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J Stanley

Publications and source records attributed to J Stanley.

At least 55 records · Page 3Linked to original sources

PCR-enzyme-linked immunosorbent assay for detection and identification of Campylobacter species: application to isolates and stool samples.

We report a PCR-enzyme-linked immunosorbent assay which identifies Campylobacter species by capture hybridization of a single-stranded 16S rRNA gene amplicon with species-specific probes in a microtiter plate format. Specificities were confirmed for both reference and field strains, but the type strain of Campylobacter coli was atypical. The assay was rapid, informative, and usable with stool-extracted DNA.

Bacterial Typing Techniques↗

Predictive fluorescent amplified-fragment length polymorphism analysis of Escherichia coli: high-resolution typing method with phylogenetic significance.

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains of Escherichia coli. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species E. coli, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselective EcoRI primer (Eco+0) and a labelled selective MseI primer (Mse+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of E. coli infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.

Bacterial Typing Techniques↗

High-resolution genotyping of Streptococcus pyogenes serotype M1 isolates by fluorescent amplified-fragment length polymorphism analysis.

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise "identical" M1 isolates as members of a clone complex.

Antigens, Bacterial↗

What determines the choice of procedure in stress incontinence surgery? The use of multilevel modeling.

The purpose of this study was to identify the determinants of choice of surgical procedure (anterior colporrhaphy, colposuspension, or needle suspension) to treat stress incontinence in women. We used multilevel modeling of data on 271 patients in 18 hospitals in England in 1993-94. Patient-related factors included sociodemographic details, anatomical diagnosis, symptom severity, symptom impact, previous treatment, parity, comorbidity, and general health status. Surgeon-related factors were specialty, grade, and annual volume of procedures undertaken. Hospital teaching status was considered. Some patient-related factors were associated with choice of procedure: women with a concomitant genital prolapse, with a history of high parity, and with no previous nonsurgical treatment were more likely to undergo an anterior colporrhaphy than a colposuspension or needle suspension (although this finding could be confounded by surgical specialty). In addition, women were more likely to be treated by colposuspension if their surgeon specialized in incontinence surgery (measured by annual volume of cases). Finally, being treated by needle suspension depended on there being a consultant surgeon familiar with the procedure at the hospital attended. While choice of surgical procedure depends partly on the patient's anatomical diagnosis, it is also dependent on the specialty of the surgeon whom she consults and the hospital that she attends. This variability, in turn, could have implications for the patient (as the relative effectiveness of the different procedures is unknown) and for the purchasers of care (as the relative cost-effectiveness of procedures is also unknown).

Adult↗

Detection of campylobacter in gastroenteritis: comparison of direct PCR assay of faecal samples with selective culture.

The prevalence of campylobacter gastroenteritis has been estimated by bacterial isolation using selective culture. However, there is evidence that certain species and strains are not recovered on selective agars. We have therefore compared direct PCR assays of faecal samples with campylobacter culture, and explored the potential of PCR for simultaneous detection and identification to the species level. Two hundred unselected faecal samples from cases of acute gastroenteritis were cultured on modified charcoal cefoperazone deoxycholate agar and subjected to DNA extraction and PCR assay. Culture on CCDA indicated that 16 of the 200 samples contained 'Campylobacter spp.'. By contrast, PCR assays detected campylobacters in 19 of the 200 samples, including 15 of the culture-positive samples, and further identified them as: C. jejuni (16), C. coli (2) and C. hyointestinalis (1). These results show that PCR offers a different perspective on the incidence and identity of campylobacters in human gastroenteritis.

Campylobacter↗

Analysis of methicillin-resistant Staphylococcus aureus by IS1181 profiling.

Variation in the genomic location and copy number of the insertion element IS1181 in methicillin-resistant Staphylococcus aureus (MRSA) was investigated. Sixty-three isolates representing the Jevons type strain (NCTC 10442), phage-propagating strains, and epidemic strains were examined. A PCR amplicon of the insertion element was used to probe genomic restriction endonuclease digests. HindIII genomic digests gave 25 distinct IS1181 patterns, while EcoRI digests gave 20 patterns. EMRSA-01, -02, -04, -06, -07, -09, -10, -11, -13 and -14 contained the element but could not be subtyped by profiling it. EMRSA-16 did not contain IS1181, consistent with a unique evolutionary origin for this major UK epidemic strain. Marked heterogeneity was observed among isolates of EMRSA-03. Each EMRSA-03 strain examined gave a unique pattern, thereby allowing subtyping of an important epidemic phage type for the purposes of hospital cross-infection control.

