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Biomedical subjects

A Berry

Publications and source records attributed to A Berry.

At least 37 records · Page 2Linked to original sources
PubMed2003

[Diagnosis of imported malaria with multiplex PCR on LighCycler apparatus].

For the diagnosis of imported malaria, a competitive multiplex PCR using LightCycler was developed and compared for 3 months with a traditional PCR method. Hundred eighty three patients were tested by these 2 techniques of molecular diagnosis: 60 were positive for P. falciparum, 9 were positive for other Plasmodium species and 114 were negative. The LightCycler method was found in total agreement with the traditional PCR.

Animals↗
PubMed2002

A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli.

Class II fructose 1,6-bisphosphate aldolases (FBP-aldolases) catalyse the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP). Analysis of the structure of the enzyme from Escherichia coli in complex with a transition state analogue (phosphoglycolohydroxamate, PGH) suggested that substrate binding caused a conformational change in the beta5-alpha7 loop of the enzyme and that this caused the relocation of two glutamate residues (Glu181 and Glu182) into the proximity of the active site. Site-directed mutagenesis of these two glutamate residues (E181A and E182A) along with another active site glutamate (Glu174) was carried out and the mutant enzymes characterised using steady-state kinetics. Mutation of Glu174 (E174A) resulted in an enzyme which was severely crippled in catalysis, in agreement with its position as a zinc ligand in the enzyme's structure. The E181A mutant showed the same properties as the wild-type enzyme indicating that the residue played no major role in substrate binding or enzyme catalysis. In contrast, mutation of Glu182 (E182A) demonstrated that Glu182 is important in the catalytic cycle of the enzyme. Furthermore, the measurement of deuterium kinetic isotope effects using [1(S)-(2)H]DHAP showed that, for the wild-type enzyme, proton abstraction was not the rate determining step, whereas in the case of the E182A mutant this step had become rate limiting, providing evidence for the role of Glu182 in abstraction of the C1 proton from DHAP in the condensation direction of the reaction. Glu182 lies in a loop of polypeptide which contains four glycine residues (Gly176, Gly179, Gly180 and Gly184) and a quadruple mutant (where each glycine was converted to alanine) showed that flexibility of this loop was important for the correct functioning of the enzyme, probably to change the microenvironment of Glu182 in order to perturb its pK(a) to a value suitable for its role in proton abstraction. These results highlight the need for further studies of the dynamics of the enzyme in order to fully understand the complexities of loop closure and catalysis in this enzyme.

Amino Acid Substitution↗
PubMed2002

Application of metabolic engineering to improve both the production and use of biotech indigo.

A fermentation process was developed for production of indigo from glucose using recombinant Escherichia coli. This was achieved by modifying the tryptophan pathway to cause high-level indole production and adding the Pseudomonas putida genes encoding naphthalene dioxygenase (NDO). In comparison to a tryptophan-over-producing strain, the first indigo-producing strain made less than half of the expected amount of indigo. Severe inactivation of the first enzyme of aromatic biosynthesis, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (the aroGfbr gene product), was observed in cells collected from indigo fermentations. Subsequent in vitro experiments revealed that DAHP synthase was inactivated by exposure to the spontaneous chemical conversion of indoxyl to indigo. Indigo production was thereafter improved by increasing the gene dosage of aroGfbr or by increasing substrate availability to DAHP synthase in vivo by either amplifying the tktA (transketolase) gene or inactivating both isozymes of pyruvate kinase. By combining all three strategies for enhancing DAHP formation in the cell, a 60% increase in indigo production was achieved. Metabolic engineering was then further applied to eliminate a byproduct of the spontaneous conversion of indoxyl to indigo, thereby solving a serious problem with the use of bio-indigo in the final denim dyeing application.

Bioreactors↗
PubMed2002

A stability analysis of a decentralized adaptive feedback active control system of sinusoidal sound in free space.

In some cases, the implementation of active control of sound in free space requires a large number of secondary sources and error sensors. In terms of control hardware, this may translate into considerable processing power requirement. A practical method to decrease processing power is to decentralize the control; that is, implement many single-input, single-output independent controllers operating simultaneously instead of a large multiple-input, multiple-output system. The main drawback of decentralized control is the risk of global instability. The purpose of this paper is to derive conditions under which globally stable control system behavior can be obtained in the case of adaptive feedback decentralized control for a sinusoidal disturbance. The main objective is to give practical conditions derived from the small gain theorem and the Nyquist criterion for the stability of the control system. These conditions only take into account the geometrical arrangement of the secondary sources and error sensors. This analysis involves a new parameter beta called "performance index," which is associated with both the convergence of the individual controllers and the global stability of the system. Simulation and experimental results are shown to illustrate the effectiveness of the developed analytical tools.

