| increased frequency of detection of ureaplasma urealyticum and mycoplasma genitalium in aids patients without urethral symptoms. | the roles of mycoplasma genitalium and ureaplasma urealyticum in nongonococcal urethritis are not yet well established. the aim of this study was to determine the presence of these microorganisms in the urethral tracts of 187 human immunodeficiency virus type 1 (hiv-1)-infected male patients with no clinical signs of urethritis. the results indicate that the prevalence of m. genitalium and u. urealyticum was higher in aids patients than in asymptomatic, hiv-1-infected patients and in healthy ind ... | 1999 | 10325375 |
| gene identification in bacterial and organellar genomes using genescan. | the performance of the genescan algorithm for gene identification has been improved by incorporation of a directed iterative scanning procedure. application is made here to the cases of bacterial and organnellar genomes. the sensitivity of gene identification was 100% in plasmodium falciparum plastid-like genome (35 kb) and in 98% in the mycoplasma genitalium genome (approximately 580 kb) and the haemophilus influenzae rd genome (approximately 1.8 mb). sensitivity was found to improve in both th ... | 1999 | 10353188 |
| development and evaluation of a polymerase chain reaction assay using the 16s rrna gene for detection of eperythrozoon suis infection. | the 16s ribosomal rna (rrna) gene of eperythrozoon suis was amplified using gene-specific primers developed from genbank sequence accession u88565. the gene was subsequently cloned and sequenced. based on these sequence data, 3 sets of e. suis-specific primers were designed. these primers selectively amplified 1394, 690, and 839 base-pair (bp) fragments of the 16s rrna gene from dna of e. suis extracted from the blood of an experimentally infected pig during a parasitemic episode. no polymerase ... | 1999 | 10353353 |
| advances in structural genomics. | new computational techniques have allowed protein folds to be assigned to all or parts of between a quarter (caenorhabditis elegans) and a half (mycoplasma genitalium) of the individual protein sequences in different genomes. these assignments give a new perspective on domain structures, gene duplications, protein families and protein folds in genome sequences. | 1999 | 10361097 |
| 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 ... | 1999 | 10373003 |
| 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 ... | 1999 | 10404619 |
| 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 ... | 1999 | 10421521 |
| detection of viral and bacterial infections in women with normal and abnormal colposcopy. | signs and symptoms of sexually-transmitted diseases (std) do not allow any etiological diagnosis in women. colposcopic findings are seldom pathognomic. consequently, the microbiology laboratory with the recent availability of molecular diagnostic tools is required to detect the infectious bacterial and/or viral agents involved in std. in cervical samples of women submitted to gynaecological screening for past or present signs and symptoms of inflammation and with different colposcopic findings, ... | 1999 | 10422688 |
| 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 ... | 1999 | 10448065 |
| detection of chlamydia trachomatis, neisseria gonorrhoeae, ureaplasma urealyticum, and mycoplasma genitalium in first-void urine specimens by multiplex polymerase chain reaction. | background: sexually transmitted diseases are often caused by one or more microorganisms, and asymptomatic carriage and transmission may be of significance. testing for more than one organism in a single assay could be a useful approach to laboratory diagnosis. methods and results: a multiplex polymerase chain reaction (pcr) assay was developed that employed specific primers targeted to the 7.5-kb cryptic plasmid of chlamydia trachomatis, the cppb gene of the 4.2-kb cryptic plasmid of neisseria ... | 1997 | 10462605 |
| 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 ... | 1999 | 10463176 |
| analysis of base-pairing potentials between 16s rrna and 5' utr for translation initiation in various prokaryotes. | it is well accepted that the 3' end of 16s rrna is directly involved in prokaryotic translation initiation by pairing with the shine-dalgarno (sd) sequence, which is located in the ribosome-binding site of mrna. according to shine and dalgarno, escherichia coli 's 5' utr has the pattern of 'aggagg' (sd sequence), which is complementary to the 3' end sequence of 16s rrna. in this work, we systematically calculated free-energy values of the base pairing between the 3' end of 16s rrna and the 5' ut ... | 1999 | 10487865 |
| amplified-fragment length polymorphism fingerprinting of mycoplasma species. | amplified-fragment length polymorphism (aflp) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. the potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including mycoplasma genitalium (n = 11), mycoplasma pneumoniae (n = 5), mycoplasma hominis (n = 5), mycoplasma hyopneumoniae (n = 9), myco plasma flocculare (n = 5), mycoplasma hyosynoviae (n = 10), and mycoplasma di ... | 1999 | 10488196 |
| aminoacylation of trnas encoded by chlorella virus cvk2. | viruses that infect certain strains of the unicellular green alga, chlorella, have a large, linear dsdna genome that is 330-380 kb in size; this genomic size is the largest known among viruses and is equivalent to approximately 60% of the smallest prokaryotic genome of mycoplasma genitalium (580 kb). besides many putative protein-coding genes, a cluster of 10-15 trna genes is present in these viral genomes. some of these trna genes contain peculiar insertions. in infected host cells, the viral t ... | 1999 | 10544096 |
| [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 ... | 1999 | 10544808 |
