A NEW PCR METHOD OF CHARACTERIZING SEAFISH FRESHNESS

Objective criteria used to assess the fish freshness in the laboratory are currently inadequate. During contamination of muscle tissue, bacteria reduce trimethylamine oxide (TMAO) to trimethylamine (TMA) in the absence of oxygen. Based on this reaction, we envisaged a new approach and have developed and optimized a PCR method which targets the tor A gene sequence that encodes TMAO reductase. We applied this method to two fish species (Whiting (Merlangus merlangus) and Pouting (Gadus luscus)) during monitoring of spoilage, in parallel with assay of TVBN and enumeration of total aerobic flora. The PCR results tally with the chemical and microbiological findings. Used in quantitative PCR, this method could characterize fish freshness.     

Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping

To test whether plucked hairs are a reliable source of DNA for genotyping microsatellite loci, we carried out experiments using one, three, or 10 hairs per extract for 50 alpine marmots. For each extract, seven independent genotypings were performed for the same locus (multiple-tubes approach). Two types of genotyping errors were recorded: a false homozygote defined as the detection of only one allele of a true heterozygote, and a false allele defined as a PCR-generated allele that was not one of the alleles of the true genotype. Using DNA extracted from one, three, or 10 hairs, the overall error rate was 14.00%, 4.86%, and 0.29%, respectively. Based on our results, we conclude that 10 hairs should be used to obtain consistently reliable genotypings using the single-tube approach, and that a single plucked hair could represent a reliable source of DNA if the multiple-tubes approach is used. For future studies of dinucleotide repeat diversity using DNA extracted from one to three shed or plucked hairs, we strongly recommend initiating an appropriate pilot study to quantify the error rate and to determine the reliability of the single-tube approach.     

Recent divergence between two morphologically differentiated subspecies of bluethroat (Aves: Muscicapidae: Luscinia svecica) inferred from mitochondrial DNA sequence variation

We assessed the mitochondrial DNA sequence divergence of a 718 bp fragment of the control region and 1007 bp of the cytochrome b gene between two allopatric morphologically different subspecies of bluethroat ( Luscinia svecica ). None of the 17 total haplotypes was shared between L. s. namnetum and L. s. svecica . However, the mean distances between subspecies were very low for both fragments (0.00168 ± 0.00001 (mean ± SE) for the control region; 0.00306 ± 0.00016 for the cytochrome b gene). Only one substitution made the two subspecies genetically differentiated, highlighting their recent divergence. Interestingly, the control region was not more variable than the cytochrome b gene.     

Theoretical habitat templets, species traits, and species richness: amphibians in the Upper Rhône River and its floodplain

• 1 The purpose of this study was to test predictions of the habitat templet and the patch dynamics concept by analysing the relationship between either the species traits or species richness of amphibians and the spatial–temporal variability of eight habitat types of the Upper Rhône River and its floodplain, France.
• 2 The information on species traits of the twelve amphibian species was accumulated primarily from the literature; that on habitat utilization was based on field surveys. The information was ‘fuzzy coded’, analysed by ordination techniques, and finally linked to the spatial–temporal variability of habitat types elaborated elsewhere in this issue.
• 3 After elimination of the variance caused by the differences between urodeles and anurans, correspondence analysis of the matrix of species traits demonstrated that the flexibility of the temporal pattern of reproduction was the major source of variation among amphibian species. A less significant source of variation within anurans was related to traits usually linked to the concept of r–K selection (potential number of descendants per reproductive cycle and ratio of egg size to female size).
• 4 A correspondence analysis of habitat utilization by amphibian species separated four groups of habitat types, corresponding to different degrees of influence that the active channel had on adjacent waters in the floodplain (i.e. from habitats that are most frequently disturbed by floods, to habitats of braided sections, old oxbow lakes, and the more terrestrialized habitats).
• 5 A co-inertia analysis of the relationship between species traits and habitat utilization separated two habitat types (terrestrialized former meanders and oxbow lakes) from the others. Species of terrestrialized habitats had a reproductive display, a low number of descendants per reproductive cycle, and a high ratio of egg size to female size. Species of oxbow lakes were early or synchronous breeders, and laid a single clutch.
• 6 Neither the predictions of the habitat templet concept nor those of the patch dynamics concept were validated. Species traits were not significantly correlated to the axes of the spatial–temporal variability templet. The highest species richness was observed in habitat types with the highest temporal variability; in addition, richness did not peak at highest spatial variability.
• 7 Deviation from the predictions of the river habitat templet could be explained by: (i) the over-simplification of this model with regard to the evolution of the complex life cycles of the amphibians; and (ii) an underestimation of the importance of phylogenetic constraints and the evolution of community interactions.

