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PubMedDate not supplied

Detection of Clostridium difficile toxin by an indigenously developed latex agglutination assay.

An indigenously developed latex agglutination assay using C. sordelli antitoxin was used to screen 211 stool samples received from hospitalized patients. Of 126 samples from patients receiving single to multiple antibiotics for various ailments, 38 (30%) were positive by the toxin assay, whereas only 6/85 (7%) of samples of patients not receiving antibiotics were also positive. Thus, of 211 samples a total of 44 (20.8%) were positive by our toxin assay, giving titers ranging from 1 in 5 to 1 in 320. The test developed by us is simple, rapid, easy and reliable and can be easily adapted to all microbiology laboratories.

Anti-Bacterial Agents↗

PubMed1993

A combined polymerase chain reaction-colour development hybridization assay in a microtitre format for the detection of Clostridium spp.

We have developed a rapid and sensitive assay for the detection of clostridial cells or spores in liquid food samples. The method recognizes Clostridium 16S (small ribosomal subunit RNA) rDNA (ribosomal DNA) sequences by a polymerase chain reaction-digoxigenin-labelling protocol, coupled to a capture oligonucleotide immobilized on a microtitre plate. The positive results are revealed by means of a colour reaction. In 6 h of non-intensive labour, we can detect as few as two to five clostridial cells or spores in experimentally contaminated soft drinks.

Bacteriological Techniques↗

PubMed2026

Identification of lineage-associated polymorphisms in the ROP18 3' flanking region and development of molecular assays for differentiation of Toxoplasma gondii lineages.

BACKGROUND: Toxoplasma gondii (T. gondii) exhibits substantial genetic diversity, and different parasite lineages are associated with distinct epidemiological distributions and biological characteristics. Accurate molecular characterization of T. gondii strains is important for understanding parasite population structure and transmission patterns. However, existing genotyping approaches often require multiple loci, extensive experimental procedures, or complex data analysis. Therefore, simplified and reliable molecular markers for rapid lineage differentiation are still needed. METHODS: In this study, comparative genomic analysis was performed using representative T. gondii strains with well-defined genetic backgrounds and virulence phenotypes. The ROP18 genomic region, including partial genomic sequences, 5' flanking regions, coding sequence (CDS), and 3' flanking regions, was analyzed to identify informative polymorphic signatures. A short conserved sequence region containing lineage-associated polymorphic sites was identified within the ROP18 3' flanking region. Based on these sequence signatures, HRM-PCR and TaqMan MGB probe-based real-time PCR assays were developed and evaluated using plasmid standards and representative T. gondii genomic DNA samples. RESULTS: Phylogenetic analyses based on different ROP18 genomic regions demonstrated distinct clustering patterns among analyzed strains. Although the ROP18 3' flanking region was highly conserved, a short conserved sequence region containing informative polymorphic sites was identified, and the combination of these sites generated three distinct lineage-associated ROP18 patterns. Analysis of publicly available genomic datasets further demonstrated that individual strains contained one of these defined patterns rather than multiple patterns simultaneously. The developed HRM-PCR assay successfully discriminated the three ROP18-associated patterns based on distinct melting profiles with good reproducibility. Furthermore, the TaqMan MGB probe-based assay enabled specific identification of different ROP18-associated patterns through defined probe-recognition combinations and showed good analytical performance. CONCLUSION: This study identifies novel lineage-associated molecular signatures within the ROP18 3' flanking region and establishes complementary HRM-PCR and TaqMan MGB probe-based approaches for rapid molecular differentiation of T. gondii strains. These findings highlight the potential of conserved non-coding regions adjacent to functionally important genes as informative targets for parasite genotyping and provide a practical complementary tool for epidemiological surveillance and strain characterization.

HRM-PCR↗

PubMed1988

A newly developed immunofluorescent assay for determining the Pichinde virus-inhibitory effects of selected nucleoside analogues.

