References of "Stroobants, Aurore"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailScreening of two agricultural genomic DNA libraries to seek new glycoside hydrolases
Stroobants, Aurore ULg; Portetelle, Daniel ULg; Vandenbol, Micheline ULg

Poster (2014, February 07)

Soils are very rich environments where the diversity of microorganisms is very high. These microorganisms play an important role in the degradation of organic matter with enzymes able to degrade it. This ... [more ▼]

Soils are very rich environments where the diversity of microorganisms is very high. These microorganisms play an important role in the degradation of organic matter with enzymes able to degrade it. This work aims to discover, by functional screening, new microbial glycoside hydrolases from soils collected in winter and spring in a winter wheat crop. The genomic DNA was extracted from both soils to construct two libraries in Escherichia coli. These libraries were then screened for beta-glucosidase activities on 2YT agar media containing 0.5% esculin and 0.1% ammonium iron (III) citrate. At this time, about 250.000 clones from each library have been screened. Two beta-glucosidases have already been found in the winter library while five beta-glucosidases and two glycosyltransferases were identified in the spring library. Sequence analyses with the BLASTX program revealed putative enzymes showing between 25% and 72% sequence identity with known enzymes and belonging to three glycoside hydrolase families (GH1, GH3 and GH20) and to two probably new glycosyltransferase families. Biochemical characterisation of the candidates at several pH values and temperatures, and with four substrates, is in progress. [less ▲]

Detailed reference viewed: 18 (3 ULg)
Full Text
Peer Reviewed
See detailImpact of agricultural practices on soil microbial communities in Belgium
Degrune, Florine ULg; Taminiau, Bernard ULg; Dufrêne, Marc ULg et al

Poster (2013, December 11)

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on ... [more ▼]

The use of fertilizers in agricultural soils is becoming a real environmental issue (an obvious example is eutrophication caused by leaching of phosphorus and nitrates). Much research has focused on finding ways to reduce the use of chemicals, and investigating microbial life may lead to solutions. We know that bacteria and fungi are deeply involved in nutrient cycles. Recently the emergence of massive parallel sequencing has enabled us to realize that microbial diversity is huger than we expected. With such a tool it should be possible to study how soil management practices affect the microbial diversity of agricultural soils. A few such studies have been conducted, most of them focusing on bacteria. For Belgium in particular, there is a lack of data on this topic. Here the aim was to see how residue management and tillage practices affect communities of both bacteria and fungi in Belgian agricultural soils. For this we used 454 pyrosequencing of 16S bacterial and 28S fungal rRNA genes. Soil samples came from an experiment in which faba beans were grown with four soil management practices (tillage and no tillage, with and without crop residues), each repeated four times in a Latin square. Several chemical and physical characteristics were measured on each sample. The results show that fungi and bacteria are both impacted by Tillage practices. The main soil drivers are Magnesium and Phosphorus for Fungi communities, and Phosphorus and Potassium for bacteria communities. Finally, the fungi variance observed between plots is explained at 38% by Tillage, Magnesium and phosphorus. And the bacteria variance is explained at 28% by Tillage, Phosphorus and Potassium. [less ▲]

Detailed reference viewed: 43 (9 ULg)
Full Text
Peer Reviewed
See detailFunctional screening of a winter and a spring genomic DNA libraries obtained from soils in a winter wheat crop
Stroobants, Aurore ULg; Portetelle, Daniel ULg; Vandenbol, Micheline ULg

Poster (2013, June 10)

Soils are very rich environments where the diversity of microorganisms is very high. These microorganisms play important role in the degradation of organic matter with enzymes able to degrade it. The aim ... [more ▼]

Soils are very rich environments where the diversity of microorganisms is very high. These microorganisms play important role in the degradation of organic matter with enzymes able to degrade it. The aim of this work is to discover by functional screening new enzymatic activities of microorganisms from soils collected in winter and spring in a winter wheat crop. The genomic DNA was extracted from both soils to construct two libraries in Escherichia coli. These libraries were then screened for several enzymes such as lipase, beta-glucosidase, cellulase, α-amylase,… At this time, 2 beta-glucosidases and 3 lipases have already been found in the winter library and 3 beta-glucosidases and 1 lipase in the spring library. Sequence analyses with the BLASTX program revealed that two beta-glucosidases have less than 65% of sequence identity with known beta-glucosidases, one have 64% of identity with a known beta-galactosidase and one have 59% of identity with a glycoside hydrolase. The fifth seems to be a phosphorylase kinase (54% identity) which have a glucoamylase domain responsible for the activity. This ORF is interrupted by a transposase. Three of the four lipases have less than 60% of sequence identity with known lipases/esterases. The fourth show 55% of identity with a known beta-lactamase. [less ▲]

