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Direct detection of the common Mediterranean beta-thalassemia gene with synthetic DNA probes. An alternative approach for prenatal diagnosis.

The most common form of beta-thalassemia among Mediterraneans results from a single nucleotide substitution within the first intervening sequence (IVS-1) of the beta-globin gene. This particular mutation is not detectable in uncloned DNA by restriction enzyme analysis. Using synthetic DNA of 19-nucleotides in length corresponding to the normal and mutant IVS-1 sequences as probes, we have developed a direct assay for this gene defect. Under carefully controlled experimental conditions these synthetic probes detect only their homologous sequences in restriction digests of both cloned and uncloned DNA samples. The method is sufficiently sensitive to establish the genotype of individuals with respect to this defect using approximately 20 micrograms total DNA. This assay provides an alternative to fetal blood and DNA linkage analysis for the prenatal diagnosis of this variety of beta-thalassemia, particularly among Greek families where it is especially common.

Cloning, Molecular↗

Evaluation of a polymerase chain reaction-based universal heteroduplex generator assay for direct detection of rifampin susceptibility of Mycobacterium tuberculosis from sputum specimens.

In a double-blind study, 655 sputum specimens were obtained from individuals suspected of having tuberculosis and were analyzed for the presence of Mycobacterium tuberculosis and rifampin susceptibility with use of a polymerase chain reaction (PCR)-based universal heteroduplex generator assay (PCR/UHG-Rif). Of the specimens containing viable M. tuberculosis, 100% of the smear-positive (n = 41) and 50% of the smear-negative (n = 6) specimens tested positive for the organism by PCR/UHG-Rif. Nineteen of 537 culture-negative specimens tested positive for M. tuberculosis by PCR/UHG-Rif and were from patients with confirmed tuberculosis who were receiving antituberculosis therapy at the time of specimen collection. Thirty-five specimens contained nontuberculous mycobacteria and were negative by PCR/UHG-Rif. Genotypic evidence of rifampin resistance in five of six culture-confirmed, rifampin-resistant isolates was obtained by PCR/UHG-Rif, yielding a sensitivity and specificity for the assay of 83% and 98.2%, respectively. These results demonstrate the feasibility of using a PCR-based assay directly on sputum specimens for simultaneous detection of M. tuberculosis and rifampin susceptibility, and they suggest that patients with smear-positive, untreated tuberculosis and those presenting with suspected drug-resistant tuberculosis are the most appropriate groups for testing by PCR/UHG-Rif.

Antibiotics, Antitubercular↗

DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells.

By means of a selective DNA amplification technique called polymerase chain reaction, proviral sequences of the human immunodeficiency virus (HIV-1) were identified directly in DNA isolated from peripheral blood mononuclear cells (PBMCs) of persons seropositive but not in DNA isolated from PBMCs of persons seronegative for the virus. Primer pairs from multiple regions of the HIV-1 genome were used to achieve maximum sensitivity of provirus detection. HIV-1 sequences were detected in 100% of DNA specimens from seropositive, homosexual men from whom the virus was isolated by coculture, but in none of the DNA specimens from a control group of seronegative, virus culture-negative persons. However, HIV-1 sequences were detected in 64% of DNA specimens from seropositive, virus culture-negative homosexual men. This method of DNA amplification made it possible to obtain results within 3 days, whereas virus isolation takes up to 3 to 4 weeks. The method may therefore be used to complement or replace virus isolation as a routine means of determining HIV-1 infection.

Acquired Immunodeficiency Syndrome↗

Development and application of a novel screening PCR assay for direct detection of 'Helicobacter heilmannii'-like organisms in human gastric biopsies in Southeast England.

