Browsing
     by title


0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

or enter first few letters:   
OK
Full Text
See detailIdentification of asthma-related trans-acting epistatic eQTLs using Model-Based Multifactor Dimensionality Reduction (MB-MDR)
Bessonov, Kyrylo ULg

Poster (2013, October 22)

Epistasis is likely to underlie most complex traits, including gene expression, yet it is very difficult to detect using standard approaches. SNPs located inside a gene coding region or in its vicinity (i ... [more ▼]

Epistasis is likely to underlie most complex traits, including gene expression, yet it is very difficult to detect using standard approaches. SNPs located inside a gene coding region or in its vicinity (i.e. ≤2 Mb from each 5’ and 3’ side) can influence the corresponding gene expression levels. These expression quantitative trait loci (eQTLs) are referred to as cisSNPs. In contrast, eQTLs that are outside the aforementioned gene range can also influence the gene’s expression, in which case, they are called transSNPS to that gene. In this study we considered significant cisSNPs previously identified via generalized least squares (GLS) regression modeling. We then identified those genes transcripts whose expression is regulated by cis/transSNP interaction. In this work we aimed at identifying transcripts whose expression is regulated by a cis/transSNP interactions using Model-Based Multifactor Dimensionality Reduction (MB-MDR) [2]. This model-free approach to detect trans-epistasis involves reducing a high-dimensional GxG space to GxG factor levels that either exhibit high evidence, low evidence or no evidence at all for their association to gene expression levels of interest. Our protocol was applied on real-life data from the childhood asthma management program (CAMP) [1]. It involved coupling a traditional a priori eQTL search to an a posteriori trans-epistasis analysis to identify genetic modifiers to statistically significant cisSNPs. Such an approach allows to reveal previously unreported inter-dependencies that may be important in understanding of biological mechanisms underlying human complex diseases such as asthma. The proposed protocol identified a large number trans-epistasis gene-gene effects of eQTLs. [less ▲]

Detailed reference viewed: 35 (11 ULg)
Full Text
See detailIdentification of bacteria community associated with earthworm gut
Lemtiri, Aboulkacem ULg; Alabi, Taofic; Bodson, Bernard ULg et al

Poster (2012, July 26)

The role of earthworms in soil fertility and transformation of organic waste was regulary cited to be of first importance. Associated to these macro-invertebrates, a large diversity of micro-orgnisms are ... [more ▼]

The role of earthworms in soil fertility and transformation of organic waste was regulary cited to be of first importance. Associated to these macro-invertebrates, a large diversity of micro-orgnisms are found indirectly in their closed environment or directly in their gut. Functional aspects of these interactions and symbiosis in relation with soil characteristics and fertility rates are poorly developed. Here, the micro-organisms diversity and potential related functions of earthworm gut were investigated using a proteiomic approach for both protein and micro-organism identifications. Microbial community investigation was detected by proteomic approach based on bidimensional electrophoresis coupled with mass spectrometry using Matrix Assisted Laser Desorption Ionisation – time of flight (Maldi-Tof). Diversity of gut associated bacterial communities was discussed. Indeed, application of particular crop production practices such as crop residue management at the field level could regulate the gut bacterial communities in earthworm but also microbials in soils. Agricultural systems had to consider the microbial and associated organisms in the soil to enhance fertlility and crop production in sustainable ways. [less ▲]

Detailed reference viewed: 77 (15 ULg)
Full Text
Peer Reviewed
See detailIdentification of bacterial strains isolated from the traditional date product "Btana" produced in south regions of Algeria
Abekhti, Abdelkader; Taminiau, Bernard ULg; Kihal, Mabrouk et al

in Folia Microbiologica (in press)

Eleven samples of the traditional date product " Btana" prepared by direct (DBM) and indirect method (UBM) were analysed to characterize their bacterial diversity. A total of 42 representative isolates ... [more ▼]

