Showing papers by "Michael McClelland published in 2003"
TL;DR: This study shows that exposure of S. typhimurium to sublethal concentrations of CAMP activates the PhoP/PhoQ and RpoS virulence regulons, while repressing the transcription of genes required for flagella synthesis and the invasion‐associated type III secretion system.
Abstract: Summary Cationic antimicrobial peptides (CAMP) represent a conserved and highly effective component of innate immunity. During infection, the Gram-negative patho- gen Salmonella typhimurium induces different mech- anisms of CAMP resistance that promote pathogenesis in animals. This study shows that expo- sure of S. typhimurium to sublethal concentrations of CAMP activates the PhoP/PhoQ and RpoS virulence regulons, while repressing the transcription of genes required for flagella synthesis and the invasion- associated type III secretion system. We further dem- onstrate that growth of S. typhimurium in low doses of the a -helical peptide C18G induces resistance to CAMP of different structural classes. Inducible resis- tance depends on the presence of PhoP, indicating that the PhoP/PhoQ system can sense sublethal con- centrations of cationic antimicrobial peptides. Growth of S. typhimurium in the presence of CAMP also leads to RpoS-dependent protection against hydrogen per- oxide. Because bacterial resistance to oxidative stress and CAMP are induced during infection of ani- mals, CAMP may be an important signal recognized by bacteria on colonization of animal tissues.
257 citations
TL;DR: Results show that csrA controls a number of gene classes in addition to those required for invasion, some of them unique to Salmonella, and suggests a co‐ordinated bacterial response to conditions that exist at the site of bacterial invasion, the intestinal tract of a host animal.
Abstract: CsrA is a regulator of invasion genes in Salmonella enterica serovar Typhimurium. To investigate the wider role of CsrA in gene regulation, we compared the expression of Salmonella genes in a csrA mutant with those in the wild type using a DNA microarray. As expected, we found that expression of Salmonella pathogenicity island 1 (SPI-1) invasion genes was greatly reduced in the csrA mutant, as were genes outside the island that encode proteins translocated into eukaryotic cells by the SPI-1 type III secretion apparatus. The flagellar synthesis operons, flg and fli, were also poorly expressed, and the csrA mutant was aflagellate and non-motile. The genes of two metabolic pathways likely to be used by Salmonella in the intestinal milieu also showed reduced expression: the pdu operon for utilization of 1,2-propanediol and the eut operon for ethanolamine catabolism. Reduced expression of reporter fusions in these two operons confirmed the microarray data. Moreover, csrA was found to regulate co-ordinately the cob operon for synthesis of vitamin B12, required for the metabolism of either 1,2-propanediol or ethanolamine. Additionally, the csrA mutant poorly expressed the genes of the mal operon, required for transport and use of maltose and maltodextrins, and had reduced amounts of maltoporin, normally a dominant protein of the outer membrane. These results show that csrA controls a number of gene classes in addition to those required for invasion, some of them unique to Salmonella, and suggests a co-ordinated bacterial response to conditions that exist at the site of bacterial invasion, the intestinal tract of a host animal.
210 citations
TL;DR: Overall, almost one quarter of the entire S. enterica sv Typhimurium genome may have been introduced by LGT, which plays an important role in diversity among Salmonella.
138 citations
TL;DR: This non- redundant array was used to measure changes in gene copy number in DNA from actively growing versus stationary Typhi and to reveal the transcriptional response of Typhi to peroxide, a stress similar to that experienced when they are phagocytosed by macrophages.
Abstract: A microarray with sequences from the annotated open reading frames (ORFs) in Salmonella enterica subspecies 1, serovar Typhimurium was supplemented with annotated chromosomal ORFs from serovar Typhi that are divergent from Typhimurium (>10% DNA sequence divergence). This non- redundant array was used to (i) measure changes in gene copy number in DNA from actively growing versus stationary Typhi and (ii) to reveal the transcriptional response of Typhi to peroxide, a stress similar to that experienced when they are phagocytosed by macrophages. In S.enterica subspecies 1, pairs of genomes differ in the presence or absence of approximately 10% of their genes. An array twice the size of that needed to cover all ORFs for one genome could carry close homologs of all the ORFs for 10 genomes. Non-redundant DNA arrays could be constructed for any group of closely related organisms that differ by the presence and absence of a few genes.
77 citations
TL;DR: Expression microarray analyses combined with binding data promise new ways to identify stage specific cancer markers, to aid in patient risk assessment and in therapeutic choices.
Abstract: Egr1 is a multifunctional transcription factor regulating a remarkable spectrum of cellular responses from survival to apoptosis, growth to growth arrest, differentiation to transformation, senescence as well as memory and learning effects. In prostate cancer, Egr1 levels are constitutively high and closely linked to cancer development and progression. This zinc-finger protein is a short-lived, immediate early growth response gene known to be induced by a large number of extracellular stimuli such as irradiation (all wavelengths tested), hypoxia, hyperoxia, chemotherapy agents, and more. Therefore the target genes that Egr1 regulates in prostate cancer cells play an important role in generating many of the cellular responses that characterize these cells. After Egr1 binds to its binding sites on gene promoters, specificity of response is determined by whether Egr1 transcriptionally up- or downregulates the target genes. Expression microarray analyses combined with binding data promise new ways to identify stage specific cancer markers, to aid in patient risk assessment and in therapeutic choices.
