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PubMed2004

Evaluation of variable number tandem repeat (VNTR) loci in molecular typing of Mycobacterium bovis isolates from Ireland.

Various sets of short tandem repeats such as the exact tandem repeats (ETRs), mycobacterial interspersed repetitive units (MIRUs) and variable number tandem repeat (VNTR) loci, have recently been described as effective tools in strain typing M. tuberculosis complex isolates, representative of global diversity. This study extends our previous study, evaluating the discrimination of a further 17 MIRU_VNTR loci individually and comparing the resolution of published VNTR sets and spoligotyping using a panel of 47 local M. bovis field isolates, including known epidemiologically linked isolates and 9 M. tuberculosis complex reference isolates. Individual loci differed greatly in their discrimination. The discriminatory capacity of novel combinations of the most discriminating VNTR loci was also assessed. In the panel of 47 M. bovis isolates, 17 unique profiles were resolved using VNTR set 1, whilst the MIRUs and ETRs resolved the panel into 11 and 6 profiles, respectively. A novel combination of 10 highly discriminatory VNTRs was determined, which resolved 30 unique profiles. The configuration of a multi-locus VNTR-based assay and its ability to provide a flexible, convenient and high-resolution genotyping method is discussed. We suggest a panel of VNTR markers which may be widely suitable for molecular epidemiological studies of M. bovis. However, the number and combination of informative VNTR markers selected needs to be determined empirically with reference to locally prevalent strains and will depend on the epidemiological study requirements.

Alleles↗

PubMed1975

Chilled food systems. Effects of chilled holding on quality of beef loaves.

Following storage at 32 degrees or 42 degrees +/- 1 degrees F. for zero (4 hr.), and one, two, four, seven, and nine days, beef loaves which had either been cooked; cooked and pasteurized; or cooked, frozen, and thawed prior to storage were compared with a freshly prepared, freshly cooked loaf. Loaves were initially cooked to an internal temperature of 165 degrees F. and reheated to the same temperature prior to testing. A freshly prepared loaf cooked immediately prior to evaluation statistically had a shorter heating time, less cooking losses, higher moisture content, lower thiobarbituric acid (TBA) scores, and higher taste panel scores for odor, juiciness, flavor, and appearance. In all quality-related properties evaluated, the reference loaf rated higher. Pasteurized loaves were not significantly different from refrigerated loaves. Frozen, thawed loaves had significantly different values for TBA scores for all taste panel evaluations; these differences were indicative of reduced quality. Taste panel scores decreased and TBA scores increased significantly over nine-day storage. The hypothesis that changes over time were linear was not rejected. The only significant difference noted for the two storage temperatures of 32 degrees and 42 degrees F. was for total heating time. Standard plate counts for aerobic bacteria were extremely low when samples were taken after storage and after reheating. Only two loaves sampled had counts per gram above 100. The absence of microbial growth pattern indicated that increases in TBA scores and decreases in odor and flavor scores were produced by autoxidation of lipids.

Cooking↗

PubMed2005

Use of novel immunohistochemical markers expressed in colonic adenocarcinoma to distinguish primary ovarian tumors from metastatic colorectal carcinoma.

