Biomedical subjects

Jacques Nicolas

Publications and source records attributed to Jacques Nicolas.

11 recordsLinked to original sources

PubMed2006

Browsing repeats in genomes: Pygram and an application to non-coding region analysis.

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.

Codon↗

PubMed2006

Use of experimental design methodology to prepare Maillard reaction products from glucose and cysteine inhibitors of polyphenol oxidase from eggplant (Solanum melongena).

Polyphenol oxidase (PPO) from eggplant was extracted and partially purified by a two-step fractionation-precipitation using ammonium sulfate and phenylsepharose hydrophobic interaction chromatography. The eggplant PPO extract was characterized concerning its kinetic properties. Optimal conditions to obtain Maillard reaction products (MRPs) with a maximal inhibitory potency (IP) toward PPO activity were determined using the surface response methodology and a four-factor and five-level experimental design. The MRPs were prepared from cysteine (0.25 M) and glucose (0-1 M), at several initial pH values (2-6) and at differing heating times (3-19 h) and temperatures (95-115 degrees C). The maximal IP was obtained after heating a model system of glucose/cysteine (1/0.25 M) at pH 2 for 3 h 20 min at 115 degrees C. The soluble part of this MRP, called MRP(IPmax), was a noncompetitive inhibitor toward eggplant PPO. The IP of MRP(IPmax) on PPO activity was very potent as compared to that displayed by benzoic, p-coumaric, and t-cinnamic acids, as well as sorbic acid and 4-hexylresorcinol. The activity of preincubated PPO at 0 degrees C with MRP(IPmax) was only slightly restored after dialysis or gel filtration.

Benzoic Acid↗

PubMed2006

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

MOTIVATION: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains. RESULTS: Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method. AVAILABILITY: DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

Algorithms↗

PubMed2005

Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.

SUMMARY: We have developed STAN (suffix-tree analyser), a tool to search for nucleotidic and peptidic patterns within whole chromosomes. Pattern syntax uses a string variable grammar-like formalism which allows the description of complex patterns including ambiguities, insertions/deletions, gaps, repeats and palindromes. STAN is based on a reduction to multipart matching on a suffix-tree data structure and can handle large DNA sequences, whether assembled or not.

Amino Acid Sequence↗

PubMed2005

The dog and rat olfactory receptor repertoires.

BACKGROUND: Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors (ORs) that specifically bind odorant molecules are encoded by the largest gene family sequenced in mammals so far. RESULTS: We identified five amino acid patterns characteristic of ORs in the recently sequenced boxer dog and brown Norway rat genomes. Using these patterns, we retrieved 1,094 dog genes and 1,493 rat genes from these shotgun sequences. The retrieved sequences constitute the olfactory receptor repertoires of these two animals. Subsets of 20.3% (for the dog) and 19.5% (for the rat) of these genes were annotated as pseudogenes as they had one or several mutations interrupting their open reading frames. We performed phylogenetic studies and organized these two repertoires into classes, families and subfamilies. CONCLUSION: We have established a complete or almost complete list of OR genes in the dog and the rat and have compared the sequences of these genes within and between the two species. Our results provide insight into the evolutionary development of these genes and the local amplifications that have led to the specific amplification of many subfamilies. We have also compared the human and rat ORs with the human and mouse OR repertoires.

Animals↗

PubMed2005

Maillard reaction products as "natural antibrowning" agents in fruit and vegetable technology.

The effects of Maillard reaction products (MRPs), synthesized from a sugar (pentose, hexose, or disaccharide) and either a cysteine-related compound, an amino acid, or a sulfur compound, were investigated on polyphenoloxidase (PPO) activity from apple, mushroom, and eggplant. The optimal conditions for the production of inhibitory MRPs were performed using two-factor and five-level central experimental designs. It resulted that thiol-derived MRPs were highly prone to give rise to inhibitory compounds of PPO activity. Technological assays were also performed to test the efficiency of selected MRPs in the prevention of enzymatic browning in raw and minimally processed fruits and vegetables.

Agaricales↗

PubMed2004

Separation and quantification by high-performance liquid chromatography with light scattering detection of the main wheat flour phospholipids during dough mixing in the presence of phospholipase.

Phospholipids (PL) are minor components of wheat flour involved in baking quality and exogenous phospholipids are used as emulsifiers giving better loaf volume and crumb grain. Few biochemical data are available on the phospholipid evolution during mixing, probably because of the time-consuming methods proposed for their extraction, separation and quantification. In the present study, the extraction, separation and quantification of the main wheat flour phospholipids were carried out. Total lipids (2% dry mass of wheat flour) were extracted from flour or dough by a mixture of chloroform-methanol-water (1:1:1 (v/v)). The phospholipids were separated from the lipid extract on silica cartridge by solid-phase extraction (SPE) procedure under a 1.5-4 mmHg vacuum, at a 0.8 mL min(-1) flow rate (1 mmHg = 133.322 Pa). The recovery of the lipid extract was 100%, whereas the SPE yield for the PLs was 50%. The resulting fraction was then submitted to HPLC with evaporative light scattering detection on a Diol stationary phase allowing the separation and quantification of each class of phospholipids, in less than 16 min. The developed method allowed to quantify the phospholipid amounts from eight wheat flours as well as their evolution during mixing in the presence of phospholipase.