Feedback↗
PubMed2002

One year's experience with the polymerase chain reaction as a routine method for the diagnosis of imported malaria.

Given the problems encountered in westernized countries with the laboratory diagnosis of malaria, namely sensitivity of the conventional methods and detection of mixed infections, a polymerase chain reaction (PCR)-based diagnosis has been developed and routinely used. The PCR used two sets of primers to simultaneously detect any infection due to the genus Plasmodium, or to the species P. falciparum. The PCR results were available within six hours. Five hundred twenty-nine patients were tested, of whom 136 were found positive by the PCR, and only 104 by the quantitative buffy coat (QBC) method. The 32 discrepancies were analyzed on the basis of the clinical data, and technical, molecular, and sequencing findings to ascertain the presence of Plasmodium DNA. The PCR-based diagnosis of malaria appeared to be a useful tool that was suitable as a second-line method when the results of conventional techniques were negative in patients presenting a syndromeconsistent with malaria, as well as yielding an accurate species identification.

Adult↗
PubMed2001

AP-1 activation and altered AP-1 composition in association with increased phosphorylation and expression of specific Jun and Fos family proteins induced by vinblastine in KB-3 cells.

Vinblastine and other microtubule inhibitors are important antitumor agents that cause mitotic arrest, and induce apoptosis through poorly understood mechanisms, in a wide variety of cell lines. The activating protein 1 (AP-1) transcription factor is a major target of the c-Jun NH2-terminal kinase (JNK) signaling pathway, which is activated by microtubule inhibitors. Therefore, we examined the effect of vinblastine on AP-1 composition and activity in human KB-3 carcinoma cells. Vinblastine caused highly selective effects on AP-1 proteins in a concentration- and time-dependent manner. Specifically, c-Jun, expressed at a low level in control cells, was greatly increased and phosphorylated, Jun D was phosphorylated, Jun B underwent phosphorylation and subsequently became undetectable, and Fra 1 expression was also greatly increased. In contrast. Fra 2, c-Fos, and Fos B were relatively unchanged by vinblastine. Changes in AP-1 preceded caspase 3 activation and, therefore, occurred prior to the commitment phase of apoptosis. With the exception of c-Jun, which was not affected by paclitaxel, the same alterations in AP-1 proteins occurred after exposure to vincristine, paclitaxel, and colchicine, demonstrating that these are general responses to microtubule inhibition. Supershift assays demonstrated that in control cells, AP-1 binding activity was mediated by Jun D/Fra 2 heterodimers, whereas after vinblastine treatment, AP-1 complexes also containing c-Jun and Fra 1 were present, suggesting that induction of these latter proteins by vinblastine is functionally significant. Consistent with these observations, vinblastine stimulated AP-1-dependent luciferase reporter gene transcription. These findings suggest that alterations in AP-1 composition and activity may be key events in the early response of KB-3 cells to microtubule inhibitors.

Antineoplastic Agents, Phytogenic↗
PubMed2001

Enteral human IgG for prevention of necrotising enterocolitis: a placebo-controlled, randomised trial.

BACKGROUND: Neonatal necrotising enterocolitis is a serious, commonly fatal disease in premature neonates. Although feeding with expressed breast milk and other good nursery practices are partly protective, preventive measures are needed. Treating neonates enterally with a mixture of human IgA and IgG, prepared from donated blood, has been claimed to protect against necrotising enterocolitis. However, no IgA preparation is available in Australia. Our aim, therefore, was to identify whether or not enteral IgG could prevent the disorder. METHODS: We did a multicentre, double-blind, placebo- controlled trial. We randomly assigned 768 infants to receive human IgG 1200 mg/kg daily, and 761 to receive placebo, for up to 28 days. Treatment began at the same time as enteral feeding. The primary outcome measure was the proportion of infants who developed definite necrotising enterocolitis during the trial, and any deaths that resulted from the disorder in the treatment and placebo groups. Analysis was on an intention-to-treat basis. FINDINGS: 43 infants developed definite necrotising enterocolitis in the IgG group, ten of whom died. In the placebo group, 41 infants contracted the disorder and six died (p=0.47). 25 infants on IgG and 36 on placebo had suspect necrotising enterocolitis (p=0.14). INTERPRETATION: Supplementation of enteral feeds with human IgG does not reduce necrotising enterocolitis.