Distinguishing primary ovarian carcinoma, particularly endometrioid and mucinous subtypes, from metastatic colorectal carcinoma to the ovary is often difficult on histologic examination alone. Recently, three immunohistochemical markers CDX2, a homeobox gene encoding an intestine-specific transcription factor; alpha-methylacyl-CoA racemase (AMACR/P504S), a mitochondrial and peroxisomal enzyme with fairly restricted expression in selective tumors and beta-catenin, an adenomatous polyposis coli (APC) mutation product resulting in activation of the Wnt pathway, have been reported to have specific and sensitive expression in colorectal carcinomas. We evaluated a panel consisting of antibodies to CDX2, beta-catenin and P504S in 23 primary ovarian adenocarcinomas (13 mucinous and 10 endometrioid) and compared the findings to 22 metastatic colorectal adenocarcinomas (seven mucinous and 15 nonmucinous tumors with endometrioid-like morphology hereafter referred to as pseudo-endometrioid) to the ovary stained with the same panel. Twenty (91%) metastatic tumors expressed at least two markers and seven (32%) expressed all three. In contrast, only three (13%) primary ovarian tumors expressed at least two markers and none expressed all three. Strong (2+, 3+) and diffuse (>40%) expression for CDX2 was noted in 21 (95%) metastatic tumors and five (22%) primary ovarian tumors (three mucinous, two endometrioid). P504S was similarly expressed in seven (32%) metastatic and none of the primary ovarian carcinomas. Nuclear expression of beta-catenin was noted in 13 (59%) metastatic tumors and in eight cases (36%), it was diffuse and strong. In contrast, four (19%) primary tumors showed nuclear expression of this protein with only one (5%) case expressing it in a diffuse pattern. Immunohistochemical expression of gene products and enzymes of colorectal carcinogenesis in some primary ovarian carcinomas suggest that the morphologic similarities between colorectal and mucinous/endometrioid carcinoma of the ovary extends to the genetic level, although differences in the level of expression exist between these tumors. Diffuse expression of all three markers (CDX2, beta-catenin and P504S) in a tumor in the ovary was found to be virtually diagnostic of metastasis from a colorectal primary in this study.

Adenocarcinoma↗

PubMed2001

[Reference values of serum lipid].

The guideline for the reference value of serum lipid(total cholesterol, LDL-cholesterol, HDL-cholesterol and triglyceride) was proposed by the Japan Atherosclerosis Society in 1997. These values are utilized for the diagnosis and treatment of hyperlipidemia to protect patients from ischemic heart disease. The upper limit of reference value was not determined by the 95 percentile range from healthy subjects, but on the basis of clinical data on serum lipid in the Japanese. This way to determine the reference value will be suitable in case of lipid, because there is a tendency to increase cholesterol level in the Japanese for these thirty years. The standardization for each lipid assay is crucial. The CDC-established Reference Methods for measuring total cholesterol(TC), HDL-C. LDL-C, and triglyceride(TG) are used to set reference values for the serum pools used for LSP(Lipid Standardization Panel) standardization. In Japan, the routine methods for cholesterol and triglyceride have been proposed by the special committee in the Japan Society of Clinical Chemistry. In contrast, homogeneous assay for HDL- and LDL-C, which are used routinely at present, have still some problems in the point of accuracy. A new ELISA for Lp(a) has been developed using antibody not reacting to kringle IV type 2. Its standardized assay, thus, will be available sooner or later. With respect to other lipid-related test such as RLP(remnant-like particles) and oxidized LDL, it is necessary to accumulate more clinical data for the determination of reference value.

Apoproteins↗

PubMed1992

Anaerobic yeast killer systems.

The influence of anaerobic conditions on the expression of the killer phenomenon of several yeast isolates belonging to recognized killer systems coded by different genetic determinants (Pichia spp., Kluyveromyces lactis, Saccharomyces cerevisiae) was studied. Anaerobiosis influenced the activity of killer toxins from some individual isolates of the genera Pichia and Saccharomyces on sensitive strains of P. anomala, K. lactis and Candida albicans. However, no influence was detectable on a S. cerevisiae sensitive isolate. Thus, anaerobic conditions seem to interfere more with the metabolic process of sensitive strains than with toxin production by killer yeasts. The selection of a panel of killer yeasts, able to display their activity against reference sensitive yeast isolates under anaerobic conditions in a medium that favored the growth of anaerobes, allowed the use of the killer system to type Bacteroides fragilis isolates for epidemiological purposes.

Anaerobiosis↗

PubMed1995

Identification of two highly polymorphic CA-repeats (D21S1224 and D21S1261) on human chromosome 21q22.3.