| benchmarking psi-blast in genome annotation. | the recognition of remote protein homologies is a major aspect of the structural and functional annotation of newly determined genomes. here we benchmark the coverage and error rate of genome annotation using the widely used homology-searching program psi-blast (position-specific iterated basic local alignment search tool). this study evaluates the one-to-many success rate for recognition, as often there are several homologues in the database and only one needs to be identified for annotating th ... | 1999 | 10547299 |
| significant differences between the g+c content of synonymous codons in orthologous genes and the genomic g+c content. | the relationship between the overall g+c content of the genome (gc) and the gc content at the third codon positions (gc3) of genes, which we refer to as a gc3-plot, was examined using 15 currently available complete genome sequences. a remarkably linear relationship was found between these two quantities, confirming previous observations of a strong positive correlation in the gc3-plot. in order to conduct a more detailed analysis of the gc3-plot, we examined the gc3 content by separating orthol ... | 1999 | 10570981 |
| studies of codon usage and trna genes of 18 unicellular organisms and quantification of bacillus subtilis trnas: gene expression level and species-specific diversity of codon usage based on multivariate analysis. | we examined codon usage in bacillus subtilis genes by multivariate analysis, quantified its cellular levels of individual trnas, and found a clear constraint of trna contents on synonymous codon choice. individual trna levels were proportional to the copy number of the respective trna genes. this indicates that the trna gene copy number is an important factor to determine in cellular trna levels, which is common with escherichia coli and yeast saccharomyces cerevisiae. codon usage in 18 unicellu ... | 1999 | 10570992 |
| global transposon mutagenesis and a minimal mycoplasma genome. | mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. global transposon mutagenesis was used to identify nonessential genes in an effort to learn whether the naturally occurring gene complement is a true minimal genome under laboratory growth conditions. the positions of 2209 transposon insertions in the completely sequenced genomes of m. genitalium and its close relative m. pneumoniae were determined by sequencing across t ... | 1999 | 10591650 |
| three views of microbial genomes. | we describe here genomeatlases as a method for visualising three different aspects of complete microbial chromosomes: repeats, dna structural characteristics, and base composition. we have applied this method to all publicly available genomes, and find a general strand preference of global repeats. the atlas for the mycoplasma genitalium genome is presented as an example, and results from all three views are consistent with known characteristics of the genome. | 1999 | 10673014 |
| in vitro activity of gemifloxacin (sb 265805; lb20304a) against human mycoplasmas. | the in vitro activity of gemifloxacin, a new broad-spectrum fluoroquinolone, was compared with those of ciprofloxacin, erythromycin, azithromycin and doxycycline against 29 human respiratory or urogenital tract mycoplasmas. gemifloxacin was highly active against all of the mycoplasma and ureaplasma species tested (mic range 0.001-0.25 mg/l) and was 5- to 100-fold more active than ciprofloxacin. doxycycline was less active than gemifloxacin against the mycoplasmas (mic range 0.01-1 mg/l) but had ... | 2000 | 10702559 |
| the proteome of mycoplasma genitalium. chaps-soluble component. | mycoplasma genitalium is the smallest member of the class mollicutes, with a genome size of 580 kb. it has the potential to express 480 gene products, and is therefore considered to be an excellent model to assess: (a) the minimum metabolism required by a free living cell; and (b) proteomic technologies and the information obtained by proteome analysis. here, we report on the most complete proteome observed at 73% (expected proteome), and analysed at 33% (reported proteome). the use of four over ... | 2000 | 10712586 |
| 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 ... | 2000 | 10721721 |
| 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 ... | 2000 | 10754070 |
| 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 ... | 2000 | 10762276 |
| 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. | 2000 | 10782745 |
| phylogenetic depth of the bacterial genera aquifex and thermotoga inferred from analysis of ribosomal protein, elongation factor, and rna polymerase subunit sequences. | the phylogenetic placement of the aquifex and thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins s10, l3, l4, l23, l2, s19, l22, and s3 encoded in the s10 operon (833 aa positions); (ii) the joint sequences of the elongation factors tu(1alpha) and g(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint rna polymerase beta- and beta'-type subunits encoded in the rpobc operon (1130 aa positions). phylogenies of r-protein and ef sequenc ... | 2000 | 10795828 |
| identification of a small rna within the pdh gene cluster of mycoplasma pneumoniae and mycoplasma genitalium. | a highly abundant and heterogeneous small rna about 205 to 210 bases long named mp200 rna has been identified in mycoplasma pneumoniae. it was localized on the genome within a 319-bp-long intergenic space of the pyruvate dehydrogenase (pdh) gene cluster. a database search at the dna level revealed the highest similarity to a sequence located within the pdh gene cluster of mycoplasma genitalium that was also shown to be transcribed into two abundant, but smaller rnas than the ones in mycoplasma p ... | 2000 | 10809712 |
| 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 ... | 2000 | 10824029 |
| 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 ... | 2000 | 10824113 |
