Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations

<p>Abstract</p> <p>Background</p> <p><it>Zymomonas mobilis </it>ZM4 (ZM4) produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. <it>Z. mobilis </it>performs best under anaerobic conditions, but is an aerotolerant organism. However, the genetic and physiological basis of ZM4's response to various stresses is understood poorly.</p> <p>Results</p> <p>In this study, transcriptomic and metabolomic profiles for ZM4 aerobic and anaerobic fermentations were elucidated by microarray analysis and by high-performance liquid chromatography (HPLC), gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analyses. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Greater amounts of other end-products such as acetate, lactate, and acetoin were detected under aerobic conditions and at 26 h there was only 1.7% of the amount of ethanol present aerobically as there was anaerobically. In the early exponential growth phase, significant differences in gene expression were not observed between aerobic and anaerobic conditions via microarray analysis. HPLC and GC analyses revealed minor differences in extracellular metabolite profiles at the corresponding early exponential phase time point.</p> <p>Differences in extracellular metabolite profiles between conditions became greater as the fermentations progressed. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 contained lower levels of amino acids such as alanine, valine and lysine, and other metabolites like lactate, ribitol, and 4-hydroxybutanoate under anaerobic conditions relative to aerobic conditions. Stationary phase microarray analysis revealed that 166 genes were significantly differentially expressed by more than two-fold. Transcripts for Entner-Doudoroff (ED) pathway genes (<it>glk, zwf, pgl, pgk, and eno</it>) and gene <it>pdc</it>, encoding a key enzyme leading to ethanol production, were at least 30-fold more abundant under anaerobic conditions in the stationary phase based on quantitative-PCR results. We also identified differentially expressed ZM4 genes predicted by The Institute for Genomic Research (TIGR) that were not predicted in the primary annotation.</p> <p>Conclusion</p> <p>High oxygen concentrations present during <it>Z. mobilis </it>fermentations negatively influence fermentation performance. The maximum specific growth rates were not dramatically different between aerobic and anaerobic conditions, yet oxygen did affect the physiology of the cells leading to the buildup of metabolic byproducts that ultimately led to greater differences in transcriptomic profiles in stationary phase.</p

New adamantan-2-ol and adamantan-1-methanol derivatives as potent antibacterials. Synthesis, antibacterial activity and lipophilicity studies

Two series of active adamantane-group-bearing trialkylamines and their quaternary ammonium salts were synthesized and their biological properties were tested. One series includes 2-(3-dialkylaminopropyl)tricyclo[3.3.1.13,7]decan-2-ols and the other α,α-bis(3-dialkylaminopropyl)tricyclo[3.3.1.13,7]decyl-1-methanols. Some of the synthesized molecules proved to be very active antibacterials. The minimum inhibitory concentration (MIC) values of the most potent compounds were determined. The observed differences were investigated. The antibacterial activity of the compounds was found to be enhanced as the length of the nitrogen-attached carbon chain extends from CH3 to C12H25. The lipophilicity of the synthesized molecules was also studied and its relationship with the antibacterial activity was investigated

Reactions of indole derivatives with cardioprotective activity with reactive oxygen species. Comparison with melatonin

We have previously reported on the synthesis of novel indole derivatives containing an amine-triazole moiety (1a - d, 2a - c), and their antioxidant activity on in vitro non-enzymatic rat hepatic microsomal lipid peroxidation. Some of the compounds showed protective activity against oxidative injury of ischemic myocardium. In the present paper we investigated the interactions of these derivatives with reactive oxygen species, in order to find a mechanism of their antioxidant capacity and to identify structural characteristics responsible for these properties. These interactions were compared with melatonin, which is also an indole derivative. The antioxidant profiles of the compounds were established by different in vitro protocols as follows: 1) by the interaction of the compounds with the 1,1-diphenyl-2-picrylhydrazyl (DPPH) stable free radical, 2) their scavenging effects on superoxide anions using an enzymic system of xanthine-xanthine oxidase, 3) their inhibitory effects on xanthine oxidase and 4) their ability to scavenge hydroxyl radicals by comparison with dimethyl sulfoxide (DMSO) for .OH. All compounds were found to interact with DPPH, most of them to be superoxide anion scavengers and to be strong hydroxyl radical scavengers. Derivatives 1a and 1d substituted on the nitrogen of the indolic nucleus were found to have better antioxidant properties than the reference compounds used and melatonin. © 2003 Pharmaceutical Society of Japan

Synthesis and biological evaluation of indole containing derivatives of thiosemicarbazide and their cyclic 1,2,4-triazole and 1,3,4-thiadiazole analogs

New indolic derivatives of thiosemicarbazides and some cyclic 1,2,4- triazol-5-thione analogs were synthesized. The newly synthesized compounds as well as some indole containing thiosemicarbazides, 1,2,4-triazoles and 1,3,4- thiadiazoles, which have been reported previously, were investigated for antimicrobial, antifungal and antiphage activity. Certain thiosemicarbazide derivatives and the corresponding cyclic 1,2,4-triazole analogs showed selective antimicrobial or antifungal activity, while they lack any antiphage activity. Antiphage activity was detected for one compound, bearing the 1,3,4-thiadiazole nucleus. The selectively active compounds cover a wide range of lipophilicity. Structure-activity relations show a remarkably similarity in the antimicrobial and antifungal behaviour of the thiosemicarbazides and their cyclic triazo-thien-5-yl analogs, while α- naphtyl substitution in the non indolic portion of the molecule is favorable. C5 substitution on the indolic nucleus may also be critical for selective activity

