PubMed

Deletion of glycerol channel aquaporin-9 (Aqp9) impairs long-term blood glucose control in C57BL/6 leptin receptor-deficient (db/db) obese mice. Physiol Rep. 2015 Sep;3(9) Authors: Spegel P, Chawade A, Nielsen S, Kjellbom P, Rützler M Abstract Deletion of the glycerol channel aquaporin-9 (Aqp9) reduces postprandial blood glucose levels in leptin receptor-deficient (db/db) obese mice on a C57BL/6 × C57BLKS mixed genetic background. Furthermore, shRNA-mediated reduction of Aqp9 expression reduces liver triacylglycerol (TAG) accumulation in a diet-induced rat model of obesity. The aim of this study was to investigate metabolic effects of Aqp9 deletion in coisogenic db/db mice of the C57BL/6 background. Aqp9(wt) db/db and Aqp9(-/-) db/db mice did not differ in body weight and liver TAG contents. On the C57BL/6 genetic background, we observed elevated plasma glucose in Aqp9(-/-) db/db mice (+1.1 mmol/L, life-time average), while plasma insulin concentration was reduced at the time of death. Glucose levels changed similarly in pentobarbital anesthetized, glucagon challenged Aqp9(wt) db/db and Aqp9(-/-) db/db mice. Liver transcriptional profiling did not detect differential gene expression between genotypes. Metabolite profiling revealed a sex independent increase in plasma glycerol (+55%) and glucose (+24%), and reduction in threonate (all at q < 0.1) in Aqp9(-/-) db/db mice compared to controls. Metabolite profiling thus confirms a role of AQP9 in glycerol metabolism of obese C57BL/6 db/db mice. In this animal model of obesity Aqp9 gene deletion elevates plasma glucose and does not alleviate hepatosteatosis. PMID: 26416971 [PubMed]

Detection of metabolites discriminating subtypes of thyroid cancer: molecular profiling of FFPE samples using the GC/MS approach. Mol Cell Endocrinol. 2015 Sep 25; Authors: Wojakowska A, Chekan M, Marczak Ł, Polanski K, Lange D, Pietrowska M, Widlak P Abstract One of the critical issues in thyroid cancer diagnostic is differentiation between follicular adenoma, follicular carcinoma and the follicular variant of papillary carcinoma, which in some cases is not possible based on histopathological features only. In this paper we performed molecular profiling of thyroid tissue aiming to identify metabolites characteristic for different types of thyroid cancer. FFPE tissue specimens were analysed from 5 different types of thyroid malignancies (follicular, papillary/classical variant, papillary/follicular variant, medullary and anaplastic cancers), benign follicular adenoma and normal thyroid. Extracted metabolites were identified and semi-quantified using the GC/MS approach. There were 28 metabolites identified, whose abundances were significantly different among different types of thyroid tumours, including lipids, carboxylic acids, and saccharides. We concluded, that multi-component metabolome signature could be used for classification of different subtypes of follicular thyroid lesions. Moreover, potential applicability of the GC/MS-based analysis of FFPE tissue samples in diagnostics of thyroid cancer has been proved. PMID: 26415588 [PubMed - as supplied by publisher]

Related Articles Intervention effects of puerarin on blood stasis in rats revealed by a (1)H NMR-based metabonomic approach. Phytomedicine. 2015 Mar 15;22(3):333-43 Authors: Zou ZJ, Liu ZH, Gong MJ, Han B, Wang SM, Liang SW Abstract Puerarin possesses a wide spectrum of biological activities including ameliorating effects on blood stasis, but the definite mechanism of this effect is still not known. In this study, a (1)H NMR-based plasma and urinary metabonomic approach was applied to comprehensively and holistically investigate the therapeutic effects of puerarin on blood stasis and its underlying mechanisms. Puerarin was injected intraperitoneally once daily for consecutive 7 days. The blood stasis rat model was established by placing the rats in ice-cold water during the time interval between two injections of adrenaline. With pattern recognition analysis, a clear separation of blood stasis model group and healthy control group was achieved and puerarin pretreatment group was located much closer to the control group than the model group, which was consistent with results of hemorheology studies. 15 and 10 potential biomarkers associated with blood stasis in plasma and urine, respectively, which were mainly involved in energy metabolism, lipid and membrane metabolisms, amino acid metabolism and gut microbiota metabolism, were identified. Puerarin could prevent blood stasis through partially regulating the disturbed metabolic pathways. This work highlights that metabonomics is a valuable tool for studying the essence of blood stasis as well as evaluating the efficacy of the corresponding drug treatment. PMID: 25837270 [PubMed - indexed for MEDLINE]

