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PubMedDate not supplied

alpha 1-antitrypsin deficiency detection by direct analysis of the mutation in the gene.

A deficiency in the plasma protease inhibitor alpha 1-antitrypsin can cause chronic obstructive emphysema or infantile liver cirrhosis. This deficiency results from a single amino acid substitution created by a G to A transition in the gene for alpha 1-antitrypsin. Chemically synthesized specific oligonucleotide probes (19-mer) have been used to develop a sensitive and direct test for the presence or absence of the mutant gene in any individual, which can be used for prenatal diagnosis of the deficiency syndrome.

Base Sequence↗
PubMed1989

The quantitative spectrum of inositol phosphate metabolites in avian erythrocytes, analysed by proton n.m.r. and h.p.l.c. with direct isomer detection.

The spectrum of inositol phosphate isomers present in avian erythrocytes was investigated in qualitative and quantitative terms. Inositol phosphates were isolated in micromolar quantities from turkey blood by anion-exchange chromatography on Q-Sepharose and subjected to proton n.m.r. and h.p.l.c. analysis. We employed a h.p.l.c. technique with a novel, recently described complexometric post-column detection system, called 'metal-dye detection' [Mayr (1988) Biochem. J. 254, 585-591], which enabled us to identify non-radioactively labelled inositol phosphate isomers and to determine their masses. The results indicate that avian erythrocytes contain the same inositol phosphate isomers as mammalian cells. Denoted by the 'lowest-locant rule' [NC-IUB Recommendations (1988) Biochem. J. 258, 1-2] irrespective of true enantiomerism, these are Ins(1,4)P2, Ins(1,6)P2, Ins(1,3,4)P3, Ins(1,4,5)P3, Ins(1,3,4,5)P4, Ins(1,3,4,6)P4, Ins(1,4,5,6)P4, Ins(1,3,4,5,6)P5, and InsP6. Furthermore, we identified two inositol trisphosphate isomers hitherto not described for mammalian cells, namely Ins(1,5,6)P3 and Ins(2,4,5)P3. The possible position of these two isomers in inositol phosphate metabolism and implications resulting from absolute abundances of inositol phosphates are discussed.

Animals↗
PubMed1995

Major changes in complex I activity in mitochondria from aged rats may not be detected by direct assay of NADH:coenzyme Q reductase.

We have investigated the respiratory activities and the concentrations of respiratory chain components of mitochondria isolated from the livers and hearts of two groups of rats aged 6 and 24 months respectively. In comparison with the adult controls (6 months), in aged rats there was a decline in total aerobic NADH oxidation in both tissues; only minor (non-significant) changes, however, were found in NADH:coenzyme Q reductase and cytochrome oxidase activities, and there was no change in ubiquinol-cytochrome c reductase activity. The coenzyme Q levels were slightly decreased in mitochondria from both organs of aged rats. The lowered NADH oxidase activity is not due to the slight decrease observed in the coenzyme Q levels, but is the result of decreased Complex I activity. Since the assay of NADH:coenzyme Q reductase requires quinone analogues, none of which can evoke its maximal turnover [Estornell, Fato, Pallotti and Lenaz (1993) FEBS Lett. 332, 127-131], its activity has been calculated indirectly by taking advantage of the relationship that exists between NADH oxidation and ubiquinol oxidation through the coenzyme Q pool. The results, expressed in this way, show a drastic loss of activity of Complex I in both the heart and the liver of aged animals in comparison with adult controls.

Aging↗
PubMed2006

Quantum-state resolved reaction dynamics at the gas-liquid interface: direct absorption detection of HF(v,J) product from F(2P)+squalane.

