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PubMed2001

The distributed annotation system.

BACKGROUND: Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. RESULTS: Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. CONCLUSIONS: The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

Base Sequence↗

PubMed2002

Comparison of cytogenetic and molecular cytogenetic detection of chromosome abnormalities in 240 consecutive adult patients with acute myeloid leukemia.

PURPOSE: To prospectively compare cytogenetic and molecular cytogenetic analysis for the detection of the most relevant chromosome abnormalities in a large series of patients with acute myeloid leukemia (AML). PATIENTS AND METHODS: Two hundred forty consecutive adult patients with AML entered onto the multicenter treatment trial AML HD93 were studied. Chromosome banding and fluorescence in situ hybridization (FISH) applying a comprehensive set of genomic DNA probes were performed in a single reference laboratory. RESULTS: Two cases of inv(16), three cases of t(11q23), and three cases of t(8;21)var were only detected by molecular cytogenetics. By FISH, aberrations were identified in three cases with normal karyotypes: inv(16), -Y (in a patient with low metaphase yield on chromosome banding) and a 12p microdeletion. Additional aneuploidies, in particular +8q and +11q, were diagnosed by FISH; however, virtually all these aberrations occurred in patients with complex karyotypes or as an additional abnormality in leukemias with an AML-specific translocation. Finally, aberrations were detected by FISH in eight of 14 patients with no assessable metaphases. CONCLUSION: In most cases of AML, conventional cytogenetic study reliably detects chromosomal abnormalities, and this method should not be replaced by FISH. FISH should be used as a complementary method for the detection of more subtle abnormalities, such as inv(16) and t(11q23), in all patients with newly diagnosed AML and for suspected t(8;21)var. Furthermore, molecular cytogenetics using this comprehensive set of DNA probes provides a valuable diagnostic tool for patients with poor chromosome morphology, low or no yields of metaphase cells, or both.

Acute Disease↗

PubMed2000

Identification of a new missense mutation (Gly95Glu) in a highly conserved codon within the high-mobility group box of the sex-determining region Y gene: report on a 46,XY female with gonadal dysgenesis and yolk-sac tumor.

Leydig cells and Sertoli cells of the testes produce hormones that cause male differentiation, if receptors are present. The Y chromosomal SRY gene (sex determining Region Y gene) acts as TDF and is required for regular male sex determination. SRY represents a transcription factor belonging to the superfamily of genes sharing the HMG-box motif(high-mobility group-box), which acts as DNA binding region. Here, we describe a nonmosaic XY sex-reversed female with pure gonadal dysgenesis (46,XY karyotype, completely female external genitalia, normal Müllerian ducts, absence of Wolffian ducts, streak gonads) who harbored a yolk-sac tumor and was referred for the assessment of primary amenorrhea. Using genomic PCR analysis, a 423-bp PCR product, encompassing the HMG-box of the SRY gene, was amplified from the proposita, her father, and her three brothers, whereas no band was visible in the patient's mother and her three sisters. The PCR products were sequenced for mutations subsequently. A new de novo missense mutation within the HMG-box of the SRY gene was discovered in the proposita. A G is replaced by an A in codon 95 at position +284, resulting in the replacement of the nonpolar aminoacid glycine by the polar amino acid glutamate. The glycine at codon 95 is highly conserved between the family of HMG-box proteins and between species. This point mutation has not been described earlier and brings the total number of SRY mutations described so far to 36, each mutation being unique. This mutation was not detected in the patient's father and her male siblings. The present data provide further evidence to support the functional importance of the putative DNA binding activity of the SRY HMG-box domain.

Adult↗

PubMed2002

The serum resistance-associated gene as a diagnostic tool for the detection of Trypanosoma brucei rhodesiense.

