Biomedical subjects

John Robinson

Publications and source records attributed to John Robinson.

At least 19 recordsLinked to original sources

PubMed2006

Proteomic analysis of pharmacological preconditioning: novel protein targets converge to mitochondrial metabolism pathways.

Ischemic preconditioning is characterized by resistance to ischemia reperfusion injury in response to previous short ischemic episodes, a protective effect that can be mimicked pharmacologically. The underlying mechanism of protection remains controversial and requires greater understanding before it can be fully exploited therapeutically. To investigate the overall effect of preconditioning on the myocardial proteome, isolated rabbit ventricular myocytes were treated with drugs known to induce preconditioning, adenosine or diazoxide (each at 100 micromol/L for 60 minutes). Their protein profiles were then compared with vehicle-treated controls (n=4 animals per treatment) using a multitiered 2D gel electrophoresis approach. Of 28 significantly altered protein spots, 19 nonredundant proteins were identified (5 spots remained unidentified). The majority of these proteins are involved in mitochondrial energetics, including subunits of tricarboxylic acid cycle enzymes and oxidative phosphorylation complexes. These changes were not indiscriminate, with only a small number of enzymes or complex subunits altered, indicating a very specific and targeted affect of these 2 preconditioning mimetics. Among the changes were shifts in the extent of posttranslational modification of 4 proteins. One of these, the adenosine-induced phosphorylation of the ATP synthase beta subunit, was fully characterized with the identification of 5 novel phosphorylation sites. This proteomics approach provides an overall assessment of the cellular response to pharmacological treatment with adenosine and diazoxide and identifies a distinct subset of enzymes and protein complex subunit that may underlie the preconditioned phenotype.

Adenosine↗

PubMed2006

Genetic analysis of the balhimycin (vancomycin-type) oxygenase genes.

In the balhimycin biosynthesis three oxygenases OxyA, OxyB and OxyC are responsible for the oxidative phenol coupling reactions, which lead to the ring-closures between the aromatic amino acid side chains in the heptapeptide aglycone. These ring-closures constrain the peptide backbone into the cup-shaped conformation that is required for binding to the Lys-D-Ala-D-Ala-terminus of the cell wall precursor peptide and represent one of the essential features of glycopeptide antibiotics. In the balhimycin biosynthetic gene cluster the oxygenase genes oxyA, oxyB and oxyC have been identified downstream of the peptide synthetase genes. Reverse transcription (RT)-PCR analyses revealed that these oxygenase genes in Amycolatopsis balhimycina are co-transcribed. Non-polar mutants (NPoxyA, DeltaoxyB and DeltaoxyC) were constructed, cultivated in production medium and assayed for the presence of glycopeptides and glycopeptide precursors by HPLC-ESI-MS. The mutant NPoxyA produces mainly monocyclic, the mutant DeltaoxyB linear and the mutant DeltaoxyC bicyclic peptides. These results definitely confirm the sequence of the three oxidative ring-closing steps (OxyB-OxyA-OxyC). The heterologous complementation of the mutant strains with the corresponding oxygenase genes from the vancomycin producer A. orientalis restored the production of balhimycin, which proves the functional equivalence of the oxygenases from the balhimycin and vancomycin producer. For the first time it is now possible to combine the genetic data obtained from the balhimycin producer with the biochemical and structural data obtained from the vancomycin producer.

Actinomycetales↗

PubMed2006

Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.

MOTIVATION: Most phylogenetic methods assume that the sequences of nucleotides or amino acids have evolved under stationary, reversible and homogeneous conditions. When these assumptions are violated by the data, there is an increased probability of errors in the phylogenetic estimates. Methods to examine aligned sequences for these violations are available, but they are rarely used, possibly because they are not widely known or because they are poorly understood. RESULTS: We describe and compare the available tests for symmetry of k-dimensional contingency tables from homologous sequences, and develop two new tests to evaluate different aspects of the evolutionary processes. For any pair of sequences, we consider a partition of the test for symmetry into a test for marginal symmetry and a test for internal symmetry. The proposed tests can be used to identify appropriate models for estimation of evolutionary relationships under a Markovian model. Simulations under more or less complex evolutionary conditions were done to display the performance of the tests. Finally, the tests were applied to an alignment of small-subunit ribosomal RNA sequences of five species of bacteria to outline the evolutionary processes under which they evolved. AVAILABILITY: Programs written in R to do the tests on nucleotides are available from http://www.maths.usyd.edu.au/u/johnr/testsym/

Base Pair Mismatch↗

PubMed2006

Defining the origins and evolution of the chemokine/chemokine receptor system.

