Boolean dynamics revisited through feedback interconnections

Boolean models of physical or biological systems describe the global dynamics of the system and their attractors typically represent asymptotic behaviors. In the case of large networks composed of several modules, it may be difficult to identify all the attractors. To explore Boolean dynamics from a novel viewpoint, we will analyse the dynamics emerging from the composition of two known Boolean modules. The state transition graphs and attractors for each of the modules can be combined to construct a new asymptotic graph which will (1) provide a reliable method for attractor computation with partial information; (2) illustrate the differences in dynamical behavior induced by the updating strategy (asynchronous, synchronous, or mixed); and (3) show the inherited organization/structure of the original network’s state transition graph.publishe

Hidden heterochromatin: Characterization in the Rodentia species Cricetus cricetus, Peromyscus eremicus (Cricetidae) and Praomys tullbergi (Muridae)

The use of in situ restriction endonuclease (RE) (which cleaves DNA at specific sequences) digestion has proven to be a useful technique in improving the dissection of constitutive heterochromatin (CH), and in the understanding of the CH evolution in different genomes. In the present work we describe in detail the CH of the three Rodentia species, Cricetus cricetus, Peromyscus eremicus (family Cricetidae) and Praomys tullbergi (family Muridae) using a panel of seven REs followed by C-banding. Comparison of the amount, distribution and molecular nature of C-positive heterochromatin revealed molecular heterogeneity in the heterochromatin of the three species. The large number of subclasses of CH identified in Praomys tullbergi chromosomes indicated that the karyotype of this species is the more derived when compared with the other two genomes analyzed, probably originated by a great number of complex chromosomal rearrangements. The high level of sequence heterogeneity identified in the CH of the three genomes suggests the coexistence of different satellite DNA families, or variants of these families in these genomes

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy

Background -- The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. Results -- Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org. Conclusions -- Because it uses novel mapping algorithms VISMapper is remarkably faster than previous available programs. It also provides a useful graphical interface to analyze the integration sites found in the genomic context

A comparative study of qualitative and quantitative dynamic models of biological regulatory networks

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Assessing health centre systems for guiding improvement in diabetes care

BACKGROUND: Aboriginal people in Australia experience the highest prevalence of diabetes in the country, an excess of preventable complications and early death. There is increasing evidence demonstrating the importance of healthcare systems for improvement of chronic illness care. The aims of this study were to assess the status of systems for chronic illness care in Aboriginal community health centres, and to explore whether more developed systems were associated with better quality of diabetes care. METHODS: This cross-sectional study was conducted in 12 Aboriginal community health centres in the Northern Territory of Australia. Assessment of Chronic Illness Care scale was adapted to measure system development in health centres, and administered by interview with health centre staff and managers. Based on a random sample of 295 clinical records from attending clients with diagnosed type 2 diabetes, processes of diabetes care were measured by rating of health service delivery against best-practice guidelines. Intermediate outcomes included the control of HbA1c, blood pressure, and total cholesterol. RESULTS: Health centre systems were in the low to mid-range of development and had distinct areas of strength and weakness. Four of the six system components were independently associated with quality of diabetes care: an increase of 1 unit of score for organisational influence, community linkages, and clinical information systems, respectively, was associated with 4.3%, 3.8%, and 4.5% improvement in adherence to process standards; likewise, organisational influence, delivery system design and clinical information systems were related to control of HbA1c, blood pressure, and total cholesterol. CONCLUSION: The state of development of health centre systems is reflected in quality of care outcome measures for patients. The health centre systems assessment tool should be useful in assessing and guiding development of systems for improvement of diabetes care in similar settings in Australia and internationally