NetEvo: A computational framework for the evolution of dynamical complex networks

NetEvo is a computational framework designed to help understand the evolution of dynamical complex networks. It provides flexible tools for the simulation of dynamical processes on networks and methods for the evolution of underlying topological structures. The concept of a supervisor is used to bring together both these aspects in a coherent way. It is the job of the supervisor to rewire the network topology and alter model parameters such that a user specified performance measure is minimised. This performance measure can make use of current topological information and simulated dynamical output from the system. Such an abstraction provides a suitable basis in which to study many outstanding questions related to complex system design and evolution

Assaying protein palmitoylation in plants

<p>Abstract</p> <p>Background</p> <p>Protein S-acylation (also known as palmitoylation) is the reversible post-translational addition of acyl lipids to cysteine residues in proteins through a thioester bond. It allows strong association with membranes. Whilst prediction methods for S-acylation exist, prediction is imperfect. Existing protocols for demonstrating the S-acylation of plant proteins are either laborious and time consuming or expensive.</p> <p>Results</p> <p>We describe a biotin switch method for assaying the S-acylation of plant proteins. We demonstrate the technique by showing that the heterotrimeric G protein subunit AGG2 is S-acylated as predicted by mutagenesis experiments. We also show that a proportion of the Arabidopsis alpha-tubulin subunit pool is S-acylated <it>in planta</it>. This may account for the observed membrane association of plant microtubules. As alpha-tubulins are ubiquitously expressed they can potentially be used as a positive control for the S-acylation assay regardless of the cell type under study.</p> <p>Conclusion</p> <p>We provide a robust biotin switch protocol that allows the rapid assay of protein S-acylation state in plants, using standard laboratory techniques and without the need for expensive or specialised equipment. We propose alpha-tubulin as a useful positive control for the protocol.</p

HEV in the pork food chain in United Kingdom

Hepatitis E virus (HEV) is responsible of acute viral hepatitis in people and it is endemic in developing countries where it is transmitted mainly through faecal contamination of drinking water. Some of the cases in developed countries are autochthonous

Towards an engineering theory of evolution

Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems

Adaptive statistical iterative reconstruction improves image quality without affecting perfusion CT quantitation in primary colorectal cancer

Objectives: To determine the effect of Adaptive Statistical Iterative Reconstruction (ASIR) on perfusion CT (pCT) parameter quantitation and image quality in primary colorectal cancer. Methods: Prospective observational study. Following institutional review board approval and informed consent, 32 patients with colorectal adenocarcinoma underwent pCT (100 kV, 150 mA, 120 s acquisition, axial mode). Tumour regional blood flow (BF), blood volume (BV), mean transit time (MTT) and permeability surface area product (PS) were determined using identical regions-of-interests for ASIR percentages of 0%, 20%, 40%, 60%, 80% and 100%. Image noise, contrast-to-noise ratio (CNR) and pCT parameters were assessed across ASIR percentages. Coefficients of variation (CV), repeated measures analysis of variance (rANOVA) and Spearmanâ rank order correlation were performed with statistical significance at 5%. Results: With increasing ASIR percentages, image noise decreased by 33% while CNR increased by 61%; peak tumour CNR was greater than 1.5 with 60% ASIR and above. Mean BF, BV, MTT and PS differed by less than 1.8%, 2.9%, 2.5% and 2.6% across ASIR percentages. CV were 4.9%, 4.2%, 3.3% and 7.9%; rANOVA P values: 0.85, 0.62, 0.02 and 0.81 respectively. Conclusions: ASIR improves image noise and CNR without altering pCT parameters substantially. Keywords: Perfusion imaging, Multidetector computed tomography, Colorectal neoplasms, Computer-assisted image processing, Radiation dosag

Circadian rhythmicity in emerging mood disorders: state or trait marker?

