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Biomedical subjects

D Faure

Publications and source records attributed to D Faure.

At least 19 recordsLinked to original sources
PubMed2005

Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties.

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJN(T), was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJN(T) and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98.7 %) and Burkholderia phenazinium (98.5 %). Analysis of whole-cell protein profiles and DNA-DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJN(T) had a DNA G+C content of 61.0 mol%. Only low levels of DNA-DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJN(T) and closely related species were identified. The predominant fatty acids in strain PsJN(T) were 16 : 0, 18 : 1omega7c and summed feature 3 (comprising 16 : 1omega7c and/or iso-15 : 0 2-OH). Isolate PsJN(T) showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJN(T) and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJN(T) (=LMG 22146(T) = CCUG 49060(T)).

4-Butyrolactone↗
PubMed2005

Radar-based alert system to operate a sewerage network: relevance and operational effectiveness after several years of use.

Since January 2000, the sewerage network of a very urbanised catchment area in the Greater Nancy Urban Community has been operated according to the alarms generated in real time by a storm alert system using weather radar data. This alert system is based on an automatic identification of intense rain cells in the radar images. This paper presents the characteristics of this alert system and synthesises the main results of two complementary studies realised in 2002 in order to estimate the relevance and the operational effectiveness of the alert system. The first study consisted in an off-line analysis of almost 50,000 intense rain cells detected in four years of historical radar data. The second study was an analysis of the experience feedback after two years of operational use of this alert system. The results of these studies are discussed in function of the initial operational objectives.

Cities↗
PubMed2004

[Violacein: a molecule of biological interest originating from the soil-borne bacterium Chromobacterium violaceum].

INTRODUCTION: Soil micro-organisms have evolved functions that allow them to withstand the strong competition for survival that characterizes most of their habitats. The production of antibiotic or antifungal compounds is one of these mechanisms. The relevant molecules often exhibit valuable therapeutic properties. EXEGESIS: Chromobacterium violaceum is a soil-borne bacterium producing a characteristic antibiotic termed violacein. It is part of a series of compounds released by C. violaceum to oppose competitors and predators in the soil and water environments. Violacein, and one of these compounds, i.e. structure FR901228, exhibit antiparasitic and antitumoral activities of potential medical interest. Genes involved in the synthesis of these compounds are available, the genome sequence of C. violaceum (strain ATCC 12472) being published. CONCLUSIONS: The above example, involving Chromobacterium, is not an exception: soil constitutes a reservoir of molecules, enzymatic activities and micro-organisms of biological interest, the study of which will undoubtedly lead to developments in fields as diverse as agronomy or animal and human therapeutics.

Agriculture↗
PubMed2004

Genomic changes arising in long-term stab cultures of Escherichia coli.

Genomic scans of clones isolated from long-term stab cultures of Escherichia coli K-12 showed the loss of two large segments of the genome, with each lost segment being approximately 20 kb long. A detailed analysis of one of the deletions, located between 5.4 and 5.9 min, revealed that similar deletions had arisen in several other stab cultures. All deletions of this type exhibited a right terminus ending precisely at an IS5A element and a left terminus that varied over an approximately 5-kb range but was bordered in all but two cases by sequences belonging to the preferred consensus target sequence for IS5, YTAR. The ubiquity of such deletions in independent stab cultures and the increase in their frequency over time argue that they have a selective advantage. It is speculated that the loss of the crl locus is responsible for the selective advantage of the deletions.

DNA Transposable Elements↗
PubMed2003

Purification and characterization of a membrane glycoprotein from the fish pathogen Flavobacterium psychrophilum.