Bacteriophage Typing↗

Recognition of desmoglein 3 by autoreactive T cells in pemphigus vulgaris patients and normals.

Pemphigus vulgaris (PV) is an autoimmune blistering disease of the skin and is caused by autoantibodies against desmoglein 3 (Dsg3) on epidermal keratinocytes. Because the production of autoantibodies is presumably T cell dependent, Dsg3-specific T cell reactivity was investigated in 14 PV patients and 12 healthy donors. Peripheral blood mononuclear cells from seven PV patients with active disease showed a primary in vitro response to a recombinant protein containing the extracellular portion (EC1-5) of Dsg3, whereas two of seven PV patients in remission or under immunosuppressive treatment exhibited only secondary (2 degrees) or tertiary (3 degrees) T cell responses to Dsg3. T cell responses to Dsg3 were also observed in four of 12 healthy individuals upon 2 degrees or 3 degrees stimulation with Dsg3. Both PV patients and healthy responders were either positive for DRbeta1*0402 -- which is highly prevalent in PV -- or positive for DR11 alleles homologous to DRbeta1*0402. Two CD4+ Dsg3-specific T cell lines and 12 T cell clones from two PV patients and two CD4+ T cell lines and eight T cell clones from two normals were also stimulated by a Dsg3 protein devoid of the EC2-3 (deltaN1), suggesting that epitopes were located in the EC1, EC4, and/or EC5. Using Dsg3 peptides, one immunodominant peptide (residues 161-177) was also identified in the EC2. These observations demonstrate that T cell responses to Dsg3 can be detected in PV patients and in healthy donors carrying major histocompatibility class II alleles identical or similar to those highly prevalent in PV.

Antibody Specificity↗

Axonal damage correlates with disability in patients with relapsing-remitting multiple sclerosis. Results of a longitudinal magnetic resonance spectroscopy study.

It has been difficult to establish a strong correlation between total brain T2-weighted lesion volume on MRI and clinical disability in multiple sclerosis, in part because of the lack of pathological specificity of T2-weighted MRI signal changes. Proton magnetic resonance spectroscopy studies have shown that measurements of the resonance intensity of N-acetylaspartate (which is localized exclusively in neurons and neuronal processes in the mature brain) can provide a specific index of axonal damage or dysfunction. Here we report a 30-month longitudinal study of 29 patients with multiple sclerosis who had either a relapsing or a secondary progressive clinical course. Conventional brain MRI and single-voxel proton magnetic resonance spectroscopy examinations were obtained at intervals of 6-8 months with concurrent clinical evaluation. At the onset of the study, the brain N-acetylaspartate:creatine resonance intensity ratio was abnormally low for the whole group of patients (control mean = 2.93 +/- 0.2, patient mean = 2.56 +/- 0.4, P < 0.005). There were no significant differences between the relapsing and secondary progressive subgroups. Over the follow-up period, there was a trend towards a decrease (8%) in the brain N-acetylaspartate:creatine ratio for the 11 relapsing patients and a significant (P < 0.001) correlation between changes in the brain N-acetylaspartate:creatine ratio and expanded disability scale scores for the patients in this group. This correlation was even more evident for the patients who had clinically relevant relapses during the 30 months of follow-up (seven of 11 patients). Increases in T2-weighted lesion volumes (35% in 30 months for the group as a whole, P < 0.0001, without differences between the subgroups) did not correlate with disability either in the group of patients as a whole or in the different subgroups. We conclude that indices of axonal damage or loss such as brain N-acetylaspartate may provide a specific measure of pathological changes relevant to disability. Total T2-weighted lesion volumes, although more sensitive to changes with time than brain N-acetylaspartate, may be less relevant to understanding the progression of disability.

Aspartic Acid↗

Recombination between viral DNA and the transgenic coat protein gene of African cassava mosaic geminivirus.

Nicotiana benthamiana was transformed with three different constructs (pCRA1, pCRA2 and pJC1) containing the coat protein coding sequence of African cassava mosaic virus (ACMV). Transformed plants were inoculated with a coat protein deletion mutant of ACMV that induces mild systemic symptoms in control plants. Several inoculated plants of transgenic lines CRA1/3, CRA1/4, CRA2/1 and CRA2/2 developed severe systemic symptoms typical of ACMV. DNA analysis revealed that, in these plants, recombination had occurred between the mutant viral DNA and the integrated construct DNA, resulting in the production of recombinant virus progeny with 'wild-type' characteristics. No reversion of mutant to 'wild-type' virus was observed in pJC1-transformed plants. Recombinant virus from several transgenic plants was analysed by PCR and parts of DNA A of virus progeny were cloned. Sequence analysis revealed that only a few nucleotides were changed from the published sequence.