| mycoplasma genitalium in non-gonococcal urethritis--a study in swedish male std patients. | urethral swab specimens obtained from 101 men attending an std clinic were examined for the presence of mycoplasma genitalium by polymerase chain reaction (pcr) amplification. fifty patients had non-gonococcal urethritis (ngu), and 51 patients were included as controls without urethritis. m. genitalium dna was detected in 13 (26%) of the urethritis patients and in 5 (10%) of the control patients (p=0.06). no patient positive for m. genitalium had a simultaneous chlamydial infection. thus, in the ... | 2000 | 10824937 |
| occurrence and treatment of mycoplasma genitalium in patients visiting std clinics in sweden. | two hundred and thirty-three men and 85 women visiting std clinics in western sweden between april 1997 and march 1998 were examined for mycoplasma genitalium and chlamydia trachomatis. the bacteria were identified by the polymerase chain reaction (pcr) technique. three women (3.5%) and 18 men (7%) were positive for m. genitalium. seventeen (14%) of the 115 men with urethritis were infected but only one of the men was without urethritis. after treatment with tetracyclines for 10 days, one woman ... | 2000 | 10824941 |
| molecular characterization of the mycoplasma gallisepticum pvpa gene which encodes a putative variable cytadhesin protein. | a putative cytadhesin-related protein (pvpa) undergoing variation in its expression was identified in the avian pathogen mycoplasma gallisepticum. the pvpa gene was cloned, expressed in escherichia coli, and sequenced. it exhibits 54 and 52% homology with the p30 and p32 cytadhesin proteins of the human pathogens mycoplasma pneumoniae and mycoplasma genitalium, respectively. in addition, 50% homology was found with the mgc2 cytadhesin of m. gallisepticum and 49% homology was found with a stretch ... | 2000 | 10858209 |
| enhanced genome annotation using structural profiles in the program 3d-pssm. | a method (three-dimensional position-specific scoring matrix, 3d-pssm) to recognise remote protein sequence homologues is described. the method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. the method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (scop) database to obtain a structu ... | 2000 | 10860755 |
| the association of mycoplasma hominis, ureaplasma urealyticum and mycoplasma genitalium with bacterial vaginosis: observations on heterosexual women and their male partners. | the prevalence of 3 mycoplasmas (mycoplasma hominis, ureaplasma urealyticum and mycoplasma genitalium) was determined in a cohort of women with or without bacterial vaginosis (bv) and in their respective male partners. heterosexual women with or without bv and their male partners were recruited and genital sampling for these microorganisms was performed. seventeen women with bv and 21 women with normal flora, and their respective male partners, were recruited. m. hominis was present in 9 (53%) o ... | 2000 | 10872907 |
| the prevalence of urethral infections amongst asymptomatic young men in hat yai, southern thailand. | the aim of this study was to survey sexual behaviour and estimate the prevalence of urethral infections amongst male vocational college students. a cross-sectional survey was performed among 479 young men attending 2 vocational colleges in hat yai, southern thailand. polymerase chain reaction (pcr) tests of first-void urine (fvu) samples were used to detect infection with chlamydia trachomatis, neisseria gonorrhoeae, ureaplasma urealyticum, mycoplasma genitalium and mycoplasma hominis. girlfrien ... | 2000 | 10872914 |
| the association of chlamydia trachomatis and mycoplasma genitalium with non-gonococcal urethritis: observations on heterosexual men and their female partners. | our objectives were to study the distribution of chlamydia trachomatis and mycoplasma genitalium in men with or without non-gonococcal urethritis (ngu) and their respective female partners. a case-control study was carried out to which men with or without ngu and their female partners were recruited. all study participants were tested for the presence of c. trachomatis and m. genitalium. an analysis firstly of the distribution of each of these microorganisms among men with or without urethritis ... | 2000 | 10919484 |
| proteomics of mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome. | we present the results of a comprehensive analysis of the proteome of mycoplasma genitalium (mg), the smallest autonomously replicating organism that has been completely sequenced. our aim was to identify and characterize all soluble proteins in mg that are structurally and functionally uncharacterized. we were particularly interested in identifying proteins that differed significantly from typical globular proteins, for example, proteins which are unstructured in the absence of a 'partner' mole ... | 2000 | 10931922 |
| predicting protein function by genomic context: quantitative evaluation and qualitative inferences. | various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. the types of genomic context that they use are type i: the fusion of genes; type ii: the conservation of gene-order or co-occurrence of genes in potential operons; and type iii: the co-occurrence of genes across genomes (phylogenetic profiles). here we compare these types for their coverage, their correlations with various types of functional interaction, and th ... | 2000 | 10958638 |
| causal analysis of cpg suppression in the mycoplasma genome. | some bacterial genomes are known to have low cpg dinucleotide frequencies. while their causes are not clearly understood, the frequency of cpg is suppressed significantly in the genome of mycoplasma genitalium, but not in that of mycoplasma pneumoniae. we compared orthologous gene pairs of the two closely related species to analyze cpg substitution patterns between these two genomes. we also divided genome sequences into three regions: protein-coding, noncoding, and rna-coding, and obtained the ... | 2000 | 11011765 |
| reactive arthritis: preliminary microbiologic analysis of the human temporomandibular joint. | the presence of chlamydia trachomatis has been previously shown in the temporomandibular joint (tmj). this study investigated whether the presence of other bacteria associated with reactive arthritis (rea) can be identified in the tmj. | 2000 | 11021709 |
