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Biomedical subjects

P Nicolas

Publications and source records attributed to P Nicolas.

At least 19 recordsLinked to original sources
PubMed2006

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.

Bacterial Proteins↗
PubMed2006

Microvessel density and VEGF expression are prognostic factors in colorectal cancer. Meta-analysis of the literature.

We performed a meta-analysis of all published studies relating intratumoural microvessel density (MVD) (45 studies) or vascular endothelial growth factor (VEGF) expression (27 studies), both reflecting angiogenesis, to relapse free (RFS) and overall survival (OS) in colorectal cancer (CRC). For each study, MVD impact was measured by risk ratio between the two survival distributions with median MVD as cutoff. Eleven studies did not mention survival data or fit inclusion criteria, six were multiple publications of same series, leaving 32 independent studies for MVD (3496 patients) and 18 for VEGF (2050 patients). Microvessel density was assessed by immunohistochemistry, using antibodies against factor VIII (16 studies), CD31 (10 studies) or CD34 (seven studies). Vascular endothelial growth factor expression was mostly assessed by immunohistochemistry. Statistics were performed for MVD in 22 studies (the others lacking survival statistics) including nine studies (n = 957) for RFS and 18 for OS (n = 2383) and for VEGF in 17 studies, including nine studies for RFS (n = 1064) and 10 for OS (n = 1301). High MVD significantly predicted poor RFS (RR = 2.32 95% CI: 1.39-3.90; P < 0.001) and OS (RR = 1.44; 95% CI: 1.08-1.92; P = 0.01). Using CD31 or CD34, MVD was inversely related to survival, whereas it was not using factor VIII. Vascular endothelial growth factor expression significantly predicted poor RFS (RR = 2.84; 95% CI: 1.95-4.16) and OS (RR=1.65; 95% CI: 1.27-2.14). To strengthen our findings, future prospective studies should explore the relation between MVD or VEGF expression and survival or response to therapy (e.g. antiangiogenic therapy). Assessment of these angiogenic markers should be better standardised in future studies.

Adenocarcinoma↗
PubMed2006

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

Bacterial Proteins↗
PubMed2006

[Use of multilocus sequence typing and pulsed-field gel electrophoresis for the study of serogroup B Neisseria meningitidis isolates from Casablanca (Morocco)].

A previous study showed that B:4:P1.15 was the most frequent phenotype of Neisseria meningitidis isolated in Casablanca (Morocco). To determine if there was an epidemic clone, MLST and PFGE were used to compare 13 B:4:P1.15 strains isolated from September 1999 to December 2000. MLST showed 4 Sequence Types (ST): ST-33 was the most frequent ST (9/13 strains) and 4 strains belonged to 3 newly described STs. Twelve stains belonged to ST-32 complex, and one strain presenting a new ST (ST-2502) did not belong to any known ST complex. The analysis by PFGE showed that the strains were subdivided into 7 clusters, and that there was no epidemic clone. MLST is useful for long-term epidemiological studies on N. meningitidis strains from varied geographical origins. PFGE seemed to be well adapted to the comparison of a small number of strains isolated during a short period within a defined community.

Bacterial Typing Techniques↗
PubMed2005

Resistance of sunflower to the biotrophic oomycete Plasmopara halstedii is associated with a delayed hypersensitive response within the hypocotyls.

The biotrophic oomycete Plasmopara halstedii is the causal agent of downy mildew in sunflower. It penetrates the roots of both susceptible and resistant sunflower lines and grows through the hypocotyls towards the upper part of the seedling. RT-PCR analysis has shown that resistance is associated with the activation of a hsr203J-like gene, which is a molecular marker of the hypersensitive reaction in tobacco. Activation of this gene was specifically observed during the incompatible interaction and coincided with cell collapse in the hypocotyls. This HR was also associated with the early and local activation of the NPR1 gene which is a key component in the establishment of the SAR. No such HR or a significant activation of the hsr203J-like gene were observed during the compatible combination. These results suggest that the resistance of sunflower to P. halstedii is associated with an HR which fails to halt the parasite. By contrast, this HR triggers a SAR which takes places in the upper part of the hypocotyls and eventually leads to the arrest of parasite growth. A model describing the resistance of plants to root-infecting oomycetes is proposed.

Gene Expression Regulation, Plant↗
PubMed2005

Pharyngeal carriage of serogroup W135 Neisseria meningitidis in Hajjees and their family contacts in Morocco, Oman and Sudan.

