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Global Stage-Specific Gene Regulation during the Developmental Cycle of Chlamydia trachomatis. Tracy L. Nicholson, 2003.Distinct morphological changes associated with the complex development cycle of the obligate intracellular bacterial pathogen Chlamydia trachomatis have been historically well characterized by microscopy . A number of temporally regulated genes have been characterized previously, suggesting that the chlamydial developmental cycle is regulated at the transcriptional level . This hypothesis was tested by microarray analysis in which the entire C . trachomatis genome was analyzed, providing a comprehensive assessment of global gene regulation throughout the chlamydial developmental cycle . Seven temporally cohesive gene clusters were identified, with 22% (189 genes) of the genome differentially expressed during the developmental cycle . The correlation of these gene clusters with hallmark morphological events of the chlamydial developmental cycle suggests three global stage-specific networks of gene regulation . Repression of the Staphylococcus aureus Accessory Gene Regulator in Serum and In Vivo. Jeremy M. Yarwood, 2002.Subgenomic DNA microarrays were employed to evaluate the expression of the accessory gene regulator (agr locus) as well as multiple virulence-associated genes in Staphylococcus aureus . Gene expression was examined during growth of S . aureus in vitro in standard laboratory medium and rabbit serum and in vivo in subcutaneous chambers implanted in either nonimmune rabbits or rabbits immunized with staphylococcal enterotoxin B . Expression of RNAIII, the effector molecule of the agr locus, was dramatically repressed in serum and in vivo, despite the increased expression of secreted virulence factors sufficient to cause toxic shock syndrome (TSS) in the animals . Statistical analysis and clustering of virulence genes based on their expression profiles in the various experimental conditions demonstrated no positive correlation between the expression of agr and any staphylococcal virulence factors examined . Disruption of the agr locus had only a minimal effect on the expression in vivo of the virulence factors examined . An effect of immunization on the expression of agr and virulence factors was also observed . These results suggest that agr activation is not necessary for development of staphylococcal TSS and that regulatory circuits responding to the in vivo environment override agr activity . Effects of Alternative Dietary Substrates on Competition between Human Colonic Bacteria in an Anaerobic Fermentor System. Sylvia H. Duncan, 2003.Duplicate anaerobic fermentor systems were used to examine changes in a community of human fecal bacteria supplied with different carbohydrate energy sources . A panel of group-specific fluorescent in situ hybridization probes targeting 16S rRNA sequences revealed that the fermentors supported growth of a greater proportion of Bacteroides and a lower proportion of gram-positive anaerobes related to Faecalibacterium prausnitzii, Ruminococcus flavefaciens-Ruminococcus bromii, Eubacterium rectale-Clostridium coccoides, and Eubacterium cylindroides than the proportions in the starting fecal inoculum . Nevertheless, certain substrates, such as dahlia inulin, caused a pronounced increase in the number of bacteria related to R . flavefaciens-R . bromii and E . cylindroides. The ability of three strictly anaerobic, gram-positive bacteria to compete with the complete human fecal flora was tested in the same experiment by using selective plating to enumerate the introduced strains . The Roseburia-related strain A2-183F was able to grow on all substrates despite the fact that it was unable to utilize complex carbohydrates in pure culture, and it was assumed that this organism survived by cross-feeding . In contrast, Roseburia intestinalis L1-82R and Eubacterium sp . strain A2-194R survived less well despite the fact that they were able to utilize polysaccharides in pure culture, except that A2-194R was stimulated 100-fold by inulin . These results suggest that many low-G+C-content gram-positive obligate anaerobes may be selected against during in vitro incubation, although several groups were stimulated by inulin . Thus, considerable caution is necessary when workers attempt to predict the in vivo effects of probiotics and prebiotics from their effects in vitro . Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics. Newton C. Marcial Gomes, 2003.The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data . Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years . A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing . A rhizosphere effect was observed for fungal populations at all stages of plant development . In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE . Similar types of fingerprints were observed in two consecutive growth periods . No major differences were detected in the fungal patterns of the two cultivars . Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands . The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced . The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands . Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants .
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