Decomposing Noise in Biochemical Signaling Systems Highlights the Role of Protein Degradation

AbstractStochasticity is an essential aspect of biochemical processes at the cellular level. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others. Here we propose a method that allows us to calculate contributions of individual reactions to the total variability of a system’s output. We demonstrate that reactions differ significantly in their relative impact on the total noise and we illustrate the importance of protein degradation on the overall variability for a range of molecular processes and signaling systems. With our flexible and generally applicable noise decomposition method, we are able to shed new, to our knowledge, light on the sources and propagation of noise in biochemical reaction networks; in particular, we are able to show how regulated protein degradation can be employed to reduce the noise in biochemical systems

Coupled oscillators as models of phantom and scalar field cosmologies

We study a toy model for phantom cosmology recently introduced in the literature and consisting of two oscillators, one of which carries negative kinetic energy. The results are compared with the exact phase space picture obtained for similar dynamical systems describing, respectively, a massive canonical scalar field conformally coupled to the spacetime curvature, and a conformally coupled massive phantom. Finally, the dynamical system describing exactly a minimally coupled phantom is studied and compared with the toy model.Comment: 18 pages, LaTeX, to appear in Physical Review

Earth system justice needed to identify and live within Earth system boundaries

Living within planetary limits requires attention to justice as biophysical boundaries are not inherently just. Through collaboration between natural and social scientists, the Earth Commission defines and operationalizes Earth system justice to ensure that boundaries reduce harm, increase well-being, and reflect substantive and procedural justice. Such stringent boundaries may also affect ‘just access’ to food, water, energy and infrastructure. We show how boundaries may need to be adjusted to reduce harm and increase access, and challenge inequality to ensure a safe and just future for people, other species and the planet. Earth system justice may enable living justly within boundaries

Theory and Applications of Non-Relativistic and Relativistic Turbulent Reconnection

Realistic astrophysical environments are turbulent due to the extremely high Reynolds numbers. Therefore, the theories of reconnection intended for describing astrophysical reconnection should not ignore the effects of turbulence on magnetic reconnection. Turbulence is known to change the nature of many physical processes dramatically and in this review we claim that magnetic reconnection is not an exception. We stress that not only astrophysical turbulence is ubiquitous, but also magnetic reconnection itself induces turbulence. Thus turbulence must be accounted for in any realistic astrophysical reconnection setup. We argue that due to the similarities of MHD turbulence in relativistic and non-relativistic cases the theory of magnetic reconnection developed for the non-relativistic case can be extended to the relativistic case and we provide numerical simulations that support this conjecture. We also provide quantitative comparisons of the theoretical predictions and results of numerical experiments, including the situations when turbulent reconnection is self-driven, i.e. the turbulence in the system is generated by the reconnection process itself. We show how turbulent reconnection entails the violation of magnetic flux freezing, the conclusion that has really far reaching consequences for many realistically turbulent astrophysical environments. In addition, we consider observational testing of turbulent reconnection as well as numerous implications of the theory. The former includes the Sun and solar wind reconnection, while the latter include the process of reconnection diffusion induced by turbulent reconnection, the acceleration of energetic particles, bursts of turbulent reconnection related to black hole sources as well as gamma ray bursts. Finally, we explain why turbulent reconnection cannot be explained by turbulent resistivity or derived through the mean field approach.Comment: 66 pages, 24 figures, a chapter of the book "Magnetic Reconnection - Concepts and Applications", editors W. Gonzalez, E. N. Parke

Neotropical and Afrotropical freshwater copepods: recent advances

peer reviewedI present new perspectives and advances on the knowledge of free-living copepods in large tropical river basins. Currently, the greatest copepod diversity is known from the Palearctic region, with a surface about twice or thrice that of the Neotropical and Afrotropical areas, respectively. Interestingly, biological diversity estimators suggest a much higher and largely unexplored diversity in the two latter regions, potentially reaching or exceeding that of the Palearctic. I show trends for both regions, focused on Brazil and Congo Basins. Brazil comprises almost 40 % of the Neotropical region surface, including four rivers among the 20 largest in the world. Based on the literature review, there are 190 free-living copepod species in the country. Among the 12 hydrographic regions in Brazil, the richest are the Amazon and the Paraná basins, with the largest surface. Taxonomical studies on Brazilian copepods were predominant until 1979, yet, between 1980 and 1989 ecologically-oriented works were developed and became a main trend after 1990, representing over 80% of copepod studies after 2000. Molecular diversity and functional ecology are still poorly studied. Ecological studies with molecular-based diversity parameters, functional attributes or comprehensive spatialtemporal data of copepod species behavior and environmental variables have been used to detect effects of environmental changes both at population and community levels. Cyclopoid copepods composition and abundance changes according to the trophic level, but calanoids appear to be influenced by conductivity. The presence of cyanobacteria and phytoplankton of lower nutritional value can cause a bottom-up effect on the copepods, resulting in low functional diversity and increase of functional uniformity. Large filtering copepods can be replaced by small cyclopoids at increasing eutrophicated conditions. The Afrotropical region comprises four of the largest rivers worldwide. The most studied environments have been the great lakes of the rift valley (e.g. Tanganyika, Victoria, Kivu), the Nile River, and several places in South Africa. The Congo River, the second largest in the world, is almost entirely unknown in terms of copepod composition and ecology. Herein, I show initial data revealing the lack of knowledge of the l extant Congo copepod diversity, with a high potential for new species. Two expeditions made in 2013 and 2015 along the Congo and the Kasai River revealed 15 copepod species, but rarefaction and extrapolation diversity curves suggest the presence of at least double of this number. There are four large groups of copepods species in the Congo Basin, being the two largest separated by differences in primary productivity (white waters rivers) or microbial food web (black waters rivers). Copepods within the main channel of the Congo River seem to be less dissimilar than tributaries, thus reinforcing the effect of upstream basins, a trend observed in other large tropical river basins. Each large river has different copepod species especially for diaptomid calanoids and also for some Cyclopoida species, but just the last have shared species between Afrotropical and Neotropical regions. The river continuum and the flood pulse concepts were applied in these large tropical rivers, but both were disrupted by reservoirs. The large rivers of these tropical regions appear seem proportionally equal in copepod diversity according to this surface, and linked to their historical biogeography

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011