Eleven samples of the traditional date product " Btana" prepared by direct (DBM) and indirect method (UBM) were analysed to characterize their bacterial diversity. A total of 42 representative isolates have been chosen for molecular identification. 16S rRNA gene sequencing revealed the presence of 20 species within 30.9% belonged to the genus Bacillus, 28.6% of the Staphylococcus, and Enterococcus genus. Within the minority represented species, two isolates were identified as Paenibacillus (isolated from UBM exclusively), Streptococci salivarius, Lactobacillus sakei and Klebsiella pneumoniae. Preliminary results indicate that IBM is more selective for spore former bacilli contrary to DBM that show more diversity in the bacterial flora with a prevalence of Enterococcus. API ZYM test showed that the bacilli species have a weak hydrolase activity. [less ▲]

Detailed reference viewed: 19 (5 ULg)
Full Text
Peer Reviewed
See detailIdentification of Bayesian posteriors for coefficients of chaos expansions
Arnst, Maarten ULg; Ghanem, Roger; Soize, Christian

in Journal of Computational Physics (2010), 229(9), 3134-3154

This article is concerned with the identification of probabilistic characterizations of random variables and fields from experimental data. The data used for the identification consist of measurements of ... [more ▼]

This article is concerned with the identification of probabilistic characterizations of random variables and fields from experimental data. The data used for the identification consist of measurements of several realizations of the uncertain quantities that must be characterized. The random variables and fields are approximated by a polynomial chaos expansion, and the coefficients of this expansion are viewed as unknown parameters to be identified. It is shown how the Bayesian paradigm can be applied to formulate and solve the inverse problem. The estimated polynomial chaos coefficients are hereby themselves characterized as random variables whose probability density function is the Bayesian posterior. This allows to quantify the impact of missing experimental information on the accuracy of the identified coefficients, as well as on subsequent predictions. An illustration in stochastic aeroelastic stability analysis is provided to demonstrate the proposed methodology. [less ▲]

Detailed reference viewed: 32 (7 ULg)
Full Text
See detailIdentification of biochemical reaction networks using a parameter-free coordinate system
Fey, Dirk ULg; Findeisen, Rolf; Bullinger, Eric ULg

in Iglesias, P. A.; Ingalls, B. (Eds.) Control-Theoretic Approaches in Systems Biology (2009)

A fundamental step in systems biology is the estimation of kinetic parameters, such as association and dissociation constants. Often, their direct estimation from in-vivo studies on isolated reactions is ... [more ▼]

A fundamental step in systems biology is the estimation of kinetic parameters, such as association and dissociation constants. Often, their direct estimation from in-vivo studies on isolated reactions is expensive, time-consuming or even infeasible. Therefore, it is necessary to estimate them from indirect measurements, such as time-series data. This chapter proposes an observer-based parameter estimation methodology particularly suited for biochemical reaction networks in which the reaction kinetics are described by polynomial or rational functions. The parameter estimation is performed in three steps. First, the system is transformed into a new set of coordinates in which the system is parameter-free. This facilitates the design of a standard observer in the second step. Finally, the parameter estimates are obtained in a straight-forward way from the observer states, transforming them back to the original coordinates. The approach is illustrated by an example of a MAP kinase signaling pathway. [less ▲]

Detailed reference viewed: 123 (13 ULg)
See detailIdentification of Biochemical reaction networks: challenges and possible solutions
Bullinger, Eric ULg

Scientific conference (2008, April 25)

Detailed reference viewed: 5 (0 ULg)
Full Text
Peer Reviewed
See detailIdentification of bioindicator species among Ephemeroptera, Plecoptera and Trichoptera in a survey of streams belonging to the rhithral classification in the Grand Duchy of Luxembourg
Dohet, A.; Dolisy, D.; Hoffmann, L. et al

in Verhandlungen der Internationalen Vereinigung für Theoretische und Angewandte Limnologie = Proceedings of the International Association of Theoretical and Applied Limnology (2002), 28