Background: Circadian rhythm disturbances overlap with the symptoms of mood episodes and may trigger or prolong mood symptoms. There is limited research on the role of circadian disturbances in mood disorders in young people and/or first episode cases of unipolar and bipolar disorders. Methods: Actigraphy was undertaken for about 14 days in 63 post-pubertal individuals aged 13–25 years with a recent onset of a mood disorder meeting recognised diagnostic criteria. We examined associations between three easily interpretable markers of circadian rhythm activity (amplitude, acrophase and rhythmicity index) and demography and clinical characteristics. Then, circadian markers were compared between diagnostic groups, controlling for potential confounders. Results: Longer duration of illness was correlated with reduced circadian rhythmicity and lower levels of activity over 24 h. A delay in the timing of maximum activity was associated with the level of manic but not depressive symptoms. The circadian rhythmicity index differentiated unipolar from bipolar cases, and in bipolar but not unipolar disorder, the rhythmicity was less robust in those with more severe manic or depressive symptoms. Conclusions: Less robust circadian rhythmicity, especially associated with increasing symptom severity, may represent a more specific or a trait marker of young people with mood disorders who are at higher risk of a bipolar course of illness

Understanding metabolic flux behaviour in whole-cell model output

Whole-cell modelling is a newly expanding field that has many applications in lab experiment design and predictive drug testing. Although whole-cell model output contains a wealth of information, it is complex and high dimensional and thus hard to interpret. Here, we present an analysis pipeline that combines machine learning, dimensionality reduction, and network analysis to interpret and visualise metabolic reaction fluxes from a set of single gene knockouts simulated in the Mycoplasma genitalium whole-cell model. We found that the reaction behaviours show trends that correlate with phenotypic classes of the simulation output, highlighting particular cellular subsystems that malfunction after gene knockouts. From a graphical representation of the metabolic network, we saw that there is a set of reactions that can be used as markers of a phenotypic class, showing their importance within the network. Our analysis pipeline can support the understanding of the complexity of in silico cells without detailed knowledge of the constituent parts, which can help to understand the effects of gene knockouts and, as whole-cell models become more widely built and used, aid genome design

Progenitors for the corneal endothelium and trabecular meshwork: a potential source for personalized stem cell therapy in corneal endothelial diseases and glaucoma

Several adult stem cell types have been found in different parts of the eye, including the corneal epithelium, conjunctiva, and retina. In addition to these, there have been accumulating evidence that some stem-like cells reside in the transition area between the peripheral corneal endothelium (CE) and the anterior nonfiltering portion of the trabecular meshwork (TM), which is known as the Schwalbe's Ring region. These stem/progenitor cells may supply new cells for the CE and TM. In fact, the CE and TM share certain similarities in terms of their embryonic origin and proliferative capacity in vivo. In this paper, we discuss the putative stem cell source which has the potential for replacement of lost and nonfunctional cells in CE diseases and glaucoma. The future development of personalized stem cell therapies for the CE and TM may reduce the requirement of corneal grafts and surgical treatments in glaucoma.published_or_final_versio

Small Amplitude Reciprocating Wear Performance of Diamond-like Carbon Films: Dependence of Film Composition and Counterface Material

Small amplitude (50 μm) reciprocating wear of hydrogen-containing diamond-like carbon (DLC) films of different compositions has been examined against silicon nitride and polymethyl-methacrylate (PMMA) counter-surfaces, and compared with the performance of an uncoated steel substrate. Three films were studied: a DLC film of conventional composition, a fluorine-containing DLC film (F-DLC), and silicon-containing DLC film. The films were deposited on steel substrates from plasmas of organic precursor gases using the Plasma Immersion Ion Implantation and Deposition (PIIID) process, which allows for the non-line-of-sight deposition of films with tailored compositions. The amplitude of the resistive frictional force during the reciprocating wear experiments was monitored in situ, and the magnitude of film damage due to wear was evaluated using optical microscopy, optical profilometry, and atomic force microscopy. Wear debris was analyzed using scanning electron microscopy and energy dispersive spectroscopy. In terms of friction, the DLC and silicon-containing DLC films performed exceptionally well, showing friction coefficients less than 0.1 for both PMMA and silicon nitride counter-surfaces. DLC and silicon-containing DLC films also showed significant reductions in transfer of PMMA compared with the uncoated steel. The softer F-DLC film performed similarly well against PMMA, but against silicon nitride, friction displayed nearly periodic variations indicative of cyclic adhesion and release of worn film material during the wear process. The results demonstrate that the PIIID films achieve the well-known advantageous performance of other DLC films, and furthermore that the film performance can be significantly affected by the addition of dopants. In addition to the well-established reduction of friction and wear that DLC films generally provide, we show here that another property, low adhesiveness with PMMA, is another significant benefit in the use of DLC films