We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. These models reduce to boolean networks in one limiting case of a parameter, and their asymptotic dynamics approaches that of a differential equation in another limiting case of this parameter. For intermediate values, the model present an original phenomenology which is argued to be due to delay effects. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle - with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.
Guanabara Bay is the second largest bay in the coast of Brazil, with an area of 384 km2. In its surroundings live circa 16 million inhabitants, out of which 6 million live in Rio de Janeiro city, one of the largest cities of the country, and the host of the 2016 Olympic Games. Anthropogenic interference in Guanabara Bay area started early in the XVI century, but environmental impacts escalated from 1930, when this region underwent an industrialization process. Herein we present an overview of the current environmental and sanitary conditions of Guanabara Bay, a consequence of all these decades of impacts. We will focus on microbial communities, how they may affect higher trophic levels of the aquatic community and also human health. The anthropogenic impacts in the bay are flagged by heavy eutrophication and by the emergence of pathogenic microorganisms that are either carried by domestic and/or hospital waste (e.g., virus, KPC-producing bacteria, and fecal coliforms), or that proliferate in such conditions (e.g., vibrios). Antibiotic resistance genes are commonly found in metagenomes of Guanabara Bay planktonic microorganisms. Furthermore, eutrophication results in recurrent algal blooms, with signs of a shift toward flagellated, mixotrophic groups, including several potentially harmful species. A recent large-scale fish kill episode, and a long trend decrease in fish stocks also reflects the bay’s degraded water quality. Although pollution of Guanabara Bay is not a recent problem, the hosting of the 2016 Olympic Games propelled the government to launch a series of plans to restore the bay’s water quality. If all plans are fully implemented, the restoration of Guanabara Bay and its shores may be one of the best legacies of the Olympic Games in Rio de Janeiro.
This Letter presents a study of the flavor-changing neutral current radiative B AE → K AE π ∓ π AE γ decays performed using data collected in proton-proton collisions with the LHCb detector at 7 and 8 TeV centerof-mass energies. In this sample, corresponding to an integrated luminosity of 3 fb −1 , nearly 14 000 signal events are reconstructed and selected, containing all possible intermediate resonances with a K AE π ∓ π AE final state in the ½1.1; 1.9 GeV=c 2 mass range. The distribution of the angle of the photon direction with respect to the plane defined by the final-state hadrons in their rest frame is studied in intervals of K AE π ∓ π AE mass and the asymmetry between the number of signal events found on each side of the plane is obtained. The first direct observation of the photon polarization in the b → sγ transition is reported with a significance of 5.2σ.
A B S T R A C TThe rising of cold water from deeper levels characterizes coastal upwelling systems. This flow makes nutrients available in the euphotic layer, which enhances phytoplankton production and growth. On the Brazilian coast, upwelling is most intense in the Cabo Frio region (RJ). The basic knowledge of this system was reviewed in accordance with concepts of biophysical interactions. The high frequency and amplitude of the prevailing winds are the main factor promoting the rise of South Atlantic Central Water, but meanders and eddies in the Brazil Current as well as local topography and coast line are also important. Upwelling events are common during spring/summer seasons. Primary biomass is exported by virtue of the water circulation and is also controlled by rapid zooplankton predation. Small pelagic fish regulate plankton growth and in their turn are preyed on by predatory fish. Sardine furnishes an important regional fish stock. Shoreline irregularities define the embayment formation of the Marine Extractive Reserve of Arraial do Cabo making it an area with evident different intensities of upwelled water that harbors high species diversity. Consequently, on a small spatial scale there are environments with tropical and subtropical features, a point to be explored as a particularity of this ecosystem. R E S U M OOs sistemas costeiros de ressurgência são caracterizados pela ascensão de águas frias que tornam os nutrientes disponíveis na camada eufótica para o crescimento e aumento da produção fitoplanctônica. No Brasil, a região do Cabo Frio (RJ) é o principal sistema de ressurgência costeira. O objetivo desse artigo foi revisar o atual conhecimento desse sistema através dos conceitos sobre interações biofísicas. A ascensão da Água Central do Atlântico Sul ocorre devido à alta frequência e amplitude dos ventos, à presença de meandros e vórtices na Corrente do Brasil, além da topografia local e da linha de costa. Os eventos de ressurgência são comuns durante os períodos de primavera/verão e a biomassa primária é exportada devido à circulação da água, sendo também controlada pela rápida predação zooplanctônica. Os pequenos peixes pelágicos regulam o crescimento do plâncton e são consumidos pelos peixes predadores, resultando em um importante estoque pesqueiro regional. A irregularidade da costa define as enseadas do Cabo Frio, na Reserva Extrativista Marinha do Arraial do Cabo, apresentando distintas influências das águas ressurgidas e resultando em grande diversidade de espécies. Consequentemente, ambientes com características tropicais e subtropicais são observados dentro de uma pequena escala espacial, o que constitui uma particularidade desse ecossistema.