An immunofluorescent assay (IFA) for Pichinde virus (PCV), a member of the family Arenaviridae, was developed for antiviral drug assays against the virus. The assay was performed by adding fluorescein-labeled anti-PCV monoclonal antibody to virus-infected cells at 24 h after the initial infection and counting the infected cells with an epifluorescence microscope. The average 50% effective dose (ED50) for a series of nucleoside analogues tested against PCV using this IFA was: 2-beta-D-ribofuranosylselenazole-4-carboxamide (selenazofurin), less than 1.0 microgram/ml; 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide (ribavirin), 6.0 micrograms/ml; ammonium 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide- 5'-phosphate hydrate (ribavirin-5'-monophosphate), 15.8 micrograms/ml; ammonium 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide-5'-hemisuccinate (ribavirin-5'-hemisuccinate), 14.7 micrograms/ml; ammonium 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide-5'-(2,3- dimethyl)hemisuccinate [ribavirin-5'-(2,3-dimethyl)hemisuccinate], 213.5 micrograms/ml; 4-hydroxy-1-beta-D-ribofuranosyl-2-pyridone (3-deazauridine), 5.2 micrograms/ml; and (S)-9-(2,3-dihydroxypropyl)adenine, ([S]-DHPA), 471.0 micrograms/ml. In comparison, the ED50 of ribavirin using inhibition of marginal PCV-induced cytopathogenic effect after 12 days was 6.0 micrograms/ml and using plaque reduction after 5 days was 2.5 micrograms/ml, indicating that this IFA was of comparable sensitivity to these other tests.

Animals↗

PubMed2005

Development of a reliable assay protocol for identification of diseases (RAPID)-bioactive amplification with probing (BAP) for detection of bovine ephemeral fever virus.

A rapid, sensitive, and specific assay, RAPID-BAP assay, was developed to detect and quantify the G protein-encoding gene of bovine ephemeral fever virus (BEFV). This new technique uses a nested PCR and magnetic bead-based DNA probing assay. The optimal conditions for the assay were examined. By applying a nested PCR, a minimum of 1 copy/mul of the BEFV plasmid DNA could be detected by the assay. The optimal hybridization conditions at 50 degrees C in 5x SSC and 0.5% SDS with a 20-min incubation allowed clear discrimination between negative and positive controls. The assay was also highly specific as all negative controls failed to show any positive detection. The diagnostic sensitivity of the RAPID-BAP assay, real-time RT-PCR, and conventional RT-PCR in the detection of 34 clinical blood samples suspected to have BEFV infections were 72.73, 36.36, and 18.18%, respectively. The results indicated that the RAPID-BAP assay developed in this study was more sensitive than the conventional RT-PCR and real-time RT-PCR assays for the detection of BEFV. The novel RAPID-BAP assay is an excellent diagnostic tool with high sensitivity, specificity, and fast turnaround time.

Animals↗

PubMedDate not supplied

Recent progress in the development of assays suited for histone deacetylase inhibitor screening.

Histone deacetylase (HDAC) inhibitors have an unprecedented potential to occupy a major position in the future market of anticancer agents. However, progress in the development of these new chemotherapeutics is largely dependent on the existence of bioassays well-suited for inhibitor screening. Herein, we summarize recent developments in HDAC assay technology and, particularly, discuss different assay types with respect to their suitability for high-throughput screening programs.

Acetylation↗

PubMed1996

A newly developed PCR assay of H. pylori in gastric biopsy, saliva, and feces. Evidence of high prevalence of H. pylori in saliva supports oral transmission.

We have recently developed a new PCR assay for the detection of H. pylori. In this study, the polymerase chain reaction (PCR) assay was used to detect H. pylori in 88 gastric biopsy, 85 saliva, and 71 fecal specimens from 88 patients. H. pylori infection was confirmed in 71 of 88 patients by culture and/or histological stain of gastric biopsies. Serum IgG antibody to H. pylori was also measured and resulted in 97% sensitivity and 94% specificity. H. pylori DNA was detected by the PCR assay in gastric biopsy specimens from all 71 patients (100% sensitivity) with proven gastric H. pylori infection but not from 17 noninfected patients (100% specificity). In saliva specimens, H. pylori DNA was identified in 57 of the 68 patients (84%) with proven gastric H. pylori infection and in three of the 17 patients without gastric H. pylori infection. However, the PCR assay was only able to detect H. pylori DNA in the feces from 15 of 61 patients (25%) with proven gastric H. pylori infection and one of the 10 patients without gastric H. pylori infection. The results show that the PCR assay is reliable for detecting the presence of H. pylori in gastric biopsy and saliva specimens. The data indicate that H. pylori exists in a higher prevalence in saliva than feces and that the fecal-oral route may be an important means of transmission of this infection in developing countries but not as significant as previously suspected in the developed countries. It is likely that the oral-oral route is more prominent.