The chemokine system has a critical role in mammalian immunity, but the evolutionary history of chemokines and chemokine receptors are ill-defined. We used comparative whole genome analysis of fruit fly, sea urchin, sea squirt, pufferfish, zebrafish, frog, and chicken to identify chemokines and chemokine receptors in each species. We report 127 chemokine and 70 chemokine receptor genes in the 7 species, with zebrafish having the most chemokines, 63, and chemokine receptors, 24. Fruit fly, sea urchin, and sea squirt have no identifiable chemokines or chemokine receptors. This study represents the most comprehensive analysis of the chemokine system to date and the only complete characterization of chemokine systems outside of mouse and human. We establish a clear evolutionary model of the chemokine system and trace the origin of the chemokine system to approximately 650 million years ago, identifying critical steps in their evolution and demonstrating a more extensive chemokine system in fish than previously thought.

Animals↗

PubMed2006

Continence: sizing and fitting a penile sheath.

Male patients suffering from urinary incontinence can benefit from being fitted with a penile sheath and drainage bag rather than using incontinence pads or having to have an indwelling catheter to treat or manage their problem. In selecting a penile sheath it is important to select the correct size of sheath to fit onto the shaft of penis and length of sheath. A penile sheath fitted too small may cause problems not only in drainage of urine but also by restricting blood circulation to the shaft of the penis. A penile sheath fitted too large will cause creases to form, allowing urine leakage and causing the sheath to fail and fall off. This article explains what is required before fitting a penile sheath, examines various sheaths and alternatives, and how to fit one correctly.

Activities of Daily Living↗

PubMed2006

Intermittent self-catheterization appliances for disabled patients.

Occasionally, district nurses may be asked to teach a patient intermittent self-catheterization (ISC). However, if the patient has some form of physical disability that reduces their manual dexterity or limits their movement, should this stop the patient undertaking the procedure? This article outlines some of the appliances available to help disabled patients undertake ISC.

Activities of Daily Living↗

PubMed2006

Intermittent self-catheterization: principles and practice.

Intermittent self-catheterization (ISC) is becoming more widely used by patients to drain their urinary bladder rather than having a long-term indwelling urinary catheter. ISC can be undertaken by people of all ages to empty their bladder of urine or by a nurse or doctor to measure residual urine after the patient has passed urine. Those patients unable to undertake the procedure themselves may have the procedure undertaken by a parent, spouse, carer or nurse to drain their bladder of urine. Modern day intermittent catheters can be used almost anywhere when drainage of the urinary bladder is required.

Activities of Daily Living↗

PubMed2006

Climate change and sustainable development: realizing the opportunity.

Manifold linkages exist between climate change and sustainable development. Although these are starting to receive attention in the climate exchange literature, the focus has typically been on examining sustainable development through a climate change lens, rather than vice versa. And there has been little systematic examination of how these linkages may be fostered in practice. This paper examines climate change through a sustainable development lens. To illustrate how this might change the approach to climate change issues, it reports on the findings of a panel of business, local government, and academic representatives in British Columbia, Canada, who were appointed to advise the provincial government on climate change policy. The panel found that sustainable development may offer a significantly more fruitful way to pursue climate policy goals than climate policy itself. The paper discusses subsequent climate change developments in the province and makes suggestions as how best to pursue such a sustainability approach in British Columbia and other jurisdictions.

British Columbia↗

PubMed2005

Environmental enrichment reduces Abeta levels and amyloid deposition in transgenic mice.

Cerebral deposition of beta-amyloid (Abeta) peptides is an invariant pathological hallmark in brains of patients with Alzheimer's disease (AD) and transgenic mice coexpressing familial AD-linked APP and PS1 variants. We now report that exposure of transgenic mice to an "enriched environment" results in pronounced reductions in cerebral Abeta levels and amyloid deposits, compared to animals raised under "standard housing" conditions. The enzymatic activity of an Abeta-degrading endopeptidase, neprilysin, is elevated in the brains of "enriched" mice and inversely correlated with amyloid burden. Moreover, DNA microarray analysis revealed selective upregulation in levels of transcripts encoded by genes associated with learning and memory, vasculogenesis, neurogenesis, cell survival pathways, Abeta sequestration, and prostaglandin synthesis. These studies provide evidence that environmental enrichment leads to reductions in steady-state levels of cerebral Abeta peptides and amyloid deposition and selective upregulation in levels of specific transcripts in brains of transgenic mice.