63 citations
TL;DR: It is shown that the selection of MM cells for increased ECM‐independent local growth was accompanied by overexpression of macrophage migration inhibiting factor (MIF), an important modulator of both cell cycle progression and angiogenesis, and cathepsin Z, a novel member of the family of matrix degrading proteinases.
Abstract: Currently, the scale and consistency of changes of gene expression profiles in models of melanoma progression are largely unknown. Therefore, we investigated siblings of cell lines of malignant melanomas (MM), which have been selected by nude mouse passages for (a) increased tumorigenicity (local ECM-independent growth), (b) metastatic potential, or (c) selected for increased invasiveness using the Boyden chamber. cDNA array analysis surveying more than 27.000 transcripts per cell line showed that 1.5–2.8% of all detectable transcripts were consistently differentially regulated during the selection processes in those models. Using array analysis, we identified 33 individual transcripts that exhibited significant differential hybridization paralleling the increased aggressiveness of the selected progeny. Because some of those genes could play a significant functional role in the progression of MM, we additionally proved their regulative pattern using Northern blotting. Among others, progressive overexpression of osteonectin/SPARC, a molecule that is known to be involved in tissue remodeling and angiogenesis, was found in the selected offspring from all three experimental models and may therefore be considered as a potential marker for aggressive MM as well as a promising therapeutic target. We further show that the selection of MM cells for increased ECM-independent local growth was accompanied by overexpression of macrophage migration inhibiting factor (MIF), an important modulator of both cell cycle progression and angiogenesis, and cathepsin Z, a novel member of the family of matrix degrading proteinases.
61 citations
TL;DR: Comparative genomic hybridization revealed differences in gene content that indicate that even within a highly clonal bacterial population the genomic reservoir is unstable.
Abstract: We used a nonredundant microarray of the Salmonella enterica serovar Typhimurium LT2 and Typhi CT18 genomes to assess the genomic content of a diverse set of isolates of serovar Typhi. Comparative genomic hybridization revealed 13 regions of absent or divergent gene content in the eight Typhi strains examined compared to Typhi CT18. In particular, two Typhi CT18 prophage regions, STY1048 to STY1077 and STY2038 to STY2077, as well as a five-gene islet (STY3188 to STY3193) were absent or divergent in all other Typhi strains examined. Seven Typhi strains lacked most or all of the IS1 elements present in strain CT18, and three Typhi strains lacked a P4-like phage (STY4821 to STY4834). One strain was devoid of a 149-gene region (STY4521 to STY4680), which encodes numerous phage genes and the Vi antigen biosynthesis and export gene cluster, a type IV pilus, and numerous phage genes. In Typhi strain 26T25, an amplification of an entire inter-ribosomal region encompassing 31 genes has occurred. Furthermore, a 257-gene region (STY1360 to STY1639) showed an aberrant replication pattern in three Typhi isolates. Overall, these differences in gene content indicate that even within a highly clonal bacterial population the genomic reservoir is unstable.
55 citations
TL;DR: Despite its rare occurrence in humans and animals, Salmonella enterica serovar California was found to be the predominantserovar in Spanish feed mills.
Abstract: We performed an epidemiological study on Salmonella isolated from raw plant-based feed in Spanish mills. Overall, 32 different Salmonella serovars were detected. Despite its rare occurrence in humans and animals, Salmonella enterica serovar California was found to be the predominant serovar in Spanish feed mills. Different typing techniques showed that isolates of this serovar were genetically closely related, and comparative genomic hybridization using microarray technology revealed 23 S. enterica serovar Typhimurium LT2 gene clusters that are absent from serovar California.
42 citations
TL;DR: EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome, is described.
Abstract: We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.
31 citations
Patent•
25 Jun 2003
TL;DR: In this article, a method for detecting organisms by identifying the presence, absence, size or sequence polymorphism of intronic regions is presented. But the method involves selecting intronic region from nuclear or organellar gene sequences that are useful for differentiating between and among taxonomic groupings of organisms.
Abstract: The present invention provides novel methods for characterizing organisms by identifying the presence, absence, size or sequence polymorphism of intronic regions. The method involves selecting intronic regions from nuclear or organellar gene sequences that are useful for differentiating between and among taxonomic groupings of organisms. Such intronic regions can be analyzed directly or after amplification in a primer extension reaction. The amplification product is then analyzed by, for example, size fractionation, nucleotide sequencing or (RFLP). Intronic regions that contain an open reading frame encoding all or a portion of a protein can be used to generate antibodies to detect the presence or absence of the protein, which indicates the presence or absence of the intronic region. Methods of detecting an organism in a sample by detecting the presence or absence of one or more intronic regions also are provided using nucleic acid based or immunological based approaches. Kits are provided for practicing the methods of the invention.
1 citations