Two highly polymorphic CA-repeat microsatellites (D21S1224 and D21S1261) are reported. The clones containing these CA-repeats (ABM-C60 and ABM-C29) have been isolated from a human chromosome-21-specific library (LA21NS01) and have been localised to the q22.3 band using a specific chromosome 21 somatic cell hybrid panel. Both polymorphisms showed heterozygosities of 0.83 in the unrelated reference parents from the Centre d'Etude du Polymorphisme Humain. These new markers should improve the map of the 21q22.3 region, which is believed to contain a large number of genes.

Base Sequence↗

PubMed1988

Bacterial expression and characterization of nine polypeptides encoded by segments of the envelope gene of human immunodeficiency virus.

Nine envelope (Env) polypeptides, encoding different regions of HIV gp120 and gp41 Env proteins, and accounting for approx. 96% of the entire Env precursor glycoprotein complex (gp160) were expressed in Escherichia coli at levels ranging from approx. 2 to 20% of total cellular protein. The recombinant polypeptides were produced either as hybrid products fused to the cII gene fragment of the lambda vector or in an unfused form without interfering cII products. Partially purified protein fractions of each polypeptide were characterized serologically by Western-blot analysis against a panel of well characterized human immunodeficiency virus (HIV)-positive human reference sera. Most of the Env polypeptides were highly immunoreactive with anti-gp120/gp41 antibodies present in the sera of patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related diseases, but the patterns of reactivity were different. These results demonstrate that some of the antigenic determinants residing on the viral gp160 complex are retained on the surfaces of the recombinant Env polypeptides, and suggest that these sites are differentially immunogenic. These results are therefore interpreted in the context of an ongoing process towards using bacterially expressed HIV Env polypeptides to help define biological and structural epitopes to aid in the development of more sensitive diagnostic and therapeutic reagents in the fight against AIDS.

Cloning, Molecular↗

PubMed2001

Intrastromal corneal ring segments for low myopia: a report by the American Academy of Ophthalmology.

OBJECTIVE: This document describes intrastromal corneal ring segments (Intacs) inserts technology and examines the evidence to answer the key question about whether the treatment is safe and effective in correcting low myopia. METHODS: A literature search that was conducted in September 2000 retrieved 13 relevant citations, and the reference lists of these articles were consulted for additional citations. Panel members reviewed this information and articles were rated according to the strength of evidence. RESULTS: Prospective multicenter phase II and III clinical trials (Level II evidence rating) of Intacs inserts for myopia of -1.00 to -3.00 diopters (D), with a maximum of +1.00 D of astigmatism, enrolled a total of 452 subjects, with a total of 454 surgical attempts. The results from phase II and phase III were pooled for much of the analysis. At 1 year, 97% of patients who completed follow-up had 20/40 or better uncorrected visual acuity (UCVA). Seventy-four percent of patients had 20/20 or better UCVA. Ninety-two percent of eyes were within +/-1 D of intended refractive correction, and 69% were within 0.5 D of intended refractive correction. At 3 months, 90% of patients had less than 1.0 D of change from the previous examination performed at 1 month. The ocular complication rate, which was defined as clinically significant events but not resulting in permanent sequelae, was 11% at 12 months. The adverse event rate was 1.1%, defined as a serious event if untreated. Nearly 9% of patients requested to have their inserts removed and a total of 3.8% of patients required a secondary surgical intervention. CONCLUSIONS: To date, evidence suggests that low myopia (-1 to -3 D) in a well-defined group of patients who have a stable manifest refraction and less than +1.0 D of astigmatism can be treated with Intacs inserts with a reasonable assurance of safety and effectiveness. Additional clinical research is needed to determine the long-term effectiveness of treatment and the comparative safety, effectiveness, and costs with other treatment modalities, including laser-assisted in-situ keratomileusis (LASIK) and photorefractive keratectomy (PRK).

Academies and Institutes↗

PubMed2005

Development and validation of a fluorescence polarization-based competitive peptide-binding assay for HLA-A*0201--a new tool for epitope discovery.