Exothermic reactive scattering of F atoms at the gas-liquid interface of a liquid hydrocarbon (squalane) surface has been studied under single collision conditions by shot noise limited high-resolution infrared absorption on the nascent HF(v,J) product. The nascent HF(v,J) vibrational distributions are inverted, indicating insufficient time for complete vibrational energy transfer into the surface liquid. The HF(v=2,J) rotational distributions are well fit with a two temperature Boltzmann analysis, with a near room temperature component (T(TD) approximately equal to 290 K) and a second much hotter scattering component (T(HDS) approximately equal to 1040 K). These data provide quantum state level support for microscopic branching in the atom abstraction dynamics corresponding to escape of nascent HF from the liquid surface on time scales both slow and fast with respect to rotational relaxation.

Journal Article↗
PubMed2006

Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase.

The Fe(II)- and alpha-ketoglutarate (alphaKG)-dependent dioxygenases use mononuclear nonheme iron centers to effect hydroxylation of their substrates and decarboxylation of their cosubstrate, alphaKG, to CO(2) and succinate. Our recent dissection of the mechanism of taurine:alphaKG dioxygenase (TauD), a member of this enzyme family, revealed that two transient complexes accumulate during catalysis in the presence of saturating substrates. The first complex contains the long-postulated C-H-cleaving Fe(IV)-oxo intermediate, J, and the second is an enzyme.product(s) complex. Here, we demonstrate the accumulation of two transient complexes in the reaction of a prolyl-4-hydroxylase (P4H), a functional homologue of human alphaKG-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing. The kinetic and spectroscopic properties of these two P4H complexes suggest that they are homologues of the TauD intermediates. Most notably, the first exhibits optical absorption and Mössbauer spectra similar to those of J and, like J, a large substrate deuterium kinetic isotope on its decay. The close correspondence of the accumulating states in the P4H and TauD reactions supports the hypothesis of a conserved mechanism for substrate hydroxylation by enzymes in this family.

Absorption↗
PubMed1979

IgM receptors on human lymphocytes: detection by direct binding.

Radioiodinated IgM isolated from a patient with Waldenström macroglobulinemia binds with high avidity (apparent Ka = 2.5 x 10(9) M-1) to freshly isolated human peripheral blood lymphocytes. Binding occurred through the Fc region of the molecule and involved a receptor specific for immunoglobulins of the IgM class. The avidity and specificity of this binding are consistent with a biologic role for IgM receptors on lymphocytes.

Antigen-Antibody Complex↗
PubMed2001

Detection and direct genomic sequencing of multiple rare unknown flanking DNA in highly complex samples.

By identifying the sequence of retro- and lentiviral integration sites in peripheral blood leukocytes, the clonal composition and fate of genetically modified hematopoietic progenitor and stem cells could be mapped in vitro and in vivo. Previously available methods have been limited to the analysis of mono- or oligoclonal integration sites present in high copy numbers. Here, we perform characterization of multiple rare retroviral and lentiviral integration sites in highly complex DNA samples. The reliability of this method results from nontarget DNA removal via magnetic extension primer tag selection (EPTS) preceding solid-phase ligation-mediated PCR. EPTS/LM-PCR allowed the simultaneous direct genomic sequencing of multiple proviral LTR-flanking sequences of retro- and lentiviral vectors even if only 1 per 100 to 1000 cells contained the provirus. A primer walking "around" the integration locus demonstrated the adaptability of EPTS/LM-PCR to study unknown flanking DNA regions unrelated to proviruses. The technique is fast, inexpensive, and sensitive in minimal samples. It enables studies of retro- and lentiviral integration, viral vector tracking in gene therapy, insertional mutagenesis, transgene integration, and direct genomic sequencing that until now have been difficult or impossible to perform.

Animals↗
PubMed1993

Direct enzymic detection of endogenous oxidative base damage in human lymphocyte DNA.

The endogenous production of oxidative damage in DNA by free radicals released as a by-product of respiration is a likely cause of mutations which, if they occur in appropriate genes, may lead to cancer. Using an endonuclease specific for oxidized pyrimidines, in conjunction with the highly sensitive method of single cell gel electrophoresis, we have detected significant oxidative damage in untreated, freshly isolated lymphocytes from normal, healthy individuals.

