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PubMed1998

Accurate sequencing by hybridization for DNA diagnostics and individual genomics.

Medical DNA diagnostics will increasingly rely on an accurate and inexpensive identification of mutations that affect the function of a gene. To validate diagnostic sequencing by hybridization (SBH), a number of p53 samples were analyzed with the complete set of 8192 noncomplementary 7-mer oligonucleotides. In four repeated, blind experiments we accurately sequenced 1.1 kb per each of 12 homozygote and heterozygote samples possessing base substitutions, insertions, and deletions. This SBH variant offers a high throughput platform to inexpensively sequence individual gene or pathogen genome samples within the clinical laboratory setting.

DNA↗
PubMed2002

Mutations in the DNAH11 (axonemal heavy chain dynein type 11) gene cause one form of situs inversus totalis and most likely primary ciliary dyskinesia.

Primary ciliary dyskinesia (PCD; MIM 242650) is an autosomal recessive disorder of ciliary dysfunction with extensive genetic heterogeneity. PCD is characterized by bronchiectasis and upper respiratory tract infections, and half of the patients with PCD have situs inversus (Kartagener syndrome). We characterized the transcript and the genomic organization of the axonemal heavy chain dynein type 11 (DNAH11) gene, the human homologue of murine Dnah11 or lrd, which is mutated in the iv/iv mouse model with situs inversus. To assess the role of DNAH11, which maps on chromosome 7p21, we searched for mutations in the 82 exons of this gene in a patient with situs inversus totalis, and probable Kartagener syndrome associated with paternal uniparental disomy of chromosome 7 (patUPD7). We identified a homozygous nonsense mutation (R2852X) in the DNAH11 gene. This patient is remarkable because he is also homozygous for the F508del allele of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Sequence analysis of the DNAH11 gene in an additional 6 selected PCD sibships that shared DNAH11 alleles revealed polymorphic variants and an R3004Q substitution in a conserved position that might be pathogenic. We conclude that mutations in the coding region of DNAH11 account for situs inversus totalis and probably a minority of cases of PCD.

Axonemal Dyneins↗
PubMed1997

Identification of a promoter for the latent membrane protein 1 gene of Epstein-Barr virus that is specifically activated in human epithelial cells.

Latent membrane protein 1 (LMP 1) is one of two Epstein-Barr virus (EBV)-encoded proteins that expressed in nasopharyngeal carcinoma (NPC) cells. Previous studies showed that a 3.5-kb transcript of the LMP 1 gene, in addition to the 2.8-kb transcript, was detected in a B95-8-EBV-containing, nude mice-passaged NPC tumor, C15. This indicated that a transcript was initiated from a region 5' to the putative promoter, ED-L1. We have isolated an EBV variant from a NPC tissue, and this virus strain contained a more pathogenic LMP 1 gene. DNA sequence analysis of the 5'-upstream region showed distinct variations as compared to that of B95-8 strain. To test if the LMP 1 gene of the NPC strain also contained an upstream promoter, we generated a series of deletion plasmids encompassing positions -1,030 to +20 of the LMP 1 promoter and tested for their abilities to drive the expression of the reporter gene in human epithelial cell lines, C-33A and NPC-TW076. We found that the region between -643 and -496 contained a promoter activity that was approximately five-fold higher than the putative promoter, ED-L1. This region between -643 and -496 was designated as ED-L1E. C-33A cells containing the genomic clone pT7(E) or the clone that had deleted a 94-bp ED-L1 sequence (delta94) was used to determine the transcription initiation sites by RNase protection assay. Results showed that a transcription initiation site was located at nucleotide 170,099 ("A") of EBV genome. The transcript was expressed in NPC biopsies and in human primary normal epithelial cells transfected with pT7(E) and delta94, respectively, as examined by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Furthermore, the ED-L1E was not regulated by the EBV-encoded nuclear antigen 1-mediated transcriptional enhancer family of repeats (FR) in C-33A cells. Our results suggested that the ED-L1E was specifically activated in epithelial cells. The biological significance of the selective usage of the ED-L1E promoter was discussed.

B-Lymphocytes↗
PubMed2000

A new Shiga toxin 2 variant (Stx2f) from Escherichia coli isolated from pigeons.

We have isolated Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from the feces of feral pigeons which contained a new Stx2 variant gene designated stx(2f). This gene is most similar to sltIIva of patient E. coli O128:B12 isolate H.I.8. Stx2f reacted only weakly with commercial immunoassays. The prevalence of STEC organisms carrying the stx(2f) gene in pigeon droppings was 12.5%. The occurrence of a new Stx2 variant in STEC from pigeons enlarges the pool of Stx2 variants and raises the question whether horizontal gene transfer to E. coli pathogenic to humans may occur.

