PubMed

Urinary metabolite profiling provides potential differentiation to explore the mechanisms of adjuvant-induced arthritis in rats. Biomed Chromatogr. 2016 Feb 8; Authors: Jiang H, Liu J, Wang T, Gao JR, Sun Y, Huang CB, Meng M, Qin XJ Abstract To explore the pathogenesis of rheumatoid arthritis (RA) from the perspective of metabolomics, gas chromatography time-of-flight mass spectrometry (GC-TOF/MS) technology was used to observe changes in the metabolic profiles of urine output from rats with adjuvant-induced arthritis (AA). Spague-Dawley (SD) rats were randomly divided into control group (NC) and experimental group, with 8 in each. Rats in experimental group were induced by intracutaneous innoculation of 0.1mL Freund's complete adjuvant (FCA) to right paws. On day 20 after immunization, the metabolic profiles between rat control and experimental groups were compared by combining GC-TOF/MS technology with multivariate statistical approaches, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projections to latent structures-discriminant analysis (OPLS-DA). Nine potential biomarkers were identified, including 2,2-dimethylsuccinic acid, tartronic acid, dehydroshikimic acid, hippuric acid, adenine, phenaceturic acid, L-dopa, 1,4-dihydroxy-2-naphthoic acid and melibiose. The findings indicate that the rats with AA are disturbed in metabolism of purine, amino acid, fat and energy. This study also demonstrates that the dysfunction in a range of biosynthetic and catabolic pathways, which leads to increased oxygen free radicals and inflammation, could cause underlying pathogenesis of RA. This article is protected by copyright. All rights reserved. PMID: 26856389 [PubMed - as supplied by publisher]

Related Articles Resolvin E1 inhibits dendritic cell migration in the skin and attenuates contact hypersensitivity responses. J Exp Med. 2015 Oct 19;212(11):1921-30 Authors: Sawada Y, Honda T, Hanakawa S, Nakamizo S, Murata T, Ueharaguchi-Tanada Y, Ono S, Amano W, Nakajima S, Egawa G, Tanizaki H, Otsuka A, Kitoh A, Dainichi T, Ogawa N, Kobayashi Y, Yokomizo T, Arita M, Nakamura M, Miyachi Y, Kabashima K Abstract Resolvin E1 (RvE1) is a lipid mediator derived from ω3 polyunsaturated fatty acids that exerts potent antiinflammatory roles in several murine models. The antiinflammatory mechanism of RvE1 in acquired immune responses has been attributed to attenuation of cytokine production by dendritic cells (DCs). In this study, we newly investigated the effect of RvE1 on DC motility using two-photon microscopy in a contact hypersensitivity (CHS) model and found that RvE1 impaired DC motility in the skin. In addition, RvE1 attenuated T cell priming in the draining lymph nodes and effector T cell activation in the skin, which led to the reduced skin inflammation in CHS. In contrast, leukotriene B4 (LTB4) induced actin filament reorganization in DCs and increased DC motility by activating Cdc42 and Rac1 via BLT1, which was abrogated by RvE1. Collectively, our results suggest that RvE1 attenuates cutaneous acquired immune responses by inhibiting cutaneous DC motility, possibly through LTB4-BLT1 signaling blockade. PMID: 26438363 [PubMed - indexed for MEDLINE]

Related Articles The role of group IIF-secreted phospholipase A2 in epidermal homeostasis and hyperplasia. J Exp Med. 2015 Oct 19;212(11):1901-19 Authors: Yamamoto K, Miki Y, Sato M, Taketomi Y, Nishito Y, Taya C, Muramatsu K, Ikeda K, Nakanishi H, Taguchi R, Kambe N, Kabashima K, Lambeau G, Gelb MH, Murakami M Abstract Epidermal lipids are important for skin homeostasis. However, the entire picture of the roles of lipids, particularly nonceramide lipid species, in epidermal biology still remains obscure. Here, we report that PLA2G2F, a functionally orphan-secreted phospholipase A2 expressed in the suprabasal epidermis, regulates skin homeostasis and hyperplasic disorders. Pla2g2f(-/-) mice had a fragile stratum corneum and were strikingly protected from psoriasis, contact dermatitis, and skin cancer. Conversely, Pla2g2f-overexpressing transgenic mice displayed psoriasis-like epidermal hyperplasia. Primary keratinocytes from Pla2g2f(-) (/-) mice showed defective differentiation and activation. PLA2G2F was induced by calcium or IL-22 in keratinocytes and preferentially hydrolyzed ethanolamine plasmalogen-bearing docosahexaenoic acid secreted from keratinocytes to give rise to unique bioactive lipids (i.e., protectin D1 and 9S-hydroxyoctadecadienoic acid) that were distinct from canonical arachidonate metabolites (prostaglandins and leukotrienes). Ethanolamine lysoplasmalogen, a PLA2G2F-derived marker product, rescued defective activation of Pla2g2f(-/-) keratinocytes both in vitro and in vivo. Our results highlight PLA2G2F as a previously unrecognized regulator of skin pathophysiology and point to this enzyme as a novel drug target for epidermal-hyperplasic diseases. PMID: 26438362 [PubMed - indexed for MEDLINE]

