PubMed

Irinotecan (CPT-11)-induced elevation of bile acids potentiates suppression of IL-10 expression. Toxicol Appl Pharmacol. 2015 Dec 16; Authors: Fang ZZ, Zhang D, Cao YF, Xie C, Lu D, Sun DX, Tanaka N, Jiang C, Chen Q, Chen Y, Wang H, Gonzalez FJ Abstract Irinotecan (CPT-11) is a first-line anti-colon cancer drug, however; CPT-11-induced toxicity remains a key factor limiting its clinical application. To search for clues to the mechanism of CPT-11-induced toxicity, metabolomics was applied using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry. Intraperitoneal injection of 50mg/kg of CPT-11 induced loss of body weight, and intestine toxicity. Changes in gallbladder morphology suggested alterations in bile acid metabolism, as revealed at the molecular level by analysis of the liver, bile, and ileum metabolomes between the vehicle-treated control group and the CPT-11-treated group. Analysis of immune cell populations further showed that CPT-11 treatment significantly decreased the IL-10-producing CD4 T cell frequency in intestinal lamina propria lymphocytes, but not in spleen or mesenteric lymph nodes. In vitro cell culture studies showed that the addition of bile acids deoxycholic acid and taurodeoxycholic acid accelerated the CPT-11-induced suppression of IL-10 secretion by activated CD4(+) naive T cells isolated from mouse splenocytes. These results showed that CPT-11 treatment caused metabolic changes in the composition of bile acids that altered CPT-11-induced suppression of IL-10 expression. PMID: 26706406 [PubMed - as supplied by publisher]

Metabolomic profiling from leaves and roots of tomato (Solanum lycopersicum L.) plants grown under nitrogen, phosphorus or potassium-deficient condition. Plant Sci. 2015 Dec;241:55-64 Authors: Sung J, Lee S, Lee Y, Ha S, Song B, Kim T, Waters BM, Krishnan HB Abstract Specific metabolic network responses to mineral deficiencies are not well-defined. Here, we conducted a detailed broad-scale identification of metabolic responses of tomato leaves and roots to N, P or K deficiency. Tomato plants were grown hydroponically under optimal (5mM N, 0.5mM P, or 5mM K) and deficient (0.5mM N, 0.05mM P, or 0.5mM K) conditions and metabolites were measured by LC-MS and GC-MS. Based on these results, deficiency of any of these three minerals affected energy production and amino acid metabolism. N deficiency generally led to decreased amino acids and organic acids, and increased soluble sugars. P deficiency resulted in increased amino acids and organic acids in roots, and decreased soluble sugars. K deficiency caused accumulation of soluble sugars and amino acids in roots, and decreased organic acids and amino acids in leaves. Notable metabolic pathway alterations included; (1) increased levels of α-ketoglutarate and raffinose family oligosaccharides in N, P or K-deficient tomato roots, and (2) increased putrescine in K-deficient roots. These findings provide new knowledge of metabolic changes in response to mineral deficiencies. PMID: 26706058 [PubMed - in process]

