Reconstruction of Cellular Signal Transduction Networks Using Perturbation Assays and Linear Programming

Perturbation experiments for example using RNA interference (RNAi) offer an attractive way to elucidate gene function in a high throughput fashion. The placement of hit genes in their functional context and the inference of underlying networks from such data, however, are challenging tasks. One of the problems in network inference is the exponential number of possible network topologies for a given number of genes. Here, we introduce a novel mathematical approach to address this question. We formulate network inference as a linear optimization problem, which can be solved efficiently even for large-scale systems. We use simulated data to evaluate our approach, and show improved performance in particular on larger networks over state-of-the art methods. We achieve increased sensitivity and specificity, as well as a significant reduction in computing time. Furthermore, we show superior performance on noisy data. We then apply our approach to study the intracellular signaling of human primary nave CD4⁺ T-cells, as well as ErbB signaling in trastuzumab resistant breast cancer cells. In both cases, our approach recovers known interactions and points to additional relevant processes. In ErbB signaling, our results predict an important role of negative and positive feedback in controlling the cell cycle progression.     

Enhancement of iodinin solubility by encapsulation into cyclodextrin nanoparticles

Phenazine is known to regroup planar nitrogen-containing heterocyclic compounds. It was used here to enhance the bioavailability of the biologically important compound iodinin, which is near insoluble in aqueous solutions. Its water solubility has led to the development of new formulations using diverse amphiphilic α-cyclodextrins (CDs). With the per-[6-desoxy-6-(3-perfluorohexylpropanethio)-2,3-di-O-methyl]-α-CD, we succeeded to get iodinin-loaded nanoformulations with good parameters such as a size of 97.9?nm, 62% encapsulation efficiency and efficient control release. The study presents an interesting alternative to optimizing the water solubility of iodinin by chemical modifications of iodinin.     

Targeted and global pharmacometabolomics in everolimus-based immunosuppression: association of co-medication and lysophosphatidylcholines with dose requirement

Introduction

The immunosuppressive therapy with everolimus (ERL) after heart transplantation is characterized by a narrow therapeutic window and a substantial variability in dose requirement. Factors explaining this variability are largely unknown.

Objectives

Our aim was to evaluate factors affecting ERL metabolism and to identify novel metabolites associated with the individual ERL dose requirement to elucidate mechanisms underlying ERL dose response variability.

Method

We used liquid chromatography coupled with mass spectrometry for quantification of ERL metabolites in 41 heart transplant patients and evaluated the effect of clinical and genetic factors on ERL pharmacokinetics. Non-targeted plasma metabolic profiling by ultra-performance liquid chromatography and high resolution quadrupole-time-of-flight mass spectrometry was used to identify novel metabolites associated with ERL dose requirement.

Results

The determination of ERL metabolites revealed differences in metabolite patterns that were independent from clinical or genetic factors. Whereas higher ERL dose requirement was associated with co-administration of sodium-mycophenolic acid and the CYP3A5 expressor genotype, lower dose was required for patients receiving vitamin K antagonists. Global metabolic profiling revealed several novel metabolites associated with ERL dose requirement. One of them was identified as lysophosphatidylcholine (lysoPC) (16:0/0:0). Subsequent targeted analysis revealed that high levels of several lysoPCs were significantly associated with higher ERL dose requirement.

Conclusion

For the first time, this study describes distinct ERL metabolite patterns in heart transplant patients and detected potentially new drug–drug interactions. The global metabolic profiling facilitated the discovery of novel metabolites associated with ERL dose requirement that might represent new clinically valuable biomarkers to guide ERL therapy.

     

Life cycle inventory modeling of phosphorus substitution,losses and crop uptake after land application of organic waste products

Purpose

Life cycle assessments (LCAs) that attempt to provide advice on treatment options for phosphorus (P) containing organic waste products encounter problems related to the quantification of mineral P fertilizer substitution, P loss and crop P uptake after land application. The purpose of this study was to develop a relatively easy to use life cycle inventory model, known as PLCI, that could be used to estimate these values.

Methods

A life cycle inventory model for P was developed, which estimates the effect of an application of organic waste followed by ordinary fertilizer management in the modeling period. This was compared with a simulation without the initial waste application. The difference in mineral P fertilizer application (substitution), P loss and crop P uptake was then calculated and expressed as a proportion of the amount of waste applied. As an example, the effect of an initial application of mineral fertilizer, sewage sludge and ash on two farm types was simulated. These results were applied in an LCA case study of different sewage sludge treatment options.