Chromatography, High Pressure Liquid↗

PubMed2004

Analysis and modeling of the ferulic acid oxidation by a glucose oxidase-peroxidase association. Comparison with a hexose oxidase-peroxidase association.

A commercial glucose oxidase (GOX) from Aspergillus niger was partially characterized. The enzyme exhibited a two-step transfer mechanism, and the kinetic constants toward glucose and oxygen were determined. Under conditions similar to dough making (glucose concentration and pH), GOX does not exhibit maximum activity. A hexose oxidase (HOX) from Chondrus crispus was partially characterized as well. The HOX activity is not far from the optimum in the kneading conditions (pH and glucose concentration). A peroxidase (POD) purified from wheat germ was used to oxidize ferulic acid in the presence of GOX or HOX. Hydrogen peroxide produced during the glucose oxidation activates the wheat germ POD. Ferulic acid oxidation in solutions containing different ratios of POD + GOX or HOX + POD was followed by UV spectrophotometry. For the same dosage, the HOX-POD system is the most efficient for peroxidase activation. Using absorbance data and kinetic constants of GOX and POD, a mathematical model describing the release or consumption of the different reactants (hydrogen peroxide, oxygen, and ferulic acid) in the medium was developed, and experimental data correlated well with calculated values. The results obtained will be applied to investigate the effect of GOX and HOX activities on the rheological properties of dough.

Alcohol Oxidoreductases↗

PubMed2004

Separation and identification by gel filtration and high-performance liquid chromatography with UV or electrochemical detection of the disulphides produced from cysteine and glutathione oxidation.

Methods for quantification of oxidised and reduced forms of glutathione (GSSG and GSH) and cysteine (CSSC and CSH) and the disulphide glutathione-cysteine (GSSC) resulting from the oxidation of the mixture of CSH and GSH are performed by RP-HPLC with coulometric and UV detection after separation of these compounds by size-exclusion fast protein liquid chromatography. The fractionation of the disulphides (GSSG, GSSC and CSSC) was achieved by size exclusion using a Superdex peptide column coupled with an UV detection at 254 nm. The conditions of separation of these compounds by RP-HPLC were optimised using the response surface methodology. Optimal peak resolution and retention times were obtained on a C18 YMC ODS AQ column with 20 mM of ammonium phosphate at pH 2.5 and 2% of acetonitrile in the elution phase. In these experimental conditions, CSH, CSSC, GSH and GSSG were eluted within 20 min. Coulometric detection enabled a sensitivity 100 times higher for the disulphides than the UV detection at 220 nm. These methods were applied to follow the consumption of thiols and the disulphide formation by three oxidising systems, sulphydryl oxidase, glutathione dehydroascorbate oxidoreductase and potassium bromate. This study revealed that the relative proportions of the disulphides formed were similar for the three oxidising systems when the reactions are in their state of equilibrium.

Chromatography, Gel↗

PubMed2003

The use of sensor arrays for environmental monitoring: interests and limitations.

Continuous, in situ monitoring of air, water and land quality is fundamental to most environmental applications. Low cost and non-invasive chemical sensor arrays provide a suitable technique for in situ monitoring. Their ability and performance under realistic conditions is discussed in this paper. Published studies report promising results despite a number of limitations that are associated with both the technology itself and its application in ever changing ambient conditions. Early investigations include the analysis of single substances as well as odour and wastewater organic load monitoring. Reported applications typically highlight the sensitivity of the currently available sensors to changes in temperature, humidity and flow rate. Two types of approaches are recommended to deal with these effects: either working under fixed experimental conditions or measuring the external parameters to numerically compensate for their change. The main challenge associated with the use of non-specific sensor arrays lies in establishing a relationship between the measured multivariate signals and the standards metrics that are traditionally used for quality assessment of gas mixtures. For instance, odour monitoring requires calibration against olfactometric measurements while investigations of wastewater samples still need to be correlated with organic pollution parameters such as BOD, COD or TOC. On the other hand, results obtained in the field have demonstrated how sensor arrays can be readily used as simple alarm devices or as early warning systems based on a general air/water quality index.

Air Movements↗

PubMed2002

Oxidation of ferulic acid or arabinose-esterified ferulic acid by wheat germ peroxidase.

The oxidation of ferulic acid (FA) or 5-O-(trans-feruloyl)-L-arabinose (EFA) by a purified wheat germ peroxidase was followed by UV spectrophotometry and high-performance liquid chromatography using an electrochemical detection. Wheat peroxidase (POD) exhibits a ping-pong bireactant mechanism forming phenoxy radicals more rapidly from FA than from EFA in routine assay conditions. When both the free and the esterified forms of FA are present, the reverse was found. This result could be due to a nonenzymatic cooxidation of FA by the phenoxy radicals of EFA leading to the formation of phenoxy radicals of FA and the EFA regeneration. Addition of ascorbic acid (AA) provokes a delay of FA consumption. AA reduced very rapidly the phenoxy radicals formed by POD back to initial phenol avoiding the formation of ferulate dimers until it was completely oxidized in dehydroascorbic acid. Conversely, cysteine addition slowed but did not delay the FA consumption. The thiol reduced a fraction of the phenoxy radicals produced by wheat POD and was oxidized into cystine, while the other part of phenoxy radicals formed ferulate dimers. These results could be of interest to understand the POD effect on the wheat dough rheological properties.

Arabinose↗