A human cancer-associated truncation of MBD4 causes dominant negative impairment of DNA repair in colon cancer cells

MBD4 binds to methylated DNA and acts as a thymine DNA glycosylase in base excision repair. Deficiency of MBD4 in mice enhances mutation at CpG sites and alters apoptosis in response to DNA damage, but does not increase tumorigenesis in mismatch repair-deficient mice. However, in humans, frameshift mutation of MBD4, rather than deletion, is what occurs in up to 43% of microsatellite unstable colon cancers. There is no murine equivalent of this mutation. We now show that recombinant truncated MBD4 (MBD4tru) inhibits glycosylase activities of normal MBD4 or Uracil DNA glycosylase in cell-free assays as a dominant negative effect. Furthermore, overexpression of MBD4tru in Big Blue (lacI)-transfected, MSI human colorectal carcinoma cells doubled mutation frequency, indicating that the modest dominant negative effect on DNA repair can occur in living cells in short-term experiments. Intriguingly, the whole mutation spectrum was increased, not only at CpG sites, suggesting that truncated MBD4 has a more widespread effect on genomic stability. This demonstration of a dominant negative effect may be of significance in tumour progression and acquisition of drug resistance

Practice belief scales among private general dental practitioners

The document attached has been archived with permission from the Australian Dental Association (8th Jan 2008). An external link to the publisher’s copy is included.Background: Practice beliefs have been related to service rate variation. The aims of this study were to replicate practice belief scales in Australia and investigate associations with dentist and practice characteristics and services. Method: A random sample of Australian dentists completed mailed questionnaires (response rate 60.3 per cent). Results: Private general practitioners (n=345) provided service data from a typical day. Eight practice belief items were recorded on a five-point Likert scale, yielding four factor-based scales. Approximately 85 per cent of responses were on the agreement side of the midpoint for the scales of Information giving and Patient influence, 45 per cent for Preventive orientation and approximately 10 per cent for Controlling active disease rather than developing better preventive advice. Capital city dentists had higher agreement with the Preventive orientation scale, while males and older dentists showed less disagreement with the Controlling active disease item (Mann-Whitney, Kruskal-Wallis P<0.05). Those agreeing with the scales (that is scores ≤ the median) showed (Poisson regression P<0.05): a higher rate of crown and bridge, a rate ratio (RR) of 1.31, but lower rates of extraction (RR=0.76) and prosthodontic services (RR=0.64) for the Information giving scale; a higher rate of restorative (RR=1.22) and total services per visit (RR=1.06) for the Preventive orientation scale; a higher rate of preventive services (RR=1.14), but a lower rate of crown and bridge services (0.78) for the Patient influence scale; and higher rates of crown and bridge (RR=1.40) and prosthodontic (RR=1.59) but lower rates of periodontic (RR=0.60) and extraction services (RR=0.62) for the Controlling active disease item. Conclusions: These findings confirm the factor structure of practice beliefs and demonstrate small to moderate associations with variation in service rates.DS Brennan and AJ Spence

Predicting functional associations from metabolism using bi-partite network algorithms

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity.</p> <p>Results</p> <p>We present new, fast methods to infer functional associations in metabolic networks. A local method, the degree-corrected Poisson score, is based only on the metabolites shared by two enzymes, but uses the known metabolite degree distribution. A global method, based on graph diffusion kernels, predicts associations between enzymes that do not share metabolites. Both methods are robust to high-degree metabolites. They out-perform previous methods in predicting shared Gene Ontology (GO) annotations and in predicting experimentally observed synthetic lethal genetic interactions. Including cellular compartment information improves GO annotation predictions but degrades synthetic lethal interaction prediction. These new methods perform nearly as well as computationally demanding methods based on flux balance analysis.</p> <p>Conclusions</p> <p>We present fast, accurate methods to predict functional associations from metabolic networks. Biological significance is demonstrated by identifying enzymes whose strong metabolic correlations are missed by conventional annotations in GO, most often enzymes involved in transport vs. synthesis of the same metabolite or other enzyme pairs that share a metabolite but are separated by conventional pathway boundaries. More generally, the methods described here may be valuable for analyzing other types of networks with long-tailed degree distributions and high-degree hubs.</p

Involvement of glomerular renin−angiotensin system (RAS) activation in the development and progression of glomerular injury