In 2000 the global outbreak that began in Saudi Arabia was caused by a W135:2a:P1.5,2 strain of Neisseria meningitidis belonging to the ET-37 complex and to ST-11. There was concern that introduction of this epidemic clone (EC) might lead to a wave of outbreaks in the African meningitis belt. The WHO therefore initiated studies of meningococcal carriage among pilgrims and their family contacts in Morocco, Oman and Sudan, 3 to 12 months after the Hajj 2000. In Morocco, 1186 persons were swabbed 3 times. Ninety-five meningococcal strains were isolated from 2.7% of the specimens. Pulsed-field gel electrophoresis showed that 32 (33.6%) were identical with the EC. In Sudan, 5 strains identical with the EC were obtained after sampling 285 persons. In Oman, among 18 meningococcal strains isolated from 399 subjects, 11 (61.1%) belonged to the EC. The important pharyngeal carriage of W135 (EC) and its role in the 2001-2002 outbreaks in Burkina Faso argues for the necessity of reinforcing surveillance, and adapting and planning responses in Africa and the Middle East using the most appropriate vaccine.

Carrier State↗
PubMed2005

Molecular epidemiology of meningococci isolated in Niger in 2003 shows serogroup A sequence type (ST)-7 and serogroup W135 ST-11 or ST-2881 strains.

In 2003, in the Zinder and Maradi regions (Niger), epidemics were due to serogroup A:4:P1.9 meningococci belonging to sequence type 7 (ST-7). In Niamey, only sporadic cases were reported: 55% of the meningococcus strains were in serogroup A, and 38% were in serogroup W135 and could be placed in ST-11, identical to the 2002 Burkina Faso epidemic clone, and in ST-2881, a new ST.

Electrophoresis, Gel, Pulsed-Field↗
PubMed2005

In situ hybridization localization of TRH precursor and TRH receptor mRNAs in the brain and pituitary of Xenopus laevis.

We examined the distribution of the mRNAs encoding proTRH and the three TRH receptor subtypes (xTRHR1, xTRHR2, and xTRHR3) in the Xenopus laevis CNS and pituitary. A positive correlation was generally observed between the expression patterns of proTRH and xTRHR mRNAs. xTRHRs were widely expressed in the telencephalon and diencephalon, where two or even three xTRHR mRNAs were often simultaneously observed within the same brain structures. In the pituitary, xTRHR2 was selectively expressed in the distal lobe, and xTRHR3 was found exclusively in the intermediate lobe of white background-adapted animals, indicating that, in amphibians, the effect of TRH on alpha-melanotropin (alpha-MSH) secretion from melanotrope cells is mediated through the novel receptor subtype xTRHR3.

Animals↗
PubMed2005

[Correlation between rainfall and meningococcal meningitis in Niger].

The term "meningitis belt" was coined by Lapeyssonnie in 1963 to describe a zone in Africa where epidemic meningitis occurs sporadically during the dry season. The purpose of this study was to evaluate the relationship between the recorded rainfall and reported incidence of meningococcal meningitis in Niger from 1996 to 2002. A total of 58 277 cases of meningococcal meningitis were reported in Niger during the study period. The mean annual incidence was 82.2 per 10(5) inhabitants. Two epidemic years occurred during the study period, i.e., 1996 with 183 cases per 105 inhabitants and 2000 with 140 cases per 10(5). The incidence increased during the dry season and decreased at the beginning of the rainy season. Calculation of the correlation coefficient between rainfall and incidence of meningococcal meningitis showed a statistically significant negative correlation (r = -0.27; P = 0.01). Neisseria meningitidis sero-group A was predominant but strains of Neisseria meningitidis sero-group W135 have been found in specimens collected since 2002. Outbreaks of meningococcal meningitis epidemics are multi-factorial. Multivariate analysis of all factors would allow implementation of preventive measures earlier than the epidemic prediction strategy based on threshold rates proposed by the World Health Organization.

Humans↗
PubMed2004

Induction of a sunflower CC-NBS-LRR resistance gene analogue during incompatible interaction with Plasmopara halstedii.

