PubMed

Rapid on-line analysis of single cyanobacteria and algae cells under nitrogen-limited conditions using aerosol time-of-flight mass spectrometry. Anal Chem. 2015 Aug 3; Authors: Cahill JF, Darlington TK, Fitzgerald CK, Schoepp NG, Beld J, Burkart MD, Prather KA Abstract Metabolomics studies typically perform measurements on populations of whole cells which provide the average representation of a collection of many cells. However key mechanistic information can be lost using this approach. Investigating chemistry at the single cell level yields a more accurate representation of the diversity of populations within a cell sample, however this approach has many analytical challenges. In this study, an aerosol time-of-flight mass spectrometer (ATOFMS) was used for rapid analysis of single algae and cyanobacteria cells with diameters ranging from 1-8 µm. Cells were aerosolized by nebulization and directly transmitted into the ATOFMS. Whole cells were determined to remain intact inside the instrument through a combination of particle sizing and imaging measurements. Differences in cell populations were observed after perturbing Chlamydomonas reinhardtii cells via nitrogen deprivation. Thousands of single cells were measured over a period of 4 days for nitrogen-replete and nitrogen-limited conditions. A comparison of the single cell mass spectra of the cells sampled under the two conditions revealed an increase in the dipalmitic acid sulfolipid sulfoquinovosyldiacylglycerol (SQDG), a chloroplast membrane lipid, under nitrogen-limited conditions. Single cell peak intensity distributions demonstrate the ability of the ATOFMS to measure metabolic differences of single cells. The ATOFMS provides an unprecedented maximum throughput of 50 Hz, enabling the rapid on-line measurement of thousands of single cell mass spectra. PMID: 26237223 [PubMed - as supplied by publisher]

Related Articles Metabolomics changes in a rat model of obstructive jaundice: mapping to metabolism of amino acids, carbohydrates and lipids as well as oxidative stress. J Clin Biochem Nutr. 2015 Jul;57(1):50-9 Authors: Long Y, Dong X, Yuan Y, Huang J, Song J, Sun Y, Lu Z, Yang L, Yu W Abstract The study examined the global metabolic and some biochemical changes in rats with cholestasis induced by bile duct ligation (BDL). Serum samples were collected in male Wistar rats with BDL (n = 8) and sham surgery (n = 8) at day 3 after surgery for metabolomics analysis using a combination of reversed phase chromatography and hydrophilic interaction chromatography (HILIC) and quadrupole-time-of-flight mass spectrometry (Q-TOF MS). The serum levels of malondialdehyde (MDA), total antioxidative capacity (T-AOC), glutathione (GSH) and glutathione disulfide (GSSG), the activities of superoxide dismutase (SOD) and glutathion peroxidase (GSH-Px) were measured to estimate the oxidative stress state. Key changes after BDL included increased levels of l-phenylalanine, l-glutamate, l-tyrosine, kynurenine, l-lactic acid, LysoPC(c) (14:0), glycine and succinic acid and decreased levels of l-valine, PC(b) (19:0/0:0), taurine, palmitic acid, l-isoleucine and citric acid metabolism products. And treatment with BDL significantly decreased the levels of GSH, T-AOC as well as SOD, GSH-Px activities, and upregulated MDA levels. The changes could be mapped to metabolism of amino acids and lipids, Krebs cycle and glycolysis, as well as increased oxidative stress and decreased antioxidant capability. Our study indicated that BDL induces major changes in the metabolism of all 3 major energy substances, as well as oxidative stress. PMID: 26236101 [PubMed]