In the search for new diagnostic methods that would distinguish Trypanosoma brucei rhodesiense from T. b. brucei and T. b. gambiense, we have developed two polymerase chain reaction (PCR) primer sets. The first primer set was derived from the serum resistance-associated (SRA) gene of T. b. rhodesiense that confers resistance to lysis by normal human serum (NHS). The specificity of the SRA-based PCR was tested on 97 different trypanosome populations originating from various taxonomic groups, host species, and geographic regions. Only one of 25 T. b. rhodesiense samples was negative in this PCR, and none of 72 other samples were positive in this assay. Interestingly, a reference T. brucei strain (TREU927/4) currently used for genome sequencing was negative for the SRA gene; however, this strain was resistant to lysis by NHS. The second primer set was derived from a specific variant surface glycoprotein (VSG) expression site where the SRA gene is expressed (R-ES). This primer set identified the strain as T. b. rhodesiense in 17 of 17 SRA gene-positive strains in which it was tested. These data strongly suggest that expression of the SRA gene is generally involved in resistance to lysis by NHS in T. b. rhodesiense strains.

Amino Acid Sequence↗

PubMed1999

Use of RAPD-PCR fingerprinting to detect genetic diversity of soil Streptomyces isolates.

Random amplified polymorphic DNA (RAPD) was used for identification and assessment of genetic diversity between isolates of Streptomyces from soil. Genomic DNA from 18 Streptomyces isolates and 2 reference strains were amplified using four different 10-mer primers. Different DNA fingerprinting patterns were obtained for all the isolates. Electrophoretic and cluster analysis of the amplification products revealed incidence of polymorphism among the isolates and none of them was identical to the reference strains although there were some common amplification bands. Two highly divergent groups were determined among the isolates. The results indicate that RAPD is an efficient method for discriminating and studying genetic diversity of Streptomyces isolates.

DNA, Bacterial↗

PubMed2000

Clinical significance of hepatitis C virus genotypes and quasispecies.

Hepatitis C virus (HCV) is a major cause of morbidity and mortality worldwide. The infection becomes chronic in about 85% of infected individuals, in the face of a strong humoral and cellular immune response. One of the most important features of HCV is its high degree of genetic variability, which is due to the inherent low fidelity of the viral replication machinery. As a consequence, HCV circulates in vivo as a population of divergent, albeit closely related, genomes exhibiting a distribution that follows the model referred to as a quasispecies. The genetic variability of HCV is complex and has been classified into four hierarchical strata: genotypes, subgenotypes, isolates, and quasispecies. Over the past few years, an extraordinary interest has been focused on the biologic and clinical implications of the genetic variability of HCV. Although there is consensus that the genotypes may influence the out come of antiviral therapy, their clinical significance in the natural history of the disease, as well as in transmission, infectivity, and pathogenesis of HCV infection, remains elusive. Conversely, evidence has accumulated that the quasispecies nature of HCV provides a large reservoir of biologically different viral variants that may have important clinical implications for viral persistence by immune escape mechanisms, for the generation of antiviral drug resistance, and for the development of an effective vaccine. This article reviews the state of the art on the biologic and clinical implications of the genetic variability of HCV.

DNA Replication↗

PubMed1978

[The smallpox vaccination strain MVA: marker, genetic structure, experience gained with the parenteral vaccination and behavior in organisms with a debilitated defence mechanism (author's transl)].

The MVA virus is a lab virus ideally suited for vaccination of both man and animal which can be differentiated from the known Vaccinia strains by the use of numerous biological markers. Its reduced virulence for the chick embryo, for experimental animals and for man is a particularly characteristic feature. With the exception of chick embryo fibroblasts, the MVA virus grows in cell cultures only abortively. This applies particularly to cells of human origin in which the cytopathic effect and plaque formation are completely missing. The restriction analysis of the DNS of the MVA virus demonstrates that its genetic structure differs from that of the CVA basic virus and other orthopox viruses. In contrast to the WHO reference strain Elstree, the MVA virus has a genome shortened by about 9 per cent. The use of the MVA virus for human vaccination is particularly indicated in persons to be vaccinated for the first time and likely to entail a risk (on account of allergies etc.) because it brings about a state of revaccination without complications. The MVA virus can be administered in intracutaneous, subcutaneous or intramuscular injections. Innocuoursness and successful vaccination have been demonstrated in more than 120000 persons. While other Vaccinia strains, such as the Elstree virus, experience a drastic increase of virulence in the immunosuppressed organism (subjected to whole-body irradiation), the MVA virus cannot be activated not even in this situation.