Aim Topographic complexity is widely accepted as a key driver of biodiversity, but at the patch‐scale, complexity–biodiversity relationships may vary spatially and temporally according to the environmental stressors complexity mitigates, and the species richness and identity of potential colonists. Using a manipulative experiment, we assessed spatial variation in patch‐scale effects of complexity on intertidal biodiversity. Location 27 sites within 14 estuaries/bays distributed globally. Time period 2015–2017. Major taxa studied Functional groups of algae, sessile and mobile invertebrates. Methods Concrete tiles of differing complexity (flat; 2.5‐cm or 5‐cm complex) were affixed at low–high intertidal elevation on coastal defence structures, and the richness and abundance of the colonizing taxa were quantified after 12 months. Results The patch‐scale effects of complexity varied spatially and among functional groups. Complexity had neutral to positive effects on total, invertebrate and algal taxa richness, and invertebrate abundances. However, effects on the abundance of algae ranged from positive to negative, depending on location and functional group. The tidal elevation at which tiles were placed accounted for some variation. The total and invertebrate richness were greater at low or mid than at high intertidal elevations. Latitude was also an important source of spatial variation, with the effects of complexity on total richness and mobile mollusc abundance greatest at lower latitudes, whilst the cover of sessile invertebrates and sessile molluscs responded most strongly to complexity at higher latitudes. Conclusions After 12 months, patch‐scale relationships between biodiversity and habitat complexity were not universally positive. Instead, the relationship varied among functional groups and according to local abiotic and biotic conditions. This result challenges the assumption that effects of complexity on biodiversity are universally positive. The variable effect of complexity has ramifications for community and applied ecology, including eco‐engineering and restoration that seek to bolster biodiversity through the addition of complexity.
An experiment was undertaken at Farol Island, Brazil, to examine colonization of bare aluminium surfaces by microbes and meiofauna. It was hypothesized that a primary source of meiofaunal colonists was sediment resuspended during upwelling events, two of which occurred during the experiment. Microbial biofilms formed on the experimental substrata within 1 day, and continued to develop throughout the experimental period. Among meiofaunal groups copepods also appeared on the first day, and nematodes on the second. Meiofaunal community structure developed in three main phases: an initial phase of 2 days, characterized by low abundances of copepods; a second phase during the first upwelling period characterized by higher abundances of copepods and also by turbellarians; and a third phase from day 13 onwards characterized by relatively stable abundances of a range of taxa including copepods, cirripedes, nematodes and ostracods. Nematode assemblages also developed in three phases, but with different timings coinciding with upwelling events: an initial phase, from the beginning of the experiment to day 9, characterized by few species and low (or no) abundances; a second phase following the first upwelling characterized by moderate abundances of Chromadorina, Chromadorella, Daptonema and Euchromadora sp. 3; a third phase following the second upwelling period (from day 26 onwards) in which Daptonema disappeared and the assemblage was characterized by moderate to high abundances of Euchromadora (species 1 and 2) and Chromadorella. Although shifts in nematode assemblage structure coincided with upwelling events no evidence was found for sediments being the primary source of colonizers on the aluminium substrata, in contrast to our hypothesis.
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