Alleles↗
PubMed2005

Analysis of LRRK2 functional domains in nondominant Parkinson disease.

A comprehensive sequence analysis of 29 exons that code for the functional domains of LRRK2 in 160 nondominant Parkinson disease (PD) patients was performed. Novel variant screening in a further 470 sporadic PD patients and 630 controls revealed two novel variants (R1067Q and IVS33 + 6 T>A), which are likely to be pathogenic in five patients. One patient presented initially with a typical essential tremor phenotype, expanding the phenotypic spectrum of LRRK2 mutations.

Adult↗
PubMed1983

[Clinical features of schizophrenia manifesting itself as transitory psychoses].

The clinical features as well as prognosis of schizophrenia manifesting by acute transient psychoses at a mature age were studied in 80 patients. Two types of manifesting attacks were described: the first one developed as an affective delirious state with fantastic subject matter of delirious emotional experience and with clouded consciousness; the second one developed as an acute paranoid. The latent period characterized by contractive reactive lability preceded transient psychoses as the disease manifestation. Psychic disorders that followed depended on the reactive lability of the latent period. The clinical course was slow-progressive; the repeated "clishe"-like attacks developed transiently. External pathogenic effects influence on transient psychoses clinical course is discussed. The peculiar variants of schizophrenic psychosis developing as transient attacks, which appeared to be reactions by their mechanism but fhyft by their clinical matter, are also discussed.

Adult↗
PubMed2002

Lack of Bcl10 gene mutations in laryngeal squamous cell carcinoma.

The Bcl10 gene encodes a protein probably involved in some apoptotic regulatory pathways. Bcl10 mutations lead to the translation of truncated proteins that show gain-of-function transforming activity; it has been suggested that Bcl10 may represent a major target gene for inactivation in many human cancers. To define the frequency of Bcl10 mutations in laryngeal squamous cell carcinoma and their possible association with tumour progression, we investigated a large panel of tumours representative of all grades and stages of malignancy. To detect pathogenic mutations in exons 1, 2 and 3 of the Bcl10 gene, we performed a silver-staining polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis followed by direct DNA sequencing. We revealed the presence of SSCP variants in 18 out of 91 laryngeal tumours. Direct DNA sequencing showed previously described polymorphisms but no pathogenic mutations. We have strong evidence that the Bcl10 gene is not involved in laryngeal carcinogenesis.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Presence of autoantibody against ATTR Val30Met after sequential liver transplantation.

BACKGROUND: Recently, sequential liver transplantation has been performed with an explanted liver from a patient with familial amyloidotic polyneuropathy (FAP) because of the shortage of donors. However, metabolism of amyloidogenic transthyretin (ATTR), the pathogenic protein of FAP, has not been well studied in patients who have undergone sequential liver transplantation. The purpose of this study was to examine the changes in serum ATTR levels and to investigate the presence of an autoantibody in patients who underwent sequential liver transplantation with an explanted organ from a patient with heterozygotic FAP (FAP ATTR Val30Met). METHODS: This was a case study performed at the Kumamoto University School of Medicine, Kumamoto, Japan, and Kyoto University School of Medicine, Kyoto, Japan. Intervention occurred by sequential liver transplantation with an explanted FAP patient's liver. Levels of normal TTR and ATTR in the two patients who received the transplanted liver were analyzed by means of an enzyme-linked immunosorbent assay (ELISA) and a matrix-assisted laser desorption/time-of-flight mass spectrometry. In addition, the presence of an autoantibody against ATTR Val30Met was evaluated via ELISA using purified ATTR Val30Met from homozygotic FAP patients' sera. RESULTS: After the operation, the variant TTR levels were unexpectedly lower than levels of normal TTR in serum samples from patients with a transplanted liver from the FAP patient. An autoantibody against the variant TTR was detected on day 3 after the operation in the serum of those patients and continued to be present for at least 2 months after the operation. CONCLUSIONS: An autoantibody against the variant TTR may reduce the serum levels of variant TTR. Although the antibody may play a beneficial role in reducing the pathogenic protein, the long-term effect of the antibody must be investigated further.

Adolescent↗
PubMed1992

Genetic differences accounting for evolution and pathogenicity of simian immunodeficiency virus from a sooty mangabey monkey after cross-species transmission to a pig-tailed macaque.

