Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus

Chronic disease risk factors associated with health service use in the elderly

<p>Abstract</p> <p>Background</p> <p>To examine the association between number and combination of chronic disease risk factors on health service use.</p> <p>Methods</p> <p>Data from the 1995 Nova Scotia Health Survey (n = 2,653) was linked to provincial health services administrative databases. Multivariate regression models were developed that included important interactions between risk factors and were stratified by sex and at age 50. Negative-binomial regression models were estimated using generalized estimating equations assuming an autoregressive covariance structure.</p> <p>Results</p> <p>As the number of chronic disease risk factors increased so did the number of annual general practitioner visits, specialist visits and days spent in hospital in people aged 50 and older. This was not seen among individuals under age 50. Comparison of smokers, people with high blood pressure and people with high cholesterol showed no significantly different impact on health service use.</p> <p>Conclusion</p> <p>As the number of chronic disease risk factors increased so did health service use among individuals over age 50 but risk factor combination had no impact.</p

Dose-Response Aligned Circuits in Signaling Systems

Cells use biological signal transduction pathways to respond to environmental stimuli and the behavior of many cell types depends on precise sensing and transmission of external information. A notable property of signal transduction that was characterized in the Saccharomyces cerevisiae yeast cell and many mammalian cells is the alignment of dose-response curves. It was found that the dose response of the receptor matches closely the dose responses of the downstream. This dose-response alignment (DoRA) renders equal sensitivities and concordant responses in different parts of signaling system and guarantees a faithful information transmission. The experimental observations raise interesting questions about the nature of the information transmission through DoRA signaling networks and design principles of signaling systems with this function. Here, we performed an exhaustive computational analysis on network architectures that underlie the DoRA function in simple regulatory networks composed of two and three enzymes. The minimal circuits capable of DoRA were examined with Michaelis-Menten kinetics. Several motifs that are essential for the dynamical function of DoRA were identified. Systematic analysis of the topology space of robust DoRA circuits revealed that, rather than fine-tuning the network's parameters, the function is primarily realized by enzymatic regulations on the controlled node that are constrained in limiting regions of saturation or linearity

The Prostate Care Questionnaire for Patients (PCQ-P): Reliability, validity and acceptability

<p>Abstract</p> <p>Background</p> <p>In England, prostate cancer patients report worse experience of care than patients with other cancers. However, no standard measure of patient experience of prostate cancer care is currently available. This paper describes an evaluation of the reliability, validity and acceptability of the PCQ-P, a newly developed instrument designed to measure patient experience of prostate cancer care.</p> <p>Methods</p> <p>The reliability, acceptability and validity of the PCQ-P were tested through a postal survey and interviews with patients. The PCQ-P was posted to 1087 prostate cancer patients varying in age, occupation, and overall health status, sampled from five hospitals in England. Nonresponders received one reminder. To assess criterion validity, 935 patients were also sent sections of the National Centre for Social Research Shortened Questionnaire; and to assess test-retest reliability, 296 patients who responded to the questionnaire were resent it a second time three weeks later. A subsample of 20 prostate cancer patients from one hospital took part in qualitative interviews to assess validity and acceptability of the PCQ-P. Acceptability to service providers was evaluated based on four hospitals' experiences of running a survey using the PCQ-P.</p> <p>Results</p> <p>Questionnaires were returned by 865 patients (69.2%). Missing data was low across the sections, with the proportion of patients completing less than 50% of each section ranging from 4.5% to 6.9%. Across the sections of the questionnaire, internal consistency was moderate to high (Cronbach's alpha ranging from 0.63 to 0.80), and test-retest stability was acceptable (intraclass correlation coefficients ranging from 0.57 to 0.73). Findings on criterion validity were significant. Patient interviews indicated that the PCQ-P had high face validity and acceptability. Feedback from hospitals indicated that they found the questionnaire useful, and highlighted important considerations for its future use as part of quality improvement initiatives.</p> <p>Conclusion</p> <p>The PCQ-P has been found to be acceptable to patients and service providers, and is ready for use for the measurement of patient experience in routine practice, service improvement programmes, and research.</p

Membrane Recruitment of Scaffold Proteins Drives Specific Signaling

Cells must give the right response to each stimulus they receive. Scaffolding, a signaling process mediated by scaffold proteins, participates in the decoding of the cues by specifically directing signal transduction. The aim of this paper is to describe the molecular mechanisms of scaffolding, i.e. the principles by which scaffold proteins drive a specific response of the cell. Since similar scaffold proteins are found in many species, they evolved according to the purpose of each organism. This means they require adaptability. In the usual description of the mechanisms of scaffolding, scaffold proteins are considered as reactors where molecules involved in a cascade of reactions are simultaneously bound with the right orientation to meet and interact. This description is not realistic: (i) it is not verified by experiments and (ii) timing and orientation constraints make it complex which seems to contradict the required adaptability. A scaffold protein, Ste5, is used in the MAPK pathway of Saccharomyces Cerevisiae for the cell to provide a specific response to stimuli. The massive amount of data available for this pathway makes it ideal to investigate the actual mechanisms of scaffolding. Here, a complete treatment of the chemical reactions allows the computation of the distributions of all the proteins involved in the MAPK pathway when the cell receives various cues. These distributions are compared to several experimental results. It turns out that the molecular mechanisms of scaffolding are much simpler and more adaptable than previously thought in the reactor model. Scaffold proteins bind only one molecule at a time. Then, their membrane recruitment automatically drives specific, amplified and localized signal transductions. The mechanisms presented here, which explain how the membrane recruitment of a protein can produce a drastic change in the activity of cells, are generic and may be commonly used in many biological processes

