Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

Positional information in developing embryos is specified by spatial gradients of transcriptional regulators. One of the classic systems for studying this is the activation of the hunchback (hb) gene in early fruit fly (Drosophila) segmentation by the maternally-derived gradient of the Bicoid (Bcd) protein. Gene regulation is subject to intrinsic noise which can produce variable expression. This variability must be constrained in the highly reproducible and coordinated events of development. We identify means by which noise is controlled during gene expression by characterizing the dependence of hb mRNA and protein output noise on hb promoter structure and transcriptional dynamics. We use a stochastic model of the hb promoter in which the number and strength of Bcd and Hb (self-regulatory) binding sites can be varied. Model parameters are fit to data from WT embryos, the self-regulation mutant hb(14F), and lacZ reporter constructs using different portions of the hb promoter. We have corroborated model noise predictions experimentally. The results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, rather than on Bcd fluctuations. The constructs and mutant, which lack self-regulation, indicate that the multiple Bcd binding sites in the hb promoter (and their strengths) also play a role in buffering noise. The model is robust to the variation in Bcd binding site number across a number of fly species. This study identifies particular ways in which promoter structure and regulatory dynamics reduce hb output noise. Insofar as many of these are common features of genes (e. g. multiple regulatory sites, cooperativity, self-feedback), the current results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development.

Quantum system under the actions of two counteracting baths: A model for the attenuation-amplification interplay

We analyze the dynamical behavior of a quantum system under the actions of two counteracting baths: the inevitable energy draining reservoir and, in opposition, exciting the system, an engineered Glauber's amplifier. We follow the system dynamics towards equilibrium to map its distinctive behavior arising from the interplay of attenuation and amplification. Such a mapping, with the corresponding parameter regimes, is achieved by calculating the evolution of both the excitation and the Glauber-Sudarshan P function. Techniques to compute the decoherence and the fidelity of quantum states under the action of both counteracting baths, based on the Wigner function rather than the density matrix, are also presented. They enable us to analyze the similarity of the evolved state vector of the system with respect to the original one, for all regimes of parameters. Applications of this attenuation-amplification interplay are discussed.

Fluorescence spectroscopy for the detection of tongue carcinoma - validation in an animal model

The efficacy of fluorescence spectroscopy to detect squamous cell carcinoma is evaluated in an animal model following laser excitation at 442 and 532 nm. Lesions are chemically induced with a topical DMBA application at the left lateral tongue of Golden Syrian hamsters. The animals are investigated every 2 weeks after the 4th week of induction until a total of 26 weeks. The right lateral tongue of each animal is considered as a control site (normal contralateral tissue) and the induced lesions are analyzed as a set of points covering the entire clinically detectable area. Based on fluorescence spectral differences, four indices are determined to discriminate normal and carcinoma tissues, based on intraspectral analysis. The spectral data are also analyzed using a multivariate data analysis and the results are compared with histology as the diagnostic gold standard. The best result achieved is for blue excitation using the KNN (K-nearest neighbor, a interspectral analysis) algorithm with a sensitivity of 95.7% and a specificity of 91.6%. These high indices indicate that fluorescence spectroscopy may constitute a fast noninvasive auxiliary tool for diagnostic of cancer within the oral cavity. (C) 2008 Society of Photo-Optical Instrumentation Engineers.

Statistics of opinion domains of the majority-vote model on a square lattice

The existence of juxtaposed regions of distinct cultures in spite of the fact that people's beliefs have a tendency to become more similar to each other's as the individuals interact repeatedly is a puzzling phenomenon in the social sciences. Here we study an extreme version of the frequency-dependent bias model of social influence in which an individual adopts the opinion shared by the majority of the members of its extended neighborhood, which includes the individual itself. This is a variant of the majority-vote model in which the individual retains its opinion in case there is a tie among the neighbors' opinions. We assume that the individuals are fixed in the sites of a square lattice of linear size L and that they interact with their nearest neighbors only. Within a mean-field framework, we derive the equations of motion for the density of individuals adopting a particular opinion in the single-site and pair approximations. Although the single-site approximation predicts a single opinion domain that takes over the entire lattice, the pair approximation yields a qualitatively correct picture with the coexistence of different opinion domains and a strong dependence on the initial conditions. Extensive Monte Carlo simulations indicate the existence of a rich distribution of opinion domains or clusters, the number of which grows with L(2) whereas the size of the largest cluster grows with ln L(2). The analysis of the sizes of the opinion domains shows that they obey a power-law distribution for not too large sizes but that they are exponentially distributed in the limit of very large clusters. In addition, similarly to other well-known social influence model-Axelrod's model-we found that these opinion domains are unstable to the effect of a thermal-like noise.

