in cardiac hypertrophy and failure. Metabolomic analysis of the failing heart has revealed global changes in mitochondrial substrate metabolism. Peroxisome proliferator-activated receptor alpha (PPARα) plays a critical role in synergistic regulation of cardiac metabolism through transcriptional control. Metabolic reprogramming via PPARα signaling in heart failure ultimately propagates into myocardial energetics. However, emerging evidence suggests that the expression level of PPARα per se does not always explain the energetic state in the heart...
June 23, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28646020/mcam-mediates-chemoresistance-in-small-cell-lung-cancer-via-the-pi3k-akt-sox2-signaling-pathway
#5
Satyendra C Tripathi, Johannes F Fahrmann, Muge Celiktas, Mitzi Aguilar, Kieren D Marini, Mohit Kumar Jolly, Hiroyuki Katayama, Hong Wang, Eunice N Murage, Jennifer B Dennison, D Neil Watkins, Herbert Levine, Edwin J Ostrin, Ayumu Taguchi, Samir M Hanash
Despite favorable responses to initial therapy, small cell lung cancer (SCLC) relapse occurs within a year and exhibits resistance to multiple drugs. Due to limited accessibility of patient tissues for research purposes, SCLC-patient derived xenografts (PDX) have provided the best opportunity to address this limitation. Here we sought to identify novel mechanisms involved in SCLC chemoresistance. Through in-depth proteomic profiling, we identified MCAM as a markedly upregulated surface receptor in chemoresistant SCLC cell lines and in chemoresistant PDX compared to matched treatment-naïve tumors...
June 23, 2017: Cancer Research
https://www.readbyqxmd.com/read/28645790/vitamin-e-deficiency-during-embryogenesis-in-zebrafish-causes-lasting-metabolic-and-cognitive-impairments-despite-refeeding-adequate-diets
#6
Melissa McDougall, Jaewoo Choi, Lisa Truong, Robert Tanguay, Maret G Traber
Vitamin E (α-tocopherol; VitE) is a lipophilic antioxidant required for normal embryonic development in vertebrates, but the long-term effects of embryonic VitE deficiency, and whether they are ameliorated by feeding VitE-adequate diets, remain unknown. We addressed these questions using a zebrafish (Danio rerio) model of developmental VitE deficiency followed by dietary remediation. Adult zebrafish maintained on VitE-deficient (E-) or sufficient (E+) diets were spawned to obtained E- and E+ embryos, respectively, which we evaluated up to 12 days post-fertilization (dpf)...
June 20, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28645211/akr1c3-mediated-adipose-androgen-generation-drives-lipotoxicity-in-women-with-polycystic-ovary-syndrome
#7
Michael W O'Reilly, Punith Kempegowda, Mark Walsh, Angela E Taylor, Konstantinos N Manolopoulos, J William Allwood, Robert K Semple, Daniel Hebenstreit, Warwick B Dunn, Jeremy W Tomlinson, Wiebke Arlt
Context: Polycystic ovary syndrome (PCOS) is a prevalent metabolic disorder, occurring in up to 10% of women of reproductive age. PCOS is associated with insulin resistance and cardiovascular risk. Androgen excess is a defining feature of PCOS and has been suggested as causally associated with insulin resistance; however, mechanistic evidence linking both is lacking. We hypothesized that adipose tissue is an important site linking androgen activation and metabolic dysfunction in PCOS...
June 22, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#8
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28644610/mzmine-2-data-preprocessing-to-enhance-molecular-networking-reliability
#9
Florent Olivon, Gwendal Grelier, Fanny Roussi, Marc Litaudon, David Touboul
Molecular networking is becoming more and more popular into the metabolomic community to organize tandem mass spectrometry (MS2) data. Even though this approach allows the treatment and comparison of large data sets, several drawbacks related to the MS-Cluster tool routinely used on the Global Natural Product Social Molecular Networking platform (GNPS) limit its potential. MS-Cluster cannot distinguish between chromatography well-resolved isomers as retention times are not taken into account. Annotation with predicted chemical formulas is also not implemented and semi-quantification is only based on the number of MS2 scans...