| intracellular dna replication and long-term survival of pathogenic mycoplasmas. | we examined intracellular survival and growth of pathogenic mycoplasmas (mycoplasma penetrans, mycoplasma pneumoniae and mycoplasma genitalium) in cultured human cells. by using the eukaryotic nuclear dna synthesis inhibitor, aphidicolin, we detected the selective synthesis of mycoplasma (my) and mitochondria (mt) dna, which could be further differentiated by restriction enzyme analyses. also, intracellular m. pneumoniae and m. penetrans infectivity of human cells was detected over 6 months usin ... | 2000 | 11031124 |
| distribution of ecto 5'-nucleotidase on mycoplasma species associated with arthritis. | the enzyme ecto 5'-nucleotidase (5'n) was found to be active on 8/14 strains of mycoplasma fermentans, k(m) (+/-s.d.) 3.8+/-2.8 microm 5'-amp, and on the type strain of mycoplasma pulmonis, k(m) 0.63 microm 5'-amp. the six m. fermentans strains lacking 5'n activity were related by restriction fragment length polymorphism typing. at ph 8.5, the type strains of mycoplasma arthritidis, mycoplasma buccale and ureaplasma urealyticum showed a relatively non-specific phosphatase activity against 5'-amp ... | 2000 | 11040429 |
| host-pathogen interactions in mycoplasma pathogenesis: virulence and survival strategies of minimalist prokaryotes. | despite their very small genomes mycoplasmas are successful pathogens of man and a wide range of animal hosts. because of the lack of effective therapeutics and vaccines, mycoplasma diseases continue to be a significant problem for public health as well as livestock production with major socio-economic consequences worldwide. recent outbreaks and epidemiological studies predict that the incidence of human and animal mycoplasma diseases might increase which indicates the urgent need to develop ne ... | 2000 | 11043978 |
| the complete sequence of the mucosal pathogen ureaplasma urealyticum. | the comparison of the genomes of two very closely related human mucosal pathogens, mycoplasma genitalium and mycoplasma pneumoniae, has helped define the essential functions of a self-replicating minimal cell, as well as what constitutes a mycoplasma. here we report the complete sequence of a more distant phylogenetic relative of those bacteria, ureaplasma urealyticum (parvum biovar), which is also a mucosal pathogen of humans. it is the third mycoplasma to be sequenced, and has the smallest seq ... | 2000 | 11048724 |
| e-cell: software environment for whole cell simulation. | we present e-cell, a generic computer software environment for modeling a cell and conducting experiments in silico. the e-cell system allows a user to define functions of proteins, protein-protein interactions, protein-dna interactions, regulation of gene expression and other features of cellular metabolism, in terms of a set of reaction rules. the system then executes those reactions iteratively, and the user can observe, through a computer display, dynamic changes in concentrations of protein ... | 1997 | 11072314 |
| genomic analysis of the genes encoding ribosomal proteins in eight eubacterial species and saccharomyces cerevisiae. | the complete genomic nucleotide sequence data of more than 10 unicellular organisms have become available. during the past years, we have been focusing our attention to the analysis of the structure and function of the ribosome and its protein components. by making use of the genomic sequence data, our work can now be extended to comparative analysis of the ribosomal components at the genomic level. such analysis will contribute to our understanding of the structure-function relationship of the ... | 1998 | 11072316 |
| horizontal gene transfer in bacterial and archaeal complete genomes. | there is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. we have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. it is based on the analysis of g+c contents, codon usage, amino acid usage, and gene position. when we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of ... | 2000 | 11076857 |
| analysis of cytadherence-deficient, gapa-negative mycoplasma gallisepticum strain r. | comparison of the phenotypic expression of mycoplasma gallisepticum strain r low (passage 15) to that of strain r high (passage 164) revealed that three proteins, i.e., the cytadhesin molecule gapa, a 116-kda protein (p116), and a 45-kda protein (p45), are missing in strain r high. sequence analysis confirmed that the insertion of an adenine 105 bp downstream of the gapa translational start codon resulted in premature termination of translation in r high. a second adenine insertion had also occu ... | 2000 | 11083776 |
| association of mycoplasma genitalium with nongonococcal urethritis in heterosexual men. | chlamydia trachomatis and neisseria gonorrhoeae are universally acknowledged as urethral pathogens, yet the etiology in the majority of cases of urethritis is unclear. our case-control study assessed the association of mycoplasma genitalium, ureaplasma urealyticum, and other potential pathogens with acute nongonococcal urethritis (ngu) in heterosexual men presenting to an urban sexually transmitted diseases clinic. m. genitalium was detected in 27 (22%) of 121 ngu case patients and in 5 (4%) of ... | 2001 | 11120932 |
| high prevalence of chlamydia trachomatis, neisseria gonorrhoeae and mycoplasma genitalium in female commercial sex workers in japan. | our objectives were to explore the prevalence of chlamydia trachomatis, neisseria gonorrhoeae, and mycoplasma genitalium in japanese female commercial sex workers (csws), in comparison with pregnant women as controls. a high-risk group of 174 female csws and 90 asymptomatic pregnant women were enrolled in this study. detection of c. trachomatis, n. gonorrhoeae, and m. genitalium on the endocervix of the women was performed mainly by using polymerase chain reaction (pcr)-based assays. the prevale ... | 2000 | 11138913 |