Alzheimer Disease↗

PubMed2005

Clinical performance of the LCx HCV RNA quantitative assay.

This study was conducted to assess the performance of the Abbott laboratories LCx HCV RNA Quantitative Assay (LCx assay) in the clinical setting. Four clinical laboratories measured LCx assay precision, specificity, and linearity. In addition, a method comparison was conducted between the LCx assay and the Roche HCV Amplicor Monitor, version 2.0 (Roche Monitor 2.0) and the Bayer VERSANT HCV RNA 3.0 Assay (Bayer bDNA 3.0) quantitative assays. For precision, the observed LCx assay intra-assay standard deviation (S.D.) was 0.060-0.117 log IU/ml, the inter-assay S.D. was 0.083-0.133 log IU/ml, the inter-lot S.D. was 0.105-0.177 log IU/ml, the inter-site S.D. was 0.099-0.190 log IU/ml, and the total S.D. was 0.113-0.190 log IU/ml. The specificity of the LCx assay was 99.4% (542/545; 95% CI, 98.4-99.9%). For linearity, the mean pooled LCx assay results were linear (r=0.994) over the range of the panel (2.54-5.15 log IU/ml). A method comparison demonstrated a correlation coefficient of 0.881 between the LCx assay and Roche Monitor 2.0, 0.872 between the LCx assay and Bayer bDNA 3.0, and 0.870 between Roche Monitor 2.0 and Bayer bDNA 3.0. The mean LCx assay result was 0.04 log IU/ml (95% CI, -0.08, 0.01) lower than the mean Roche Monitor 2.0 result, but 0.57 log IU/ml (95% CI, 0.53, 0.61) higher than the mean Bayer bDNA 3.0 result. The mean Roche Monitor 2.0 result was 0.60 log IU/ml (95% CI, 0.56, 0.65) higher than the mean Bayer bDNA 3.0 result. The LCx assay quantitated genotypes 1-4 with statistical equivalency. The vast majority (98.9%, 278/281) of paired LCx assay-Roche Monitor 2.0 specimen results were within 1 log IU/ml. Similarly, 86.6% (240/277) of paired LCx assay and Bayer bDNA 3.0 specimen results were within 1 log, as were 85.6% (237/277) of paired Roche Monitor 2.0 and Bayer specimen results. These data demonstrate that the LCx assay may be used for quantitation of HCV RNA in HCV-infected individuals.

DNA, Viral↗

PubMed2005

Sexual dysfunction after radical prostatectomy: prevalence, treatments, restricted use of treatments and distress.

PURPOSE: Cancer of the prostate (CAP) is one of the most common malignancies affecting North American men with about 215,000 new cases and 35,800 CAP related deaths annually. The most prevalent intervention for localized CAP is radical prostatectomy (RP) with 10-year survival rates approaching 90%. Studies of men in post-RP recovery indicate that 44% to 75% experience sexual dysfunction and more than 60% experience distress in reaction to sexual dysfunction problems. These findings are increasingly significant as prostate specific antigen testing continues to increase CAP detection rates, resulting in more and younger post-RP patients confronting sexual dysfunction. MATERIALS AND METHODS: A MEDLINE database search was performed for articles published from 1966 to September 2004. RESULTS: Despite effectiveness 30% to 50% of patients who turn to sexually assistive aids after RP discontinue use within a year. This suggests that the achievement of physical responsiveness to an aid is necessary but it is not a sufficient factor in long-term sexual adaptation. Current research exploring this gap between effectiveness and ongoing use supports a broader perspective of sexual dysfunction emphasizing several factors, including perceptions of inadequacy, anxieties in regard to performance and depression in each member of the couple, overly enthusiastic expectations, partner physical/emotional readiness to resume active sex, the meaning to the couple of using a sexual aid and the quality of the nonsexual relationship of the couple. CONCLUSIONS: Our findings reveal the need to explore broader strategies for improving patient coping ability and adaptation. They also point to the need to explore the role of resumed satisfying sexuality in overall quality of life following treatment.