Related Articles Metabolic Effect Level Index Links Multivariate Metabolic Fingerprints to Ecotoxicological Effect Assessment. Environ Sci Technol. 2015 Jul 7;49(13):8096-104 Authors: Riedl J, Schreiber R, Otto M, Heilmeier H, Altenburger R, Schmitt-Jansen M Abstract A major goal of ecotoxicology is the prediction of adverse outcomes for populations from sensitive and early physiological responses. A snapshot of the physiological state of an organism can be provided by metabolic fingerprints. However, to inform chemical risk assessment, multivariate metabolic fingerprints need to be converted to readable end points suitable for effect estimation and comparison. The concentration- and time-dependent responsiveness of metabolic fingerprints to the PS-II inhibitor isoproturon was investigated by use of a Myriophyllum spicatum bioassay. Hydrophilic and lipophilic leaf extracts were analyzed with gas chromatography-mass spectrometry (GC-MS) and preprocessed with XCMS. Metabolic changes were aggregated in the quantitative metabolic effect level index (MELI), allowing effect estimation from Hill-based concentration-response models. Hereby, the most sensitive response on the concentration scale was revealed by the hydrophilic MELI, followed by photosynthetic efficiency and, 1 order of magnitude higher, by the lipophilic MELI and shoot length change. In the hydrophilic MELI, 50% change compares to 30% inhibition of photosynthetic efficiency and 10% inhibition of dry weight change, indicating effect development on different response levels. In conclusion, aggregated metabolic fingerprints provide quantitative estimates and span a broad response spectrum, potentially valuable for establishing adverse outcome pathways of chemicals in environmental risk assessment. PMID: 26020363 [PubMed - indexed for MEDLINE]

Related Articles Quantification of cellular viability by automated microscopy and flow cytometry. Oncotarget. 2015 Apr 20;6(11):9467-75 Authors: Sauvat A, Wang Y, Segura F, Spaggiari S, Müller K, Zhou H, Galluzzi L, Kepp O, Kroemer G Abstract Cellular viability is usually determined by measuring the capacity of cells to exclude vital dyes such as 4',6-diamidino-2-phenylindole (DAPI), or by assessing nuclear morphology with chromatinophilic plasma membrane-permeant dyes, such as Hoechst 33342. However, a fraction of cells that exclude DAPI or exhibit normal nuclear morphology have already lost mitochondrial functions and/or manifest massive activation of apoptotic caspases, and hence are irremediably committed to death. Here, we developed a protocol for the simultaneous detection of plasma membrane integrity (based on DAPI) or nuclear morphology (based on Hoechst 33342), mitochondrial functions (based on the mitochondrial transmembrane potential probe DiOC6(3)) and caspase activation (based on YO-PRO®-3, which can enter cells exclusively upon the caspase-mediated activation of pannexin 1 channels). This method, which allows for the precise quantification of dead, dying and healthy cells, can be implemented on epifluorescence microscopy or flow cytometry platforms and is compatible with a robotized, high-throughput workflow. PMID: 25816366 [PubMed - indexed for MEDLINE]