| identification of a plasmid-encoded gene from haemophilus ducreyi which confers nad independence. | members of the family pasteurellaceae are classified in part by whether or not they require an nad supplement for growth on laboratory media. in this study, we demonstrate that this phenotype can be determined by a single gene, nadv, whose presence allows nad-independent growth of haemophilus influenzae and actinobacillus pleuropneumoniae. this gene was cloned from a 5.2-kb plasmid which was previously shown to be responsible for nad independence in haemophilus ducreyi. when transformed into a. ... | 2001 | 11157928 |
| [detection of mycoplasma genitalium in throat by nested polymerase chain reaction and analysis of dna sequencing in pediatric patients with acute upper respiratory tract infections]. | to explore the relation between mycoplasma genitalium (mg) and acute upper respiratory tract infection in pediatric patients by using nested polymerase chain reaction(npcr) and analysis of dna sequencing techniques. | 2000 | 11225033 |
| a primordial trna modification required for the evolution of life? | the evolution of reading frame maintenance must have been an early event, and presumably preceded the emergence of the three domains archaea, bacteria and eukarya. features evolved early in reading frame maintenance may still exist in present-day organisms. we show that one such feature may be the modified nucleoside 1-methylguanosine (m(1)g37), which prevents frameshifting and is present adjacent to and 3' of the anticodon (position 37) in the same subset of trnas from all organisms, including ... | 2001 | 11226173 |
| genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. | gene order in prokaryotes is conserved to a much lesser extent than protein sequences. only several operons, primarily those that code for physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. nevertheless, even the limited conservation of operon organization that is observed can provide valuable evolutionary and functional clues through multiple genome comparisons. a program for constructing gapped local alignments of conserved gene strings in two ... | 2001 | 11230160 |
| etiology of urethral discharge in west africa: the role of mycoplasma genitalium and trichomonas vaginalis. | to determine the etiological role of pathogens other than neisseria gonorrhoeae and chlamydia trachomatis in urethral discharge in west african men. | 2001 | 11242818 |
| rho is not essential for viability or virulence in staphylococcus aureus. | we have identified the gene for transcription termination factor rho in staphylococcus aureus. deletion of rho in s. aureus reveals that it is not essential for viability or virulence. we also searched the available bacterial genomic sequences for homologs of rho and found that it is broadly distributed and highly conserved. exceptions include streptococcus pneumoniae, streptococcus pyogenes, mycoplasma genitalium, mycoplasma pneumoniae, ureaplasma urealyticum, and synechocystis sp. strain pcc68 ... | 2001 | 11257021 |
| role of mycoplasma genitalium and ureaplasma urealyticum in acute and chronic nongonococcal urethritis. | one hundred fourteen heterosexual men with acute nongonococcal urethritis (ngu) and 64 patients without ngu were studied. we determined that chlamydia trachomatis and mycoplasma genitalium were strongly associated with acute ngu after controlling, by means of multivariate analysis, for age, race, sexual lifestyle, and coinfection (odds ratio [or], 13.0, 95% confidence interval [ci], 2.6-64.5; and or, 17.9, 95% ci, 2.0-160, respectively). eighty-six men with acute ngu reattended at least once 10- ... | 2001 | 11264026 |
| aetiology of urethral discharge in bangui, central african republic. | to determine the aetiology of urethritis in bangui, central african republic. | 2001 | 11287692 |
| failure of mycoplasma pneumoniae infection to confer protection against mycoplasma genitalium: observations from a mouse model. | mycoplasma pneumoniae and m. genitalium are genomically distinct but share antigens that induce some serological cross-reactivity. therefore, the possibility that m. pneumoniae infection of the human respiratory tract might provide immunity to m. genitalium infection of the genital tract was considered. because of the difficulty of assessing this proposition in man, it was evaluated experimentally in a mouse model. female balb/c mice were susceptible to infection of the vagina with m. pneumoniae ... | 2001 | 11289524 |
| identification of novel essential escherichia coli genes conserved among pathogenic bacteria. | we deleted a subset of 27 open reading frames (orfs) from escherichia coli which encode previously uncharacterized, probably soluble gene products homologous to proteins from a broad spectrum of bacterial pathogens such as haemophilus influenzae, staphylococcus aureus, streptococcus pneumoniae and enterococcus faecalis and only distantly related to eukaryotic proteins. six novel bacteria-specific genes essential for growth in complex medium could be identified through a combination of bioinforma ... | 2001 | 11361082 |
| gene re-arrangement and fusion in mycoplasma gallisepticum thya-nrdfei locus. | sequencing of mycoplasma gallisepticum genome fragment containing thymidylate synthase and ribonucleotide reductase gene clusters reveals both its unusual organization and gene content. sequence analysis indicates the presence of a gene whose product can be considered as a fusion of two full size proteins: the n-terminal part shows significant similarity to mycoplasmal dihydrofolate reductases, while the c-terminal part of the polypeptide chain shows significant similarity to eukaryotic deoxycyt ... | 2001 | 11410345 |
| the role of mycoplasma genitalium in non-gonococcal urethritis. | | 2001 | 11463919 |
| sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. | functional annotation of proteins encoded in newly sequenced genomes can be expected to meet two conflicting objectives: (i) provide as much information as possible, and (ii) avoid erroneous functional assignments and over-predictions. the continuing exponential growth of the number of sequenced genomes makes the quality of sequence annotation a critical factor in the efforts to utilize this new information. when dubious functional assignments are used as a basis for subsequent predictions, they ... | 1998 | 11471243 |
| association of mycoplasma genitalium persistence in the urethra with recurrence of nongonococcal urethritis. | most patients with recurrent symptomatic nongonococcal urethritis receive negative test results for chlamydia trachomatis and ureaplasma urealyticum, and the cause of such recurrence usually is unknown. | 2001 | 11473221 |
| midtrimester vaginal mycoplasma genitalium in women with subsequent spontaneous preterm birth. | we sought to determine the midtrimester prevalence of mycoplasma genitalium in women who had subsequent spontaneous preterm birth. | 2001 | 11483922 |
| assignment of the 1h, 13c and 15n resonances of the ppiase domain of the trigger factor from mycoplasma genitalium. | | 2001 | 11495256 |
| serological investigation of mycoplasma genitalium in infertile women. | the role of mycoplasma genitalium in the pathogenesis of pelvic inflammatory disease has not been characterized. | 2001 | 11527890 |
| peptide methionine sulfoxide reductase (msra) is a virulence determinant in mycoplasma genitalium. | mycoplasma genitalium is the smallest self-replicating microorganism and is implicated in human diseases, including urogenital and respiratory infections and arthritides. m. genitalium colonizes host cells primarily through adherence mechanisms mediated by a network of surface-associated membrane proteins, including adhesins and cytadherence-related proteins. in this paper, we show that cytadherence in m. genitalium is affected by an unrelated protein known as peptide methionine sulfoxide reduct ... | 2001 | 11544227 |
| zooming-in on the proteome: very narrow-range immobilised ph gradients reveal more protein species and isoforms. | two-dimensional gel electrophoresis (2-de) enables separation of complex mixtures of proteins on a single polyacrylamide gel according to isoelectric point, molecular weight, solubility, and relative abundance. for this reason, 2-de together with mass spectrometry (ms) has become a key technology in proteome analysis. the introduction of immobilised ph gradients (ipgs) for isoelectric focusing of proteins affords improved reproducibility and permits full-scale proteome analyses to be undertaken. ... | 2001 | 11565781 |
| isolation and identification of mycoplasma genitalium from high risk populations of sexually transmitted diseases in china. | to investigate mycoplasma genitalium (mg) infection in high risk populations of sexually transmitted diseases (stds) in china by means of culture, mg-dna detection, observation under an electron microscope (em) and an atomic force microscope (afm). | 1999 | 11601323 |
| analysis of the gyra and parc genes of mycoplasma genitalium detected in first-pass urine of men with non-gonococcal urethritis before and after fluoroquinolone treatment. | | 2001 | 11679571 |
| how many genes can make a cell: the minimal-gene-set concept. | several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. a comparison of the first two completed bacterial genomes, those of the parasites haemophilus influenzae and mycoplasma genitalium, produced a version of the minimal gene set co ... | 2000 | 11701626 |
| nongonococcal and nonchlamydial cervicitis. | cervicitis encompasses a variety of gynecologic conditions. although inflammation on a papanicolaou smear may be indicative of true cervical inflammation, establishing a diagnosis of mucopurulent cervicitis (mcp) is more clinically useful. mcp seems to be analogous to nongonococcal urethritis in men. many cases of mcp are related to chlamydia trachomatis infection, but the majority of cases have other potential causes. other possible pathogens include neisseria gonorrhoeae, trichomonas vaginalis ... | 2001 | 11722812 |
| phylogeny-based rapid identification of mycoplasmas and ureaplasmas from urethritis patients. | some strains of mycoplasmas and ureaplasmas (family mycoplasmataceae) are associated with nongonococcal urethritis (ngu) or other genitourinary infections. we have developed a rapid and reliable method of identifying the presence and prevalence of mycoplasmas and ureaplasmas in men with ngu. this method is based on the amplification of a part of the 16s rrna gene by pcr and phylogenetic analysis. a portion of the 16s rrna gene from 15 prototype strains was amplified with a set of common primers, ... | 2002 | 11773101 |
| molecular epidemiologic study of mycoplasma genitalium infection in high risk populations of sexually transmitted diseases in china. | to detect mycoplasma genitalium (mg) infection in high risk populations of sexually transmitted diseases (stds) from several cities in china and to clarify the possible role of mg in the pathogenesis of non-gonococcal urethritis. | 2000 | 11776115 |
| stability of cytadherence-related proteins p140/p110 in mycoplasma genitalium requires mg218 and unidentified factors. | tip-mediated cytadherence in mycoplasma genitalium requires the structural and functional stability of the p140 adhesin, its operon-related protein p110, and the high molecular weight protein mg218 (190-kda). disruption mutants of mg218 unable to express mg218 exhibit both a non-cytadhering phenotype and p140/p110 instability, while disruption mutants that synthesize a truncated mg218 (160 kda) retain the stability of p140/p110 and are >95% cytadhering. however, the origin of the mg218 truncated ... | 2002 | 11825623 |
| mycoplasma genitalium: another important pathogen of nongonococcal urethritis. | we reviewed findings on the pathogenic role of mycoplasma genitalium in nongonococcal urethritis and the treatment of men with m. genitalium positive nongonococcal urethritis. | 2002 | 11832700 |