Detailed reference viewed: 13 (1 ULg)
Full Text
Peer Reviewed
See detailCharacterization of new bacterial glycoside hydrolases isolated from agricultural soils using a functional metagenomic approach
Biver, Sophie ULg; Dubois, Benjamin; Stroobants, Aurore ULg et al

Poster (2013, June 10)

Microorganisms play key roles in soil ecosystem functioning, notably through their ability to degrade plant cell wall polymers. For this, bacteria and fungi produce various enzymes such as cellulases ... [more ▼]

Microorganisms play key roles in soil ecosystem functioning, notably through their ability to degrade plant cell wall polymers. For this, bacteria and fungi produce various enzymes such as cellulases, xylanases, glucosidases, esterases or laccases. Finding new enzymes hydrolyzing cellulose, hemicellulose or lignin is not only interesting for a better understanding of the roles of the soil microflora still largely unknown but these enzymes are also useful for various biotechnological applications such as the production of renewable energy from lignocellulosic material. So here, we used a functional metagenomic approach to isolate new bacterial β-glucosidases, which were then biochemically characterized. The new enzymes were identified by functional analysis of agricultural-soil metagenomic libraries hosted in Escherichia coli and screened on medium containing esculin. After sequence analysis and preliminary estimation of the activity of the new β-glucosidases using p-nitrophenol derivatives on intact bacterial cells, the coding sequences of three of them were cloned into a bacterial expression vector so as to overproduce and purify them by affinity chromatography. The chosen enzymes show only 52-64% sequence identity to known family 3 (GH3) or 1 (GH1) glycoside hydrolases of different phyla (Actinobacteria, Acidobacteria and Proteobacteria). Analysis of the E. coli cells expressing each of them revealed that both GH1 proteins (ASEsc9 and ASEsc10) are thermophilic enzymes more active at mildly acidic to neutral pH while the GH3 enzyme (ASEsc6) is an alkaline, mesophilic, β-glucosidase also displaying xylosidase activity. Their coding sequences have been cloned in fusion with a carboxy-terminal His-tag and placed under the control of the IPTG-inducible promoter of the pET-30b vector. The proteins will be overproduced and purified for further characterization. [less ▲]

Detailed reference viewed: 184 (14 ULg)
Full Text
Peer Reviewed
See detailStudy of bacterial diversity in the topsoil and below the hardpan in an agricultural soil by metagenomics following by two analysis pipelines
Stroobants, Aurore ULg; Lambert, Christrophe; Degrune, Florine ULg et al

Poster (2013, June 10)

On earth, Bacteria are ubiquitous and even present in extreme environments (pH, temperature,…). In soils in particular, bacteria are very abundant (up to 109 cells per gram of soil) but still poorly ... [more ▼]

On earth, Bacteria are ubiquitous and even present in extreme environments (pH, temperature,…). In soils in particular, bacteria are very abundant (up to 109 cells per gram of soil) but still poorly characterized. Thus, it is of paramount importance to use relevant study and analysis procedures to ensure that the results obtained closely reflect the real-life conditions. In the present work, we analyze the bacterial diversity in the topsoil and below the hardpan in an agricultural soil using the metagenomics approach, with the Ion Torrent PGM sequencer. The soil samples was collected at three depths : 10 cm (topsoil), 25 cm (topsoil above the hardpan) and 45 cm (below the hardpan), in a tilled and a no tilled plot. The taxonomic analysis of the reads obtained are carried out according to two different procedures with the RDP classifier program and with a confidence score threshold of 0 and 0.99. The 0 threshold is used to assign a species to all reads, each read being therefore assigned to its most closest known species. The threshold of 0.99 enables us to focus on reads being assigned to a species with a high degree of confidence. In this case, each read is assigned to the most specific rank having a confidence score higher than 0.99. The bacterial diversity was then compared between the different conditions. Results obtained demonstrate that the bacterial communities were not the same in the two horizons. For example, some classes of Acidobacteria were up to 11 fold more numerous in topsoil while others was until 12 fold more represented below the hardpan. The biomass and the bacterial diversity (Shannon index) were also greatly different between the two depths. [less ▲]

Detailed reference viewed: 113 (9 ULg)
Full Text
See detail2. Implantation des cultures
Eylenbosch, Damien ULg; Pierreux, Jérome ULg; Dufranne, Delphine et al

in Bodson, Bernard; Destain, Jean-Pierre (Eds.) Livre Blanc - Céréales (2013, February 27)

Detailed reference viewed: 52 (29 ULg)
Full Text
Peer Reviewed
See detailImpact of the depth on bacterial diversity in an agricultural soil
Stroobants, Aurore ULg; Degrune, Florine ULg; Lambert, Christophe et al

Poster (2013, February 08)

Bacteria are the most abundant and diverse microorganisms in soils. They play an important role in soil formation, contribute to plant nutrition and are involved in various processes in agroecosystems ... [more ▼]