Related Articles Metabolic biomarkers for chronic kidney disease. Arch Biochem Biophys. 2015 Jul 30; Authors: Breit M, Weinberger KM Abstract Chronic kidney disease (CKD) is an increasingly recognized burden for patients and health care systems with high (and growing) global incidence and prevalence, significant mortality, and disproportionately high treatment costs. Yet, the available diagnostic tools are either impractical in clinical routine or have serious shortcomings impeding a well-informed disease management although optimized treatment strategies with proven benefits for the patients have become available. Advances in bioanalytical technologies have facilitated studies that identified genomic, proteomic, and metabolic biomarker candidates, and confirmed some of them in independent cohorts. This review summarizes the CKD-related markers discovered so far, and focuses on compounds and pathways, for which there is quantitative data, substantiating evidence from translational research, and a mechanistic understanding of the processes involved. Also, multiparametric marker panels have been suggested that showed promising diagnostic and prognostic performance in initial analyses although the data basis from prospective trials is very limited. Large-scale studies, however, are underway and will provide the information for validating a set of parameters and discarding others. Finally, the path from clinical research to a routine application is discussed, focusing on potential obstacles such as the use of mass spectrometry, and the feasibility of obtaining regulatory approval for targeted metabolomics assays. PMID: 26235490 [PubMed - as supplied by publisher]

Related Articles Are Isoursenol and γ-Amyrin Rare Triterpenes in Nature or Simply Overlooked by Usual Analytical Methods? Org Lett. 2015 Aug 2; Authors: Shan H, Wilson WK, Castillo DA, Matsuda SP Abstract Among pentacyclic triterpenes commonly found in plants, γ-amyrin and isoursenol are seldom reported and considered rare in nature. It was hypothesized that these triterpenes are instead routinely overlooked due to inadequate spectral characterization. γ-Amyrin was prepared by HCOOH isomerization of α-amyrin, and isoursenol was isolated from products of a heterologously expressed oxidosqualene cyclase. With precise NMR and GC-MS data, a metabolomics strategy was used to identify isoursenol and γ-amyrin in a wide range of plants. PMID: 26235440 [PubMed - as supplied by publisher]

Related Articles The roles of IP3 receptor in energy metabolic pathways and reactive oxygen species homeostasis revealed by metabolomic and biochemical studies. Biochim Biophys Acta. 2015 Jul 30; Authors: Wen H, Xu WJ, Jin X, Oh S, Phan CH, Song J, Lee SK, Park S Abstract Inositol 1,4,5-trisphosphate receptors (IP3R) are calcium channels modulating important calcium-mediated processes. Recent studies implicate IP3R in cell metabolism, but specific evidence is missing regarding IP3R's effects on actual metabolic pathways and key energy metabolites. Here, we applied metabolomics and molecular biology to compare DT40 cell lines devoid of IP3R (KO) and its wild-type (WT) counterpart. NMR and LC-MS metabolomics data showed that the KO cell line has a very different basic energy metabolism from the WT cell line, showing enhanced Warburg effect. In particular, the KO cells exhibited significant perturbation in energy charge, reduced glutathione and NADPH ratios with slower cellular growth rate. Subsequent flow cytometry results showed that the KO cell line has a higher level of general reactive oxygen species (ROS) but a lower level of peroxynitrites. This ROS disturbance could be explained by observing lower expression of superoxide dismutase 2 (SOD2) and unchanged expression of catalase. The higher ROS seems involved in the slower growth rate of the KO cells, with an ROS scavenger increasing their growth rate. However, the KO and WT cell lines did not show noticeable difference in AMPK and phosphorylated AMPK levels, suggesting possible saturation of AMPK-mediated metabolic regulatory circuit in both cells. Overall, our study reveals IP3R's roles in ROS homeostasis and metabolic pathways as well as the effects of its KO on cellular phenotypes. PMID: 26235438 [PubMed - as supplied by publisher]

