No description available.

The central nature of nicotinamide in metabolic processes as a part of the NAD and NADP coenzyme systems prompted the synthesis of a series of N-nicotinyl- and N-isonicotinyl-N'- (substituted)ureas as potential metabolite antagonists of the vitamin. The compounds which were synthesized may be represented by the following general structure, where R = hydrogen, methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, n-hexyl, cyclohexyl, phenyl and a-naphthyl. The observed toxicity of the N-nicotinyl-N'-(substituted)urea analogs may be attributed to the formation of a non-functional N-nicotinyl-N'-(substituted)urea-NAD analog through an exchange reaction catalyzed by NAD-ases in the cell. Support for this view was obtained by an in vitro enzymic synthesis of Nnicotinyl- N'-ethylurea-NAD analog employing N-nicotinyl-7- 1 4CN'- ethylurea. The labeled derivative was characterized through spectral, chromatographic, and chemical reaction studies.

No description available.

Metal-reducing microorganisms reduce a variety of metals in metabolic processes coupled to the oxidation of organic compounds. These bacteria play an important role in the biogeochemical cycling of metals and organic matter in anaerobic aquatic and sediment ecosystems. It has been proposed recently that metal-reducing microorganisms also are active in deep subsurface environments such as petroleum reservoirs. Only two metal-reducing bacteria have been isolated from petroleum reservoir fluids, Shewanella putrefaciens and Deferribacter thermophilus. This project studied the occurrence and distribution of metal-reducing microorganisms in petroleum reservoirs. The research focused on the isolation, characterisation and identification of anaerobic bacteria from petroleum reservoirs that were capable of reducing metals and the potential roles of these isolates in the microbial ecology and biogeochemical cycling of petroleum reservoirs. Petroleum reservoirs were selected for this study on the basis of physio-chemical conditions such as temperature, salinity, pH and the presence of organic and inorganic compounds, that were likely to provide a suitable environment for anaerobic bacteria capable of reducing metals. Factors such as the stratigraphic features of the sedimentary basin, age of reservoir and past oil field practices also were considered in choosing the reservoir for study. Seven petroleum reservoirs in the USA and Azerbaijan were chosen for extensive investigations. The physico-chemical conditions in these reservoirs varied substantially. A systematic study of the production water from these petroleum reservoirs revealed a consistent presence of iron- and manganese-reducing microorganisms. It was found that salinity and temperature play a significant and defining role in the occurrence and distribution of these metal-reducing microorganisms. Biotic metal reduction was detected from production waters from all but one of the oil wells sampled. It was significant that the water from this well (Neftcala #1074) was the most saline (78 g/l NaCI). Metal-reducing activity was detected at temperatures up to 70°C. Two pure cultures, strains RED1 for Redwash petroleum reservoir (USA) and NEF1 from the Neftcala petroleum reservoir (Azerbaijan) were isolated and characterized. The strains had diverse physiological and metabolic properties including the ability to oxidize a wide range of carbon compounds and reduce a variety of metals. Their temperature, salinity and pH optima varied markedly. Phylogenetic analyses of the 16S rRNA of strain RED1 showed that the strain represented a new species of a new genus in the domain Bacteria. The bacterium most closely related to strain RED1 is the fermentative Fe(III)-reducer, Pelobacter acetylenicus (similarity value, 92.8%). Strain NEF1 possesses a unique combination of phenotypic traits and a low mol % G+C. From preliminary analyses and comparative biochemistry, NEF1 appears to be a novel metal-reducing bacterium of the Flexistipes group. The bacteria isolated in this study were able to grow at temperatures and salinities consistent with the reservoir from which they were isolated. This indicated that petroleum reservoirs are a new source of physiologically diverse, novel, metal-reducing microorganisms. The bacteria isolated also demonstrated a number of characteristics that would enable them to survive and persist in extreme subsurface conditions and develop a selective ecological advantage in petroleum reservoir environments. Significantly, the metal-reducing bacteria isolated were able to utilize an array of metabolic products produced by bacteria indigenous to petroleum reservoirs. This has resulted in a new proposed model for the ecological succession of bacteria in petroleum reservoirs.

