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random priming pcr strategy to amplify and clone trace amounts of dna.here we report a new methodology to study trace amounts of dna of unknown sequence using a two-step pcr strategy to amplify and clone target dna. the first pcr is carried out with a partial random primer comprised of a specific 21-nucleotide 5' sequence, a random heptamer, and a 3' tggc clamp. the second pcr is carried out with a single 19-nucleotide primer that matches the specific 5' sequence of the partial random primer. using human and mycoplasma genitalium dna as examples, we demonstrated t ...200314579741
the presence of bacteria in the synovial fluid of the temporomandibular joint and clinical significance: preliminary study.the objective of this study was to find any relation between the presence of specific bacterial species in the synovial fluid of the temporomandibular joint (tmj) and clinical parameters.200314586850
the pyruvate dehydrogenase complex of mycoplasma hyopneumoniae contains a novel lipoyl domain arrangement.the genes encoding the pyruvate dehydrogenase (pdh) complex (pdha, pdhb, pdhc and pdhd) from mycoplasma hyopneumoniae have been cloned and sequenced. the genes are arranged into two operons, designated pdhab and pdhcd, which are not found together in the chromosome. the pdha, pdhb, pdhc and pdhd genes encode proteins of predicted molecular masses of 44.2 kda (pyruvate dehydrogenase major subunit; e1alpha), 36.6 kda (pyruvate dehydrogenase minor subunit; e1beta), 33.1 kda (dihydrolipoyl acetyltra ...200314597175
estimating the accuracy of polymerase chain reaction-based tests using endpoint dilution.polymerase chain reaction (pcr)-based tests for various microorganisms or target dna sequences are generally acknowledged to be highly "sensitive," yet the concept of sensitivity is ill-defined in the literature on these tests. we propose that sensitivity should be expressed as a function of the number of target dna molecules in the sample (or specificity, when the target number is 0). however, estimating this "sensitivity curve" is problematic, since it is difficult to construct samples with a ...200314601751
gene essentiality determines chromosome organisation in bacteria.in escherichia coli and bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. although essential genes tend to be coded in the leading replicating strand, the underlying selective constraints and the evolutionary extent of these findings have still not been subject to comparative studies. here, we extend our previous analysis to the genomes of low g + c firmicutes and gamma-proteobacteria, and in a second step to all sequenced ba ...200314602916
[mycoplasma genitalium--a reply]. 200314619068
[genital mycoplasmas].the mycoplasmas frequently isolated in genital tract, and potentially pathogenic, are m. hominis, u. urealyticum and m. genitalium. m. hominis and u. urealyticum are very frequent in the vaginal tract and they can be, according to circumstances, either commensal or pathogenic. m. hominis and/or u. urealyticum, have been considered as responsible for many types of genital infectious diseases (such as cervicitis, pelvis inflammatory disease), for infertility, obstetrical pathologies (premature del ...200314623561
transcriptional starts for cytadherence-related operons of mycoplasma genitalium.one mechanism of mycoplasma cytadherence possessed by several mycoplasmas, including mycoplasma genitalium, necessitates coordination of multiple adhesins and adherence-associated proteins. the genes encoding these adherence-related proteins are located in three different regions of the m. genitalium genome and exhibit an operon-like organization with surrounding genes. to understand whether genes encoding adherence-related proteins in m. genitalium are regulated as operons, we performed transcr ...200314659545
mycoplasma genitalium: the aetiological agent of urethritis and other sexually transmitted diseases.mycoplasma genitalium was first isolated in 1980 from two of 13 men with non-gonococcal urethritis (ngu). it shares several features with m. pneumoniae, a recognized respiratory tract pathogen. it is extremely difficult to isolate by culture. the development of sensitive and specific polymerase chain reaction (pcr) assays in the early 1990s made clinical studies possible and a significant number of publications have shown a strong association between m. genitalium and ngu, independent of chlamyd ...200414678525
molligen, a database dedicated to the comparative genomics of mollicutes.bacteria belonging to the class mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. at this time six genome sequences have been publicly released (mycoplasma genitalium, mycoplasma pneumoniae, ureaplasma urealyticum-parvum, mycoplasma pulmonis, mycoplasma penetrans and mycoplasma gallisepticum) and as the number of available mollicute genomes inc ...200414681420
diagnostic assessment of mycoplasma genitalium in culture-positive women.detection of mycoplasma genitalium-mediated, chlamydia-negative nongonococcal urethritis and other m. genitalium-linked infectious etiologies has been very challenging. although m. genitalium is considered a leading cause of genitourinary symptoms in men and women, extreme difficulties in its cultivation due to its highly fastidious nature and the lack of routine and effective diagnostic tests have slowed the generation of clinical data which directly implicate the presence of m. genitalium in d ...200414715754
use of taqman 5' nuclease real-time pcr for quantitative detection of mycoplasma genitalium dna in males with and without urethritis who were attendees at a sexually transmitted disease clinic.mycoplasma genitalium is a cause of nongonococcal urethritis, particularly in patients not infected with chlamydia trachomatis. a quantitative 5' nuclease assay (taqman pcr) was developed and validated. the assay detected a fragment of the mgpa adhesin gene by use of a taqman mgb (minor groove binder) probe and included an internal processing control to detect pcr inhibition. urethral swab specimens and first-void urine samples from m. genitalium-positive men were examined, and the m. genitalium ...200414766837