Cohort Profile: The Framingham Heart Study (FHS): overview of milestones in cardiovascular epidemiology. Int J Epidemiol. 2015 Dec;44(6):1800-13 Authors: Tsao CW, Vasan RS Abstract The Framingham Heart Study (FHS) has conducted seminal research defining cardiovascular disease (CVD) risk factors and fundamentally shaping public health guidelines for CVD prevention over the past five decades. The success of the Original Cohort, initiated in 1948, paved the way for further epidemiological research in preventive cardiology. Due to the keen observations suggesting the role of shared familial factors in the development of CVD, in 1971 the FHS began enroling the second generation cohort, comprising the children of the Original Cohort and the spouses of the children. In 2002, the third generation cohort, comprising the grandchildren of the Original Cohort, was initiated to additionally explore genetic contributions to CVD in greater depth. Additionally, because of the predominance of White individuals of European descent in the three generations of FHS participants noted above, the Heart Study enrolled the OMNI1 and OMNI2 cohorts in 1994 and 2003, respectively, aimed to reflect the current greater racial and ethnic diversity of the town of Framingham. All FHS cohorts have been examined approximately every 2-4 years since the initiation of the study. At these periodic Heart Study examinations, we obtain a medical history and perform a cardiovascular-focused physical examination, 12-lead electrocardiography, blood and urine samples testing and other cardiovascular imaging studies reflecting subclinical disease burden.The FHS has continually evolved along the cutting edge of cardiovascular science and epidemiological research since its inception. Participant studies now additionally include study of cardiovascular imaging, serum and urine biomarkers, genetics/genomics, proteomics, metabolomics and social networks. Numerous ancillary studies have been established, expanding the phenotypes to encompass multiple organ systems including the lungs, brain, bone and fat depots, among others. Whereas the FHS was originally conceived and designed to study the epidemiology of cardiovascular disease, it has evolved over the years with staggering expanded breadth and depth that have far greater implications in the study of the epidemiology of a wide spectrum of human diseases. The FHS welcomes research collaborations using existing or new collection of data. Detailed information regarding the procedures for research application submission and review are available at [http://www.framinghamheartstudy.org/researchers/index.php]. PMID: 26705418 [PubMed - in process]

A metabolomics study of retrospective forensic data from whole blood samples of humans exposed to 3,4-methylenedioxymethamphetamine (MDMA) - A new approach for identifying drug metabolites and changes in metabolism related to drug consumption. J Proteome Res. 2015 Dec 25; Authors: Nielsen KL, Telving R, Andreasen MF, Hasselstrøm JB, Johannsen M Abstract The illicit drug 3,4-methylenedioxymethamphetamine (MDMA) has profound physiological cerebral, cardiac and hepatic effects that are reflected in the blood. Screening of blood for MDMA and other narcotics are routinely performed in forensics analysis using ultra-performance liquid chromatography with high-resolution time-of-flight mass spectrometry (UPLC-HR-TOFMS). The aim of this study was to investigate whether such UPLC-HR-TOFMS data collected over a two year period could be used for untargeted metabolomics to determine MDMA metabolites as well as endogenous changes related to drug response and toxicology. Whole blood samples from living Danish drivers' positive for MDMA in different concentrations were compared to negative control samples using various statistical methods. The untargeted identification of known MDMA metabolites was used to validate the methods. The results further revealed changes of several acylcarnitines, adenosine monophosphate (AMP), adenosine, inosine, thiomorpholine 3-carboxylate (TMC), tryptophan, S-adenosyl-L-homocysteine (SAH) and lysophospatidylcholine (lysoPC) species in response to MDMA. These endogenous metabolites could be implicated in an increased energy demand and mechanisms related to the serotonergic syndrome as well as drug induced neurotoxicity. The findings showed that it was possible to extract meaningful results from retrospective UPLC-HR-TOFMS screening data for metabolic profiling in relation to drug metabolism, endogenous physiological effects, and toxicology. PMID: 26705142 [PubMed - as supplied by publisher]

Personalized Radiation Therapy (PRT) for Lung Cancer. Adv Exp Med Biol. 2016;890:175-202 Authors: Jin JY, Kong FS Abstract This chapter reviews and discusses approaches and strategies of personalized radiation therapy (PRT) for lung cancers at four different levels: (1) clinically established PRT based on a patient's histology, stage, tumor volume and tumor locations; (2) personalized adaptive radiation therapy (RT) based on image response during treatment; (3) PRT based on biomarkers; (4) personalized fractionation schedule. The current RT practice for lung cancer is partially individualized according to tumor histology, stage, size/location, and combination with use of systemic therapy. During-RT PET-CT image guided adaptive treatment is being tested in a multicenter trial. Treatment response detected by the during-RT images may also provide a strategy to further personalize the remaining treatment. Research on biomarker-guided PRT is ongoing. The biomarkers include genomics, proteomics, microRNA, cytokines, metabolomics from tumor and blood samples, and radiomics from PET, CT, SPECT images. Finally, RT fractionation schedule may also be personalized to each individual patient to maximize therapeutic gain. Future PRT should be based on comprehensive considerations of knowledge acquired from all these levels, as well as consideration of the societal value such as cost and effectiveness. PMID: 26703805 [PubMed - as supplied by publisher]