Various approaches are currently proposed to successfully develop therapies for the prevention and treatment of infectious diseases and cancer. One of the most promising approaches is the development of vaccines that elicit cytotoxic T lymphocyte (CTL) responses. Consequently, identification and exact definition of molecular parameters involved in peptide-MHC class-I interactions of putative CTL epitopes are of prime importance for the development of immunomodulating compounds. To better facilitate epitope discovery, we developed and validated a novel state-of-the-art biochemical HLA-A0201 assay, which is comprised of technologically advanced cutting edge reagents. The technique is based on competition and uses a FITC-labeled reference peptide and highly purified soluble HLA-A0201 molecules to quantitatively measure the binding capacity of nonlabeled peptide candidates. Detection by fluorescence polarization allows real-time measurement of binding ratios without separation steps. During standardization, the problem of assay parameter variation is discussed, showing the dramatic influence of HLA and reference peptide concentrations as well as the choice of the reference peptide itself on IC(50) determinations. For validation, a panel of 15 well-defined HLA-A0201 ligands from various sources covering a broad range of binding affinities was tested. Binding data were used to compare against pre-existing quantitative assay systems. The results obtained demonstrated significant correlation among assay procedures, suggesting that the application of fluorescence polarization in combination with recombinant sHLA molecules is highly advantageous for the accurate assessment of peptide binding. Furthermore, the assay also features high-throughput screening capacity, providing uniquely efficient means of identifying and evaluating immune target molecules.

Binding Sites↗

PubMed2003

The scientific basis of recent US guidance on sugars intake.

Most fruits and dairy products are high in sugars, and thus naturally occurring sugars are consumed as part of a healthy diet. Sugars are also added to foods during processing or preparation, primarily to enhance taste. Monosaccharides and disaccharides added to foods are chemically indistinguishable from naturally occurring forms. However, concern has been expressed about the apparent increasing consumption of added sugars and their possible role in displacing or diluting nutrients in the diet and contributing to the epidemic of obesity in developed countries. One of the 2000 Dietary Guidelines for Americans states, "Choose beverages and foods to moderate your intake of sugars." The Dietary Guidelines Advisory Committee discussed whether to specify added sugars rather than the broader term sugars but decided that it was not possible to conclude that added sugars per se play a negative role in the public's health. The Dietary Guidelines Advisory Committee issued a call for more definitive studies of the role of sugars in current diets and the potential effect of a reduction in added sugars on both dietary quality and energy intake. The American Heart Association recently released a statement advising consumers to limit sugars consumption. The macronutrient report for the dietary reference intakes addresses many of these same issues; the expert panel concluded that it was not appropriate to set a tolerable upper intake level for added sugars but suggested a maximal intake level of 25% of energy from added sugars because of concerns about reduced intakes of essential micronutrients.

Adolescent↗

PubMed2005

Unrecognized heart failure in elderly patients with stable chronic obstructive pulmonary disease.

AIMS: To establish the prevalence of unrecognized heart failure in elderly patients with a diagnosis of chronic obstructive pulmonary disease, in a stable phase of their disease. METHODS AND RESULTS: In a cross-sectional study, patients >/=65 years of age, classified as having chronic obstructive pulmonary disease by their general practitioner and not known with a cardiologist-confirmed diagnosis of heart failure, were invited to our out-patient clinic. Four hundred and five participants underwent an extensive diagnostic work-up, including medical history and physical examination, followed by chest radiography, electrocardiography, echocardiography, and pulmonary function tests. As reference (i.e. 'gold') standard the consensus opinion of an expert panel was used. The panel based the diagnosis of heart failure on all available results from the diagnostic assessment, guided by the diagnostic principles of the European Society of Cardiology (ESC) for heart failure (i.e., symptoms and echocardiographic systolic and/or diastolic dysfunction). The diagnosis of chronic obstructive pulmonary disease was based on the diagnostic criteria of the Global Initiative (GOLD) for chronic obstructive pulmonary disease. Of 405 participating patients with a diagnosis of chronic obstructive pulmonary disease, 83 (20.5%, 95% CI 16.7-24.8) had previously unrecognized heart failure (42 patients systolic, 41 'isolated' diastolic, and none right-sided heart failure). In total, 244 (60.2%) patients had chronic obstructive pulmonary disease according to the GOLD criteria and 50 (20.5%, 95% CI 15.6-26.1) patients combined with unrecognized heart failure. CONCLUSION: Unrecognized heart failure is very common in elderly patients with stable chronic obstructive pulmonary disease. Closer co-operation among general practitioners, pulmonologists, and cardiologists is necessary to improve detection and adequate treatment of heart failure in this large patient population.