| genital mycoplasmas, including mycoplasma genitalium, as sexually transmitted agents. | mycoplasmas are the smallest free-living organisms, widespread in nature. several mycoplasma species have been isolated from humans. for 6 of them: mycoplasma hominis, ureaplasma urealyticum, m. primatum, m. genitalium, m. spermatophilum and m. penetrans, the genital tract is the main site of colonization. this review is concentrated on the role of mycoplasmas as sexually transmitted agents, with the emphasis to m. genitalium infections. m. hominis and u. urealyticum are isolated from the genita ... | 2002 | 11839161 |
| mycoplasma genitalium -- an up-date. | mycoplasma genitalium was first isolated from men with non-gonococcal urethritis (ngu) more than 20 years ago. use of polymerase chain reaction technology has shown it to be a cause of acute ngu and probably chronic ngu, almost independently of chlamydia trachomatis, but there is no substantial evidence that it causes acute or chronic prostatitis. in women, m. genitalium is not associated with bacterial vaginosis, but it is strongly associated with cervicitis and endometritis and serologically w ... | 2002 | 11860689 |
| association between mycoplasma genitalium and acute endometritis. | up to 70% of cases of pelvic inflammatory disease do not have a known cause. we recruited 115 women who had presented to a clinic for sexually transmitted diseases in nairobi, kenya with pelvic pain that had persisted for 14 days or less, to look for an association between mycoplasma genitalium and endometritis. with pcr, we detected m genitalium in the cervix, endometrium, or both in nine (16%) of 58 women with histologically confirmed endometritis and in one (2%) of 57 women without endometrit ... | 2002 | 11888591 |
| extreme genome reduction in buchnera spp.: toward the minimal genome needed for symbiotic life. | buchnera is a mutualistic intracellular symbiont of aphids. their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. during this coevolutionary process, buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. previous studies reported that genome size in buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lin ... | 2002 | 11904373 |
| quantitative detection of mycoplasma genitalium from first-pass urine of men with urethritis and asymptomatic men by real-time pcr. | we developed a taqman-based real-time pcr assay for quantifying mycoplasma genitalium. this assay is able to specifically quantify concentrations of the m. genitalium 16s rrna gene ranging from 10(7) to 10 copies/reaction. using the taqman assay, we quantified the m. genitalium 16s rrna gene in first-pass urine of men with urethritis and asymptomatic men who were positive for m. genitalium by pcr- and phylogeny-based assay. of 130 men with gonococcal urethritis (gu), five were positive for m. ge ... | 2002 | 11923372 |
| a genome-wide strategy for the identification of essential genes in staphylococcus aureus. | to address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, staphylococcus aureus, using a rapid shotgun antisense rna method. staphylococcus aureus chromosomal dna fragments were cloned into a xylose-inducible expression plasmid and transformed into s. aureus. homology comparisons between 658 s. aureus genes identified in this particular antisense screen and the mycoplasma genitalium genome, which contai ... | 2002 | 11952893 |
| ab initio protein structure prediction on a genomic scale: application to the mycoplasma genitalium genome. | an ab initio protein structure prediction procedure, touchstone, was applied to all 85 small proteins of the mycoplasma genitalium genome. touchstone is based on a monte carlo refinement of a lattice model of proteins, which uses threading-based tertiary restraints. such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. selection of the nati ... | 2002 | 11959918 |
| genomic repeats, genome plasticity and the dynamics of mycoplasma evolution. | mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. we have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of mycoplasma pneumoniae, mycoplasma genitalium, ureaplasma urealyticum and mycoplasma pulmonis. this allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potential ... | 2002 | 11972343 |
| observations on the microbiology of urethritis in black south african men. | the occurrence of neisseria gonorrhoeae, chlamydia trachomatis and mycoplasma genitalium was determined by molecular techniques in urine specimens from 182 black south african men who had symptoms and/or overt signs of urethritis. eighty-six (47.3%) of these men were infected with n. gonorrhoeae. there were 185 men without overt evidence of urethritis, 16 (8.6%) of whom were also infected with n. gonorrhoeae. of the 96 men who had non-gonococcal urethritis, 14 (14.6%) were infected with c. trach ... | 2002 | 11972936 |
| adhesion and inhibition assay of mycoplasma genitalium and m. pneumoniae by immunofluorescence microscopy. | adhesion of mycoplasma pneumoniae and the closely related m. genitalium to hep-2 cells was investigated. the main surface proteins known to be involved in adhesion are p1 of m. pneumoniae and its homologue, mgpa, of m. genitalium. both proteins are also immunodominant proteins. protein p116 is another immunodominant protein of m. pneumoniae. these immunogenic proteins were investigated for their surface exposure and involvement in adhesion to host epithelial cells. immunofluorescence microscopy ... | 2002 | 11990488 |
| high prevalence of mycoplasma genitalium in the lower genitourinary tract of women attending a sexually transmitted disease clinic in paris, france. | previous studies have suggested that mycoplasma genitalium is associated with cervicitis and may be a cause of pelvic inflammatory disease. this study attempted to investigate further the possible role of m genitalium in genital symptoms of women attending a sexually transmitted disease (std) clinic. | 2002 | 12035026 |