Double-Blind Method↗
PubMed2001

An improved procedure for characterization of spatial and temporal evolution of immobilized cells in gel membranes.

An improved procedure that allows the simple and reproducible characterization of spatial and temporal distribution of immobilized biomass in gel membranes was developed. This procedure involves three main steps in the preparation of membrane samples, the use of a standard microtome to obtain membrane slices, and the measurement of cell concentration by spectrophotometry. The key improvement in this procedure is to prepare the membrane samples by clamping them between two glass plates and storing them in a -80 degrees C freezer for a specified period of time depending on the membrane thickness. With this simple pre-treatment, the membrane samples were frozen in an ideal physical state to be cut into flat, consistent, slices using a commercial freezing sledge microtome, thus providing accurate and reproducible results. As a validation case study, a gel membrane bioreactor was constructed in which an alginate gel membrane with immobilized Lactobacillus rhamnosus cells was flanked by two well-mixed chambers with identical fermentation media. The improved procedure was employed to experimentally determine the intra-membrane cell distribution in the alginate membranes during fermentation. The experimental results showed a heterogeneous "U-shape" biomass distribution across the membrane, with the highest cell concentration at the membrane-solution interface. High reproducibility and accuracy were verified by a low average standard deviation (<5%) and a high biomass recovery ratio (>90%), respectively.

Alginates↗
PubMed2001

Isolation and characterization of the UBASH3A gene on 21q22.3 encoding a potential nuclear protein with a novel combination of domains.

In order to identify candidate genes for Down syndrome phenotypes or monogenic disorders that map to human chromosome 21q22.3, we have used genomic sequence and expressed sequence tags mapping to an autosomal recessive deafness (DFNB10) critical region to isolate a novel 2.5-kb cDNA that maps between TFF1 and D21S49. A semi-quantitative reverse transcription/polymerase chain reaction method revealed that UBASH3A gene expression is limited to only a few tissues, with its highest expression in spleen, peripheral blood leukocytes, and bone marrow. The putative 661-amino-acid protein shows considerable homology to a hypothetical protein from Drosophila melanogaster but only domain homologies to other organisms. Both the human and D. melanogaster proteins contain protein-protein interaction domains, viz., SH3 and ubiquitin-associated (UBA) domains, in addition to a novel domain also containing a nuclear localization signal. This is the first protein described containing both UBA and SH3 domains. The gene, thus called UBASH3A, spans 40 kb and is divided into 15 exons. Mutation analysis excluded UBASH3A as being responsible for DFNB10.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Reduction of peptic ulcer disease and Helicobacter pylori infection but increase of reflux esophagitis in Western Sydney between 1990 and 1998.

We aimed to determine if changes in the patterns of upper gastrointestinal diseases at endoscopy have occurred over the past decade. Retrospectively, 917 consecutive patients were selected based on upper endoscopy between June 1 and August 31, in 1990 (n = 217), 1994 (n = 270), and 1998 (n = 430). Demographic, clinical, endoscopic, and histological information were extracted from the medical records on a standardized case record form. Over the eight-year period, follow-up of peptic ulcer (15%, 5%, and 5%, respectively, in 1990, 1994, and 1998, df = 2, P < 0.001), bleeding (22%, 14%, and 13%, P = 0.008), and nausea/vomiting (15%, 16%, and 10%, df = 2, P = 0.003) had become less frequent, but reflux (21%, 19%, and 34%, df = 2, P < 0.001) and dyspepsia (24%, 43%, and 32%, df = 2, P < 0.001) more frequent indications for upper endoscopy. The prevalence of peptic ulcer disease decreased (22%, 15%, and 13%, df = 2, P = 0.025), but the prevalence of reflux esophagitis increased significantly (29%, 30%, and 39%, df = 2, P = 0.010). The prevalence of both the use of nonsteroidal antiinflammatory drugs (NSAIDs) (18%, 20%, and 11%, respectively, in 1990, 1994, and 1998, df = 2, P = 0.004) and H. pylori infection (39% in 1994 and 30% in 1998, df = 1, P = 0.032) decreased. Overall, NSAID use was independently associated with gastric ulcers (OR = 2.39, 95% CI 1.21-4.73, chi2 = 6.31, df = 1, P = 0.012), but not esophagitis. H. pylori infection was independently associated with duodenal ulcers (OR = 4.74, 95% CI 2.30-9.77, chi2 = 17.8, df = 1, P < 0.001), histologically chronic (OR = 166.8, 95% CI 76.1-365.4, chi2 = 313.0, df = 1, P < 0.001) and active (OR = 30.1, 95% CI 17.0-53.5, chi2 = 189.7, df = 1, P < 0.001) gastritis and lymphoid aggregates (OR = 5.49, 95% CI 3.02-9.97, chi2 = 36.3, df = 1, P < 0.001). In conclusion, the prevalence of peptic ulcer disease appears to have been decreasing, whereas reflux esophagitis has been increasing over the past decade in Western Sydney. The decreased use of NSAIDs and decline of H. pylori infection have likely both contributed to the reduction of peptic ulcer disease, but the increase in reflux esophagitis remains to be fully explained.