Related Articles Application of Systems Theory in Longitudinal Studies on the Origin and Progression of Alzheimer's Disease. Methods Mol Biol. 2016;1303:49-67 Authors: Lista S, Khachaturian ZS, Rujescu D, Garaci F, Dubois B, Hampel H Abstract This chapter questions the prevailing "implicit" assumption that molecular mechanisms and the biological phenotype of dominantly inherited early-onset alzheimer's disease (EOAD) could serve as a linear model to study the pathogenesis of sporadic late-onset alzheimer's disease (LOAD). Now there is growing evidence to suggest that such reductionism may not be warranted; these suppositions are not adequate to explain the molecular complexities of LOAD. For example, the failure of some recent amyloid-centric clinical trials, which were largely based on the extrapolations from EOAD biological phenotypes to the molecular mechanisms in the pathogenesis of LOAD, might be due to such false assumptions. The distinct difference in the biology of LOAD and EOAD is underscored by the presence of EOAD cases without evidence of familial clustering or Mendelian transmission and, conversely, the discovery and frequent reports of such clustering and transmission patterns in LOAD cases. The primary thesis of this chapter is that a radically different way of thinking is required for comprehensive explanations regarding the distinct complexities in the molecular pathogenesis of inherited and sporadic forms of Alzheimer's disease (AD). We propose using longitudinal analytical methods and the paradigm of systems biology (using transcriptomics, proteomics, metabolomics, and lipidomics) to provide us a more comprehensive insight into the lifelong origin and progression of different molecular mechanisms and neurodegeneration. Such studies should aim to clarify the role of specific pathophysiological and signaling pathways such as neuroinflammation, altered lipid metabolism, apoptosis, oxidative stress, tau hyperphosphorylation, protein misfolding, tangle formation, and amyloidogenic cascade leading to overproduction and reduced clearance of aggregating amyloid-beta (Aβ) species. A more complete understanding of the distinct difference in molecular mechanisms, signaling pathways, as well as comparability of the various forms of AD is of paramount importance. The development of knowledge and technologies for early detection and characterization of the disease across all stages will improve the predictions regarding the course of the disease, prognosis, and response to treatment. No doubt such advances will have a significant impact on the clinical management of both EOAD and LOAD patients. The approach propped here, combining longitudinal studies with the systems biology paradigm, will create a more effective and comprehensive framework for development of prevention therapies in AD. PMID: 26235059 [PubMed - in process]

Related Articles The acute impact of polyphenols from Hibiscus sabdariffa in metabolic homeostasis: an approach combining metabolomics and gene-expression analyses. Food Funct. 2015 Aug 3; Authors: Beltrán-Debón R, Rodríguez-Gallego E, Fernández-Arroyo S, Senan-Campos O, Massucci FA, Hernández-Aguilera A, Sales-Pardo M, Guimerà R, Camps J, Menendez JA, Joven J Abstract We explored the acute multifunctional effects of polyphenols from Hibiscus sabdariffa in humans to assess possible consequences on the host's health. The expected dynamic response was studied using a combination of transcriptomics and metabolomics to integrate specific functional pathways through network-based methods and to generate hypotheses established by acute metabolic effects and/or modifications in the expression of relevant genes. Data were obtained from healthy male volunteers after 3 hours of ingestion of an aqueous Hibiscus sabdariffa extract. The data were compared with data obtained prior to the ingestion, and the overall findings suggest that these particular polyphenols had a simultaneous role in mitochondrial function, energy homeostasis and protection of the cardiovascular system. These findings suggest beneficial actions in inflammation, endothelial dysfunction, and oxidation, which are interrelated mechanisms. Among other effects, the activation of the heme oxygenase-biliverdin reductase axis, the systemic inhibition of the renin-angiotensin system, the inhibition of the angiotensin-converting enzyme, and several actions mirroring those of the peroxisome proliferator-activated receptor agonists further support this notion. We also found concordant findings in the serum of the participants, which include a decrease in cortisol levels and a significant increase in the active vasodilator metabolite of bradykinin (des-Arg(9)-bradykinin). Therefore, our data support the view that polyphenols from Hibiscus sabdariffa play a regulatory role in metabolic health and in the maintenance of blood pressure, thus implying a multi-faceted impact in metabolic and cardiovascular diseases. PMID: 26234931 [PubMed - as supplied by publisher]