Detailed reference viewed: 55 (8 ULg)
Full Text
See detailIdentification of biomarkers of hemostatic, endothelial and immune function in sepsis
GOTHOT, André ULg; GOSSET, Christian ULg; FOGUENNE, Jacques ULg et al

in Belgian Journal of Hematology (2013)

Detailed reference viewed: 20 (14 ULg)
Full Text
Peer Reviewed
See detailIdentification of biomarkers to estrogen exposure using MCF-7/BOS cell line exposed to 17β-estradiol and phytoestrogens
Collodoro, Mike ULg; Bertrand, Virginie ULg; Lemaire, Pascale ULg et al

Poster (2009, June)

Use of an estrogen responsive cell line and proteomic for biomarker discovery and the screening of xenoestrogen

Detailed reference viewed: 72 (10 ULg)
Full Text
Peer Reviewed
See detailIdentification of bla(IMP-22) in Pseudomonas spp. in urban wastewater and nosocomial environments: biochemical characterization of a new IMP metallo-enzyme variant and its genetic location.
Pellegrini, Cristina; Mercuri, Paola ULg; Celenza, Giuseppe et al

in The Journal of antimicrobial chemotherapy (2009), 63(5), 901-8

OBJECTIVES: The aim of the study was the biochemical characterization of a new variant of the metallo-beta-lactamase, IMP-22. Moreover, the genetic environment of the bla(IMP-22) gene was investigated in ... [more ▼]

OBJECTIVES: The aim of the study was the biochemical characterization of a new variant of the metallo-beta-lactamase, IMP-22. Moreover, the genetic environment of the bla(IMP-22) gene was investigated in Pseudomonas fluorescens and Pseudomonas aeruginosa collected from urban wastewater and a teaching hospital in L'Aquila, Italy. METHODS: Molecular characterization of genetic elements was carried out by PCR and DNA sequencing methods. The new enzyme was purified from recombinant Escherichia coli BL21(DE)Rosetta/pBC-SK/IMP-22. Steady-state kinetic parameters (K(m) and V(max)) were determined for a large pattern of substrates. RESULTS: A new IMP metallo-beta-lactamase gene was found in a class 1 integron and in one case, in a plasmid of Pseudomonas spp. The bla(IMP-22) encodes for a pre-protein of 246 amino acids and the N-terminus of the mature beta-lactamase (NH(2)-PDLK) was also determined. The molecular mass and pI were 24 930 Da and 6.2, respectively. On the basis of the kinetic parameters calculated (K(m) and V(max)), IMP-22 was found to hydrolyse narrow- and extended-spectrum beta-lactams. Enzyme activity was found to be inhibited by metal chelators such as EDTA, 1,10-o-phenathroline and dipicolinic acid with an IC(50) of 800, 750 and 300 microM, respectively. CONCLUSIONS: The finding of the bla(IMP-22) gene in P. fluorescens environmental strains and P. aeruginosa clinical isolate suggests the ongoing spread of bla(MBL) genes in several bacterial species and in different environments. [less ▲]

Detailed reference viewed: 18 (2 ULg)
Full Text
Peer Reviewed
See detailIdentification of BlaR, the signal transducer for β-lactamase production in Bacillus licheniformis, as a penicillin-binding protein with strong homology to the OXA-2 β-lactamase (class D) of Salmonella typhimurium
Zhu, Ying-Fang; Curran, Ivan H. A.; Joris, Bernard ULg et al

in Journal of Bacteriology (1990), 172(2), 1137-1141

The blaR gene of Bacillus licheniformis encodes the signal transducer for induction of the class A beta-lactamase. The protein product, BlaR, has a hydrophilic carboxy region that binds beta-lactams and ... [more ▼]

