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PubMed2003

Provirus variants of bovine leukemia virus in naturally infected cattle from Argentina and Japan.

A serologic subgroup of bovine leukemia virus (BLV) has not been identified, whereas genetic diversity among BLVs has been reported by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). To investigate the distribution of BLV provirus variants, 42 isolates from Argentina and Japan were examined by nested PCR for a segment of the env gene, followed by DNA sequencing. The nucleotide sequences were compared with other previously characterized BLV variants from different geographical areas (Belgium, France, Italy, North America, Australia, Japan and Argentina). The majority of analyzed segments had a tendency for nucleotide substitution without changing the amino acid. The constructed phylogenetic tree showed the relations and differences between proviruses and within each one. Most of the samples in Argentina formed one cluster. The samples in Japan, except one, also formed one cluster and some of them showed high homology with the isolates from Australia and the USA. Considering the sequence analysis of env PCR products of all Japanese and Argentine samples and comparing them with the other previously isolated sequences, the variation was up to 3.5% and was characterized geographically in each area.

Amino Acid Sequence↗

PubMed1997

Polymerase chain reaction on cerebrospinal fluid cells in the detection of leptomeningeal involvement by B-cell lymphoma and leukaemia: a novel strategy and its implications.

In the search of B-cell lymphoma/leukaemia dissemination to cerebrospinal fluid (CSF), we used the highly sensitive semi-nested PCR (snPCR) for the analysis of IgH gene rearrangements. This method detects a rearranged IgH gene from a single B lymphocyte which may or may not represent the neoplastic B-cell population. We therefore performed multiple snPCR (three to five) experiments on the same CSF sample, postulating that the detection of a band of the same size and sequence in different PCR runs was highly indicative of a clonal population. 17 consecutive cases with a differential diagnosis of primary (PCNSL) (n=10) or secondary (SCNSL) (n=7) CNS lymphoma or leukaemia were investigated by the new strategy. The clonal nature of the B-cell population was confirmed in 3/10 of suspected PCNSL, and in six other cases the PCR study was indicative of reactive lymphocytosis. One case revealed a clonal B-cell population in the clinical context of an autoimmune disorder. Evidence of clonal B-cell population was found in 4/7 of suspected SCNSL. In one of these cases the detected band and its sequence proved identical to that of the primary nodal lymphoma. We believe that the evaluation of B-cell clonality in CSF requires multiple snPCR amplification on the same sample to compare the size of the products and, if necessary, the DNA sequences to ascertain the diagnosis of malignancy in equivocal cytologic and clinical findings.

Adult↗

PubMed2002

Lymph nodes in gastric B-cell lymphoma: pattern of involvement and early histological changes.

AIMS: This study aims to analyse the histological pattern of nodal involvement in gastric B-cell lymphoma and to detect early involvement of the lymph nodes. METHODS AND RESULTS: Histological findings of 37 resected primary gastric lymphomas with 1313 regional lymph nodes were analysed. The primary tumour was classified into four groups: MALT lymphoma, MALT lymphoma with a minor large B-cell lymphoma (<20%), large B-cell lymphoma with MALT lymphoma, and large B-cell lymphoma without MALT lymphoma. Histological patterns of nodal involvement were divided into sinusoidal, subsinusoidal/marginal, follicular, and diffuse patterns. Semi-nested polymerase chain reaction (PCR) analysis for IgH gene rearrangement was performed. Nodal involvement was found in 2/13 (15%) MALT lymphomas, 5/6 (83%) MALT lymphomas with a minor large B-cell lymphoma, 9/12 (75%) large B-cell lymphomas with MALT lymphoma, and 6/6 (100%) large B-cell lymphomas without MALT lymphoma. The MALT lymphoma and MALT lymphoma with a minor large B-cell lymphoma showed a predominantly sinusoidal and subsinusoidal pattern, whereas diffuse pattern predominated in large B-cell lymphomas without MALT lymphoma and large B-cell lymphomas with MALT lymphoma. The follicular pattern was least common, being observed in 10.2% of large B-cell lymphomas without MALT lymphoma and large B-cell lymphomas with MALT lymphoma. Sinusoidal obliteration with permeation of small monocytoid cells into subsinusoidal zone is a characteristic finding suggesting early nodal involvement of MALT lymphoma. CONCLUSIONS: Histological patterns of nodal involvement in gastric B-cell lymphoma vary according to the histological grade. Immunostaining for CD20 with or without PCR analysis for IgH gene rearrangement would be a useful ancillary method to confirm lymphomatous involvement.

