Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection.

Understanding the structure and function of complex gene regulatory networks using classical genetic assays is an error-prone procedure that frequently generates ambiguous outcomes. Even some of the best-characterized gene networks contain interactions whose validity is not conclusively proven. Founded on dynamic experimental data, mechanistic mathematical models are able to offer detailed insights that would otherwise require prohibitively large numbers of genetic experiments. Here we attempt mechanistic modeling of the transcriptional network formed by the four GATA-factor proteins, a well-studied system of central importance for nitrogen-source regulation of transcription in the yeast Saccharomyces cerevisiae. To resolve ambiguities in the network organization, we encoded a set of five interactions hypothesized in the literature into a set of 32 mathematical models, and employed Bayesian model selection to identify the most plausible set of interactions based on dynamic gene expression data. The top-ranking model was validated on newly generated GFP reporter dynamic data and was subsequently used to gain a better understanding of how yeast cells organize their transcriptional response to dynamic changes of nitrogen sources. Our work constitutes a necessary and important step towards obtaining a holistic view of the yeast nitrogen regulation mechanisms; on the computational side, it provides a demonstration of how powerful Monte Carlo techniques can be creatively combined and used to address the great challenges of large-scale dynamical system inference.

Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome.

Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system-wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi-level dynamic data remains challenging. Here, we co-designed dynamic experiments and a probabilistic, model-based method to infer causal relationships between metabolism, signaling, and gene regulation. We analyzed the dynamic regulation of nitrogen metabolism by the target of rapamycin complex 1 (TORC1) pathway in budding yeast. Dynamic transcriptomic, proteomic, and metabolomic measurements along shifts in nitrogen quality yielded a consistent dataset that demonstrated extensive re-wiring of cellular networks during adaptation. Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.

Helping networks in community home care for the elderly: types of team.

Changes in the delivery of health care have led to a shift in the location of care from the institution to the community. This has resulted in a need to re-examine current models of health-care practice in terms of their applicability and relevance to the community setting. The purpose of this study was to determine the relevance of traditional models of multidisciplinary teams by examining interrelationships amongst community-dwelling seniors with arthritis, their families, and health and community service providers (HCSPs). In-depth interviews or focus groups were conducted with clients, family members, and HCSPs. Participants described 4 different types of interaction within the helping network, with no interaction whatsoever being the most common except for with the seniors themselves. Three types of team emerged: client-centred, case manager-centred, and discipline-specific. No evidence of formal collaborative interdisciplinary teams was found, with HCSPs most valuing the discipline-specific model.

The development of a helpline for chronic obstructive pulmonary disease (COPD).

BACKGROUND: The goal of the helpline is to assist individuals with chronic obstructive pulmonary disease (COPD) better manage their disease through improved understanding of COPD, its symptoms and treatment. OBJECTIVES: The purpose of this project was to develop and validate a protocol for a COPD helpline. METHODS: Ten key informants with expertise in helpline development or COPD were interviewed. Fifty individuals with COPD participated in content validation of the protocol. RESULTS: An initial protocol for the helpline aimed to provide: (1) information and education regarding COPD and its management via the telephone and with written materials; (2) guidance regarding course of management; (3) resource links to other support services and programs locally, provincially, and/or nationally; and (4) caring support and reassurance to those with COPD and their families. The majority of the calls from individuals with COPD sought medical information (74%) and required 36.6 +/- 14.5 min (range: 15-85) to complete. Many different topics were discussed, with medication and exercise being the most common. The availability of the call center was identified as one means of replacing information sought from other health care providers, mainly physicians and pulmonary rehabilitation staff. CONCLUSION: A protocol of a helpline for COPD has been developed based on the literature, theoretical knowledge, and input from key informants and individuals with COPD.

Adaptation to disability in chronic obstructive pulmonary disease: neglected relationships to older adults' perceptions of independence.

PURPOSE: This study extends understanding of the relationship between disability and independence in older adults with COPD. METHODS: An interviewer-administered questionnaire was used to examine disability, adaptation, perceptions of independence, and self-efficacy in a sample of 50 community-dwelling older adults. Odds ratios were used to investigate relationships between variables. RESULTS: Participants used a wide range of behavioural strategies to adapt to their disability including: limiting activities, optimizing performance (e.g. taking rests), compensating for lost function (e.g. using equipment), and obtaining help from others. The relative use of these adaptations varied across five domains of activity: personal care, in-home mobility, household activities, community mobility, and valued activities. Most participants felt very or extremely independent in all domains. In personal care, those who reported greater disability (O.R. = 0.26), more frequent attempts to optimize performance (O.R. = 0.57), or greater reliance on help from others (O.R. = 0.79) were significantly (p < 0.05) less likely to feel very or extremely independent. CONCLUSIONS: The relationship between disability and perceptions of independence depends on the nature of the activity and is influenced by factors that are amenable to study and intervention. In particular, the vast array of behavioural strategies available to older adults with COPD enables them to feel highly independent despite disability.

The S. Typhimurium effector SopE induces caspase-1 activation in stromal cells to initiate gut inflammation.

In the healthy intestinal mucosa, homeostasis between the immune system and commensal microflora prevents detrimental inflammatory responses. Infection with acute enteropathogens such as Salmonella enterica serovar Typhimurium disturbs this homeostasis and triggers inflammation, but the underlying mechanisms are poorly understood. We found that bacterial delivery or ectopic expression of the S. Typhimurium type III effector protein SopE, a known activator of host cellular Rho GTPases, led to proinflammatory caspase-1 activation and consequent maturation and secretion of the cytokine IL-1beta. In vivo, SopE triggered mucosal inflammation in wild-type but not caspase-1(-/-), IL-1R(-/-), or IL-18(-/-) mice. Bone marrow chimeras indicated that caspase-1 was more important in stromal cells, most likely enterocytes, than in bone marrow-derived cells. SopE-mediated caspase-1 activation in vitro was mediated by cellular Rho GTPases Rac-1 and Cdc42. These findings implicate SopE-driven Rho GTPase-mediated caspase-1 activation in stromal cells as a mechanism eliciting mucosal inflammation during S. Typhimurium infection.