Identification of meat spoilage gene biomarkers in Pseudomonas putida using gene profiling

While current food science research mainly focuses on microbial changes in food products that lead to foodborne illnesses, meat spoilage remains as an unsolved problem for the meat industry. This can result in important economic losses, food waste and loss of consumer confidence in the meat market. Gram-negative bacteria involved in meat spoilage are aerobes or facultative anaerobes. These represent the group with the greatest meat spoilage potential, where Pseudomonas tend to dominate the microbial consortium under refrigeration and aerobic conditions. Identifying stress response genes under different environmental conditions can help researchers gain an understanding of how Pseudomonas adapts to current packaging and storage conditions. We examined the gene expression profile of Pseudomonas putida KT2440, which plays an important role in the spoilage of meat products. Gene expression profiles were evaluated to select the most differentially expressed genes at different temperatures (30 °C and 10 °C) and decreasing glucose concentrations, in order to identify key genes actively involved with the spoilage process. A total of 739 and 1269 were found to be differentially expressed at 30 °C and 10 °C respectively; of which 430 and 568 genes were overexpressed, and 309 and 701 genes were repressed at 30 °C and 10 °C respectively

This better be interesting:A speaker's decision to speak cues listeners to expect informative content

In anticipating upcoming content, comprehenders are known to rely on real-world knowledge. This knowledge can be deployed directly in favor of upcoming content about typical situations (implying a transparent mapping between the world and what speakers say about the world). Such knowledge can also be used to estimate the likelihood of speech, whereby atypical situations are the ones newsworthy enough to merit reporting (i.e., a nontransparent mapping in which improbable situations yield likely utterances). We report four forced-choice studies (three preregistered) testing this distinction between situation knowledge and speech production likelihood. Comprehenders are shown to anticipate situation-atypical meanings more when guessing content (a) that a speaker announces (rather than thinks), (b) that is said out of the blue (rather than produced when prompted), and (c) that is addressed to a large audience (rather than a single listener). The findings contrast with prior work that emphasizes a comprehension bias in favor of typicality, and they highlight the need for comprehension models that incorporate expectations for informativity (as one of a set of inferred speaker goals) alongside expectations for content plausibility

Reasoning About the Transfer of Control

We present DCL-PC: a logic for reasoning about how the abilities of agents and coalitions of agents are altered by transferring control from one agent to another. The logical foundation of DCL-PC is CL-PC, a logic for reasoning about cooperation in which the abilities of agents and coalitions of agents stem from a distribution of atomic Boolean variables to individual agents -- the choices available to a coalition correspond to assignments to the variables the coalition controls. The basic modal constructs of DCL-PC are of the form coalition C can cooperate to bring about phi. DCL-PC extends CL-PC with dynamic logic modalities in which atomic programs are of the form agent i gives control of variable p to agent j; as usual in dynamic logic, these atomic programs may be combined using sequence, iteration, choice, and test operators to form complex programs. By combining such dynamic transfer programs with cooperation modalities, it becomes possible to reason about how the power of agents and coalitions is affected by the transfer of control. We give two alternative semantics for the logic: a direct semantics, in which we capture the distributions of Boolean variables to agents; and a more conventional Kripke semantics. We prove that these semantics are equivalent, and then present an axiomatization for the logic. We investigate the computational complexity of model checking and satisfiability for DCL-PC, and show that both problems are PSPACE-complete (and hence no worse than the underlying logic CL-PC). Finally, we investigate the characterisation of control in DCL-PC. We distinguish between first-order control -- the ability of an agent or coalition to control some state of affairs through the assignment of values to the variables under the control of the agent or coalition -- and second-order control -- the ability of an agent to exert control over the control that other agents have by transferring variables to other agents. We give a logical characterisation of second-order control

Expression of the Inhibitory CD200 Receptor Is Associated with Alternative Macrophage Activation

Classical macrophage activation is inhibited by the CD200 receptor (CD200R). Here, we show that CD200R expression was specifically induced on human in vitro polarized macrophages of the alternatively activated M2a subtype, generated by incubation with IL-4 or IL-13. In mice, peritoneal M2 macrophages, elicited during infection with the parasites Taenia crassiceps or Tryponosoma brucei brucei, expressed increased CD200R levels compared to those derived from uninfected mice. However, in vitro stimulation of mouse peritoneal macrophages and T crassiceps infection in IL-4-/- and IL-4R-/- mice showed that, in contrast to humans, induction of CD200R in mice was not IL-4 or IL-13 dependent. Our data identify CD200R as a suitable marker for alternatively activated macrophages in humans and corroborate observations of distinct species- and/or site-specific mechanisms regulating macrophage polarization in mouse and man. Copyright (C) 2009 S. Karger AG, Base

Clustering of contacts relevant to the spread of infectious disease.

OBJECTIVE: Infectious disease spread depends on contact rates between infectious and susceptible individuals. Transmission models are commonly informed using empirically collected contact data, but the relevance of different contact types to transmission is still not well understood. Some studies select contacts based on a single characteristic such as proximity (physical/non-physical), location, duration or frequency. This study aimed to explore whether clusters of contacts similar to each other across multiple characteristics could better explain disease transmission. METHODS: Individual contact data from the POLYMOD survey in Poland, Great Britain, Belgium, Finland and Italy were grouped into clusters by the k medoids clustering algorithm with a Manhattan distance metric to stratify contacts using all four characteristics. Contact clusters were then used to fit a transmission model to sero-epidemiological data for varicella-zoster virus (VZV) in each country. RESULTS AND DISCUSSION: Across the five countries, 9-15 clusters were found to optimise both quality of clustering (measured using average silhouette width) and quality of fit (measured using several information criteria). Of these, 2-3 clusters were most relevant to VZV transmission, characterised by (i) 1-2 clusters of age-assortative contacts in schools, (ii) a cluster of less age-assortative contacts in non-school settings. Quality of fit was similar to using contacts stratified by a single characteristic, providing validation that single stratifications are appropriate. However, using clustering to stratify contacts using multiple characteristics provided insight into the structures underlying infection transmission, particularly the role of age-assortative contacts, involving school age children, for VZV transmission between households

Topology of SU(N) gauge theories at T=0 and T=Tc

We calculate the topological charge density of SU(N) lattice gauge fields for values of N up to N=8. Our T=0 topological susceptibility appears to approach a finite non-zero limit at N=infinity that is consistent with earlier extrapolations from smaller values of N. Near the deconfining temperature Tc we are able to investigate separately the confined and deconfined phases, since the transition is quite strongly first order. We find that the topological susceptibility of the confined phase is always very similar to that at T=0. By contrast, in the deconfined phase at larger N there are no topological fluctuations except for rare, isolated and small instantons. This shows that as N->infinity the large-T suppression of large instantons and the large-N suppression of small instantons overlap, even at T=Tc, so as to suppress all topological fluctuations in the deconfined phase. In the confined phase by contrast, the size distribution is much the same at all T, becoming more peaked as N grows, suggesting that D(rho) is proportional to a delta function at N=infinity, centered on rho close to 1/Tc.Comment: 31 page