Related Articles Drug Metabolism and Pharmacokinetic Diversity of Ranunculaceae Medicinal Compounds. Curr Drug Metab. 2015 Aug 3; Authors: Hao DC, Ge GB, Xiao PG, Wang P, Yang L Abstract The wide-reaching distributed angiosperm family Ranunculaceae has approximately 2200 species in around 60 genera. Chemical components of this family include several representative groups: benzylisoquinoline alkaloid (BIA), ranunculin, triterpenoid saponin and diterpene alkaloid, etc. Their extensive clinical utility has been validated by traditional uses of thousands of years and current evidence-based medicine studies. Drug metabolism and pharmacokinetic (DMPK) studies of plant-based natural products are an indispensable part of comprehensive medicinal plant exploration, which could facilitate conservation and sustainable utilization of Ranunculaceae pharmaceutical resources, as well as new chemical entity development with improved DMPK parameters. However, DMPK characteristics of Ranunculaceae derived medicinal compounds have not been summarized. Black cohosh (Cimicifuga) and goldenseal (Hydrastis) raise concerns of herbdrug interaction. DMPK studies of other Ranunculaceae genera, e.g., Nigella, Delphinium, Aconitum, Trollius, and Coptis, are also rapidly increasing and becoming more and more clinically relevant. In this contribution, we highlight the up-to-date awareness, as well as the challenges around the DMPK-related issues in optimization of drug development and clinical practice of Ranunculaceae compounds. Herb-herb interaction of Ranunculaceae herb-containing traditional Chinese medicine (TCM) formula could significantly influence the in vivo pharmacokinetic behavior of compounds thereof, which may partially explain the complicated therapeutic mechanism of TCM formula. Although progress has been made on revealing the absorption, distribution, metabolism, excretion and toxicity (ADME/T) of Ranunculaceae compounds, there is a lack of DMPK studies of traditional medicinal genera Aquilegia, Thalictrum and Clematis. Fluorescent probe compounds could be promising substrate, inhibitor and/or inducer in future DMPK studies of Ranunculaceae compounds. A better understanding of the important herb-drug/herb-herb interactions, bioavailability and metabolomics aspects of Ranunculaceae compounds will bolster future natural product-based drug design and the comprehensive investigation of inter-individual inconsistency of drug metabolism. PMID: 26234707 [PubMed - as supplied by publisher]

Related Articles Chronic liver disease questionnaire would be a primary screening tool of neuropsychiatric test detecting minimal hepatic encephalopathy of cirrhotic patients. Hepatol Res. 2015 Jul 31; Authors: Hirano H, Saito M, Yano Y, Momose K, Yoshida M, Tanaka A, Azuma T Abstract AIM: The neuropsychiatric test (NP test) is a clinically available modality to confirm minimal hepatic encephalopathy (MHE), but it takes at least 30 minutes for outpatients to complete. An easier primary screening tool of the NP test would be helpful to predict MHE in routine testing on the public METHODS: We performed a prospective cohort study on 59 cirrhotic outpatients at Kobe University Hospital. Laboratory measurements, the NP test, and the chronic liver disease questionnaire (CLDQ) were performed. As an indicator of MHE, cases with and without two abnormal subsets or more in the NP test were compared, and the independent risk factors were statistically examined. Predictive scoring systems of the risk of MHE were established using multivariate logistic regression. RESULTS: CLDQ worry (WO) was the best predictive factor of MHE diagnosed by the NP test (p = 0.006). The predictive model using CLDQ WO discriminated well between patients with and without MHE (AUC: 0.714; 95% CI: 0.582 to 0.824). The predictive scores of MHE enable the patient-specific probability to be easily looked up. CONCLUSIONS: CLDQ WO was shown to be an independent factor associated with the NP test to diagnose MHE in cirrhotic patients. The easy predictive scoring system of the risk of MHE using CLDQ WO could become a primary screening tool before performing the NP test in a social setting. PMID: 26234673 [PubMed - as supplied by publisher]