Related Articles The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology (Bethesda). 2015 Mar;30(2):97-106 Authors: Wang Q, Cen Z, Zhao J Abstract Thermophiles are referred to as microorganisms with optimal growth temperatures of >60 °C. Over the past few years, a number of studies have been conducted regarding thermophiles, especially using the omics strategies. This review provides a systematic view of the survival physiology of thermophiles from an "omics" perspective, which suggests that the adaptive ability of thermophiles is based on a cooperative mode with multi-dimensional regulations integrating genomics, transcriptomics, and proteomics. PMID: 25729055 [PubMed - indexed for MEDLINE]

Related Articles [Metabonomic analysis of the serum from rat model with abnormal balgam syndrome of Uyghur medicine]. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2015 Jan;40(1):18-24 Authors: Mosha G, Nurmaimaiti A, Zhang J, Abudula M, Huang J, Yunusi K Abstract OBJECTIVE: To investigate correlation between the change in metabolic components of serum and the abnormal balgam syndrome by using a rat model of abnormal balgam syndrome. METHODS: Male Wistar rats were randomly divided into a control group and a test group. According to Uyghur medicine theory, the test group of rats were given wet cold diet (seeds of spinach and parsley, 24 hours) in a cold (6 °C) and humid (85%-95%, 10 hours) environment for 40 days to establish the rat model of abnormal balgam syndrome. 1H MR based metabonomic analysis of serum was performed. Data was analyzed using Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) software. RESULTS: Compared with the control group, the serum components including glutamate, phenylalanine, tyrosine, citric acid, β-hydrocxy butyrate, acetoacetate, pyruvic acid and creatine were decreased, while the glucose, lactic acid, low density lipoprotein and very low density lipoprotein were increased in the test group (P<0.05). CONCLUSION: The low energy production and consumption in the rat model of abnormal balgam syndrome suggests that the dysfunctional metabolisms of three major nutrients might be the molecular basis for the abnormal balgam syndrome. PMID: 25652368 [PubMed - indexed for MEDLINE]

Related Articles Chemical imaging of latent fingerprints by mass spectrometry based on laser activated electron tunneling. Anal Chem. 2015 Mar 3;87(5):2693-701 Authors: Tang X, Huang L, Zhang W, Zhong H Abstract Identification of endogenous and exogenous chemicals contained in latent fingerprints is important for forensic science in order to acquire evidence of criminal identities and contacts with specific chemicals. Mass spectrometry has emerged as a powerful technique for such applications without any derivatization or fluorescent tags. Among these techniques, MALDI (Matrix Assisted Laser Desorption Ionization) provides small beam size but has interferences with MALDI matrix materials, which cause ion suppressions as well as limited spatial resolution resulting from uneven distribution of MALDI matrix crystals with different sizes. LAET (Laser Activated Electron Tunneling) described in this work offers capabilities for chemical imaging through electron-directed soft ionization. A special film of semiconductors has been designed for collection of fingerprints. Nanoparticles of bismuth cobalt zinc oxide were compressed on a conductive metal substrate (Al or Cu sticky tape) under 10 MPa pressure. Resultant uniform thin films provide tight and shining surfaces on which fingers are impressed. Irradiation of ultraviolet laser pulses (355 nm) on the thin film instantly generates photoelectrons that can be captured by adsorbed organic molecules and subsequently cause electron-directed ionization and fragmentation. Imaging of latent fingerprints is achieved by visualization of the spatial distribution of these molecular ions and structural information-rich fragment ions. Atomic electron emission together with finely tuned laser beam size improve spatial resolution. With the LAET technique, imaging analysis not only can identify physical shapes but also reveal endogenous metabolites present in females and males, detect contacts with prohibited substances, and resolve overlapped latent fingerprints. PMID: 25647159 [PubMed - indexed for MEDLINE]