AIMS: The cell envelope of the fish pathogen Flavobacterium psychrophilum contains more than 50 polypeptides resolved by sodium dodecyl sulphate-polyacrylaminde gel electrophoresis analysis including a major component named P60. Here, we have developed a simple and efficient procedure for the purification of P60 and therefore permitting its biochemical characterization. METHODS AND RESULTS: Membrane proteins were selectively extracted from isolated cell envelopes with the mild non-ionic detergent Triton X-100. About 10 polypeptides were identified from the detergent fraction, including P60. The P60-enriched fraction was thereafter subjected to an anion exchange chromatographic step in the presence of Triton X-100. The molecule was purified at the milligram level (yield, about 75%; purification factor, 6.2). Analyses performed by charge shift electrophoresis, Triton X-114 phase separation and by detection of sugar-modified components showed that P60 is a true amphiphilic membrane-associated glycoprotein. CONCLUSIONS: The method described in this paper provides pure and non-denaturated P60 and should prove to be easily scaled-up. As sugar-modified protein, P60 should be included in the growing list of glycosylated prokaryotic proteins. SIGNIFICANCE AND IMPACT OF THE STUDY: It offers the possibility of obtaining P60 in amounts allowing the testing of the potential of P60 as a candidate for anti-flavobacteria subunit vaccines, as P60 is one of the major antigens.

Animals↗
PubMed2003

The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-Acyl homoserine lactonase activity.

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.

4-Butyrolactone↗
PubMed2003

Radiation and functional specialization of the family-3 glycoside hydrolases.

A phylogenetic analysis of the glycoside hydrolases of family 3 (GH3s) was conducted in order to infer particular trends in its evolution: functional specialization, gene transfer events, gene duplications and paralogous evolution, and gene deletions. The phylogenetic analysis of GH3s revealed six clusters, i.e., A, B, C, D, E, and F that could fit the definition of 3 sub-families, i.e., AB, AB' and AB". While the sub-families AB' and AB" contain a single cluster, F and E, respectively, the AB sub-family is sub-divided into four clusters. Global analysis of the GH3 phylogenetic tree suggests a primary burst of amplification of the GH3s that might have led to these sub-families. Specializations, gene transfers, and gene duplications among each of these sub-families and phylogenetic clusters might then have occurred and have been inferred. The fine comparison of the enzyme properties and phylogenetic relationships of GH3s allowed to detect common functional groups that belong to the same cluster (D, E or F), or sub-cluster (A1, A2 or B2). The prokaryotic and eukaryotic beta-xylosidases and beta-glucosidases belong to the AB and AB' sub-families, and the N-acetylglucosaminidases are in sub-family AB" (in cluster E). In some instances (B1, B2, C1, C2, and C3), the lack of data and/or the high heterogeneity of the hydrolytic properties did not allow to infer a particular link between an enzyme functional group and a phylogenetic cluster, suggesting the emergence of some highly specialized GH3s.

Computational Biology↗
PubMed2002

Development and application of a nested PCR to monitor brood stock salmonid ovarian fluid and spleen for detection of the fish pathogen Flavobacterium psychrophilum.

AIMS: To develop a nested PCR to detect Flavobacterium psychrophilum based on the intergenic spacer region 16S-23S rRNA and in 16S rRNA for analysis of brood stock salmonid fish samples. METHODS AND RESULTS: The sensitivity and specificity of the test was evaluated using pure cultures, spiked and naturally contaminated samples. Samples were internal organs (spleen and kidney), eggs and ovarian fluid from rainbow trout and coho salmon from European fish farms (France, Spain). This nested PCR was more specific and sensitive that the nested PCR based on 16S rRNA sequences primers only. The detection limit of this PCR assay was one bacterium per PCR tube corresponding to 10 bacteria/mg of spleen and 5 bacteria/ml from ovarian fluid. Analysis of mixed ovarian fluid samples from reproductive salmonids in various French hatcheries demonstrated that 69% of hatcheries were contaminated with Fl. psychrophilum. The analysis of individual samples demonstrated that 39% of rainbow trout (Oncorhynchus mykiss) and 62.5% of coho salmon (O. kisutch) samples were contaminated. CONCLUSIONS: The results demonstrated a very sensitive and specific detection of this fish pathogen and that most of the female rainbow trout and coho salmon breeders analysed carry Fl. psychrophilum in the ovarian fluid. SIGNIFICANCE AND IMPACT OF THE STUDY: The understanding of Fl. psychrophilum dissemination and transmission and the detection of asymptomatic carriers is important for the development of free breeders stock and for significantly decreasing Flavobacteriose.

