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At least 721 records · Page 40Linked to original sources
PubMed2006

7E olfactory receptor gene clusters and evolutionary chromosome rearrangements.

Olfactory receptor (OR) genes of the 7E subfamily have been duplicated to multiple regions throughout the human genome. Segmental duplications containing 7E OR genes have been associated with both pathological and evolutionary chromosome rearrangements. Many of these breakpoint regions coincide with breaks of chromosomal synteny in the mouse, rat and/or chicken genomes. Collectively, these data suggest that 7E OR-containing regions represent hot spots of genomic instability.

Animals↗
PubMed1997

Oral isotretinoin treatment policy. Do we all agree?

A consensus meeting was held in Brussels in 1995 to review current oral isotretinoin (Roaccutane/Accutane) treatment policies among internationally renowned experts and to improve service to needy patients by proposing treatment guidelines based upon a review of 1,000 acne patients who received this therapy. The group agreed that acne conditions warranting oral isotretinoin treatment include severe acne and poorly responsive acne which improves less than 50% after 6 months of therapy with combined oral and topical antibiotics. Furthermore, acne which relapses, scars or induces consequential psychological distress should be treated with oral isotretinoin. Other indications are gram-negative folliculitis, inflammatory rosacea such as rhinophyma, pyoderma faciale, acne fulminans and hidradenitis suppurativa. Treatment was usually initiated at a daily dose of 0.5 mg/kg (but may be higher) and increased to 1.0 mg/kg. Aiming at a total does of 120-150 mg/kg per treatment course treatment lasted 4-7 months depending upon daily doses. The same dosage guidelines were applied to repeated courses of oral isotretinoin therapy with no evidence of increased risk. Mucocutaneous side-effects were predictable; dose-dependent and systemic side-effects were rarely problematic. Acne patients gain immeasurable physical and emotional relief from isotretinoin treatment and society benefits from limiting bacterial resistance evolution and reducing health care costs.

Acne Vulgaris↗
PubMed2005

A computational approach for identifying pathogenicity islands in prokaryotic genomes.

BACKGROUND: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. RESULTS: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs. CONCLUSION: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.

Bacteria↗
PubMed2005

Genome-wide localization of mobile elements: experimental, statistical and biological considerations.

BACKGROUND: The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial isolates. The information about the genomic locations of IS elements is available in public sequence databases. However, the locations of mobile elements may vary from strain to strain and within the population of an individual strain. Tools that allow de novo localization of IS elements and are independent of existing sequence information are essential to map insertion elements and advance our knowledge of the role that such elements play in gene regulation and genome plasticity in bacteria. RESULTS: In this study, we present an efficient and reliable method for linear mapping of mobile elements using whole-genome DNA microarrays. In addition, we describe an algorithm for analysis of microarray data that can be applied to find DNA sequences physically juxtaposed with a target sequence of interest. This approach was used to map the locations of the IS5 elements in the genome of Escherichia coli K12. All IS5 elements present in the E. coli genome known from GenBank sequence data were identified. Furthermore, previously unknown insertion sites were predicted with high sensitivity and specificity. Two variants of E. coli K-12 MG1655 within a population of this strain were predicted by our analysis. The only significant difference between these two isolates was the presence of an IS5 element upstream of the main flagella regulator, flhDC. Additional experiments confirmed this prediction and showed that these isolates were phenotypically distinct. The effect of IS5 on the transcriptional activity of motility and chemotaxis genes in the genome of E. coli strain MG1655 was examined. Comparative analysis of expression profiles revealed that the presence of IS5 results in a mild enhancement of transcription of the flagellar genes that translates into a slight increase in motility. CONCLUSION: In summary, this work presents a case study of an experimental and analytical application of DNA microarrays to map insertion elements in bacteria and gains an insight into biological processes that might otherwise be overlooked by relying solely on the available genome sequence data.

DNA Transposable Elements↗
PubMed2006

Nucleotide sequences and organization of the genes for carotovoricin (Ctv) from Erwinia carotovora indicate that Ctv evolved from the same ancestor as Salmonella typhi prophage.

Carotovoricin Er (CtvEr), which is produced by a plant soft rot disease causative agent, Erwinia carotovora subsp. carotovora Er, is a high-molecular-weight bacteriocin showing Myoviridae phage-tail-like morphology with contractile sheath and plural tail fibers. We determined the complete nucleotide sequences of CtvEr genes on the E. carotovora Er chromosome and report that CtvEr genes consist of lysis cassette, major and minor structural protein gene clusters. Four promoters were identified. The lysis gene cassette, which is composed of the genes for lysis enzyme and holin, was also identified and characterized. The nucleotide sequences and organization of the genes for CtvCGE, which is produced by E. carotovora strain CGE234-M403 with the morphology similar to CtvEr, were also determined and compared to that of CtvEr, and it was found that CtvCGE is almost identical to CtvEr except for tail fibers which are involved in the killing spectra of both bacteriocins. We also explain that the gene organization and the deduced amino acid sequences of both carotovoricins are very close to those of prophage, which is lysogenized in the chromosome on Salmonella enterica serovar Typhi CT18. These findings strongly suggest that Ctv evolved as a phage tail-like bacteriocin from a common ancestor with Salmonella typhi prophage.