Adult↗

PubMed1987

Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322.

The specificity of deletion formation was studied using tests involving reversion of palindromic insertion mutations. Insertions of a Tn5-related transposon at 13 sites in the ampicillin-resistance (amp) gene of plasmid pBR322 were shortened to a nested set of perfect palindromes, 22, 32 and 90 bp long. We monitored frequencies of reversion to Ampr, which is the result of deletion of the palindrome plus one copy of the flanking 9 bp direct repeats (which had been formed by transposition). Revertant frequencies were found to depend on the location and the sequence of the palindromic insert. Changing a 45-kb interrupted palindrome to a 22-bp perfect palindrome stimulated deletion formation by factors of from fourfold to 545-fold among the 13 sites, while elongation of the perfect palindrome from 22 to 90 bp stimulated deletion formation by factors of from eight- to 18,000-fold. We conclude that deletion formation is strongly affected by subtle features of DNA sequence or conformation, both inside and outside the deleted segment, and that these effects may reflect specific interactions of DNA processing proteins with template DNAs.

Base Sequence↗

PubMed1993

Direct DNA amplification and restriction pattern analysis of Helicobacter pylori in patients with duodenal ulcer and their families.

Sera from 14 patients with duodenal ulcer and their families were tested for IgG antibodies to Helicobacter pylori. Fourteen serologically negative patients and their families served as controls. Index patients and their family members who were serologically positive were advised to undergo endoscopic biopsy. Gastric biopsy tissues were subjected to HaeIII restriction analysis of nested polymerase chain reaction products of the urease gene. By serology, 28 (49.0%) of 57 in index families and 11 (27.5%) of 40 in control families tested positive. A higher prevalence rate was found in children of index patients (11/31, 35.5%) than in those of control patients (1/18, 5.6%; P < .05). On DNA analysis, 11 patterns were found in 13 patients, and 6 families underwent endoscopy. Children in 5 families exhibited identical patterns to those of their siblings and, in 3 of the 5 families, identical to the pattern of 1 of the parents. These results suggest that parent-to-child transmission and common infection source are probable causes of intrafamilial clustering of H. pylori.

Adult↗

PubMed1996

Identification of a Gly862 to Ser substitution in the type I collagen gene from a single spermatozoon.

Individual spermatozoa from the father of two affected infants with osteogenesis imperfecta were separated by dilution and micromanipulation. A segment of the type I collagen gene containing the mutant region was amplified by nested polymerase chain reaction and sequenced. Among 40 individual spermatozoa, 15 specimens were identified as mutants with a substitution of guanine3208 to adenine (glycine862 to serine) while 18 and seven specimens were of the wild and mixed types respectively. Through this study, we have established a molecular procedure that can be considered as prerequisite for preimplantation diagnosis of genetic disorders with a single point mutation.

Collagen↗

PubMedDate not supplied

Esterase variation at three loci in meat ants.

The meat ant (Iridomyrmex purpureus) occurs in a number of color forms, with uncertain taxonomic status. Gel electrophresis of meat ant extracts, followed by nonspecific esterase staining, reveals several zones of activity. Allelic variation at three loci is proposed to account for variation in some of these zones. Two of the loci (Es-1, Es-2) appear to have recessive null alleles, whose frequencies have been estimated by the method of maximum likelihood. Geographic variation in allele frequency is attributed to behavioral and geographic subdivision of the population. Apparent disturbances in segregation ratios and deviations from Hardy-Weinberg equilibrium can be accounted for if it is argued that some nests contain more than one queen. Differences in gene frequency between sympatric populations of the red and blue forms of I. purpureus are observed, confirming their reproductive is isolation and sibling species status.

Alleles↗

PubMed2005

Molecular and serological evidence of Pneumocystis circulation in a social organization of healthy macaques (Macaca fascicularis).