Application of bioengineering technologies for enhanced biological hydrogen production is a promising approach that may play a vital role in sustainable energy. Due to the ability of several naturally occurring microorganisms to generate hydrogen through varying metabolic processes, biological hydrogen has become an attractive alternative energy and fuel source. One area of particular interest is the production of biological hydrogen in organically-rich engineered systems, such as those associated with waste treatment. Despite the potential for high energy yields, hydrogen yields generated by bacteria in waste systems are often limited due to a focus on microbial utilization of organic material towards cellular growth rather than production of biogas. To address this concern and to improve upon current technological applications, metabolic engineering approaches may be applied to known hydrogen producing organisms. However, to successfully modify metabolic pathways, full understanding of metabolic networks involved in expression of microbial traits in hydrogen producing organisms is necessary. Because microbial communities associated with hydrogen production are capable of exhibiting a number of phenotypes, attempts to apply metabolic engineering concepts have been restricted due to limited information regarding complex metabolic processes and regulatory networks involved in expression of microbial traits associated with biohydrogen production. To bridge this gap, this dissertation focuses on identification of phenotype-related biochemical processes within sets of phenotype-expressing organisms. Specifically, through co-development and application of evolutionary genome-scale phenotype-centric comparative network analysis tools, metabolic and cellular components related to three phenotypes (i.e., dark fermentative, hydrogen production and acid tolerance) were identified. The computational tools employed for the systematic elucidation of key phenotype-related genes and subsystems consisted of two complementary methods. The first method, the Network Instance-Based Biased Subgraph Search (NIBBS) algorithm, identified phenotype-related metabolic genes and subsystems through comparative analysis of multiple genome-scale metabolic networks. The second method was the multiple alignments of metabolic pathways for identification of conserved metabolic sub-systems in small sets of phenotype-expressing microorganisms. For both methodologies, key metabolic genes and sub-systems that are likely to be related to hydrogen production and acid-tolerance were identified and hypotheses regarding their role in phenotype expression were generated. In addition, analysis of hydrogen producing enzymes generated by NIBBS revealed the potential interplay, or cross-talk, between metabolic pathways. To identify phenotype-related subnetworks, three complementary approaches were applied to individual, and sets of phenotype-expressing microorganisms. In the first method, the Dense ENriched Subgraph Enumeration (DENSE) algorithm, partial "prior knowledge" about the proteins involved in phenotype-related processes are utilized to identify dense, enriched sets of known phenotype-related proteins in Clostridium acetobutylicum. The second approach utilized a bi-clustering algorithm to identify phenotype-related functional association modules associated with metabolic controls of phenotype-related pathways. Last, through comparison of hundreds of genome-scale networks of functionally associated proteins, the á, â-motifs approach, was applied to identify phenotype-related subsystems. Application of methodologies for identification of subnetworks resulted in detection of regulatory proteins, transporters, and signaling proteins predicted to be related to phenotype-expression. Through analysis of protein interactions, clues to the functional roles and associations of previously uncharacterized proteins were identified (DENSE) and hypotheses regarding potentially important acid-tolerant mechanisms were generated (á, â-motifs). Similar to the NIBBS algorithm, analysis of functional modules predicted by the bi-clustering algorithm suggest cross-talk is occurring between pathways associated with hydrogen production. The ability of these phenotype-centric comparative network analysis tools to identify both known and potentially new biochemical process is important for providing further understanding and insights into metabolic networks and system controls involved in the expression of microbial traits. In particular, identification of phenotype-related metabolic components through a systems approach provides the underlying foundation for the development of improved bioengineering technologies and experimental design for enhanced biological hydrogen production.

La cetogènesi és el procés mitocondrial pel qual es sintetitzen els cossos cetònics (acetoacetat, 3-hidroxibutirat i acetona) a partir de l’acetil-CoA provinent de la degradació dels àcids grassos. És un procés mitocondrial i l’enzim clau de la via és la 3-hidroxi-3-metilglutaril-CoA sintasa mitocondrial (HMGCS2). La regulació de l’HMGCS2 ha estat àmpliament estudiada i es coneixen les hormones (glucagó, insulina, dexametasona), situacions metabòliques (dieta grassa, dejuni-realimentació, lactància, exercici perllongat) o patològiques (diabetis) que la regulen. Durant la darrera dècada s’atribueix als cossos cetònics un paper com a molècules senyalitzadores. Per tal d’aprofundir en l’estudi d’aquest paper, en la present tesi doctoral ens hem plantejat estudiar les conseqüències de la modificació de l’expressió del gen HMGCS2. Amb aquest objectiu, hem realitzat experiments en cèl·lules HepG2 de sobreexpressió i disminució de l’expressió del gen HMGCS2 que ens han permès demostrar que l’HMGCS2 és necessària per la inducció de l’oxidació d’àcids grassos mitjançada per PPARα. També hem demostrat que l’HMGCS2 regula positivament l’expressió d’FGF21, un gen diana de PPARα implicat en l’homeòstasi energètica per un mecanisme que implica la sirtuina SIRT1. D’altra banda, s’ha reduït l’expressió del gen HMGCS2 en ratolins de forma aguda mitjançant la injecció d’adenovirus codificants per shRNAs i se n’ha analitzat el fenotip. S’ha identificat, mitjançant un anàlisi massiu d’expressió gènica, el gen Fat specific protein 27 (Fsp27/CIDEC), una proteïna implicada en la formació de gotes lipídiques, com a potencial gen diana de l’HMGCS2. Finalment, s’ha aprofundit en els mecanismes de regulació del gen Fsp27/CIDEC demostrant que aquest s’indueix fortament durant el dejuni a nivell hepàtic. / Ketogenesis is a mitochodrial pathway by which ketone bodies (acetoacetat, 3-hydroxybutyrate and acetone) are syntesized from the acetyl- CoA comming from fatty acid oxidation. The key enzyme of this pathway is mitochondrial 3-hydroxy-3-metylglutaryl-CoA synthase (HMGCS2). The regulation of HMGCS2 has been widely studied: it is known that hormones (glucagon, insulin, dexamethasone), metabolic situations (dietary fat, fastfeeding, lactation, prolonged exercise) or pathologies (diabetes) regulate its expression. During the last decade, evidence is emerging that ketone bodies could act as signaling molecules. To further study this role, in this thesis we studied the consequences of the modification of HMGCS2 gene expression. To this end, we performed experiments in HepG2 cells by overexpression and down regulation of HMGCS2 gene, which allowed us to demonstrate that HMGCS2 is necessary for the induction of fatty acid oxidation mediated by PPARα. We have also shown that HMGCS2 positively regulates the expression of FGF21, a PPARα target gene involved in energy homeostasis by a mechanism that involves sirtuin SIRT1. On the other hand, we have down regulated HMGCS2 acutely in mice by injection of adenovirus encoding for shRNAs and we have analysed the phenotype of these mice. Through a massive analysis of gene expression, we have identified Fat specific protein 27 (Fsp27/CIDEC), a protein involved in the formation of lipid droplets, as a potential target of HMGCS2. Finally, we explored the mechanisms of Fsp27/CIDEC gene regulation demonstrating that it is strongly induced during fasting in liver.