Bacteria are the most abundant and diverse microorganisms in soils. They play an important role in soil formation, contribute to plant nutrition and are involved in various processes in agroecosystems such as nutrient cycling. The aim of this study was to evaluate the impact of the depth on bacterial diversity and quantity in an agricultural soil. Samples was collected on May 2011 and May 2012 at three different depths : 10, 25 and 45 centimeters. The quantity of total bacteria was measured by real time PCR and the analysis of the diversity was performed by the high throughput sequencing technology. Results obtained by these methods show that the biomass and the bacterial quantity and diversity (Shannon index) decrease with the depth, particularly at 45 centimeters. The biomass is, in average, 6.5 fold less important at 45 cm than at 10 cm and the quantity is 17 fold lower at 45 cm than at 10 cm. Our results also indicate that many taxa, such as Betaprotebacteria, Deltaproterobacteria, Gammaproteobacteria, Acidobacteria and Burkholderiales are influenced by the depth. The results will be presented in more details on the poster. [less ▲]

Detailed reference viewed: 84 (21 ULg)
Full Text
Peer Reviewed
See detailSTUDY OF BACTERIAL DIVERSITY IN AN AGRICULTURAL SOIL
Stroobants, Aurore ULg; Bodson, Bernard ULg; Portetelle, Daniel ULg et al

Poster (2012, August 19)

Bacterial growth in soil is dependent on soil characteristics. In this experiment, we have studied the evolution of bacterial diversity during a winter wheat crop and the impacts caused by the tillage and ... [more ▼]

Bacterial growth in soil is dependent on soil characteristics. In this experiment, we have studied the evolution of bacterial diversity during a winter wheat crop and the impacts caused by the tillage and residue incorporation. Three growth stages of wheat was chosen for this work : germination, tillering and booting. The analyse of bacterial diversity in these conditions was performed by the Next Generation Sequencing technology. Results obtained by this method indicate that the soil is composed, in average, by 38,02 (±4,81)% Proteobacteria; 19,71(±3,88)% Actinobacteria; 7,77(±1,44)% Firmicutes; 6,94(±1,58)% Fibrobacteres/Acidobacteria group; 5(±3,21)% Bacteroidetes/Chlorobi group; 3,89(±1,36)% Chloroflexi; 2,96(±0,67)% Planctomycetes; 2,87(±1,58)% Verrucomicrobia; 1,42(±0,41)% Cyanobacteria and 15,38(±2,64)% others. The tillage influences mostly the Deltaproteobacteria, Gammaproteobacteria, Actinobacteridae, Bacteroidetes/Chlorobi group and Verrucomicrobia. Residue incorporation has an impact on Betaproteobacteria, Gammaproteobacteria, Actinobacteridae, Acidimicrobidae, Firmicutes and Bacteroidetes/Chlorobi group. The wheat growth stages affect especially Betaproteobacteria, Deltaproteobacteria, Actinomycetales, Acidibacteria, Fibrobacteres and Bacillales. The results will be presented and discussed on the poster. [less ▲]

Detailed reference viewed: 77 (9 ULg)
Full Text
Peer Reviewed
See detailIMPACT OF DEPTH AND SOIL COMPACTION ON BACTERIAL DIVERSITY IN SOIL
Stroobants, Aurore ULg; Degrune, Florine; Olivier, Claire et al

Poster (2012, August 19)

Bacteria are the most abundant and diverse microorganisms in soils. The amount of bacteria in soils can reach 10^10 cells per gram of soil. These organisms are involved in various processes in ... [more ▼]

Bacteria are the most abundant and diverse microorganisms in soils. The amount of bacteria in soils can reach 10^10 cells per gram of soil. These organisms are involved in various processes in agroecosystems such as nutrient cycling, contributing to plant nutrition, plant health and soil structure. The knowledge about this diversity is limited because only one percent of these organisms can be cultured by laboratory methods. During the last decades, many molecular-based techniques have been developed to assess the diversity of bacterial communities. The aim of this study was to determine the quantity and diversity of bacteria in two agricultural soils with differents soil management practices (tillage and no tillage) at different depths (10, 30 and 45 centimeters) and different compaction levels (high and low). Quantity was evaluated by real time PCR and diversity was analysed by the DGGE (Denaturing Gradient Gel Electrophoresis) technique. The results show that soil management has an impact on bacterial quantity at 45 centimeters and quantity is higher in till soil. Compaction level affects the bacterial quantity in till soil, quantity is higher in low compaction. And finally, depth influences the bacterial quantity in till and no till soil. In both soils, quantity decreases with the depth. The results will be presented and discussed on the poster. [less ▲]