Age Distribution↗

PubMed2005

Validation of verbal autopsy procedures for adult deaths in China.

BACKGROUND: Vital registration of causes of death in China is incomplete with poor coverage of medical certification. Information on the leading causes of mortality will continue to rely on verbal autopsy (VA) methods. A new international VA form is being considered for data collection in China, but it first needs to be validated to determine its operating characteristics. METHODS: Detailed medical records and clinical evidence for 3290 deaths (mostly adults) among residents of six cities representative of the urban Chinese population were reviewed by a panel of physicians and coded by experts to establish a reference underlying cause of death. Independently, families of the deceased were interviewed using a structured symptomatic questionnaire and a separate death certificate was prepared for each matching case (2102). Validity of the VA procedure was assessed using standard measurement criteria of sensitivity, specificity, and positive predictive value. RESULTS: VA methods perform reasonably well in identifying deaths from several leading causes of adult deaths including stroke, several major cancer sites (lung, liver, stomach, oesophagus, and colorectal), and transport accidents. Sensitivity was less satisfactory in detecting deaths from several causes of major public health concern in China including ischaemic heart disease, chronic obstructive pulmonary disease, diabetes, and tuberculosis, and was particularly poor in diagnosing deaths from viral hepatitis, hypertension, and kidney diseases. CONCLUSIONS: VA is an imprecise tool for detecting leading causes of death among adults. However, much of the misclassification generally occurs within broad cause groups (e.g. CVD, respiratory diseases, and liver diseases). Moreover, compensating patterns of misclassification would appear to suggest that, in urban China at least, the method yields population-level cause-specific estimates that are reasonably reliable. These results suggest the possible utility of these methods in rural China, to back up the low coverage of medical certification of cause of death owing to poor access to health facilities there.

Adolescent↗

PubMed2003

Development of appropriateness criteria for colonoscopy: comparison between a standardized expert panel and an evidence-based medicine approach.

OBJECTIVES: To assess the degree of agreement between appropriateness criteria for the use of colonoscopy developed by a standardized expert panel method and evidence from published studies. DESIGN: Descriptive, agreement study. SETTING: Multidisciplinary panel; primary care practice in Switzerland. PARTICIPANTS: Nine national experts; 577 primary care patients referred for colonoscopy, 154 published papers. INTERVENTIONS: Evaluation of the appropriateness of 402 possible clinical indications for colonoscopy, based on a comprehensive review of the literature. MAIN OUTCOMES MEASURES: Proportion of agreement (weighted kappa), between panel- and literature-based appropriateness categories (appropriate, uncertain, inappropriate) for theoretical and actual indications encountered. RESULTS: Nineteen of 402 indications rated by the panel could be based on the evidence retrieved from eight randomized clinical trials. A 68% agreement (kappa = 0.52) was found between panel- and study-based criteria. The addition of an uncontrolled trial and seven observational studies yielded a 71% agreement (kappa = 0.63). Agreement was similar when examining 577 actual cases: 69% agreement, kappa = 0.47. Agreement between panel-based indications and published evidence was not influenced by the perceived comprehensiveness and the apparent quality of the published reports. CONCLUSIONS: Evidence for the appropriateness of most indications for colonoscopy could not be derived directly from the published literature. Agreement between appropriateness criteria developed by an expert panel and evidence from published studies was moderate to good, where available. New approaches should be sought in order to systematically integrate complementary evidence obtained from clinical trials and expert panels into practice guidelines.

