Showing papers by "Institut national de la recherche agronomique published in 1997"

The complete genome sequence of the Gram-positive bacterium Bacillus subtilis

Abstract: Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Catalase is a sink for H2O2 and is indispensable for stress defence in C3 plants.

Abstract: Hydrogen peroxide (H 2 O 2 ) has been implicated in many stress conditions. Control of H 2 O 2 levels is complex and dissection of mechanisms generating and relieving H 2 O 2 stress is difficult, particularly in intact plants. We have used transgenic tobacco with ∼10% wild‐type catalase activity to study the role of catalase and effects of H 2 O 2 stress in plants. Catalase‐deficient plants showed no visible disorders at low light, but in elevated light rapidly developed white necrotic lesions on the leaves. Lesion formation required photorespiratory activity since damage was prevented under elevated CO 2 . Accumulation of H 2 O 2 was not detected during leaf necrosis. Alternative H 2 O 2 ‐scavenging mechanisms may have compensated for reduced catalase activity, as shown by increased ascorbate peroxidase and glutathione peroxidase levels. Leaf necrosis correlated with accumulation of oxidized glutathione and a 4‐fold decrease in ascorbate, indicating that catalase is critical for maintaining the redox balance during oxidative stress. Such control may not be limited to peroxisomal H 2 O 2 production. Catalase functions as a cellular sink for H 2 O 2 , as evidenced by complementation of catalase deficiency by exogenous catalase, and comparison of catalase‐deficient and control leaf discs in removing external H 2 O 2 . Stress analysis revealed increased susceptibility of catalase‐deficient plants to paraquat, salt and ozone, but not to chilling.

Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis.

Abstract: The bacterial community structure of a fluidized-bed reactor fed by vinasses (wine distillation waste) was analyzed. After PCR amplification, four small-subunit (SSU) rDNA clone libraries of Bacteria, Archaea, Procarya, and Eucarya populations were established. The community structure was determined by operational taxonomic unit (OTU) phylogenetic analyses of 579 partial rDNA sequences (about 500 bp long). A total of 146 OTUs were found, comprising 133, 6, and 7 from the Bacteria, Archaea, and Eucarya domains, respectively. A total of 117 bacterial OTU were affiliated with major phyla: low-G+C gram-positive bacteria, Cytophaga-Flexibacter-Bacteroides, Proteobacteria, high-G+C gram-positive bacteria, and Spirochaetes, where the clone distribution was 34, 26, 17, 6, and 4%, respectively. The other 16 bacterial OTUs represent 13% of the clones. They were either affiliated with narrow phyla such as Planctomyces-Chlamydia, green nonsulfur bacteria, or Synergistes, or deeply branched on the phylogenetic tree. A large number of bacterial OTUs are not closely related to any other hitherto determined sequences. The most frequent bacterial OTUs represents less than 5% of the total bacterial SSU rDNA sequences. However, the 20 more frequent bacterial OTUs describe at least 50% of these sequences. Three of the six Archaea OTUs correspond to 95% of the Archaea population and are very similar to already known methanogenic species: Methanosarcina barkeri, Methanosarcina frisius, and Methanobacterium formicicum. In contrast, the three other Archaea OTUs are unusual and are related to thermophilic microorganisms such as Crenarchaea or Thermoplasma spp. Five percent of the sequences analyzed were chimeras and were removed from the analysis.

Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions.

Abstract: Using grafting procedures, we investigated the transmission of co-suppression of nitrate reductase and nitrite reductase host genes and transgenes and of post-transcriptional silencing of a uidA transgene encoding glucuronidase in tobacco. We demonstrate that silencing is transmitted with 100% efficiency from silenced stocks to non-silenced scions expressing the corresponding transgene. Transmission is unidirectional from stock to scion, transgene specific, locus independent and requires the presence of a transcriptionally active transgene in the target scion. The transmission of co-suppression occurs when silenced stocks and non-silenced target scions are physically separated by up to 30 cm of stem of a non-target wild-type plant. Taken together, these results suggest that a non-metabolic, transgene-specific, diffusable messenger mediates the propagation of de novo post-transcriptional silencing through the plant.

Cellular basis of hypocotyl growth in Arabidopsis thaliana.

