Comparisons of mitochondrial DNA (mtDNA) sequences (16S rRNA gene) between oviparous and viviparous strains of Lacerta vivipara: a preliminary study

The lizard Lacerta vivipara has allopatric oviparous and viviparous populations. The mitochondrial DNA (mtDNA) gene coding for the 16S rRNA was sequenced for several viviparous lizard populations from France, Switzerland, Bulgaria, Czech Republic, The Netherlands, Sweden, and for oviparous lizard populations from the Pyrenean and Cantabric Mountains. Seven distinct groups (three oviparous and four viviparous) were identified. The net nucleotide divergence between oviparous and viviparous haplotypes was 1.3% +/- 0.5 (mean +/- standard deviation). These results on mtDNA, together with other data obtained previously, led us to formulate a biogeographical scenario that could be tested by further research.     

Influence of rainfall seasonality on African lowland vegetation during the Late Quaternary: pollen evidence from Lake Masoko, Tanzania

Aim  To determine if changes in the key bioclimatic parameters associated with rainfall seasonality can be quantified from fossil sequences and to distinguish them from changes in the total annual rainfall.
Location  Lake Masoko, southern Tanzania (9°20' S, 33°45' E, 840 m a.s.l.).
Methods  Fossil pollen was extracted from a long and well-dated sedimentary sequence spanning the period 45,000–4400 cal. yr bp . The modern habitat, geographical distribution and climatic range (mean annual rainfall and temperature, and length of the dry season) of selected East African plants were used to infer past rainfall attributes for the most characteristic fossil pollen taxa identified from the sediments of Lake Masoko.
Results  In the Masoko pollen sequence it has been possible to identify changes in the length/severity of the dry season during the last 45,000 cal. yr bp , which are interpreted to reflect shifts in the mean position of the Intertropical Convergence Zone (ITCZ) over the southern tropics. We suggest that this bioclimatic parameter has been the main driver of the vegetation dynamics in this area. The major inferred change occurred at the Younger Dryas–Holocene transition c . 11,800 cal. yr bp , when semi-deciduous forest disappeared, being replaced in the lake catchment by woodland, which persists to the present day in spite of locally high rainfall.
Main conclusions  In tropical regions under the influence of the ITCZ, the position and strength of which determine the distribution of rainfall through the year, more attention must be paid to the impact of the length and intensity of the dry season on the modern and past distribution and dynamics of the vegetation. This climatic parameter is as important as the total annual amount of rainfall, and probably one of the most relevant in lowland areas.     

Occurrence of Virulence and Antimicrobial Resistance Genes in Escherichia coli Isolates from Different Aquatic Ecosystems within the St. Clair River and Detroit River Areas

Although the number of Escherichia coli bacteria in surface waters can differ greatly between locations, relatively little is known about the distribution of E. coli pathotypes in surface waters used as sources for drinking or recreation. DNA microarray technology is a suitable tool for this type of study due to its ability to detect high numbers of virulence and antimicrobial resistance genes simultaneously. Pathotype, phylogenetic group, and antimicrobial resistance gene profiles were determined for 308 E. coli isolates from surface water samples collected from diverse aquatic ecosystems at six different sites in the St. Clair River and Detroit River areas. A higher frequency (48%) of E. coli isolates possessing virulence and antimicrobial resistance genes was observed in an urban site located downstream of wastewater effluent outfalls than in the other examined sites (average of 24%). Most E. coli pathotypes were extraintestinal pathogenic E. coli (ExPEC) pathotypes and belonged to phylogenetic groups B2 and D. The ExPEC pathotypes were found to occur across all aquatic ecosystems investigated, including riverine, estuarine, and offshore lake locations. The results of this environmental study using DNA microarrays highlight the widespread distribution of E. coli pathotypes in aquatic ecosystems and the potential public health threat of E. coli pathotypes originating from municipal wastewater sources.     

Molecular characterization of nosRZDFYLX genes coding for denitrifying nitrous oxide reductase of Bradyrhizobium japonicum

The nosRZDFYLX gene cluster for the respiratory nitrous oxide reductase from Bradyrhizobium japonicum strain USDA110 has been cloned and sequenced. Seven protein coding regions corresponding to nosR, nosZ, the structural gene, nosD, nosF, nosY, nosL, and nosX were detected. The deduced amino acid sequence exhibited a high degree of similarity to other nitrous oxide reductases from various sources. The NosZ protein included a signal peptide for protein export. Mutant strains carrying either a nosZ or a nosR mutation accumulated nitrous oxide when cultured microaerobically in the presence of nitrate. Maximal expression of a P nosZ-lacZ fusion in strain USDA110 required simultaneously both low level oxygen conditions and the presence of nitrate. Microaerobic activation of the fusion required FixLJ and FixK(2).     

