Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma

BACKGROUND: Rhabdomyosarcoma is a relatively common tumour of the soft tissue, probably due to regulatory disruption of growth and differentiation of skeletal muscle stem cells. Identification of genes differentially expressed in normal skeletal muscle and in rhabdomyosarcoma may help in understanding mechanisms of tumour development, in discovering diagnostic and prognostic markers and in identifying novel targets for drug therapy. RESULTS: A Perl-code web client was developed to automatically obtain genome map positions of large sets of genes. The software, based on automatic search on Human Genome Browser by sequence alignment, only requires availability of a single transcribed sequence for each gene. In this way, we obtained tissue-specific chromosomal maps of genes expressed in rhabdomyosarcoma or skeletal muscle. Subsequently, Perl software was developed to calculate gene density along chromosomes, by using a sliding window. Thirty-three chromosomal regions harbouring genes mostly expressed in rhabdomyosarcoma were identified. Similarly, 48 chromosomal regions were detected including genes possibly related to function of differentiated skeletal muscle, but silenced in rhabdomyosarcoma. CONCLUSION: In this study we developed a method and the associated software for the comparative analysis of genomic expression in tissues and we identified chromosomal segments showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma, appearing as candidate regions for harbouring genes involved in origin of alveolar rhabdomyosarcoma representing possible targets for drug treatment and/or development of tumor markers

REEF: searching REgionally Enriched Features in genomes

BACKGROUND: In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. RESULTS: REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at . CONCLUSION: REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role

A multistep bioinformatic approach detects putative regulatory elements in gene promoters

BACKGROUND: Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs. RESULTS: Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of them are localized in the proximal portion of promoters, less variable in central region than in lateral regions and similar to known regulatory sequences. COOP software and reference manual are freely available upon request to the Authors. CONCLUSION: The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role

Proposta de um PSS para um sistema de compartilhamento de bicicletas na UFSC utilizando a gestão da qualidade

Problemas relacionados ao trânsito são um inconveniente para muitas cidades, e essa situação tende a piorar quando envolve locais com grande concentração de pessoas. Na Universidade Federal de Santa Catarina – UFSC o fluxo de veículos aos redores tem sido um problema para frequentadores do local. PSS (Product-Service System - Sistema Produto-Serviço) são sistemas de negócio que unem produtos e serviços visando ofertar um valor diferenciado aos clientes. Este trabalho tem como objetivo apresentar uma proposta de PSS para compartilhamento de bicicletas dentro da UFSC utilizando técnicas de gestão da qualidade, e visando oferecer aos clientes um meio de transporte sustentável. Foram levantadas informações sobre a universidade, sugerido um ciclo PDCA (Plan, Do, Check, Action – Planejar, Executar, Verificar, Agir) e identificadas propostas de melhoria dentro da abordagem gestão da qualidade. O uso da gestão da qualidade, com a identificação de alguns pontos fortes e fracos, mostrou a possível viabilidade de um projeto piloto com quantidade reduzida de bicicletas, auxilio de um aplicativo, e gratuidade na utilização do sistema por alunos e servidore

Toward the Development of a Hybrid Active and Measuring Exoskeleton for Upper Limbs of Heavy-duty Harbor Workers

The paper presents the study of a novel exoskeleton designed for the upper limbs of heavy-duty port operators responsible for lashing containers. This exoskeleton is designed to measure initially its configuration and operational times, once positioned on the workers, to pass to a partial activeness introducing motors for the shoulder, the intra-extra rotation of the forearm, and the elbow. The key concept revolves around the shoulder joint, with particular emphasis on the scapula and its motion. The scapula plays a fundamental role in moving the center of rotation of the humerus, contributing to its exceptional mobility. The fundamental objective is to develop a system that provides support for the vertical motion of the operator's arms, with a specific focus on allowing initially the vertical motion of the scapula to remain unrestricted. This approach aims to collect essential data, which, in a subsequent phase, will likely enable the addition of vertical support to the scapula, possibly with the assistance of AI. Meanwhile, the horizontal motion will consistently be left unrestricted. This exoskeleton design is inspired by previous work that conceptualized a fully measuring exoskeleton, and a corresponding patent application has been presented

A new locus for arrhythmogenic right ventricular cardiomyopathy (ARVD2) maps to chromosome 1q42-q43

Autosomal dominant arrhythmogenic right ventricular cardiomyopathy (ARVD, MIM 107970) is one of the major causes of juvenile sudden death. We have previously assigned the disease locus to chromosome 14q23-q24. Here we report on a novel variant of ARVD, which is transmitted associated to 1q42-q43 and is characterized by a concealed form, showing effort-induced polymorphic tachycardias. Since both loci ARVD1 and ARVD2 map in proximity of a-actinin genes, the possible implication of these myofibrillar proteins in the pathogenesis of ARVD is discussed. Two additional ARVD families, tested with markers of chromosomes 1q42-q43 and 14q23-q24, failed to show linkage, providing evidence of further genetic heterogeneit

Genomic expression during human myelopoiesis

<p>Abstract</p> <p>Background</p> <p>Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization.</p> <p>Results</p> <p>Gene expression data from 24 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset of 9,425 genes, each reliably associated to a unique genomic position and chromosomal coordinate. Lists of genes constitutively expressed or silent during myelopoiesis and of genes differentially expressed in commitment phase of myelopoiesis were first identified using a classical data analysis procedure. Then, the genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. This approach allowed identifying specific chromosomal regions significantly highly or weakly expressed, and clusters of differentially expressed genes and of transcripts related to specific functional modules.</p> <p>Conclusion</p> <p>The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.</p