Abstract: The Arabidopsis thaliana hypocotyl is widely used to study the effects of light and plant growth factors on cell elongation. To provide a framework for the molecular-genetic analysis of cell elongation in this organ, here we describe, at the cellular level, its morphology and growth and identify a number of characteristic, developmental differences between light-grown and dark-grown hypocotyls. First, in the light epidermal cells show a characteristic differentiation that is not observed in the dark. Second, elongation growth of this organ does not involve significant cortical or epidermal cell divisions. However, endoreduplication occurs, as revealed by the presence of 4C and 8C nuclei. In addition, 16C nuclei were found specifically in dark-grown seedlings. Third, in the dark epidermal cells elongate along a steep, acropetal spatial and temporal gradient along the hypocotyl. In contrast, in the light all epidermal cells elongated continuously during the entire growth period. These morphological and physiological differences, in combination with previously reported genetic data (T. Desnos, V. Orbovic, C. Bellini, J. Kronenberger, M. Caboche, J. Traas, H. Hofte [1996] Development 122: 683-693), illustrate that light does not simply inhibit hypocotyl growth in a cell-autonomous fashion, but that the observed growth response to light is a part of an integrated developmental change throughout the elongating organ.

N Uptake and Distribution in Plant Canopies

Abstract: Nitrogen (N) is often considered to be the most important limiting factor, after water deficiency, for biomass production in natural ecosystems. In arable and forage cropping, N fertilization practices can provide a sufficient N supply for plants to achieve the potential growth allowed by the amount of energy intercepted by the crop. However, to ensure that this potential yield is reached, the N inputs are often higher than the minimum required for maximum crop growth: this is particularly true because N fertilizers are relatively cheap compared to the expected economic benefits from a maximized crop yield.

Estimation of a Hedonic Price Equation for Bordeaux Wine: Does Quality Matter?

Abstract: In this paper the hedonic price technique is applied to Bordeaux wine. In the hedonic price function we include not only the ‘objective’ characteristics appearing on the label of the bottle, but also the sensory characteristics of the wine. Our data come from an experimental study in which juries have evaluated and graded a sample of Bordeaux wines. The estimation of the hedonic price equation shows that the market price is essentially determined by the objective characteristics. The estimation of a jury grade equation shows that quality, unlike the market price, is essentially determined by the sensory characteristics.

Physiology and genetics of the dimorphic fungus Yarrowia lipolytica

Abstract: The ascomycetous yeast Yarrowia lipolytica (formerly Candida, Endomycopsis, or Saccharomyces lipolytica) is one of the more intensively studied 'non-conventional' yeast species. This yeast is quite different from the well-studied yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe with respect to its phylogenetic evolution, physiology, genetics, and molecular biology. However, Y. lipolytica is not only of interest for fundamental research, but also for biotechnological applications. It secretes several metabolites in large amounts (i.e. organic acids, extracellular proteins) and the tools are available for overproduction and secretion of foreign proteins. This review presents a comprehensive overview on the available data on physiology, cell biology, molecular biology and genetics of Y. lipolytica.

Phylogeographic structure of white oaks throughout the European continent

Abstract: Patterns of chloroplast DNA (cpDNA) variation were studied in eight white oak species by sampling 345 populations throughout Europe. The detection of polymorphisms by restriction analysis of PCR-amplified cpDNA fragments allowed the identification of 23 haplotypes that were phylogenetically ordered. A systematic hybridization and introgression between the eight species studied is evident. The levels of subdivision for unordered (GST) and ordered (NST) alleles are very high and close (0.83 and 0.85). A new statistical approach to the quantitative study of phylogeography is presented, which relies on the coefficients of differentiation GST and NST and the Mantel's test. Based on pairwise comparisons between populations, the significance of the difference between both coefficients is evaluated at a global and a local scale. The mapped distribution of the haplotypes indicates the probable routes of postglacial recolonization followed by oak populations that had persisted in southern refugia, especially in the Iberian peninsula, Italy and the Balkans. Most cpDNA polymorphisms appear to be anterior to the beginning of the last recolonization. A subset of the preexisting haplotypes have merely expanded north, while others were left behind in the south.

