PubMed

Related Articles Metabolic Profiling and Identification of Shikonins in Root Periderm of Two Invasive Echium spp. Weeds in Australia. Molecules. 2017 Feb 21;22(2): Authors: Skoneczny D, Weston PA, Zhu X, Gurr GM, Callaway RM, Barrow RA, Weston LA Abstract Metabolic profiling can be successfully implemented to analyse a living system's response to environmental conditions by providing critical information on an organism's physiological state at a particular point in time and allowing for both quantitative and qualitative assessment of a specific subset(s) of key metabolites. Shikonins are highly reactive chemicals that affect various cell signalling pathways and possess antifungal, antibacterial and allelopathic activity. Based on previous bioassay results, bioactive shikonins, are likely to play important roles in the regulation of rhizosphere interactions with neighbouring plants, microbes and herbivores. An effective platform allowing for rapid identification and accurate profiling of numerous structurally similar, difficult-to-separate bioactive isohexenylnaphthazarins (shikonins) was developed using UHPLC Q-TOF MS. Root periderm tissues of the invasive Australian weeds Echium plantagineum and its congener E. vulgare were extracted overnight in ethanol for shikonin profiling. Shikonin production was evaluated at seedling, rosette and flowering stages. Five populations of each species were compared for qualitative and quantitative differences in shikonin formation. Each species showed little populational variation in qualitative shikonin production; however, shikonin was considerably low in one population of E. plantagineum from Western New South Wales. Seedlings of all populations produced the bioactive metabolite acetylshikonin and production was upregulated over time. Mature plants of both species produced significantly higher total levels of shikonins and isovalerylshikonin > dimethylacrylshikonin > shikonin > acetylshikonin in mature E. plantagineum. Although qualitative metabolic profiles in both Echium spp. were nearly identical, shikonin abundance in mature plant periderm was approximately 2.5 times higher in perennial E. vulgare extracts in comparison to those of the annual E. plantagineum. These findings contribute to our understanding of the biosynthesis of shikonins in roots of two related invasive plants and their expression in relation to plant phenological stage. PMID: 28230806 [PubMed - in process]

Related Articles Omics and cachexia. Curr Opin Clin Nutr Metab Care. 2017 Feb 21;: Authors: Twelkmeyer B, Tardif N, Rooyackers O Abstract PURPOSE OF REVIEW: The purpose of this review is to recapture recent advances in cachexia-related diseases, mainly cancer cachexia, and treatment using genomic, transcriptomics, proteomic, and metabolomics-related techniques. RECENT FINDINGS: From recent studies in the cancer cachexia field it is clear that the tumor has a direct effect on distant organs via its secretome. The affected pathways on the other hand were largely known from earlier studies with changes in energy-related pathways (mainly lipid metabolism) and the protein degradation pathways. Treatment-oriented studies use mostly rodent models and in-vivo cultures and it is too early for human studies. SUMMARY: Omics tools are powerful if used in the right way. Omics research has identified the tumor as an important player in cancer cachexia and some interesting novel treatments have been found in experimental models. PMID: 28230703 [PubMed - as supplied by publisher]

Related Articles Paradoxical Inhibition of Glycolysis by Pioglitazone Opposes the Mitochondriopathy Caused by AIF Deficiency. EBioMedicine. 2017 Feb 16;: Authors: Bénit P, Pelhaître A, Saunier E, Bortoli S, Coulibaly A, Rak M, Schiff M, Kroemer G, Zeviani M, Rustin P Abstract Mice with the hypomorphic AIF-Harlequin mutation exhibit a highly heterogeneous mitochondriopathy that mostly affects respiratory chain complex I, causing a cerebral pathology that resembles that found in patients with AIF loss-of-function mutations. Here we describe that the antidiabetic drug pioglitazone (PIO) can improve the phenotype of a mouse Harlequin (Hq) subgroup, presumably due to an inhibition of glycolysis that causes an increase in blood glucose levels. This glycolysis-inhibitory PIO effect was observed in cultured astrocytes from Hq mice, as well as in human skin fibroblasts from patients with AIF mutation. Glycolysis inhibition by PIO resulted from direct competitive inhibition of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Moreover, GAPDH protein levels were reduced in the cerebellum and in the muscle from Hq mice that exhibited an improved phenotype upon PIO treatment. Altogether, our results suggest that excessive glycolysis participates to the pathogenesis of mitochondriopathies and that pharmacological inhibition of glycolysis may have beneficial effects in this condition. PMID: 28229909 [PubMed - as supplied by publisher]