A novel PCR assay (HHLO-16) to screen for presence of 'Helicobacter heilmannii'-like organisms (HHLO) direct from gastric biopsies is described. As 'H. heilmannii' is generally uncultivable, diagnosis of infection is reliant on histology; thus prevalence may be underestimated. Analysis of an HHLO histology-positive human gastric biopsy and 15 gastric biopsies from domestic cats demonstrated that the HHLO-16 assay was more sensitive than an alternative available species-specific PCR assay. Further testing of 131 gastric biopsies from dyspeptic patients demonstrated an HHLO prevalence rate of 2.3% in Southeast England. Subsequent combination of the HHLO-16 assay with a H. pylori-specific PCR assay in a multiplex format (HpHh assay), and repeat analysis of the 131 biopsies showed the HpHh assay was as sensitive as each individual test. This novel PCR assay provides simple concomitant testing of dyspeptic patients for both HHLOs and H. pylori, thereby rapidly identifying individuals requiring eradication therapy.

Base Sequence↗

Evaluation of DNA-DNA hybridization for the direct detection of enterotoxigenic Escherichia coli in stool blots.

The simplicity of enterotoxigenic Escherichia coli (ETEC) stool blot hybridization, where the total bacterial growth of a fecal inoculum is examined directly for the presence of enterotoxin genes, has been marred by reports of unsatisfactory sensitivity and/or specificity. To assess the accuracy of stool blot hybridization and to study the effect of varying proportions of ETEC among fecal E. coli (ETEC/E. coli) on test performance, a detailed 'blind' study of 166 stool specimens from children with diarrhea was performed. Oligonucleotide probes were found to be superior to polynucleotide probes, having a sensitivity of 80%, a specificity of 99%, a positive predictive value of 89% and a negative predictive value of 97%. The sensitivity was found to be 100% when ETEC/E. coli > 2/12, as compared with 20% when ETEC/E. coli < or = 2/12 (p = 0.001), showing that the proportion of ETEC among fecal E. coli is of paramount importance for test sensitivity.

Bacteriological Techniques↗

A prozone phenomenon interferes in islet cell antibody detection: direct comparison of two methods in subjects at risk of diabetes and in insulin dependent diabetics at onset.

A recent international workshop documented marked interlaboratory variation in end point titers of standard islet cell antibody (ICA) positive sera. End titers were lower using a modified assay which utilizes fluorescein labeled protein A (ICA-pA) rather than fluoresceinated anti-IgG (ICA-IgG) to detect antibody binding to islets. In this study we sought to compare directly two ICA assays with respect to future development of IDDM. Sera were obtained from 26 prospectively evaluated high risk subjects identified by family screening or history of transient hyperglycemia and 12 normal controls. As expected, end point titers for ICA positive sera were 10 times greater using the ICA-IgG assay than with the ICA-pA assay. However, despite higher end point titers, the ICA-IgG assay failed to detect more 'prediabetics' and showed a prozone effect. Fourteen subjects were positive at a 1:2 dilution using the ICA-pA assay. Only 10 of these 14 were positive at a 1:2 dilution using the ICA-IgG assay but all became positive at greater sera dilutions. No normal controls were positive using either assay. A similar prozone was observed with anti-islet monoclonal antibodies A2B5 and 4F2. Sera from 14 long-standing IDDM patients (where titers of ICA may have decreased relative to time of onset of diabetes) which were negative using ICA-pA were also assayed using ICA-IgG. Five sera positive for ICA-IgG but negative for ICA-pA were identified. In addition two sera in which a prozone effect was seen with ICA-pA were identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Agglutination Tests↗

Direct detection constraints on superheavy dark matter.

The dark matter in the Universe might be composed of superheavy particles (mass greater, similar 10(10) GeV). These particles can be detected via nuclear recoils produced in elastic scatterings from nuclei. We estimate the observable rate of strongly interacting supermassive particles (simpzillas) in direct dark matter search experiments. The simpzilla energy loss in Earth and in the experimental shields is taken into account. The most natural scenarios for simpzillas are ruled out based on recent EDELWEISS and CDMS results. The dark matter can be composed of superheavy particles only if these interact weakly with normal matter or if their mass is above 10(15) GeV.

Journal Article↗

Direct detection of methylation in genomic DNA.

The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote.

5-Methylcytosine↗

Direct detection and identification of radicals generated during the hydroxyl radical-induced degradation of hyaluronic acid and related materials.