DNA Damage↗
PubMed1996

Direct genetic detection of Dobrava virus in Greek and Albanian patients with hemorrhagic fever with renal syndrome.

Blood samples were collected from an Albanian and a Greek patient with hemorrhagic fever with renal syndrome and tested by reverse transcriptase-polymerase chain reaction. The genetic detection assay amplified hantavirus-specific DNA fragments from RNA extracted from the blood of the patients; nucleotide sequence analysis revealed that the causative agent of the disease was Dobrava virus. These findings suggest that Dobrava virus (which was originally isolated from the lungs of an Apodenws flavicollis mouse in Slovenia) is endemic throughout the Balkan States and causes overt human disease.

Adult↗
PubMed1988

Conformational mutation in human mtDNA detected by direct sequencing of enzymatically amplified DNA.

Restriction enzyme analysis of 241 human mtDNAs revealed polymorphism in the electrophoretic mobility of a fragment corresponding to part of the ND4 gene. Enzymatic amplification and direct sequencing of this fragment demonstrates that a single T--C transition correlates with the faster mobility exhibited by the fragment in seven mtDNAs from Papua New Guinea. The enhanced mobility caused by this transition could result from disrupting an AT-rich region near the middle of the fragment that might make it curve. An analogous mutation at an adjacent position in a European mtDNA causes a similar but more pronounced alteration in mobility. The seven New Guineans with this substitution are all from the Eastern Highlands Province and constitute one clade in a genealogical tree based upon restriction analysis. The additional information provided by sequencing allows refinement of the genealogical tree but does not require modification of higher order branching structure.

Base Sequence↗
PubMed1995

Small bowel bacterial overgrowth in systemic sclerosis: detection using direct and indirect methods and treatment outcome.

Twenty-four patients with proven systemic sclerosis and with symptoms suggestive of malabsorption (i.e. chronic diarrhoea and weight loss) were investigated for small bowel bacterial overgrowth. Of the patients selected, six were suffering from the diffuse form of the disease. Jejunal aspiration was performed in all patients, and in nine normal volunteers. A specially designed double-lumen sterile catheter was used for this purpose and was introduced via a gastroscope. Twenty of these patients underwent a glucose hydrogen breath test. Eight patients (33%) had significant bacterial counts: > 10(5) colony forming units per ml (cfu/ml) of jejunal fluid. Less than 10(2) cfu/ml were found in the jejunal fluid from the nine control subjects. Glucose hydrogen breath testing was positive in seven patients, all of whom had significant jejunal bacterial growth. Diarrhoea rather than weight loss was shown to be the symptom which correlated best with the presence of bacterial overgrowth. Ciprofloxacin was used in six patients whose diarrhoeal symptoms ceased dramatically within 48 h of commencing the antibiotic. Trimethoprim produced a partial response despite bacterial sensitivity. A disadvantage of the hydrogen breath test is that subsequent antibacterial therapy cannot be specific, as bacterial species, antibiotic sensitivity and resistance are unknown. Systemic sclerosis involving the small intestine in the past has been said to more prevalent in patients with diffuse disease, whereas this study showed a preponderance of patients with long-standing limited cutaneous systemic sclerosis and small bowel involvement.

Adult↗
PubMed2003

Direct WIMP detection with cryogenic detectors.

Cryogenic detectors have been developed since the mid 1980s and have been applied successfully to dark-matter searches since the mid 1990s. Among the advantages of cryogenic detectors are their high sensitivity to nuclear recoil, their low detection thresholds, the wide choice of target materials and the possibility of implementing event type recognition on an event-by-event basis. I explain the basics of cryogenic detectors, review various implementations, discuss advantages and drawbacks and give an overview of current dark-matter-search experiments based upon cryogenic detectors.

Journal Article↗
PubMed1991

Two-dimensional 1H, 15N-NMR investigation of uniformly 15N-labeled ribonuclease T1. Complete assignment of 15N resonances.