Related Articles Effects of Boron Supplementation on Peripartum Dairy Cows' Health. Biol Trace Elem Res. 2017 Feb 22;: Authors: Basoglu A, Baspinar N, Tenori L, Vignoli A, Gulersoy E Abstract Although many different dietary studies on the prevention of negative energy balance related diseases are often encountered, this is the first study investigating the effects of boron supplementation on peripartum dairy cows' health in the light of an omics approach. Twenty-eight healthy cows (1 control and 3 experimental groups) were enrolled from 2 months before predicted calving until 2 months after calving. Experimental groups were assigned to receive boron at increasing doses as an oral bolus. Production parameters, biochemical profile, Nuclear Magnetic Resonance based metabolomics profile, and mRNA abundance of gluconeogenic enzymes and lipid oxidation genes were determined. Pivotal knowledge was obtained on boron distribution in the body. Production parameters and mRNA abundance of the genes were not affected by the treatments. Postpartum nonesterified fatty acids, β-hydroxybutyrate, and triglyceride concentrations were significantly decreased in experimentals. The primary differences among groups were in lipid-soluble metabolites. There were significant differences in metabolites including postpartum valine, β-hydroxybutyrate, polyunsaturated fatty acid and citrate, propionate, isobutyrate, choline metabolites (betaine, phosphatidylcholine, and sphingomyelin), and some types of fatty acids and cholesterol in experimentals. Boron appears to be effective in minimizing negative energy balance and improving health of postpartum dairy cows. PMID: 28229388 [PubMed - as supplied by publisher]

Related Articles Implications of SDHB genetic testing in patients with sporadic pheochromocytoma. Langenbecks Arch Surg. 2017 Feb 22;: Authors: Maignan A, Guerin C, Julliard V, Paladino NC, Kim E, Roche P, Castinetti F, Essamet W, Mancini J, Imperiale A, Clifton-Bligh R, Romanet P, Barlier A, Pacak K, Sebag F, Taïeb D Abstract PURPOSE: Succinate dehydrogenase B (SDHB) associated pheochromocytomas (PHEOs) are associated with a higher risk of tumor aggressiveness and malignancy. The aim of the present study was to evaluate (1) the frequency of germline SDHB mutations in apparently sporadic patients with PHEO who undergo preoperative genetic testing and (2) the ability to predict pathogenic mutations. METHODS: From 2012 to 2016, 82 patients underwent a PHEO surgical resection. Sixteen were operated in the context of hereditary PHEO and were excluded from analysis. Among the 66 remaining cases, 48 were preoperatively screened for an SDHB mutation. In addition to imaging studies with specific radiopharmaceuticals ((123)I-MIBG or (18)F-FDOPA) for exclusion of multifocality/metastases, 36 patients underwent (18)F-FDG PET/CT. RESULTS: From the 48 genetically screened patients, genetic testing found a germline SDHB variant in two (4.2%) cases: a variant of unknown significance, exon 1, c.14T>G (p.Val5Gly), and a most likely pathogenic mutation, exon 5, c.440A>G (p.Tyr147Cys), according to in silico analysis. Structural and functional analyses of the protein predicted that p.Tyr147Cys mutant was pathogenic. Both tumors exhibited moderate (18)F-FDG PET uptake with similar uptake patterns to non-SDHB mutated PHEOs. The two patients underwent total laparoscopic adrenalectomies. Of the remaining patients, 44 underwent a laparoscopic adrenalectomy, and two had an open approach. Pathological analysis of the tumors from patients bearing two germline SDHB variants revealed a typical PHEO (PASS 0 and 2). Ex-vivo analyses (metabolomics, SDHB immunohistochemistry, loss of heterozygosity analysis) allowed a reclassification of the two SDHB variants as probably non-pathogenic variants. CONCLUSIONS: This study illustrates that SDHx mutational analysis can be misleading, even if structural and functional analyses are done. Surgeons should be aware of the difficulty of classifying new SDHB variants prior to implementing SDHB mutation status into a tailored surgical management strategy of a patient. PMID: 28229225 [PubMed - as supplied by publisher]