     

Theoretical habitat templets, species traits, and species richness: ostracods (Crustacea) in the Upper Rhône River and its floodplain

• 1 Ostracods occurring at two sections of the Upper Rhône River, France, were examined to determine relationships among species traits, habitat utilization, the relationship between species traits and habitat utilization, and trends in species traits and species richness in the context of spatial and temporal variability of habitats. Twenty regularly sampled species were used in this study and fifteen species traits were considered.
• 2 Throe groups can be distinguished according to their species traits: group 1 has species of mixed sizes with high reproductive rates, short life span, spherical shape, long swimming bristles, low thigmotactism, and high resistance to desiccation; group 2 has medium-sized species with low reproductive rates, long life span, low or no tolerance to desiccation, geometric (trapezoidal, triangular) or streamlined carapace shape, no swimming bristles, and a strong thigmotactism; group 3 has the largest species with parthenogenetic reproduction, medium-sized swimming bristles, and flattened or cylindric carapace shape.
• 3 Ostracod habitat utilization segregates the superficial and interstitial habitats along a gradient from the main channel to the abandoned arms and to the temporary waters.
• 4 The co-structure (= relationship) between species traits and habitat utilization indicates that the species use particular habitats with a particular set of species trait modalities. Species with long life spans, late maturity, low fecundity, and low migratory ability are restricted to the interstitial habitats; the epigean species with long life spans, large size, and parental care are more abundant in permanent flowing and standing surface waters; the epigean species with short life spans, high migratory ability, and high tolerance to desiccation are more abundant in temporary ponds.
• 5 The analyses of the distribution of the species traits in a river habitat templet of spatial and temporal variability emphasized that the main disturbance structuring the Rhône River ostracod assemblage is desiccation.
• 6 Of the trends predicted for species traits in the framework of the river habitat templet, five (size, body form, attachment, reproductive technique, and mobility) are clearly opposite for ostracods (because the predictions were mainly established for flood-related disturbances) but four (life span, number of reproductive cycles per year, age at first reproduction, and desiccation tolerance) are in agreement.
• 7 No trends in ostracod species richness in the framework of spatial–temporal habitat variability were evident.

     

Influence of Protein Factors on the Activation of NADP–malate Dehydrogenase by Dithiothreitol

Leaves of Phaseolus vulgaris L. contained malate dehydrogenase activity dependent on NADP (E. C. 1.1.1.82); it could be detected in extracts only when a dithiol such as dithiothreitol was present. After the addition of dithiothreitol, the activity increased with time, passed through a maximum and then diminished. The activation rate and/or the maximum level of activity were essentially dependent on dithiothreitol concentration, pH, and temperature. The presence of bovine serum albumine or glycerol in the medium decreased the inactivation rate; equivalent results were obtained at low temperatures. A mathematical model was established showing an apparent first-order rate for activation and inactivation only under conditions of alkaline pH near 8.3. These data allowed us to demonstrate that compounds other than dithiothreitol were necessary for the activation process. Evidence suggested that these compounds were protein factors of low molecular weights which increased the activation rate and the maximum level of activity when added to the incubation medium at pH 7.3. Their efficiency in the enzyme activation was higher at alkaline pH than at acid or neutral pH.