Cell Adhesion Molecules and Ubiquitination-Functions and Significance. Biology (Basel). 2015;5(1) Authors: Homrich M, Gotthard I, Wobst H, Diestel S Abstract Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous system. All members of the Ig superfamily are intensively posttranslationally modified. However, many aspects of their cellular functions are not yet known. Since a few years ago it is known that some of the Ig superfamily members are modified by ubiquitin. Ubiquitination has classically been described as a proteasomal degradation signal but during the last years it became obvious that it can regulate many other processes including internalization of cell surface molecules and lysosomal sorting. The purpose of this review is to summarize the current knowledge about the ubiquitination of cell adhesion molecules of the Ig superfamily and to discuss its potential physiological roles in tumorigenesis and in the nervous system. PMID: 26703751 [PubMed]

Related Articles Blood transcriptomics and metabolomics for personalized medicine. Comput Struct Biotechnol J. 2016;14:1-7 Authors: Li S, Todor A, Luo R Abstract Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine. PMID: 26702339 [PubMed]

Related Articles Simvastatin and a plant galactolipid protect animals from septic shock by regulating oxylipin mediator dynamics through the MAPK-cPLA2 signaling pathway. Mol Med. 2015 Dec 14; Authors: Apaya MK, Lin CY, Chiou CY, Yang CC, Ting CY, Shyur LF Abstract Sepsis remains a major medical issue despite decades of research. Identification of important inflammatory cascades and key molecular mediators are crucial for developing intervention and prevention strategies. In this study, we conducted a comparative oxylipin metabolomics study to gain a comprehensive picture of lipid mediator dynamics during the initial hyper-inflammatory phase of sepsis, and demonstrated, in parallel, the efficacy of simvastatin and plant galactolipid, 1,2-di-O-α-linolenoyl-3-O-β-galactopyranosyl-sn-glycerol (dLGG) in the homeostatic regulation of the oxylipin metabolome using a lipopolysaccharide (LPS)-induced sepsis C57BL/6J mouse model. LPS increased the systemic and organ levels of pro-inflammatory metabolites of linoleic acid including leukotoxin diols, i.e., 9,10-DHOME, 12,13-DHOME, and octadecadienoic acids, i.e., 9-HODE and 13-HODE; and arachidonic acid-derived prostanoid, PGE2, and hydroxyeicosatetraenoic acids, i.e., 8, 12- and 15-HETE. Treatment with either compound decreased the levels of pro-inflammatory metabolites and elevated pro-resolution lipoxin A4, 5(6)-EET, 11(12)-EET and 15-deoxy-PGJ2. dLGG and simvastatin ameliorated the effects of LPS-induced MAPK-dependent activation of cPLA2, cyclooxygenase-2, lipoxygenase, cytochrome P450, and/or epoxide hydrolase, lowered systemic TNF-α and IL-6 levels and aminotransferase activities and decreased organ-specific infiltration of inflammatory leukocytes and macrophages, and septic shock-induced multiple organ damage. Furthermore, both dLGG and simvastatin increased the survival rates in the cecal ligation and puncture (CLP) sepsis model. This study provides new insights into the role of oxylipins in sepsis pathogenesis and highlights the potential of simvastatin and dLGG in sepsis therapy and prevention. PMID: 26701313 [PubMed - as supplied by publisher]