17 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2015/09/29PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Syst Biol. 2015;9(1):64 Authors: Millard P, Portais JC, Mendes P Abstract BACKGROUND: Isotope labeling experiments (ILEs) are increasingly used to investigate the functioning of metabolic systems. Some enzymes are subject to kinetic isotope effects (KIEs) which modulate reaction rates depending on the isotopic composition of their substrate(s). KIEs may therefore affect both the propagation of isotopes through metabolic networks and their operation, and ultimately jeopardize the biological value of ILEs. However, the actual impact of KIEs on metabolism has never been investigated at the system level. RESULTS: First, we developed a framework which integrates KIEs into kinetic and isotopic models of metabolism, thereby accounting for their system-wide effects on metabolite concentrations, metabolic fluxes, and isotopic patterns. Then, we applied this framework to assess the impact of KIEs on the central carbon metabolism of Escherichia coli in the context of (13)C-ILEs, under different situations commonly encountered in laboratories. Results showed that the impact of KIEs strongly depends on the label input and on the variable considered but is significantly lower than expected intuitively from measurements on isolated enzymes. The global robustness of both the metabolic operation and isotopic patterns largely emerge from intrinsic properties of metabolic networks, such as the distribution of control across the network and bidirectional isotope exchange. CONCLUSIONS: These results demonstrate the necessity of investigating the impact of KIEs at the level of the entire system, contradict previous hypotheses that KIEs would have a strong effect on isotopic distributions and on flux determination, and strengthen the biological value of (13)C-ILEs. The proposed modeling framework is generic and can be used to investigate the impact of all the isotopic tracers ((2)H, (13)C, (15)N, (18)O, etc.) on different isotopic datasets and metabolic systems. By allowing the integration of isotopic and metabolomics data collected under stationary and/or non-stationary conditions, it may also assist interpretations of ILEs and facilitate the development of more accurate kinetic models with improved explicative and predictive capabilities. PMID: 26410690 [PubMed - as supplied by publisher]

Related Articles High-throughput approaches to unravel hepatitis C virus-host interactions. Virus Res. 2015 Sep 24; Authors: Colpitts CC, El-Saghire H, Pochet N, Schuster C, Baumert TF Abstract Hepatitis C virus (HCV) remains a major global health burden, with more than 130 million individuals chronically infected and at risk for the development of hepatocellular carcinoma (HCC). The recent clinical licensing of direct-acting antivirals enables viral cure. However, limited access to therapy and treatment failure in patient subgroups warrants a continuing effort to develop complementary antiviral strategies. Furthermore, once fibrosis is established, curing HCV infection does not eliminate the risk for HCC. High-throughput approaches and screens have enabled the investigation of virus-host interactions on a genome-wide scale. Gain- and loss-of-function screens have identified essential host-dependency factors in the HCV viral life cycle, such as host cell entry factors or regulatory factors for viral replication and assembly. Network analyses of systems-scale data sets provided a comprehensive view of the cellular state following HCV infection, thus improving our understanding of the virus-induced responses of the target cell. Interactome, metabolomics and gene expression studies identified dysregulated cellular processes potentially contributing to HCV pathogenesis and HCC. Drug screens using chemical libraries led to the discovery of novel antivirals. Here, we review the contribution of high-throughput approaches for the investigation of virus-host interactions, viral pathogenesis and drug discovery. PMID: 26410623 [PubMed - as supplied by publisher]

Related Articles Vitamin D metabolite profiling using liquid chromatography-tandem mass spectrometry (LC-MS/MS). J Steroid Biochem Mol Biol. 2015 Sep 24; Authors: Jones G, Kaufmann M Abstract Liquid chromatography tandem mass spectrometry (LC-MS/MS) has emerged as the latest technology to be used to assay the metabolites of vitamin D. The method uses molecular mass as a detection technique after straightforward extraction and chromatography steps. LC-MS/MS assay provides a level of accuracy and reproducibility not seen before with other methods and is beginning to rival antibody-based methods in terms of sensitivity and convenience. Methods for detection of underivatized and DMEQ-TAD derivatized vitamin D metabolites are evaluated. Sensitivity is improved by 10-100 fold with derivatization and allows for the simultaneous assay of multiple vitamin D metabolites, a process termed vitamin D metabolite profiling. Clinical and research applications of vitamin D metabolite profiling are discussed. PMID: 26409684 [PubMed - as supplied by publisher]