Adaptation, Psychological↗

PubMed2005

Intersegmental recombination between the haemagglutinin and matrix genes was responsible for the emergence of a highly pathogenic H7N3 avian influenza virus in British Columbia.

In February 2004 a highly pathogenic avian influenza (HPAI) outbreak erupted in British Columbia. Investigations indicated that the responsible HPAI H7N3 virus emerged suddenly from a low pathogenic precursor. Analysis of the haemagglutinin (HA) genes of the low and high pathogenic viruses isolated from the index farm revealed the only difference to be a 21 nt insert at the HA cleavage site of the highly pathogenic avian influenza virus. It was deduced that this insert most probably arose as a result of non-homologous recombination between the HA and matrix genes of the same virus. Over the course of the outbreak, a total of 37 isolates with, and 3 isolates without inserts were characterized. The events described here appear very similar to those which occurred in Chile in 2002 where the virulence shift of another H7N3 virus was attributed to non-homologous recombination between the HA and nucleoprotein genes.

Animals↗

PubMed2005

Suprapubic catheterization: challenges in changing catheters.

Suprapubic catheterization of the bladder is used as a short- or long-term alternative to urethral catheterization. As with any indwelling urinary catheter, correct insertion, care and removal are vitally important to minimize problems. A particular problem that affects suprapubic catheters is 'cuffing', which on its own or combined with encrustation can potentially cause a great deal of difficulty on removal or discomfort for the patient. This article discusses the causes of cuffing, and suggests using catheters with integral balloons to reduce the incidence of the problem.

Catheterization↗

PubMed2005

Removing indwelling catheters: trial without catheter in the community.

Indwelling urinary catheters are inserted to drain the bladder for a variety of reasons, but are an intervention of last resort. Unless contraindicated, patients with an indwelling catheter should therefore have at least one trial without catheter to assess if they can pass urine without having a catheter in situ. The commonest method in undertaking trial without catheter is to remove a indwelling urethral catheter and monitor urinary output over a period of time. Another method is when the catheter is not removed in patients who have a suprapubic catheter. Instead the catheter is clamped, and urethral urine output monitored. This is followed by immediately measuring any residue of urine drained via the supra-pubic catheter. This article looks at undertaking a 'trial without catheter' using both methods and examines the arguments concerning when to remove catheters, midnight or early in the morning.

Clinical Trials as Topic↗

PubMed2005

Changing indwelling urinary catheters using bladder infill.

The commonest method used in changing indwelling urinary catheters, either urethral or supra-pubic, is to remove the catheter and proceed to re-catheterise. When removing the catheter with patients using drainage bags on continual drainage, the urinary bladder becomes empty of urine. This may then leave the practitioner following re-catheterisation and often with no immediate drainage of urine, if the catheter has been safely inserted. A method which the author has used for many years and has experienced no problems is re-catheterisation using bladder infill. This article explains what is meant by bladder infill and how re-catheterisation can be undertaken safely using this method.

Adult↗

PubMed2004

Clodronate reduces vertebral fracture risk in women with postmenopausal or secondary osteoporosis: results of a double-blind, placebo-controlled 3-year study.