Antibodies, Bacterial↗

PubMed1984

Chemical analysis of marker substances.

The development of chemical assay procedures for potential marker substances will depend on, and be determined by, three basic factors: (1) the nature of the substance used, (2) the characteristics of the biological samples obtained, and (3) the varieties of information required. Once these have been delineated, the analytical methodology can be specifically characterized in terms of specificity and sensitivity; accuracy, precision, and reliability; and ease, cost, and safety. The specific details of a method must be based on the three factors mentioned above. Thus, a procedure having an ultimate sensitivity limit of more than a micromole per milliliter will be useless if the maximum expected marker concentration in the sample is less than a micromole per milliliter. Similarly, a procedure utilizing gas-liquid chromatography mass spectrometry costing many thousands of dollars is overkill if only a simple, inexpensive thin-layer chromatography procedure is needed to merely confirm the presence of the marker in a sample of urine or blood. Finally, the potential utility of the marker substance will be constrained by nonscientific factors such as cost, time, and convenience. These factors may depend on the ultimate applications of marker substance use, but they must also be addressed in any assay development program. The overall characteristics of a chemical assay procedure for marker substances will be discussed in terms of a model based on similar procedures for the chemical assay of foreign organic compounds in biological materials.

Costs and Cost Analysis↗

PubMed2003

Detection of the factor V Leiden mutation by a modified photo-cross-linking oligonucleotide hybridization assay.

BACKGROUND: Our previously developed assay for detection of the factor V Leiden mutation (G1691A) based on a nucleic acid photo-cross-linking technology used two allele-specific capture probes and six fluorescein-modified signal-generating reporter probes. We wished to improve the sensitivity and performance of the method. METHODS: We developed new reporter probes with approximately 10-fold more fluorescein molecules than the original probes. The single, cross-linker-modified capture probe was replaced by a three-probe system, separating the probe-target cross-linking function and the allelic differentiation function. The capture probe cross-linked to either or both of two flanking probes through stem structures at the capture-probe/flanking-probe junctions. The flanking probes cross-linked to target DNA through two cross-linking sites each. Genomic DNA was extracted from 0.2 mL of whole blood and restriction-enzyme digested to create a defined 677 bp target sequence. Preliminary genotype ranges were determined for the assay by testing of pre-typed samples. We then tested 1054 clinical samples, using an automated sample processor. RESULTS: The new assay had a 10-fold increase in signal-to-background ratio. Genotype results for 1039 of 1054 clinical samples (98.6%) agreed with those of a PCR-based method. Of the 15 remaining samples, 10 produced an indeterminate result outside the defined genotype ranges, 2 yielded insufficient signal to be genotyped, and 3 gave a discordant result. All 15 samples were genotyped correctly after re-extraction of genomic DNA and retesting. CONCLUSION: The modified photo-cross-linking assay for factor V Leiden detection is a sensitive non-PCR-based assay with potential for use in high-throughput clinical laboratories.

Autoanalysis↗

PubMed1978

Improved assay procedures for thyroid peroxidase; application to normal and adenomatous human thyroid tissue.

