Project description:Microarray comparative genome hybridization (mCGH) data was collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae, and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491, and FAM18 and N. gonorrhoeae FA1090.
2007-04-04 | E-TIGR-129 | ArrayExpress
Project description:Whole genome sequencing of Neisseria carriage study isolates from the United Kingdom
Project description:Plasmids are one of the important mobile genetic elements in bacterial evolution. In this study, to evaluate the generality of the impact of plasmid carriage on host cell between different plasmids, we compared the response of Pseudomonas putida KT2440 to harboring three natural plasmids; RP4 (IncP-1, multidrug resistance, 60,099-bp), pCAR1 (IncP-7, carbazole-degradative, 200,231-bp) and NAH7 (IncP-9, naphthalene-degradative, 82,232-bp). We prepared two sets of plasmid-harboring strains from independent conjugation events to elucidate the reproducibility of the impact of the plasmid carriage. As results, the fitness was reduced by the carriage of RP4 and pCAR1 in liquid medium, while it was unaffected or even improved for NAH7-harboring strains. RP4-harboring KT2440 formed smaller colonies than the plasmid-free strain on solid medium (1.6% agar). The host cells were elongated by the carriage of the all plasmids, respectively. Copy number determination by quantitative PCR showed that the amount of each plasmid DNA in the host cell did not differed drastically. Whole genome resequencing showed that 13 SNPs (RP4), 24 SNPs (pCAR1) and 5 SNPs (NAH7) were the total differences between the two substrains for each plasmid-harboring strains. Transcriptome analyses showed that the impact of plasmid carriage was constantly larger in RP4-harboring strain than the other two plasmid-harboring strains. Genes involved in metal acquisition and metabolism were commonly affected by the carriage of the three plasmid. Indeed, plasmid-harboring strains showed greater growth inhibition than plasmid-free strains under iron-limiting condition. This feature could become future target to control plasmid spreading. Overall design: Transcriptome analysis was performed using Pseudomonas putida KT2440 harboring one of the three plasmid (RP4, pCAR1, NAH7), respectively. RNA maps of the donor or the plasmid-free strain were used as controls. Biologically duplicated data were obtained.
Project description:Baart2007 - Genome-scale metabolic network of
Neisseria meningitidis (iGB555)
This model is described in the article:
meningitidis metabolism: from genome to metabolic fluxes.
Baart GJ, Zomer B, de Haan A, van
der Pol LA, Beuvery EC, Tramper J, Martens DE.
Genome Biol. 2007; 8(7): R136
BACKGROUND: Neisseria meningitidis is a human pathogen that
can infect diverse sites within the human host. The major
diseases caused by N. meningitidis are responsible for death
and disability, especially in young infants. In general, most
of the recent work on N. meningitidis focuses on potential
antigens and their functions, immunogenicity, and pathogenicity
mechanisms. Very little work has been carried out on Neisseria
primary metabolism over the past 25 years. RESULTS: Using the
genomic database of N. meningitidis serogroup B together with
biochemical and physiological information in the literature we
constructed a genome-scale flux model for the primary
metabolism of N. meningitidis. The validity of a simplified
metabolic network derived from the genome-scale metabolic
network was checked using flux-balance analysis in chemostat
cultures. Several useful predictions were obtained from in
silico experiments, including substrate preference. A minimal
medium for growth of N. meningitidis was designed and tested
successfully in batch and chemostat cultures. CONCLUSION: The
verified metabolic model describes the primary metabolism of N.
meningitidis in a chemostat in steady state. The genome-scale
model is valuable because it offers a framework to study N.
meningitidis metabolism as a whole, or certain aspects of it,
and it can also be used for the purpose of vaccine process
development (for example, the design of growth media). The flux
distribution of the main metabolic pathways (that is, the
pentose phosphate pathway and the Entner-Douderoff pathway)
indicates that the major part of pyruvate (69%) is synthesized
through the ED-cleavage, a finding that is in good agreement
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Project description:Deep sequencing of cDNA from Neisseria gonorrhoeae bacteria and human neutrophils, alone and after coincubation. Overall design: Total RNA was isolated from Neisseria gonorrhoeae strains FA1090/H041 and adherent primary human neutrophils, alone and after co-culture over time. Ribosomal RNA was depleted and the remaining RNA was reverse-transcribed into a cDNA library for Illumina sequencing. Reads were mapped to the FA1090, H041 and/or human genomes.