The blaR gene of Bacillus licheniformis encodes the signal transducer for induction of the class A beta-lactamase. The protein product, BlaR, has a hydrophilic carboxy region that binds beta-lactams and shows high sequence homology to the class D beta-lactamases, particularly the OXA-2 beta-lactamase of Salmonella typhimurium. The BlaR-beta-lactam complex is stable and may provide the continuing stimulus needed for the prolonged production of the enzyme. [less ▲]

Detailed reference viewed: 32 (0 ULg)
See detailIdentification of bovine and porcine colistin-resistant mcr1-positive Escherichia coli.
Mainil, Jacques ULg; Muylaert, Adeline ULg; Saulmont, Marc et al

Conference (2016, September)

OBJECTIVE Polymyxins, especially colistin, have been used for years in veterinary medicine and were rediscovered a few years ago as last resort antibiotics in human medicine against multi-resistant Gram ... [more ▼]

OBJECTIVE Polymyxins, especially colistin, have been used for years in veterinary medicine and were rediscovered a few years ago as last resort antibiotics in human medicine against multi-resistant Gram negative bacterial pathogens. For years, only chromosome-mediated resistance to colistin was identified as a consequence of mutation(s) in lipid A-encoding genes. Recently, however, a plasmid-located gene (mcr1) was identified in Gram-negative enterobacteria and has since been found by PCR in several, but not all, bovine, human, porcine and poultry colistin-resistant Escherichia coli (Liu YY et al. Lancet Infect Dis, 2016, 16(2), 161-168; Nordmann P and Poirel L. Clin Microbiol Infect, 2016, 22, 398-400 ; Schwarz S and Johnson AP. J Antimicrob Chemother, 2016, in press, doi: 10.1093/jac/dkw274). The purpose of this study was to compare phenotypic and genetic for the detection of resistance to colistin and of the mcr1 gene in a collection of Escherichia coli isolated from different animal species and from humans. METHODS More than 3000 E. coli isolates from cattle, pigs, dogs, cats, horses, rabbits, chickens ducks and humans were tested for resistance to colistin by growing them on agar plates with 1g/ml of colistin. The Minimal Inhibitory Concentrations (MIC) of and the presence of the mcr1 gene in all growing isolates were determined using the E test® and colony hybridization assay with a mcr1 specific gene probe, respectively. The probe-positive isolates were further tested with the mcr1 gene specific PCR. RESULTS A total of 410 E. coli isolated grew on 1g/ml colistin-containing agar plates. The majority of isolates grew well, but several grew sparsely with only few isolated colonies. As determined by the E test®, MIC of 273 isolates (67%) was 1g/ml of colistin and higher; conversely, MIC of 137 isolates (33%) was lower than 1g/ml of colistin. Of those 410 E. coli isolates, 34 from pigs and bovines (9% of isolates growing on colistin-containing agar plates; 25% of isolates with MIC higher than 1g/ml) hybridized with the mcr1 gene-derived probe: 5 from pigs and 11 from bovines gave black spots (including five from the same calf), while 18 from pigs and one from bovine gave grey spots. All but one pig isolate had a MIC between 1.5 and 16 g/ml of colistin. Fifteen “black spot” probe-positive isolates tested positive with the mcr1 gene specific PCR as did 3 porcine “grey spot” probe-positive isolates, while the remaining 16 isolates repeatedly tested negative even after lowering the annealing temperature. CONCLUSION This study confirms that (i) the results of phenotypic assays for the detection of colistin resistance can not be always trusted; (ii) the mcr1 gene is not the only one mechanism of resistance to colistin; (iii) mcr1 variants may exist that can not be detected by the classical PCR. Phenotypic assays like growth on colistin-containing agar plates can still represent a first base screening assay, although the MIC determination using the E test® confirms a >1g/ml MIC for only 2 out of 3 growing isolates. Presence of mcr1 gene and putative variants (like the most recently described mcr2 gene; Xavier BB et al., Eurosurveillance, 21, 7 July 2016) in all probe-positive isolates will be confirmed after Whole Genome Sequencing that will also allow comparing the mcr1-positive plasmids and isolates from pigs and cattle to similar human E. coli isolates. Further studies should also be performed to identify the colistin resistance mechanism in mec-negative isolates. [less ▲]