Simian populations represent valuable models for understanding the epidemiology of human pneumocystosis. The present study aims to describe the circulation of Pneumocystis organisms within a social organization of healthy crab-eating macaques (Macaca fascicularis) living in a natural setting in France. Animals were followed for up to 2 years. Deep nasal swab and blood samples were collected monthly from each animal under general anaesthesia. Environmental air was sampled for a 1 week period every month in the park where the macaques dwelt. Pneumocystis DNA was detected by nested-PCR of mitochondrial large subunit rRNA (mtLSU) gene in nasal swab and air samples. Anti-Pneumocystis IgG antibodies were detected in serum samples by indirect immuno-fluorescence assay. Pneumocystis DNA was detected in 168 of 500 swab samples examined (33.6 %). The number of macaques with detectable Pneumocystis DNA was highly variable from one month to another. Positive detection of Pneumocystis DNA was not related to the detection of serum anti-Pneumocystis antibody. During the second year of the study, Pneumocystis DNA was amplified more frequently from unweaned macaques than from adults or subadults. The mtLSU sequence showed marked polymorphism with eight Pneumocystis sequence types representing two distinct groups. On the whole, a constant and intensive circulation of Pneumocystis organisms within the community was observed. However, the implication of the various members of the colony was probably different and several levels of colonization by Pneumocystis may occur in immunocompetent macaques.

Animals↗

PubMed2006

Effects of parental effort on blood stress protein HSP60 and immunoglobulins in female blue tits: a brood size manipulation experiment.

1. Physiological stress in animals may impose a limit for investment in current reproduction in the wild. A brood manipulation experiment was conducted in a population of blue tits Cyanistes caeruleus to study the effect of parental effort on changes in two types of proteins related with stress: the blood stress protein HSP60 and the plasma immunoglobulins. 2. Levels of HSP60 were reduced across the experiment for females attending reduced broods, and females attending enlarged broods experienced a reduction of immunoglobulin levels. Moreover, the overall changes in the levels of both proteins were positively related. 3. By controlling for the change in immunoglobulin levels we found an increase in HSP60 for females in the enlarged treatment, presumably to offset deleterious effects derived from increased effort. 4. Maternal effort was able to partially compensate for the effect of treatment as nestlings did not differ in mass and levels of immunoglobulins and HSP60 among treatments. 5. Physiological stress as reflected in stress and immunoglobulin proteins may limit maternal effort in breeding blue tits.

Animals↗

PubMed1991

Identification of a surface-exposed immunodominant epitope on outer membrane protein P1 of Haemophilus influenzae type b.

Eight murine monoclonal antibodies (MAbs) directed against outer membrane protein P1 of Haemophilus influenzae type b were generated and characterized. Seven of the eight MAbs reacted with recombinant P1 and purified P1 protein from H. influenzae type b strains MinnA and 1613; MAb P1.8 was specific for the latter strain. A panel of 32 nontypeable and 140 encapsulated Haemophilus strains recovered worldwide representing the major clonal families of serotypes a, b, and d was used to evaluate the distribution among Haemophilus strains of the epitopes identified by the P1-specific MAbs. The epitope reactive with the seven MAbs which recognized P1 from strains MinnA and 1613 was shared by 92% of the encapsulated Haemophilus isolates tested. The epitope is present in the H. influenzae type b strains from clonal families commonly recovered from cases of invasive disease in North America and Europe. A series of nested 5' and 3' deletions of the P1 gene were constructed and analyzed to localize the determinants on P1 recognized by the MAbs. MAbs P1.2, P1.4, P1.5, P1.6, and P1.7 recognized an epitope localized to the carboxy-terminal portion of P1. Murine MAbs P1.1 and P1.3 and two human MAbs, HiH-7 and HiH-10, recognized a complex epitope which was partially localized to the carboxy-terminal portion of the P1 protein. These data indicate that an immunodominant surface-exposed epitope is present on the carboxy-terminal portion of the P1 protein of type b Haemophilus isolates responsible for the majority of invasive disease in North America.

Amino Acid Sequence↗

PubMed1996

DNA sequences identical to Pneumocystis carinii f. sp. carinii and Pneumocystis carinii f. sp. hominis in samples of air spora.

Samples of ambient air collected with three different types of spore traps in a rural location were examined for the presence of Pneumocystis carinii by screening for P. carinii-specific DNA sequences by DNA amplification. Eleven spore trap samples were analyzed by nested PCR, using oligonucleotide primers designed for the gene encoding the mitochondrial large subunit rRNA of P. carinii f. sp. carinii and P. carinii f. sp. hominis. The samples were collected over a 3-year period during the months of May to September, with a range of sampling times from 9 to 240 h. One air sample from an animal facility housing P. carinii-infected rats was also examined. P. carinii-specific amplification products were obtained from samples from each of the spore traps. The amplification products from eight air samples were cloned and sequenced. The majority of the recombinants from each of these samples had sequences identical to those of P. carinii f. sp. carinii and P. carinii f. sp. hominis, and a number of clones had single-base differences. These data suggest that sequences identical to those of P. carinii f. sp. carinii and P. carinii f. sp. hominis can be detected in samples of air collected in a rural location and that P. carinii may be a component of the air spora of rural Oxfordshire.