Related Articles Upregulation of energy metabolism-related, p53-target TIGAR and SCO2 in HuH-7 cells with p53 mutation by geranylgeranoic acid treatment. Biomed Res. 2015;36(6):371-81 Authors: Iwao C, Shidoji Y Abstract Metabolic alternation in cancer cells is one of the most common characteristics that distinguish malignant cells from normal cells. Many studies have explained the Warburg hypothesis that cancer cells obtain more energy from aerobic glycolysis than mitochondrial respiration. Here, we show that a branched-chain C-20 polyunsaturated fatty acid, geranylgeranoic acid (GGA), induces upregulation of the cellular protein levels of TP53-induced glycolysis and apoptosis regulator (TIGAR) and synthesis of cytochrome c oxidase 2 (SCO2) in human hepatoma-derived HuH-7cells harboring the mutant TP53 gene, suggesting that GGA may shift an energetic state of the tumor cells from aerobic glycolysis to mitochondrial respiration. In addition, UPLC/TOF/MS-based metabolomics analysis supported the GGA-induced energetic shift, as it revealed that GGA induced a time-dependent increase in the cellular contents of fructose 6-phosphate and decrease of fructose 1,6-diphosphate. Furthermore, metabolomics analysis revealed that GGA rapidly induced spermine accumulation with slight decrease of spermidine. Taken together, the present study strongly suggests that GGA may shift HuH-7 cells from aerobic glycolysis to mitochondrial respiration through the immediate upregulation of TIGAR and SCO2 protein levels. PMID: 26700591 [PubMed - in process]

Related Articles Ethyl Esterification for MALDI-MS Analysis of Protein Glycosylation. Methods Mol Biol. 2016;1394:151-62 Authors: Reiding KR, Lonardi E, Hipgrave Ederveen AL, Wuhrer M Abstract Ethyl esterification is a technique for the chemical modification of sialylated glycans, leading to enhanced stability when performing matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS), as well as allowing the efficient detection of both sialylated and non-sialylated glycans in positive ion mode. In addition, the method shows specific reaction products for α2,3- and α2,6-linked sialic acids, leading to an MS distinguishable mass difference. Here, we describe the ethyl esterification protocol for 96 glycan samples, including enzymatic N-glycan release, the aforementioned ethyl esterification, glycan enrichment, MALDI target preparation, and the MS(/MS) measurement. PMID: 26700047 [PubMed - in process]

Related Articles CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress. Biochem J. 2015 Dec 23; Authors: Holyoake LV, Hunt S, Sanguinetti G, Cook GM, Howard MJ, Rowe ML, Poole RK, Shepherd M Abstract The glutathione/cysteine exporter CydDC maintains redox balance in Escherichia coli . A cydD mutant strain was used to probe the influence of CydDC upon reduced thiol export, gene expression, metabolic perturbations, intracellular pH homeostasis, and tolerance to nitric oxide (NO). Loss of CydDC was found to decrease extracytoplasmic thiol levels, whereas overexpression diminished the cytoplasmic thiol content. Transcriptomic analysis revealed a dramatic up-regulation of protein chaperones, protein degradation (via phenylpropionate/phenylacetate catabolism), β-oxidation of fatty acids, and genes involved in nitrate/nitrite reduction. (1)H NMR metabolomics revealed elevated methionine and betaine and diminished acetate and NAD(+) in cydD cells, which was consistent with the transcriptomics-based metabolic model. The growth rate and ΔpH, however, were unaffected, although the cydD strain did exhibit sensitivity to the NO-releasing compound NOC-12. These observations are consistent with the hypothesis that the loss of CydDC-mediated reductant export promotes protein misfolding, adaptations to energy metabolism, and sensitivity to NO. The addition of both glutathione and cysteine to the medium was found to complement the loss of bd -type cytochrome synthesis in a cydD strain (a key component of the pleiotropic cydDC phenotype), providing the first direct evidence that CydDC substrates are able to restore the correct assembly of this respiratory oxidase. These data provide an insight into the metabolic flexibility of E. coli , highlight the importance of bacterial redox homeostasis during nitrosative stress, and report for the first time the ability of periplasmic low molecular weight thiols to restore haem incorporation into a cytochrome complex. PMID: 26699904 [PubMed - as supplied by publisher]