determination of infectious load of mycoplasma genitalium in clinical samples of human vaginal cells.mycoplasma genitalium is a leading cause of chlamydia-negative, nongonoccocal urethritis and has been directly implicated in numerous other genitourinary as well as extragenitourinary tract pathologies. detection of m. genitalium has relied almost entirely on pcr amplification of clinical specimens and evidence of seroconversion since these mycoplasmas are highly fastidious and culture isolation by microbiological techniques is very rare. we have established a combinatorial strategy using confoc ...200414766847
mycoplasma genitalium in chronic non-gonococcal urethritis.seventy-eight men with a history of chronic urethritis were referred for investigation. of 52 men diagnosed as having persistent or recurrent non-gonococcal urethritis (ngu) at the time of referral, 11 (21%) were infected with mycoplasma genitalium and three with chlamydia trachomatis. men who were m. genitalium-positive had not previously received less antibiotic, in terms of treatment duration, than those who were m. genitalium-negative, suggesting a possible resistance to the antibiotics give ...200414769166
evolution. transitions from nonliving to living matter. 200414963315
evolutionary lability of context-dependent codon bias in bacteria.in bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. in particular, we focus on two contextual biases previously identified in escherichia coli; the avoidance of out-of-frame stop ...200010754070
simultaneous detection and identification of common cell culture contaminant and pathogenic mollicutes strains by reverse line blot hybridization.we have developed a reverse line blot (rlb) hybridization assay to detect and identify the commonest mollicutes causing cell line contamination (mycoplasma arginini, mycoplasma fermentans, mycoplasma hyorhinis, mycoplasma orale, and acholeplasma laidlawii) and human infection (mycoplasma pneumoniae, mycoplasma hominis, mycoplasma genitalium, ureaplasma parvum, and ureaplasma urealyticum). we developed a nested pcr assay with "universal" primers targeting the mollicute 16s-23s rrna intergenic spa ...200415006769
dna methylation and mycoplasma genomes.dna methylation is one of the many hypotheses proposed to explain the observed deficiency in cpg dinucleotides in a variety of genomes covering a wide taxonomic distribution. recent studies challenged the methylation hypothesis on empirical grounds. first, it cannot explain why the mycoplasma genitalium genome exhibits strong cpg deficiency without dna methylation. second, it cannot explain the great variation in cpg deficiency between m. genitalium and m. pneumoniae that also does not have cpg- ...200315008400
essential eukaryotic core.the aids-related fungal pathogen pneumocystis carinii is unusual in having a remarkably compact genome of 7.7 megabase pairs (mbp) whose small size presents the opportunity to identify the essential eukaryotic core of genes. the essential eukaryotic core is defined to be a collection of essential genes shared by all eukaryotes. sequencing the 3' ends of more than 5500 cdnas from p. carinii allowed us to identify about 200 genes shared with its nearest known but distant relative, schizosaccharomy ...200415068361
comparison of multiplex pcr assay with culture for detection of genital mycoplasmas.ureaplasma, spp. mycoplasma genitalium, and mycoplasma hominis are associated with infection of the genitourinary tract, reproductive failure, and neonatal morbidity and mortality. we have developed a multiplex pcr for the detection of these mycoplasmatales in a single amplification reaction. the analytical sensitivities of this assay were 10.8, 10.8, and 8.8 cfu for each organism, respectively. this multiplex pcr was compared to culture on 26 cervical swabs, 2 vaginal swabs, 4 female urine spec ...200415070999
geneorder3.0: software for comparing the order of genes in pairs of small bacterial genomes.an increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. in parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. geneorder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. it was originally developed for comparing virus, mitochondrion and chloroplast genomes. th ...200415128433
[studies on the infection status of seven species mycoplasma, three species of chlamydia, neisseria gonorrhoeae and garderella vaginalis in 76 patients with sexual transmitted diseases].to study the infectious status of seven species of mycoplasma, three species of chlamydia, neisseria gonorrhoeae and garderella vaginalis in the 76 male sexual transmitted disease (std) patients in yangzhou city.200415132870
a conserved hypothetical protein from mycoplasma genitalium shows structural homology to nusb proteins. 200415146506
shaping and moving a spiroplasma.the mollicutes (spiroplasma, mycoplasma and acholeplasma) are the most minimal cells known to exist, being the smallest and simplest free-living and self-replicating forms of life. phylogenetically, the mollicutes are related to gram-positive bacteria and have evolved, by regressive evolution and genome reduction, from clostridia. the smallest genome in this group (mycoplasma genitalium - 5.77 x 10(5) bp) is only twice that of a large virus (e.g., entomopox viruses). the largest mollicute genome ...200415170406
quantifying intrachromosomal gc heterogeneity in prokaryotic genomes.the sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (gc) heterogeneity, largely in view of lateral transfers. we present here a brief overview of some methods for visualizing and quantifying gc variation in prokaryotes. we used these methods to examine heterogeneity levels in sequenced prokaryotes, for a range of scales or stringencies. some species are consistently homogeneous, whereas others are markedly heterogen ...200415177687
characterization of sodium dodecylsulfate polyacrylamide gel electrophoresis-separated m. agalactiae membrane antigens by mass spectrometry.mycoplasma membrane proteins are generally designated according to their apparent molecular weight measured by sds-page. several results about mycoplasma membrane antigens are conflicting because some doubts are emerging about the accuracy of the method utilised to identify the antigens. aim of this work, was to characterise proteins separated after sodium dodecylsulfate polyacrylamide gel electrophoresis (sds-page)-mass spectrometry to allow an uncontroversial designation of the antigens. fifte ...200415187300