Time-Lapse Imaging of the Dynamics of CNS Glial-Axonal Interactions In Vitro and Ex Vivo

Myelination is an exquisite and dynamic example of heterologous cell-cell interaction, which consists of the concentric wrapping of multiple layers of oligodendrocyte membrane around neuronal axons. Understanding the mechanism by which oligodendrocytes ensheath axons may bring us closer to designing strategies to promote remyelination in demyelinating diseases. The main aim of this study was to follow glial-axonal interactions over time both in vitro and ex vivo to visualize the various stages of myelination.We took two approaches to follow myelination over time: i) time-lapse imaging of mixed CNS myelinating cultures generated from mouse spinal cord to which exogenous GFP-labelled murine cells were added, and ii) ex vivo imaging of the spinal cord of shiverer (Mbp mutant) mice, transplanted with GFP-labelled murine neurospheres. We demonstrate that oligodendrocyte-axonal interactions are dynamic events with continuous retraction and extension of oligodendroglial processes. Using cytoplasmic and membrane-GFP labelled cells to examine different components of the myelin-like sheath, we provide evidence from time-lapse fluorescence microscopy and confocal microscopy that the oligodendrocytes' cytoplasm-filled processes initially spiral around the axon in a corkscrew-like manner. This is followed subsequently by focal expansion of the corkscrew process to form short cuffs, which then extend longitudinally along the axons. We predict from this model that these spiral cuffs must extend over each other first before extending to form internodes of myelin.These experiments show the feasibility of visualizing the dynamics of glial-axonal interaction during myelination over time. Moreover, these approaches complement each other with the in vitro approach allowing visualization of an entire internodal length of myelin and the ex vivo approach validating the in vitro data

Reversal of aberrant cancer methylome and transcriptome upon direct reprogramming of lung cancer cells

10.1038/srep00592Scientific Reports2

Survivors of intensive care with type 2 diabetes and the effect of shared care follow-up clinics: study protocol for the SWEET-AS randomised controlled feasibility study

Published online: 13 October 2016Background: Many patients who survive the intensive care unit (ICU) experience long-term complications such as peripheral neuropathy and nephropathy which represent a major source of morbidity and affect quality of life adversely. Similar pathophysiological processes occur frequently in ambulant patients with diabetes mellitus who have never been critically ill. Some 25 % of all adult ICU patients have diabetes, and it is plausible that ICU survivors with co-existing diabetes are at heightened risk of sequelae from their critical illness. ICU follow-up clinics are being progressively implemented based on the concept that interventions provided in these clinics will alleviate the burdens of survivorship. However, there is only limited information about their outcomes. The few existing studies have utilised the expertise of healthcare professionals primarily trained in intensive care and evaluated heterogenous cohorts. A shared care model with an intensivist- and diabetologist-led clinic for ICU survivors with type 2 diabetes represents a novel targeted approach that has not been evaluated previously. Prior to undertaking any definitive study, it is essential to establish the feasibility of this intervention. Methods: This will be a prospective, randomised, parallel, open-label feasibility study. Eligible patients will be approached before ICU discharge and randomised to the intervention (attending a shared care follow-up clinic 1 month after hospital discharge) or standard care. At each clinic visit, patients will be assessed independently by both an intensivist and a diabetologist who will provide screening and targeted interventions. Six months after discharge, all patients will be assessed by blinded assessors for glycated haemoglobin, peripheral neuropathy, cardiovascular autonomic neuropathy, nephropathy, quality of life, frailty, employment and healthcare utilisation. The primary outcome of this study will be the recruitment and retention at 6 months of all eligible patients. Discussion: This study will provide preliminary data about the potential effects of critical illness on chronic glucose metabolism, the prevalence of microvascular complications, and the impact on healthcare utilisation and quality of life in intensive care survivors with type 2 diabetes. If feasibility is established and point estimates are indicative of benefit, funding will be sought for a larger, multi-centre study. Trial registration: ANZCTR ACTRN12616000206426Yasmine Ali Abdelhamid, Liza Phillips, Michael Horowitz and Adam Dean

Hospitalizations for acetaminophen overdose: a Canadian population-based study from 1995 to 2004

<p>Abstract</p> <p>Background</p> <p>Acetaminophen overdose (AO) is the most common cause of acute liver failure. We examined temporal trends and sociodemographic risk factors for AO in a large Canadian health region.</p> <p>Methods</p> <p>1,543 patients hospitalized for AO in the Calgary Health Region (population ~1.1 million) between 1995 and 2004 were identified using administrative data.</p> <p>Results</p> <p>The age/sex-adjusted hospitalization rate decreased by 41% from 19.6 per 100,000 population in 1995 to 12.1 per 100,000 in 2004 (<it>P </it>< 0.0005). This decline was greater in females than males (46% vs. 29%). Whereas rates fell 46% in individuals under 50 years, a 50% increase was seen in those ≥ 50 years. Hospitalization rates for intentional overdoses fell from 16.6 per 100,000 in 1995 to 8.6 per 100,000 in 2004 (2004 vs. 1995: rate ratio [RR] 0.49; <it>P </it>< 0.0005). Accidental overdoses decreased between 1995 and 2002, but increased to above baseline levels by 2004 (2004 vs. 1995: RR 1.24;<it>P </it>< 0.0005). Risk factors for AO included female sex (RR 2.19; <it>P </it>< 0.0005), Aboriginal status (RR 4.04; <it>P </it>< 0.0005), and receipt of social assistance (RR 5.15; <it>P </it>< 0.0005).</p> <p>Conclusion</p> <p>Hospitalization rates for AO, particularly intentional ingestions, have fallen in our Canadian health region between 1995 and 2004. Young patients, especially females, Aboriginals, and recipients of social assistance, are at highest risk.</p