Search results for " GENOMICS"
showing 10 items of 390 documents
Listeria monocytogenes Differential Transcriptome Analysis Reveals Temperature-Dependent Agr Regulation and Suggests Overlaps with Other Regulons
2012
Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its Delta agrA mutant at the saprophytic temperature of 25 degrees C and in vivo temperature of 37 degrees C. Variations of transcriptome were higher at 37 degrees C than at 25 degrees C. Results suggested that AgrA may be involved in the regu…
The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps
2015
Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium "Candidatus Tremblaya" maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have "Candidatus Tremblaya phenacola" as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every "Candidatus Tremblaya princeps" cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, co…
Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth.
2013
Abstract Background In all branches of life there are plenty of symbiotic associations. Insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. Essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps. Results We report the genome sequencing …
Genomics of intracellular symbionts in insects
2010
Endosymbiotic bacteria play a vital role in the evolution of many insect species. For instance, endosymbionts have evolved metabolically to complement their host's natural diet, thereby enabling them to explore new habitats. In this paper, we will review and give some examples of the nature of the metabolic coupling of different primary and secondary endosymbionts that have evolved in hosts with different nutritional diets (i.e., phloem, xylem, blood, omnivores, and grain). Particular emphasis is given to the evolutionary functional convergence of phylogenetically distant endosymbionts, which are evolving in hosts with similar diets.
Comparative genomics of yeast species: new insights into their biology
2003
The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of D…
Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
2021
A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, m…
Isolation and Characterization of High-Efficiency Rhizobia From Western Kenya Nodulating With Common Bean.
2021
Common bean is one of the primary protein sources in third-world countries. They form nodules with nitrogen-fixing rhizobia, which have to be adapted to the local soils. Commercial rhizobial strains such as Rhizobium tropici CIAT899 are often used in agriculture. However, this strain failed to significantly increase the common bean yield in many places, including Kenya, due to the local soils’ low pH. We isolated two indigenous rhizobial strains from the nodules of common bean from two fields in Western Kenya that have never been exposed to commercial inocula. We then determined their ability to fix nitrogen in common beans, solubilize phosphorus, and produce indole acetic acid. In greenhou…
Live genomics for pathogen monitoring in public health.
2014
Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in a short lapse of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the “local” level, such as in the event of a recurrent …
Effects of different simplified milk recording methods on genetic evaluation with Test-Day animal model
2007
The aims of the present study were to compare estimated breeding values (EBV) for milk yield using different testing schemes with a test-day animal model and to evaluate the effect of different testing schemes on the ranking of top sheep. Alternative recording schemes that use less information than that currently obtained with a monthly test-day schedule were employed to estimate breeding values. A random regression animal mixed model that used a spline function of days in milk was fitted. EBVs obtained with alternative recording schemes showed different degrees of Spearman correlation with EBVs obtained using the monthly recording scheme. These correlations ranged from 0.77 to 0.92. A redu…
Comprehensive yeast genome database (CYGD)
2015
Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.