Uniformly 15N-enriched ribonuclease T1 (RNase T1) was obtained from Escherichia coli by recombinant techniques. Heteronuclear 1H, 15N-shift correlation spectra were recorded utilizing proton detection. Direct 1H, 15N connectivities were established applying the heteronuclear multiple-quantum coherence technique. Additional 1H, 1H-TOCSY or 1H, 1H-NOESY transfer steps allowed for sequential assignments. Nitrogen atoms without directly bonded protons were detected by means of the heteronuclear multiple-bond correlation experiment. Signals emerging from 15NH and 15NH2 groups were distinguished by heteronuclear triple-quantum filtering methods. 119 nitrogen resonances out of the expected 127 were assigned unambiguously; in addition, previously obtained proton assignments were extended. Preliminary 1H, 15N NMR investigation were performed on the RNase-T1-3'GMP inhibitor complex. Results were interpreted with respect to nucleotide binding.

Magnetic Resonance Spectroscopy↗
PubMed2002

Homonucleotide stretches in chromosomal DNA of Campylobacter jejuni display high frequency polymorphism as detected by direct PCR analysis.

Homopolymeric nucleotide tracts have been previously identified in the genome sequence of Campylobacter jejuni 11168 [Parkhill et al., Nature 403 (2000) 665-668]. These tracts are believed to regulate contingency genes but as yet no phenotypic variation has been identified associated with many of these genes. To investigate homopolymeric tracts for genes for which there is no observable phenotype, a method was designed to visualise profiles of the various tract lengths directly at the genomic level by means of PCR and denatured polyacrylamide gel electrophoresis. Six of the seven contingency genes investigated displayed variation in the length of the respective homonucleotide tracts. Surprisingly, each contingency gene gave a typical peak profile that represented a conserved size distribution of polymorphic forms. For each gene studied, peak profiles were conserved between strains of C. jejuni. Duplicated genes, containing homonucleotide stretches, displayed locus-specific peak distributions for each gene copy. Contingency genes were polymorphic within single colonies, and the observed complex peak profiles suggested a frequency of slippage several orders of magnitude higher than reported for other organisms. No G7 (or C7) stretch was ever observed, and their absence from the complete genome suggests strong selection against their presence. In view of the predictable outcome of the process leading to these polymorphisms, it is hypothesised that the formation and/or selection of these tracts is not a random process, but is driven by as yet unknown mechanism(s). High-frequency polymorphism of these genes may be a mechanism by which C. jejuni survives selection bottlenecks between opportunities for growth within a host.

Animals↗
PubMed1985

Mechanically isolated hepatocytes are unsuitable to detect antibodies directed against plasma membrane determinants.

The ultrastructural morphology of mechanically and enzymatically isolated hepatocytes was compared. Plasma membrane integrity was evaluated by electron microscopy, both in the absence and in the presence of ruthenium red, which stains cell coat glycoproteins and makes it possible to identify even partially permeable cells, and by indirect immunofluorescence using experimental antibodies directed against epithelial submembranous components (prekeratin, actin). In order to evaluate the antigenic integrity of the hepatocellular plasma membrane after the isolation procedures, an immuno-electronmicroscopical technique (Staph. pA-colloidal gold) was applied using the IgG fraction from two liver-kidney microsomal antibody (LKM) positive sera, known to react with both plasma membranes and smooth endoplasmic reticulum (SER). Enzymatic procedure made it possible to isolate hepatocytes with a good preservation of both plasma membranes and subcellular organelles. Ruthenium red staining was confined to plasma membranes, thus indicating the preservation of both cell-coat glycoproteins and plasma membrane. Most cells were negative after exposure to experimental antibodies. After exposure to LKM positive sera colloidal gold was strictly confined to the plasma membrane. On the other hand, mechanically isolated hepatocytes showed wide interruptions of the plasma membrane and gross alterations of subcellular organelles. Most cells were stained by ruthenium red, thus confirming the plasma membrane permeability. In addition, a linear peripheral positivity was found in the vast majority of the cells tested with anti-prekeratin and anti-actin antibodies. LKM-colloidal gold complexes were found at the level of both residual plasma membrane and SER.(ABSTRACT TRUNCATED AT 250 WORDS)

Actins↗
PubMed1998

Direct spectroscopic detection of molecular dynamics and interactions of the calcium pump and phospholamban.