Related Articles A metabolomics approach to studying the effects of Jinxin oral liquid on RSV-infected mice using UPLC/LTQ-Orbitrap mass spectrometry. J Ethnopharmacol. 2015 Jul 30; Authors: Du LN, Xie T, Xu JY, Kang A, Di LQ, Shan JJ, Wang SC Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Jinxin oral liquid (JOL) is a traditional Chinese medicine (TCM) formula modified from ma-xing-shi-gan-tang, an ancient formula widely used in the treatment of respiratory diseases such as bronchitis, pneumonia, and asthma. In our previous studies, JOL was shown to safely and effectively treat viral pneumonia, especially that involving respiratory syncytial virus (RSV). AIM OF THE STUDY: To investigate the mechanism of the effect of JOL in RSV infected mice, using a metabolomics approach based on ultra-performance liquid chromatography coupled with linear ion trap quadrupole - Orbitrap mass spectrometry (UPLC/LTQ-Orbitrap-MS). MATERIALS AND METHODS: BALB/c mice were divided into four groups, the control group (saline inoculation/no treatment), RSV group (RSV inoculation/saline treatment), RSV+JOL group (RSV inoculation/JOL treatment), and RSV+Riba group (RSV inoculation/ribavirin treatment). Plasma and lung tissue samples were collected 7 days after the inoculation/treatment protocols, and UPLC/LTQ-Orbitrap-MS method based on metabolomics was developed. Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were utilized to identify biomarkers potentially associated with the anti-RSV activity of JOL. RESULTS: JOL was associated with reduced inflammatory responses in RSV-infected lung tissue. The combination of PCA and OPLS-DA revealed deviations in 11 biomarkers in plasma, and 16 biomarkers in lung tissue induced by RSV that were corrected with JOL treatment. These biomarkers were primarily components of metabolic pathways involving glycerophosphocholines, sphingolipids, and glycerolipids. JOL was able to restore the abnormal levels of these biomarkers detected in the plasma and lung tissue of RSV-infected mice to approximately normal levels. CONCLUSIONS: This study suggested that JOL can treat RSV pneumonia effectively, partially by ameliorating the associated disturbances to lipid metabolism. The results provided insight into the anti-RSV mechanism of JOL, and also demonstrated that metabolomics is a valuable tool for investigating the efficacy of TCM treatment for RSV pneumonia, and the associated biomarkers involved. PMID: 26234176 [PubMed - as supplied by publisher]

Related Articles NMR-Based Metabolic Profiling Reveals Neurochemical Alterations in the Brain of Rats Treated with Sorafenib. Neurotox Res. 2015 Aug 2; Authors: Du C, Shao X, Zhu R, Li Y, Zhao Q, Fu D, Gu H, Kong J, Luo L, Long H, Deng P, Wang H, Hu C, Zhao Y, Cen X Abstract Sorafenib, an active multi-kinase inhibitor, has been widely used as a chemotherapy drug to treat advanced clear-cell renal cell carcinoma patients. In spite of the relative safety, sorafenib has been shown to exert a negative impact on cognitive functioning in cancer patients, specifically on learning and memory; however, the underlying mechanism remains unclear. In this study, an NMR-based metabolomics approach was applied to investigate the neurochemical effects of sorafenib in rats. Male rats were once daily administrated with 120 mg/kg sorafenib by gavage for 3, 7, and 28 days, respectively. NMR-based metabolomics coupled with histopathology examinations for hippocampus, prefrontal cortex (PFC), and striatum were performed. The (1)H NMR spectra data were analyzed by using multivariate pattern recognition techniques to show the time-dependent biochemical variations induced by sorafenib. Excellent separation was obtained and distinguishing metabolites were observed between sorafenib-treated and control rats. A total of 36 differential metabolites in hippocampus of rats treated with sorafenib were identified, some of which were significantly changed. Furthermore, these modified metabolites mainly reflected the disturbances in neurotransmitters, energy metabolism, membrane, and amino acids. However, only a few metabolites in PFC and striatum were altered by sorafenib. Additionally, no apparent histological changes in these three brain regions were observed in sorafenib-treated rats. Together, our findings demonstrate the disturbed metabonomics pathways, especially, in hippocampus, which may underlie the sorafenib-induced cognitive deficits in patients. This work also shows the advantage of NMR-based metabolomics over traditional approach on the study of biochemical effects of drugs. PMID: 26233726 [PubMed - as supplied by publisher]