Three dimensional multicell tumor spheroids (MCTS) provide an experimental model where the influence of microenvironmental conditions on protein expression can be determined. Sequential trypsin digestion of HT29 colon carcinoma MCTS enabled segregation into four populations comprising proliferating cells from the surface (SL), an intermediate region (IR), nonproliferating hypoxic cells from the perinecrotic region (PN), and a necrotic core (NC). Total protein was extracted from each population and subjected to iTRAQ-based quantitative proteomics analysis. From a total of 887 proteins identified, 209 were observed to be up-regulated and 114 were down-regulated in the PN and NC regions relative to the SL. Among the up-regulated proteins, components of glycolysis, TCA cycle, lipid metabolism, and steroid biosynthesis increased progressively toward the PN and NC regions. Western blotting, immunohistochemistry, and enzyme assays confirmed that significant changes in the expression of proteins involved in cellular metabolism occur in the nonproliferating fraction of cells within the viable rim. The presence of full length, functional proteins within the NC was unexpected, and further analysis demonstrated that this region contains cells that are undergoing autophagy. This study has identified possible targets that may be suitable for therapeutic intervention, and further studies to validate these are required.

Glucosyltransferases, or GTs, are enzymes which perform glucosylation reactions. These glucosylation reactions involve attaching a UDP-activated glucose molecule to acceptor molecules specific to the enzyme. The products of these reactions are observed to have a myriad of effects on metabolic processes, including stabilization of structures, solubility modification, and regulation of compound bioavailability. The enzyme which our lab focuses its research on is a flavonol-specific 3-O-GT found in Citrus paradisi, or grapefruit. This enzyme is part of the class of enzymes known as flavonoid GTs, which are responsible for, among other things, the formation of compounds which can affect the taste of citrus. Our lab focuses its research on performing site-directed mutagenesis on Citrus paradisi 3-O-GT in an attempt to modify its substrate specificity and regiospecificity. In this poster, we report our findings thus far concerning the addition of specific residues to the 3-O-GT's amino acid sequence based on an alignment with the sequence of a putative flavonoid GT found in Citrus sinensis.

Glucosyltransferases (GTs) are enzymes which perform glucosylation reactions, which involve attaching a UDP-activated glucose molecule to acceptor molecules specifi c to the enzyme. The enzyme which our lab focuses its research on is a fl avonol-specifi c 3-OGT found in Citrus paradisi, or grapefruit (Cp3GT). This enzyme is part of the class of enzymes known as fl avonoid GTs, which are responsible for, among other things, the formation of compounds which can affect the taste of citrus. Our lab focuses its research on performing site-directed mutagenesis on Cp3GT in an attempt to discover the residues important for substrate and regiospecifi city. In this study, we are testing the basis of substrate septicity of Cp3GT. We hypothesize that incorporation of fi ve amino acids specifi c to Citrus sinensis GT (CsGT) into Cp3GT at 308th position may facilitate mCp3GT to use anthocyanidins as one of the substrates. We report our fi ndings thus far concerning the addition of specifi c residues to the Cp3GT’s amino acid sequence based on an alignment with the sequence of a putative fl avonoid GT found in Citrus sinensis.