Related Articles Modeling non-clinical and clinical drug tests in Gaucher disease. Conf Proc IEEE Eng Med Biol Soc. 2016 Aug;2016:1434-1438 Authors: Phelix CF, Bourdon AK, Villareal G, LeBaron RG, Phelix CF, Bourdon AK, Villareal G, LeBaron RG, LeBaron RG, Phelix CF, Bourdon AK, Villareal G Abstract There is need for modeling biological systems to accelerate drug pipelines for treating metabolic diseases. The eliglustat treatment for Gaucher disease is approved by the FDA with a companion genomic test. The Transcriptome-To-Metabolome™ biosimulation technology was used to model, in silico, a standard non-clinical eliglustat test with an in vitro canine kidney cell system over-expressing a human gene; and a clinical test using human fibroblasts from control and Gaucher disease subjects. Protein homology modeling and docking studies were included to gather affinity parameters for the kinetic metabolic model. Pharmacodynamics and metabolomics analyses of the results replicated published findings and demonstrated that processing and transport of lysosomal proteins alone cannot explain the metabolic disorder. This technology shows promise for application to other diseases. PMID: 28226774 [PubMed - in process]

Top-down Metabolomic Approaches for Nitrogen-Containing Metabolites. Anal Chem. 2017 Feb 22;: Authors: Nakabayashi R, Hashimoto K, Toyooka K, Saito K Abstract Streamlining the processes that reveal heteroatom-containing metabolites and their biosynthetic genes is essential in integrated metabolomics studies. These metabolites are especially targeted for their potential pharmaceutical activities. By using a Fourier-transform ion cyclotron resonance-mass spectrometry (FTICR-MS) instrument, we provide top-down targeted metabolomic analyses using ultrahigh-resolution liquid chromatography-mass spectrometry (LC-MS), high-resolution matrix-assisted laser desorption/ionization (MALDI), and high-resolution imaging mass spectrometry (IMS) with (15)N labeling of nitrogen-containing metabolites. In this study, we efficiently extract known and unknown chemicals and spatial information from the medicinal plant Catharanthus roseus, which sources several cancer drugs. The ultrahigh-resolution LC-MS analysis showed that the molecular formula of 65 N-metabolites were identified using the petals, peduncles, leaves, petioles, stems, and roots of the non- and (15)N-labeled Catharanthus plants. The high resolution MALDI analysis showed the molecular formula of 64 N-metabolites using the petals, leaves, and stems of the non- and (15)N-labeled Catharanthus. The chemical assignments using molecular formulas stored in databases identified known and unknown metabolites. The comparative analyses using the assigned metabolites revealed that most of the organ-specific ions are derived from unknown N-metabolites. The high-resolution IMS analysis characterized the spatial accumulation patterns of 32 N-metabolites using the buds, leaves, stems, and roots in Catharanthus. The comparative analysis using the non- and (15)N-labeled IMS data showed the same spatial accumulation patterns of a non- and (15)N-labeled metabolite in the organs, showing that top-down analysis can be performed even in IMS analysis. PMID: 28225596 [PubMed - as supplied by publisher]