Air Microbiology↗

PubMed1998

Diagnosis of Mycoplasma pneumoniae infection in autopsy and open-lung biopsy tissues by nested PCR.

A nested PCR specific for the Mycoplasma pneumoniae P1 gene was used to diagnose mycoplasma infection in two cohort patients with severe pneumonia within 24 h of tissue receipt. A postmortem diagnosis of M. pneumoniae infection was obtained for the first patient, who died without the collection of appropriate paired samples for serodiagnosis. An open-lung biopsy obtained from the second patient allowed a quick, definitive diagnosis and proper selection of therapy.

Adult↗

PubMed2000

Failure to detect Chlamydia pneumoniae in the late-onset Alzheimer's brain.

Epidemiological studies have yet to identify a single cause for the most common late-onset form of Alzheimer's disease. The common respiratory pathogen Chlamydia pneumoniae recently has been implicated as a risk factor for this form of Alzheimer's disease. Were this true, there would be a dramatic shift in current paradigms of Alzheimer's disease research and treatment. In the absence of published confirmation, we obtained postmortem brain tissue from late-onset Alzheimer's disease patients (n = 15) and representative controls (n = 5) and extracted DNA from up to six separate brain regions in each instance, including those areas particularly relevant to Alzheimer's disease neuropathology. Each sample of DNA (n = 101) was assayed five times or more for the presence of C. pneumoniae DNA using a nested-PCR protocol targeting a species-specific gene sequence coding for the major outer membrane protein of this organism. We were unable unequivocally to detect C. pneumoniae in any of the 101 samples tested by PCR and failed to culture the organism from tissue samples. We conclude that C. pneumoniae is neither strongly nor uniquely associated with the neuropathology seen in late-onset Alzheimer's disease.

Aged↗

PubMed1993

Definition of a subset of human peripheral blood mononuclear cells that are permissive to human cytomegalovirus infection.

The identity of cells responsible for transmission of human cytomegalovirus (HCMV) in blood products or bone marrow transplants is unknown. We have tested the capacity of HCMV to in vitro infect human peripheral blood mononuclear cells (PBMC) from healthy donors and found that certain PBMC are permissive to HCMV infection. In vitro-infected viable cells were double stained for surface expression of different HMCV proteins and for cell-type-specific antigens to allow the identification of sensitive cells. All analysis were performed on viable cells, using HCMV-specific monoclonal antibodies and automated flow cytofluorimetry. PBMC were infected either with the laboratory-adapted HCMV strain AD169 or with a virus isolate obtained from a viremic patient. Up to 25% of all PBMC could express the major immediate-early antigen as well as the pp65 antigen, known at the lower matrix protein. Infected cells were mainly CD14+ monocytes, but also a small population of large CD8+ cells were susceptible to HCMV infection. CD19+ B lymphocytes were resistant to HCMV infection. Different populations of infected cells were enriched by using Dynabeads coated with cell-type-specific antibodies, and the presence of infectious virus was demonstrated by incubating the selected and sonicated cell material on human fibroblasts. Only material from infected monocytes and from CD3+ CD8+ cells gave rise to HCMV-specific plaques. The presence of HCMV mRNA as a sign of active viral transcription of the major immediate-early and late pp150 genes in infected cells was demonstrated by using nested reversed polymerase chain reaction. A common denominator was found for all cells that could be infected with HCMV. The CD13 antigen, a 130- to 150-kDa integral membrane protein identical to the enzyme aminopeptidase N, was expressed on all HCMV-permissive cells.

Antigens, CD↗

PubMed2004

Hepatitis B virus infection in Haemodialysis Centres from Santa Catarina State, Southern Brazil. Predictive risk factors for infection and molecular epidemiology.