Detailed reference viewed: 60 (1 ULg)
See detailIdentification of bovine methicillin resistant staphylococci from Europe, Africa and North America by colony hybridization, PCR and antibiotic sensitivity.
Ngassam Tchamba, Cyrille ULg; Thiry, Damien ULg; Bardiau, Marjorie et al

Conference (2016, September)

Mastitis is the costliest pathology in dairy cattle and staphylococci are the most prevalent bacterial mastitis pathogens worldwide. Antimicrobial treatment of mastitis has led to the selection of ... [more ▼]

Mastitis is the costliest pathology in dairy cattle and staphylococci are the most prevalent bacterial mastitis pathogens worldwide. Antimicrobial treatment of mastitis has led to the selection of resistant staphylococci, of which the Methicillin Resistant S. aureus (MRSA) are the most studied ones. Still, MR has also been described for non-aureus staphylococci (MRS) species. Bovine MRS(A) represent not only a problem in the treatment of mastitis, but also a potential hazard in public health via the inter-Staphylococcus transferability of the mobile “Staphylococcal Cassette Chromosome” (SCC) carrying the mec genes encoding MR and the zoonotic potential of some Staphylococcus species. The aim of this study is the comparison of genetic and phenotypic methods for the identification of MRS(A) isolated from bovine mastitis in European, African and North-American countries. A total of 1168 mastitis-associated staphylococci were isolated between 2005 and 2014 in Belgium, Italy, Switzerland, Senegal, Niger and Canada, and kept at -80°C until further use. Out of them, 867 isolates were identified to S. aureus while 301 isolates were non aureus staphylococci. All 1168 staphylococci were tested genetically by the dot blot hybridization assay on positively charged nylon membranes (Roche) after DNA extraction with 32P-radioactively labelled probes derived from the mecA and mecC genes and phenotypically by growth on “Chrom MRSA ID®” agar plates. Isolates positive at both or either tests were further studied by PCR targeting the same two genes and by the disk diffusion assay to oxacillin and cefoxitin. A total of 265 isolates (23%) were positive at both or either tests. Out of them, 27 S. aureus (10%) but no non-aureus (0%) tested positive both for DNA hybridization with the mecA probe and for growth on “Chrom MRSA ID®” plates. No isolate tested positive with the mecC probe. In addition, 32 S. aureus (12%) and 15 non aureus (6%) were positive with the mecA probe only and 169 S. aureus (64%) and 22 non aureus (8%) grew on “Chrom MRSA ID®” plates only. The S. aureus originate from Belgium (105), Italy (6), Canada (31), Senegal (38) and Niger (48) whereas the non-aureus originate from Belgium (25), Italy (1) and Niger (11). All of them are being tested with the PCR targeting the mecA gene and by the disk diffusion assay to oxacillin and cefoxitin. Most isolates (72%) grew on “Chrom MRSA ID®” plates only while few (18%) were positive to the hybridization with the mecA probe only. This high difference between the results of both tests could be explained by the weak specificity of phenotypic tests comparing to genetic tests. The others 10% of the isolates (S. aureus) which are positive with the two methods (dot blot hybridization and “Chrom MRSA ID®”) can be considered as MRSA mediated by the mecA gene. However, results of PCR and disk diffusion assay will confirm respectively the presence of mec genes and which of the two methods is the most suitable for identifying MRS from mastitis cases in cattle. Comparison of the results of phenotypic and genetic assays will indicate whether other variant(s) than mecA and mecC may be present in MRS. Further genetic and phenotypic studies are needed to (i) identify the non-aureus isolates to the species level; (ii) compare the MRS(A) isolated in the different countries by their biotypes, serotypes, lysotypes, and virulotypes, without forgetting their SCCmec and their clonal complex; and (iii) identify the mec gene variant present in hybridization-positive PCR-negative isolates, if any. [less ▲]

