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Content available remote Petri Nets for Modelling and Analysing Trophic Networks
We consider trophic networks, a kind of networks used in ecology to represent feeding interactions (what-eats-what) in an ecosystem. Starting from the observation that trophic networks can be naturally modelled as Petri nets, we explore the possibility of using Petri nets for the analysis and simulation of trophic networks. We define and discuss different continuous Petri net models, whose level of accuracy depends on the information available for the modelled trophic network. The simplest Petri net model we construct just relies on the topology of the network. We also propose a technique for deriving a more refined model that embeds into the Petri net the known constraints on the transition rates that represent the knowledge on metabolism and diet of the species in the network. Finally, if the information of the biomass amounts for each species at steady state is available, we discuss a way of further refining the Petri net model in order to represent dynamic behaviour. We apply our Petri net technology to a case study of the Venice lagoon and analyse the results.
Content available remote Characterization of lacosamide metabolites by UHPLC–ESI–HRMS method
In this study, the in vitro phase I metabolism of lacosamide was characterized with the use of ultra-high-performance liquid chromatography combined with high-resolution mass spectrometry (quadrupole time-of-flight). The use of two metabolism simulation techniques (photocatalysis and human liver microsomes) allowed the characterization of a polar metabolite of parent compound, not yet described. The experiment with the participation of HLM gave the ability to describe the full liver metabolic pathway of lacosamide. It has been proven that this molecule undergoes deacetylation, demethylation, and during liver tissue metabolism. Photocatalysis with the use of a TiO2 catalyst was proved to be a complementary technique in mimicking in vitro drug metabolism.
Previous studies on electrochemical reduction of the HTV reverse transcriptase inhibitor, 3'-azido-3'-deoxy thymidine (Zidovudine, AZT) and several of its analogues, have been extended to 2'-AZdT and two of the intracellular metabolites of AZT, the 5'-0-glucuronide (GAZT) and the 5'-phosphate (AZTMP). Also investigated were azido nucleosides with aglycons susceptible to electrochemical reduction, cytosine and adenine. The surface activities of these compounds at the mercury electrode were examined. In all instances, reduction of the azido group was a two-electron process, with conversion to an amino group. For an azido adenine nucleoside, it proved possible to reduce the azido group without affecting the aglycon. Electrochemical reduction is shown to provide a simple one-step synthesis of amino nucleosides from the available azido nucleosides. The reduced compounds, several hitherto unknown, are useful reference standards for following intracellular metabolism of azido nucleosides, and may also prove of interest as new potential antimetabolites.
Content available Struktura i funkcje białka βKlotho
The βKlotho gene was identified on 2000, based on sequence similarity with the αKlotho gene. The KLB gene encoded single-pass transmembrane protein, which is expressed predominantly in liver and white adipose tissue. KLB–/–mice, unlike αKL–/– mice, grow and develop quite normally, but they exhibit increased bile acid synthesis and resistance to gallstone formation. Similar phenotype was also observed in mice lacking FGFR4 or FGF15. These observations led to hypothesis, that βKlotho interacts with FGFR4 and functions as a coreceptor for FGF15. Subsequent studies have shown, that βKlotho form complex with FGFR1c and function as coreceptor for FGF21. It was found, that via FGF-FGFR signalling pathway βKlotho can regulate many cellular processes. Functions as coreceptor for FGF19 (the orthologous protein in humans), KLB can regulate inter alia bile acids metabolism and energy homeostasis. Function as coreceptor for FGF21 protein can mediate promotion of lypolisis in white adipose tissue and ketogenesis in liver.
Gen βKlotho (KLB) odkryty został w roku 2000, jako homolog genu αKlotho. Gen KLB koduje monotopowe białko przezbłonowe, ulegające ekspresji głównie w wątrobie i białej tkance tłuszczowej. W odróżnieniu od myszy αKL–/–, myszy KLB–/– rozwijają się prawidłowo, jednakże wykazują one znaczny wzrost biosyntezy kwasów żółciowych oraz oporność na tworzenie się kamieni żółciowych. Podobny fenotyp obserwuje się również u myszy z wyłączonym genem FGFR4 lub FGF15. Dane te były podstawą sugestii, że białko βKlotho oddziałuje z FGFR4 i pełni rolę koreceptora dla FGF15. Dalsze analizy pokazały, że βKlotho tworzy również kompleks z receptorem FGFR1c, funkcjonując jako koreceptor dla czynnika FGF21. Wykazano, że poprzez działanie na szlaku FGF-FGFR, białko βKlotho zaangażowane jest w regulację licznych procesów komórkowych. Funkcjonując jako koreceptor dla czynnika FGF19 (ortolog FGF15 u człowieka), KLB wpływa na metabolizm kwasów żółciowych oraz homeostazę energetyczną. Natomiast jako koreceptor dla FGF21, białko KLB wpływa na promocję lipolizy w białek tkance tłuszczowej oraz ketogenezy w wątrobie.