Related Articles Circulating levels of antioxidant vitamins correlate with better lung function and reduced exposure to ambient pollution. Am J Respir Crit Care Med. 2015 May 15;191(10):1203-7 Authors: Menni C, Metrustry SJ, Mohney RP, Beevers S, Barratt B, Spector TD, Kelly FJ, Valdes AM PMID: 25978575 [PubMed - indexed for MEDLINE]

Related Articles Maternal intravenous administration of azithromycin results in significant fetal uptake in a sheep model of second trimester pregnancy. Antimicrob Agents Chemother. 2014 Nov;58(11):6581-91 Authors: Kemp MW, Miura Y, Payne MS, Jobe AH, Kallapur SG, Saito M, Stock SJ, Spiller OB, Ireland DJ, Yaegashi N, Clarke M, Hahne D, Rodger J, Keelan JA, Newnham JP Abstract Treatment of intrauterine infection is likely key to preventing a significant proportion of preterm deliveries before 32 weeks of gestation. Azithromycin (AZ) may be an effective antimicrobial in pregnancy; however, few gestation age-approriate data are available to inform the design of AZ-based treatment regimens in early pregnancy. We aimed to determine whether a single intra-amniotic AZ dose or repeated maternal intravenous (i.v.) AZ doses would safely yield therapeutic levels of AZ in an 80-day-gestation (term is 150 days) ovine fetus. Fifty sheep carrying single pregnancies at 80 days gestation were randomized to receive either: (i) a single intra-amniotic AZ administration or (ii) maternal intravenous AZ administration every 12 h. Amniotic fluid, maternal plasma, and fetal AZ concentrations were determined over a 5-day treatment regimen. Markers of liver injury and amniotic fluid inflammation were measured to assess fetal injury in response to drug exposure. A single intra-amniotic administration yielded significant AZ accumulation in the amniotic fluid and fetal lung. In contrast, repeated maternal intravenous administrations achieved high levels of AZ accumulation in the fetal lung and liver and a statistically significant increase in the fetal plasma drug concentration at 120 h. There was no evidence of fetal injury in response to drug exposure. These data suggest that (i) repeated maternal i.v. AZ dosing yields substantial fetal tissue uptake, although fetal plasma drug levels remain low; (ii) transfer of AZ from the amniotic fluid is less than transplacental transfer; and (iii) exposure to high concentrations of AZ did not elicit overt changes in fetal white blood cell counts, amniotic fluid monocyte chemoattractant protein 1 concentrations, or hepatotoxicity, all consistent with an absence of fetal injury. PMID: 25155606 [PubMed - indexed for MEDLINE]

Related Articles Fingerprinting and simultaneous determination of alkaloids and limonins in Phellodendri amurensis cortex from different locations by high-performance liquid chromatography with diode array detection. J Chromatogr Sci. 2015 Jan;53(1):161-6 Authors: Wang L, Yan G, Zhang A, Shi H, Sun H, Wang X Abstract A sensitive high-performance liquid chromatography method coupled with diode array detection (HPLC-DAD) was developed for the quality control of Phellodendri amurensis cortex (PAC), the quality control included the simultaneous determination of seven major constituents, namely phellodendrine, magnoflorine, jatrorrhizine, palmatine, berberine, obaculactone and obacunone. The chromatographic separation was accomplished on a Diamonsil-C18 column (4.6 mm × 200 mm, 5 μm) with acetonitrile and 0.1% phosphoric acid (0.02 mol sodium dihydrogen phosphate per liter) by linear gradient elution. The established method was successfully validated by acceptable linearity, limits of detection and quantitation, precision, repeatability, stability and accuracy. The HPLC-DAD fingerprint chromatograph under 220 nm consisting of 21 peaks was constructed for the evaluation of the 11 batches of PAC. The HPLC fingerprints were analyzed by similarity analysis, hierarchical clustering analysis and principal component analysis. The results indicated that the combination of multicomponent determination method and chromatographic fingerprint analysis could be employed for the quantitative analysis and identification of PAC, as well as pharmaceutical products containing this herbal material. PMID: 24872523 [PubMed - indexed for MEDLINE]