Animals↗

PubMed1998

Rapid detection of enteroviral RNA in cerebrospinal fluid (CSF) from patients with aseptic meningitis by reverse transcription-nested polymerase chain reaction.

The aim of this study was to compare conventional enterovirus isolation with rapid detection of enteroviral RNA by a reverse transcription-nested polymerase chain reaction (RT-nPCR) method amplifying the 5' nontranslated region of the enteroviral genome in specimens from patients with aseptic meningitis. Reference enterovirus strains and clinical enterovirus isolates were analyzed to evaluate assay sensitivity and specificity. All known enteroviral serotypes tested, but one (echovirus type 22), were detected by RT-nPCR. A series of unrelated viral isolates as well as CSF samples from patients with meningitis/encephalitis or neurological syndromes unrelated to enterovirus infection were included as controls. A total of 47 specimens (31 CSF, 12 rectal swabs, 4 throat swabs) from 30 patients with aseptic meningitis were available for the study. Of the 31 CSF samples tested from 30 patients, 17 from 17 patients (54.8%) were positive by RT-nPCR, while only 10 from 10 patients (32.2%) were positive by culture. Thus, RT-nPCR allowed diagnosis of enterovirus meningitis in 7 additional patients compared to cell culture. The cytopathic effect was observed 5-15 days after inoculation of CSF specimens onto cell cultures, while direct detection of viral RNA in CSF samples by RT-nPCR permitted diagnosis of enteroviral meningitis within 1-2 days. On the whole, viral isolation was positive in 12/47 (25.5%) specimens, whereas viral RNA was detected by RT-nPCR in 11 additional samples (23/47, 48.9%). Specimens of the control group were consistently negative by both viral isolation and RT-nPCR. Restriction endonuclease analysis of PCR products (RFLP) was applied to differentiate poliovirus (PV) from non-polio enteroviruses (NPEV). All enterovirus strains detected in clinical samples (n = 23) were identified as NPEV by RFLP. Clinical isolates were typed by neutralization as echovirus type 30 (n = 6), while 6 were not typed. In conclusion, detection of enteroviral RNA in CSF by RT-nPCR allows: i) rapid diagnosis of enteroviral meningitis; ii) increased sensitivity with respect to virus isolation; iii) differentiation between PV and NPEV infections of the central nervous system.

Adolescent↗

PubMed2006

Effect of various normalization methods on Applied Biosystems expression array system data.

BACKGROUND: DNA microarray technology provides a powerful tool for characterizing gene expression on a genome scale. While the technology has been widely used in discovery-based medical and basic biological research, its direct application in clinical practice and regulatory decision-making has been questioned. A few key issues, including the reproducibility, reliability, compatibility and standardization of microarray analysis and results, must be critically addressed before any routine usage of microarrays in clinical laboratory and regulated areas can occur. In this study we investigate some of these issues for the Applied Biosystems Human Genome Survey Microarrays. RESULTS: We analyzed the gene expression profiles of two samples: brain and universal human reference (UHR), a mixture of RNAs from 10 cancer cell lines, using the Applied Biosystems Human Genome Survey Microarrays. Five technical replicates in three different sites were performed on the same total RNA samples according to manufacturer's standard protocols. Five different methods, quantile, median, scale, VSN and cyclic loess were used to normalize AB microarray data within each site. 1,000 genes spanning a wide dynamic range in gene expression levels were selected for real-time PCR validation. Using the TaqMan assays data set as the reference set, the performance of the five normalization methods was evaluated focusing on the following criteria: (1) Sensitivity and reproducibility in detection of expression; (2) Fold change correlation with real-time PCR data; (3) Sensitivity and specificity in detection of differential expression; (4) Reproducibility of differentially expressed gene lists. CONCLUSION: Our results showed a high level of concordance between these normalization methods. This is true, regardless of whether signal, detection, variation, fold change measurements and reproducibility were interrogated. Furthermore, we used TaqMan assays as a reference, to generate TPR and FDR plots for the various normalization methods across the assay range. Little impact is observed on the TP and FP rates in detection of differentially expressed genes. Additionally, little effect was observed by the various normalization methods on the statistical approaches analyzed which indicates a certain robustness of the analysis methods currently in use in the field, particularly when used in conjunction with the Applied Biosystems Gene Expression System.