Mass Spectral Feature List Optimizer (MS-FLO): a tool to minimize false positive peak reports in untargeted LC-MS data processing. Anal Chem. 2017 Feb 22;: Authors: Defelice BC, Mehta SS, Samra S, Cajka T, Wancewicz B, Fahrmann JF, Fiehn O Abstract Untargeted metabolomics by liquid chromatography-mass spectrometry generates data rich chromatograms in form of m/z-retention time features. Managing such datasets is a bottleneck. Many popular data processing tools, including XCMS-online and MZmine2, yield numerous false positive peak detections. Flagging and removing such false peaks manually is a time consuming task and prone to human error. We present a web application, MS Feature List Optimizer (MS-FLO), to improve the quality of feature lists after initial processing to expedite the process of data curation. The tool utilizes retention time alignments, accurate mass tolerances, Pearson's correlation analysis, and peak height similarity to identify ion-adducts, duplicate peak reports and isotopic features of the main monoisotopic metabolites. Removing such erroneous peaks reduces the overall number of metabolites in data reports and improves the quality of subsequent statistical investigations. To demonstrate the effectiveness of MS-FLO, we processed 28 biological studies and uploaded raw and results data to the metabolomicsworkbench.org, encompassing 1,481 chromatograms produced by two different data processing programs used in-house (MZmine2 and later MS-DIAL). Post-processing of datasets with MS-FLO yielded a 7.8% automated reduction of total peak features and flagged an additional 7.9% of features, per dataset, for review by the user. When manually curated, 87% of these additional flagged features were verified false positives. MS-FLO is an open source web application that is freely available for use at http://msflo.fiehnlab.ucdavis.edu. PMID: 28225594 [PubMed - as supplied by publisher]

Urinary metabolic signatures and early triage of acute radiation exposure in rat model. Mol Biosyst. 2017 Feb 22;: Authors: Zhao M, Lau KK, Zhou X, Wu J, Yang J, Wang C Abstract After a large-scale radiological accident, early-response biomarkers to assess radiation exposure over a broad dose range are not only the basis of rapid radiation triage, but are also the key to the rational use of limited medical resources and to the improvement of treatment efficiency. Because of its high throughput, rapid assays and minimally invasive sample collection, metabolomics has been applied to research into radiation exposure biomarkers in recent years. Due to the complexity of radiobiological effects, most of the potential biomarkers are both dose-dependent and time-dependent. In reality, it is very difficult to find a single biomarker that is both sensitive and specific in a given radiation exposure scenario. Therefore, a multi-parameters approach for radiation exposure assessment is more realistic in real nuclear accidents. In this study, untargeted metabolomic profiling based on gas chromatography-mass spectrometry (GC-MS) and targeted amino acid profiling based on LC-MS/MS were combined to investigate early urinary metabolite responses within 48 h post-exposure in a rat model. A few of the key early-response metabolites for radiation exposure were identified, which revealed the most relevant metabolic pathways. Furthermore, a panel of potential urinary biomarkers was selected through a multi-criteria approach and applied to early triage following irradiation. Our study suggests that it is feasible to use a multi-parameters approach to triage radiation damage, and the urinary excretion levels of the relevant metabolites provide insights into radiation damage and repair. PMID: 28225098 [PubMed - as supplied by publisher]

A Comprehensive Analysis of Metabolomics and Transcriptomics in Cervical Cancer. Sci Rep. 2017 Feb 22;7:43353 Authors: Yang K, Xia B, Wang W, Cheng J, Yin M, Xie H, Li J, Ma L, Yang C, Li A, Fan X, Dhillon HS, Hou Y, Lou G, Li K Abstract Cervical cancer (CC) still remains a common and deadly malignancy among females in developing countries. More accurate and reliable diagnostic methods/biomarkers should be discovered. In this study, we performed a comprehensive analysis of metabolomics (285 samples) and transcriptomics (52 samples) on the potential diagnostic implication and metabolic characteristic description in cervical cancer. Sixty-two metabolites were different between CC and normal controls (NOR), in which 5 metabolites (bilirubin, LysoPC(17:0), n-oleoyl threonine, 12-hydroxydodecanoic acid and tetracosahexaenoic acid) were selected as candidate biomarkers for CC. The AUC value, sensitivity (SE), and specificity (SP) of these 5 biomarkers were 0.99, 0.98 and 0.99, respectively. We further analysed the genes in 7 significantly enriched pathways, of which 117 genes, that were expressed differentially, were mainly involved in catalytic activity. Finally, a fully connected network of metabolites and genes in these pathways was built, which can increase the credibility of our selected metabolites. In conclusion, our biomarkers from metabolomics could set a path for CC diagnosis and screening. Our results also showed that variables of both transcriptomics and metabolomics were associated with CC. PMID: 28225065 [PubMed - in process]