Clinical Trials as Topic↗

PubMed2002

Dorsal root entry zone lesioning used to treat central neuropathic pain in patients with traumatic spinal cord injury: a systematic review.

STUDY DESIGN: A systematic review was conducted for studies of any design. OBJECTIVES: To evaluate the effectiveness and safety of dorsal root entry zone lesioning in treating central neuropathic pain of patients with traumatic spinal cord injury. SUMMARY OF BACKGROUND DATA: Central neuropathic pain has a great impact on the quality of life of many patients with traumatic spinal cord injury. Dorsal root entry zone lesioning has become one of several treatment options. No previous systematic reviews were found that address this indication for the procedure. METHODS: Several computerized databases were searched along with reference lists of eligible articles and personal files of advisory panel members. Only primary studies of patients older than 13 years with both traumatic spinal cord injury and central neuropathic pain receiving dorsal root entry zone lesioning were included. Two assessors independently performed data extraction and quality assessment for all the studies. RESULTS: The selection criteria were met by 11 studies. All were case series of 5 to 54 patients. As reported by 10 of the studies, at least 50% of the patients attained more than 50% pain relief or experienced no pain limitation of activity and no need for narcotics. However, all the studies had poorly defined eligibility criteria or none at all, no control groups, and inadequate reporting of adverse effects. Only one study provided adequate patient description. None of the studies reported the validity, reliability, or responsiveness of outcome measures. CONCLUSIONS: Reviewed studies indicate promising results from dorsal root entry zone lesioning for the treatment of central neuropathic pain in selected patients with traumatic spinal cord injury. However, the strength of the evidence provided by the studies was poor in terms of study design, outcome measures, reports on the severity of adverse effects, patient selection criteria, and patient description. For these reasons, the evidence is weak for the use of dorsal root entry zone lesioning to relieve central neuropathic pain in patients with traumatic spinal cord injury.

Adult↗

PubMed1986

Continuing education and peer review in internal medicine (CEPRIME).

Research in adult education shows that educational initiatives are most effective when they are related to perceived needs. The CEPRIME system was devised as a means of using peer review to reveal the educational needs of physicians. Sixteen physicians volunteered to test the system, by allowing a panel of specialists to review copies of their reports to referring general practitioners. The comments of the reviewers, both commendatory and critical, were referred back to the participants, and their evaluation of the system was sought. Although the method was found to have limitations relating both to the adequacy of the report as a document for review, and to the objectivity and relevance of the comments made about it, the results were such as to encourage further development of CEPRIME as a means of appraising physicians of their specific educational needs.

Australia↗

PubMed2004

Comparison between the two systems to evaluate the appropriateness of endoscopy of the upper digestive tract.