In order to test molecular models of cardiac calcium transport regulation, we have used spectroscopy to probe the structures, dynamics, and interactions of the Ca pump (Ca-ATPase) and phospholamban (PLB) in cardiac sarcoplasmic reticulum (SR) and in reconstituted membranes. Electron paramagnetic resonance (EPR) and phosphorescence of probes bound to the Ca pump show that the activity of the pump is quite sensitive to its oligomeric interactions. In cardiac SR, PLB aggregates and inhibits the pump, and both effects are reversed by PLB phosphorylation. Previous analyses of PLB's oligomeric state were only in detergent solutions, so we used EPR and fluorescence to determine the oligomeric structure of PLB in its native state in lipid bilayers. Wild-type PLB is primarily oligomeric in the membrane, while the mutant L37A-PLB is monomeric. For both proteins, phosphorylation shifts the dynamic monomer-oligomer equilibrium toward oligomers, and induces a similar structural change, as indicated by tyrosine fluorescence; yet L37A-PLB is more effective than wild-type PLB in inhibiting and aggregating the pump. Fluorescence energy transfer shows that the Ca pump increases the fraction of monomeric PLB, indicating that the pump preferentially binds monomeric PLB. These results support a reciprocal aggregation model for Ca pump regulation, in which the Ca pump is aggregated and inhibited by association with PLB monomers, and phosphorylation of PLB reverses these effects while decreasing the concentration of PLB monomers. To investigate the structure of the PLB pentamer in more detail, we measured the reactivities of cysteine residues in the transmembrane domain of PLB, and recorded EPR spectra of spin labels attached to these sites. These results support an atomic structural model, based on molecular dynamics simulations and mutagenesis studies, in which the PLB pentamer is stabilized by a leucine-isoleucine zipper within the transmembrane domain.

Animals↗
PubMed2000

Strategies to improve the signal and noise performance of active matrix, flat-panel imagers for diagnostic x-ray applications.

A theoretical investigation of factors limiting the detective quantum efficiency (DQE) of active matrix flat-panel imagers (AMFPIs), and of methods to overcome these limitations, is reported. At the higher exposure levels associated with radiography, the present generation of AMFPIs is capable of exhibiting DQE performance equivalent, or superior, to that of existing film-screen and computed radiography systems. However, at exposure levels commonly encountered in fluoroscopy, AMFPIs exhibit significantly reduced DQE and this problem is accentuated at higher spatial frequencies. The problem applies both to AMFPIs that rely on indirect detection as well as direct detection of the incident radiation. This reduced performance derives from the relatively large magnitude of the square of the total additive noise compared to the system gain for existing AMFPIs. In order to circumvent these restrictions, a variety of strategies to decrease additive noise and enhance system gain are proposed. Additive noise could be reduced through improved preamplifier, pixel and array design, including the incorporation of compensation lines to sample external line noise. System gain could be enhanced through the use of continuous photodiodes, pixel amplifiers, or higher gain x-ray converters such as lead iodide. The feasibility of these and other strategies is discussed and potential improvements to DQE performance are quantified through a theoretical investigation of a variety of hypothetical 200 microm pitch designs. At low exposures, such improvements could greatly increase the magnitude of the low spatial frequency component of the DQE, rendering it practically independent of exposure while simultaneously reducing the falloff in DQE at higher spatial frequencies. Furthermore, such noise reduction and gain enhancement could lead to the development of AMFPIs with high DQE performance which are capable of providing both high resolution radiographic images, at approximately 100 microm pixel resolution, as well as variable resolution fluoroscopic images at 30 fps.

Feasibility Studies↗