DNA double‐strand breaks caused by replication arrest

Abstract: We report here that DNA double‐strand breaks (DSBs) form in Escherichia coli upon arrest of replication forks due to a defect in, or the inhibition of, replicative DNA helicases. The formation of DSBs was assessed by the appearance of linear DNA detected by pulse‐field gel electrophoresis. Processing of DSBs by recombination repair or linear DNA degradation was abolished by mutations in recBCD genes. Two E.coli replicative helicases were tested, Rep, which is essential in recBC mutants, and DnaB. The proportion of linear DNA increased up to 50% upon shift of rep recBTS recCTS cells to restrictive temperature. No increase in linear DNA was observed in the absence of replicating chromosomes, indicating that the formation of DSBs in rep strains requires replication. Inhibition of the DnaB helicase either by a strong replication terminator or by a dnaBTS mutation led to the formation of linear DNA, showing that blocked replication forks are prone to DSB formation. In wild‐type E.coli , linear DNA was detected in the absence of RecBC or of both RecA and RecD. This reveals the existence of a significant amount of spontaneous DSBs. We propose that some of them may also result from the impairment of replication fork progression.

Accumulation of nitrate in the shoot acts as a signal to regulate shoot‐root allocation in tobacco†

Abstract: Mutants and transformants of tobacco (Nicotiania tabacum L. cv Gatersleben 1) with decreased expression of nitrate reductase have been used to investigate whether nitrate accumulation in the shoot acts as a signal to alter allocation between shoot and root growth. (a) Transformants with very low (1–3% of wild-type levels) nitrate reductase activity had growth rates, and protein, amino acid and glutamine levels similar to or slightly lower than a nitrate-limited wild-type, but accumulated large amounts of nitrate. These plants should resemble a nitrate-limited wild-type, except in responses where nitrate acts as a signal. (b) Whereas the shoot:root ratio decreases from about 3.5 in a well-fertilized wild-type to about 2 in a nitrate-limited wild-type, the transformants had a very high shoot:root ratio (8–10) when they were grown on high nitrate. When they were grown on lower nitrate concentrations their shoot:root ratio declined progressively to a value similar to that in nitrate-limited wild-types. Mutants with a moderate (30–50%) decrease of nitrate reductase also had a small but highly significant increase of their shoot:root ratio, compared to the wild-type. The increased shoot:root ratio in the mutants and transformants was due to a stimulation of shoot growth and an inhibition of root growth. (c) There was a highly significant correlation between leaf nitrate content and the shoot:root ratio for eight genotypes growing at a wide range of nitrate supply. (d) A similar increase of the shoot:root ratio in nitrate reductase-deficient plants, and correlation between leaf nitrate content and the shoot:root ratio, was found in plants growing on ammonium nitrate. (f) Split-root experiments, in which the transformants were grown with part of their root system in high nitrate and the other part in low nitrate, showed that root growth is inhibited by the accumulation of nitrate in the shoot. High concentrations of nitrate in the rooting medium actually stimulate local root growth. (g) The inhibition of root growth in the transformants was relieved when the transformants were grown on limiting phosphate, even though the nitrate content of the root remained high. This shows that the nitrate-dependent changes in allocation can be overridden by other signals that increase allocation to root growth. (h) The reasons for the changed allocation were investigated in transformants growing normally, and in split-root culture. Accumulation of nitrate in the shoot did not lead to decreased levels of amino acids or protein in the roots. However, it did lead to a strong inhibition of starch synthesis and turnover in the leaves, and to decreased levels of sugars in the root. The rate of root growth was correlated with the root sugar content. It is concluded that these changes of carbon allocation could contribute to the changes in shoot and root growth.

Effect of soluble or partly soluble dietary fibres supplementation on absorption and balance of calcium, magnesium, iron and zinc in healthy young men