Comparison of multivariate curve resolution strategies in quantitative LCxLC: Application to the quantification of furanocoumarins in apiaceous vegetables. Anal Chim Acta. 2017 Apr 08;961:49-58 Authors: Cook DW, Burnham ML, Harmes DC, Stoll DR, Rutan SC Abstract Comprehensive two-dimensional liquid chromatography (LC × LC) has been gaining popularity for the analysis of complex samples in a wide range of fields including metabolomics, environmental analysis, and food analysis. While LC × LC can provide greater chromatographic resolution than one-dimensional LC (1D-LC), overlapping peaks are often still present in separations of complex samples, a problem that can be alleviated by chemometric curve resolution techniques such as multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS has also been previously shown to assist in the quantitative analysis of LC x LC data by isolating pure analyte signals from background signals which are often present at higher levels in LC x LC compared to 1D-LC. In this work we present the analysis of a dataset from the LC × LC analyses of parsley, parsnip and celery samples for the presence and concentrations of 14 furanocoumarins. Several MCR-ALS implementations are compared for the analysis of LC × LC data. These implementations include analyzing the LC x LC chromatogram alone, analyzing the one-dimensional chromatogram alone, as well as two hybrid approaches that make use of both the first and second dimension chromatograms. Furthermore, we compared manual integration of resolved chromatograms versus a simple summation approach, using the resolved chromatographic peaks in both cases. It is found that manual integration of the resolved LC × LC chromatograms provides the best quantification as measured by the consistency between replicate injections. If the summation approach is desired for automation, the choice of MCR-ALS implementation has a large effect on the precision of the analysis. Based on these results, the concentrations of the 14 furanocoumarins are determined in the three apiaceous vegetable types by analyzing the LC × LC chromatograms with MCR-ALS and manual integration for peak area determination. The concentrations of the analytes are found to vary greatly between samples, even within a single vegetable type. PMID: 28224908 [PubMed - in process]

Related Articles Untargeted Metabotyping Lolium perenne Reveals Population-Level Variation in Plant Flavonoids and Alkaloids. Front Plant Sci. 2017;8:133 Authors: Cao M, Fraser K, Jones C, Stewart A, Lyons T, Faville M, Barrett B Abstract Metabolomics provides a powerful platform to characterize plants at the biochemical level, allowing a search for underlying genes and associations with higher level complex traits such as yield and nutritional value. Efficient and reliable methods to characterize metabolic variation in economically important species are considered of high value to the evaluation and prioritization of germplasm and breeding lines. In this investigation, a large-scale metabolomic survey was performed on a collection of diverse perennial ryegrass (Lolium perenne L.) plants. A total of 2,708 data files, derived from liquid chromatography coupled to high resolution mass spectrometry (LCMS), were selected to assess the effectiveness and efficiency of applying high throughput metabolomics to survey chemical diversity in plant populations. The data set was generated from 23 ryegrass populations, with 3-25 genotypes per population, and five clonal replicates per genotype. We demonstrate an integrated approach to rapidly mine and analyze metabolic variation from this large, multi-batch LCMS data set. After performing quality control, statistical data mining and peak annotation, a wide range of variation for flavonoid glycosides and plant alkaloids was discovered among the populations. Structural variation of flavonoids occurs both in aglycone structures and acetylated/malonylated/feruloylated sugar moieties. The discovery of comprehensive metabolic variation among the plant populations offers opportunities to probe into the genetic basis of the variation, and provides a valuable resource to gain insight into biochemical functions and to relate metabolic variation with higher level traits in the species. PMID: 28223996 [PubMed - in process]