Related Articles Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species. Plant Cell Physiol. 2015 May;56(5):843-51 Authors: Li D, Ono N, Sato T, Sugiura T, Altaf-Ul-Amin M, Ohta D, Suzuki H, Arita M, Tanaka K, Ma Z, Kanaya S Abstract Curcuminoids, namely curcumin and its analogs, are secondary metabolites that act as the primary active constituents of turmeric (Curcuma longa). The contents of these curcuminoids vary among species in the genus Curcuma. For this reason, we compared two wild strains and two cultivars to understand the differences in the synthesis of curcuminoids. Because the fluxes of metabolic reactions depend on the amounts of their substrate and the activity of the catalysts, we analyzed the metabolite concentrations and gene expression of related enzymes. We developed a method based on RNA sequencing (RNA-Seq) analysis that focuses on a specific set of genes to detect expression differences between species in detail. We developed a 'selection-first' method for RNA-Seq analysis in which short reads are mapped to selected enzymes in the target biosynthetic pathways in order to reduce the effect of mapping errors. Using this method, we found that the difference in the contents of curcuminoids among the species, as measured by gas chromatography-mass spectrometry, could be explained by the changes in the expression of genes encoding diketide-CoA synthase, and curcumin synthase at the branching point of the curcuminoid biosynthesis pathway. PMID: 25637373 [PubMed - indexed for MEDLINE]

Emerging role of novel biomarkers in the diagnosis of inflammatory bowel disease. World J Gastrointest Pharmacol Ther. 2016 Feb 6;7(1):41-50 Authors: Soubières AA, Poullis A Abstract There is currently no gold standard test for the diagnosis of inflammatory bowel disease (IBD). Physicians must rely on a number of diagnostic tools including clinical and endoscopic evaluation as well as histologic, serologic and radiologic assessment. The real difficulty for physicians in both primary and secondary care is differentiating between patients suffering from functional symptoms and those with true underlying IBD. Alongside this, there is always concern regarding the possibility of a missed, or delayed diagnosis of ulcerative colitis (UC) or Crohn's disease. Even once the diagnosis of IBD has been made, there is often uncertainty in distinguishing between cases of UC or Crohn's. As a consequence, in cases of incorrect diagnosis, optimal treatment and management may be adversely affected. Endoscopic evaluation can be uncomfortable and inconvenient for patients. It carries significant risks including perforation and in terms of monetary cost, is expensive. The use of biomarkers to help in the diagnosis and differentiation of IBD has been increasing over time. However, there is not yet one biomarker, which is sensitive of specific enough to be used alone in diagnosing IBD. Current serum testing includes C-reactive protein and erythrocyte sedimentation rate, which are cheap, reliable but non-specific and thus not ideal. Stool based testing such as faecal calprotectin is a much more specific tool and is currently in widespread clinical use. Non-invasive sampling is of the greatest clinical value and with the recent advances in metabolomics, genetics and proteomics, there are now more tools available to develop sensitive and specific biomarkers to diagnose and differentiate between IBD. Many of these new advances are only in early stages of development but show great promise for future clinical use. PMID: 26855811 [PubMed - as supplied by publisher]

Predicting chronic copper and nickel reproductive toxicity to Daphnia pulex-pulicaria from whole-animal metabolic profiles. Environ Pollut. 2016 Feb 5;212:325-329 Authors: Taylor NS, Kirwan JA, Johnson C, Yan ND, Viant MR, Gunn JM, McGeer JC Abstract The emergence of omics approaches in environmental research has enhanced our understanding of the mechanisms underlying toxicity; however, extrapolation from molecular effects to whole-organism and population level outcomes remains a considerable challenge. Using environmentally relevant, sublethal, concentrations of two metals (Cu and Ni), both singly and in binary mixtures, we integrated data from traditional chronic, partial life-cycle toxicity testing and metabolomics to generate a statistical model that was predictive of reproductive impairment in a Daphnia pulex-pulicaria hybrid that was isolated from an historically metal-stressed lake. Furthermore, we determined that the metabolic profiles of organisms exposed in a separate acute assay were also predictive of impaired reproduction following metal exposure. Thus we were able to directly associate molecular profiles to a key population response - reproduction, a key step towards improving environmental risk assessment and management. PMID: 26854702 [PubMed - as supplied by publisher]

