ABSTRACT
The CRISPR-Cas system is involved in bacterial immunity, virulence, gene regulation, biofilm formation and sporulation. In Salmonella enterica serovar Typhi, this system consists of five transcriptional units including antisense RNAs. It was determined that these genetic elements are expressed in minimal medium and are up-regulated by pH. In addition, a transcriptional characterization of cas3 and ascse2-1 is included herein.
Subject(s)
CRISPR-Associated Proteins/genetics , CRISPR-Cas Systems/genetics , DNA Helicases/genetics , Gene Expression Regulation, Bacterial/genetics , RNA, Antisense/genetics , Salmonella typhi/genetics , Chloramphenicol O-Acetyltransferase/metabolism , Electrophoretic Mobility Shift Assay , Transcription, Genetic/genetics , Transcriptional Activation/genetics , Up-Regulation/geneticsABSTRACT
Recent evidence suggests that most influenza A virus gene segments can contribute to the pathogenicity of the virus. In this regard, the hemagglutinin (HA) subtype of the circulating strains has been closely surveyed, but the reassortment of internal gene segments is usually not monitored as a potential source of an increased pathogenicity. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origins of the eight segments of the influenza virus genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 neuraminidase (NA) subtypes. Viral genetic material was amplified by reverse transcription-PCR (RT-PCR) with primers specific to the conserved 5' and 3' ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3 labeling. The microarray unambiguously determined the clades for all eight influenza virus genes in 74% (28/38) of the samples. The microarray was validated with reference strains from different animal origins, as well as from human, swine, and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed for the determination of the time and place that strains with the same genomic pattern were previously reported. PhyloFlu is useful for characterizing and surveying the genetic diversity and variation of animal viruses circulating in different environmental niches and for obtaining a more detailed surveillance and follow up of reassortant events that can potentially modify virus pathogenicity.
Subject(s)
DNA Fingerprinting/methods , Genome, Viral , Genotyping Techniques/methods , Influenza A virus/classification , Influenza, Human/virology , Microarray Analysis/methods , Paramyxoviridae Infections/veterinary , Animals , Cluster Analysis , Humans , Influenza A virus/genetics , Influenza A virus/isolation & purification , Paramyxoviridae Infections/virology , Phylogeny , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction , Virology/methodsABSTRACT
The transcriptional network of Escherichia coli is currently the best-understood regulatory network of a single cell. Motivated by statistical evidence, suggesting a hierarchical modular architecture in this network, we identified eight modules with well-defined physiological functions. These modules were identified by a clustering approach, using the shortest path to trace regulatory relationships across genes in the network. We report the type (feed forward and bifan) and distribution of motifs between and within modules. Feed-forward motifs tend to be embedded within modules, whereas bi-fan motifs tend to link modules, supporting the notion of a hierarchical network with defined functional modules.