Algorithms↗

PubMed2004

Effect of sex and age on serum biochemical reference ranges in C57BL/6J mice.

The C57BL/6J mouse strain is widely used as a common genomic background for many gene-modified murine models. However, few data on its clinical biochemistry are available. Therefore, we conducted a study to provide new protocols for serum biochemical screening and developed the reference range for a set of 13 analytes that pertain to lipoprotein metabolism, electrolyte balance, and data reflecting function of the heart, liver, kidneys, and pancreas. Male and female mice were studied, and blood samples were obtained at six and 20 weeks of age. Of 13 parameters studied, 12 were affected by age and sex. Briefly, male mice had higher triglycerides, cholesterol, high-density lipoprotein cholesterol, glucose, and amylase values. With age, mice of both sexes developed higher triglycerides and glucose concentrations, as well as aspartate and alanine transaminase activities. A significant difference between mice and humans was noted for amylase activity, which is extremely high in this healthy mouse strain. Therefore, we suggest that caution should be taken when data are interpreted to indicate gastrointestinal disease in murine models. The reference values for murine clinical biochemical analytes obtained during the study reported here should be useful for characterizing the biochemical phenotype of experimental mice.

Aging↗

PubMed2005

Characterization of hMLH1 and hMSH2 gene dosage alterations in Lynch syndrome patients.

BACKGROUND & AIMS: A significant proportion of Lynch syndrome cases are believed to be due to large genomic alterations in the mismatch repair genes hMLH1 and hMSH2. However, previous studies have not adequately identified the frequency and scope of such mutations, and routine clinical Lynch syndrome testing often does not include analysis for these mutations. Our aim was to characterize hMLH1 and hMSH2 genomic rearrangements in a large population of suspected Lynch syndrome patients. METHODS: A total of 365 samples from probands referred for genetic testing for Lynch syndrome were analyzed for the presence of large genomic alterations in hMLH1 or hMSH2 by using a combination of techniques. Samples with a deletion in exons 1-6 in hMSH2 were further characterized by polymerase chain reaction to establish the presence of the hMSH2 American founder deletion. RESULTS: An hMLH1 or hMSH2 mutation was identified in 153 cases, and, of these, 12 of 67 (17.9%) and 39 of 86 (45.3%) had a large genomic alteration in hMLH1 and hMSH2, respectively. Overall, 6 different hMLH1 and 12 different hMSH2 deletions/duplications, including 10 novel mutations, were identified. Analysis of the hMSH2 exon 1-6 deletion samples showed that 13 of 18 (72.2%) had the American founder deletion. CONCLUSIONS: These data show a high frequency and diverse spectrum of large genomic alterations in hMLH1 and hMSH2 in suspected Lynch syndrome patients. Thus, a comprehensive mutation identification strategy that includes the ability to detect large genomic rearrangements is imperative for the clinical genetic identification of Lynch syndrome patients and families.

Adaptor Proteins, Signal Transducing↗

PubMedDate not supplied

Tissue subtraction DNA in situ hybridization (TSDISH): in situ detection of DNA abnormalities in formalin-fixed paraffin-embedded tissue sections by subtraction hybridization with whole genomic DNA.

We have developed a novel in situ histochemical method of screening for genetic alterations of human malignancies by subtraction hybridization of genomic DNA without employing specific probes to give a colorimetric reaction. We identified a t(13;14) chromosome abnormality in the chromosome spread of a patient with multiple myeloma. In situ hybridization of a whole cell preparation of MCF-7 cell demonstrated reaction products as intranuclear dots-in all MCF-7 cells. We subsequently examined the cells of different foci of esophageal squamous cell carcinoma(10) and esophageal biopsy specimens (9) by this method. Hybridization with genomic DNA from the patients demonstrated no reaction products in the stromal cells of the esophagus. However, hybridization with reference DNA from a healthy individual demonstrated intranuclear reaction products in the stromal cells, possibly due to individual genomic differences. There were more intranuclear reaction products in the carcinoma cells than in the stromal cells when hybridized with reference DNA. When hybridized with the reference DNA above, the cells of the non-pathologic epithelium of 8 of 10 malignant esophagi demonstrated significantly more reaction product than the stromal cells of the some specimens. This was not detected in the cells of normal epithelium obtained from non-cancerous esophagi suggesting the accumulation of genetic alterations of the non-malignant epithelium of the cancerous esophagus. This method is thought to detect DNA alterations, including those which have not been previously identified, using genomic DNA for hybridization, and the results can be correlated with the morphological findings. Application of this in situ method, together with other molecular genetic techniques may contribute to the analysis of various genetic alterations of human malignancies using archival material.