comparison of first void urine and urogenital swab specimens for detection of mycoplasma genitalium and chlamydia trachomatis by polymerase chain reaction in patients attending a sexually transmitted disease clinic.the objective of this study was to compare urogenital swab specimens and first void urine (fvu) specimens from male and female patients at a sexually transmitted disease clinic for the detection of mycoplasma genitalium and chlamydia trachomatis infections using in-house, inhibitor-controlled polymerase chain reaction (pcr).200415273584
symptomatic urethritis is more prevalent in men infected with mycoplasma genitalium than with chlamydia trachomatis.to study the prevalence, symptoms, and signs of mycoplasma genitalium and chlamydia trachomatis infections in men attending a swedish std clinic and to study the criteria for urethritis.200415295128
[up to date in sexually transmitted infections: epidemiology, diagnostic approaches and treatments].in the last years, there have been important advances in sexually transmitted infections such as genome sequencing of treponema pallidum, chlamydia trachomatis or mycoplasma genitalium; the new taxonomic position of calymmatobacterium granulomatis; commercial diagnostic systems based on nucleic acid amplification; the emergence of quinolone resistance in neisseria gonorrhoeae; new therapeutic approaches in vulvovaginal candidiasis that include boric acid; the demonstration that valacyclovir redu ...200415355770
aetiology of male urethritis in patients recruited from a population with a high hiv prevalence.the aetiology of urethritis, the significance of potential pathogens and the relation of urethritis to hiv infection were determined in 335 men (cases) with and 100 men (controls) without urethral symptoms. urethral swab specimens were tested for different organisms by pcr or by culture for neisseria gonorrhoeae. the prevalence of n. gonorrhoeae and chlamydia trachomatis was 52 and 16%, respectively. the potential pathogens: mycoplasma genitalium, ureaplasma urealyticum, trichomonas vaginalis an ...200415364299
mycoplasma genitalium urethritis in men.mycoplasma genitalium was first isolated from two men with non-gonococcal urethritis (ngu) and thereafter shown to produce urethritis in subhuman primates, inoculated intraurethrally. this mycoplasma has been detected significantly more often in patients with acute ngu, particularly in patients with non-chlamydial ngu, than in subjects without urethritis. the prevalence of m. genitalium-positive non-chlamydial ngu ranges from 18 to 46% of all non-chlamydial ngu cases. in addition, the persistenc ...200415364301
detection of mycoplasma genitalium, mycoplasma hominis, ureaplasma parvum (biovar 1) and ureaplasma urealyticum (biovar 2) in patients with non-gonococcal urethritis using polymerase chain reaction-microtiter plate hybridization.to use polymerase chain reaction (pcr)-microtiter plate hybridization assays to detect mycoplasma genitalium, mycoplasma hominis, ureaplasma parvum (biovar 1) and ureaplasma urealyticum (biovar 2) in first-voided urine specimens from patients with non-gonococcal urethritis (ngu).200415379939
high prevalence of genital mycoplasmas among sexually active young adults with urethritis or cervicitis symptoms in la crosse, wisconsin.sexually active young adults in the small college town of la crosse, wisconsin, were evaluated for conventional sexually transmitted pathogens and tested for infections with mycoplasmas. the prevalence in 65 symptomatic men or women and 137 healthy volunteers (67 men and 70 women) was compared. urine specimens from both cohorts were tested by ligase chain reaction for chlamydia trachomatis or neisseria gonorrhoeae. in addition, the urethral or cervical swabs from the symptomatic subjects were te ...200415472322
single-nucleotide polymorphisms in the rrna operon and variable numbers of tandem repeats in the lipoprotein gene among mycoplasma genitalium strains from clinical specimens.we characterized the single-nucleotide polymorphisms in the rrna operon and variable numbers of tandem repeats in the lipoprotein gene mg309 among mycoplasma genitalium strains from clinical specimens by pcr and sequencing. analysis of 31 m. genitalium-infected patient specimens and 7 american type culture collection strains identified six types of rrna sequences and 11 different numbers of mg309 repeats. examination of sequential specimens from 10 patients showed that these genotypes were stabl ...200415472369
conjunctivitis associated with mycoplasma genitalium infection.conjunctival and first-void urine specimens from a patient with unilateral conjunctivitis and urethritis were found to be positive for mycoplasma genitalium but negative for chlamydia trachomatis, by polymerase chain reaction analysis. identical m. genitalium dna sequences were found in both types of specimens.200415472835
chronic prostatitis: charlottesville to seattle.since few men with chronic prostatitis/chronic pelvic pain syndrome (cp/cpps) have culturable bacteria by traditional approaches, we used sensitive molecular methods to determine presence of fastidious microorganisms.200415538207
methods for assessing the accuracy of pcr-based tests: comparisons and extensions.polymerase chain reaction (pcr) based tests are commonly used to diagnose various infections. such tests are assumed to be highly 'sensitive', however, no consensus definition of, or method for estimating, sensitivity exists. hughes and totten proposed that sensitivity be defined as a function of the number of target dna molecules in the sample with specificity corresponding to the case where there is no target dna molecule present. they then developed parametric, non-parametric and semi-paramet ...200515568209