Abstract: Objectives: This study is aimed at investigating the effect of feeding a soluble or partly soluble fibre rich-diet on the apparent absorption and balance of calcium, magnesium, iron and zinc in healthy young men, by using a chemical balance technique. Study design: Nine healthy young men were given a control diet or the same diet complemented with either inulin (soluble) or sugar beet fibre (partly soluble) during 28 d periods according to a 3×3 latin square design with three repetitions. During the 20 d adaptation period to fibre ingestion, experimental fibres were incorporated into bread (60%) and liquid foods (40%) up to a maximum of 40 g/d. Ca, Mg, Fe and Zn were measured in diets and in a 8 d urine and faecal composites to assess mineral absorption and balance. Results: The dietary mineral intake provided (mg/d) 859±196 of Ca; 311±43 of Mg; 11.6±1.7 of Fe; and 11.1±1.6 of Zn from the control diet. The apparent absorption of minerals from the control diet was (%) Ca: 21.3±12.5; Mg: 46.3±10.9; Fe: 21.8±12.3 and Zn: 14.0±14.5 (mean±s.d.). Ingestion of inulin significantly increased the apparent absorption and the balance of Ca. Sugar beet fibre ingestion resulted in a significant increase in Ca intake and balance, without modification its apparent absorption. Apparent absorption and balance of Mg, Fe and Zn were not significantly altered by the ingestion of either experimental fibre. Conclusions: Addition of the two experimental fibres (inulin or sugar beet fibre) to normal mixed diets can improve Ca balance without adverse effects on other mineral retention. Sponsorship: This project was supported by the French Ministry of Agriculture, Fisheries and Foods (programme Aliment #2002-Aliment Demain; No. 906335). The authors acknowledge the societe Agro Industries, Recherche et Developpement (Mr R. De Baynast) who supplied them with the experimental fibres.

Chloroplast DNA footprints of postglacial recolonization by oaks.

Abstract: Recolonization of Europe by forest tree species after the last glaciation is well documented in the fossil pollen record. This spread may have been achieved at low densities by rare events of long-distance dispersal, rather than by a compact wave of advance, generating a patchy genetic structure through founder effects. In long-lived oak species, this structure could still be discernible by using maternally transmitted genetic markers. To test this hypothesis, a fine-scale study of chloroplast DNA (cpDNA) variability of two sympatric oak species was carried out in western France. The distributions of six cpDNA length variants were analyzed at 188 localities over a 200 × 300 km area. A cpDNA map was obtained by applying geostatistics methods to the complete data set. Patches of several hundred square kilometers exist which are virtually fixed for a single haplotype for both oak species. This local systematic interspecific sharing of the maternal genome strongly suggests that long-distance seed dispersal events followed by interspecific exchanges were involved at the time of colonization, about 10,000 years ago.

Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos

Abstract: In the mouse embryo, transcriptional activation begins during S/G2 phase of the first cell cycle when paternal and maternal chromatin are still in separate nuclear entities within the same cytoplasm. At this time, the male pronucleus exhibits greater transcriptional activity than the female pronucleus. Since acetylation of histones in the nucleosome octamer exerts a regulatory influence on gene expression, we investigated changes in histone acetylation during the remodeling of paternal and maternal chromatin from sperm entry through to minor genome activation and mitosis. We found (1) neither mature sperm nor metaphase II maternal chromatin stained for hyperacetylated histone H4; (2) immediately following fertilization, hyperacetylated H4 was associated with paternal but not maternal chromatin while, in parthenogenetically activated oocytes, maternal chromatin became hyperacetylated; (3) in zygotes, differential levels and patterns of hyperacetylated H4 between male and female pronuclei persisted throughout most of G1 with histone deacetylases and acetyltransferases already active at this time; (4) when transcriptional differences are observed in S/G2, male and female pronuclei have equivalent levels of H4 hyperacetylation and DNA replication was not required to attain this equivalence and (5) in contrast to the lack of H4 hyperacetylation on gametic chromatin, chromosomes at the first mitosis showed distinct banding patterns of H4 hyperacetylation. These results suggest that sperm chromatin initially out-competes maternal chromatin for the pool of hyperacetylated H4 in the oocyte, that hyperacetylated H4 participates in the process of histone-protamine exchange in the zygote, and that differences in H4 acetylation in male and female pronuclei during G1 are translated across DNA replication to transcriptional differences in S/G2. Prior to fertilization, neither paternal nor maternal chromatin show memory of H4 hyperacetylation patterns but, by the end of the first cell cycle, before major zygotic genome activation at the 2-cell stage, chromosomes already show hyperacetylated H4 banding patterns.