Adult↗
PubMed2001

Eosinophil cationic protein as a possible marker of active human Toxocara infection.

BACKGROUND: Human toxocariasis is a common, worldwide helminthozoonosis that may elicit syndromes including various allergy symptoms. The diagnosis relies upon specific serology. However, this parasitosis is often self-limiting, and many subjects have residual antibodies, thus making differential diagnosis quite difficult when blood eosinophilia, a commonly accepted criterion of active helminthiasis due to tissue-dwelling parasites, is lacking. METHODS AND RESULTS: We present a patient with chronic irritant cough displaying negative allergologic screening, normal blood eosinophilia, but positive toxocariasis immunodiagnosis. Therefore, this case presented the fortuitous association of an unexplained allergic picture with residual anti-Toxocara antibodies. In an attempt to distinguish between active and past toxocaral infection, the subject's level of eosinophil cationic protein (ECP) was assessed and then compared to those of four control groups, namely, healthy volunteers, subjects presenting anti-Toxocara residual antibodies, patients with various helminthiases, and patients with active toxocaral disease. Since the patient's ECP level was found to be sharply elevated, we hypothesized that viable Toxocara larvae were still present in the tissues, and the patient was given anthelmintic therapy. At the control checkup, the cough had waned and the ECP level had decreased to below the mean value observed in both healthy subjects and in subjects with past toxocaral infections. CONCLUSIONS: These data suggest, first, that patients presenting unexplained allergic syndromes should be checked for helminthiases, even if blood eosinophilia is lacking, and, second, in such subjects displaying positive toxocariasis immunodiagnosis, ECP assessment would be a useful marker to distinguish between active and past toxocaral disease.

Animals↗
PubMed2001

Insertion of beta-satellite repeats identifies a transmembrane protease causing both congenital and childhood onset autosomal recessive deafness.

Approximately 50% of childhood deafness is caused by mutations in specific genes. Autosomal recessive loci account for approximately 80% of nonsyndromic genetic deafness. Here we report the identification of a new transmembrane serine protease (TMPRSS3; also known as ECHOS1) expressed in many tissues, including fetal cochlea, which is mutated in the families used to describe both the DFNB10 and DFNB8 loci. An 8-bp deletion and insertion of 18 monomeric (approximately 68-bp) beta-satellite repeat units, normally present in tandem arrays of up to several hundred kilobases on the short arms of acrocentric chromosomes, causes congenital deafness (DFNB10). A mutation in a splice-acceptor site, resulting in a 4-bp insertion in the mRNA and a frameshift, was detected in childhood onset deafness (DFNB8). This is the first description of beta-satellite insertion into an active gene resulting in a pathogenic state, and the first description of a protease involved in hearing loss.

Adult↗
PubMed2001

Identification of some rabbit allergens as lipocalins.