detection of mycoplasma genitalium in urogenital specimens by real-time pcr and by conventional pcr assay.a real-time lightcycler pcr (lc-pcr) with hybridization probes for detection of mycoplasma genitalium in endocervical and first void urine specimens was developed and compared to a conventional pcr. the primers for both assays were identical and designed to amplify a 427 bp fragment of the 16s rrna gene of m. genitalium. the lc-pcr assay had a detection limit of < 5 bacterial genomes per reaction when dilutions of genomic dna from a type strain of m. genitalium were tested. first void urine from ...200515591251
the influence of environmental adaptation on bacterial genome structure.researchers have long been puzzled by the diversity of life. now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa. the aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches.200515612996
prevalence of mycoplasma genitalium in early pregnancy and relationship between its presence and pregnancy outcome.mycoplasma genitalium is associated with cervicitis and pelvic inflammatory disease but little is known about its role in pregnancy. we investigated the prevalence of m. genitalium by polymerase chain reaction assay on urine specimens from 1216 pregnant women (mean age 31years) presenting before 10 weeks of gestation in 32 general practices. the prevalence of m. genitalium was 0.7% (6/915, 95% ci 0.1-1.2). it was more common in women aged < 20 years, women of afro-caribbean or black african ethn ...200415663138
mycoplasma genitalium: an organism commonly associated with cervicitis among west african sex workers.to identify the contribution of mycoplasma genitalium to the aetiology of cervicitis in sub-saharan africa and its relative importance in the overall burden of sexually transmitted infections among female sex workers (fsw).200515681727
signs and symptoms of urethritis and cervicitis among women with or without mycoplasma genitalium or chlamydia trachomatis infection.to study the prevalence, symptoms, and signs of mycoplasma genitalium and chlamydia trachomatis infections in women attending a swedish std clinic, accessible for both sexes, and in a group of young women called in the cervical cancer screening programme.200515681728
sexually transmitted infections in rural madagascar at an early stage of the hiv epidemic: a 6-month community-based follow-up study.sexually transmitted infections (stis) in madagascar have primarily been monitored in selected groups of patients attending sti clinics in major cities as part of the hiv surveillance program in madagascar.200515729151
the use of enzyme-linked immunosorbent assay for detection of mycoplasma hominis antibodies in infertile women serum samples.besides chlamydiae trachomatis and mycoplasma genitalium, mycoplasma hominis may also cause infertility due to damage of the fallopian tubes. therefore serum samples from infertile women were analyzed for antibodies to m. hominis.200515734761
prevalence of ureaplasma urealyticum and mycoplasma genitalium in men with non-gonococcal urethritis.this study in teheran, islamic republic of iran, investigated the prevalence of ureaplasma urealyticum and mycoplasma species in men with non-gonococcal urethritis. urethral swab samples were collected from 125 cases and 125 healthy men as a control group. the samples were then investigated by culture methods. the rates of detected bacteria in case and control groups were 19.2% and 7.2% for u. urealyticum, 7.2% and 0.8% for m. genitalium, and 2.4% and 1.6% for m. hominis respectively. statistica ...200315751921
detecting of mycoplasma genitalium in male patients with urethritis symptoms in turkey by polymerase chain reaction.the aim of this study was to investigate the incidence of mycoplasma genitalium in the urine samples of 63 male patients who had urethritis symptoms. along with neisseria gonorrhoeae (n. gonorrhoeae) and chlamydia trachomatis (c. trachomatis). we also investigated mycoplasma hominis (m. hominis) and ureaplasma urealyticum (u. urealyticum), both of which are known to cause urethritis.200515756355
symptoms of non-gonococcal urethritis in heterosexual men: a case control study.to determine microbial and behavioural factors contributing to non-gonococcal urethral symptoms in men.200515800097
expression of uga-containing mycoplasma genes in bacillus subtilis.we used bacillus subtilis to express uga-containing mycoplasma genes encoding the p30 adhesin (one uga) of mycoplasma pneumoniae and methionine sulfoxide reductase (two ugas) of mycoplasma genitalium. due to natural uga suppression, these mycoplasma genes were expressed as full-length protein products, but at relatively low efficiency, in recombinant wild-type bacillus. the b. subtilis-expressed mycoplasma proteins appeared as single bands and not as multiple bands compared to expression in reco ...200010762276
increased prevalence of leukocytes and elevated cytokine levels in semen from schistosoma haematobium-infected individuals.in this study, we investigated the seminal inflammatory response to egg infestation of the urogenital organs in 240 semen-donating men aged 15-49 years living in a schistosoma haematobium-endemic area of madagascar. in 29 subjects (12%) with excretion of > or =5 ova/ejaculate, leukocytospermia (>10(6) leukocytes/ml) and the presence of seminal lymphocytes and eosinophil leukocytes were each significantly more prevalent than in 74 subjects (31%) who were s. haematobium negative (p<.01). in additi ...200515838790
comparison of first void urine and urogenital swab specimens for detection of mycoplasma genitalium and chlamydia trachomatis by polymerase chain reaction in patients attending a sexually transmitted disease clinic. 200515879800
should we still be testing for asymptomatic non-specific urethritis in departments of genitourinary medicine?it has recently been advocated that non-invasive testing with first-catch urine specimens using nucleic acid amplification techniques, to detect chlamydia trachomatis and neisseria gonorrhoeae, should replace routine microscopy on asymptomatic men. although it is assumed that this strategy will be cost effective, the available evidence suggests that this will result in fewer sexually transmitted infections being averted than continuing the current practice of screening for urethritis and testing ...200515899076