OBJECTIVES: The aim of this study was to compare the diagnostic performance of the two systems for the evaluation of the appropriateness of upper digestive endoscopy suggested by the American Society of Gastrointestinal Endoscopy (ASGE) and by the European Panel on the Appropriateness of Gastrointestinal Endoscopy (EPAGE). METHODS: Patients referred for the upper digestive endoscopy (EGD) to a University Outpatients Clinic of Northeastern Italy were consecutively included in this prospective observational study. Before the EGD, the endoscopist assigned the patients to one of the ASGE appropriateness classes; another endoscopist then identified the detailed clinical scenario for the patients, which corresponds to scenarios examined by EPAGE by using a nine-point scale: 1-3 inappropriate; 4-6 uncertain; and 7-9 appropriate. The relationship between the appropriateness of use and the presence of relevant endoscopic lesions (neoplasms, ulcers, esophagitis, erosive gastritis/duodenitis, stenosis, and varices) was assessed, calculating the sensitivity and the specificity for each of the ASGE criteria, and each of the EPAGE scores, and plotting them to form a receiver operating characteristic (ROC) curve. The area under the ROC curve (AUC) provides a summary measure of test performance, and can vary from a minimum of 0.5 to a maximum of 1.0. We compared the AUC of the ROC curve derived from the ASGE criteria against that derived from the EPAGE criteria. RESULTS: A total of 2,300 consecutive patients were included in the study (42% men; mean age: 57.3; range: 12-99); comparison of appropriateness criteria according to the ASGE and EPAGE could be made for 2,000 patients. The AUC of the ROC curve derived from the ASGE criteria was 0.553 (95% CI: 0.527-0.579), significantly higher than the AUC of the ROC curve derived from the EPAGE score: 0.523 (95% CI: 0.497-0.549; p < 0.05). CONCLUSIONS: We suggest that the diagnostic yield for relevant endoscopic findings obtained by both the systems (ASGE and EPAGE) is low; slightly better results could be accomplished by the ASGE criteria.

Adolescent↗

PubMed1986

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and monoclonal antibodies as tools for the subgrouping of Escherichia coli lipopolysaccharide O18 and O23 antigens.

The lipopolysaccharide (LPS) of Escherichia coli O18 isolated from a wide variety of sources was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Four different LPS types, designated O18A, O18A1, O18B, and O18B1, were identified. Most O18 strains possess O18A, O18A1, or O18B LPS types, and these types are clonally associated. A reference test strain with the classical O18ab designation possessed O18B LPS, while two reference O18ac strains possessed O18A and O18A1 LPS, respectively. A panel of 15 anti-O18A B-cell hybridomas was isolated. Enzyme-linked immunosorbent assays revealed that some of the monoclonal antibodies produced by these cells recognize different epitopes. Four of these antibodies suffice to distinguish the four O18 types. Numerous strains whose LPS had been typed by SDS-PAGE were tested by agglutination with seven monoclonal antibodies whose specificities had been determined by enzyme-linked immunosorbent assays. The results indicated a perfect correlation between the two methods. Rabbit antisera raised against O18A bacteria agglutinated boiled bacteria of each of the O18 LPS types efficiently. The antisera were adsorbed with bacteria possessing each of the LPS types. The adsorbed sera only distinguished between two groups: O18A and O18A1 versus O18B and O18B1, as shown by agglutination assays and Western blotting. E. coli O4 and O23 and Serratia marcescens O8 antigens, which are reputed to cross-react with O18, were also analyzed. One O4, one O8, and four O23 strains were tested. All made an LPS which was distinguishable from O18 LPS types by SDS-PAGE. Each O23 strain synthesized a different LPS, and three of them synthesized only few short chains. Some of the monoclonal antibodies reacted with O4, O8, and O23A LPSs. The results are interpreted as indicating that numerous E. coli O serogroups will prove to be chemically heterogeneous and that future analyses of subgroup heterogeneity should be guided by results from SDS-PAGE and rely preferentially on monoclonal antibodies as opposed to rabbit hyperimmune sera.

Antibodies, Bacterial↗

PubMed1999

Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms.

The performance of a silica chip-based resequencing method, the Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix assay), was evaluated on a panel of well-characterized nonclade B viral isolates and on isolates exhibiting length polymorphisms. Sequencing of human immunodeficiency virus type 1 (HIV-1) pol cDNAs from clades A, C, D, E, and F resulted in clade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spurious resistance polymorphisms. The Affymetrix assay failed to detect the presence of additional serine codons distal to reverse transcriptase (RT) codon 68 that are associated with multinucleoside RT inhibitor resistance. The increasing prevalence of non-clade B HIV-1 strains in the United States and Europe and the identification of clinically relevant pol gene length polymorphisms will impact the generalizability of the Affymetrix assay, emphasizing the need to accommodate this expanding pool of pol genotypes in future assay versions.

Acquired Immunodeficiency Syndrome↗