Amino Acid Sequence↗
PubMed2006

An integrative method for accurate comparative genome mapping.

We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying "maximal similar segments," and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes.

Algorithms↗
PubMed2006

The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci.

The innate and adaptive immune systems of vertebrates possess complementary, but intertwined functions within immune responses. Receptors of the mammalian innate immune system play an essential role in the detection of infected or transformed cells and are vital for the initiation and regulation of a full adaptive immune response. The genes for several of these receptors are clustered within the leukocyte receptor complex (LRC). The purpose of this study was to carry out a detailed analysis of the chicken (Gallus gallus domesticus) LRC. Bacterial artificial chromosomes containing genes related to mammalian leukocyte immunoglobulin-like receptors were identified in a chicken genomic library and shown to map to a single microchromosome. Sequencing revealed 103 chicken immunoglobulin-like receptor (CHIR) loci (22 inhibitory, 25 activating, 15 bifunctional, and 41 pseudogenes). A very complex splicing pattern was found using transcript analyses and seven hypervariable regions were detected in the external CHIR domains. Phylogenetic and genomic analysis showed that CHIR genes evolved mainly by block duplications from an ancestral inhibitory receptor locus, with transformation into activating receptors occurring more than once. Evolutionary selection pressure has led not only to an exceptional expansion of the CHIR cluster but also to a dramatic diversification of CHIR loci and haplotypes. This indicates that CHIRs have the potential to complement the adaptive immune system in fighting pathogens.

Alternative Splicing↗
PubMed2005

Identification of a genomic island of Actinobacillus actinomycetemcomitans.

BACKGROUND: Horizontal gene transfer (HGT) is a process by which bacteria acquire genes from organisms of distant taxa. HGT is now recognized as a major driving force in the evolution of bacterial pathogens. Through this process, bacteria may accumulate blocks of DNA such as genomic islands (GEIs) that encode fitness or virulence factors. The periodontal pathogen A. actinomycetemcomitans has been known to exhibit variable virulence potential. It is postulated that GEIs may play a role in modifying the virulence potential of A. actinomycetemcomitans. This study was initiated to identify and determine the distribution of GEIs in A. actinomycetemcomitans. METHODS: Forty-seven A. actinomycetemcomitans strains of serotypes a through f were examined. Strain-specific variant DNA in the genomes of A. actinomycetemcomitans was identified by polymerase chain reaction (PCR) genomic mapping and sequenced to identify GEIs. The distribution of the GEIs among test strains of A. actinomycetemcomitans was determined by PCR analysis and Southern hybridization assays. RESULTS: An approximately 22 kb GEI of A. actinomycetemcomitans, designated AAI-1, was identified in five serotype b strains. The AAI-1 exhibits low %G+C and encodes proteins of phage, restriction modification systems, mobile elements, and other hypothetical proteins of unknown functions. The insertion of AAI-1 was found to cause truncation of A. actinomycetemcomitans genes at the insertion site. CONCLUSIONS: Some A. actinomycetemcomitans strains may harbor GEIs, which were acquired via HGT by the bacteria. The GEIs may increase the gene repertoire of A. actinomycetemcomitans. However, the insertion of the GEIs in A. actinomycetemcomitans may also cause truncation and inactivation of resident genes at the insertion sites. The virulence significance of such gain and loss of genes in A. actinomycetemcomitans remains to be determined.

Aggregatibacter actinomycetemcomitans↗
PubMed2004

Vancomycin susceptibility within methicillin-resistant Staphylococcus aureus lineages.

Methicillin-resistant Staphylococcus aureus (MRSA) with reduced vancomycin susceptibility vancomycin-intermediate S. aureus (VISA) has been reported from many countries. Whether resistance is evolving regularly in different genetic backgrounds or in a single clone with a genetic predisposition, as early results suggest, is unclear. We have studied 101 MRSA with reduced vancomycin susceptibility from nine countries by multilocus sequence typing (MLST), characterization of SCCmec (staphylococcal chromosomal cassette mec), and agr (accessory gene regulator). We found nine genotypes by MLST, with isolates within all five major hospital MRSA lineages. Most isolates (88/101) belonged to two of the earliest MRSA clones that have global prevalence. Our results show that reduced susceptibility to vancomycin has emerged in many successful epidemic lineages with no clear clonal disposition. Increasing antimicrobial resistance in genetically distinct pandemic clones may lead to MRSA infections that will become increasingly difficult to treat.

Anti-Bacterial Agents↗
PubMed2006

Predominance of ancestral lineages of Mycobacterium tuberculosis in India.

