Genomic characterization of POS5, the Saccharomyces cerevisiae mitochondrial NADH kinase

Disruption of the Saccharomyces cerevisiae mitochondrial NADH kinase POS5 increases the mitochondrial mutation rate 50-fold. Whereas most multicellular eukaryotic genomes have one NADH kinase gene, the yeast genome contains three distinct genes encoding NAD/H kinase activity. To determine if all three genes are essential for viability we constructed combinations of gene knockouts. We show that only the pos5Deltautr1Delta combination is synthetically lethal, demonstrating an essential overlapping function, and showing that NAD/H kinase activity is essential for eukaryotic viability. The single human NAD/H kinase gene can rescue the lethality of the double knockout in yeast, demonstrating that the single human gene can fill the various functions provided by the three yeast genes. The human NAD/H kinase gene harbors very common sequence variants, but all of these equally complement the synthetic lethality in yeast, illustrating that each of these are functionally wild-type. To understand the molecular mechanism of the mitochondrial genome instability of pos5 mutation we performed gene expression analysis on the pos5Delta. The pos5Delta resulted in an increase in expression of most of the iron transport genes including key genes involved in iron-sulfur cluster assembly. Decreased expression occurred in many genes involved in the electron transport chain. We show that the pos5Delta expression pattern is similar to the frataxin homolog knockout (yfh1Delta), the yeast model for Friedreich's ataxia. These combined data show that the POS5 NAD/H kinase is an important protein required for a variety of essential cellular pathways and that deficient iron-sulfur cluster assembly may play a critical role in the mitochondrial mutator phenotype observed in the pos5Delta.     

Geotrichum candidum dominates in yeast population dynamics in Livarot, a French red-smear cheese

The diversity and dynamics of yeast populations in four batches of Livarot cheese at three points of ripening were determined. Nine different species were identified by Fourier transform infrared spectroscopy and/or sequencing, and each batch had its own unique yeast community. A real-time PCR method was developed to quantify the four main yeast species: Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces sp. and Yarrowia lipolytica. Culture and molecular approaches showed that G. candidum was the dominant yeast in Livarot cheese. When D. hansenii was added as a commercial strain, it codominated with G. candidum. Kluyveromyces lactis was present only at the start of ripening. Yarrowia lipolytica appeared primarily at the end of ripening. We propose a scheme for the roles and dynamics of the principal Livarot yeasts.     

Synthesis and physicochemical and dynamic mechanical properties of a water-soluble chitosan derivative as a biomaterial

The physicochemical and rheological properties of a water-soluble chitosan (WSC) derivative were characterized in order to facilitate its use as a novel material for biomedical applications. The WSC was prepared by conjugating glycidyltrimethylammonium chloride (GTMAC) onto chitosan chains. Varying the molar ratio of GTMAC to chitosan from 3:1 to 6:1 produced WSCs with a degree of substitution (DS) that ranged from 56% to 74%. The WSC with the highest DS was soluble in water up to concentrations of 25 g/dL at room temperature. An increase in the polymer concentration gradually increased both the pH and conductivity of the WSC solutions. The rheological properties of the WSC solutions were found to be dependent on the salt and polymer concentrations as well as the DS value. In the absence of salt, the rheological behavior of the WSC was found to be typical of that for a polyelectrolyte in the dilute solution regime. However, the addition of salt decreased the viscosity of the polymer solution due to the reduction of electrostatic repulsions by the positively charged trimethylated ammonium groups of the WSC. In the concentrated regime, the viscosity of the WSCs was found to follow a power-law expression. The lowest DS WSC had the more favorable viscoelastic properties that were attributed to its high molecular weight, as confirmed by the stress relaxation spectra and intrinsic viscosity measurements. The effect of DS on the degree of interaction between WSC and the lipid egg phosphatidylcholine was investigated by FTIR analysis. Overall, the lower DS WSC had enhanced rheological properties and was capable of engaging in stronger intermolecular physical interactions.     