We have developed assays for thyroid peroxidase in crude thyroid tissue preparations, in which a linear relationship between activity and amount of tissue could be demonstrated. Linear assays were developed based on the following peroxidase catalyzed reactions in the presence of H2O2:(1) oxidation of I- to I(-3), (2) oxidation of guaiacol, and (3) iodination of human goiter thyroglobulin. To attain satisfactory linearity we found it necessary to solubilize the enzyme beforehand. This was accomplished by a brief treatment of the particulate fraction with trypsin and deoxycholate, followed by centrifugation at 40 000 X g and dialysis. Not only did this treatment facilitate the development of linear assays, but it also resulted in a substantial increase in enzyme activity compared with that in the untreated particulate fraction. The use of a Polytron homogenizer for the initial disruption of the tissue also proved helpful in developing these assay procedures. The three different assays were used to measure peroxidase activities in human thyroid adenomas and in normal tissue derived from adenomatous glands. T he adenomas generally displayed a higher level of peroxidase activity than normal tissue. The greatest difference was observed with the iodination assay and the smallest difference with the guaiacol assay.

Adenoma↗

PubMed1988

The hemizona assay (HZA): development of a diagnostic test for the binding of human spermatozoa to the human hemizona pellucida to predict fertilization potential.

The authors present their initial results with the hemizona assay (HZA), which was developed to predict the fertilizing potential of spermatozoa. The HZA uses the matching halves of a human zona pellucida from a nonfertilizable and nonliving oocyte, providing an internal control on zona-to-zona variability. Maximal binding of human sperm to the hemizona usually occurred after 4 to 5 hours of coincubation. Sperm from fertile men exhibited significantly higher binding capacity to hemizonae compared with sperm from men who had fertilization failure during in vitro fertilization (IVF) treatment. The HZA index is calculated as follows: (bound sperm from subfertile male) divided by (bound sperm from fertile male) X 100. These findings demonstrate that the HZA may be a useful diagnostic tool in male infertility evaluations.

Female↗

PubMedDate not supplied

Non-pretreatment digoxin assays and developments in immunoanalyzers.

OBJECTIVE: The performance of a new, non-pretreatment digoxin assay for the Abbott IMx analyzer (Abbott Park IL) was evaluated to determine its reliability and suitability for routine clinical use. The operational characteristics of 1st, 2nd and 3rd generation immunoanalyzers are compared and contrasted. DESIGN: Within-run and day-to-day precision of the assay was determined, as well as its limit of detection. The effect of digoxin-like immunoreactive factors and carryover were evaluated. Serum from patients receiving digoxin was analyzed using the Dade Stratus II (Miami FL) digoxin test as the reference method and the IMx digoxin test as the comparison method. SETTING: An independent reference laboratory specializing in serving long-term care facilities. PATIENT POPULATION: Specimens were analyzed from geriatric patients in long-term care facilities who receive digoxin as a therapeutic drug for cardiac arrhythmias. Specimens were also tested from individuals in this same population, not receiving digoxin but demonstrating the presence of digoxin-like immunoreactive factors. MAIN OUTCOME MEASURE: Comparability of results from a new nonpretreatment digoxin with the standard digoxin assay (Stratus II) was used to determine the suitability of the new test for routine clinical use. RESULTS: The limit of detection is 0.27 ng/mL; day-to-day precision ranges from 3.4% CV to 5.9% CV. Linear regression analysis generated the following equation: IMx = 0.968 Stratus + 0.1043, r = 0.9776, n = 237. No significant interference from digitoxin-like immunoreactive factors was noted. CONCLUSION: The IMx nonpretreatment digoxin assay's performance matches the manufacturer's claims, compares favorably with another common automated digoxin test, and is suitable for routine clinical use.

Aged↗

PubMed1989

Assessment of chemically-induced alterations in brain development using assays of neuron- and glia-localized proteins.

Chemical-induced injury of the developing central nervous system (CNS) is often manifested by alterations in the cellular ontogeny of specific neuroanatomical regions. Within the affected area, critical developmental processes encompassing a variety of neuronal and glial cell types may be transiently or permanently altered. Because the cellular heterogeneity of the developing CNS is expressed by unique neuronal and glial proteins, we proposed that radioimmunoassays of these proteins can be used to define normal and chemically- altered patterns of CNS development. We are testing this hypothesis by administering prototype neurotoxicants to the developing rat and then assessing the effects of these agents on previously characterized neuronal and glial proteins. Using this approach, we have characterized several features associated with perinatal chemical exposure: (1) region-dependent patterns of altered brain development are revealed by changes in the amounts of specific neuronal and glial proteins; (2) chemical-induced changes in neuronal and glial proteins depend on the time of exposure and nature of the insult; and (3) significant changes in neuron- and glial-localized proteins can be observed in the absence of cytopathology or decreases in brain weight. Data obtained from studies of toxicant-induced injury of the CNS will be presented as models for the use of neuron- and glial-localized proteins as biochemical indicators of altered brain development.