HO. attack on hyaluronic acid, related polymers and monomers has been studied by both direct, rapid-flow, EPR (ESR) and EPR spin trapping using a variety of traps. Evidence has been obtained, with the monomers, for essentially random hydrogen-atom abstraction at all the ring C -- H bonds with glucuronic acid, and at all sites except the N-acetyl side chain and C(2) with N-acetylglucosamine. The initial radicals do not undergo rapid rearrangement reactions at pH 4; however at both lower and higher pH values, acid- and base-catalysed rearrangement process, respectively, result in the loss of these species. The rate of loss of these species is dependent on the substrate, with those derived from N-acetylglucosamine undergoing slowed acid-catalysed rearrangement than the glucuronic acid-derived species. This is rationalised in terms of a rearrangement reaction of 1.2-dihydroxyalkyl(1.2-dio) radicals involving an electron-deficient radical-cation intermediate; the formation of this species would be disfavoured by the electron-withdrawing N-acetyl substituent. The base-catalysed process, which is believed to involve a radical-anion intermediate, occurs rapidly at pH 7.4, and appears to be less substrate dependent. In the case of glucuronic acid- (but not N-acetylglucosamine-) derived species this latter process results in the detection of ring-opened semidione species. With equimolar mixtures of the two monomers essentially random attack occurs on the two rings. However with chondroitin sulphate A, attack appears to be much more selective, with a radical generated at C(5) on the glucuronic acid ring present at highest concentration. The initial radicals obtained with this polysaccharide also undergo base- and acid-catalysed rearrangements; this leads to strand-breakage and the formation of low-molecular-weight material. Spin-trapping experiments carried out with hyaluronic acid, and a number of other polysaccharides, resulted in the detection of a number of novel spin adducts, the formation of which are consistent with attack on both the sugar rings in the polymer. The pH dependence of the observed spectra, and the detection of additional species at some pH values, suggest that at least some of the initial radicals undergo base-catalysed rearrangement reactions which result in strand-breakage and the formation of low-molecular-weight fragments. The extent of fragmentation at a particular pH, is also affected by the radical flux, with high radical yields giving more low-molecular-weight material. These observations suggest that pH-independent processes also contribute to strand-cleavage; this may be due to beta-cleavage of the radicals formed at C(1) on either ring, C(3) on N-acetylglucosamine or C(4) on the glucuronic acid ring.

Acetylglucosamine↗

UV-vis spectroscopic study directly detecting inorganic phosphorus in urine and our reagent kit.

The determination of inorganic phosphorus in human urine is very important, since it has diagnostic value in some clinical cases. Here we apply a simple, sensitive and direct method to determine inorganic phosphorus in urine. This new ensemble is prepared by adding ytterbium chloride and pyrocatechol violet in a 2:1 molar ratio in an aqueous solution of 10 mM 2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acid buffer at pH 7.0. The addition of the urine sample turned the blue ensemble yellow and altered the UV-vis absorption spectra. The ensemble exhibits excellent selectivity for inorganic phosphorus over other constituents of urine. We validate the accuracy of our method by the standard procedure (molybdenum blue assay for phosphate). The detection results are basically consistent with normal excretion of phosphate. Furthermore, we fabricated a new kind of inorganic phosphorus reagent kit, which enables us to inspect phosphate concentrations of urine with the naked eye. Fit for all kinds of various clinic uses, our reagent kit is a hopeful substitute for the molybdenum reagent kit.

Benzenesulfonates↗

In vitro selection of DNA aptamer against abrin toxin and aptamer-based abrin direct detection.

Abrin toxin as the target protein, belongs to class II ribosome-inactivating proteins family, has high toxicity to eukaryotic cells. Here, we firstly report the DNA aptamers, isolated by in vitro selection, recognize abrin toxin with high affinity and specificity, and have the advantage of no cross-reaction with structure-similar protein ricin toxin over antibodies. Then, a highly selective and sensitive aptamer-based abrin assay was established using a molecular light switching reagent [Ru(phen)(2)(dppz)](2+) with a limit of detection of 1 nM and a wide linear range from 1 to 400 nM with the correlation coefficient of 0.993. This assay can be successfully directly performed not only in physiological buffer but also in more complicated biological matrix, such as diluted serum.