Anaerobic digestion of organic matter results from the metabolic activity of many groups of microorganisms. Interactions between microorganisms during acidogenesis, acetogenesis and methanogenesis, source of inoculum, type of feedstock and operational conditions determine metabolic pathways in bioreactors and consequently the efficiency of fermentation processes. In innovative installations it is desirable to separate acidogenesis from acetogenesis and methanogenesis to favour respectively the production of biohydrogen or biomethane under controlled conditions.
10-Methoxycamptothecin (MCPT) and 10-hydroxycamptothecin (HCPT) are the indole alkaloids isolated from a Chinese tree, Camptotheca acuminata, and have a wide spectrum of anticancer activity in vitro and in vivo mainly through inhibitory effects on topoisomerase I. HCPT is a major metabolite of MCPT in rats; the pharmacokinetic analysis and tissue distribution of MCPT and HCPT in rats have also been determined after i.v. injection of MCPT, but the excretion of MCPT and its metabolite HCPT has not been assessed up to now. In the present study, the excretion study of MCPT and its metabolite HCPT in rat bile, feces, and urine after i.v. administration of MCPT (5 mg kg-1) was performed by high performance liquid chromatography (HPLC) method coupled with a fluorescence detector. The results showed that MCPT mainly biotransformed to HCPT and excreted in the form of HCPT and MCPT in bile, urine, and feces after i.v. administration of MCPT. It was excreted about 1.24 ± 0.07% as MCPT and 5.49 ± 0.40% as HCPT in bile within 6 h after i.v. administration. The cumulative excretions of MCPT and HCPT were mainly within 24 h after i.v. administration, which were 0.41 ± 0.10% and 7.66 ± 1.43% of the dosage in urine and about 0.16 ± 0.04% and 20.30 ± 3.35% of the dosage in feces. The total excretion of MCPT in urine, bile, and feces was 1.81 ± 0.09% in the form of original MCPT and 33.45 ± 1.57%. detected as the metabolite HCPT in urine, bile, and feces, suggesting that MCPT might undergo other biotransformation.
W ciągu ostatniego dziesięciolecia obszary bioinformatyki i genomiki zidentyfikowały .śruby. i .nakrętki. maszyny, która tworzy żywą komórkę. Równolegle rozwijany jest nowy kierunek badań, którego celem jest zrozumienie systemów biologicznych, związanych z modelowaniem, symulacją i wizualizacją dynamicznego zachowania się tych złożonych systemów. W pracy przedstawiono proces budowy modeli matematycznych opisujących metabolizm węgla i energii drobnoustrojów.
Over the last decade, the areas of bioinformatics and genomics have identified the nuts and bolts of the machinery that make up a living cell. In parallel with such data-driven research, a new approach which aims at understanding of life mechanisms by modeling, simulating and visualization of the dynamic behaviors of complex biological systems is being developed. In this study, the process of building mathematical models of carbon and energy metabolism for microbial organisms is described.
Comparison was made of reactions of two species: Tribolium castaneum (Herbst) - strain cl and T. confusum (Duval) - strain bIV and their two phenotypes characterised by different number of instars during development (6- and 7-instar) in each species to two diets: wheat flour with yeast (standard medium) and flour without yeast (altered medium). Medium deprived of yeast did not affect substantially survival of phenotypic groups of both species during embryonic and larval development. Lack of yeast in the diet significantly decreased fecundity (especially in T. castaneum), increased oxygen consumption mainly in larval stages, and increased body calorific value (stronger in T. confusum), decreased reproductive effort (stronger in T. castaneum). Lack of yeast in diet caused decrease in energy expenditure for maturation in T. confusum (with much smaller effect in T. castaneum). There was no significant difference in reaction to diet change in the two phenotypes within both strains
Oxygen consumption, thermal conductance and body temperature of Meriones unguiculatus (Milne-Edwards, 1867) were measured at a temperature range from 5 to 40°C. The lowest mean metabolic rate tBMR) was 2.13 ± 0.14 ml02 g~ 1 h , which is higher than the predicted values based on their body mass. The thermal neutral zone (TNZ) was 26 to 38°C. Mean body temperature below the TNZ was 38.4 ± 0.5°C. Mean thermal conductance below the TNZ was 0.179 ± 0.037 ml02 g-1 • h-1 • °C which is also higher than predicted values based on their body mass. Thermoregulatory characteristics of Mongolian gerbils are very different from that found in arid-adapted small mammals. The extreme severe climate perhaps is the main selective force faced by Mongolian gerbils during their evolution with their macroenvironments.
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