UNLABELLED: The efficacy of oral clodronate 800 mg daily to reduce vertebral fractures was studied in 593 women with postmenopausal or secondary osteoporosis. The incidence of vertebral fractures was significantly reduced by 46%. The effect was not modified by the underlying cause of osteoporosis or other baseline factors including bone mineral density, QUS, weight, and smoking. INTRODUCTION: This study aimed to determine if the bisphosphonate, clodronate (Bonefos), reduced the incidence of vertebral fractures in osteoporotic women. MATERIALS AND METHODS: Women fulfilling the WHO criteria for osteoporosis at the lumbar spine (T-score </= -2.5) and/or with at least one prevalent vertebral fracture were recruited to a 3-year double-blind, placebo-controlled study. A total of 593 patients were randomized to two strata comprised of women with postmenopausal osteoporosis (I, n = 483) and secondary osteoporosis (II, n = 110). They received either clodronate 800 mg daily orally (n = 292) or an identical placebo (n = 301). All patients received a calcium supplement of 500 mg daily. BMD was measured at 6, 12, 24, and 36 months, and lateral spine radiographs were obtained at baseline and annually thereafter for vertebral morphometry. RESULTS: Treatment with clodronate was associated with a significant increase in mean spine BMD over 3 years (percent change from baseline, 4.35 +/- 6.34% versus 0.64 +/- 6.02% in the placebo group, p < 0.0001). At the hip, clodronate maintained total BMD, whereas a significant decrease was observed in the placebo group (percent change from baseline 0.70 +/- 5.67% versus -3.03 +/- 6.32% in the placebo group, p < 0.0001). The changes at the spine and hip were similar in both strata. Incident vertebral fractures at 3 years were observed in 63 women in the placebo group and 33 patients receiving clodronate (relative risk, 0.54; 95% CI, 0.37-0.80; p = 0.001). Clodronate significantly reduced vertebral fracture risk in both strata and in women with or without prior vertebral fracture at baseline. Nonvertebral osteoporosis-associated fractures occurred in 21 women in the placebo group and in 14 women treated with clodronate. Treatment was well tolerated, with no significant difference in adverse event rates, including esophagitis, during clodronate treatment. CONCLUSION: We conclude that clodronate 800 mg daily is a safe and effective treatment to reduce fracture risk in women with osteoporosis, regardless of causation.

Aged↗

PubMed2004

Venn analysis as part of a bioinformatic approach to prioritize expressed sequence tags from cardiac libraries.

OBJECTIVES: We needed to sort expressed sequence tags (ESTs) from human cardiac expression libraries. DESIGN AND METHODS: We annotated DNA sequence text files of 35,152 cardiac ESTs using our search and annotation tool called Multiblast.pl. We generated lists of the most prevalent ESTs in each library, and using a novel Venn tool, we grouped ESTs that were common to all or exclusive to particular libraries. RESULTS: Hypothetical protein KIAA0553 was expressed 120 times among 917 ESTs from an adult cardiac library (13.1%) compared only once among 8075 ESTs from fetal cardiac libraries (P < 10(-114)), this was confirmed using Northern analysis. We collated biochemical features of KIAA0553 and determined DNA polymorphism frequencies. We also used the Venn tool to specify genes that were uniquely expressed in hypertrophic cardiomyocytes. CONCLUSIONS: Annotating ESTs and sorting them using Venn analysis can help specify new candidate disease genes from the current lists of "hypothetical proteins".

Amino Acid Sequence↗

PubMed2004

Performance attributes of the LCx HCV RNA quantitative assay.

The LCx HCV RNA quantitative assay (Abbott Laboratories, North Chicago, IL) is designed to use competitive reverse transcriptase-polymerase chain reaction (RT-PCR) and microparticle enzyme immunoassay (MEIA), in combination with a modified Qiagen sample preparation method, to measure the level of hepatitis C virus (HCV) in human plasma and serum. The assay provides quantitative results in international units (IU) of HCV RNA/ml, in copies of HCV RNA/ml, or their log (base 10) equivalents. A conversion study determined that 1IU equals 4.3 copies. The LCx HCV assay detected HCV RNA transcripts representative of genotypes 1-6 with near equal efficiency. The assay did not cross-react with high concentrations of 21 potentially cross-reactive microorganisms or with 100 HCV-negative specimens. The lower limit of detection was demonstrated to be 23IU/ml. The LCx assay had similar sensitivity to the Roche Amplicor HCV (version 2.0) qualitative assay when used to test panels containing 6, 12, 23, and 47IU/ml. The assay linear range was shown to extend from 23 to 2.3millionIU/ml. The intra-assay standard deviation (S.D.) was < or =0.066 logIU/ml for the four HCV positive samples tested, while for the same samples the observed inter-assay S.D. was < or =0.075 logIU/ml. The overall mean assay quantitation value for seven HCV-positive WHO-standardized Acrometrix NAP linearity panel members was within 0.06 logIU/ml of the mean assigned value. The assay was demonstrated to correlate acceptably against the Roche Amplicor HCV monitor test (version 2.0). These data suggest that the assay is standardized appropriately against the WHO standard across its linear range and can be used for quantitation of HCV. In addition, with a sensitivity of 23IU/ml, the assay can be used to determine if post-therapy viral clearance has occurred.

Cross Reactions↗