Animals↗
PubMed2002

Management of a detention-settling basin using radar data and risk notion.

This paper presents a practical application of sewage network management strategy using radar data to control a detention-settling basin. This practical application, used in operational mode since January 2000, is based on three main notions. Firstly, the use of radar data without rainfall estimation. Secondly, the definition of some gradual risk levels for the sewage network by a detailed modelling of the sewage system functioning. Thirdly the definition of relations between risk levels for the sewage network and types of rain events defined from radar data. The operational application produces gradual alarms for decision-making assistance: no risk, potential risk and confirmed risk.

Cities↗
PubMed2001

Detection and activity of insertion sequences in environmental strains of Burkholderia.

The presence of two insertion sequences, IS406 and IS407, was tested by polymerase chain reaction (PCR) amplification in 25 strains representing 15 Burkholderia species and the close relative Ralstonia pickettii. A total of 50% of the 25 strains contained at least one of the two insertion sequences (ISs) and a statistically significant correlation was found between the occurrences of IS406 and IS407. Moreover, PCR-RFLP studies of the amplified fragments showed that IS406 is largely conserved among all the strains tested, whereas IS407 is rather polymorphic. Transposition activity was studied in Burkholderia vietnamiensis TVV75, using the pGBG1 target plasmid. This entrapping plasmid permitted the isolation and characterization of three active IS, able to activate the plasmid-borne tetA gene after transposition. Sequencing permitted the identification of these mobile genetic elements as isoforms of IS402, IS407 and IS1416. PCR amplification products provided IS probes, which were used to determine the copy-numbers of IS402, IS407 and IS1416 in the genome of B. vietnamiensis TVV75, by Southern blotting. Copy numbers are 12, 3 and 11 respectively. To our knowledge, this is the first description of active insertion sequences in B. vietnamiensis.

Blotting, Southern↗
PubMed2001

The celA gene, encoding a glycosyl hydrolase family 3 beta-glucosidase in Azospirillum irakense, is required for optimal growth on cellobiosides.

The CelA beta-glucosidase of Azospirillum irakense, belonging to glycosyl hydrolase family 3 (GHF3), preferentially hydrolyzes cellobiose and releases glucose units from the C(3), C(4), and C(5) oligosaccharides. The growth of a DeltacelA mutant on these cellobiosides was affected. In A. irakense, the GHF3 beta-glucosidases appear to be functional alternatives for the GHF1 beta-glucosidases in the assimilation of beta-glucosides by other bacteria.

Amino Acid Sequence↗
PubMed2001

An evolutionary alternative system for aryl beta-glucosides assimilation in bacteria.

Some bacteria of the soil microflora or of the digestive systems of mammals can grow on aryl beta-glucosides as sole carbon sources. The bgl operon of E. coli is the paradigm for such a catabolic pathway. In Azospirillum irakense, the two adjacent genes salAB encode beta-glucosidases which are required for salicin assimilation. In this report, we analyse the sequence of salC, the last gene to be identified in the salCAB operon and investigate the phylogenetic origins of the sal and bgl genes. The results suggest an alternative model for the assimilation of aryl beta-glucosides in bacteria.

Amino Acid Sequence↗
PubMed2001

Use of real time control modelling on the urban sewage system of Nancy.