LIMIT THEOREMS FOR A GENERAL STOCHASTIC RUMOUR MODEL

We study a general stochastic rumour model in which an ignorant individual has a certain probability of becoming a stifler immediately upon hearing the rumour. We refer to this special kind of stifler as an uninterested individual. Our model also includes distinct rates for meetings between two spreaders in which both become stiflers or only one does, so that particular cases are the classical Daley-Kendall and Maki-Thompson models. We prove a Law of Large Numbers and a Central Limit Theorem for the proportions of those who ultimately remain ignorant and those who have heard the rumour but become uninterested in it.

Eddy Formation in the Tropical Atlantic Induced by Abrupt Changes in the Meridional Overturning Circulation

The variability of the meridional overturning circulation (MOC) in the upper tropical Atlantic basin is investigated using a reduced-gravity model in a simplified domain. Four sets of idealized numerical experiments are performed: (i) switch-on of the MOC until a fixed value when a constant northward flow is applied along the western boundary; (ii) MOC with a variable flow; (iii) MOC in a quasi-steady flow; and (iv) shutdown of the MOC in the Northern Hemisphere. Results from experiments (i) show that eddies are generated at the equatorial region by shear instability and detached northward; eddies are responsible for an enhancement of the mean flow and the variability of the MOC. Results from experiments (ii) show a transitional behavior of the MOC related to the eddy generation in interannual-decadal time scales as the Reynolds number varies due to the variations in the MOC. In experiments (iii), a critical Reynolds number Re(c) around 30 is found, above which eddies are generated. Experiments (iv) demonstrate that even after the collapse of MOC in the Northern Hemisphere, eddies can still be generated and carry energy across the equator into the Northern Hemisphere; these eddies act to attenuate the impact of the MOC shutdown on short time scales. The results described here may be particularly pertinent to ocean general circulation models in which the Reynolds number lies close to the bifurcation point separating the laminar and turbulent regimes.

The impact of the subtropical South Atlantic SST on South American precipitation

The Community Climate Model (CCM3) from the National Center for Atmospheric Research (NCAR) is used to investigate the effect of the South Atlantic sea surface temperature (SST) anomalies on interannual to decadal variability of South American precipitation. Two ensembles composed of multidecadal simulations forced with monthly SST data from the Hadley Centre for the period 1949 to 2001 are analysed. A statistical treatment based on signal-to-noise ratio and Empirical Orthogonal Functions (EOF) is applied to the ensembles in order to reduce the internal variability among the integrations. The ensemble treatment shows a spatial and temporal dependence of reproducibility. High degree of reproducibility is found in the tropics while the extratropics is apparently less reproducible. Austral autumn (MAM) and spring (SON) precipitation appears to be more reproducible over the South America-South Atlantic region than the summer (DJF) and winter (JJA) rainfall. While the Inter-tropical Convergence Zone (ITCZ) region is dominated by external variance, the South Atlantic Convergence Zone (SACZ) over South America is predominantly determined by internal variance, which makes it a difficult phenomenon to predict. Alternatively, the SACZ over western South Atlantic appears to be more sensitive to the subtropical SST anomalies than over the continent. An attempt is made to separate the atmospheric response forced by the South Atlantic SST anomalies from that associated with the El Nino - Southern Oscillation (ENSO). Results show that both the South Atlantic and Pacific SSTs modulate the intensity and position of the SACZ during DJF. Particularly, the subtropical South Atlantic SSTs are more important than ENSO in determining the position of the SACZ over the southeast Brazilian coast during DJF. On the other hand, the ENSO signal seems to influence the intensity of the SACZ not only in DJF but especially its oceanic branch during MAM. Both local and remote influences, however, are confounded by the large internal variance in the region. During MAM and JJA, the South Atlantic SST anomalies affect the magnitude and the meridional displacement of the ITCZ. In JJA, the ENSO has relatively little influence on the interannual variability of the simulated rainfall. During SON, however, the ENSO seems to counteract the effect of the subtropical South Atlantic SST variations on convection over South America.