Aggregate stability and assessment of soil crustability and erodibility: II. Application to humic loamy soils with various organic carbon contents

Abstract: Summary Surface crusting results from aggregate breakdown under raindrop impact. It reduces the infiltration rate and may induce erosion by increasing runoff. Soil crustability and erodibility generally increase as organic carbon content decreases. Samples of topsoil were collected from fields cropped continuously for maize after land clearance at various dates. Organic carbon content ranged 4–30 g kg-1. Aggregate stability was assessed by measuring fragment size distribution after different treatments. Samples were also subjected to simulated rainfall. The size of fragments forming the seal when the rain ceased and the infiltration rate during the rainfall were measured to characterize seal structure and hydraulic properties. Development of the seal and infiltration capacity were related to aggregate stability, which was itself a function of organic carbon content. The relations between aggregate breakdown, crusting and infiltration enabled us to predict soil physical behaviour from measurements of aggregate stability which are easier to make than direct measurements under rainfall. The proposed tests offer the opportunity to evaluate actual or potential soil physical degradation and erosion risks without extensive field measurements.

An enlarged set of consensus primers for the study of organelle DNA in plants

Abstract: Recently, there has been a growing interest in the use of the chloroplast genome (cpDNA) in population genetics studies of plants. Indeed, despite its low substitution rate (Wolfe et al. 1987), its typically uniparental mode of transmission, and hence clonal mode of evolution is a unique feature of cytoplasmic genomes of great interest for evolution studies. The plant mitochondrial genome (mtDNA) shares these characteristics, with however, an even slower substitution rate, but is much less studied because it varies enormously in size and gene arrangement (Palmer 1992). Consensus primers which are homologous to the most conserved coding regions of cpDNA or mtDNA but amplify the more variable noncoding regions are likely therefore to be very useful. Here, we greatly enlarge a previous list of primers published in this journal (Demesure et al. 1995). A total of seven pairs of cpDNA primers and nine pairs of mtDNA primers are described. Moreover, the degree of conservation of the whole set (16 and 12 pairs of cpDNA and mtDNA primers, respectively) is tested by amplification on five species, three angiosperms (two dicotyledons and one monocotyledon), a pine (gymnosperm) and a fern (pteridophyte), i.e. on a broader taxonomic range than in the former study. The primers are also evaluated by comparison with sequences available in the molecular databases. The primers were designed in order to be as consensual as possible, although the chloroplast genome of tobacco (i.e. a dicotyledon) was used as reference, and full homology with dicotyledon sequences was also given priority in the case of the mtDNA primers. Their design was facilitated by the availability of an increasing number of complete sequences in the molecular databases. Conserved coding sequences flanking the regions to be amplified were identified with the computer software BLAST (Altschul et al. 1990). The cpDNA primers are all located in the relatively variable large single-copy region (Palmer 1985). For the mtDNA primers, introns of genes available in the molecu

Digestion and metabolism of dietary fat in farm animals

Abstract: Fat digestion and metabolism differ widely between animal species. In ruminants, dietary fats are hydrogenated in the rumen before intestinal absorption so that absorbed fatty acids (FA) are more saturated than dietary FA. In non-ruminants, intestinal FA digestibility depends on the level of saturation of dietary FA. Fat supplementation of the diet of cows decreases milk protein and has a variable effect on milk fat, depending on the source of dietary lipids. When encapsulated lipids are used, the linoleic acid content of milk is increased, but the organoleptic quality of milk may be altered. Supplementary lipids are incorporated into non-ruminant body fat, whereas de novo lipogenesis is reduced. There is a close relationship between the nature of dietary FA and non-ruminant body FA.

Use of the extended BBCH scale—general for the descriptions of the growth stages of mono; and dicotyledonous weed species

Abstract: Summary The extended BBCH scale is a system for a uniform coding of phenologicaliy similar growth stages of all mono- and dicotyledonous plant species, based on the well known cereal code of Zadoks et al. (1974). The BBCH key is it decimal system, with 10 principal growth stages and up to 10 secondary ones, starting with seed germination, sprouting of perennials, progressing through leaf production and extension growth to flowering and senescence. Therefore, it can also be a suitable tool to define the growth stages of different weed species. To encourage further use of the BBCH scale in weed research, definitions of the codes have been more closely adapted to weeds. Possible problems are discussed and guidelines for correct use are given.