Since 1991, European Legislation on the urban treatment of wastewater requires local authorities to take into account the treatment of polluted water transported by the sewerage system and this during dry and wet weather conditions. In the seventies, the urban Community of Grand Nancy constructed storage tanks in its sewerage system in order to prevent flooding and wish today to use them to reduce and control the pollution discharges into the receiving water. This action is a part of a European LIFE project 1996-2000. The main aim of this project was to assess the effectiveness of reducing pollution of one particular retention basin, the 12,000 m3 Gentilly tank. This one has two operating modes: protection against floods during heavy rain and reduction of pollutant overflows during lighter rain. To assess its effect on the pollutant discharge, the HYDROWORKS DM software and its Real Time Control Module have been used, calibrated and validated. As this study is still in progress, this paper describes the studied site and the modelling results under different weather conditions and shows that the mathematical model can be used to simulate the operation of the catchment area and its associated sewerage system realistically.

Cities↗
PubMed2000

A broad-host-range plasmid for isolating mobile genetic elements in gram-negative bacteria.

Plasmid pGBG1 was constructed to isolate mobile genetic elements in a wide variety of gram-negative bacteria. The mutation target, carried on a broad-host-range vector, allows positive selection for tetracycline resistance. In tests using several gram-negative bacteria we could detect transposition events of either insertion sequences or transposons. A new insertion sequence (IS) element was identified in Ralstonia eutropha.

Agrobacterium tumefaciens↗
PubMed2000

The salCAB operon of Azospirillum irakense, required for growth on salicin, is repressed by SalR, a transcriptional regulator that belongs to the Lacl/GalR family.

The salAB genes of Azospirillum irakense KBC1, which encode two aryl-beta-glucosidases, are required for growth on salicin. In the 4-kb region upstream of the salAB genes, two additional genes, salC and salR, were identified. SalC shows characteristics of the outer membrane receptors in the FepA/FhuA family. The salC AB genes are transcribed as a polycistronic mRNA. The salR gene encodes a protein homologous to the LacI/GalR family of transcriptional repressors. Expression of the sal operon, measured by means of a salC-gusA translational fusion in A. irkense KBC1, requires the presence of aryl-beta-glucosides such as arbutin and salicin. Expression is markedly enhanced when a simple carbon source, like glucose, cellobiose or malate, is added to the medium. In a salR mutant, expression of the salC-gusA fusion does not require an aryl-beta-glucoside inducer. Expression of a salR-gusA fusion is constitutive. The product of arbutin hydrolysis (hydroquinone) partly inhibits the expression of a salC-gusA fusion in arbutin- or salicin-containing minimal medium. This effect is independent of SalR. Salicylalcohol, the hydrolysis product of salicin, also partly inhibits salC expression in a SalR-independent fashion, but only in salicin-containing minimal medium.

Amino Acid Sequence↗
PubMed1999

Growth of Azospirillum irakense KBC1 on the aryl beta-glucoside salicin requires either salA or salB.

The rhizosphere nitrogen-fixing bacterium Azospirillum irakense KBC1 is able to grow on pectin and beta-glucosides such as cellobiose, arbutin, and salicin. Two adjacent genes, salA and salB, conferring beta-glucosidase activity to Escherichia coli, have been identified in a cosmid library of A. irakense DNA. The SalA and SalB enzymes preferentially hydrolyzed aryl beta-glucosides. A Delta(salA-salB) A. irakense mutant was not able to grow on salicin but could still utilize arbutin, cellobiose, and glucose for growth. This mutant could be complemented by either salA or salB, suggesting functional redundancy of these genes in salicin utilization. In contrast to this functional homology, the SalA and SalB proteins, members of family 3 of the glycosyl hydrolases, show a low degree of amino acid similarity. Unlike SalA, the SalB protein exhibits an atypical truncated C-terminal region. We propose that SalA and SalB are representatives of the AB and AB' subfamilies, respectively, in glycosyl hydrolase family 3. This is the first genetic implication of this beta-glucosidase family in the utilization of beta-glucosides for microbial growth.

Amino Acid Sequence↗
PubMed1995

Oligonucleotide probes based on 16S rRNA sequences for the identification of four Azospirillum species.

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.

Azospirillum↗