INTERANNUAL VARIABILITY IN TROPICAL ESTUARINE COPEPOD ASSEMBLAGES OFF NORTHEASTERN BRAZIL

We studied copepod assemblage variability among years, seasons, and tidal states in the Mucuri River estuary (Bahia State, Brazil). Zooplankton samples were collected seasonally through five years (2002-2006) at three sampling stations, one of which was sampled over a complete tidal cycle (two ebb and two flood tides). Temperature, salinity, river flux, and rainfall data were collected. Winter and summer represented dry and wet seasons, respectively. Copepod abundances ranged from 40 to 63% of the total zooplankton assemblage and comprised 46 taxa, among which, common estuarine species such as Temora turbinata (first record for the studied area), Parvocalanus crassirostris, Acartia lilljeborgi, Oithona hebes were the most abundant (euryhaline species). Interannual and seasonal variations were most marked in stenohaline species, e.g.. Notodiaptomus sp. and Thermocyclops minutus; density variations of euryhaline species, which made up the majority of the abundant taxa, were most closely related to tides. Diversity and richness also followed an intertidal pattern of variation.

Intraspecific variability of dihydrochalcone, chromenes and benzoic acid derivatives in leaves of Piper aduncum L. (Piperaceae)

Chemical analysis carried out in leaves of 18 specimens of Piper aduncum L. (Piperaceae) occurring at Ripasa Reserve, Araraquara, SP, Brazil indicated two distinct populations when investigated over a period of 14 months (January 2000 to February 2001) and then submitted to cluster analysis. The two groups were characterized by accumulation of prenylated benzoic acids, chromenes and dihydrochalcone, respectively. A total of seven compounds were identified by HPLC analysis and compared with standards including two prenylated benzoic acid [aduncumene (1) and 3-(3'-7'-dimethyl-2'-6'-octadienyl)-4-methoxy-benzoic acid (5)], four chromenes [methyl 2,2-dimethyl-8-(3'-methyl-2'-butenyl)-2H-1-chromene-6-carboxylate (4), methyl 2,2-dimethyl-2H-1-chromene-6-carboxylate (2b), methyl 8-hydroxy-2,2-dimethyl-2H-1-chromene-6-carboxylate (3) and 2,2-dimethyl-2H-1-chromene-6-carboxylic acid (2a)] and one dihydrochalcone [2',6'-dihydroxy-4'-methoxy-dihydrochalcone (6)].

Mechanism and model of the oscillatory electro-oxidation of methanol

A mechanism for the kinetic instabilities observed in the galvanostatic electro-oxidation of methanol is suggested and a model developed. The model is investigated using stoichiometric network analysis as well as concepts from algebraic geometry (polynomial rings and ideal theory) revealing the occurrence of a Hopf and a saddle-node bifurcation. These analytical solutions are confirmed by numerical integration of the system of differential equations. (C) 2010 American Institute of Physics

Environmental and grazing influence on spatial variability of intertidal biofilm on subtropical rocky shores

Epilithic biofilm on rocky shores is regulated by physico-chemical and biological factors and is important as a source of food for benthic organisms. The influences of environmental and grazing pressure on spatial variability of biomass of biofilm were evaluated on shores on the north coast of Sao Paulo State (SE Brazil). A general trend of greater abundance of microalgae was observed lower on the shore, but neither of the environmental factors evaluated (wave exposure and shore level) showed consistent effects, and differences were found among specific shores or times (September 2007 and March 2008). The abundance of slow-moving grazers (limpets and littorinids) showed a negative correlation with chlorophyll a concentration on shores. However, experimental exclusion of these grazers failed to show consistent results at small spatial scales. Observations of divergent abundances of the isopod Ligia exotica and biomass of biofilm on isolated boulders on shores led to a short exclusion experiment, where the grazing pressure by L. exotica significantly decreased microalgal biomass. The result suggests that grazing activities of this fast-moving consumer probably mask the influence of slow-moving grazers at small spatial scales, while both have an additive effect at larger scales that masks environmental influences. This is the first evaluation of the impact of the fast-moving herbivore L. exotica on microalgal biomass on rocky shores and opens an interesting discussion about the role of these organisms in subtropical coastal environments.