Chromosome Aberrations↗

PubMed2006

New commercially available PCR and microplate hybridization assay for detection and differentiation of human polyomaviruses JC and BK in cerebrospinal fluid, serum, and urine samples.

JC and BK human polyomaviruses (family Polyomaviridae) may cause severe neurological or urinary tract pathologies in immunocompromised hosts. In the present study, we evaluated a new commercially available PCR and microplate colorimetric hybridization assay for the standardized differential detection of JC virus (JCV) and BK virus (BKV) genomes in clinical samples. This JC/BK Consensus test was first evaluated by testing serial dilutions of JCV or BKV plasmid DNA standards and was then compared with an in-house reference PCR assay for the detection of JC and BK virus genomes in 70 cerebrospinal fluid (CSF) samples of patients with neurological disorders and in 75 serum or plasma samples and 125 urine samples of renal graft recipients. This new test allowed a limit of detection of 10 copies and 1 copy of JC and BK virus genomes, respectively, and was able to differentiate various levels of JCV, BKV, and mixed JCV and BKV DNA genomes in a single reaction tube. Our results showed 100% specificity and sensitivity for the JC/BK Consensus test with CSF samples. With serum or plasma samples, this test had a sensitivity and a specificity of 100% for both JCV and mixed JCV and BKV DNA detection and a sensitivity and a specificity of 100 and 97.8% for BKV DNA detection, respectively. With urine samples, the sensitivity and specificity were 100 and 96.6%, respectively, for JCV DNA detection; 100 and 89.4%, respectively, for BKV DNA detection; and 44.4 and 100%, respectively, for mixed JCV and BKV DNA detection. In conclusion, our data indicate that this new test, the JC/BK Consensus test, is valuable for the sensitive and specific differential detection of single JCV and BKV infections in CSF, serum or plasma, and urine samples. The use of this reliable PCR assay would improve the routine virological diagnosis as well as the clinical care of immunocompromised patients with polyomavirus-related pathologies.

Adult↗

PubMed2006

Designing new methodologies for integrating biomedical information in clinical trials.

OBJECTIVES: To propose a modification to current methodologies for clinical trials, improving data collection and cost-efficiency. To describe a system to integrate distributed and heterogeneous medical and genetic databases for improving information access, retrieval and analysis of biomedical information. METHODS: Data for clinical trials can be collected from remote, distributed and heterogeneous data sources. In this distributed scenario, we propose an ontologybased approach, with two basic operations: mapping and unification. Mapping outputs the semantic model of a virtual repository with the information model of a specific database. Unification provides a single schema for two or more previously available virtual repositories. In both processes, domain ontologies can improve other traditional approaches. RESULTS: Private clinical databases and public genomic and disease databases (e.g., OMIM, Prosite and others) were integrated. We successfully tested the system using thirteen databases containing clinical and biological information and biomedical vocabularies. CONCLUSIONS: We present a domain-independent approach to biomedical database integration, used in this paper as a reference for the design of future models of clinico-genomic trials where information will be integrated, retrieved and analyzed. Such an approach to biomedical data integration has been one of the goals of the IST INFOBIOMED Network of Excellence in Biomedical Informatics, funded by the European Commission, and the new ACGT (Advanced Clinico-Genomic Trials on Cancer) project, where the authors will apply these methods to research experiments.

Clinical Trials as Topic↗

PubMed1998

A comparative analysis of ABC transporters in complete microbial genomes.

The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an "ortholog group table" by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set for functional assignment in four additional genomes. In general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. In Synechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.