is mycoplasma genitalium a cause of pelvic inflammatory disease?the evidence for m genitalium as a sexually acquired infection in women is strong, and the organism has been associated with cervicitis and urethritis. in vitro evidence supports the concept that m genitalium causes inflammation in the fallopian tube epithelium, and animal studies have demonstrated the potential for infection to spread from the lower to the upper genital tract. serologic data in humans who have pid are somewhat conflicting, but studies in infertile women suggest a link between m ...200515963879
transcriptional analysis of the conserved ftsz gene cluster in mycoplasma genitalium and mycoplasma pneumoniae.several experimental approaches were used to construct a detailed transcriptional profile of the phylogenetically conserved ftsz cell division gene cluster in both mycoplasma genitalium and its closest relative, mycoplasma pneumoniae. we determined initiation and termination points for the cluster, as well as an absolute steady-state rna level for each gene. transcription of this cluster in both these organisms was shown to be highly strand specific. while the four genes in this cluster are cotr ...200515968065
polymerase chain reaction-based subtyping of ureaplasma parvum and ureaplasma urealyticum in first-pass urine samples from men with or without urethritis.our previous study suggested a significant association between ureaplasma urealyticum and nongonococcal urethritis (ngu). however, association of the serovars of u. urealyticum with ngu remains unclear. a polymerase chain reaction (pcr)-based assay can distinguish 4 serovars of ureaplasma parvum from each other and categorize 10 serovars of u. urealyticum into 3 subtypes: subtype 1 (serovars 2, 5, 8, and 9), subtype 2 (serovars 4, 10, 12, and 13), and subtype 3 (serovars 7 and 11).200515976604
development of a quantitative real-time pcr assay for detection of mycoplasma genitalium.mycoplasma genitalium is known to cause nonchlamydial, nongonococcal urethritis in men and to be associated with pelvic inflammatory disease in women. specific and sensitive pcr methods are needed for diagnosis of this bacterium because it is very difficult to culture from patient samples. to determine the bacterial load in patients' specimens, a quantitative real-time lightcycler pcr was developed. the housekeeping gene gap encoding glyceraldehyde-3-phosphate dehydrogenase was chosen as the tar ...200516000423
crystal structure of a putative type i restriction-modification s subunit from mycoplasma genitalium.the crystal structure of the eubacteria mycoplasma genitalium orf mg438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 a resolution, reveals the organization of s subunits from the type i restriction and modification system. the structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel alpha-helices. the globular domains correspond to the variable target recognition domains (trds), as previously defi ...200516038930
genome sequencing in microfabricated high-density picolitre reactors.the proliferation of large-scale dna-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. the apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. to achieve an approximately ...200516056220
prevalence survey on condom use and infection of urogenital mycoplasmas in female sex workers in china.we evaluated the prevalence of condom use and the effects of condom use on urogenital mycoplasma infection in female sex workers in jinjiang, china.200516102559
[mycoplasma genitalium--a new challenge in sexually transmitted diseases].although mycoplasma genitalium was described 20 years ago, the knowledge concerning it is still limited. the publications in the area are surprisingly few in number, especially considering that the pathogen is rather common and has been connected with a number of different urogenital diseases. the pcr technique has made it possible to perform investigations on a large scale, which might elucidate the pathogenic role of m. genitalium in the urogenital tract. however, it seems well established tha ...200516138971
mycoplasma genitalium in males with nongonococcal urethritis: prevalence and clinical efficacy of eradication.mycoplasma genitalium is regarded as a potential pathogen of the human urogenital tract based on prevalence findings of several european studies.200010782745
in vitro activity of fluoroquinolones against mycoplasma genitalium and their bacteriological efficacy for treatment of m. genitalium-positive nongonococcal urethritis in men.we investigated the minimum inhibitory concentrations of some fluoroquinolones for mycoplasma genitalium and their bacteriological efficacy in the treatment of m. genitalium-positive nongonococcal urethritis. in vitro, levofloxacin was less active than gatifloxacin, tosufloxacin, and sparfloxacin. in vivo, the bacteriological efficacy of gatifloxacin was superior to that of levofloxacin or tosufloxacin.200516206116
structural genomics of minimal organisms and protein fold space.the initial aim of the berkeley structural genomics center is to obtain a near-complete structural complement of two minimal organisms, closely related pathogens mycoplasma genitalium and m. pneumoniae. the former has fewer than 500 genes and the latter fewer than 700 genes. to achieve this goal, the current protein targets have been selected starting with those predicted to be most tractable and likely to yield new structural and functional information. during the past 3 years, the semi-automat ...200516211501
mycoplasma genitalium.mycoplasma genitalium was initially isolated from men with nongonococcal urethritis in 1980. subsequent studies to assess the association of m. genitalium with human disease were inhibited however because on repeated attempts the organism proved extremely difficult to culture. fortunately, the development and use of specific polymerase chain reaction assays allowed progress in this arena and provided evidence of the association between m. genitalium and urethritis, cervicitis, and endometritis. ...200516225783
synthetic biology. synthetic biology remakes small genomes. 200516272096