Related Articles Alterations in Spinal Cord Metabolism during Treatment of Neuropathic Pain. J Neuroimmune Pharmacol. 2015 Aug 2; Authors: Johnson CH, Patti GJ, Courade JP, Shriver LP, Hoang LT, Manchester M, Siuzdak G Abstract Therapeutic options for neuropathic pain have improved over the last 20 years yet still only provide partial relief with numerous side effects. Recently, metabolomics revealed that the concentration of the endogenous metabolite N,N-dimethylsphingosine (DMS) is increased in the spinal cord in a model of neuropathic pain. Additionally, it was shown that introduction of DMS to the central nervous system (CNS) resulted in mechanical allodynia. Here, we have examined two compounds; pregabalin (Lyrica®), a drug used to treat neuropathic pain, and N-oleoylethanolamine (NOE), an endogenous endocannabinoid-like compound that is known to affect multiple lipid pathways. We found that the concentration of DMS in the spinal cord was not significantly altered upon pregabalin treatment of rats suffering from neuropathic pain. We further explored whether modulating lipid metabolism may impact neuropathic pain by testing NOE as a potential novel therapeutic. PMID: 26232265 [PubMed - as supplied by publisher]

Related Articles An Extensive Library of Surrogate Peptides for all Human Proteins. J Proteomics. 2015 Jul 28; Authors: Mohammed Y, Borchers CH Abstract Selecting the most appropriate surrogate peptides to represent a target protein is a major component of experimental design in Multiple Reaction Monitoring (MRM). Our software PeptidePicker with its v-score remains distinctive in its approach of integrating information about the proteins, their tryptic peptides, and the suitability of these peptides for MRM that is available online in UniProtKB, NCBI's dbSNP, ExPASy, PeptideAtlas, PRIDE, and GPMDB. The scoring algorithm reflects our "best knowledge" for selecting candidate peptides for MRM, based on the uniqueness of the peptide in the targeted proteome, its physiochemical properties, and whether it has previously been observed. Here we present an updated approach where we have already compiled a list of all possible surrogate peptides of the human proteome. Using our stringent selection criteria, the list includes 165k suitable MRM peptides covering 17k proteins of the human reviewed proteins in UniProtKB. Compared to average of 2-4 minutes per protein for retrieving and integrating the information, the precompiled list includes all peptides available instantly. This allows a more cohesive and faster design of a multiplexed MRM experiment and provides insights into evidence for a protein's existence. We will keep this list up-to-date as proteomics data repositories continue to grow. BIOLOGICAL SIGNIFICANCE: A list of all possible surrogate peptides of the human proteome has been compiled using our tool PeptidePicker. This list enables a cohesive and faster design of multiplexed MRM experiments. We used stringent selection criteria on the human reviewed proteins in UniProtKB to create the list which includes 165k MRM-suitable peptides covering 17k proteins. Compared to average of a few minutes per protein for retrieving and integrating the information from online repositories using our automatic workflow, the pre-compiled list has the information for all of the peptides available instantly. The list also provides interesting insights into the proteins' evidence of existence. 3,389 proteins reported in UniProtKB as having only a "lower level" of existence evidence actually have mass spectrometric evidence of existence in online data repositories. PMID: 26232110 [PubMed - as supplied by publisher]