ATP-Binding Cassette Transporters↗

PubMed2004

Cross-sectional analysis of clinical and environmental isolates of Pseudomonas aeruginosa: biofilm formation, virulence, and genome diversity.

Chronic lung infections with Pseudomonas aeruginosa biofilms are associated with refractory and fatal pneumonia in cystic fibrosis (CF). In this study, a group of genomically diverse P. aeruginosa isolates were compared with the reference strain PAO1 to assess the roles of motility, twitching, growth rate, and overproduction of a capsular polysaccharide (alginate) in biofilm formation. In an in vitro biofilm assay system, P. aeruginosa displayed strain-specific biofilm formation that was not solely dependent on these parameters. Compared with non-CF isolates, CF isolates expressed two opposing growth modes: reduced planktonic growth versus efficient biofilm formation. Planktonic cells of CF isolates showed elevated sensitivity to hydrogen peroxide, a reactive oxygen intermediate, and decreased lung colonization in an aerosol infection mouse model. Despite having identical genomic profiles, CF sequential isolates produced different amounts of biofilm. While P. aeruginosa isolates exhibited genomic diversity, the genome size of these isolates was estimated to be 0.4 to 19% (27 to 1,184 kb) larger than that of PAO1. To identify these extra genetic materials, random amplification of polymorphic DNA was coupled with PAO1-subtractive hybridization. Three loci were found within the genomes of two CF isolates encoding one novel homolog involved in retaining a Shigella virulence plasmid (mvpTA) and two divergent genes that function in removing negative supercoiling (topA) and biosynthesis of pyoverdine (PA2402). Together, P. aeruginosa biodiversity could provide one cause for the variation of morbidity and mortality in CF. P. aeruginosa may possess undefined biofilm adhesins that are important to the development of an antibiofilm therapeutic target.

Animals↗

PubMed2006

Determination of genomic damage in neuroblastic tumors by arbitrarily primed PCR: MYCN amplification as a marker for genomic instability in neuroblastomas.

The aim of this study is to establish an estimation of the global genomic alteration in neuroblastic tumors (ganglioneuromas, ganglioneuroblastomas and neuroblastomas) and correlate them with different clinical parameters (age, sex, diagnosis, Shimada index, proliferation index, tumor location, and 1p and v-myc avian myelocitomatosis viral-related (MYCN) status) in order to find new molecular and/or prognostic markers for neuroblastoma. To assess the genomic damage in neuroblastic tumors, we used an arbitrarily primed PCR approach, a technique based on the reproducibility of band profiles obtained by a PCR with a low annealing temperature in its first cycles. Genomic damage was assessed by comparing band profiles of tumors and normal paired samples. Gains and losses in the intensity of the bands were computerized and referred to the total number of bands analyzed. We found a higher genomic damage fraction (GDF) in the female's group (U-Mann-Whitney, P = 0.025), but we could not find any association between GDF and tumor location, proliferation index, diagnosis or age of the patient. There was no relationship between 1p status and GDF, but tumors with MYCN amplification had a slightly higher GDF. MYCN amplification might in some way contribute to genomic instability of neuroblastomas.

Child, Preschool↗

PubMed2003

Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates.

We previously reported that laboratory reference strains of Chlamydia trachomatis differing in infection organotropism correlated with inactivating mutations in the pathogen's tryptophan synthase (trpBA) genes. Here, we have applied functional genomics to extend this work and find that the paradigm established for reference serovars also applies to clinical isolates - specifically, all ocular trachoma isolates tested have inactivating mutations in the synthase, whereas all genital isolates encode a functional enzyme. Moreover, functional enzyme activity was directly correlated to IFN-gamma resistance through an indole rescue mechanism. Hence, a strong selective pressure exists for genital strains to maintain a functional synthase capable of using indole for tryptophan biosynthesis. The fact that ocular serovars (serovar B) isolated from the genital tract were found to possess a functional synthase provided further persuasive evidence of this association. These results argue that there is an important host-parasite relationship between chlamydial genital strains and the human host that determines organotropism of infection and the pathophysiology of disease. We speculate that this relationship involves the production of indole by components of the vaginal microbial flora, allowing chlamydiae to escape IFN-gamma-mediated eradication and thus establish persistent infection.

Antigens, Bacterial↗