target selection and deselection at the berkeley structural genomics center.at the berkeley structural genomics center (bsgc), our goal is to obtain a near-complete structural complement of proteins in the minimal organisms mycoplasma genitalium and m. pneumoniae, two closely related pathogens. current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. we report on the process used to select these proteins, as well as our t ...200616276528
mycoplasma amphoriforme sp. nov., isolated from a patient with chronic bronchopneumonia.a mycoplasma was isolated from the sputum of an immunodeficient patient with recurrent bronchitis. the isolate designated strain a39t was very fastidious and atypical for a mycoplasma in its colonial appearance. classical biochemical tests for mycoplasma speciation could not differentiate the isolate from the pathogens mycoplasma pneumoniae and mycoplasma genitalium and serological identification as a recognized mycoplasma species was lacking. specific pcr detection for these two species was neg ...200516280532
a review on pelvic inflammatory disease.pelvic inflammatory disease (pid) remains a significant cause of morbidity worldwide, with the potential to result in serious reproductive complications. much of the definitive work regarding pid was completed in the 1960s and 1970s. more recently, however, there have been a range of studies published that have contributed to our understanding of pid. aetiologically, the main pathogens are chlamydia and gonorrhoea, but may include mycoplasma genitalium and anaerobic gram-negative rods. risk fact ...200516303062
mycoplasma genitalium and asymptomatic chlamydia-negative non-gonococcal urethritis revisited. 200516303076
mycoplasmas in semen of chronic prostatitis patients.to evaluate the occurrence of mycoplasmas in the semen of chronic prostatitis patients.200516303724
antibiotic susceptibility testing of mycoplasma genitalium by taqman 5' nuclease real-time pcr.mycoplasma genitalium is an important pathogen in male nongonococcal urethritis (ngu). isolation of m. genitalium from clinical specimens by axenic culture is very difficult and time-consuming, and very few strains are available for antibiotic susceptibility testing. primary isolation of m. genitalium by coculture with vero cells improves the isolation rate significantly. however, some strains cannot be adapted to axenic culture. in this study, we determined the antibiotic susceptibility of m. g ...200516304163
mycoplasma genitalium: prevalence, clinical significance, and transmission.to study the prevalence, symptoms and signs of mycoplasma genitalium and chlamydia trachomatis infections in std clinic attendees and in partners of m genitalium infected patients.200516326846
detection of mycoplasma genitalium in women with laparoscopically diagnosed acute salpingitis.mycoplasma genitalium has been associated with cervicitis, endometritis, and tubal factor infertility. because the ability of this bacterium to ascend and infect the fallopian tube remains undefined, we performed an investigation to determine the prevalence of m genitalium in fallopian tube, endometrial, and cervical specimens from women laparoscopically diagnosed with acute salpingitis in nairobi, kenya.200516326847
etiologies of nongonococcal urethritis: bacteria, viruses, and the association with orogenital exposure.the purpose of the present study was to determine pathogens and behaviors associated with nongonococcal urethritis (ngu) and the usefulness of the urethral smear in predicting the presence of pathogens.200616388480
interstitial cystitis and infectious agents.interstitial cystitis (ic) is a syndrome consisting of severe refractory bladder symptoms of unknown etiology. the disease tends to affect caucasian women with a mean age of 40 years, with 25% of patients under the age of 30. few population based epidemiological studies of ic have been performed. we analyzed a case of interstitial cystitis in a 42-year-old non-smoker woman. in two biopsy samples the presence of viral dna of human polyomavirus bk (bkv), human herpes virus type 1 and type 2 (hhv- ...200516388730
association between preterm birth and vaginal colonization by mycoplasmas in early pregnancy.to examine the association between colonization by two newly classified species of genital ureaplasmas (ureaplasma parvum and u. urealyticum) in early pregnancy and subsequent late abortion or preterm birth at <34 weeks of gestation, four species of genital mycoplasmas--mycoplasma genitalium, m. hominis, u. parvum, and u. urealyticum--as well as chlamydia trachomatis and neisseria gonorrhoeae were examined by pcr-based methods in a prospective cohort study of 877 women with singleton pregnancies ...200616390947
essential genes of a minimal bacterium.mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. it has a minimal metabolism and little genomic redundancy. consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. none of the 43 rna-coding genes were disrupted. herein, we identify 382 o ...200616407165
[mycoplasma genitalium should be suspected in unspecific urethritis and cervicitis. a study from vasterbotten confirms the high prevalence of the bacteria].the microbe mycoplasma genitalium has in several studies been proposed as an individual cause of non-gonococcal urethritis (ngu) in men, and has been associated with pelvic inflammatory disease (pid) and salpingitis. the prevalence of m genitalium has generally been 50-90% of the prevalence of c trachomatis, and this seems to be the case in sweden as well. this is the first study of the pathogenesis and prevalence of m genitalium in northern sweden. in total 823 samples, 340 from women and 483 f ...200516408391
comparative analysis of antibiotic resistance gene markers in mycoplasma genitalium: application to studies of the minimal gene complement.mycoplasma genitalium has been proposed as a suitable model for an in-depth understanding of the biology of a free-living organism. this paper reports that the expression of the aminoglycoside resistance gene aac(6')-aph(2''), the only selectable marker hitherto available for m. genitalium genetic studies, correlates with a growth impairment of the resistant strains. in light of this finding, a tetm438 construction based on the tetracycline resistance gene tetm was developed; it can be used effi ...200616436439