Animals↗

PubMed2004

Development of PCR assay based on ITS2 rDNA polymorphism for the detection and differentiation of Fusarium sporotrichioides.

A polymerase chain reaction assay was developed for detection of Fusarium sporotrichioides, a plant pathogen in many parts of the world. Based on small nucleotide differences in ITS2 (Internal Transcribed Spacer) rDNA of our local isolate of F. sporotrichioides (Accession No. AY510069) and other isolates found in NCBI/GeneBank database, species specific primer FspITS2K was selected. Primer pair FspITS2K and P28SL amplified a fragment of 288 bp containing a portion of ITS2 and 28S rDNA of all the F. sporotrichioides isolates tested, originated from different hosts and regions of the world but did not amplify any other species of Fusarium and plant's DNA. To use the PCR assay in seed health testing, a protocol was setup for the rapid and effective preparations of fungal DNA from wheat seeds. The method developed may be useful for the rapid detection and identification of F. sporotrichioides both from culture and from plant tissue.

Base Sequence↗

PubMed2001

Seroepidemiological study of hepatitis E virus infection in Japan using a newly developed antibody assay.

PURPOSE: A seroepidemiological study of hepatitis E virus (HEV) infection was conducted in Japan, where HEV infection is not considered endemic. METHODS: IgG and IgM class antibodies to HEV were measured with a newly developed enzyme-linked immunosorbent assay in which recombinant virus-like particles were used as an antigen. A total of 1253 individuals (401 males and 852 females; age range, 6-89 years) were enrolled from two different areas: area 1 (n = 478), in which hepatitis C was endemic; and area 2 (n = 775), in which it was not endemic. RESULTS: The HEV antibody (IgG class) positive rate was 6.7% in area 1 and 4.6% in area 2. Similarly, the HAV antibody (IgG class) positive rates were 65.3% and 72.3%. The age- and sex-specific prevalence of both HAV and HEV antibodies was quite similar in the two areas, and the HAV antibody positive rate clearly increased with age in both males and females. On the other hand, the HEV antibody positive rate showed a slight tendency to increase with age in males, but not in females. None of the 32 individuals with the HEV antibody who were interviewed had a history of visiting countries in which hepatitis E was endemic. In both areas, the mean age, percentage of males, and HAV antibody positive rate were significantly higher in the group of individuals with the HEV antibody than in the group of those without it, according to conventional statistical analyses. Of the three factors age, male sex, presence of HAV antibody, and the area factor, only male sex was statistically significant (P < 0.001) on multivariate logistic regression analysis. Two (0.2%) of the total of 1253 individuals were positive for the IgM class antibody to HEV. CONCLUSIONS: Our results suggest the possibility that HEV infection is circulating in Japan at a low level. HEV infection was associated with male sex, but not with HAV infection.

Adolescent↗

PubMed1991

Preparation and characterization of labelled interferon-gamma and the development of radioreceptor assay for interferon-gamma.

A 125I-labelled recombinant interferon-gamma (IFN-gamma) was prepared by the lactoperoxidase-glucose oxidase method. The specific activity of the labelled IFN-gamma was 31 Bq U-1 and its molecular weight, immunoreactivity and receptor binding ability remained the same after the labelling. Using the labelled IFN-gamma and FL5(-1) cells from human amniotic membrane, a radioreceptor assay was developed. Natural IFN-gamma, recombinant IFN-gamma and the labelled IFN-gamma were observed to bind to the same binding sites on the cells with similar affinity (Kd = 1.3-2.2 x 10(-10) M). The radioreceptor assay was more specific than a bioassay because the labelled IFN-gamma did not compete with IFN-alpha or IFN-beta. It was much more sensitive (90 pM) than conventional competitive radioimmunoassay (300 pM) using the same labelled IFN-gamma, and as sensitive as immunoenzymometric assay (60 pM). The radioreceptor assay should be useful not only for research on IFN-gamma but also for the determination of biological activity in process control and/or quality control of IFN-gamma manufacturing.