Perturbation of pharmacologically relevant polyphenolic compounds in Moringa oleifera against photo-oxidative damages imposed by gamma radiation. J Photochem Photobiol B. 2016 Jan 26;156:79-86 Authors: Ramabulana T, Mavunda RD, Steenkamp PA, Piater LA, Dubery IA, Madala NE Abstract Oxidative stress is a physiological state associated with almost all biotic and abiotic stresses in plants. This phenomenon occurs due to imbalances which result from the overproduction of reactive oxygen species (ROS). Plants, however, have developed sophisticated mechanisms to mitigate the effect of ROS. In this regard, plant polyphenolic metabolites such as flavonoids are known to possess high antioxidant activities. In the current study, changes in the levels of phenolic compounds from Moringa oleifera after gamma radiation treatment were investigated with reverse phase liquid chromatography and mass spectrometric techniques in combination with multivariate data models such as principal component analysis and orthogonal projection to latent structures discriminant analysis. Our results revealed several polyphenolic compounds such as hydroxycinnamoyl derivatives and flavonoid molecules to be down-regulated post-radiation treatment. Interestingly, other flavonoid molecules were found to be up-regulated post-radiation treatment, thereby suggesting a possible compensatory phenomenon. The existence and involvement of structurally similar metabolites (such as regio-isomers of chlorogenic acids) in M. oleifera towards mitigating photo-oxidative damages are in support of the proposed evolutionary existence of a large pool of polyphenolics which contribute to the state of readiness, aptly described as a "better safe than sorry" phenomenon. Our study thus reaffirms the involvement of phenolic compounds as a first line of constitutive/preformed protection against oxidative stress. Furthermore, the obtained data supports M. oleifera as a source of versatile and pharmacologically relevant metabolites that may be exploited for ameliorating the oxidative damages imposed by several metabolic disorders in humans. PMID: 26854613 [PubMed - as supplied by publisher]

Integrating omics to unravel the stress response mechanisms in probiotic bacteria: approaches, challenges, and prospects. Crit Rev Food Sci Nutr. 2016 Feb 6;:0 Authors: Gandhi A, Shah NP Abstract Identifying the stress response mechanism of probiotic bacteria has always captivated the interest of the food producers. It is crucial to identify probiotic bacteria that have increased stress tolerance to survive during production, processing, and storage of food products. However, in order to achieve high resistance to environmental factors, there is a need to better understand the stress induced responses and adaptive mechanisms. With the advances in bacterial genomics, there has been an upsurge in application of other omics platforms such as transcriptomics, proteomics, metabolomics, and some more recent ones such as interactomics, fluxomics, and phenomics. These omics technologies have revolutionized the functional genomics and their application. There have been several studies implementing the various omics technologies to investigate the stress responses of probiotic bacteria. Integrated omics has the potential to provide in-depth information about the mechanisms of stress-induced responses in bacteria. However, there still remain challenges in integrating the information from different omics platforms. This review discusses the current omics techniques and the challenges faced in integrating various omics platforms with focus on their use in stress response studies. PMID: 26853094 [PubMed - as supplied by publisher]

An R package for the integrated analysis of metabolomics and spectral data. Comput Methods Programs Biomed. 2016 Jan 14; Authors: Costa C, Maraschin M, Rocha M Abstract Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as nuclear magnetic resonance, gas or liquid chromatography, mass spectrometry, infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines. PMID: 26853041 [PubMed - as supplied by publisher]

Related Articles Biomarkers in Pharmaceutical Research. Clin Chem. 2015 Nov;61(11):1343-53 Authors: Zhao X, Modur V, Carayannopoulos LN, Laterza OF Abstract BACKGROUND: Biomarkers are important tools in drug development and are used throughout pharmaceutical research. CONTENT: This review focuses on molecular biomarkers in drug development. It contains sections on how biomarkers are used to assess target engagement, pharmacodynamics, safety, and proof-of-concept. It also covers the use of biomarkers as surrogate end points and patient selection/companion diagnostics and provides insights into clinical biomarker discovery and biomarker development/validation with regulatory implications. To survey biomarkers used in drug development--acknowledging that many pharmaceutical development biomarkers are not published--we performed a focused PubMed search employing "biomarker" and the names of the largest pharmaceutical companies as keywords and filtering on clinical trials and publications in the last 10 years. This yielded almost 500 entries, the majority of which included disease-related (approximately 60%) or prognostic/predictive (approximately 20%) biomarkers. A notable portion (approximately 8%) included HER2 (human epidermal growth factor receptor 2) testing, highlighting the utility of biomarkers for patient selection. The remaining publications included target engagement, safety, and drug metabolism biomarkers. Oncology, cardiovascular disease, and osteoporosis were the areas with the most citations, followed by diabetes and Alzheimer disease. SUMMARY: Judicious biomarker use can improve pharmaceutical development efficiency by helping to select patients most appropriate for treatment using a given mechanism, optimize dose selection, and provide earlier confidence in accelerating or discontinuing compounds in clinical development. Optimal application of biomarker technology requires understanding of candidate drug pharmacology, detailed modeling of biomarker readouts relative to pharmacokinetics, rigorous validation and qualification of biomarker assays, and creative application of these elements to drug development problems. PMID: 26408531 [PubMed - indexed for MEDLINE]