proximal region of the gene encoding cytadherence-related protein permits molecular typing of mycoplasma genitalium clinical strains by pcr-restriction fragment length polymorphism.restriction fragment length polymorphism (rflp) analysis of the pcr-amplified proximal region of the gene encoding cytadherence accessory protein p110 (mg192) revealed dna sequence divergences among 54 mycoplasma genitalium clinical strains isolated from the genitourinary tracts of women attending a sexually transmitted disease-related health clinic, plus one from the respiratory tract and one from synovial fluid. seven of 56 (12.5%) strains exhibited rflps following digestion of the proximal re ...200616455921
the subunit b of the f0f1-type atpase of the bacterium mycoplasma pneumoniae is a lipoprotein.the dna sequence analysis of the f0f1-atpase operon of the bacterium mycoplasma pneumoniae predicted that the subunit b, encoded by the gene atpf, is a lipoprotein of the murein lipoprotein type of escherichia coli. here we experimentally verify this prediction by metabolic labeling of subunit b with [14c]palmitic acid and by in vivo interfering with the processing of the prolipoprotein form of subunit b by the antibiotic globomycin, a specific inhibitor of the signal peptidase ii. our results s ...19989733782
persistent increase in the incidence of acute male urethritis diagnosed in general practices in france.at-risk sexual behaviour seems to have increased in europe, possibly due to the reassuring efficacy of highly active antiretroviral treatments.200616464324
quantitative detection and phylogeny-based identification of mycoplasmas and ureaplasmas from human immunodeficiency virus type 1-positive patients.more than 20 years ago, mycoplasma genitalium was first isolated from men with nongonococcal urethritis (ngu). some strains of mycoplasma and ureaplasma are associated with ngu or other genitourinary infections. it is reasonable to suggest that mycoplasmas and ureaplasmas may increase the development of acquired immunodeficiency syndrome in human immunodeficiency virus type 1 (hiv-1)-infected patients. this study investigated a rapid and reliable diagnostic method, based on a lightcycler syber g ...200616506086
cervicitis and genitourinary symptoms in women culture positive for mycoplasma genitalium.mycoplasma genitalium has been associated with male urethritis. we sought to relate m. genitalium to genitourinary signs and symptoms in women.200616533338
mycoplasma genitalium infections. diagnosis, clinical aspects, and pathogenesis. 200616542629
transcriptional heat shock response in the smallest known self-replicating cell, mycoplasma genitalium.mycoplasma genitalium is a human bacterial pathogen linked to urethritis and other sexually transmitted diseases as well as respiratory and joint pathologies. though its complete genome sequence is available, little is understood about the regulation of gene expression in this smallest known, self-replicating cell, as its genome lacks orthologues for most of the conventional bacterial regulators. still, the transcriptional repressor hrca (heat regulation at circe [controlling inverted repeat of ...200616585746
performance of the gen-probe transcription-mediated [corrected] amplification research assay compared to that of a multitarget real-time pcr for mycoplasma genitalium detection.mycoplasma genitalium (mg) can cause nongonococcal urethritis and is potentially associated with urethritis, endometritis, and cervicitis. several assays have been developed to detect mg. molecular amplification assays for organism detection can be problematic due to the potential for false-positive and false-negative results. confirmatory testing is often required in these situations, requiring additional time and resources. use of multigene targets could integrate both detection and verificati ...200616597844
mycoplasma genitalium is associated with symptomatic urethritis.in order to further investigate the epidemiology of mycoplasma genitalium, 680 men attending departments of genitourinary medicine in bristol, bath and truro were studied. m. genitalium was detected in 36 men (5.3%) and was present at all three clinics. clinically, both urethritis and the presence of a urethral discharge and/or dysuria, but not penile irritation were independently associated with the detection of m. genitalium, the former being with the strongest association (odds ratio [or] 10. ...200616643675
mycoplasma pneumoniae and mycoplasma genitalium: a comparison of two closely related bacterial species.the rapid progress in sequencing large quantities of dna will provide an increasing number of complete genome sequences of closely related bacterial species as well as of pairs of isolates from the same species with different features, such as a pathogenic and an apathogenic representative. this opens the way to apply subtractive comparative analysis as a tool to select from the large pool of all bacterial genes a relatively small set of genes that can be correlated with the expression of a cert ...199810066529
functional insights from structural predictions: analysis of the escherichia coli genome.fold assignments for proteins from the escherichia coli genome are carried out using basic, a profile-profile alignment algorithm, recently tested on fold recognition benchmarks and on the mycoplasma genitalium genome and psi blast, the newest generation of the de facto standard in homology search algorithms. the fold assignments are followed by automated modeling and the resulting three-dimensional models are analyzed for possible function prediction. close to 30% of the proteins encoded in the ...199910091664
genthreader: an efficient and reliable protein fold recognition method for genomic sequences.a new protein fold recognition method is described which is both fast and reliable. the method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. as a final step, each threaded model is evaluated by a neural network in order to produce a single measure of confidence in the proposed prediction. the speed of the method, along with its sensitivity and very low false-positive rate makes it ideal for automatic ...199910191147