Metabolic switch during adipogenesis: From branched chain amino acid catabolism to lipid synthesis. Arch Biochem Biophys. 2015 Sep 23; Authors: Halama A, Horsch M, Kastenmüller G, Möller G, Kumar P, Prehn C, Laumen H, Hauner H, Hrabĕ de Angelis M, Beckers J, Suhre K, Adamski J Abstract Fat cell metabolism has an impact on body homeostasis and its proper function. Nevertheless, the knowledge about simultaneous metabolic processes, which occur during adipogenesis and in mature adipocytes, is limited. Identification of key metabolic events associated with fat cell metabolism could be beneficial in the field of novel drug development, drug repurposing, as well as for the discovery of patterns predicting obesity risk. The main objective of our work was to provide comprehensive characterization of metabolic processes occurring during adipogenesis and in mature adipocytes. In order to globally determine crucial metabolic pathways involved in fat cell metabolism, metabolomics and transcriptomics approaches were applied. We observed significantly regulated metabolites correlating with significantly regulated genes at different stages of adipogenesis. We identified the synthesis of phosphatidylcholines, the metabolism of even and odd chain fatty acids, as well as the catabolism of branched chain amino acids (BCAA; leucine, isoleucine and valine) as key regulated pathways. Our further analysis led to identification of an enzymatic switch comprising the enzymes Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthase) and Auh (AU RNA binding protein/enoyl-CoA hydratase) which connects leucine degradation with cholesterol synthesis and which is strongly regulated during adipogenesis. In addition, propionyl-CoA, a product of isoleucine degradation, was identified as a putative substrate for odd chain fatty acid synthesis. The uncovered crosstalk's between BCAA and lipid metabolism during adipogenesis might contribute to the understanding of molecular mechanisms of obesity and have potential implications in obesity prediction. PMID: 26408941 [PubMed - as supplied by publisher]

The potential of metabolomic analysis techniques for the characterisation of α1-adrenergic receptors in cultured N1E-115 mouse neuroblastoma cells. Cytotechnology. 2015 Sep 25; Authors: Wenner MI, Maker GL, Dawson LF, Drummond PD, Mullaney I Abstract Several studies of neuropathic pain have linked abnormal adrenergic signalling to the development and maintenance of pain, although the mechanisms underlying this are not yet fully understood. Metabolomic analysis is a technique that can be used to give a snapshot of biochemical status, and can aid in the identification of the mechanisms behind pathological changes identified in cells, tissues and biological fluids. This study aimed to use gas chromatography-mass spectrometry-based metabolomic profiling in combination with reverse transcriptase-polymerase chain reaction and immunocytochemistry to identify functional α1-adrenergic receptors on cultured N1E-115 mouse neuroblastoma cells. The study was able to confirm the presence of mRNA for the α1D subtype, as well as protein expression of the α1-adrenergic receptor. Furthermore, metabolomic data revealed changes to the metabolite profile of cells when exposed to adrenergic pharmacological intervention. Agonist treatment with phenylephrine hydrochloride (10 µM) resulted in altered levels of several metabolites including myo-inositol, glucose, fructose, alanine, leucine, phenylalanine, valine, and n-acetylglutamic acid. Many of the changes observed in N1E-115 cells by agonist treatment were modulated by additional antagonist treatment (prazosin hydrochloride, 100 µM). A number of these changes reflected what is known about the biochemistry of α1-adrenergic receptor activation. This preliminary study therefore demonstrates the potential of metabolomic profiling to confirm the presence of functional receptors on cultured cells. PMID: 26408527 [PubMed - as supplied by publisher]