Downy mildew caused by Plasmopara halstedii is one of the main diseases causing economic losses in cultivated sunflower. Resistance in this host is conferred by major genes denoted Pl. The inbred sunflower line QIR8, which contains the Pl8 locus and is resistant to all known downy mildew races, was used to isolate a full-length resistance gene analogue (RGA) belonging to the CC-NBC-LRR class of plant resistance genes. The genetically incompatible combination involving downy mildew races 300 and sunflower line QIR8 was characterized by a hypersensitive-like reaction. Semi-quantitative RT-PCR analysis showed that the transcript of Ha-NTIR11g RGA was specifically induced during the incompatible reaction. The transcript was induced approximately 3 d post-infection (dpi), and then decreased by 9 dpi. The high level of transcriptional expression of this RGA coincides with a transcript accumulation of the hsr203J gene which is a marker of the hypersensitive reaction. Treatment with signalling molecules, including salicylic acid and methyl jasmonate, did not activate transcription of the Ha-NTIR11g gene, indicating that Ha-NTIR11g expression is not regulated by defence signalling pathways triggered by these molecules. Ha-NTIR11g was not induced by treatment with hydrogen peroxide or wounding. These results suggest that Ha-NTIR11g RGA may play a critical role in protecting sunflower cells against P. halstedii. The transcript accumulation of R gene-mediated signalling components was also examined.

Acetates↗
PubMed2004

Immunogenicity, safety, and memory of different schedules of Neisseria meningitidis A/C-diphtheria toxoid conjugate vaccine in infants in Niger.

We studied one to four doses of meningococcal polysaccharides A and C conjugated to diphtheria toxoid (Men D) versus A/C polysaccharide (Men PS) vaccine in 618 infants in Niger. Men PS at 24 months permitted evaluating memory. Two Men D doses (at 3 and 9 months) induced higher serum bactericidal activity (SBA) than other regimens. SBA titers after Men PS at 24 months were higher in those given Men D in infancy versus Men PS. While responses were lower for serogroup C, hyporesponsiveness was not evident. Men D was well-tolerated. A single Men D dose in infancy appeared to induce memory.

Blood Bactericidal Activity↗
PubMed2004

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.) 3. Characterisation of QTL involved in resistance to Sclerotinia sclerotiorum and Phoma macdonaldi.

One hundred and fifty F(2)-F(3) families from a cross between two inbred sunflower lines FU and PAZ2 were used to map quantitative trait loci (QTL) for resistance to white rot (Sclerotinia sclerotiorum) attacks of terminal buds and capitula, and black stem ( Phoma macdonaldii). A genetic linkage map of 18 linkage groups with 216 molecular markers spanning 1,937 cM was constructed. Disease resistances were measured in field experiments for S. sclerotiorum and under controlled conditions for P. macdonaldii. For resistance to S. sclerotiorum terminal bud attack, seven QTL were identified, each explaining less than 10% of phenotypic variance. For capitulum attack by this parasite, there were four QTL (each explaining up to 20% of variation) and for P. macdonaldii resistance, four QTL were identified, each having effects of up to 16%. The S. sclerotiorum capitulum resistance QTL were compared with those reported previously and it was concluded that resistance to this disease is governed by a considerable number of QTL, located on almost all the sunflower linkage groups.

Ascomycota↗
PubMed2004

Development of PCR markers for the Pl5/Pl8 locus for resistance to Plasmopara halstedii in sunflower, Helianthus annuus L. from complete CC-NBS-LRR sequences.

Sunflower downy mildew, caused by Plasmopara halstedii, is one of the major diseases of this crop. Development of elite sunflower lines resistant to different races of this oomycete seems to be the most efficient method to limit downy mildew damage. At least two different gene clusters conferring resistance to different races of P. halstedii have been described. In this work we report the cloning and mapping of two full-length resistance gene analogs (RGA) belonging to the CC-NBC-LRR class of plant resistance genes. The two sequences were then used to develop 14 sequence tagged sites (STS) within the Pl5/Pl8 locus conferring resistance to a wide range of P. halstedii races. These STSs will be useful in marker-assisted selection programs.

Amino Acid Sequence↗
PubMed2004

[Pharyngeal carriage of Neisseria meningitidis in a school of Niamey, Niger].

This study of pharyngeal carriage of Neisseria meningitidis in a school in Niamey, Nigeria was carried out to confirm the feasibility of evaluating the impact of conjugate vaccine on the meningococcal carriage. All 90 pupils attending the school were examined during the dry season in February 1998. All children had been vaccinated using polysaccharide A/C in 1996. Samples were collected from the soft palate and immediately seeded on selective medium. After incubation at 37 degrees C for 24 hours, suspicious colonies were re-seeded on Miller-Hinton medium. Identification of N. meningitidis was based on standard biochemical criteria, agglutination grouping and DNA fingerprinting. Seven carriers of N. meningitidis X:NT:P1.5 were found. One of these carriers also presented a strain of N. meningitis A:4:P1.9. The high prevalence of serogroup X strains coincided with an outbreak of meningitis involving the same sub-type and sequence-type in Niamey.

Adolescent↗
PubMed2003

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

Chromosome Mapping↗