Capsid↗

Mutational analysis of bean yellow dwarf virus, a geminivirus of the genus Mastrevirus that is adapted to dicotyledonous plants.

Bean yellow dwarf virus (BeYDV) is an atypical member of the geminivirus genus Mastrevirus that infects dicotyledonous plants. BeYDV DNA contains six open reading frames (ORFs) with the capacity to encode proteins in excess of 10 kDa. Two virion-sense ORFs (V1 and V2) and two complementary-sense ORFs (C1 and C2) have homologues in all mastreviruses, while ORFs C3 and C4 are not conserved. To investigate their functions, each of the ORFs has been truncated by either frame-shifting or the introduction of a stop codon. We demonstrate that an ORF V1 mutant replicated efficiently in Nicotiana tabacum protoplasts but was unable to systemically infect Phaseolus vulgaris and Datura stramonium, consistent with a role for V1 protein in virus movement. However, the mutant was able to systemically infect Nicotiana benthamiana although the onset of symptoms was appreciably delayed in comparison with wild-type virus. Disruption of ORF V2, encoding the coat protein, prevented systemic infection of all three hosts but the mutant replicated in protoplasts. Both ORF C1 and ORF C2 were essential for replication in protoplasts. Modification of the complementary-sense splice donor and acceptor sequences also prevented replication. Removal of the intron prevented systemic infection, although the intronless mutant was able to produce functional replication-associated protein (Rep) and replicated efficiently in protoplasts. ORFs C3 and C4 were not required for systemic infection. Our results indicate that four ORFs are spatially and functionally conserved in mastreviruses that infect both monocotyledonous and dicotyledonous plants.

Base Sequence↗

Fluorescent amplified-fragment length polymorphism analysis of an outbreak of group A streptococcal invasive disease.

Fluorescent amplified-fragment length polymorphism (FAFLP) analysis was carried out for an outbreak of group A streptococcal (GAS) invasive disease. Streptococcal genomic DNAs were digested with endonucleases EcoRI and MseI, site-specific adaptors were ligated, and PCR amplification was carried out with an EcoRI adaptor-specific primer labelled with fluorescent dye. Amplified fragments of up to 600 bp in size were separated on a polyacrylamide sequencing gel which contained internal size markers in each lane. These data were automatically scanned and analyzed, fragments were precisely sized (+/-1 bp), and electropherograms were generated for each genome with GeneScan 2.1 software. All isolates were compared in this way. Among 27 GAS isolates examined, we found 18 FAFLP profiles, compared with 12 macrorestriction profiles by pulsed-field gel electrophoresis. FAFLP readily distinguished genotypes for two clones of GAS serotype M77 which were responsible for outbreaks of invasive disease in a care-of-the-elderly system. It provided an automated analysis of the whole genome of bacterial isolates. It was reproducible, more discriminatory, and capable of higher throughput than other molecular typing methods. Given agreed conditions, FAFLP would be reproducible between laboratories for rapid characterization of outbreak strains.

Aged↗

Novel defective interfering DNAs associated with ageratum yellow vein geminivirus infection of Ageratum conyzoides.

Defective DNA forms of the geminivirus ageratum yellow vein virus (AYVV) have been identified in naturally infected Ageratum conyzoides plants. Several examples of the defective DNA have been cloned from purified virus-specific supercoiled DNA and characterized by sequence analysis. All are approximately half the size of AYVV genomic DNA, and all contain intergenic region sequences and the 5' terminus of gene C1 as well as additional sequences that are unrelated to the viral genomic DNA. The chimeric nature of the defective DNA distinguishes it from previously characterized geminivirus defective and satellite DNAs. The defective DNA ameliorates disease symptoms and causes a significant delay in the accumulation of viral DNA during the early stage of infection when coinoculated with the AYW genomic DNA into Nicotiana benthamiana, suggesting a biological role as a defective interfering DNA.

Base Sequence↗

Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species.

When the 23S rRNA genes from several Helicobacter species were amplified by PCR and compared with similar amplicons derived from H. pylori, they were seen to be enlarged in size. Sequencing of these enlarged genes from H. mustelae, H. canis (two strains) and H. muridarum identified insertions of novel sequence (intervening sequences, IVSs) sized between 93 and 377 bp located at nt 545, in place of an 8-nt sequence in the conventionally sized H. pylori gene. These IVSs were not present elsewhere in the genome. All strains with such IVSs lacked intact 23S rRNA which was replaced by two fragment whose sizes were consistent with cleavage at either side of the particular IVS. The predicted secondary structures of the four IVSs were characterised by base pairing at the 5' and 3' ends to form a stem. The four IVSs exhibited significant sequence inter-relationships. Further relationships were also observed between them and similar elements in both small and large subunit rRNA genes of other Helicobacter and Campylobacter species. Alignment of each IVS with the other such elements identified blocks of related sequence consistent with insertion/deletion events, indicating possible evolutionary relationships.