BACKGROUND: Patients under haemodialysis are considered at high risk to acquire hepatitis B virus (HBV) infection. Since few data are reported from Brazil, our aim was to assess the frequency and risk factors for HBV infection in haemodialysis patients from 22 Dialysis Centres from Santa Catarina State, south of Brazil. METHODS: This study includes 813 patients, 149 haemodialysis workers and 772 healthy controls matched by sex and age. Serum samples were assayed for HBV markers and viraemia was detected by nested PCR. HBV was genotyped by partial S gene sequencing. Univariate and multivariate statistical analyses with stepwise logistic regression analysis were carried out to analyse the relationship between HBV infection and the characteristics of patients and their Dialysis Units. RESULTS: Frequency of HBV infection was 10.0%, 2.7% and 2.7% among patients, haemodialysis workers and controls, respectively. Amidst patients, the most frequent HBV genotypes were A (30.6%), D (57.1%) and F (12.2%). Univariate analysis showed association between HBV infection and total time in haemodialysis, type of dialysis equipment, hygiene and sterilization of equipment, number of times reusing the dialysis lines and filters, number of patients per care-worker and current HCV infection. The logistic regression model showed that total time in haemodialysis, number of times of reusing the dialysis lines and filters, and number of patients per worker were significantly related to HBV infection. CONCLUSIONS: Frequency of HBV infection among haemodialysis patients at Santa Catarina state is very high. The most frequent HBV genotypes were A, D and F. The risk for a patient to become HBV positive increase 1.47 times each month of haemodialysis; 1.96 times if the dialysis unit reuses the lines and filters > or = 10 times compared with haemodialysis units which reuse < 10 times; 3.42 times if the number of patients per worker is more than five. Sequence similarity among the HBV S gene from isolates of different patients pointed out to nosocomial transmission.

Adolescent↗

PubMed2003

High-risk human papillomaviruses may have an important role in non-oral habits-associated oral squamous cell carcinomas in Taiwan.

To evaluate the etiologic role of human papillomavirus (HPV) in oral carcinogenesis, DNA samples were purified from 103 oral squamous cell carcinoma (OSCC) and 30 normal oral mucosal (NOM) specimens. A nested polymerase chain reaction, DNA sequencing, and gene-chip HPV typing were used to identify multiple HPV types in our samples. We found that the positive rates of all HPV types and of high-risk HPV types were significantly higher in OSCC samples (49.5% and 41.7%, respectively) than in NOM samples (6/30 [20%; P < .01] and 5/30 [17%; P < .05], respectively) and significantly higher in non-oral habits (OH)-associated OSCC samples (31/51 [61%] and 28/51 [55%], respectively) than in OH-associated OSCC samples (20/52 [38%; P < .05] and 15/52 [29%; P < .001], respectively). High-risk HPV types and all HPV types had odds ratios of 3.97 (P = .0097) and 3.92 (P = .006), respectively. Our results suggest that HPVs, particularly high-risk HPVs, might be associated with the development of OSCCs, especially the non-OH-associated OSCCs.

Adult↗

PubMedDate not supplied

No evidence of vertical transmission of HTLV-I in bottle-fed children.

The most frequent pathway of vertical transmission of HTLV-I is breast-feeding, however bottle fed children may also become infected in a frequency varying from 4 to 14%. In these children the most probable routes of infection are transplacental or contamination in the birth canal. Forty-one bottle-fed children of HTLV-I seropositive mothers in ages varying from three to 39 months (average age of 11 months) were submitted to nested polymerase chain reaction analysis (pol and tax genes). 81.5% of the children were born by an elective cesarean section. No case of infection was detected. The absence of HTLV-I infection in these cases indicates that transmission by transplacental route may be very infrequent.

Bottle Feeding↗

PubMed2000

Characterization of Lyme disease spirochetes isolated from ticks and vertebrates in North Carolina.

Borrelia burgdorferi isolates obtained from numerous locations and from different hosts in North Carolina, were compared to previously characterized strains of the Lyme disease spirochete and other Borrelia spp. The spirochete isolates were confirmed to be B. burgdorferi sensu stricto based on immunofluorescence (IFA) using a monoclonal antibody to outer surface protein A (Osp A [H5332]) and polymerase chain reaction (PCR) using a species-specific nested primer for a conserved region of the gene that encodes for flagellin. In addition, the isolates tested positive in Western blots with species-specific monoclonal antibodies for outer surface protein A and OspB (84c), and the genus-specific, monoclonal antibody to flagellin (H9724). Infectivity studies with several of these isolates were conducted using Mus musculus and Oryzomys palustris and the isolates exhibited markedly different levels of infectivity. This study demonstrates that B. burgdorferi sensu stricto is present and naturally transmitted on the Outer Banks and in the Coastal Plain and Piedmont regions of North Carolina.

Animals↗