Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation

Background: Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the species genomes were subsequently published. In this study, we performed comparative genomics on eight strains of Cronobacter, including six that we sequenced (representing six of the seven species) and two previously published, closed genomes.

Results: We identified and characterized the features associated with the core and pan genome of the genus Cronobacter in an attempt to understand the evolution of these bacteria and the genetic content of each species. We identified 84 genomic regions that are present in two or more Cronobacter genomes, along with 45 unique genomic regions. Many potentially horizontally transferred genes, such as lysogenic prophages, were also identified. Most notable among these were several type six secretion system gene clusters, transposons that carried tellurium, copper and/or silver resistance genes, and a novel integrative conjugative element.

Conclusions: Cronobacter have diverged into two clusters, one consisting of C. dublinensis and C. muytjensii (Cdub-Cmuy) and the other comprised of C. sakazakii, C. malonaticus, C. universalis, and C. turicensis, (Csak-Cmal-Cuni-Ctur) from the most recent common ancestral species. While several genetic determinants for plant-association and human virulence could be found in the core genome of Cronobacter, the four Cdub-Cmuy clade genomes contained several accessory genomic regions important for survival in a plant-associated environmental niche, while the Csak-Cmal-Cuni-Ctur clade genomes harbored numerous virulence-related genetic traits.

An experimental and numerical investigation into the seismic performance of a multi-storey concentrically braced plan irregular structure

In this investigation, the seismic torsional response of a multi-storey concentrically braced frame (CBF) plan irregular structure is evaluated numerically and experimentally through a series of hybrid tests. CBF structures have become popular in seismic design because they are one of the most efficient types of steel structures to resist earthquake loading. However, their response under plan irregular conditions has received little focus mostly in part
due to their complex behaviour under seismic loading conditions. The majority of research on the seismic response of plan irregular structures is based purely on numerical investigations. This paper provides much needed experimental investigation of the seismic response of a CBF plan irregular structure with the aim of characterising the response of this class of structure. The effectiveness of the Eurocode 8 torsional effects provision as a method of designing for
low levels of mass eccentricity is evaluated. Results indicate that some of the observations made by purely numerical models are valid in that; torsionally stiff structures perform well and the stiff side of the structure is subjected to a greater ductility demand compared to the flexible side of the structure. The Eurocode 8 torsional effects provision is shown to be adequate in terms of ductility and interstorey drift however the structure performs poorly
in terms of floor rotation. Importantly, stiffness eccentricity occurs when the provision is applied to the structure when no mass eccentricity exists and results in a significant increase in floor rotations.

Cathelicidin-like Helminth Defence Molecules (HDMs):Absence of Cytotoxic, Anti-microbial and Anti-protozoan Activities Imply a Specific Adaptation to Immune Modulation

Host defence peptides (HDPs) are expressed throughout the animal and plant kingdoms. They have multifunctional roles in the defence against infectious agents of mammals, possessing both bactericidal and immune-modulatory activities. We have identified a novel family of molecules secreted by helminth parasites (helminth defence molecules; HDMs) that exhibit similar structural and biochemical characteristics to the HDPs. Here, we have analyzed the functional activities of four HDMs derived from Schistosoma mansoni and Fasciola hepatica and compared them to human, mouse, bovine and sheep HDPs. Unlike the mammalian HDPs the helminth-derived HDMs show no antimicrobial activity and are non-cytotoxic to mammalian cells (macrophages and red blood cells). However, both the mammalian- and helminth-derived peptides suppress the activation of macrophages by microbial stimuli and alter the response of B cells to cytokine stimulation. Therefore, we hypothesise that HDMs represent a novel family of HDPs that evolved to regulate the immune responses of their mammalian hosts by retaining potent immune modulatory properties without causing deleterious cytotoxic effects.

Scalable black-box prediction models for multi-dimensional adaptation on NUMA multi-cores

This paper presents a scalable, statistical ‘black-box’ model for predicting the performance of parallel programs on multi-core non-uniform memory access (NUMA) systems. We derive a model with low overhead, by reducing data collection and model training time. The model can accurately predict the behaviour of parallel applications in response to changes in their concurrency, thread layout on NUMA nodes, and core voltage and frequency. We present a framework that applies the model to achieve significant energy and energy-delay-square (ED2) savings (9% and 25%, respectively) along with performance improvement (10% mean) on an actual 16-core NUMA system running realistic application workloads. Our prediction model proves substantially more accurate than previous efforts.

Teaching the physiology of adaptation to hypoxic stress with the aid of a classic paper on high altitude by Houston and Riley

Many pathological conditions exist where tissues exhibit hypoxia or low oxygen tension. Hypoxic hypoxia arises when there is a reduction in the amount of oxygen entering the blood and occurs in healthy people at high altitude. In 1946, research sponsored by the United States Navy led to the collection and subsequent publication of masses of data demonstrating the physiological consequences and adaptations of ascent to high altitude. This article describes how a figure from a 1947 paper from the American Physiological Society Legacy collection (Houston CS, Riley RL. Respiratory and circulatory changes during acclimatization to high altitude. Am J Physiol 149: 565-588) may be used to allow students to review their understanding of some of the generalized effects of hypoxia on the body. In particular, this figure summarizes some of the adaptive responses that take place in the oxygen transport system as a consequence of prolonged hypoxia.

Seismic Assessment of a Steel Braced Plan Mass Symmetric/Asymmetric Building Structure

This paper presents a seismic response investigation into a code designed concentrically braced frame structure that is subjected to but not designed for in-plan mass eccentricity. The structure has an accidental uneven distribution of mass in plan resulting in an increased torsional component of vibration. The level of inelasticity that key structural elements in plan mass asymmetric structures are subjected to is important when analysing their ability to sustain uneven seismic demands. In-plan mass asymmetry of moment resisting frame and shear wall type structures have received significant investigation, however, the plan asymmetric response of braced frame type structures is less well understood. A three-dimensional non-linear time history analysis (NLTHA) model is created to capture the torsional response of the plan mass asymmetric structure to quantify the additional ductility demand, interstorey drifts and floor rotations. Results show that the plan mass asymmetric structure performs well in terms of ductility demand, but poorly in terms of interstorey drifts and floor rotations when compared to the plan mass symmetric structure. New linear relationships are developed between the normalised ductility demand and normalised slenderness of the bracing on the sides of the plan mass symmetric/asymmetric structures that the mass is distributed towards and away from.