We determined the nucleotide sequences of two related isolates of simian immunodeficiency virus from the sooty mangabey monkey (SIVsmm) that exhibit dramatic differences in virulence. These isolates are separated by one experimental cross-species transmission, from sooty mangabey to pig-tailed macaque. The parental virus (SIVsmm9), nonpathogenic in the original host (sooty mangabeys), causes a chronic AIDS-like disease in macaques. In contrast, the variant virus (SIVsmmPBj14) induces an acute lethal disease in various macaque species and is also pathogenic for sooty mangabeys. The combination of necessary and sufficient mutations that determined the acutely lethal phenotype on the SIVsmm9 genetic background is included within a maximal set of 57 point mutations, plus two insertions located in the long terminal repeat (22 bp spanning an NF-kappa B-like enhancer element) and in the surface envelope glycoprotein (5 amino acids). Comparisons of synonymous and nonsynonymous nucleotide substitutions in the genome of SIVsmm indicated that selective pressures, probably due to the host immune response, favored amino acid changes in the envelope. This immunoevolutionary mechanism could explain the increase in diversity and the apparition of new virulent phenotypes after cross-species transmission.

Animals↗
PubMed1999

Antigenicity and pathogenicity characteristics of molecularly cloned chicken anaemia virus isolates obtained after multiple cell culture passages.

The Cux-1 isolate of chicken anaemia virus (CAV), which had received 310 (P310) cell culture passages, was substantially less pathogenic than virus that had been passaged 13 times (P13). Molecularly cloned virus isolates, selected from the P310 and P13 virus populations using recombinant DNA cloning and transfection procedures, reacted differently with 4 CAV-specific monoclonal antibodies (MAbs), which had been raised to low-passage Cux-1 virus. In contrast to the strong immunofluorescence (IF) reactivities exhibited by all P13 cloned isolates tested, 80% and 57% of the P310 cloned isolates reacted weakly with MAbs 2A9 and 4H4, which are directed against conformational epitopes on the capsid protein, VP1. Sequence analysis of the VP1 coding regions possessed by ten P310 and two P13 cloned isolates showed that 6 amino acid changes within VP1 had been selected by multiple-cell culture passage. One of these at position 89 in VP1 appeared to be crucial for determining reactivity with MAb 2A9. Of nine P310 cloned isolates evaluated, 8 were substantially attenuated compared to the low-passage Cux-1 virus pool. It is concluded that the individual virus variants comprising the P310 virus pool differ with regards to their antigenicity and pathogenicity.

Amino Acid Sequence↗
PubMed2001

The genomics and genetics of human infectious disease susceptibility.

A genetic basis for interindividual variation in susceptibility to human infectious diseases has been indicated by twin, adoptee, pedigree, and candidate gene studies. This has led to the identification of a small number of strong genetic associations with common variants for malaria, HIV infection, and infectious prion diseases. Numerous other genes have shown less strong associations with these and some other infectious diseases, such as tuberculosis, leprosy, and persistent hepatitis viral infections. Many immunogenetic loci influence susceptibility to several infectious pathogens. Recent genetic linkage analyses of measures of infection as well as of infectious disease, including some genome-wide scans, have found convincing evidence of genetic linkage to chromosomal regions wherein susceptibility genes have yet to be identified. These studies indicate a highly polygenic basis for susceptibility to many common infectious diseases, with some emerging examples of interaction between variants of specific polymorphic host and pathogen genes.

Communicable Diseases↗
PubMed2002

The myth of Brucella L-forms and possible involvement of Brucella penicillin binding proteins (PBPs) in pathogenicity.

Brucella spp. L-forms have been proposed to be stationary phase organisms in the evolution of new variants and enduring entities in the host in complicated cases of brucellosis and during latent brucellosis. In vitro formation of Brucella L-forms has been achieved by treating the cells with sub-lethal doses of penicillin. Interestingly, Brucella spp. have classified during the evolution into two groups, penicillin susceptible or penicillin resistant, yet both types grow on 20 microg/ml of methicillin. Strains proven susceptible to penicillin grew in the presence of methicillin as L-forms as demonstrated by light and electron microscopy. In addition, the B. melitensis vaccine strain Rev.1, a penicillin susceptible organism, responded to sheep serum by development of L-form-like structures unlike wild type, strain 16M. The two strains grew normally in sheep macrophages. We propose, for the first time, a model that associates Brucella pathogenicity with the structure and activity of two of their penicillin binding proteins (PBPs). According to the model, PBP1 has evolved as the major cell wall synthesizing enzyme of the genus, capable of responding to host serum growth factor(s) necessary for Brucella survival in the host. This property is associated with high avidity to beta-lactam antibiotics. PBP2 complements the activity of PBP1. New beta-lactam antibiotics and improved vaccines might be developed based on this property.

