Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37.

The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ϕR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ϕR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ϕR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ϕKZ. The tail of ϕR1-37 has a contractile sheath. We conclude that phage ϕR1-37 is a representative of a novel phage type that carries the dU-containing genome in a ϕKZ-like head.

Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing.

Multilocus sequence analysis of 417 strains of Yersinia pseudotuberculosis revealed that it is a complex of four populations, three of which have been previously assigned species status [Y. pseudotuberculosis sensu stricto (s.s.), Yersinia pestis and Yersinia similis] and a fourth population, which we refer to as the Korean group, which may be in the process of speciation. We detected clear signs of recombination within Y. pseudotuberculosis s.s. as well as imports from Y. similis and the Korean group. The sources of genetic diversification within Y. pseudotuberculosis s.s. were approximately equally divided between recombination and mutation, whereas recombination has not yet been demonstrated in Y. pestis, which is also much more genetically monomorphic than is Y. pseudotuberculosis s.s. Most Y. pseudotuberculosis s.s. belong to a diffuse group of sequence types lacking clear population structure, although this species contains a melibiose-negative clade that is present globally in domesticated animals. Yersinia similis corresponds to the previously identified Y. pseudotuberculosis genetic type G4, which is probably not pathogenic because it lacks the virulence factors that are typical for Y. pseudotuberculosis s.s. In contrast, Y. pseudotuberculosis s.s., the Korean group and Y. pestis can all cause disease in humans.

Penetrance and phenotype of the Thr377Met Myocilin mutation in a large Finnish family with juvenile- and adult-onset primary open-angle glaucoma.

PURPOSE: To study the role of myocilin (MYOC) as a susceptibility gene for juvenile- and adult-onset open-angle glaucoma (JOAG and POAG, respectively). METHODS: In a six-generation Finnish family with JOAG and POAG, we performed thorough ophthalmologic characterization (including assessment of the visual fields by Octopus perimetry, nerve-fiber layer thickness by photography, and disc size by Heidelberg tomography) of 51 individuals. The coding region of MYOC was screened for mutations by PCR amplification and direct sequencing. RESULTS: We detected a C > T transition at codon 377 resulting in a substitution of a threonine residue for methionine (Thr377Met) in the olfactomedin-like domain of myocilin, segregating in the family. Of the 20 individuals heterozygous for the mutation, nine (45%) were glaucomatous and two (10%) had ocular hypertension (OHT). The mean age at diagnosis of glaucoma in these individuals was 34.3 years (range: 14-66 years). Moreover, three of these individuals suffered retinal vein occlusion (RVO) in one eye, while one individual without the mutation had RVO. CONCLUSION: Our results further support the evidence that the Thr377Met mutation in MYOC may represent a susceptibility allele for glaucoma. These findings may facilitate genetic counseling, and early diagnosis and treatment of glaucoma. The possible interaction of factors contributing to RVO in conjunction with the Thr377Met mutation warrants further investigation.

Ultrastructural and chromosomal studies on manganese superoxide dismutase in malignant mesothelioma.

Mesothelioma represents an aggressive tumor type with high resistance to all treatment modalities. Its pathogenesis is strongly associated with exposure to asbestos fibers and probably with free radicals. One of the most important free radical scavenging enzymes, mitochondrial manganese superoxide dismutase (MnSOD), has been shown to be elevated in mesothelioma (K. Kahlos et al., 1998, Am. J. Respir. Cell Mol. Biol. 18:570-580). In the present study, we could detect intense ultrastructural accumulation of MnSOD in the mitochondrial compartment of malignant mesothelioma cells. There was no association between the immunohistochemical reactivity and the most common and functional polymorphic variant of MnSOD, the Ala to Val amino acid change at 9 position (16th amino acid from the beginning of the signal sequence), in the 31 mesothelioma cases investigated. Comparative genomic hybridization and fluorescence in situ hybridization did not reveal any changes in chromosome 6, where the MnSOD gene is located. Sequencing of the MnSOD promoter region in four mesothelioma cell lines showed similar nucleotide variables in the malignant and nonmalignant cells. Therefore, the intense expression of MnSOD in the mitochondria of mesothelioma cells does not appear be associated with any major chromosomal alterations or the polymorphism of MnSOD gene. Association with oxidative/nitrosative stress in mesothelioma using nitrotyrosine immunostaining pointed to a tendency for more intense reactivity in those mesotheliomas with higher MnSOD expression (P = 0.069).

The role of TIGR and OPTN in Finnish glaucoma families: a clinical and molecular genetic study.

PURPOSE: The aim of the present study was to analyze the role of the two primary open angle glaucoma (POAG) genes, trabecular meshwork-induced glucocorticoid response (TIGR/MYOC) and optineurin (OPTN), in Finnish glaucoma families originating from southern coast of Finland. METHODS: In total, 136 patients were examined to determine their ophthalmological status. Genealogical studies were performed using church records. Direct PCR-sequencing of the coding regions of the TIGR and OPTN genes was performed in 11 subjects. RESULTS: Inheritance resembling autosomal dominant mode was detected in eight families with open-angle glaucoma. Glaucoma was diagnosed in 53 subjects, of them 44 had POAG, 7 had exfoliative glaucoma (EG), and 2 had other types of glaucoma. Of the first degree relatives, 22 out of 79 (28%) were glaucoma suspects. No mutations in these families were identified. Instead, two polymorphisms in the TIGR gene and three polymorphisms in the OPTN gene, in which one was novel, were found in three phenotypes: POAG, exfoliative glaucoma, and exfoliation syndrome. CONCLUSIONS: Our results give evidence that novel, unidentified genes will underlie POAG and exfoliation syndrome in the Finnish population.

Genetic screening for maternal uniparental disomy of chromosome 7 in prenatal and postnatal growth retardation of unknown cause.

OBJECTIVE: Many short-statured children lack an etiologic explanation for their retarded growth. Recently, uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair from only 1 parent, has been associated with short stature for many chromosomes. Silver-Russell syndrome (SRS) represents an extreme syndrome of intrauterine growth retardation (IUGR) and slight dysmorphic signs, and maternal UPD of human chromosome 7 (matUPD7) has been observed in approximately 10% of SRS cases. In addition, matUPD7 has been reported in patients with only slight dysmorphic features and prenatal or postnatal growth retardation. The objectives of this study were to study the role of matUPD7 in growth failure of unknown cause and in cases of SRS, and to evaluate the efficiency of genetic testing for matUPD7 as a diagnostic tool. METHODS: DNA samples were studied from 205 children, 92 girls and 113 boys, with short stature of unknown cause and their parents. The patient cohort included 39 cases of SRS, 91 patients with IUGR and subsequent postnatal short stature, and 75 patients with postnatal growth retardation only. MatUPD7 was screened for by genotyping DNA samples from the patient, mother, and father with 13 chromosome-7-specific polymorphic microsatellite markers. RESULTS: Six (3%) of 205 matUPD7 cases were observed exclusively among 39 (15%) SRS patients studied. Patients with IUGR and/or postnatal growth retardation and with dysmorphic features did not reveal cases of matUPD7. CONCLUSIONS: Our results indicate that matUPD7 cases are predominantly observed among patients meeting the criteria of SRS, and matUPD7 is not a common cause for growth retardation. Genetic screening for cases of matUPD7 among growth-retarded patients should be focused on patients with severe IUGR and features of SRS. In addition, matUPD7 screening is advisable in individuals with cystic fibrosis and other recessive disorders mapped to chromosome 7 who have unusually short stature.