Related Articles Choline Diet and Its Gut Microbe-Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload-Induced Heart Failure. Circ Heart Fail. 2016 Jan;9(1):e002314 Authors: Organ CL, Otsuka H, Bhushan S, Wang Z, Bradley J, Trivedi R, Polhemus DJ, Tang WH, Wu Y, Hazen SL, Lefer DJ Abstract BACKGROUND: Trimethylamine N-oxide (TMAO), a gut microbe-dependent metabolite of dietary choline and other trimethylamine-containing nutrients, is both elevated in the circulation of patients having heart failure and heralds worse overall prognosis. In animal studies, dietary choline or TMAO significantly accelerates atherosclerotic lesion development in ApoE-deficient mice, and reduction in TMAO levels inhibits atherosclerosis development in the low-density lipoprotein receptor knockout mouse. METHODS AND RESULTS: C57BL6/J mice were fed either a control diet, a diet containing choline (1.2%) or a diet containing TMAO (0.12%) starting 3 weeks before surgical transverse aortic constriction. Mice were studied for 12 weeks after transverse aortic constriction. Cardiac function and left ventricular structure were monitored at 3-week intervals using echocardiography. Twelve weeks post transverse aortic constriction, myocardial tissues were collected to evaluate cardiac and vascular fibrosis, and blood samples were evaluated for cardiac brain natriuretic peptide, choline, and TMAO levels. Pulmonary edema, cardiac enlargement, and left ventricular ejection fraction were significantly (P<0.05, each) worse in mice fed either TMAO- or choline-supplemented diets when compared with the control diet. In addition, myocardial fibrosis was also significantly greater (P<0.01, each) in the TMAO and choline groups relative to controls. CONCLUSIONS: Heart failure severity is significantly enhanced in mice fed diets supplemented with either choline or the gut microbe-dependent metabolite TMAO. The present results suggest that additional studies are warranted examining whether gut microbiota and the dietary choline→TMAO pathway contribute to increased heart failure susceptibility. PMID: 26699388 [PubMed - in process]

Related Articles Metabolomic profiles investigation on atheletes' urine 35 minutes after an 800-meter race. J Sports Med Phys Fitness. 2015 Dec 23; Authors: Sun T, Wu Y, Wu X, Ma H Abstract AIM: The main energy delivery system of 800 meters run is the glycolytic system. Running the 800 meters causes significant changes in our body, yet our understanding of how these changes occur is limited. METHODS: We used an NMR-based metabolomics analysis to evaluate the metabolite profile changes in 19 young male athletes' urine samples after 800-meter runs and provide an overall picture of its impact. Various multivariate data analysis methods, including principal component analysis (PCA), partial least squares-discrimination analysis (PLS-DA), and orthogonal projection of latent-structure-discrimination analysis (OPLS-DA) were applied to analyze the NMR data and thus identify possible correlations between the metabolite profile changes and the alterations in biological pathways. RESULTS: The potential biological mechanism of an 800-meter race was finally elucidated based on the multivariate statistical analysis results. The levels of Lac, 2HIV, Leu, 2HIB, Ala, NAG, Pyr, Crn,FMA, Ino and Hyx were up-regulated in the post samples, whereas the levels of certain metabolites, including 3HIV, Cit, Tau, Gly and FOR were down-regulated in the post samples. CONCLUSION: 1Our study provides novel insights into the 800-meter race metabolic characteristic. Separation of pre- from post-exercise samples was related to the Krebs cycle, Cori cycle, Cahill cycle, HIFs and ROS. 2Besides the Lac change, the increased concentrations of Ino, 2HIV concentrations in the post-exercise urine samples represent potential indices which indicate the high percent of glycolysis during the 800-meter run. 3The increase of concentrations of Hyx, 2HB may indicated oxidative stress with concomitant ROS generation in the athletes' bodies during the 800-meter race. PMID: 26699119 [PubMed - as supplied by publisher]