Animals↗
PubMed2000

Enterohemorrhagic Escherichia coli (EHEC) strains of serogroup O118 display three distinctive clonal groups of EHEC pathogens.

A recent case report of a child infected with enterohemorrhagic Escherichia coli (EHEC) of serotype O118:H16 in Bavaria, in association with the isolation of a bovine O118 strain on the same farm (A. Weber, H. Klie, H. Richter, P. Gallien, M. Timm, and K. W. Perlberg, Berl. Muench. Tieraerztl. Wochenschr. 110:211-213, 1997), prompted us to investigate the relationship between bovine and human strains of serogroup O118. A total of 29 human O118 E. coli strains from Europe (21), Canada (4), and Peru (4) were compared by virulence typing and macrorestriction analysis with 7 bovine O118 EHEC strains isolated in Bavaria. Twenty-five of the human strains were characterized as EHEC. By serotyping and determination of the virulence-associated factors Shiga toxin (stx1 stx2 stx2 variants), intimin (eae), and EHEC hemolysin (Hly(EHEC)), three distinctive groups of O118 human pathogens were identified. Most of the strains belonged to serotype O118:H16, displaying the virulence traits Stx1, intimin, Hly(EHEC), and EspP/PssA (group 1). In addition, we identified strains of serotype O118:H12 (Stx2d only; group 2) and of serotype O118:H30 (Stx2 and intimin; group 3). Macrorestriction analysis with BlnI and XbaI revealed that all strains with a single O118 serotype profile (O118:H12, O118:H16, and O118:H30) belonged to one clonal cluster, irrespective of their origin. Group 1 strains clustered in the same clonal group as the bovine O118:H16 strains. Moreover, four pairs of strains of different origins and indistinguishable by all other methods applied were identified as group 1 strains. Our data support the direct transmission of an EHEC O118:H16 strain from a calf to a 2-year-old boy in the above-mentioned case report. Since bovine and human O118:H16 strains represent the same clones, they must be considered zoonotic EHEC pathogens. In contrast, EHEC strains of serotypes O118:H12 and O118:H30 have been isolated only from humans, indicating a reservoir for certain human O118 EHEC strains other than bovines.

Adhesins, Bacterial↗
PubMed2006

VHL P25L is not a pathogenic von Hippel-Lindau mutation: a family study.

BACKGROUND: von Hippel-Lindau (VHL) disease is a hereditary tumor syndrome in which affected individuals may develop CNS and retinal hemangioblastomas, pheochromocytomas, renal cell carcinoma, and cysts of various organs. The VHL gene has been localized to chromosome 3p25-26 and >500 germline mutations have been identified. A rare variant of the VHL gene results in the substitution of lysine for proline at position 25 (P25L) in the larger of the two VHL proteins. This VHL variant has previously been described in a limited number of cases and has been strongly suggested to be non-pathogenic, but this has not been proven. METHODS: A family with a medical history suggestive of VHL disease was investigated using DNA sequence analysis to determine the presence of the P25L variant of the VHL protein. RESULTS: Sequence analysis identified the VHL P25L variant in 7 of 14 family members, one of whom had a single retinal hemangioma, which is in itself insufficient to diagnose VHL disease. The variant was not identified in a family member with clear cell renal carcinoma, which is a hallmark feature of VHL disease. CONCLUSIONS: On the basis of these results, it is concluded that P25L is a benign variant of the VHL protein and individuals carrying this variant should not be required to undergo screening for VHL manifestations.

Aged↗
PubMed1984

Porcine parvovirus DNA: characterization of the genomic and replicative form DNA of two virus isolates.

The genomic and replicative form (RF) DNA of porcine parvovirus (PPV) have been characterized. PPV isolate NADL-8 was found to have a 5000-base single-stranded genome, and a unique strand was encapsidated in virus particles. The RF DNA of isolate NADL-8 was found to be an infectious 5000-base pair (bp) molecule. Select restriction endonuclease sites were mapped along the RF DNA of PPV (NADL-8), and oriented with respect to the viral genomic DNA. The RF DNA of a second isolate of PPV, the less pathogenic, cell culture-adapted NADL-2 virus, was also analyzed. DNA preparations isolated from NADL-2 virus-infected cells contained two viral RF DNA species: a 5000-bp infectious molecule very similar if not identical to the NADL-8 virus RF DNA, and a noninfectious 4700-bp DNA molecule. The 4700-bp RF DNA molecule found in NADL-2 DNA preparations was similar in all respects to the 5000-bp RF DNA, except for a 300-bp deletion in the region encoding the viral capsid proteins. The presence of this defective variant in PPV (NADL-2) virus preparations is discussed in relation to the reduced pathogenic potential of the NADL-2 virus as compared to the NADL-8 virus.