| characterization of the mycoplasma hominis ftsz gene and its sequence variability in mycoplasma clinical isolates. | we cloned and sequenced mycoplasma hominis chromosomal fragment containing ftsz gene. the wild-type expression of the gene was shown at rna level by reverse transcription followed by pcr amplification. we revealed that m. hominis ftsz had a comparatively low similarity to proteins of mycoplasma genitalium and mycoplasma pneumoniae. after full ftsz gene sequencing for 14 clinical isolates of m. hominis, single-nucleotide substitutions were found in 21 positions, 6 of them being common for almost ... | 2002 | 12054578 |
| nmr solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from mycoplasma genitalium compared to fk506-binding protein. | we have solved the solution structure of the peptidyl-prolyl cis-trans isomerase (ppiase) domain of the trigger factor from mycoplasma genitalium by homo- and heteronuclear nmr spectroscopy. our results lead to a well-defined structure with a backbone rmsd of 0.23 a. as predicted, the ppiase domain of the trigger factor adopts the fk506 binding protein (fkbp) fold. furthermore, our nmr relaxation data indicate that the dynamic behavior of the trigger factor ppiase domain and of fkbp are similar. ... | 2002 | 12054805 |
| the necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria: amino acid, purine and pyrimidine metabolism in mollicutes. | bacteria of the class mollicutes have no cell wall. one species, mycoplasma genitalium is the personification of the simplest form of independent cell-free life. its small genome (580 kbp) is the smallest of any cell. mollicutes have unique metabolic properties, perhaps because of their limited coding space and high mutability. based on 16s rrna analyses the mollicutes mycoplasma gallisepticum is thought to be the most mutable bacteria. enzyme activities found in most bacteria are absent from mo ... | 2002 | 12133816 |
| prostatitis: what is the role of infection. | although bacterial prostatitis is a common diagnosis, well documented infections of the prostate are uncommon. culture studies of prostate tissue led our group to hypothesize that bacterial colonization/invasion of the prostate gland might occur more commonly than is appreciated by standard microbiological techniques. specific polymerase chain reaction (pcr) assays were used for each of the pathogens previously implicated in chronic prostatitis as well as broad-spectrum pcr assays to identify te ... | 2002 | 12135836 |
| complete nucleotide sequence of the s10-spc operon of phytoplasma: gene organization and genetic code resemble those of bacillus subtilis. | an 11.4-kbp region of genomic dna containing the complete s10-spc operon was constructed by an integrative mapping technique with eight plasmid vectors carrying ribosomal protein sequences from onion yellows phytoplasma. southern hybridization analysis indicated that phytoplasmal s10-spc is a single-copy operon. this is the first complete s10-spc operon of a phytoplasma to be reported, although only a part of six serial genes of the s10 operon is reported previously. the operon has a context of ... | 2002 | 12162807 |
| coexistence of urethritis with genital ulcer disease in south africa: influence on provision of syndromic management. | to assess whether syndromic management of genital ulcer disease was sound, if based on the premise that men with genital ulcers rarely have a concomitant urethral infection. | 2002 | 12181466 |
| mycoplasma genitalium is not associated with adverse outcomes of pregnancy in guinea-bissau. | to evaluate the impact of mycoplasma genitalium on the outcome of pregnancy. | 2002 | 12181470 |
| analysis of heat shock protein 60 encoding genes of mycoplasmas and investigations concerning their role in immunity and infection. | only little is known about the heat shock proteins (hsp) and hsp-encoding genes of mycoplasmas. the aim of this study was to identify and sequence the hsp60 gene of mycoplasma agalactiae, mycoplasma arthritidis, mycoplasma bovis, and mycoplasma hyopneumoniae, and to investigate the immune response to hsp60. fragments of the hsp60 genes of m. agalactiae, m. arthritidis, m. bovis and m. hyopneumoniae representing almost the entire coding region were amplified by pcr. two fragments of a hsp60 gene ... | 2002 | 12243891 |
| longitudinal quantitative detection by real-time pcr of mycoplasma genitalium in first-pass urine of men with recurrent nongonococcal urethritis. | by using a taqman assay we monitored longitudinal changes in mycoplasma genitalium loads in five men with recurrent m. genitalium-positive nongonococcal urethritis. we observed regrowth of m. genitalium persisting in hosts after treatment and a possible association of the increase in the m. genitalium load with emergence of symptoms and signs of nongonococcal urethritis in four of these patients. | 2002 | 12354899 |
| do all men attending departments of genitourinary medicine need to be screened for non-gonococcal urethritis? | we investigated the influence of symptoms and signs on the detection of chlamydia trachomatis, mycoplasma genitalium and ureaplasma urealyticum organisms (ureaplasmas) in men with non-gonococcal urethritis (ngu). two hundred and forty-two men attending the jefferiss wing at st mary's hospital for a sexual health assessment were evaluated, of whom 169 had ngu. urethral inflammation was diagnosed if there were either > or =5 polymorphonuclear leucocytes (pmnls) per high-power field (hpf) in five o ... | 2002 | 12396535 |
| mycoplasma genitalium infections in asymptomatic men and men with urethritis attending a sexually transmitted diseases clinic in new orleans. | we report the results of a study of mycoplasma genitalium (detected with a modified polymerase chain reaction [pcr] assay) in men with urethritis and in asymptomatic control subjects at a sexually transmitted diseases clinic in new orleans. data for 97 men with urethritis and 184 asymptomatic men were available for analysis. m. genitalium infection rates in symptomatic and asymptomatic men who were negative for chlamydia trachomatis and neisseria gonorrhoeae were 25% and 7%, respectively (p=.006 ... | 2002 | 12410476 |