Related Articles Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein. FEMS Microbiol Lett. 2015 Jun;362(11) Authors: Li H, Zhang DF, Lin XM, Peng XX Abstract Antibiotic-resistant bacteria are a great threat to human health and food safety and there is an urgent need to understand the mechanisms of resistance for combating these bacteria. In the current study, comparative proteomic methodologies were applied to identify Escherichia coli K-12 outer membrane (OM) proteins related to kanamycin resistance. Mass spectrometry and western blotting results revealed that OM proteins TolC, Tsx and OstA were up-regulated, whereas MipA, OmpA, FadL and OmpW were down-regulated in kanamycin-resistant E. coli K-12 strain. Genetic deletion of tolC (ΔtolC-Km) led to a 2-fold decrease in the minimum inhibitory concentration (MIC) of kanamycin and deletion of mipA (ΔmipA-Km) resulted in a 4-fold increase in the MIC of kanamycin. Changes in the MICs for genetically modified strains could be completely recovered by gene complementation. Compared with the wild-type strain, the survival capability of ΔompA-Km was significantly increased and that of Δtsx-Km was significantly decreased. We further evaluated the role and expression of MipA in response to four other antibiotics including nalidixic acid, streptomycin, chloramphenicol and aureomycin, which suggested that MipA was a novel OM protein related to antibiotic resistance. PMID: 25940639 [PubMed - indexed for MEDLINE]

Related Articles Strategies for individual phenotyping of linoleic and arachidonic acid metabolism using an oral glucose tolerance test. PLoS One. 2015;10(3):e0119856 Authors: Saccenti E, van Duynhoven J, Jacobs DM, Smilde AK, Hoefsloot HC Abstract The ability to restore homeostasis upon environmental challenges has been proposed as a measure for health. Metabolic profiling of plasma samples during the challenge response phase should offer a profound view on the flexibility of a phenotype to cope with daily stressors. Current data modeling approaches, however, struggle to extract biological descriptors from time-resolved metabolite profiles that are able to discriminate between different phenotypes. Thus, for the case of oxylipin responses in plasma upon an oral glucose tolerance test we developed a modeling approach that incorporates a priori biological pathway knowledge. The degradation pathways of arachidonic and linoleic acids were modeled using a regression model based on a pseudo-steady-state approximated model, resulting in a parameter A that summarizes the relative enzymatic activity in these pathways. Analysis of the phenotypic parameters As suggests that different phenotypes can be discriminated according to preferred relative activity of the arachidonic and linoleic pathway. Correlation analysis shows that there is little or no competition between the arachidonic and linoleic acid pathways, although they share the same enzymes. PMID: 25786212 [PubMed - indexed for MEDLINE]

Related Articles Quercetin attenuates lactate production and extracellular matrix secretion in keratoconus. Sci Rep. 2015;5:9003 Authors: McKay TB, Lyon D, Sarker-Nag A, Priyadarsini S, Asara JM, Karamichos D Abstract Keratoconus(KC) is an ecstatic corneal disease leading to corneal-thinning and the formation of a cone-like cornea. Elevated lactate levels, increased oxidative stress, and myofibroblast formation have all been previously reported. In the current study, we assess the role of Quercetin on collagen secretion and myofibroblast formation in KC in vitro. Human corneal fibroblasts(HCFs) and human keratoconus cells(HKCs) were treated with a stable Vitamin C derivative and cultured for 4 weeks, stimulating formation of a self-assembled extracellular matrix. All samples were analyzed using Western blots and targeted tandem mass spectrometry. Our data showed that Quercetin significantly down regulates myofibroblast differentiation and fibrotic markers, such as α-smooth muscle actin (α-SMA) and Collagen III (Col III), in both HCFs and HKCs. Collagen III secretion was reduced 80% in both HCFs and HKCs following Quercetin treatment. Furthermore, Quercetin reduced lactate production by HKCs to normal HCF levels. Quercetin down regulated TGF-βR2 and TGF-β2 expression in HKCs suggesting a significant link to the TGF-β pathway. These results assert that Quercetin is a key regulator of fibrotic markers and ECM assembly by modulating cellular metabolism and TGF-β signaling. Our study suggests that Quercetin is a potential therapeutic for treatment of corneal dystrophies, such as KC. PMID: 25758533 [PubMed - indexed for MEDLINE]