disruption of gene mg218 of mycoplasma genitalium through homologous recombination leads to an adherence-deficient phenotype.although the complete genome of mycoplasma genitalium has been sequenced, the functional identification of various genes, including those involved in virulence, has not been accomplished. further compounding these difficulties has been the failure to develop genetic tools in mycoplasmas that permit the assessment of gene and operon function and regulation. to determine whether homologous recombination could be developed as a tool to analyze the function of genes in m. genitalium, a plasmid that ...199910220448
the helicobacter pylori genome: from sequence analysis to structural and functional predictions.fold assignments for proteins from the helicobacter pylori genome are carried out using basic, a profile-profile alignment algorithm recently tested on the mycoplasma genitalium and escherichia coli genomes. the fold assignments are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. over 40% of the proteins encoded in the h. pylori genome can be recognized as belonging to a protein family with known structure. previous estimates sugges ...199910373003
sequence complexity and dna curvature.a linguistic complexity measure was applied to the complete genomes of hiv-1, escherichia coli, bacillus subtilis, haemophilus influenzae, mycoplasma genitalium, and to long human and yeast genomic fragments. complexity values averaged over entire genomic sequences were compared, as were predicted average values of intrinsic dna curvature. we found that both the most curved and the least complex fragments are located preferentially in non-coding parts of the genome. analysis of location of the m ...199910404619
amass: a structured pattern matching approach to shotgun sequence assembly.in this paper, we propose an efficient, reliable shotgun sequence assembly algorithm based on a fingerprinting scheme that is robust to both noise and repetitive sequences in the data, two primary roadblocks to effective whole-genome shotgun sequencing. our algorithm uses exact matches of short patterns randomly selected from fragment data to identify fragment overlaps, construct an overlap map, and deliver a consensus sequence. we show how statistical clues made explicit in our approach can eas ...199910421521
characterization of acholeplasma laidlawii ftsz gene and its gene product.the ftsz gene was found among representatives of all bacterial groups. ftsz protein is an essential component of cell division ring. contraction of this cytoskeleton-like ring is believed to be the universal way of bacterial division. acholeplasma laidlawii possesses all features of the minimal mycoplasma cell and some traits of cell-wall bacteria and seems to be a promising object for study of basic principles of the bacterial division process. we cloned an a. laidlawii chromosomal fragment con ...199910448065
a gene family in mycoplasma imitans closely related to the pmga family of mycoplasma gallisepticum.the avian pathogen mycoplasma gallisepticum possesses a large gene family encoding lipoproteins which function as haemagglutinins. representative species of the pneumoniae phylogenetic group of mycoplasmas were examined for the presence of genes homologous to members of this multigene family. antisera against the pmga1.1 lipoprotein recognized a 35 kda protein in mycoplasma imitans, but did not recognize proteins of mycoplasma genitalium, mycoplasma pneumoniae, mycoplasma pirum, mycoplasma penet ...199910463176
[computer analysis of regulatory signals in complete bacterial genomes. translation initiation of ribosomal protein operons].signals of translation initiation of operons of haemophilus influenzae ribosomal proteins were predicted. this process is regulated by the formation of secondary rna structures to which one of the proteins encoded in a particular operon binds. in some cases, these structures imitate the region of protein binding to rrna. predictions are made by comparing with homologous operons of escherichia coli and analogous regions of rrna and by estimating the energy of secondary structure formation. it is ...199910544808
polypurine.polypyrimidine sequences in complete bacterial genomes: preference for polypurines in protein-coding regions.the genomes of methanococcus jannaschii, mycoplasma genitalium, haemophilus influenzae, archaeoglobus fulgidus, helicobacter pylori, treponema pallidum, borrelia burgdorferri, rickettsia prowazekeii, mycobacterium tuberculosis, methanobacterium thermoautotrophicum, synechocystis sp. pcc6803, bacillus subtilis, chlamydia trachomatis, pyrococcus horikoshii, aquifex aeolicus, mycoplasma pneumoniae and escherichia coli have been analysed for the presence of polypurine.polypyrimidine tracts, in order ...200010721721
comparative potency of gemifloxacin, new quinolones, macrolides, tetracycline and clindamycin against mycoplasma spp.this study determined the comparative in vitro potency of the new investigative quinolone gemifloxacin (sb-265805) using low-passaged clinical isolates and type strains of mycoplasma commonly found in the human respiratory and urogenital tracts. organisms studied were mycoplasma pneumoniae, mycoplasma hominis, mycoplasma fermentans, mycoplasma genitalium, mycoplasma penetrans and ureaplasma urealyticum, obtained from different geographical regions. comparator drugs were levofloxacin, trovafloxac ...200010824029
prolyl isomerases in a minimal cell. catalysis of protein folding by trigger factor from mycoplasma genitalium.peptidyl-prolyl cis/trans isomerases (ppiases) catalyze the isomerization of prolyl peptide bonds. distinct families of this class of enzymes are involved in protein folding in vitro, whereas their significance in free living organisms is not known. previously, we inspected the smallest known genome of a self-replicating organism and found that mycoplasma genitalium is devoid of all known ppiases except the trigger factor. despite the extensive sequence information becoming available, most genes ...200010824113
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