A worldwide survey of tomato yellow leaf curl viruses

Abstract: The name tomato yellow leaf curl virus (TYLCV) has been given to several whitefly-transmitted geminiviruses affecting tomato cultures in many tropical and subtropical regions. Hybridization tests with two DNA probes derived from a cloned isolate of TYLCV from Israel (TYLCV-ISR) were used to assess the affinities of viruses in naturally infected tomato plants with yellow leaf curl or leaf curl symptoms from 25 countries. Probe A which included most of the intergenic region was expected to detect only isolates closely related to TYLCV-ISR, especially after high stringency washes. In contrast probe B, which included the full-length genome, was expected to detect a wide range of whitefly-transmitted geminiviruses. Tomato samples from six countries in the Middle East, from Cuba or the Dominican Republic proved to be closely related to TYLCV-ISR and probably were infected by strains of the same virus. Samples from Senegal and Cape Verde Islands were also related to the Middle Eastern virus. Samples from nine other countries in the western Mediterranean area, Africa, or South-East Asia were more distantly related and probably represent one or more additional geminivirus species. Samples from five countries in Africa, Central or South America gave hybridization signals with the full-length viral genome, only after low stringency wash, indicating that these samples were infected by remote viruses. These results were supported by DNA and protein sequence comparison, which indicate that tomato geminiviruses fall into three main clusters representing viruses from 1) the Mediterranean/Middle East/African region, 2) India, the Far East and Australia, and 3) the Americas. Within the first cluster, two sub-clusters of viruses from the western Mediterranean or from the Middle East/Caribbean Islands were distinguished. The incidence of tomato yellow leaf curl diseases has increased considerably between 1990 and 1996.

Marker-Assisted Introgression of Quantitative Trait Loci

Abstract: The use of molecular markers for the introgression of one or several superior QTL alleles into a recipient line is investigated using analytic and simulation results. The positions of the markers devoted to the control of the genotype at the QTLs in a "foreground selection" step are optimized given the confidence interval of the QTL position. Results demonstrate that using at least three markers per QTL allows a good control over several generations. Population sizes that should be recommended for various numbers of QTLs are calculated and are used to determine the limit in the number of QTLs that can be monitored simultaneously. If "background selection" devoted to accelerate the return to the recipient parent genotype outside the QTL regions is applied, the positions of the markers devoted to the control of the QTLs have to be reconsidered. When several QTLs are monitored simultaneously, background selection among the limited number of individuals resulting from the foreground selection step accelerates the increase in genomic similarity with the recipient parent, with only limited costs. Background selection is even more efficient in a pyramidal backcross program where QTLs are first monitored one by one.

Control of the shift from homolactic acid to mixed-acid fermentation in Lactococcus lactis: predominant role of the NADH/NAD+ ratio.

Abstract: During batch growth of Lactococcus lactis subsp. lactis NCDO 2118 on various sugars, the shift from homolactic to mixed-acid metabolism was directly dependent on the sugar consumption rate. This orientation of pyruvate metabolism was related to the flux-controlling activity of glyceraldehyde-3-phosphate dehydrogenase under conditions of high glycolytic flux on glucose due to the NADH/NAD+ ratio. The flux limitation at the level of glyceraldehyde-3-phosphate dehydrogenase led to an increase in the pool concentrations of both glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate and inhibition of pyruvate formate lyase activity. Under such conditions, metabolism was homolactic. Lactose and to a lesser extent galactose supported less rapid growth, with a diminished flux through glycolysis, and a lower NADH/NAD+ ratio. Under such conditions, the major pathway bottleneck was most probably at the level of sugar transport rather than glyceraldehyde-3-phosphate dehydrogenase. Consequently, the pool concentrations of phosphorylated glycolytic intermediates upstream of glyceraldehyde-3-phosphate dehydrogenase decreased. However, the intracellular concentration of fructose-1,6-bisphosphate remained sufficiently high to ensure full activation of lactate dehydrogenase and had no in vivo role in controlling pyruvate metabolism, contrary to the generally accepted opinion. Regulation of pyruvate formate lyase activity by triose phosphates was relaxed, and mixed-acid fermentation occurred (no significant production of lactate on lactose) due mostly to the strong inhibition of lactate dehydrogenase by the in vivo NADH/NAD+ ratio.

“Antiplasticization” in starch-glycerol films?