Animals↗
PubMedDate not supplied

Influence of the host system on the pathogenicity, immunogenicity, and antigenicity of infectious bursal disease virus.

The effect of the host system on the pathogenicity, immunogenicity, and antigenicity of infectious bursal disease virus (IBDV) was investigated. One classic (SAL) and one variant strain (IN) of IBDV were passaged separately six times in three host systems, namely BGM-70 continuous cell line, primary chicken embryo fibroblast (CEF) cells, or embryonating chicken eggs (embryos) or one time in the bursa of Fabricius (BF) of specific-pathogen-free (SPF) chickens. Passage in BGM-70 cells or CEF cells resulted in loss of pathogenicity, but viruses passaged in embryos or BF maintained their pathogenicity. For the immunogenicity study, the viruses described above were used to prepare live and inactivated vaccines, containing 10(3) mean embryo infectious doses (EID50s) and 10(5) EID50s respectively. These vaccines induced different levels of protection. It was concluded that the antigen titration methodology employing embryonating chicken eggs was not suitable for titration of viruses propagated in other host systems because of varying degrees of adaptation and/or pathogenicity of the viruses resulting in variability in antigen mass of the tested vaccines. To test this assumption, an antigen-capture enzyme-linked immunosorbent assay was used as a titration system to compare the antigenicity of viruses propagated in BGM-70 cells or BF. Preparations containing similar antigen masses were inactivated then inoculated into two age groups of SPF chickens and antibody titers were monitored. During the experimental period, the geometric mean virus-neutralizing (VN) antibody titers of the vaccinated groups did not differ significantly (P > 0.05).

Animals↗
PubMed2001

Mitochondrial DNA transfer RNA gene sequence variations in patients with mitochondrial disorders.

Many different pathogenic mutations in the mitochondrial (mt) transfer RNA (tRNA) genes have been reported for patients with mitochondrial encephalomyopathy. Although some of them are recurrent, most have only been described once and appear to be restricted to one patient or to one family. The incidence of mt tRNA gene alterations is not known, even though the frequency of some recurrent mutations has been analysed both in patients and in the general population. In this study, we describe the results of stepwise screening for sequence variations in the mt tRNA genes of 166 patients selected according to several criteria. Extensive sequence analysis of the tRNA genes was performed using denaturing gradient gel electrophoresis. A total of 31 patients (19%) were found to harbour significant levels of a pathogenic mutation, thus confirming the importance of mt tRNA mutations in human pathology. Forty-three different sequence variations were found, illustrating the great diversity of the mtDNA sequence in humans. The functional assessment of all these sequence variations represented a difficult task; it was mostly based on indirect data, such as the phylogenetic conservation of modified nucleotides and the proportions of variant species in different tissues of the index case or in blood of maternal relatives. Direct demonstration of a correlation between the proportion of heteroplasmic sequence variations and the cytochrome c oxidase defect was performed at the single muscle-fibre level. Eleven heteroplasmic sequence variations were found, six of which are new mutations. One is a known Caucasian polymorphism but the other 10 are pathogenic. Two of them are the well-known pathogenic MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes) (A3243G) and MERRF (myoclonic epilepsy with ragged-red fibres) (A8344G) point mutations. They were found in 23 patients. The eight other mutations were restricted to one patient. The pathogenic nature of these mutations was demonstrated directly for five of them and hypothesized from indirect arguments for the other three. Thirty-two homoplasmic sequence variations were found. Twenty-nine were considered to be polymorphisms, even though 15 of these were found for the first time in our patients and two others had been reported previously as pathogenic. The pathogenic nature of three homoplasmic variants remains questionable.

Adolescent↗
PubMed1990

Nutritionally variant streptococci associated with corneal ulcers in horses: 35 cases (1982-1988).

Nutritionally variant streptococci (NVS) are nutritionally deficient viridans streptococci that require pyridoxal for growth. Although NVS are pathogenic in human beings, they have not been considered to be pathogenic in domestic animals. In 1982 and 1983, 24 isolates of NVS were recovered from horses with ulcerative keratitis. A retrospective study was done to determine the incidence of NVS in horses with corneal disease. The medical records of 249 horses (259 eyes) examined for clinical signs of corneal disease were reviewed. Nutritionally variant streptococci were isolated from approximately 13.5% of horses with ulcerative keratitis.

Animals↗