Binding, Competitive↗

PubMed2003

Comparative genomics tools applied to bioterrorism defence.

Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens that could be used as weapons of mass destruction or disruption. This sequence information must be exploited to provide rapid and accurate diagnostics to identify pathogens and distinguish them from harmless near-neighbours and hoaxes. The Chem-Bio Non-Proliferation (CBNP) programme of the US Department of Energy (DOE) began a large-scale effort of pathogen detection in early 2000 when it was announced that the DOE would be providing bio-security at the 2002 Winter Olympic Games in Salt Lake City, Utah. Our team at the Lawrence Livermore National Lab (LLNL) was given the task of developing reliable and validated assays for a number of the most likely bioterrorist agents. The short timeline led us to devise a novel system that utilised whole-genome comparison methods to rapidly focus on parts of the pathogen genomes that had a high probability of being unique. Assays developed with this approach have been validated by the Centers for Disease Control (CDC). They were used at the 2002 Winter Olympics, have entered the public health system, and have been in continual use for non-publicised aspects of homeland defence since autumn 2001. Assays have been developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. Collaborations with comparative genomics algorithm developers have enabled our LLNL team to make major advances in pathogen detection, since many of the existing tools simply did not scale well enough to be of practical use for this application. It is hoped that a discussion of a real-life practical application of comparative genomics algorithms may help spur algorithm developers to tackle some of the many remaining problems that need to be addressed. Solutions to these problems will advance a wide range of biological disciplines, only one of which is pathogen detection. For example, exploration in evolution and phylogenetics, annotating gene coding regions, predicting and understanding gene function and regulation, and untangling gene networks all rely on tools for aligning multiple sequences, detecting gene rearrangements and duplications, and visualising genomic data. Two key problems currently needing improved solutions are: (1) aligning incomplete, fragmentary sequence (eg draft genome contigs or arbitrary genome regions) with both complete genomes and other fragmentary sequences; and (2) ordering, aligning and visualising non-colinear gene rearrangements and inversions in addition to the colinear alignments handled by current tools.

Amino Acid Sequence↗

PubMed1991

Chromogenic peptide substrate assays and their clinical applications.

Chromogenic peptide substrates were first introduced into research laboratories in the early 1970s and were quickly utilised to develop assays for the determination of enzymes, proenzymes and inhibitors of the coagulation system. These assays were gradually introduced into coagulation and clinical chemistry laboratories as laboratory tools in the diagnosis and treatment of coagulation disorders. From the knowledge of the structures of the natural substrates attacked by enzymes other than those of the coagulation system or by synthesis and random screening, substrates for enzymes of the fibrinolytic, plasma and glandular kallikrein and complement systems were produced. These allowed various research groups to develop assays for components of these systems and subsequently led to the use of these assays in studies on various clinical conditions. Substrates for activated protein C ensured that assays for this enzyme and its inhibitors could be developed and introduced into the haematological routine. With the introduction of substrates for limulus lysate not only were assays for endotoxins in clinical samples produced but the control of all disposable products and injectables for endotoxin contamination can now be effected. Initially high costs and time-consuming manual assays were a hinderence to the general acceptance of the use of chromogenic peptide substrate assays and they were only used routinely in a few specialised laboratories. With the introduction of automated and microtitre plate methods however, these assays are are now available in most hospital laboratories. Since the first chromogenic peptide substrate was described thousands of articles have been published on the use of chromogenic substrate assays to measure proenzymes, enzyme activators, enzyme cofactors and inhibitors in blood and other body fluids in normal subjects and clinical material. We have endeavoured to cover as many of these as possible in this review.

Blood Chemical Analysis↗