Simulation of Soil Carbon Dynamics under Sugarcane with the CENTURY Model

Currently there is a trend for the expansion of the area cropped with sugarcane (Saccharum officinarum L.), driven by an increase in the world demand for biofuels, due to economical, environmental, and geopolitical issues. Although sugarcane is traditionally harvested by burning dried leaves and tops, the unburned, mechanized harvest has been progressively adopted. The use of process based models is useful in understanding the effects of plant litter in soil C dynamics. The objective of this work was to use the CENTURY model in evaluating the effect of sugarcane residue management in the temporal dynamics of soil C. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of soil C, validating the model through field experiment data, and finally to make predictions in the long term regarding soil C. The main focus of this work was the comparison of soil C stocks between the burned and unburned litter management systems, but the effect of mineral fertilizer and organic residue applications were also evaluated. The simulations were performed with data from experiments with different durations, from 1 to 60 yr, in Goiana and Timbauba, Pernambuco, and Pradopolis, Sao Paulo, all in Brazil; and Mount Edgecombe, Kwazulu-Natal, South Africa. It was possible to simulate the temporal dynamics of soil C (R(2) = 0.89). The predictions made with the model revealed that there is, in the long term, a trend for higher soil C stocks with the unburned management. This increase is conditioned by factors such as climate, soil texture, time of adoption of the unburned system, and N fertilizer management.

Intra and interannual variability in the Madeira River water chemistry and sediment load

Concentrations of cations (Na(+), Ca(2+), Mg(2+), K(+), NH(4) (+)), anions (HCO(3) (-), Cl(-), NO(3) (-), SO(4) (2-), PO(4) (3-)) and suspended sediments in the Madeira River water were determined near the city of Porto Velho (RO), in order to assess variation in water chemistry from 2004 to 2007. Calcium and bicarbonate were the dominant cation and anion, respectively. Significant seasonal differences were found, with highest concentrations occurring during the dry season, as expected from the drainage of Andean carbonate-rich substratum. Interannual variations were also observed, but became significant only when annual average discharge was 25% less than normal. Under this atypical discharge condition, bicarbonate was replaced by sulfate, and higher suspended sediment concentrations and loads were also observed. Compared to previously published studies, it appears that no significant changes in water chemistry have occurred during the last 20-30 years, although differences in approaches and sampling designs among this and previous studies may not allow detection of modest changes. The calculated suspended sediment load reported here is close to the values presented elsewhere, reinforcing the relative importance of this river as a sediment supplier for the Amazon Basin. Seasonality has a significant control on the chemistry of Madeira River waters, and severe decrease in discharge due to anthropogenic changes, such as construction of reservoirs or the occurrence of drier years-a plausible consequence of global climate change-may lead to modification in the chemical composition as well in the sediment deliver to the Amazon River.

Multifractal regime transition in a modified minority game model

The search for more realistic modeling of financial time series reveals several stylized facts of real markets. In this work we focus on the multifractal properties found in price and index signals. Although the usual minority game (MG) models do not exhibit multifractality, we study here one of its variants that does. We show that the nonsynchronous MG models in the nonergodic phase is multifractal and in this sense, together with other stylized facts, constitute a better modeling tool. Using the structure function (SF) approach we detected the stationary and the scaling range of the time series generated by the MG model and, from the linear (non-linear) behavior of the SF we identified the fractal (multifractal) regimes. Finally, using the wavelet transform modulus maxima (WTMM) technique we obtained its multifractal spectrum width for different dynamical regimes. (C) 2009 Elsevier Ltd. All rights reserved.

An opinion dynamics model for the diffusion of innovations

We study the dynamics of the adoption of new products by agents with continuous opinions and discrete actions (CODA). The model is such that the refusal in adopting a new idea or product is increasingly weighted by neighbor agents as evidence against the product. Under these rules, we study the distribution of adoption times and the final proportion of adopters in the population. We compare the cases where initial adopters are clustered to the case where they are randomly scattered around the social network and investigate small world effects on the final proportion of adopters. The model predicts a fat tailed distribution for late adopters which is verified by empirical data. (C) 2009 Elsevier B.V. All rights reserved.