Recently, there has been a paradigm shift away from an emphasis on the role of the endocrine (circulating) renin−angiotensin system (RAS) in the regulation of the sodium and extracellular fluid balance, blood pressure, and the pathophysiology of hypertensive organ damage toward a focus on the role of tissue RAS found in many organs, including kidney. A tissue RAS implies that RAS components necessary for the production of angiotensin II (Ang II) reside within the tissue and its production is regulated within the tissue, independent of the circulating RAS. Locally produced Ang II plays a role in many physiological and pathophysiological processes such as hypertension, inflammation, oxidative stress, and tissue fibrosis. Both glomerular and tubular compartments of the kidney have the characteristics of a tissue RAS. The purpose of this article is to review the recent advances in tissue RAS research with a particular focus on the role of the glomerular RAS in the progression of renal disease

Inducible Transgenic Rat Model for Diabetes Mellitus Based on shRNA-Mediated Gene Knockdown

The rat is an important animal model in biomedical research, but gene targeting technology is not established for this species. Therefore, we aimed to produce transgenic knockdown rats using shRNA technology and pronuclear microinjection. To this purpose, we employed a tetracycline-inducible shRNA expression system targeting the insulin receptor (IR). Doxycycline (DOX) treatment of the resulting transgenic rats led to a dose-dependent and reversible increase in blood glucose caused by ubiquitous inhibition of IR expression and signalling. We could neither detect an interferon response nor disturbances in microRNA processing after DOX treatment excluding toxic effects of shRNA expression. Low dose DOX treatment induced a chronic state of diabetes mellitus. In conclusion, we have developed a technology which allows the specific, inducible, and reversible suppression of any gene of interest in the rat. Our first transgenic rat line generated with this method represents an inducible model for diabetes mellitus

Unexpected combination of acute croup and myocarditis: Case report

BACKGROUND: Lower vaccination coverage among foreign-born children is of concern because they live in households and communities characterized by more intense exposure to infectious diseases. Because of their higher prevalence rates, there is an increasing occurrence of infectious diseases imported into developed countries. This case report emphasizes the emerging necessity for new clinicians and pathologists of having competence with old infectious disease pathology. CASE PRESENTATION: A three and a half year old girl, who presented with croup history of 5 days and has been in severe respiratory distress, was admitted to the Pediatric Intensive Care Unit in shock and acute respiratory failure. The patient was immediately intubated, and a grayish nonadherent membrane extending through the glottis down into the larynx was apparent during the procedure. Echocardiographic findings, which were consistent with acute myocarditis, confirmed poor left ventricular contractility despite escalating high doses of inotropes. Autopsy showed numerous strains of toxigenic corynobacterium diphtheriae, which also grew on the Loeffler cultures of membranes received during the intubation. CONCLUSION: It is critical that new generations of clinicians and bio-pathologists not only be trained in the subspecialty of infectious disease pathology, but that they also be willing participants in the diagnosis and investigation of infectious diseases

Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse

Recent clinical evidence suggests important role of lipid and amino acid metabolism in early pre-autoimmune stages of type 1 diabetes pathogenesis. We study the molecular paths associated with the incidence of insulitis and type 1 diabetes in the Non-Obese Diabetic (NOD) mouse model using available gene expression data from the pancreatic tissue from young pre-diabetic mice. We apply a graph-theoretic approach by using a modified color coding algorithm to detect optimal molecular paths associated with specific phenotypes in an integrated biological network encompassing heterogeneous interaction data types. In agreement with our recent clinical findings, we identified a path downregulated in early insulitis involving dihydroxyacetone phosphate acyltransferase (DHAPAT), a key regulator of ether phospholipid synthesis. The pathway involving serine/threonine-protein phosphatase (PP2A), an upstream regulator of lipid metabolism and insulin secretion, was found upregulated in early insulitis. Our findings provide further evidence for an important role of lipid metabolism in early stages of type 1 diabetes pathogenesis, as well as suggest that such dysregulation of lipids and related increased oxidative stress can be tracked to beta cells

Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databases dealing with these data comprehensively have been constructed and applied to analyzing PPI networks. However, few research on prediction interaction sites using both PPI networks and the 3D protein structures complementarily has explored.</p> <p>Results</p> <p>We propose a method of predicting interaction sites in proteins with unknown function by using both of PPI networks and protein structures. For a protein with unknown function as a target, several clusters are extracted from the neighboring proteins based on their structural similarity. Then, interaction sites are predicted by extracting similar sites from the group of a protein cluster and the target protein. Moreover, the proposed method can improve the prediction accuracy by introducing repetitive prediction process.</p> <p>Conclusions</p> <p>The proposed method has been applied to small scale dataset, then the effectiveness of the method has been confirmed. The challenge will now be to apply the method to large-scale datasets.</p