Detection of Ophthalmic Acid in Serum from Acetaminophen-Induced Acute Liver Failure Patients Is More Frequent in Non-Survivors. PLoS One. 2015;10(9):e0139299 Authors: Kaur G, Leslie EM, Tillman H, Lee WM, Swanlund DP, Karvellas CJ, US Acute Liver Failure Study Group Abstract BACKGROUND/AIM: Acetaminophen (APAP) hepatotoxicity is related to the formation of N-acetyl-p-benzoquinone imine (NAPQI), which is detoxified through conjugation with reduced glutathione (GSH). Ophthalmic acid (OA) is an analogue of GSH in which cysteine is replaced with 2-aminobutyrate. Metabolomics studies of mice with APAP-induced acute liver failure (APAP-ALF) identified OA as a marker of oxidative stress and hepatic GSH consumption. The aim of the current study was to determine whether OA is detectable in APAP-ALF human patients either early (day 2) or late (day 4) and whether OA levels were associated with in-hospital survival in the absence of liver transplant. METHODS: Serum samples from 130 APAP-ALF patients (82 survivors, 48 non-survivors) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and correlated with clinical data from the United States Acute Liver Failure Study Group (US ALFSG) Registry (2004-2011). RESULTS: Survivors had significantly lower admission bilirubin (4.2 vs. 5.7 mg/dl) and lactate levels (3.3 vs. 6.5 μmol/l, p<0.05 for all). During the first 7 days of the study, survivors were less likely to require mechanical ventilation (55% vs. 88%), vasopressor support (9.8% vs. 67%) or renal replacement therapy (26% vs. 63%, p< 0.001 for all). Non-survivors were more likely to have detectable OA levels early (31% vs. 15%, p = 0.034) and late (27% vs. 11%, p = 0.02). However there were no significant differences in mean OA levels between non-survivors and survivors (early 0.48 vs. 0.36, late 0.43 vs. 0.37, P > 0.5 for all). CONCLUSION: OA was detectable more frequently in APAP-ALF non-survivors but mean OA levels were not associated with survival. The routine clinical administration of N-acetyl cysteine could replenish GSH levels and prevent OA production. PMID: 26407170 [PubMed - as supplied by publisher]

Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges. PLoS One. 2015;10(9):e0138528 Authors: Cheng C, MacIntyre L, Abdelmohsen UR, Horn H, Polymenakou PN, Edrada-Ebel R, Hentschel U Abstract Marine sponge-associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes. PMID: 26407167 [PubMed - as supplied by publisher]

Putative identification of new p-coumaroyl glycoside flavonoids in grape by ultra-high performance liquid chromatography/high-resolution mass spectrometry. Rapid Commun Mass Spectrom. 2015 Feb 28;29(4):357-366 Authors: Panighel A, De Rosso M, Dalla Vedova A, Flamini R Abstract RATIONALE: Grape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p-coumaric acid. Until now, only p-coumaroyl anthocyanins have been found in grape. METHODS: A method of 'suspect screening analysis' by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures. RESULTS: Three putative p-coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide-3-O-p-coumaroylhexoside-like flavanone, isorhamnetin-3-O-p-coumaroylglucoside, and a chrysoeriol-p-coumaroylhexoside-like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound. CONCLUSIONS: Compounds were identified by overlapping various analytical methods according to recommendations in the MS-based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties. Copyright © 2015 John Wiley & Sons, Ltd. PMID: 26406348 [PubMed - as supplied by publisher]

Profiling of volatile compounds in APC(Min/+) mice blood by dynamic headspace extraction and gas chromatography/mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Sep 11;1003:35-40 Authors: Kakuta S, Nishiumi S, Yoshida M, Fukusaki E, Bamba T Abstract Various volatile compounds as well as hydrophilic compounds exist in the blood. For example, 2-alkenals, 4-hydroxy-2-alkenals, and ketoaldehydes have been reported as oxidized lipid-derived volatiles in blood. These specific volatiles have been associated with diseases; however, multi-volatile analyses have not been performed. In this study, volatile profiling of APC(Min/+) mouse plasma by dynamic headspace extraction was performed for multi-volatile analysis. In total, 19 volatiles were detected in the plasma of mice, based on information regarding oxidized lipid-derived volatile compounds, and eight of these compounds differed significantly between normal and diseased mice. 2-Methyl-2-butanol and benzyl alcohol were previously unreported in blood samples. Furthermore, 3,5,5-trimethyl-2(5H)-furanone was only detected in normal mice. 5-Methyl-3-hexanone and benzaldehyde have been detected in subjects with gastrointestinal diseases and lung cancer, respectively. Therefore, volatile profiling can be used to detect differences between samples and to identify compounds associated with diseases. PMID: 26406113 [PubMed - as supplied by publisher]

