Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction

BACKGROUND: The accomplishment of the various genome sequencing projects resulted in accumulation of massive amount of gene sequence information. This calls for a large-scale computational method for predicting protein localization from sequence. The protein localization can provide valuable information about its molecular function, as well as the biological pathway in which it participates. The prediction of localization of a protein at subnuclear level is a challenging task. In our previous work we proposed an SVM-based system using protein sequence information for this prediction task. In this work, we assess protein similarity with Gene Ontology (GO) and then improve the performance of the system by adding a module of nearest neighbor classifier using a similarity measure derived from the GO annotation terms for protein sequences. RESULTS: The performance of the new system proposed here was compared with our previous system using a set of proteins resided within 6 localizations collected from the Nuclear Protein Database (NPD). The overall MCC (accuracy) is elevated from 0.284 (50.0%) to 0.519 (66.5%) for single-localization proteins in leave-one-out cross-validation; and from 0.420 (65.2%) to 0.541 (65.2%) for an independent set of multi-localization proteins. The new system is available at . CONCLUSION: The prediction of protein subnuclear localizations can be largely influenced by various definitions of similarity for a pair of proteins based on different similarity measures of GO terms. Using the sum of similarity scores over the matched GO term pairs for two proteins as the similarity definition produced the best predictive outcome. Substantial improvement in predicting protein subnuclear localizations has been achieved by combining Gene Ontology with sequence information

Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrients

The systematic review demonstrates that the IM plays a major role in the breakdown and transformation of the dietary substrates examined. However, recent human data are limited with the exception of data from studies examining fibres and polyphenols. Results observed in relation with dietary substrates were not always consistent or coherent across studies and methodological limitations and differences in IM analyses made comparisons difficult. Moreover, non-digestible components likely to reach the colon are often not well defined or characterised in studies making comparisons between studies difficult if not impossible. Going forward, further rigorously controlled randomised human trials with well-defined dietary substrates and utilizing omic-based technologies to characterise and measure the IM and their functional activities will advance the field. Current evidence suggests that more detailed knowledge of the metabolic activities and interactions of the IM hold considerable promise in relation with host health

Autistic Disorder in Patients with Williams-Beuren Syndrome: A Reconsideration of the Williams-Beuren Syndrome Phenotype

International audienceBackground: Williams-Beuren syndrome (WBS), a rare developmental disorder caused by deletion of contiguous genes at 7q11.23, has been characterized by strengths in socialization (overfriendliness) and communication (excessive talkativeness). WBS has been often considered as the polar opposite behavioral phenotype to autism. Our objective was to better understand the range of phenotypic expression in WBS and the relationship between WBS and autistic disorder. Methodology: The study was conducted on 9 French individuals aged from 4 to 37 years old with autistic disorder associated with WBS. Behavioral assessments were performed using Autism Diagnostic Interview-Revised (ADI-R) and Autism Diagnostic Observation Schedule (ADOS) scales. Molecular characterization of the WBS critical region was performed by FISH. Findings: FISH analysis indicated that all 9 patients displayed the common WBS deletion. All 9 patients met ADI-R and ADOS diagnostic criteria for autism, displaying stereotypies and severe impairments in social interaction and communication (including the absence of expressive language). Additionally, patients showed improvement in social communication over time. Conclusions: The results indicate that comorbid autism and WBS is more frequent than expected and suggest that the common WBS deletion can result in a continuum of social communication impairment, ranging from excessive talkativeness and overfriendliness to absence of verbal language and poor social relationships. Appreciation of the possible co-occurrence of WBS and autism challenges the common view that WBS represents the opposite behavioral phenotype of autism, and might lead to improved recognition of WBS in individuals diagnosed with autism

Case Report - Isolated submandibular gland metastasis from an occult papillary thyroid cancer

A case of an isolated submandibular gland metastasis from a clinically occult papillary thyroid carcinoma is described in a 46-year old lady. Initial surgery was done based on the fine needle aspiration cytology (FNAC) report of adenocarcinoma of the submandibular gland. Histopathologic examination of the specimen suggested a metastatic papillary carcinoma. Occult papillary carcinoma in the thyroid was found by multiple blind FNACs. Subsequently to near-total thyroidectomy, no other site of metastasis was found on radio-iodine scanning

Tubularized incised plate urethroplasty with de-epithelialized flap

Aim: To improve the results of tubularized plate urethroplasty by adding de-epithelized flap. Patients and Methods: Twenty-five cases of hypospadias who underwent Snodgrass urethroplasty using de-epithelialized flap were studied. The minimum period of follow-up in this series was 1 year. Results: The resultant neo-meatus was vertically oriented and slit like. Glans was conical which is cosmetically well accepted. Penile raphe was in the midline. None of the patient had residual chordee, penile torsion, or glans dehiscence. Excellent cosmetic results were observed in all cases. The complication rate in our series was 8% (two cases). Two patients developed fistula. Conclusion: De-epithelialized flap is a simple method to provide additional covering to the constructed neourethra after Snodgrass urethroplasty. It achieves our goal of noncrossing suture lines and providing maximum vascularity.African Journal of Paediatric Surgery Vol. 5 (1) 2008: pp. 8-1