Results and discussion

Farm type influenced the P fertilizer substitution, loss and crop uptake factors. The application on an arable farm showed a substitution of 28 to 31%, relatively low P loss and a large spread in crop P uptake for the different P sources, compared with the pig farm. Application on a pig farm showed no mineral P substitution. For substitution, mineral fertilizer outperformed waste product fertilizer with a short modeling period, due to higher immediate P availability, which was not the case with a long period. The LCA case study showed that the P substitution factor had an influence on the environmental impact categories climate change and depletion of reserve-based abiotic resources while the P loss factor influenced freshwater eutrophication. Application of the P loss and substitution factors generated from the PLCI model resulted in higher environmental burdens and lower savings than using conventional factors.

Conclusions

The soil P status mainly affected P substitution and loss, with the fertilizer type only having a small influence when soils had a low P status. The PLCI model can facilitate more coherent and rigorous estimates of P substitution and loss to be used in LCA studies involving application of waste products on agricultural land. This is important since P substitution and loss can have an important influence on impact categories, such as freshwater eutrophication and resource depletion.

     

Rearing environment influences boldness and prey acquisition behavior,and brain and lens development of bull trout

Animals reared in barren captive environments exhibit different developmental trajectories and behaviors than wild counterparts. Hence, the captive phenotypes may influence the success of reintroduction and recovery programs for threatened and endangered species. We collected wild bull trout embryos from the Metolius River Basin, Oregon and reared them in differing environments to better understand how captivity affects the bull trout Salvelinus confluentus phenotype. We compared the boldness and prey acquisition behaviors and development of the brain and eye lens of bull trout reared in conventional barren and more structurally complex captive environments with that of wild fish. Wild fish and captive reared fish from complex habitats exhibited a greater level of boldness and prey acquisition ability, than fish reared in conventional captive environments. In addition, the eye lens of conventionally reared bull trout was larger than complex reared captive fish or same age wild fish. Interestingly, we detected wild fish had a smaller relative cerebellum than either captive reared treatment. Our results suggest that rearing fish in more complex captive environments can create a more wild-like phenotype than conventional rearing practices. A better understanding of the effects of captivity on the development and behavior of bull trout can inform rearing and reintroduction programs though prediction of the performance of released individuals.     

A realist process evaluation within the Facilitating Implementation of Research Evidence (FIRE) cluster randomised controlled international trial: an exemplar

Background

Facilitation is a promising implementation intervention, which requires theory-informed evaluation. This paper presents an exemplar of a multi-country realist process evaluation that was embedded in the first international randomised controlled trial evaluating two types of facilitation for implementing urinary continence care recommendations. We aimed to uncover what worked (and did not work), for whom, how, why and in what circumstances during the process of implementing the facilitation interventions in practice.

Methods

This realist process evaluation included theory formulation, theory testing and refining. Data were collected in 24 care home sites across four European countries. Data were collected over four time points using multiple qualitative methods: observation (372 h), interviews with staff (n?=?357), residents (n?=?152), next of kin (n?=?109) and other stakeholders (n?=?128), supplemented by facilitator activity logs. A combined inductive and deductive data analysis process focused on realist theory refinement and testing.

Results

The content and approach of the two facilitation programmes prompted variable opportunities to align and realign support with the needs and expectations of facilitators and homes. This influenced their level of confidence in fulfilling the facilitator role and ability to deliver the intervention as planned. The success of intervention implementation was largely dependent on whether sites prioritised their involvement in both the study and the facilitation programme. In contexts where the study was prioritised (including release of resources) and where managers and staff support was sustained, this prompted collective engagement (as an attitude and action). Internal facilitators’ (IF) personal characteristics and abilities, including personal and formal authority, in combination with a supportive environment prompted by managers triggered the potential for learning over time. Learning over time resulted in a sense of confidence and personal growth, and enactment of the facilitation role, which resulted in practice changes.

Conclusion

The scale and multi-country nature of this study provided a novel context to conduct one of the few trial embedded realist-informed process evaluations. In addition to providing an explanatory account of implementation processes, a conceptual platform for future facilitation research is presented. Finally, a realist-informed process evaluation framework is outlined, which could inform future research of this nature.

Trial registration

Current controlled trials ISRCTN11598502.