Related Articles Metabolic profiling of presymptomatic Huntington's disease sheep reveals novel biomarkers. Sci Rep. 2017 Feb 22;7:43030 Authors: Skene DJ, Middleton B, Fraser CK, Pennings JL, Kuchel TR, Rudiger SR, Bawden CS, Morton AJ Abstract The pronounced cachexia (unexplained wasting) seen in Huntington's disease (HD) patients suggests that metabolic dysregulation plays a role in HD pathogenesis, although evidence of metabolic abnormalities in HD patients is inconsistent. We performed metabolic profiling of plasma from presymptomatic HD transgenic and control sheep. Metabolites were quantified in sequential plasma samples taken over a 25 h period using a targeted LC/MS metabolomics approach. Significant changes with respect to genotype were observed in 89/130 identified metabolites, including sphingolipids, biogenic amines, amino acids and urea. Citrulline and arginine increased significantly in HD compared to control sheep. Ten other amino acids decreased in presymptomatic HD sheep, including branched chain amino acids (isoleucine, leucine and valine) that have been identified previously as potential biomarkers of HD. Significant increases in urea, arginine, citrulline, asymmetric and symmetric dimethylarginine, alongside decreases in sphingolipids, indicate that both the urea cycle and nitric oxide pathways are dysregulated at early stages in HD. Logistic prediction modelling identified a set of 8 biomarkers that can identify 80% of the presymptomatic HD sheep as transgenic, with 90% confidence. This level of sensitivity, using minimally invasive methods, offers novel opportunities for monitoring disease progression in HD patients. PMID: 28223686 [PubMed - in process]

Related Articles Differential TOR activation and cell proliferation in Arabidopsis root and shoot apexes. Proc Natl Acad Sci U S A. 2017 Feb 21;: Authors: Li X, Cai W, Liu Y, Li H, Fu L, Liu Z, Xu L, Liu H, Xu T, Xiong Y Abstract The developmental plasticity of plants relies on the remarkable ability of the meristems to integrate nutrient and energy availability with environmental signals. Meristems in root and shoot apexes share highly similar molecular players but are spatially separated by soil. Whether and how these two meristematic tissues have differential activation requirements for local nutrient, hormone, and environmental cues (e.g., light) remain enigmatic in photosynthetic plants. Here, we report that the activation of root and shoot apexes relies on distinct glucose and light signals. Glucose energy signaling is sufficient to activate target of rapamycin (TOR) kinase in root apexes. In contrast, both the glucose and light signals are required for TOR activation in shoot apexes. Strikingly, exogenously applied auxin is able to replace light to activate TOR in shoot apexes and promote true leaf development. A relatively low concentration of auxin in the shoot and high concentration of auxin in the root might be responsible for this distinctive light requirement in root and shoot apexes, because light is required to promote auxin biosynthesis in the shoot. Furthermore, we reveal that the small GTPase Rho-related protein 2 (ROP2) transduces light-auxin signal to activate TOR by direct interaction, which, in turn, promotes transcription factors E2Fa,b for activating cell cycle genes in shoot apexes. Consistently, constitutively activated ROP2 plants stimulate TOR in the shoot apex and cause true leaf development even without light. Together, our findings establish a pivotal hub role of TOR signaling in integrating different environmental signals to regulate distinct developmental transition and growth in the shoot and root. PMID: 28223530 [PubMed - as supplied by publisher]

Related Articles Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles. MBio. 2017 Feb 21;8(1): Authors: Doberenz S, Eckweiler D, Reichert O, Jensen V, Bunk B, Spröer C, Kordes A, Frangipani E, Luong K, Korlach J, Heeb S, Overmann J, Kaever V, Häussler S Abstract DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved sequence motif targeted by an adenine methyltransferase of a type I R-M system and quantified the presence of N(6)-methyladenine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1 methylation status were dependent on growth conditions and affected P. aeruginosa pathogenicity in a Galleria mellonella infection model. Furthermore, we found that methylated motifs in promoter regions led to shifts in sense and antisense gene expression, emphasizing the role of enzymatic DNA methylation as an epigenetic control of phenotypic traits in P. aeruginosa Since the DNA methylation enzymes are not encoded in the core genome, our findings illustrate how the acquisition of accessory genes can shape the global P. aeruginosa transcriptome and thus may facilitate adaptation to new and challenging habitats.IMPORTANCE With the introduction of advanced technologies, epigenetic regulation by DNA methyltransferases in bacteria has become a subject of intense studies. Here we identified an adenosine DNA methyltransferase in the opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA methylation of a conserved sequence motif. The methylation level of all target sequences throughout the PAO1 genome was approximated to be in the range of 65 to 85% and was dependent on growth conditions. Inactivation of the methyltransferase revealed an attenuated-virulence phenotype in the Galleria mellonella infection model. Furthermore, differential expression of more than 90 genes was detected, including the small regulatory RNA prrF1, which contributes to a global iron-sparing response via the repression of a set of gene targets. Our finding of a methylation-dependent repression of the antisense transcript of the prrF1 small regulatory RNA significantly expands our understanding of the regulatory mechanisms underlying active DNA methylation in bacteria. PMID: 28223461 [PubMed - in process]