Metabolomics for genomics: the role of vitamin D in nonalcoholic fatty liver disease. J Gastrointestin Liver Dis. 2015 Sep;24(3):394-5 Authors: Crisan D, Radu C, Suciu A, Grigorescu MD, Stefanescu H, Romanciuc F, Socaciu C, Grigorescu M PMID: 26405717 [PubMed - in process]

Autocrine signaling of type 1 interferons in successful anticancer chemotherapy. Oncoimmunology. 2015 Aug;4(8):e988042 Authors: Vacchelli E, Sistigu A, Yamazaki T, Vitale I, Zitvogel L, Kroemer G Abstract Anthracycline-based chemotherapies are particularly effective if they succeed in reinstating immunosurveillance by the induction of immunogenic cell death (ICD) in the tumor. Recently, we discovered that ICD is coupled to the induction of type 1 interferons (IFNs-I) that act in an autocrine fashion on cancer cells, thereby increasing their immunogenic potential. PMID: 26405588 [PubMed - as supplied by publisher]

A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. Genes Dev. 2015 Sep 24; Authors: Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kuśnierczyk A, Klungland A, Darnell JE, Darnell RB Abstract We adapted UV CLIP (cross-linking immunoprecipitation) to accurately locate tens of thousands of m(6)A residues in mammalian mRNA with single-nucleotide resolution. More than 70% of these residues are present in the 3'-most (last) exons, with a very sharp rise (sixfold) within 150-400 nucleotides of the start of the last exon. Two-thirds of last exon m(6)A and >40% of all m(6)A in mRNA are present in 3' untranslated regions (UTRs); contrary to earlier suggestions, there is no preference for location of m(6)A sites around stop codons. Moreover, m(6)A is significantly higher in noncoding last exons than in next-to-last exons harboring stop codons. We found that m(6)A density peaks early in the 3' UTR and that, among transcripts with alternative polyA (APA) usage in both the brain and the liver, brain transcripts preferentially use distal polyA sites, as reported, and also show higher proximal m(6)A density in the last exons. Furthermore, when we reduced m6A methylation by knocking down components of the methylase complex and then examined 661 transcripts with proximal m6A peaks in last exons, we identified a set of 111 transcripts with altered (approximately two-thirds increased proximal) APA use. Taken together, these observations suggest a role of m(6)A modification in regulating proximal alternative polyA choice. PMID: 26404942 [PubMed - as supplied by publisher]

Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach. Mar Drugs. 2015;13(10):6082-98 Authors: Adnani N, Vazquez-Rivera E, Adibhatla SN, Ellis GA, Braun DR, Bugni TS Abstract With respect to bacterial natural products, a significant outcome of the genomic era was that the biosynthetic potential in many microorganisms surpassed the number of compounds isolated under standard laboratory growth conditions, particularly among certain members in the phylum Actinobacteria. Our group, as well as others, investigated interspecies interactions, via co-culture, as a technique to coax bacteria to produce novel natural products. While co-culture provides new opportunities, challenges exist and questions surrounding these methods remain unanswered. In marine bacteria, for example, how prevalent are interspecies interactions and how commonly do interactions result in novel natural products? In an attempt to begin to answer basic questions surrounding co-culture of marine microorganisms, we have tested both antibiotic activity-based and LC/MS-based methods to evaluate Micromonosporaceae secondary metabolite production in co-culture. Overall, our investigation of 65 Micromonosporaceae led to the identification of 12 Micromonosporaceae across three genera that produced unique metabolites in co-culture. Our results suggest that interspecies interactions were prevalent between marine Micromonosporaceae and marine mycolic acid-containing bacteria. Furthermore, our approach highlights a sensitive and rapid method for investigating interspecies interactions in search of novel antibiotics, secondary metabolites, and genes. PMID: 26404321 [PubMed - in process]