Rabbits are frequently used as laboratory animals or kept as domestic pets. Rabbit serum albumin and a 17-kDa protein referred to as Ory c 1 have previously been reported as allergens. Several other allergenic proteins have been recognized by crossed immuno-electrophoresis but have not been characterized. The aim of this study was to characterize the allergenic proteins present in rabbit saliva, urine and fur on the basis of molecular size and, where possible, to determine their amino acid sequences. Extracts from the male New Zealand white rabbit were used for developing specific direct RAST and RAST inhibition assays. Proteins in the extracts were separated by SDS-PAGE and the individual allergens identified by immunoblotting with serum from rabbit-allergic individuals. The N-termini of four allergens were sequenced. Saliva was the most potent extract. In total, 26 protein bands were recognized as allergens in the three extracts: 12 in saliva, seven in urine and seven in fur. Their molecular weights ranged from an 8-kDa species in saliva to an 80-kDa protein in urine. The N terminal sequences of an 18 kDa and a 21-kDa species in saliva, were identified as lipocalins with sequence similarity to a recently described odourant binding protein. This is the first evidence that allergens from the rabbit are members of the lipocalin superfamily of proteins, suggesting that similar mechanisms may be involved in eliciting the allergic response to rabbits. The 18 kDa allergen from saliva may be the previously named rabbit allergen, Ory c 1.

Allergens↗
PubMed2001

Three-dimensional elasticity model for a decoupling coating on a rectangular plate immersed in a heavy fluid.

This paper presents an analysis of the vibroacoustic response of a finite, simply supported rectangular plate covered by a layer of decoupling material and immersed in a heavy fluid. An exact formulation using the three-dimensional theory of elasticity for the decoupling material is derived for this problem, thereby extending previous studies that were limited to infinite plates. The paper details the constitutive equations of the problem and the analytical method of solution. Numerical results show that shear waves in the decoupling material generally have little influence on the sound radiation in the heavy fluid. Comparisons with a locally reacting model of the decoupling material and with the simple model of House [Proc. I.O.A. 13(3), 166-173 (1991)] are also presented.

Journal Article↗
PubMed2000

Cloning and characterization of a putative human glycerol 3-phosphate permease gene (SLC37A1 or G3PP) on 21q22.3: mutation analysis in two candidate phenotypes, DFNB10 and a glycerol kinase deficiency.

Using multiple exons trapped from human chromosome 21 (HC21)-specific cosmids with homology to a putative Arabidopsis thaliana glycerol 3-phosphate permease, we have determined the full-length cDNA sequence of a novel HC21 gene encoding a putative sugar-phosphate transporter (HGMW-approved symbol SLC37A1, aka G3PP). The predicted protein has 12 putative transmembrane domains and is also highly homologous to bacterial glpT proteins. The transcript was precisely mapped to 21q22.3 between D21S49 and D21S113. Comparison of the SLC37A1 cDNA to genomic sequence revealed that the gene encompasses 82 kb, and it is split into 19 coding exons and 7 untranslated exons, which are alternatively spliced in a complex and tissue-specific manner. Glycerol 3-phosphate (G3P) is produced by glycerol kinase (GK) and is found in several biochemical pathways in different cellular compartments, such as the glycerol phosphate shuttle and glycerophospholipid synthesis. Thus SLC37A1 mutations may cause a phenotype similar to GK deficiency. Mutational analyses of SLC37A1 in seven patients with no mutations in the GK gene and low GK activity revealed only nonpathogenetic sequence variants, excluding SLC37A1 as the gene for the phenotype in these patients. SLC37A1 maps in the refined critical region of the autosomal recessive deafness locus, DFNB10, on 21q22.3. Mutation analyses also excluded SLC37A1 as the gene for DFNB10.

Amino Acid Sequence↗
PubMed2000

Refined localization of autosomal recessive nonsyndromic deafness DFNB10 locus using 34 novel microsatellite markers, genomic structure, and exclusion of six known genes in the region.

An autosomal recessive nonsyndromic deafness locus, DFNB10, was previously localized to a 12-cM region near the telomere of chromosome 21 (21q22.3). This locus was discovered in a large, consanguineous Palestinian family. We have identified and ordered a total of 50 polymorphic microsatellite markers in 21q22.3, comprising 16 published and 34 new markers, precisely mapped and ordered on BAC/cosmid contigs. Using these microsatellite markers, the locus for DFNB10 has been refined to an area of less than 1 Mb between markers 1016E7.CA60 and 1151C12.GT45. Six previously published cDNAs were mapped to this critical region, and their genomic structures were determined to facilitate mutation analysis in DFNB10. All six genes in this region (in order from centromere to telomere: White/ABCG1, TFF3, TFF2, TFF1, PDE9A, and NDUVF3) have been screened and eliminated as candidates for DFNB10. The new microsatellite markers and single nucleotide polymorphisms identified in this study should enable the refined mapping of other genetic diseases that map to 21q22.3. In addition, the critical region for DFNB10 has been reduced to a size amenable to an intensive positional cloning effort.

Chromosome Mapping↗