Lambda-prophage induction modeled as a cooperative failure mode of lytic repression

We analyze a system-level model for lytic repression of lambda-phage in E. coli using reliability theory, showing that the repressor circuit comprises 4 redundant components whose failure mode is prophage induction. Our model reflects the specific biochemical mechanisms involved in regulation, including long-range cooperative binding, and its detailed predictions for prophage induction in E. coli under ultra-violet radiation are in good agreement with experimental data.Comment: added referenc

Coherent addition of two dimensional array of fiber lasers

Configurations for efficient free space coherent addition of four separate fiber lasers arranged in two dimensional array are presented. They include compact and robust interferometric combiners that can be inserted either inside or outside the cavity of the combined lasers system. The results reveal that over 85% combining efficiency can be obtained.Comment: To be published in Optics Communicatio

Measurement-based modeling of bromine chemistry at the Dead Sea boundary layer ? Part 2: The influence of NO₂ on bromine chemistry at mid-latitude areas

International audienceUnderstanding the interaction between anthropogenic air pollution and Reactive Halogen Species (RHS) activity has had only limited support of direct field measurements, due to the fact that past field measurements of RHS have been mainly performed in Polar Regions. The present paper investigates the interaction between NO2 and Reactive Bromine Species (RBS) activity by model simulations based on extensive field measurements performed in the Dead Sea area, as described in a companion paper (Tas et al., 2006). The Dead Sea is an excellent natural laboratory for this investigation since elevated concentrations of BrO (up to more than 150 pptv) are frequently observed, while the average levels of NO2 are around several ppb. The results of the present study show that under the chemical mechanisms that occur at the Dead Sea, higher levels of NO2 lead to higher daily average concentrations of BrOX, as a result of an increase in the rate of the heterogeneous decomposition of BrONO2 that in turn causes an increase in the rate of the "Bromine Explosion" mechanism. The present study has shown that the influence of NO2 on BrOX production clearly reflects an enhancement of RBS activity caused by anthropogenic activity. However, above a certain threshold level of NO2 (daily average mixing ratios of 0.2 ppbv during RBS activity), the daily average concentrations of BrOX decrease for a further increase in the NO2 concentrations

Evolutionary game theory in growing populations

Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show that genuinely stochastic events can ease the dilemma by leading to a transient but robust increase in cooperationComment: 4 pages, 2 figures and 2 pages supplementary informatio

Observation of Quantum Effects in sub Kelvin Cold Reactions

There has been a long-standing quest to observe chemical reactions at low temperatures where reaction rates and pathways are governed by quantum mechanical effects. So far this field of Quantum Chemistry has been dominated by theory. The difficulty has been to realize in the laboratory low enough collisional velocities between neutral reactants, so that the quantum wave nature could be observed. We report here the first realization of merged neutral supersonic beams, and the observation of clear quantum effects in the resulting reactions. We observe orbiting resonances in the Penning ionization reaction of argon and molecular hydrogen with metastable helium leading to a sharp increase in the absolute reaction rate in the energy range corresponding to a few degrees kelvin down to 10 mK. Our method is widely applicable to many canonical chemical reactions, and will enable a breakthrough in the experimental study of Quantum Chemistry

Measurement-based modeling of bromine chemistry in the boundary layer: 1. Bromine chemistry at the Dead Sea

International audienceThe Dead Sea is an excellent natural laboratory for the investigation of Reactive Bromine Species (RBS) chemistry, due to the high RBS levels observed in this area, combined with anthropogenic air pollutants up to several ppb. The present study investigated the basic chemical mechanism of RBS at the Dead Sea using a numerical one-dimensional chemical model. Simulations were based on data obtained from comprehensive measurements performed at sites along the Dead Sea. The simulations showed that the high BrO levels measured frequently at the Dead Sea could only partially be attributed to the highly concentrated Br? present in the Dead Sea water. Furthermore, the RBS activity at the Dead Sea cannot solely be explained by a pure gas phase mechanism. This paper presents a chemical mechanism which can account for the observed chemical activity at the Dead Sea, with the addition of only two heterogeneous processes: the "Bromine Explosion" mechanism and the heterogeneous decomposition of BrONO2. Ozone frequently dropped below a threshold value of ~1 to 2 ppbv at the Dead Sea evaporation ponds, and in such cases, O3 became a limiting factor for the production of BrOx (BrO+Br). The entrainment of O3 fluxes into the evaporation ponds was found to be essential for the continuation of RBS activity, and to be the main reason for the jagged diurnal pattern of BrO observed in the Dead Sea area, and for the positive correlation observed between BrO and O3 at low O3 concentrations. The present study has shown that the heterogeneous decomposition of BrONO2 has a great potential to affect the RBS activity in areas influenced by anthropogenic emissions, mainly due to the positive correlation between the rate of this process and the levels of NO2. Further investigation of the influence of the decomposition of BrONO2 may be especially important in understanding the RBS activity at mid-latitudes

The simulation of action disorganisation in complex activities of daily living

Action selection in everyday goal-directed tasks of moderate complexity is known to be subject to breakdown following extensive frontal brain injury. A model of action selection in such tasks is presented and used to explore three hypotheses concerning the origins of action disorganisation: that it is a consequence of reduced top-down excitation within a hierarchical action schema network coupled with increased bottom-up triggering of schemas from environmental sources, that it is a more general disturbance of schema activation modelled by excessive noise in the schema network, and that it results from a general disturbance of the triggering of schemas by object representations. Results suggest that the action disorganisation syndrome is best accounted for by a general disturbance to schema activation, while altering the balance between top-down and bottom-up activation provides an account of a related disorder - utilisation behaviour. It is further suggested that ideational apraxia (which may result from lesions to left temporoparietal areas and which has similar behavioural consequences to action disorganisation syndrome on tasks of moderate complexity) is a consequence of a generalised disturbance of the triggering of schemas by object representations. Several predictions regarding differences between action disorganisation syndrome and ideational apraxia that follow from this interpretation are detailed

Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR

How brains make decisions

This chapter, dedicated to the memory of Mino Freund, summarizes the Quantum Decision Theory (QDT) that we have developed in a series of publications since 2008. We formulate a general mathematical scheme of how decisions are taken, using the point of view of psychological and cognitive sciences, without touching physiological aspects. The basic principles of how intelligence acts are discussed. The human brain processes involved in decisions are argued to be principally different from straightforward computer operations. The difference lies in the conscious-subconscious duality of the decision making process and the role of emotions that compete with utility optimization. The most general approach for characterizing the process of decision making, taking into account the conscious-subconscious duality, uses the framework of functional analysis in Hilbert spaces, similarly to that used in the quantum theory of measurements. This does not imply that the brain is a quantum system, but just allows for the simplest and most general extension of classical decision theory. The resulting theory of quantum decision making, based on the rules of quantum measurements, solves all paradoxes of classical decision making, allowing for quantitative predictions that are in excellent agreement with experiments. Finally, we provide a novel application by comparing the predictions of QDT with experiments on the prisoner dilemma game. The developed theory can serve as a guide for creating artificial intelligence acting by quantum rules.Comment: Latex file, 20 pages, 3 figure