Abrin↗

Direct detection and identification of Mycobacterium ulcerans in clinical specimens by PCR and oligonucleotide-specific capture plate hybridization.

We compared various diagnostic tests for their abilities to detect Mycobacterium ulcerans infection in specimens from patients with clinically active disease. Specimens from 10 patients from the area of Zangnanado (Department of Zou, Benin) with advanced, ulcerated active M. ulcerans infections were studied by direct smear, histopathology, culture, PCR, and oligonucleotide-specific capture plate hybridization (OSCPH). A total of 27 specimens, including 12 swabs of exudate collected before debridement and 15 fragments of tissue obtained during debridement, were submitted to bacteriologic and histopathologic analysis. The histopathologic evaluation of tissues from all six patients so tested revealed changes typical of those caused by M. ulcerans infection. Five specimens were contaminated, and M. ulcerans was cultivated on Löwenstein-Jensen medium from 12 of the remaining 22 (54.5%) specimens. Detection of mycobacteria was performed by PCR, and M. ulcerans was detected by OSCPH with a new probe (5'-CACGGGATTCATGTCCTGT-3') reacting with M. ulcerans and Mycobacterium marinum. In 10 of 22 (45.5%) specimens, M. ulcerans was identified by PCR-OSCPH. There was no statistically significant difference between the detection of M. ulcerans by culture and by PCR-OSCPH (P > 0.05). This is the first demonstration of an amplification system (PCR-OSCPH) with a sensitivity similar to that of culture for the direct and rapid recognition of M. ulcerans in clinical specimens. This system is capable of identifying M. ulcerans, even in paucibacillary lesions. Our findings suggest that PCR-OSCPH should be used in the quest for the elusive environmental reservoir(s) of M. ulcerans.

Humans↗

Direct detection of domains in phospholipid bilayers by grazing incidence diffraction of neutrons and atomic force microscopy.

The geometry of domains in phospholipid bilayers of binary (1:1) mixtures of synthetic lecithins with a difference in chain length of four methylene groups has been studied by two independent, direct and complementary methods. Grazing incidence diffraction of neutrons provided gel domain sizes of less than 10 nm in both the gel and the coexistence phase of the mixture, while no domains were detected for the fluid phase. For the coexistence region, the neutron data suggest that domains grow in number rather than in size with decreasing temperature. Atomic force microscopy was used to study gel phase size and shape of the domains. The domains imaged by atomic force microscopy exhibit a rather irregular shape with an average size of 10 nm, thus confirming the neutron results for this phase. The good agreement between atomic force microscopy and neutron results, despite the completely different nature of their observables, has potential for the future development of refined models for the interpretation of neutron data from heterogeneous membranes in terms of regularly spaced and spatially extended scatterers.

Calorimetry, Differential Scanning↗

Direct detection of Shiga toxigenic Escherichia coli strains belonging to serogroups O111, O157, and O113 by multiplex PCR.

Shiga toxigenic Escherichia coli (STEC) strains are a diverse group of organisms associated with severe gastrointestinal and systemic diseases in humans. Within the STEC family, eae-positive STEC strains, particularly those belonging to serogroups O157 and O111, appear to have greater virulence for humans. However, in spite of being eae negative, STEC strains belonging to serogroup O113 have frequently been associated with cases of severe STEC disease, including hemolytic-uremic syndrome (HUS). We have developed a modified multiplex PCR assay for detection of STEC strains belonging to these three serogroups in cultures of feces by using primers specific for portions of the genetic loci (rfb) encoding biosynthesis of the respective O antigen. These primers direct amplification of PCR products of 259, 406, and 593 bp for serogroups O157, O111, and O113, respectively. The assay was validated by testing 40 previously characterized STEC strains, with 100% agreement. It also detected STEC strains of the appropriate genotype in primary fecal cultures from 13 patients with HUS or bloody diarrhea. Thirty other primary fecal cultures from patients without evidence of STEC infection were negative.