Base Sequence↗

Transactivation of dianthin transgene expression by African cassava mosaic virus AC2.

We have recently described a novel strategy for engineering resistance to African cassava mosaic virus (ACMV) in transgenic Nicotiana benthamiana plants using a virus-inducible promoter to control the expression of a plant ribosome-inactivating protein (RIP) transgene (Y. Hong et al., Virology 220, 119-127, 1996). Here, we have used a potato virus X (PVX) vector to express the ACMV transactivator protein, AC2, in planta. We confirm that amplification of RIP activity in transgenic plants is mediated by AC2; disruption of AC2 expression by either the introduction of an in-frame stop codon or the deletion of 5'-terminal or 3'-terminal coding sequences reduced RIP expression to the basal level associated with PVX-infected plants. AC2 expression from the PVX vector induced necrosis in nontransformed plants as well as in plants containing the RIP transgene, suggesting that the protein can functionally interact with PVX and/or host factors. The potential of this system to provide a direct and sensitive assay to investigate AC2 function in planta is discussed.

Antiviral Agents↗

Malaria.

The preeminent infectious threat to unwary tropical travelers, malaria is a preventable, mosquito-borne protozoan infection of red blood cells, which causes fever, anemia, respiratory failure, coma, and death. Malaria is a true medical emergency that requires rapid diagnosis and treatment. Unfortunately, in two thirds of tropical travelers who die of malaria, either treatment is delayed or the diagnosis is simply missed. Every tropical traveler with fever or unexplained, flu-like illness must be assumed to have life-threatening malaria and must have thick and thin blood smears immediately examined to confirm the diagnosis.

Algorithms↗

Polymerase chain reaction detection and speciation of Campylobacter upsaliensis and C. helveticus in human faeces and comparison with culture techniques.

A polymerase chain reaction (PCR) assay based on the 16S rRNA gene and an improved DNA extraction procedure were developed for the direct detection and differentiation of Campylobacter upsaliensis and C. helveticus in seeded human faeces. The PCR assay was compared with culture detection by a membrane filter (MF) technique and on selective agar (SA) containing 8 mg l-1 cefoperazone. Both MF culture and the PCR assay detected 10(5) colony-forming units (cfu) g-1 faeces. Selective agar culture of some strains could detect as few as 10(3) cfu g-1 faeces. However, some strains were susceptible to cefoperazone and either failed to grow or were detected only with reduced sensitivity in the presence of the antibiotic. Detection by MF and SA both required 48-96 h incubation in a microaerobic atmosphere and did not specifically identify the isolate. By contrast, the PCR assay could be completed within 8 h and accurately identified the two phenotypically similar species, C. upsaliensis and C. helveticus.

Agar↗

Side effects of CHOP in the treatment of non-hodgkin's lymphoma.

Cyclophosphamide, doxorubicin, vincristine (Oncovin), and prednisolone (CHOP) has for many years been the standard chemotherapeutic regimen for patients with aggressive non-Hodgkin's lymphoma. Published data for side effects experienced by patients undergoing CHOP chemotherapy in the treatment of non-Hodgkin's lymphoma are limited and inconsistent. No broad descriptive work appears to have been carried out. This study aimed to describe the range of problems experienced by patients receiving CHOP and to estimate incidence and severity of side effects over the treatment period. Data were collected at each treatment cycle via a 75-item self-report questionnaire, with severity of each side effect graded on a 5-point scale. The instrument has previously been shown to be reliable and valid. Nineteen participants received 99 cycles of CHOP and returned 74 questionnaires (response rate = 75%). Patients reported a total of 80 side effects. Alopecia was the most common problem, with all patients experiencing some hair loss by cycle 3. Fatigue was the second most common side effect (incidence = 77%) and taste change the third (incidence = 74%). Patients judged postchemotherapy nausea to be the "most troublesome" problem, followed by fatigue, taste change, constipation, and difficulty sleeping. Both nausea and fatigue were most problematic in the first part of the treatment course. These results indicate that patients receiving CHOP experience a wide range of problems, many of which merit further investigation.

Adolescent↗