Similar functional activity of dendritic cells recruited to the mesenteric lymph nodes of newborn and adult mice after the rectal delivery of Mycobacterium bovis BCG

BCG rectal administration to newborn and adult mice induced protective immune responses against tuberculosis. BCG reaches the sub-epithelial site and the draining mesenteric lymph nodes (MLNs), and dendritic cells (DC) could be recruited to these sites. Using polarized Caco-2 epithelial cells, we showed that BCG translocates epithelial cells to basolateral compartment. Delayed in newborn BALB/c mice, an important recruitment of CD11c⁺ DCs, was documented in the rectal lamina propria and the MLNs during the first two weeks after rectal BCG delivery. In MLNs, two major DC subtypes were observed: conventional DCs (cDCs) (B220⁻) and plasmacytoid DCs (pDCs) (B220⁺). CIRE, mouse DC-specific intracellular adhesion molecule 3 grabbing non-integrin (DC-SIGN) is predominantly expressed on pDCs and at a higher level on pDCs from the adult compared to newborn MLNs. cDCs with a higher capacity to induce the proliferation of naïve CD4⁺ T cells than pDCs, triggered CD4⁺ T cells to produce interferon-γ whereas pDCs triggered them to release interleukin-10. Both DC subtypes equilibrates T cells as a source of microbicidal/microbiostatic signals and those acting as source of counter-inflammatory signals, preventing tissue damage and/or accelerating tissue repair. Thus, rectal delivery of BCG could be a safe and efficient route of vaccination against tuberculosis.     

Spatial patterns of the surf zone hyperbenthic fauna of Valdivia Bay (Ecuador)

The present research is a first attempt to study the hyperbenthic fauna of the surf zone of Valdivia Bay (South East Pacific--Ecuador), an exposed low tide terrace--rip beach. The aims of the study were to contribute to the inventory of the surf zone fauna of the tropical southeast Pacific coast, to investigate spatial distribution patterns along the bay and to search for possible tidal effects on the hyperbenthic composition. Samples were taken during daylight with a hyperbenthic sledge on 6 consecutive days in August 1999 at high tide, low tide and mid tide. The hyperbenthic community was characterized by quantifying the higher taxa, their density and the relative composition of the dominant groups. No tidal effect could be observed, but two main geographically distinct hyperbenthic assemblages were distinguished along the bay, related to hydrodynamic factors (local current velocity, intertidal beach slope and suspended particulate matter). In the turbulent northern part of the bay the highest densities were encountered and hyperbenthos was, next to the dominant mysid Metamysidopsissp., mainly composed of planktonic organisms (calanoid copepods, chaetognaths and fish eggs). In the calmer southern part of the bay Metamysidopsissp. dominated as well, but the community was completed with other mysid species, and early life stages of Brachyura and fish. Most striking was the general dominance of the mysid Metamysidopsis sp. in all the samples (97%, max. density of 62000 ind. 100 m^-2) and the high amount of unknown species. Penaeid shrimp larvae, important for the local shrimp industry, were only found in very low densities during the sampling period (1%). Compared to other studies on the whole surf zone hyperbenthic community of sandy beaches, the average densities encountered in Valdivia Bay can be considered to be relatively high (2500--6000 ind. 100 m^-2). Although limited in time and performed with a limited taxonomic resolution, the results indicate a high contribution of early life stages of invertebrate and fish species to the biodiversity of the intertidal hyperbenthic community in comparison with temperate regions.     

Isotopic composition of nitrate-nitrogen as a marker of riparian and benthic denitrification at the scale of the whole Seine River system

Nitrogen budgets established for large river systems reveal that up to 60% of the nitrate exported from agricultural soils is eliminated, either when crossing riparian wetlands areas before even reaching surface waters, or within the rivers themselves through benthic denitrification. The study of nitrogen isotope ratios of riverine nitrates could offer an elegant means to assess the extent of denitrification and thus confirm these budgets, as it is known that denitrification results in a natural ¹⁵N enrichment of residual nitrates. The results reported here, for the Seine river system (France), demonstrate the feasibility of this isotopic approach at the scale of large watersheds. On the basis of in situ observations carried out in a large storage reservoir in the upstream Seine catchment (Der Lake), where intensive benthic denitrification occurs, as well as on the basis of laboratory experiments of denitrification under controlled conditions, it is shown that the isotopic discrimination associated with benthic denitrification is minimal ( of NO₃-N ranging from –1.5 to –3.6), probably because the rate-limiting step of the process consists of nitrate diffusion through the water-sediment interface. Riparian denitrification on the contrary, when it implies nitrate reduction during convective transfer through reducing environements, causes a much more significant isotopic enrichment of ¹⁵N of residual nitrate ( about –18). The authors report measurements of nitrogen isotopic composition of nitrate from rivers of various stream orders in the Seine river system under summer conditions. Anomalies in the data with respect to the values expected from the mixture of the various sources of nitrate are here attributed to riparian denitrification. However, the authors show that because of the patchy distribution of actively denitrifying riparian zones within the drainage network, the isotopic signature conferred to residual nitrate in river water intrinsically provides only a minimum estimate of the extent of denitrification.     