Related Articles Hi-Jack: a novel computational framework for pathway-based inference of host-pathogen interactions. Bioinformatics. 2015 Jul 15;31(14):2332-9 Authors: Kleftogiannis D, Wong L, Archer JA, Kalnis P Abstract MOTIVATION: Pathogens infect their host and hijack the host machinery to produce more progeny pathogens. Obligate intracellular pathogens, in particular, require resources of the host to replicate. Therefore, infections by these pathogens lead to alterations in the metabolism of the host, shifting in favor of pathogen protein production. Some computational identification of mechanisms of host-pathogen interactions have been proposed, but it seems the problem has yet to be approached from the metabolite-hijacking angle. RESULTS: We propose a novel computational framework, Hi-Jack, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking. Hi-Jack searches metabolic network data from hosts and pathogens, and identifies candidate reactions where hijacking occurs. A novel scoring function ranks candidate hijacked reactions and identifies pathways in the host that interact with pathways in the pathogen, as well as the associated frequent hijacked metabolites. We also describe host-pathogen interaction principles that can be used in the future for subsequent studies. Our case study on Mycobacterium tuberculosis (Mtb) revealed pathways in human-e.g. carbohydrate metabolism, lipids metabolism and pathways related to amino acids metabolism-that are likely to be hijacked by the pathogen. In addition, we report interesting potential pathway interconnections between human and Mtb such as linkage of human fatty acid biosynthesis with Mtb biosynthesis of unsaturated fatty acids, or linkage of human pentose phosphate pathway with lipopolysaccharide biosynthesis in Mtb. AVAILABILITY AND IMPLEMENTATION: Datasets and codes are available at http://cloud.kaust.edu.sa/Pages/Hi-Jack.aspx PMID: 25758402 [PubMed - indexed for MEDLINE]

An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters. Mol Cell Proteomics. 2016 Feb 6; Authors: Gielisch I, Hardt C, Wittig I, Meierhofer D Abstract Hundreds of genes have been associated with respiratory chain disease (RCD), the most common inborn error of metabolism so far. Elimination of the respiratory electron chain by depleting the entire mitochondrial DNA (mtDNA, rho0 cells) has therefore one of the most severe impacts on the energy metabolism in eukaryotic cells. In this study, proteomic data sets including the post transcriptional modifications (PTMs) phosphorylation and ubiquitination were integrated with metabolomic data sets and selected enzyme activities in the osteosarcoma cell line 143B.TK. A shotgun based SILAC LC-MS proteomics and a targeted metabolomics approach was applied to elucidate the consequences of the rho0 state. Pathway and protein protein interaction (PPI) network analyses revealed a non-uniform down-regulation of the respiratory electron chain, the tricarboxylic acid (TCA) cycle and the pyruvate metabolism in rho0 cells. Metabolites of the TCA cycle were dysregulated, such as a reduction of citric acid and cis-aconitic acid (6- and 2.5-fold), and an increase of lactic acid, oxalacetic acid (both 2-fold), and succinic acid (5-fold) in rho0 cells. Signaling pathways such as GPCR, EGFR, G12/13 alpha and Rho GTPases were up-regulated in rho0 cells, which could be indicative for the mitochondrial retrograde response, a pathway of communication from mitochondria to the nucleus. This was supported by our phosphoproteome data, which revealed two main processes, GTPase-related signal transduction and cytoskeleton organization. Furthermore, a general de-ubiquitination in rho0 cells was observed, for example, 80S ribosomal proteins were in average 3-fold and SLC amino acid transporters 5-fold de-ubiquitinated. The latter might cause the observed significant increase of amino acids levels in rho0 cells. We conclude that an elimination of the respiratory electron chain, e.g. mtDNA depletion, not only leads to an uneven down-regulation of mitochondrial energy pathways, but also triggers the retrograde response. PMID: 26852163 [PubMed - as supplied by publisher]