Related Articles Increased lanosterol turnover: a metabolic burden for daunorubicin-resistant leukemia cells. Med Oncol. 2016 Jan;33(1):6 Authors: Stäubert C, Krakowsky R, Bhuiyan H, Witek B, Lindahl A, Broom O, Nordström A Abstract The cholesterol metabolism is essential for cancer cell proliferation. We found the expression of genes involved in the cholesterol biosynthesis pathway up-regulated in the daunorubicin-resistant leukemia cell line CEM/R2, which is a daughter cell line to the leukemia cell line CCRF-CEM (CEM). Cellular (2)H2O labelling, mass spectrometry, and isotopomer analysis revealed an increase in lanosterol synthesis which was not accompanied by an increase in cholesterol flux or pool size in CEM/R2 cells. Exogenous addition of lanosterol had a negative effect on CEM/R2 and a positive effect on sensitive CEM cell viability. Treatment of CEM and CEM/R2 cells with cholesterol biosynthesis inhibitors acting on the enzymes squalene epoxidase and lanosterol synthase, both also involved in the 24,25-epoxycholesterol shunt pathway, revealed a connection of this pathway to lanosterol turnover. Our data highlight that an increased lanosterol flux poses a metabolic weakness of resistant cells that potentially could be therapeutically exploited. PMID: 26698156 [PubMed - as supplied by publisher]

Related Articles Ultrafast polyphenol metabolomics of red wines using microLC-MS/MS. J Agric Food Chem. 2015 Dec 23; Authors: Ma Y, Tanaka N, Vaniya A, Kind T, Fiehn O Abstract The taste and quality of red wine is determined by its highly complex mixture of polyphenols and many other metabolites. While no single method can fully cover the full metabolome, even for polyphenols and related compounds, current methods proved inadequate. We optimized liquid chromatography resolution and sensitivity using 1 mm I.D. columns with microLC pumps and compared data-dependent to data-independent (SWATH) MS/MS acquisitions. A high-throughput microLC-MS method was developed with a 4 min gradient at 0.05 mL/min flow rate on a Kinetex C18 column and Sciex TripleTOF mass spectrometry. Using the novel software MS-DIAL, we structurally annotated 264 compounds including 165 polyphenols in six commercial red wines by accurate mass MS/MS matching. As proof of concept, multivariate statistics revealed the difference in the metabolite profiles of the six red wines and regression analysis linked the polyphenol contents to the taste of the red wines. PMID: 26698107 [PubMed - as supplied by publisher]

Related Articles Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations. PLoS One. 2014;9(11):e112757 Authors: Turner J, Quek LE, Titmarsh D, Krömer JO, Kao LP, Nielsen L, Wolvetang E, Cooper-White J Abstract As human embryonic stem cells (hESCs) steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic) and atmospheric (normoxic) oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that can be used in rational bioreactor design and in the development of novel culture media for hESC maintenance and expansion. PMID: 25412279 [PubMed - indexed for MEDLINE]

Related Articles Systems Biology Approaches to Understand Natural Products Biosynthesis. Front Bioeng Biotechnol. 2015;3:199 Authors: Licona-Cassani C, Cruz-Morales P, Manteca A, Barona-Gomez F, Nielsen LK, Marcellin E Abstract Actinomycetes populate soils and aquatic sediments that impose biotic and abiotic challenges for their survival. As a result, actinomycetes metabolism and genomes have evolved to produce an overwhelming diversity of specialized molecules. Polyketides, non-ribosomal peptides, post-translationally modified peptides, lactams, and terpenes are well-known bioactive natural products with enormous industrial potential. Accessing such biological diversity has proven difficult due to the complex regulation of cellular metabolism in actinomycetes and to the sparse knowledge of their physiology. The past decade, however, has seen the development of omics technologies that have significantly contributed to our better understanding of their biology. Key observations have contributed toward a shift in the exploitation of actinomycete's biology, such as using their full genomic potential, activating entire pathways through key metabolic elicitors and pathway engineering to improve biosynthesis. Here, we review recent efforts devoted to achieving enhanced discovery, activation, and manipulation of natural product biosynthetic pathways in model actinomycetes using genome-scale biological datasets. PMID: 26697425 [PubMed]

Related Articles CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing. Genom Data. 2015 Dec;6:175-81 Authors: Lambirth KC, Whaley AM, Schlueter JA, Bost KL, Piller KJ Abstract Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. PMID: 26697366 [PubMed]