Bacterial Toxins↗

Direct detection of the Philadelphia chromosome in CD20-positive lymphocytes in chronic myeloid leukemia by tri-color immunophenotyping/FISH.

Six patients with previously diagnosed chronic myelogenous leukemia (CML) were studied by a tri-color immunophenotyping/FISH method for direct determination of the Philadelphia (Ph) chromosome in B and T lymphocytes. Two patients had involvement of CD20-positive lymphocytes. CD3-positive lymphocytes in all patients were negative for the Ph chromosome.

Antigens, CD↗

Development and implementation of a direct detection, quantitation and validation system for class I MHC self-peptide epitopes.

Gene and protein expression studies demonstrate that viral-infected and malignant cells undergo a complex series of transcriptional and translational changes. As class I MHC molecules reflect the proteome (and changes therein) by presenting intracellular peptide epitopes, the development of a direct discovery and validation technology for the identification of these epitopes is needed. We developed our technology using HIV-1-infected cells as a model. A combination of hollow fiber class I HLA protein production and mass spectrometric epitope analysis indicated a 3-fold increase in the host-peptide VLMTEDIKL(720-728), [eIF4G((720))] presented by the HLA-A*0201 of HIV-1-infected cells. This peptide is derived from the host-protein translation of eukaryotic initiation factor 4-gamma (eIF4G) that plays a pivotal role in cellular protein synthesis. Direct confirmation of expression of this self-encoded antigen was performed through development of a T cell receptor mimic (TCRm) monoclonal antibody (mAb). The resulting 4F7 TCRm demonstrated specific recognition of the eIF4G((720))-A*0201 complex. Staining of normal PBMCs with 4F7 showed only low levels of endogenous eIF4G((720)) presentation by HLA-A*0201, while 4F7 staining of HIV-1-infected PBMCs revealed an approximately 3-fold increase in eIF4G((720))-A*0201. The MHC-peptide complex was initially detectable by 4F7 at 3 days post-infection, with a steady increase through day 8. We therefore demonstrate the successful development and implementation of an integrated discovery and validation technology system for direct identification and confirmation of class I MHC-peptide epitopes on cells.

Antibodies, Monoclonal↗

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells.

Base editors create precise nucleotide changes in DNA, but their off-target activity remains challenging to quantify. Here, we develop and deploy a direct, in cellulo sequencing assay that simultaneously measures both Cas9-mediated unwinding and deaminase editing of genomic DNA (beCasKAS). Our strategy nominates >460-fold more potential off-target sites than other methods by enriching for Cas9-dependent R-loops immediately preceding editing. Using beCasKAS in primary human T-cells, we observe that mRNA-encoded ABE8e and PAMless ABE8e-SpRY base editors have distinct off-target profiles that can be mitigated by optimizing mRNA dose. Finally, we combine beCasKAS with base-resolution deep learning models to risk-stratify off-target edits by their likelihood of epigenetic dysregulation. Collectively, beCasKAS offers a sensitive and facile tool to optimize the balance between base editor on- and off-target activity.

Journal Article↗

Direct detection of oxygen free radicals produced in the viscera of burned rats using electron paramagnetic resonance spectroscopy.

OBJECTIVE: To detect superoxide anion (O(-)(2)) signals in the heart, liver, lung and kidney tissues after burns. METHODS: Twenty-four male rats were randomized into 4 groups. The rats of experimental groups were immersed in 100 degrees C water for 15 seconds and 25% third-degree burn was created. Thoracotomy or laparotomy was performed at 5, 10, 15, 20 and 30 minutes after burn, and specimens of the heart, lung, liver kidney were obtained for burned rats. The specimens were then preserved in liquid nitrogen for cryo-preservation and detected immediately using EPR. RESULTS: The signals of superoxide O radical appeared in the heart, lung, 1iver and kidney specimens 10-15 minutes after burn. CONCLUSIONS: There is a direct evidence of oxygen free radicals (OFRs) injury to viscera of burned rats between 10-15 minutes after burn.

Animals↗