Detailed reference viewed: 174 (14 ULg)
Full Text
Peer Reviewed
See detailIsolation and biomass production of a Saccharomyces cerevisiae strain binding copper and zinc ions
Stroobants, Aurore ULg; Delroisse, Jean-Marc; Delvigne, Frank ULg et al

in Applied Biochemistry and Biotechnology (2009), 157(1),

Detailed reference viewed: 70 (24 ULg)
Full Text
Peer Reviewed
See detailImmunomodulatory Properties Of Two Wheat Bran Fractions - Aleurone-Enriched And Crude Fractions - In Obese Mice Fed A High Fat Diet
Neyrinck, Am.; De Backer, F.; Cani, Pd. et al

in International Immunopharmacology (2008), 8(10),

Detailed reference viewed: 25 (6 ULg)
Full Text
Peer Reviewed
See detailExpression and purification of the human Tre2 product, a putative Ypt/Rab GTPase activating protein.
Bizimungu, Christelle; Stroobants, Aurore ULg; Tricot, Catherine et al

in Archives Internationales de Physiologie et de Biochimie (2005), 191

Detailed reference viewed: 14 (7 ULg)
Full Text
See detailApplication de la technique RNAi au silençage d’un rapporteur
Stroobants, Aurore ULg

Master's dissertation (2004)

Le système d’interférence par ARN (RNAi) a été découvert récemment. A la base, il semblerait avoir constitué un mécanisme de défense naturel de l’organisme en réponse à l’expression anormale de gènes ... [more ▼]

Le système d’interférence par ARN (RNAi) a été découvert récemment. A la base, il semblerait avoir constitué un mécanisme de défense naturel de l’organisme en réponse à l’expression anormale de gènes, notamment ceux résultants de l’envahissement viral ou de transposons. A l’heure actuelle, il est exploité pour éteindre l’expression d’un gène afin de modifier de manière contrôlée un phénotype. Ce système est induit par la présence d’ARN double-brin dans la cellule. Cet ARN double-brin est débité en siRNA (short interfering RNA) de 21-23 nucléotides par le complexe Dicer. Ces siRNA seront ensuite incorporés dans un complexe RISC (RNA Induced Silencing Complex) et le guideront vers l’ARNm homologue afin de le dégrader. Le but de ce travail est de tester, de manière comparative, différentes techniques d’induction du système chez la levure Schizosaccharomyces pombe. Un gène rapporteur ura4 est choisi comme cible du système. Trois vecteurs ont été construits pour induire la production de siRNA homologues de ura4. Un premier vecteur est destiné à produire le transcrit complet du gène ura4 antisens, un deuxième vecteur une "hairpin" de 25 paires de bases et un troisième vecteur une "hairpin" de 350 paires de bases. Ces trois vecteurs, ainsi que des siRNA synthétiques, ont été transformés dans S. pombe afin d’induire le système RNAi. Aucune induction du système n’a été observée. Nous discutons les raisons possibles de cet échec. [less ▲]

Detailed reference viewed: 56 (19 ULg)
Full Text
Peer Reviewed
See detailConstruction of a set of vectors allowing inducible production of siRNA in Schizosaccharomyces pombe.
Stroobants, Aurore ULg; Tafforeau, Lionel; Guiguen, Allan et al

Poster (2004, May 14)

RNA interference (RNAi) is a sequence-specific gene silencing mechanism. It is induced by the formation of dsRNA that are recognised by the Dicer complex and processed into 21-23 long oligonucleotides ... [more ▼]

RNA interference (RNAi) is a sequence-specific gene silencing mechanism. It is induced by the formation of dsRNA that are recognised by the Dicer complex and processed into 21-23 long oligonucleotides called siRNA (short interfering RNA). Subsequently, RISC (RNA-Inducing Silencing Complex) binds siRNA that targets the complex towards its homologous mRNA (DYKXHOORN et al., 2003) which is eventually degraded. In contrast to budding yeast, the entire pathway is conserved in the fission yeast Schizosaccharomyces pombe, making it a valuable organism to both study physiological RNAi and to use it as a inducible gene knock-down tool. In an attempt to apply this method in the fission yeast, we are using three different approaches to produce siRNA. In each case, a vector containing a regulatable promoter activated in presence of tetracycline (tTA') (GOSSEN et al., 1995) is generated and the ura4 marker required for growth on medium lacking uracil serves as reporter. First, a vector expressing the full lenght antisens RNA of ura4 (800 nucleotides) (RAPONI and ARNDT, 2003) is used. Second, we are trying to generate much shorter dsRNA where both strands are linked by either a short hairpin of 25 nucleotides (BRUMMELKAMP et al., 2002) or a longer one of 350 nucleotides (SCHRAMKE and ALLSHIRE, 2003). The ability of these different dsRNA to induce silencing of ura4 will be presented. [less ▲]

Detailed reference viewed: 18 (4 ULg)