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S Burden

Publications and source records attributed to S Burden.

12 recordsLinked to original sources
PubMed2004

Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.

MOTIVATION: Although a great deal of research has been undertaken in the area of promoter prediction, prediction techniques are still not fully developed. Many algorithms tend to exhibit poor specificity, generating many false positives, or poor sensitivity. The neural network prediction program NNPP2.2 is one such example. RESULTS: To improve the NNPP2.2 prediction technique, the distance between the transcription start site (TSS) associated with the promoter and the translation start site (TLS) of the subsequent gene coding region has been studied for Escherichia coli K12 bacteria. An empirical probability distribution that is consistent for all E.coli promoters has been established. This information is combined with the results from NNPP2.2 to create a new technique called TLS-NNPP, which improves the specificity of promoter prediction. The technique is shown to be effective using E.coli DNA sequences, however, it is applicable to any organism for which a set of promoters has been experimentally defined. AVAILABILITY: The data used in this project and the prediction results for the tested sequences can be obtained from http://www.uow.edu.au/~yanxia/E_Coli_paper/SBurden_Results.xls CONTACT: alh98@uow.edu.au.

Algorithms↗
PubMed2001

Dietary treatment of irritable bowel syndrome: current evidence and guidelines for future practice.

The aim of this literature review is to produce guidelines for dietetic practice in irritable bowel syndrome (IBS) by evaluating the research available. In this area randomized control trials (RCT) only account for a small proportion of the literature and have been concentrated in the modification of dietary fibre in patients with IBS. The bulk of the literature is mainly observational trials from which no indisputable conclusions can be extracted. In this review, the evidence available has been interpreted within the context of the current knowledge base. Conclusions are drawn to facilitate the development of guidelines, enabling a starting point for discussion and an evaluation of current practice. The literature available on therapeutic dietary manipulation in IBS patients is centred around non-starch polysaccharides (NSPs), mono and disaccharide sensitivity and food intolerance. The production of these guidelines has focused on research examining the role of dietary components in the therapeutic management of patients with IBS. However, where there is a deficiency in the literature directly relating dietary intake to management of IBS patients, physiological function in relation to dietary components has been relied upon to produce practical guidelines which can be applied realistically in a clinical environment. An interpretation of the evidence has revealed a limited role for exclusion diets, a move away from high-fibre diets towards the manipulation of fibre fractions in the diet, an evaluation of the effects of caffeine on gut function and the necessity for individual dietary assessment to identify dietary issues pertinent to the patient's symptoms. These guidelines outline a positive role for dietitians in the treatment of IBS patients which draws on the unique skills possessed by dietitians regarding the assessment of habitual eating habits and therapeutic dietary manipulation.

Colonic Diseases, Functional↗
PubMed1996

Delivery of macromolecules into adherent cells via electroporation for use in fluorescence spectroscopic imaging and metabolic studies.

A method is described to introduce by electroporation membrane-impermeant molecules into adherent living cells with little perturbation. The approach uses simple, commonly available equipment to introduce small fluorescent dyes, large carrier-based dyes (e.g., fluorescein-labeled dextran), large macromolecules (e.g., antibodies), and metabolic precursors (e.g., 32P-ATP) with high efficiency. Conditions are relatively independent of cell type. Electroporation with three pulses of 300 volts at 540 microF capacitance at 4 degrees C is a good starting point for many cell types. Electrode distance from the adherent cells was critical at 1.0 +/- 0.15 mm. Suitable poration medium includes calcium-magnesium free phosphate buffered saline (PBS), PBS-buffered 0.25-3.0 M sucrose, Hepes-buffered sucrose, or unbuffered sucrose. Potential use in fluorescence imaging and metabolic studies is shown with DNA synthesis, cell replication, cell substratum attachment, 32P-ATP phosphorylation, and insulin-mediated increases in glucose uptake and its suppression by antiphosphotyrosine and antiglucose transporter protein antibodies. The ability to load foreign molecules into large numbers of adherent cells provides a means of studying these cells individually via microscopic approaches, such as fluorescence spectroscopic imaging, as well as with conventional biochemical and physiological techniques.

3T3 Cells↗
PubMed1982

Identification of an intracellular postsynaptic antigen at the frog neuromuscular junction.

A layer of amorphous, electron-dense material is situated at the cytoplasmic surface of the postsynaptic membrane of vertebrate neuromuscular synapses. The function of this structure is not clear, but its location suggests that it may have an important role in the formation and/or maintenance of the synapse. This paper demonstrates that a monoclonal antibody raised against antigens from Torpedo electric organ binds to an intracellular, postsynaptic protein at the frog neuromuscular synapse. Indirect immunofluorescence on frozen sections of frog muscle was used to demonstrate that the antigen is concentrated at synaptic sites in normal muscle. In denervated muscle, the antigen remains concentrated at synaptic sites, but is also present at extrasynaptic regions of denervated myofibers. The antigen cannot be labeled in intact, whole muscle, but only in whole muscle that has been permeabilized with nonionic detergents. The antibody staining pattern in Triton X-100-permeabilized whole-mounts of the frog neuromuscular synapse is arranged in elongate, arborized areas which are characteristic of the frog neuromuscular synapse. The stained areas are striated and the striations occur with a periodicity that corresponds to the regular folding of the postsynaptic membrane. Immunoferritin labeling of fixed, saponin-permeabilized muscle demonstrates that the antigen is associated with amorphous material that is situated between the postsynaptic membrane and an underlying layer of intermediate filaments. The antigen, solubilized from membrane and an underlying layer of intermediate filaments. The antigen, solubilized from Torpedo electric organ by high ionic strength, was identified by antibody binding to nitrocellulose replicas of SDS gels of Torpedo tissue. In Torpedo tissue, the antibody binds to a single protein band at 51,000 daltons (51 kd). The 51-kd protein shares an antigenic determinant with intermediate filament proteins, since a monoclonal antibody to all intermediate filaments reacts with the same 51-kd protein. The monoclonal antibody also reacts with a 55-kd protein in frog skin which is localized to the perinuclear region of the epithelial cells.

Animals↗
PubMedDate not supplied

Sleep apnea in end-stage renal disease patients on hemodialysis and continuous ambulatory peritoneal dialysis.

Fifteen unselected end-stage renal disease patients (nine hemodialysis [HD] and six continuous ambulatory peritoneal dialysis [CAPD]) were randomly selected from four Sydney metropolitan dialysis centers for sleep assessment by full polysomnography. Four of six CAPD patients and eight of nine HD patients were found to have clinically significant obstructive sleep apnea. An additional 21 unselected patients (10 CAPD and 11 HD patients) were assessed using overnight home monitoring of nasal airflow and arterial oxygen saturation. Of these, 8 of the 11 HD and 7 of the 10 CAPD patients were found to have obstructive sleep apnea. These data confirm the high incidence of obstructive sleep apnea in the end-stage renal disease population at large. Screening for obstructive sleep apnea should become a routine part of the management of these patients.

Adolescent↗