Related Articles Review of validation and reporting of non-targeted fingerprinting approaches for food authentication. Anal Chim Acta. 2015 Jul 23;885:17-32 Authors: Riedl J, Esslinger S, Fauhl-Hassek C Abstract Food fingerprinting approaches are expected to become a very potent tool in authentication processes aiming at a comprehensive characterization of complex food matrices. By non-targeted spectrometric or spectroscopic chemical analysis with a subsequent (multivariate) statistical evaluation of acquired data, food matrices can be investigated in terms of their geographical origin, species variety or possible adulterations. Although many successful research projects have already demonstrated the feasibility of non-targeted fingerprinting approaches, their uptake and implementation into routine analysis and food surveillance is still limited. In many proof-of-principle studies, the prediction ability of only one data set was explored, measured within a limited period of time using one instrument within one laboratory. Thorough validation strategies that guarantee reliability of the respective data basis and that allow conclusion on the applicability of the respective approaches for its fit-for-purpose have not yet been proposed. Within this review, critical steps of the fingerprinting workflow were explored to develop a generic scheme for multivariate model validation. As a result, a proposed scheme for "good practice" shall guide users through validation and reporting of non-targeted fingerprinting results. Furthermore, food fingerprinting studies were selected by a systematic search approach and reviewed with regard to (a) transparency of data processing and (b) validity of study results. Subsequently, the studies were inspected for measures of statistical model validation, analytical method validation and quality assurance measures. In this context, issues and recommendations were found that might be considered as an actual starting point for developing validation standards of non-targeted metabolomics approaches for food authentication in the future. Hence, this review intends to contribute to the harmonization and standardization of food fingerprinting, both required as a prior condition for the authentication of food in routine analysis and official control. PMID: 26231890 [PubMed - as supplied by publisher]

Related Articles Metabolomic Applications to the Characterization of the Mode-of-Action of CDK Inhibitors. Methods Mol Biol. 2016;1336:211-223 Authors: Palomino-Schätzlein M, Pineda-Lucena A Abstract Cyclin-dependent kinases (CDKs) regulate cell cycle progression, and some of them are also involved in the control of cellular transcription. Dysregulation of these critical cellular processes, due to the aberrant expression of some of these proteins, is common in many neoplastic malignancies. Consequently, the development of chemical compounds capable of inhibiting the biological activity of CDKs represents an attractive strategy in the anticancer area. CDK inhibition can trigger apoptosis and could be particularly useful in hematological malignancies, which are more sensitive to inhibition of cell cycle and apoptosis induction. Over the last few years, a number of pharmacological inhibitors of CDKs (CDKIs) belonging to different chemical families have been developed, and some of them have been tested in clinical trials. Given the complexity of the role of CDKs in cell functioning, it would be desirable to develop new tools that could facilitate a better understanding of the new insights into CDK functions and the mode-of-actions of CDKIs. In this context, this chapter describes an experimental approach to evaluate the metabolic consequences of CDKIs at the cellular level based on metabolomics by NMR. More specifically, a description of a strategy to characterize the biochemical effects of CDKIs acting on mammalian cells is provided, including protocols for the extraction of hydrophilic and lipophilic metabolites, the acquisition of 1D and 2D metabolomic Nuclear Magnetic Resonance (NMR) experiments, the identification and quantification of metabolites, and the annotation of the results in the context of biochemical pathways. PMID: 26231718 [PubMed - as supplied by publisher]

Related Articles The Role of the Epigenome in Translating Neighborhood Disadvantage Into Health Disparities. Curr Environ Health Rep. 2015 Jun;2(2):163-170 Authors: Olden K, Olden HA, Lin YS Abstract The possible causal role of the environment in health disparities is not well understood, even though it has been a national priority for many years. Progress to investigate the relationship between genetics, environmental exposures, and health outcomes has been hampered by the lack of analytical tools to quantify the combined or cumulative effect of multiple chemical and non-chemical stressors on gene expression. The studies cited here provide a strong rationale for using epigenomic analysis to assess cumulative risk from multiple environmental exposures over the life course. The environment-specific "imprints" on the genome, coupled with transcriptomics and metabolomics, can be used to advance our understanding of the relationship between neighborhood disadvantage and health disparities. PMID: 26231365 [PubMed - as supplied by publisher]

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