Biology subjects

Stewart, A.

Publications and source records attributed to Stewart, A..

3 recordsLinked to original sources

bioRxiv2018

Evolution of empathetic moral evaluation

Social norms can promote cooperation in human societies by assigning reputations to individuals based on their past actions. A good reputation indicates that an individual is worthy of help and is likely to reciprocate. A large body of research has established the norms of moral assessment that promote cooperation and maximize social welfare, assuming reputations are objective. But if there is no centralized institution to provide objective moral evaluation, then opinions about an individuals reputation may differ across a population. Here we use evolutionary game theory to study the effects of empathy - the capacity to make moral evaluations from the perspective of another person. We find that empathetic moral evaluation tends to foster cooperation by reducing the rate of unjustified defection. The norms of moral evaluation previously considered most socially beneficial depend on high levels of empathy, whereas different norms are required to maximize social welfare in populations unwilling or incapable of empathy. We demonstrate that empathy itself can evolve through social contagion and attain evolutionary stability under most social norms. We conclude that a capacity for empathetic moral evaluation represents a key component to sustaining cooperation in human societies: cooperation requires getting into the mindset of others whose views differ from our own.

evolutionary biology↗

bioRxiv2018

Characterizing Genetic Circuit Components in E. coli towards a Campylobacter jejuni Biosensor.

Campylobacter jejuni is responsible for most cases of bacterial gastroenteritis (food poisoning) in the United Kingdom. The most common routes of transmission are by contact with raw poultry. Current detection systems for the pathogen are time-consuming, expensive or inaccessible for everyday users. In this article we propose a cheaper and faster system for detection of C. jejuni using a synthetic biology approach. We aimed to detect C. jejuni by the presence of xylulose, an uncommon bacterial capsular saccharide. We characterized two sugar-based regulatory systems that displayed potential to act as tools for detection of xylulose. Using a two-plasmid reporter system in Escherichia coli, we investigated the regulatory protein component (MtlR) of the mannitol operon from Pseudomonas fluorescens. Our findings suggest that the promoter of mtlE is activated by MtlR in the presence of a variety of sugar inducer molecules, and may exhibit cross-activity with a native regulator of E. coli. Additionally, we engineered the L-arabinose transcriptional activator (AraC) of E. coli for altered ligand specificity. We performed site-specific saturation mutagenesis to generate AraC variants with altered effector specificity, with an aim to generate a mutant activated by xylulose. We characterized several mutant AraC variants which have lost the ability to respond specifically to the native L-arabinose effector. We promote this technique as a powerful tool for future iGEM teams to create regulatory circuits activated by novel small molecule ligands.

synthetic biology↗

bioRxiv2017

MRCZ - A proposed fast compressed MRC file format and direct detector normalization strategies

The introduction of high-speed CMOS detectors is fast marching the field of transmission electron microscopy into an intersection with the computer science field of big data. Automated data pipelines to control the instrument and the initial processing steps are imposing more and more onerous requirements on data transfer and archiving. We present a proposal for expansion of the venerable MRC file format to combine integer decimation and lossless compression to reduce storage requirements and improve file read/write times by >1000 % compared to uncompressed floating-point data. The integer decimation of data necessitates application of the gain normalization and outlier pixel removal at the data destination, rather than the source. With direct electron detectors, the normalization step is typically provided by the vendor and is not open-source. We provide robustly tested normalization algorithms that perform at-least as well as vendor software. We show that the generation of hot pixels is a highly dynamic process in direct electron detectors, and that outlier pixels must be detected on a stack-by-stack basis. In comparison, the low-frequency bias features of the detectors induced by the electronics on-top of the active layer, are extremely stable with time. Therefore we introduce a stochastic-based approach to identify outlier pixels and smoothly filter them, such that the degree of correlated noise in micrograph stacks is reduced. Both a priori and a posteriori gain normalization approaches that are compatible with pipeline image processing are discussed. The a priori approach adds a gamma-correction to the gain reference, and the a posteriori approach normalized by a moving average of time-adjacent stacks, with the current stack being knocked-out, known as the KOMA (knock-out moving average) filter. The combination of outlier filter and KOMA normalization over ~25 frames can reduce the correlated noise in movies to nearly zero. Sample libraries and a command-line utility are hosted at github.com/em-MRCZ and released under the BSD license.

bioinformatics↗