Detailed reference viewed: 51 (4 ULg)
Full Text
Peer Reviewed
See detailIdentification of Brucella spp. genes involved in intracellular trafficking.
Delrue, R. M.; Martinez-Lorenzo, M.; Lestrate, P. et al

in Cellular Microbiology (2001), 3(7), 487-97

After uptake by host cells, the pathogen Brucella transits through early endosomes, evades phago-lysosome fusion and replicates in a compartment associated with the endoplasmic reticulum (ER). The ... [more ▼]

After uptake by host cells, the pathogen Brucella transits through early endosomes, evades phago-lysosome fusion and replicates in a compartment associated with the endoplasmic reticulum (ER). The molecular mechanisms underlying these processes are still poorly understood. To identify new bacterial factors involved in these processes, a library of 1800 Brucella melitensis 16M mini-Tn5catkm mutants was screened for intracellular survival and multiplication in HeLa cells and J774A.1 macrophages. Thirteen mutants were identified as defective for their intracellular survival in both cell types. In 12 of them, the transposon had inserted in the virB operon, which encodes a type IV-related secretion system. The preponderance of virB mutants demonstrates the importance of this secretion apparatus in the intracellular multiplication of B. melitensis. We also examined the intracellular fate of three virB mutants (virB2, virB4 and virB9) in HeLa cells by immunofluorescence. The three VirB proteins are not necessary for penetration and the inhibition of phago-lysosomal fusion within non-professional phagocytes. Rather, the virB mutants are unable to reach the replicative niche and reside in a membrane-bound vacuole expressing the late endosomal marker, LAMP1, and the sec61beta protein from the ER membrane, proteins that are present in autophagic vesicles originating from the ER. [less ▲]

Detailed reference viewed: 36 (0 ULg)
Full Text
Peer Reviewed
See detailIdentification of cardiac repercussions after intense and prolonged concentric isokinetic exercise in young sedentary people
LE GOFF, Caroline ULg; Kaux, Jean-François ULg; Couffignal, Vincent et al

in Clinical physiology and functional imaging (2015), 35(5), 368-375

INTRODUCTION: Cardiopathies are the world's leading cause of mortality and morbidity. Although rare, cardiovascular accidents can occur during intense and infrequent sporting activity, particularly among ... [more ▼]

INTRODUCTION: Cardiopathies are the world's leading cause of mortality and morbidity. Although rare, cardiovascular accidents can occur during intense and infrequent sporting activity, particularly among those who are unaware of their heart condition. The development of cardiospecific biochemical markers has led to a reconsideration of the role of biology in the diagnosis of cardiovascular illnesses. The aim of this study therefore was, through the use of cardiac biomarker assays, to highlight the impact of sustained physical effort in the form of intense and prolonged concentric isokinetic exercise and to research potential cardiovascular risks. MATERIALS AND METHODS: Eighteen subjects participated in a maximal concentric isokinetic exercise involving 30 knee flexion-extensions for each leg. Five blood tests were taken to study the kinetics of the cardiac biomarkers. Haemodynamic parameters were measured continuously using a Portapres, and respiratory parameters were measured using a Sensormedics Vmax 29C. RESULTS: The results showed significant increases in the creatine kinase, myoglobin, homocysteine and haemoglobin cardiac markers. Evolutionary trends were also observed for the following biomarkers: NT-proBNP, myeloperoxydase and C-reactive protein. All the physiological parameters measured presented statistically significant changes. CONCLUSION: Isokinetic effort leads to the release of cardiac markers in the blood, but these do not exceed the reference values in healthy subjects. Maximal concentric isokinetic exercise does not, therefore, lead to an increased risk of cardiovascular pathologies. [less ▲]

Detailed reference viewed: 105 (44 ULg)