June 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28644019/metabolomics-analysis-to-evaluate-the-anti-inflammatory-effects-of-polyphenols-glabridin-reversed-metabolism-change-caused-by-lps-in-raw-264-7-cells
#10
Kaiqin Liu, FuWei Pi, Hongxia Zhang, Jian Ji, Shuang Xia, Fangchao Cui, Jiadi Sun, Xiulan Sun
Inflammation has been shown to play a critical role in the development of many diseases. In this study, we used metabolomics to evaluate the inflammatory effect of lipopolysaccharide (LPS) and anti-inflammatory effect of glabridin (GB, a polyphenol from Glycurrhiza glabra L. roots) in RAW 264.7 cells. Multivariate statistical analysis showed that compared with the LPS group, the metabolic profile of the GB group was more similar to that of the control group. LPS impacted the amino acid, energy and lipid metabolisms in RAW 264...
June 23, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28643618/heat-stabilised-rice-bran-consumption-by-colorectal-cancer-survivors-modulates-stool-metabolite-profiles-and-metabolic-networks-a-randomised-controlled-trial
#11
Dustin G Brown, Erica C Borresen, Regina J Brown, Elizabeth P Ryan
Rice bran (RB) consumption has been shown to reduce colorectal cancer (CRC) growth in mice and modify the human stool microbiome. Changes in host and microbial metabolism induced by RB consumption was hypothesised to modulate the stool metabolite profile in favour of promoting gut health and inhibiting CRC growth. The objective was to integrate gut microbial metabolite profiles and identify metabolic pathway networks for CRC chemoprevention using non-targeted metabolomics. In all, nineteen CRC survivors participated in a parallel randomised controlled dietary intervention trial that included daily consumption of study-provided foods with heat-stabilised RB (30 g/d) or no additional ingredient (control)...
May 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28643516/untargeted-comprehensive-two-dimensional-liquid-chromatography-coupled-with-high-resolution-mass-spectrometry-analysis-of-rice-metabolome-using-multivariate-curve-resolution
#12
Meritxell Navarro-Reig, Joaquim Jaumot, Anna Baglai, Gabriel Vivó-Truyols, Peter J Schoenmakers, Romà Tauler
In this work, a new strategy for the chemometric analysis of LC×LC-HRMS data is proposed. This approach consists of a preliminary compression step along the MS spectral dimension based on the selection of the Regions of Interest (ROI), followed by a further data compression along the chromatographic dimension by wavelet transforms. In a secondary step, the Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) method is applied to previously compressed data sets obtained in the simultaneous analysis of multiple LC×LC-HRMS chromatographic runs from multiple samples...
June 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28643099/-beyond-antibiotic-therapy-future-antiinfective-strategies-update-2017
#13
REVIEW
D Vogt, S Sperling, T Tkhilaishvili, A Trampuz, J-P Pirnay, C Willy
BACKGROUND: The key elements in the therapy of surgical site infections (SSI) are surgical debridement and local and systemic antibiotic therapy; however, due to increasing antibiotic resistance, the development of additional therapeutic measures is of great interest for future trauma and orthopedic surgery. METHOD: Against the background of our own experimental and clinical experiences and on the basis of the current literature, possible future anti-infective strategies were elaborated...
June 22, 2017: Der Unfallchirurg
https://www.readbyqxmd.com/read/28642837/environmental-influences-in-the-etiology-of-colorectal-cancer-the-premise-of-metabolomics
#14
Nicholas J W Rattray, Georgia Charkoftaki, Zahra Rattray, James E Hansen, Vasilis Vasiliou, Caroline H Johnson
PURPOSE OF REVIEW: In this review we discuss how environmental exposures predominate the etiology of colorectal cancer (CRC). With CRC being a personalized disease influenced by genes and environment, our goal was to explore the role metabolomics can play in identifying exposures, assessing the interplay between co-exposures, and the development of personalized therapeutic interventions. RECENT FINDINGS: Approximately 10 % of CRC cases can be explained by germ-line mutations, whereas the prevailing majority are caused by an initiating exposure event occurring decades prior to diagnosis...
