13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches

Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily on the correctness of the assumed stoichiometry including the presence of all reactions with a noticeable impact on the model metabolite balances. Determination of fluxes in complex metabolic networks often requires the inclusion of NADH and NADPH balances, which are subject to controversial debate. Transhydrogenation reactions that transfer reduction equivalents from NADH to NADPH or vice versa can usually not be included in the stoichiometric model, because they result in singularities in the stoichiometric matrix. However, it is the NADPH balance that, to a large extent, determines the calculated flux through the pentose phosphate pathway. Hence, wrong assumptions on the presence or activity of transhydrogenation reactions will result in wrong estimations of the intracellular flux distribution. Using 13C tracer experiments and NMR analysis, flux analysis can be performed on the basis of only well established stoichiometric equations and measurements of the labeling state of intracellular metabolites. Neither NADH/NADPH balancing nor assumptions on energy yields need to be included to determine the intracellular fluxes. Because metabolite balancing methods and the use of 13C labeling measurements are two different approaches to the determination of intracellular fluxes, both methods can be used to verify each other or to discuss the origin and significance of deviations in the results. Flux analysis based entirely on metabolite balancing and flux analysis, including labeling information, have been performed independently for a wild-type strain of Aspergillus oryzae producing alpha-amylase. Two different nitrogen sources, NH4+ and NO3-, have been used to investigate the influence of the NADPH requirements on the intracellular flux distribution. The two different approaches to the calculation of fluxes are compared and deviations in the results are discussed. Copyright 1998 John Wiley & Sons, Inc.     

Observation of the Yarrowia lipolytica peroxisome-vacuole dynamics by fluorescence microscopy with a single filter set

We constructed the fusion of peroxisomal acyl-CoA oxidase 3 and the enhanced yellow fluorescent protein (EYFP) for fluorescent labeling of Yarrowia lipolytica peroxisomes. Using the spectral overlap between EYFP and FM4-64, we developed a procedure for simultaneous observation of Y. lipolytica peroxisomes and vacuoles with the single fluorescein isothiocyanate filter set. Using this procedure we were able to follow the Y. lipolytica peroxisome-vacuole dynamics under pexophagy conditions and show that Y. lipolytica peroxisomes are degraded in the vacuoles by a macropexophagic mechanism.     

Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae

Yarrowia lipolytica was recently introduced as a new model organism to study peroxisome degradation in yeasts. Transfer of Y. lipolytica cells from oleate/ethylamine to glucose/ammonium chloride medium leads to selective macroautophagy of peroxisomes. To decipher the molecular mechanisms of macropexophagy we isolated mutants of Y. lipolytica defective in the inactivation of peroxisomal enzymes under pexophagy conditions. Through this analysis we identified the gene YlTRS85, the ortholog of Saccharomyces cerevisiae TRS85 that encodes the 85 kDa subunit of transport protein particle (TRAPP). A parallel genetic screen in S. cerevisiae also identified the trs85 mutant. Here, we report that Trs85 is required for nonspecific autophagy, pexophagy and the cytoplasm to vacuole targeting pathway in both yeasts.     

Population parameters and exploitation rate of Sarotherodon galilaeus galilaeus (Cichlidae) in Lakes Doukon and Togbadji,Benin

Growth, mortality, recruitment and relative yield per recruit of Sarotherodon galilaeus galilaeus from Lakes Doukon and Togbadji were studied. Data on total length, total weight and sex were recorded on a monthly basis between January and December 2013 for S. g. galilaeus captured by local fishers. The estimated asymptotic lengths L_∞ were 26.2 and 23.6?cm for Lakes Doukon and Togbadji, respectively, while the growth rate K was 0.73 in Lake Doukon and 0.87 in Lake Togbadji. Estimates of fishing mortality, 0.27 and 0.47 y^?1 for Doukon and Togbadji, respectively, were low relative to natural mortality, 1.51 and 1.74 y^?1, respectively. Sizes at first sexual maturity were 12.8 and 13.2?cm for females and males, respectively, in Lake Doukon, and 11.5 and 12.4?cm for females and males, respectively, in Lake Togbadji. The size at first capture was estimated at 13.3 and 12.7?cm for Lakes Doukon and Togbadji, respectively, which, in the light of the size at maturity estimates, indicates that fish spawn at least once before capture. The current exploitation rates of 0.15 for Lake Doukon and 0.21 for Lake Togbadji suggest that their stocks of S. g. galilaeus are not overexploited in either lake.     

Histopathological biomarkers and genotoxicity in gill and liver tissues of Nile tilapia Oreochromis niloticus from a polluted part of the Nile River,Egypt

Fish health is affected by water pollution. Oreochromis niloticus collected during summer 2014 from El-Serw, a polluted site on the Nile River, were compared with fish from a reference site, El-Zamalek. Histopathological changes were detected in gill and liver tissue samples using light and electron microscopy. In addition, the degree of DNA damage was measured using the comet assay. To indicate the severity of water pollution at the two sites, physico-chemical properties and heavy metal concentrations were investigated. Gill damage, including lamellar cell hyperplasia and aneurysm, was observed in the fish samples from the polluted site. The livers of fish from the polluted area showed necrosis and an increase in melanomacrophage centres. Histochemical results confirmed a marked rise of gill mucopolysaccharides and a reduction of carbohydrate stored in hepatocytes. Electron microscopy revealed clear alterations in gill and liver tissue of fish from the polluted site. The comet assay showed highly significant DNA damage in tilapia collected from the polluted site, compared to those from the reference site. Histopathological biomarkers and the comet assay may therefore be sensitive indicators of exposure to mixtures of aquatic pollutants in Nile tilapia.