The Emerging Importance of IgG Fab Glycosylation in Immunity. J Immunol. 2016 Feb 15;196(4):1435-41 Authors: van de Bovenkamp FS, Hafkenscheid L, Rispens T, Rombouts Y Abstract Human IgG is the most abundant glycoprotein in serum and is crucial for protective immunity. In addition to conserved IgG Fc glycans, ∼15-25% of serum IgG contains glycans within the variable domains. These so-called "Fab glycans" are primarily highly processed complex-type biantennary N-glycans linked to N-glycosylation sites that emerge during somatic hypermutation. Specific patterns of Fab glycosylation are concurrent with physiological and pathological conditions, such as pregnancy and rheumatoid arthritis. With respect to function, Fab glycosylation can significantly affect stability, half-life, and binding characteristics of Abs and BCRs. Moreover, Fab glycans are associated with the anti-inflammatory activity of IVIgs. Consequently, IgG Fab glycosylation appears to be an important, yet poorly understood, process that modulates immunity. PMID: 26851295 [PubMed - in process]

Reference gene selection for in vitro cell-free DNA analysis and gene expression profiling. Clin Biochem. 2016 Feb 2; Authors: Bronkhorst AJ, Aucamp J, Wentzel JF, Pretorius PJ Abstract OBJECTIVES: (i) To optimize cell-free DNA (cfDNA) and mRNA quantification using eight housekeeping genes (HKGs), (ii) to determine if there is a difference in the occurrence of HKGs in the cfDNA and mRNA of normal cells and cancer cells, and (iii) to investigate whether there is some selectivity involved in the release of cfDNA. DESIGN AND METHODS: cfDNA was isolated directly from the growth medium of 3 cultured cancer cell lines and one non-malignant, primary cell line. At the same time interval, mRNA was isolated from these cells and cDNA was synthesized. CfDNA and cDNA was then amplified with real-time PCR utilizing eight different HKGs. RESULTS: For all cell lines tested, Beta-actin (ACTB) is the most appropriate HKG to use as a control for cfDNA and mRNA quantification. There was no clear difference in the occurrence of HKGs between cancer cells and healthy cells. Lastly, there is a consistent and distinct difference between the mRNA expression and cfDNA of all cell lines. CONCLUSIONS: This study reveals a new candidate HKG for a robust control in cfDNA analysis and gene expression profiling, and should be considered for optimal analysis. Furthermore, results indicate that cfDNA is selectively released from cells into culture medium. PMID: 26851157 [PubMed - as supplied by publisher]

Chromatographic fingerprinting: An innovative approach for food 'identitation' and food authentication - A tutorial. Anal Chim Acta. 2016 Feb 25;909:9-23 Authors: Cuadros-Rodríguez L, Ruiz-Samblás C, Valverde-Som L, Pérez-Castaño E, González-Casado A Abstract Fingerprinting methods describe a variety of analytical methods that provide analytical signals related to the composition of foodstuffs in a non-selective way such as by collecting a spectrum or a chromatogram. Mathematical processing of the information in such fingerprints may allow the characterisation and/or authentication of foodstuffs. In this context, the particular meaning of 'fingerprinting', in conjunction with 'profiling', is different from the original meanings used in metabolomics. This fact has produced some confusion with the use of these terms in analytical papers. Researchers coming from the metabolomic field could use 'profiling' or 'fingerprinting' on a different way to researchers who are devoted to food science. The arrival of an eclectic discipline, named 'foodomics' has not been enough to allay this terminological problem, since the authors keep on using the terms with both meanings. Thus, a first goal of this tutorial is to clarify the difference between both terms. In addition, the chemical approaches for food authentication, i.e., chemical markers, component profiling and instrumental fingerprinting, have been described. A new term, designated as 'food identitation', has been introduced in order to complete the life cycle of the chemical-based food authentication process. Chromatographic fingerprinting has been explained in detail and some strategies which could be applied has been clarified and discussed. Particularly, the strategies for chromatographic signals acquisition and chromatographic data handling are unified in a single framework. Finally, an overview about the applications of chromatographic (GC and LC) fingerprints in food authentication using different chemometric techniques has been included. PMID: 26851080 [PubMed - in process]