Use of reversed-phase high-performance liquid chromatography in lipophilicity studies of 9H-xanthene and 9H-thioxanthene derivatives containing an aminoalkanamide or a nitrosoureido group. Comparison between capacity factors and calculated octanol-water partition coefficients

The lipophilicity of 9H-xanthene and 9H-thioxanthene derivatives, containing either a basic alkanamide or a nitrosoureido group, was studied by means of reversed-phase high-performance liquid chromatography using an octadecylsilane stationary phase, methanol as organic modifier and n-decylamine as a masking agent. Correlation of the extrapolated capacity factors with log P values calculated according to Rekker&apos;s fragmental system showed an excellent parallelism between HPLC and the octanol-water partition system and permitted the generation of a hydrophobic fragmental constant for the nitrosoureido group. Tetrahydrofuran was also tried as an organic modifier but without satisfactory results. © 1993

Analysis of PPAR-α/γ activity by combining 2-D QSAR and molecular simulation

In the present study 2D-QSAR analysis was combined with information on crystallographic data and molecular modeling, in order to investigate dual PPAR-α/γ activity for a data set of 71 compounds, compiled from literature. Using Multivariate Data Analysis, satisfactory PLS models were generated for each receptor subtype separately. The models were based on simple and easily interpretable drug-like and constitutional descriptors, while the inclusion of MOLCONN-Z descriptors in the initial pool of variables had no considerable impact in model predictivity. By simultaneous analysis of both types of activity, a consensus PLS model for dual PPAR-α/γ activity could be derived, displaying the molecular features, which may lead to a balanced activity. All models were validated by permutation tests, by dividing the data set into training and test sets, as well as by external validation using a blind test set. Detailed inspection of PPAR-α and PPAR-γ crystal structures and molecular simulation supported the differentiation of most important descriptors in the separate PLS models, e.g. the higher impact of lipophilicity and bulk descriptors in PPAR-α and PPAR-γ activity respectively, as well as the effect of specific structural descriptors. Molecular simulation provided also explanation for the behavior of certain outliers in the PLS models. Copyright © 2013 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim

Application of NMR-based metabonomics in the investigation of myocardial ischemia-reperfusion, ischemic preconditioning and antioxidant intervention in rabbits

NMR based metabonomics was applied in rabbit plasma samples during myocardial ischemia-reperfusion injury, with the following interventions: (1) Control (no intervention); (2) ischemic preconditioning (IpC); (3) administration of melatonin; (4) IpC + administration of melatonin; (5) treatment of the indole derivative C6458. The 1H NMR signal intensity ratio of lactate/glucose was found to increase in Control samples during reperfusion compared to baseline, while lactate + alanine/acetate was decreased suggesting impairment of aerobic glycolysis and concomitant lipid utilization. In contrast, after IpC or treatment with C6458, the lactate/glucose ratio was similar to baseline in accordance with the previously reported decrease in infarct size. Multivariate statistical methods such as Principal Component Analysis (PCA), and Discriminant Analysis (DA) were used for the discrimination of samples. The use of ANOVA variable preselection prior to PCA was advantageous in producing adequate models. PCA could classify the Control group in three clusters according to the condition of the heart (baseline-ischemia-reperfusion) while in the IpC groups no classification was evident. PCA discrimination upon treatment with melatonin and C6458 provided further evidence of their effect on the metabolic profile. The supervised DA resulted in fine discrimination between the different subgroups. Plasma NMR spectra in combination with pattern recognition techniques proved to be an efficient and simple method to depict the metabolic changes produced upon ischemia-reperfusion of the myocardium. © 2006 Elsevier B.V. All rights reserved

Electrochemical study of some non-steroidal anti-inflammatory drugs: Solvent effect and antioxidant activity

The electrochemical behavior of 12 non-steroidal anti-inflammatory drugs (NSAIDs) was studied by means of cyclic voltammetry at a glassy carbon electrode. The underlying solvent had a considerable effect to the oxidation potentials of the investigated NSAIDs due to the alteration of their polar intermediates&apos; solvation. Oxicams were more capable of electrochemical oxidation, and the influence of both specific and non-specific solute-solvent interactions in their reactivity was confirmed by means of Kamlet-Taft&apos;s analysis. Oxicams were further studied by chronoamperometry at the potentials of 300, 500, and 800 mV. The results obtained by the employed electroanalytical techniques were compared with the reactivity of oxicams towards 1,1- diphenyl-2-dipicrylhydrazyl (DPPH). The study showed a correlation of oxicams&apos; amperometric signal at 800 mV with their absolute reaction rate, z with DPPH. © 2010 Springer-Verlag