Related Articles Metabolomic profiling reveals distinct patterns of tricarboxylic acid disorders in blood stasis syndrome associated with coronary heart disease. Chin J Integr Med. 2016 Aug;22(8):597-604 Authors: Wang Y, Li C, Chang H, Lu LH, Qiu Q, Ouyang YL, Yu JD, Guo SZ, Han J, Wang W Abstract OBJECTIVE: To investigate the underlying metabolomic profifiling of coronary heart disease (CHD) with blood stasis syndrome (BSS). METHODS: CHD model was induced by a nameroid constrictor in Chinese miniature swine. Fifteen miniature swine were randomly divided into a model group (n=9) and a control group (n=6), respectively according to arandom number table. After 4 weeks, plasma hemorheology was detected by automatic hemorheological analyzer, indices including hematocrit, plasma viscosity, blood viscosity, rigidity index and erythrocyte sedimentation rate; cardiac function was assessed by echocardiograph to detect left ventricular end-systolic diameter (LVED), left ventricular end-diastolic diameter (LVEDd), ejection fraction (EF), fractional shortening (FS) and other indicators. Gas chromatography coupled with mass spectrometry (GC-MS) and bioinformatics were applied to analyze spectra of CHD plasma with BSS. RESULTS: The results of hemorheology analysis showed signifificant changes in viscosity, with low shear whole blood viscosity being lower and plasma viscosity higher in the model group compared with the control group. Moreover, whole blood reduction viscosity at high shear rate and whole blood reduction viscosity at low shear rate increased signifificantly (P <0.05). The echocardiograph results demonstrated that cardiac EF and FS showed signifificant difference (P <0.05), with EF values being decreased to 50% or less. The GC-MS data showed that principal component analysis can clearly separate the animals with BSS from those in the control group. The enriched Kyoto Encyclopedia of Genes and Genomes biological pathways results suggested that the patterns involved were associated with dysfunction of energy metabolism including glucose and lipid disorders, especially in glycolysis/gluconeogenesis, galactose metabolism and adenosine-triphosphate-binding cassette transporters. CONCLUSIONS: Glucose metabolism and lipid metabolism disorders were the major contributors to the syndrome classifification of CHD with BSS. PMID: 27184905 [PubMed - indexed for MEDLINE]

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Related Articles Dysregulation of Metabolic Pathways in a Mouse Model of Allergic Asthma. Allergy. 2017 Feb 18;: Authors: Quinn KD, Schedel M, Nkrumah-Elie Y, Joetham A, Armstrong M, Cruickshank-Quinn C, Reisdorph R, Gelfand EW, Reisdorph N Abstract BACKGROUND: Asthma is a complex lung disease resulting from the interplay of genetic and environmental factors. To understand the molecular changes that occur during the development of allergic asthma without genetic and environmental confounders, an experimental model of allergic asthma in mice was used. Our goals were to (1) identify changes at the small molecule level due to allergen exposure, (2) determine perturbed pathways due to disease, and (3) determine whether small molecule changes correlate with lung function. METHODS: In this experimental model of allergic asthma, matched bronchoalveolar lavage (BAL) fluid and plasma were collected from three groups of C57BL6 mice (control vs sensitized and/or challenged with ovalbumin, n=3-5/group) 6h, 24h, and 48h after the last challenge. Samples were analyzed using liquid chromatography mass spectrometry-based metabolomics. Airway hyperresponsiveness (AHR) measurements and differential cell counts were performed. RESULTS: In total, 398 and 368 dysregulated metabolites in the BAL fluid and plasma of sensitized and challenged mice were identified, respectively. These belonged to four, interconnected pathways relevant to asthma pathogenesis: sphingolipid metabolism (p=6.6x10(-5) ), arginine and proline metabolism (p=1.12x10(-7) ), glycerophospholipid metabolism (p=1.3x10(-10) ), and the neurotrophin signaling pathway (p=7.0x10(-6) ). Furthermore, within the arginine and proline metabolism pathway, a positive correlation between urea-1-carboxyate and AHR was observed in plasma metabolites, while ornithine revealed a reciprocal effect. In addition, agmatine positively correlated with lung eosinophilia. CONCLUSION: These findings point to potential targets and pathways that may be central to asthma pathogenesis and can serve as novel therapeutic targets. This article is protected by copyright. All rights reserved. PMID: 28213886 [PubMed - as supplied by publisher]