Analysis of human cytochrome P450 2C8 substrate specificity using a substrate pharmacophore and site-directed mutants

The structural determinants of substrate specificity of human liver cytochrome P450 2C8 (CYP2C8) were investigated using site-directed mutants chosen on the basis of a preliminary substrate pharmacophore and a three-dimensional (3D) model. Analysis of the structural features common to CYP2C8 substrates exhibiting a micromolar K(m) led to a substrate pharmacophore in which the site of oxidation by CYP2C8 is 12.9, 8.6, 4.4, and 3.9 A from features that could establish ionic or hydrogen bonds, and hydrophobic interactions with protein amino acid residues. Comparison of this pharmacophore with a 3D model of CYP2C8 constructed using the X-ray structure of CYP2C5 suggested potential CYP2C8 amino acid residues that could be involved in substrate recognition. Twenty CYP2C8 site-directed mutants were constructed and expressed in yeast to compare their catalytic activities using five CYP2C8 substrates that exhibit different structures and sizes [paclitaxel, fluvastatin, retinoic acid, a sulfaphenazole derivative (DMZ), and diclofenac]. Mutation of arginine 241 had marked effects on the hydroxylation of anionic substrates of CYP2C8 such as retinoic acid and fluvastatin. Serine 100 appears to be involved in hydrogen bonding interactions with a polar site of the CYP2C8 substrate pharmacophore, as shown by the 3-4-fold increase in the K(m) of paclitaxel and DMZ hydroxylation after the S100A mutation. Residues 114, 201, and 205 are predicted to be in close contact with substrates, and their mutations lead either to favorable hydrophobic interactions or to steric clashes with substrates. For instance, the S114F mutant was unable to catalyze the 6alpha-hydroxylation of paclitaxel. The S114F and F205A mutants were the best catalysts for retinoic acid and paclitaxel (or fluvastatin) hydroxylation, respectively, with k(cat)/K(m) values 5 and 2.1 (or 2.4) times higher, respectively, than those found for CYP2C8. Preliminary experiments of docking of the substrate into the experimentally determined X-ray structure of substrate-free CYP2C8, which became available quite recently [Schoch, G. A., et al. (2004) J. Biol. Chem. 279, 9497], were consistent with key roles for S100, S114, and F205 residues in substrate binding. The results suggest that the effects of mutation of arginine 241 on anionic substrate hydroxylation could be indirect and result from alterations of the packing of helix G with helix B'.     

Cryopreservation induces an apoptosis-like mechanism in bull sperm

Cryopreservation induces many changes in sperm cells, including membrane disorders and cell death. We tested the hypothesis that apoptosis, a form of programmed cell death, can contribute to the fatal effect of cryopreservation on sperm cells. A multiparametric study of apoptosis on bovine sperm is proposed, using flow cytometry, including mitochondrial membrane potential (DeltaPsi(m)), caspase activation, membrane permeability, nucleus condensation, DNA fragmentation, and phosphatidylserine (PS) externalization. The relevance of each test was first validated on a human somatic cell line, U937. Cryopreservation and/or thawing induced significant changes in all apoptotic markers in living bull sperm cells except those concerning the nucleus. After cryopreservation, 44.9% +/- 17% (vs. 11.3% +/- 10.6% before cryopreservation) of sperm cells showed low DeltaPsi(m), 12% +/- 6.3% (vs. 2.2% +/- 1.0% before) contained active caspases, and 10.8% +/- 5.8% (vs. 1.4% +/- 1.1% before) exhibited high membrane permeability. However, cryopreservation had no effect on DNA fragmentation (9.1% +/- 7.7% before vs. 11.1% +/- 5.7% after cryopreservation) or on nucleus condensation (46% +/- 12.7% before vs. 43.8% +/- 13.1% after). Cryopreservation acts as an apoptotic mechanism inducer in bovine sperm cells, where the earliest but not the latest features of cells undergoing apoptosis occur. We have named this abortive process an apoptosis-like phenomenon.