Related Articles Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport. Front Plant Sci. 2015;6:996 Authors: Zhao Y, Liu T, Luo J, Zhang Q, Xu S, Han C, Xu J, Chen M, Chen Y, Kong L Abstract Peucedanum praeruptorum Dunn is well-known traditional Chinese medicine. However, little is known in the biosynthesis and the transport mechanisms of its coumarin compounds at the molecular level. Although transcriptomic sequence is playing an increasingly significant role in gene discovery, it is not sufficient in predicting the specific function of target gene. Furthermore, there is also a huge database to be analyzed. In this study, RNA sequencing assisted transcriptome dataset and high-performance liquid chromatography (HPLC) coupled with electrospray-ionization quadrupole time-of-flight mass spectrometry (Q-TOF MS)-based metabolomics dataset of P. praeruptorum were firstly constructed for gene discovery and compound identification. Subsequently, methyl jasmonate (MeJA)-induced gene expression analysis and metabolomics analysis were conducted to narrow-down the dataset for selecting the candidate genes and the potential marker metabolites. Finally, the genes involved in coumarins biosynthesis and transport were predicted with parallel analysis of transcript and metabolic profiles. As a result, a total of 40,952 unigenes and 19 coumarin compounds were obtained. Based on the results of gene expression and metabolomics analysis, 7 cytochrome-P450 and 8 multidrug resistance transporter unigenes were selected as candidate genes and 8 marker compounds were selected as biomarkers, respectively. The parallel analysis of gene expression and metabolites accumulation indicated that the gene labeled as 23,746, 228, and 30,922 were related to the formation of the coumarin core compounds whereas 36,276 and 9533 participated in the prenylation, hydroxylation, cyclization or structural modification. Similarly, 1462, 20,815, and 15,318 participated in the transport of coumarin core compounds while 124,029 and 324,293 participated in the transport of the modified compounds. This finding suggested that integration of a decrescent transcriptome and metabolomics dataset could largely narrow down the number of gene to be investigated and significantly improve the efficiency of functional gene predication. In addition, the large amount of transcriptomic data produced from P. praeruptorum and the genes discovered in this study would provide useful information in investigating the biosynthesis and transport mechanism of coumarins. PMID: 26697023 [PubMed]

Related Articles Assessment of maternal drug intake by urinary bio monitoring during pregnancy and postpartally until the third perinatal year. Pharmacoepidemiol Drug Saf. 2015 Dec 22; Authors: Hoeke H, Roeder S, Bertsche T, Borte M, von Bergen M, Wissenbach DK Abstract PURPOSE: Although sales of prescribed and over-the-counter (OTC) medication are rising, little is known about individual drug intake. This study was aimed to obtain complementary information about drug intake. METHOD: Information on drug utilization was obtained in a female cohort for five different time points (TP): 36th week of pregnancy (n = 622), 7th perinatal week (n = 533), 3rd perinatal month (n = 340), and 1st perinatal (n = 534) and 3rd perinatal year (n = 324) by a validated urine screening method. RESULTS: Drugs were detected 807 times among all analyzed samples (n = 2353) with less drug intake for early TP compared with later TP (~24.4%, n = 152; ~33.8%, n = 180; ~23.2%, n = 79; ~42.5%, n = 227; and ~52.2%, n = 169). The diversity of drugs increased from 25 up to 40 different drugs for the investigated period. OTC drugs were detected most frequently reflected by the top three drugs: acetaminophen (~37%, n = 292), ibuprofen (~23%, n = 183), and xylometazoline (~12%, n = 98). Mainly guideline-orientated drug therapy was observed. However, contraindicated ibuprofen intake during third trimester urine samples (n = 26) and a repeated usage of acetaminophen and/or ibuprofen (n = 9), as well as xylometazoline (n = 7), reveal missing information about drug safety. CONCLUSION: Bio monitoring was applied for detection of drug intake revealing a lack of information about OTC products and their health risks. Hence, information about health risks for certain drugs and patient groups must be improved for and by pharmacists, to avoid (i) usage of contraindicated drugs and (ii) abuse of OTC drugs. Copyright © 2015 John Wiley & Sons, Ltd. PMID: 26696520 [PubMed - as supplied by publisher]