Related Articles Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut. 2017 Feb 17;: Authors: Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J Abstract OBJECTIVE: Contrary to the long-standing prerequisite of inducing selective (ie, bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterisation of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (gas chromatography mass spectrometry) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and faecal metabolites profiles. DESIGN: Faecal samples collected during a double-blind, randomised, cross-over intervention study set up to assess the effect of inulin consumption on stool frequency in healthy adults with mild constipation were analysed. Faecal microbiota composition and metabolite profiles were linked to the study's clinical outcome as well as to quality-of-life measurements recorded. RESULTS: While faecal metabolite profiles were not significantly altered by inulin consumption, our analyses did detect a modest effect on global microbiota composition and specific inulin-induced changes in relative abundances of Anaerostipes, Bilophila and Bifidobacterium were identified. The observed decrease in Bilophila abundances following inulin consumption was associated with both softer stools and a favourable change in constipation-specific quality-of-life measures. CONCLUSIONS: Ecosystem-wide analysis of the effect of a dietary intervention with prebiotic inulin-type fructans on the colon microbiota revealed that this effect is specifically associated with three genera, one of which (Bilophila) representing a promising novel target for mechanistic research. TRIAL REGISTRATION NUMBER: NCT02548247. PMID: 28213610 [PubMed - as supplied by publisher]

Related Articles Drug discovery strategies in the field of tumor energy metabolism: Limitations by metabolic flexibility and metabolic resistance to chemotherapy. Biochim Biophys Acta. 2017 Feb 14;: Authors: Amoedo ND, Obre E, Rossignol R Abstract The search for new drugs capable of blocking the metabolic vulnerabilities of human tumors has now entered the clinical evaluation stage, but several projects already failed in phase I or phase II. In particular, very promising in vitro studies could not be translated in vivo at preclinical stage and beyond. This was the case for most glycolysis inhibitors that demonstrated systemic toxicity. A more recent example is the inhibition of glutamine catabolism in lung adenocarcinoma that failed in vivo despite a strong addiction of several cancer cell lines to glutamine in vitro. Such contradictory findings raised several questions concerning the optimization of drug discovery strategies in the field of cancer metabolism. For instance, the cell culture models in 2D or 3D might already show strong limitations to mimic the tumor micro- and macro-environment. The microenvironment of tumors is composed of cancer cells of variegated metabolic profiles, supporting local metabolic exchanges and symbiosis, but also of immune cells and stroma that further interact with and reshape cancer cell metabolism. The macroenvironment includes the different tissues of the organism, capable of exchanging signals and fueling the tumor 'a distance'. Moreover, most metabolic targets were identified from their increased expression in tumor transcriptomic studies, or from targeted analyses looking at the metabolic impact of particular oncogenes or tumor suppressors on selected metabolic pathways. Still, very few targets were identified from in vivo analyses of tumor metabolism in patients because such studies are difficult and adequate imaging methods are only currently being developed for that purpose. For instance, perfusion of patients with [(13)C]-glucose allows deciphering the metabolomics of tumors and opens a new area in the search for effective targets. Metabolic imaging with positron emission tomography and other techniques that do not involve [(13)C] can also be used to evaluate tumor metabolism and to follow the efficiency of a treatment at a preclinical or clinical stage. Relevant descriptors of tumor metabolism are now required to better stratify patients for the development of personalized metabolic medicine. In this review, we discuss the current limitations in basic research and drug discovery in the field of cancer metabolism to foster the need for more clinically relevant target identification and validation. We discuss the design of adapted drug screening assays and compound efficacy evaluation methods for the discovery of innovative anti-cancer therapeutic approaches at the level of tumor energetics. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux. PMID: 28213330 [PubMed - as supplied by publisher]