Effect of smoking habit on the frequency of micronuclei in human lymphocytes: results from the Human MicroNucleus project

The effect of tobacco smoking on the frequency of micronuclei (MN) in human lymphocytes has been the object of many population studies. In most reports, the results were unexpectedly negative, and in many instances smokers had lower frequencies of MN than non-smokers. A pooled re-analysis of 24 databases from the HUMN international collaborative project has been performed with the aim of understanding the impact of smoking habits on MN frequency. The complete database included 5710 subjects, with 3501 non-smokers, 1409 current smokers, and 800 former smokers, among subjects in occupational and environmental surveys. The overall result of the re-analysis confirmed the small decrease of MN frequencies in current smokers (frequency ratio (FR) = 0.97, 95% confidence interval (CI) = 0.93-1.01) and in former smokers (FR = 0.96, 95% CI = 0.91-1.01), when compared to non-smokers. MN frequency was not influenced by the number of cigarettes smoked per day among subjects occupationally exposed to genotoxic agents, whereas a typical U-shaped curve is observed for non-exposed smokers, showing a significant increase of MN frequency in individuals smoking 30 cigarettes or more per day (FR = 1.59, 95% CI = 1.35-1.88). This analysis confirmed that smokers do not experience an overall increase in MN frequency, although when the interaction with occupational exposure is taken into account, heavy smokers were the only group showing a significant increase in genotoxic damage as measured by the micronucleus assay in lymphocytes. From these results some general recommendations for the design of biomonitoring studies involving smokers can be formulated. Quantitative data about smoking habit should always be collected because, in the absence of such data, the simple comparison of smokers versus non-smokers could be misleading. The sub-group of heavy smokers (> or =30 cigarettes per day) should be specifically evaluated whenever it is large enough to satisfy statistical requirements. The presence of an interaction between smoking habit and occupational exposure to genotoxic agents should be always tested.     

Novel bicyclic lactam inhibitors of thrombin: highly potent and selective inhibitors

The potency and selectivity of a previous series of low molecular weight thrombin inhibitors were improved through modifications of the P1 and P3 residues. Introduction of diphenyl substituted sulfonamides in the P3 moiety led to highly efficacious compounds. By correctly selecting the combination of P1 and P3 residues, high levels of potency, selectivity and in vivo efficacy were obtained.     

Rates of nitrification and carbon uptake in the Rhône River plume (northwestern Mediterranean Sea)

Nitrification rates were measured along a salinity gradient in the Rhône River estuary, using specific inhibitors (allylthiourea and chlorate) coupled with the measurement of change in nitrite concentration and inorganic carbon uptake by nitrifiers. Rates of ammonium and nitrite oxidation were similar up to 15 practical salinity units (from 1 to 2 mol N oxidized liter^-1 day^-1). For higher salinities, nitrite and ammonium oxidation rates were 0.14 and 0.23 mol N oxidized liter^-1 day^-1, respectively. Ammonium oxidizers assimilated 19–150 × 10–3 mol C liter^-1 day^-1, while nitrite oxidizers fixed 4.8–72.6 × 10–3 mol C liter^-1 day^-1. The amounts of nitrogen oxidized and C incorporated demonstrated a linear correlation (r ² > 0.99). The ratio of N oxidized to C incorporated ranged between 14.3 to 12.3 for ammonium oxidizers, and between 31.6 and 29 for nitrite oxidizers, the lower values being measured in seawater. Offprint requests to: M. Bianchi.