June 2017: Current Pharmacology Reports
https://www.readbyqxmd.com/read/28642462/metabolic-changes-in-medaka-fish-induced-by-cyanobacterial-exposures-in-mesocosms-an-integrative-approach-combining-proteomic-and-metabolomic-analyses
#15
Benoît Sotton, Alain Paris, Séverine Le Manach, Alain Blond, Gérard Lacroix, Alexis Millot, Charlotte Duval, Hélène Huet, Qin Qiao, Sophie Labrut, Giovanni Chiapetta, Joelle Vinh, Arnaud Catherine, Benjamin Marie
Cyanobacterial blooms pose serious threats to aquatic organisms and strongly impact the functioning of aquatic ecosystems. Due to their ability to produce a wide range of potentially bioactive secondary metabolites, so called cyanotoxins, cyanobacteria have been extensively studied in the past decades. Proteomic and metabolomic analyses provide a unique opportunity to evaluate the global response of hundreds of proteins and metabolites at a glance. In this study, we provide the first combined utilization of these methods targeted to identify the response of fish to bloom-forming cyanobacteria...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642310/metabolomics-analysis-identifies-sex-associated-metabotypes-of-oxidative-stress-and-the-autotaxin-lysopa-axis-in%C3%A2-copd
#16
Shama Naz, Johan Kolmert, Mingxing Yang, Stacey N Reinke, Muhammad Anas Kamleh, Stuart Snowden, Tina Heyder, Bettina Levänen, David J Erle, C Magnus Sköld, Åsa M Wheelock, Craig E Wheelock
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease and a leading cause of mortality and morbidity worldwide. The aim of this study was to investigate the sex dependency of circulating metabolic profiles in COPD.Serum from healthy never-smokers (healthy), smokers with normal lung function (smokers), and smokers with COPD (COPD; Global Initiative for Chronic Obstructive Lung Disease stages I-II/A-B) from the Karolinska COSMIC cohort (n=116) was analysed using our nontargeted liquid chromatography-high resolution mass spectrometry metabolomics platform...
June 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28642031/clustering-of-ms-2-spectra-using-unsupervised-methods-to-aid-the-identification-of-secondary-metabolites-from-pseudomonas-aeruginosa
#17
Tobias Depke, Raimo Franke, Mark Brönstrup
Pseudomonas aeruginosa is an important opportunistic pathogen that produces a large arsenal of small molecule virulence factors and quorum sensing signal molecules. The annotation of these secondary metabolites in untargeted, mass spectrometry-based metabolomics is difficult, as many of them cannot be found in common metabolite databases, and as manual annotation is tedious. We therefore developed an algorithm named CluMSID that uses cosine similarities of product ion spectra and neutral loss patterns in combination with unsupervised clustering methods such as multidimensional scaling, density based clustering and hierarchical clustering to group structurally similar compounds and hence facilitate their annotation...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28641781/pregnancy-to-postpartum-transition-of-serum-metabolites-in-women-with-gestational-diabetes
#18
Elin Chorell, Ulrika Andersson Hall, Carolina Gustavsson, Kerstin Berntorp, Jatta Puhkala, Riitta Luoto, Tommy Olsson, Agneta Holmäng
CONTEXT: Gestational diabetes is commonly linked to development of type 2 diabetes mellitus (T2DM). There is a need to characterize metabolic changes associated with gestational diabetes in order to find novel biomarkers for T2DM. OBJECTIVE: To find potential pathophysiological mechanisms and markers for progression from gestational diabetes mellitus to T2DM by studying the metabolic transition from pregnancy to postpartum. DESIGN: The metabolic transition profile from pregnancy to postpartum was characterized in 56 women by mass spectrometry-based metabolomics; 11 women had gestational diabetes mellitus, 24 had normal glucose tolerance, and 21 were normoglycaemic but at increased risk for gestational diabetes mellitus...
July 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28641411/development-of-an-lc-hrms-metabolomics-method-with-high-specificity-for-metabolite-identification-using-all-ion-fragmentation-aif-acquisition
#19
Shama Naz, Hector Gallart-Ayala, Stacey Reinke, Caroline Mathon, Richard Blankley, Romanas Chaleckis, Craig Edward Wheelock
High-resolution mass spectrometry (HRMS)-based metabolomics approaches have made significant advances. However, metabolite identification is still a major challenge and significant bottleneck in translating metabolomics data into biological context. In the current study, a liquid chromatography (LC)-HRMS metabolomics method was developed using an all ion fragmentation (AIF) acquisition approach. In order to increase the specificity in metabolite annotation, four criteria were considered: i) accurate mass (AM), ii) retention time (RT), iii) MS/MS spectrum, and iv) product/precursor ion intensity ratios...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28640973/production-of-red-flowered-oilseed-rape-via-the-ectopic-expression-of-orychophragmus-violaceus-ovpap2
#20
Wenqin Fu, Daozong Chen, Qi Pan, Fengfeng Li, Zhigang Zhao, Xianhong Ge, Zaiyun Li
Oilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower color of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up-regulated in both M4 and OvP...
June 22, 2017: Plant Biotechnology Journal
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