Although India has the highest prevalence of tuberculosis (TB) worldwide, the genetic diversity of Mycobacterium tuberculosis in India is largely unknown. A collection of 91 isolates originating from 12 different regions spread across the country were analyzed by genotyping using 21 loci with variable-number tandem repeats (VNTRs), by spoligotyping, by principal genetic grouping (PGG), and by deletion analysis of M. tuberculosis-specific deletion region 1. The isolates showed highly diverse VNTR genotypes. Nevertheless, highly congruent groupings identified by using the 4 independent sets of markers permitted a clear definition of 3 prevalent PGG1 lineages, which corresponded to the "ancestral" East African-Indian, the Delhi, and the Beijing/W genogroups. A few isolates from PGG2 lineages and a single representative of the presumably most recent PGG3 were identified. These observations suggest a predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, which supports the hypothesis that India is an ancient endemic focus of TB.

Adult↗
PubMed1999

[French National Institute for observation of prescriptions and consumption of medicines. Prescription and consumption of antibiotics in ambulatory care].

The National Research Institute for Prescriptions and Consumption of medicines which was founded under the authority of the Minister of Health, is charged with the following missions: improved evaluation of the therapeutic needs of the population; more precise knowledge of therapeutic management; the identification of possible deviations in relation to systems of reference; recommendations in favor of correct use of medicines; and the optimization of patient management. Its first report concerned the antibiotic therapy of respiratory infections. In France, the average annual increase rate of the frequency of antibiotics consumption was in the region of 3.7%, between the periods 1980-1981 and 1991-1992. It essentially concerned cephalosporins and quinolones. Between 1991 and 1996 antibiotics sales increased on average by 2.1%, in units, per year. The increase of this consumption, which was not justified by any epidemiological evolution, is partly explained by the high frequency of antibiotic prescriptions during respiratory or ENT affections presumed to be of viral etiology: in 40% of rhinopharyngitis, 80% of acute bronchitis and more than 90% of anginas, whatever the age. Moreover the antibiotic treatments were not prescribed optimally: too long duration, insufficient dosages. Such phenomena are disturbing with regard to their consequences on the evolution of bacterial resistances. A comparison between French practices and those of Germany and the United Kingdom suggests that recourse to treatment is more frequent in France for the infectious diseases mentioned above, with more intensive utilization of antibiotics, in particular broad-spectrum penicillins. Recommendations have been made in favor of a rationalisation of practices.

Ambulatory Care↗
PubMed2001

[Homologous recombination and chromosomal rearrangements in Escherichia coli strains carrying a heterozygous tandem duplication].

Heterozygous tandem duplications formed in conjugational matings in Escherichia coli provides a convenient model system for studying the evolution of bacterial chromosome. Heterozygous duplications segregate various classes of haploid and diploid recombinants that appear as a result of unequal crossing over between sister chromosomes. In this work, an extended tandem duplication in the deo operon of E. coli carrying deoA deoB::Tn5/deoC deoD thr::Tn9 alleles was examined. Recombination between homologous DNA repeats in the duplication was studied in strains carrying different combinations of recBC, sbcBC, recB::Tn10, recQ::Tn3 mutations. The frequency of recombination between homologous DNA repeats was very high in all strains and did not decrease when the RecBCD and RecF recombinational pathways were simultaneously damaged in strains with the recB sbcBC recQ (or recF) genotype. It is assumed that unequal crossing over between direct DNA repeats in duplications may proceed through a particular pathway of "adaptive" recombination.

Alleles↗
PubMed2001

[Mycoplasma].

Explore the source record for details and available documents.

Animals↗
PubMed2002

Molecular characteristics of Neisseria meningitidis strains isolated in Burkina Faso in 2001.

In the course of an epidemic of meningitis in Burkina Faso in 2001, 27 cerebrospinal fluid samples from patients in 7 districts were forwarded to Norway for isolation and characterization of the causative agents. Neisseria meningitidis was isolated from 13 (48%) samples. The isolates were analysed using serological and genetic methods. Of the 13 strains, 4 were serogroup A, serotype 21:P1.9, sequence type (ST)-5 and belonged to clonal subgroup III, while the remaining 9 strains were serogroup W135, serotype 2a:P1.5,2, ST-11 and belonged to the electrophoretic type-37 complex. PCR analyses revealed meningococcal DNA in 13/14 culture-negative samples. Sequence analysis of the PCR products demonstrated that at least 3 different meningococcal strains were responsible for these 13 cases. Our results show that the W135 strain associated with the 2000 hajj (Muslim pilgrimage) outbreak was a significant cause of disease in Burkina Faso in 2001. Further studies are warranted to determine whether W135 is about to replace serogroup A in sub-Saharan Africa.

Adolescent↗
PubMedDate not supplied

[Gene typing of infectious tularemia strains isolated from the Stavropol and Krasnodar Territories].

The typing of F. tularensis strains by four variable number of tandem repeats (VNTR) loci has been carried out. Among the strains isolated in the Stavropol and Krasnodar Territories seven genotypes have been detected and their spread in different natural foci has been analyzed. The data thus obtained suggest that the VNTR analysis may become an important instrument for studying the structure of the natural foci of tularemia and evolutionary relationships between individual areas of these foci.

Alleles↗