Abstract: Calorimetric, mechanical, and thermomechanical properties have been measured on starch films with various glycerol/water contents. For calorimetric measurements, a continuous decrease in Tg was observed as glycerol increases from 0 to 25%. Mechanical properties exhibit a minimum of elongation at break for glycerol content ∼ 12%. In slightly hydrated starch films not containing another plasticizer, a β relaxation is detected by DMTA around −68°C. This relaxation is modified by the presence of glycerol, the α relaxation of which appears in the same temperature range. Results are discussed comparing with the well-known antiplasticization effect in synthetic polymers such as PVC and PC. The combination of the plasticizer α mode and the polymer β mode is considered. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 63: 1047–1053, 1997

Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris Nodules

Abstract: Thirty-one strains of two new genomic species (genomic species 1 and 2) of rhizobia isolated from root nodules of Phaseolus vulgaris and originating from various locations in France were compared with reference strains of rhizobia by performing a numerical analysis of 64 phenotypic features. Each genomic species formed a distinct phenon and was separated from the other rhizobial species. A comparison of the complete 16S rRNA gene sequences of a representative of genomic species 1 (strain R602spT) and a representative of genomic species 2 (strain H152T) with the sequences of other rhizobia and related bacteria revealed that each genomic species formed a lineage independent of the lineages formed by the previously recognized species of rhizobia. Genomic species 1 clustered with the species that include the bean-nodulating rhizobia, Rhizobium leguminosarum, Rhizobium etli, and Rhizobium tropici, and branched with unclassified rhizobial strain OK50, which was isolated from root nodules of Pterocarpus klemmei in Japan. Genomic species 2 was distantly related to all other Rhizobium species and related taxa, and the most closely related organisms were Rhizobium galegae and several Agrobacterium species. On the basis of the results of phenotypic and phylogenetic analyses and genotypic data previously published and reviewed in this paper, two new species of the genus Rhizobium, Rhizobium gallicum and Rhizobium giardinii, are proposed for genomic species 1 and 2, respectively. Each species could be divided in two subgroups on the basis of symbiotic characteristics, as shown by phenotypic (host range and nitrogen fixation effectiveness) and genotypic data. For each species, one subgroup had the same symbiotic characteristics as R. leguminosarum biovar phaseoli and R. etli biovar phaseoli. The other subgroup had a species-specific symbiotic phenotype and genotype. Therefore, we propose that each species should be subdivided into two biovars, as follows: R. gallicum biovar gallicum and R. gallicum biovar phaseoli; and R. giardinii biovar giardinii and R. giardinii biovar phaseoli.

Administration of Transgalacto-Oligosaccharides Increases Fecal Bifidobacteria and Modifies Colonic Fermentation Metabolism in Healthy Humans

Abstract: Transgalacto-oligosaccharides are a mixture of oligosaccharides consisting of glucose and galactose; they are not digested in the human small intestine. In vitro, they specifically stimulate the growth of bifidobacteria. The aim of the present work was to assess tolerance of transgalacto-oligosaccharides and the effects of their prolonged administration on bifidobacteria and fermentative activity of colonic flora. Eight healthy subjects were given 10 g of transgalacto-oligosaccharides per day for 21 d in two daily doses. A breath test and stool sample collection were carried out on d 1, 7, 14 and 21 of transgalacto-oligosaccharides ingestion. The stools of three subjects were collected and mixed before the study, and then inoculated in vitro into a fermentor to which 10 g transgalacto-oligosaccharides was added daily for 14 d. In the eight volunteers, administration of transgalacto-oligosaccharides led to a significant decrease in breath hydrogen excretion (P < 0.01) and a significant increase in fecal concentrations of bifidobacteria from (means +/- SEM) 8.6 +/- 0.6 to 9.7 +/- 0.5, 9.7 +/- 0.6 and 9.5 +/- 0.6 log colony-forming units (CFU)/g on d 1, 7, 14 and 21, respectively (P < 0.05). Fecal concentrations of enterobacteria, as well as stool weight, fecal water and pH did not change during the study. In vitro, transgalacto-oligosaccharides fermentation became more efficient and faster with time. In addition, metabolic alterations such as a rise in acetate proportion and lactate formation after 7 d of fermentation were observed, indicating the transformation of the inoculated fecal flora into an acid-resistant lactic flora. Prolonged administration of transgalacto-oligosaccharides, at a dose which does not induce digestive symptoms, increases the number of bifidobacteria and alters the fermentative activity of colonic flora in humans.