Assigning Degrees of Stochasticity to Blazar Light Curves in the Radio Band Using Complex Networks.

We focus on characterizing the high-energy emission mechanisms of blazars by analyzing the variability in the radio band of the light curves of more than a thousand sources. We are interested in assigning complexity parameters to these sources, modeling the time series of the light curves with the method of the Horizontal Visibility Graph (HVG), which allows us to obtain properties from degree distributions, such as a characteristic exponent to describe its stochasticity and the Kullback-Leibler Divergence (KLD), presenting a new perspective to the methods commonly used to study Active Galactic Nuclei (AGN). We contrast these parameters with the excess variance, which is an astronomical measurement of variability in light curves; at the same time, we use the spectral classification of the sources. While it is not possible to find significant correlations with the excess variance, the degree distributions extracted from the network are detecting differences related to the spectral classification of blazars. These differences suggest a chaotic behavior in the time series for the BL Lac sources and a correlated stochastic behavior in the time series for the FSRQ sources. Our results show that complex networks may be a valuable alternative tool to study AGNs according to the variability of their energy output.

A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization.

The genome tridimensional (3D) organization and its role towards the regulation of key cell processes such as transcription is currently a main question in biology. Interphase chromosomes are spatially segregated into "territories," epigenetically-defined large domains of chromatin that interact to form "compartments" with common transcriptional status, and insulator-flanked domains called "topologically associating domains" (TADs). Moreover, chromatin organizes around nuclear structures such as lamina, speckles, or the nucleolus to acquire a higher-order genome organization. Due to recent technological advances, the different hierarchies are being solved. Particularly, advances in microscopy technologies are shedding light on the genome structure at multiple levels. Intriguingly, more and more reports point to high variability and stochasticity at the single-cell level. However, the functional consequences of such variability in genome conformation are still unsolved. Here, I will discuss the implication of the cell-to-cell heterogeneity at the different scales in the context of newly developed imaging approaches, particularly multiplexed Fluorescence in situ hybridization methods that enabled "chromatin tracing." Extensions of these methods are now combining spatial information of dozens to thousands of genomic loci with the localization of nuclear features such as the nucleolus, nuclear speckles, or even histone modifications, creating the fast-moving field of "spatial genomics." As our view of genome organization shifts the focus from ensemble to single-cell, new insights to fundamental questions begin to emerge.

Viability of the vaquita, Phocoena sinus (Cetacea: Phocoenidae) population, threatened by poaching of Totoaba macdonaldi (Perciformes: Sciaenidae) / Viabilidad de la población de vaquita marina, Phocoena sinus (Cetacea: Phocoenidae), amenazada por la pesca ilegal de Totoaba macdonaldi (Perciformes: Sciaenidae)

Abstract Introduction: Despite extensive science-based conservation policy recommendations, with fewer than 20 individuals remaining, the vaquita (Phocoena sinus) -endemic to the Gulf of California- is the world's most endangered marine mammal due to incidental catch in fishing nets and whether it can recover is unclear. Objective: Assess expectations for vaquita over the next two decades. Methods: We identified factors affecting the vaquita, constructed life tables, derived demographic parameters for different scenarios and conducted a population viability analysis using stochastic age-structured matrix Leslie models. Results: Analytical results indicate that the vaquita net growth rate is particularly sensitive to juvenile survival. We find that intensive, ongoing bycatch in gillnets used to poach totoaba (Totoaba macdonaldi) over the past decade brought the vaquita population to its current critically low size. Currently this seems to be exacerbated by demographic stochasticity and a potential Allee effect. Conclusions: If totoaba poaching is eliminated immediately, demographically, vaquita can recover; its long-term survival will depend on its uncertain genetic status, although a recent study found encouraging results in this regard.

Resumen Introducción: Pese a las acciones de conservación basadas en la ciencia y las políticas recomendadas, con menos de 20 individuos sobrevivientes, la vaquita (Phocoena sinus) -endémica del Golfo de California- es el mamífero marino más amenazado del mundo debido a su muerte incidental en redes de pesca; una pregunta relevante es si su población se puede recuperar. Objetivo: Evaluar las expectativas para la vaquita marina durante los próximos 20 años. Métodos: Identificamos los factores que afectan a la vaquita marina, construimos tablas de vida, derivamos parámetros demográficos para diferentes escenarios y realizamos un análisis de viabilidad poblacional utilizando matrices estocásticas de Leslie, estructuradas por edad. Resultados: La tasa de crecimiento neto de la vaquita es muy sensible a la supervivencia de los juveniles. Encontramos que la captura incidental intensiva y continua en redes de enmalle para la pesca furtiva de totoaba (Totoaba macdonaldi) durante la última década llevó a la población de vaquitas a su actual estado crítico. Esto parece agravarse por la estocasticidad demográfica y un potencial efecto Allee. Conclusiones: Si la pesca furtiva de totoaba se elimina de inmediato, demográficamente la vaquita puede recuperarse; su supervivencia a largo plazo dependerá de su incierto estatus genético, aunque los resultados de un estudio reciente son alentadores en este sentido.

Community size can affect the signals of ecological drift and niche selection on biodiversity.

Ecological drift can override the effects of deterministic niche selection on small populations and drive the assembly of some ecological communities. We tested this hypothesis with a unique data set sampled identically in 200 streams in two regions (tropical Brazil and boreal Finland) that differ in macroinvertebrate community size by fivefold. Null models allowed us to estimate the magnitude to which ß-diversity deviates from the expectation under a random assembly process while taking differences in richness and relative abundance into account, i.e., ß-deviation. We found that both abundance- and incidence-based ß-diversity was negatively related to community size only in Brazil. Also, ß-diversity of small tropical communities was closer to stochastic expectations compared with ß-diversity of large communities. We suggest that ecological drift may drive variation in some small communities by changing the expected outcome of niche selection, increasing the chances of species with low abundance and narrow distribution to occur in some communities. Habitat destruction, overexploitation, pollution, and reductions in connectivity have been reducing the size of biological communities. These environmental pressures might make smaller communities more vulnerable to novel conditions and render community dynamics more unpredictable. Incorporation of community size into ecological models should provide conceptual and applied insights into a better understanding of the processes driving biodiversity.

Adaptive Physiological and Morphological Adjustments Mediated by Intestinal Stem Cells in Response to Food Availability in Mice.

Several studies have evaluated plastic changes in the morphology of the digestive tract in rodents subjected to caloric restriction or restricted availability. Nevertheless, studies that link these morphological responses to physiological consequences are scarce. In order to investigate short-term plastic responses in the intestine, we acclimated adult Mus musculus (BALB/c) males for 20 days to four distinctive treatments: two caloric regimens (ad libitum and 60% of calorie ingestion) and two levels of periodicity of the regimens (continuous and stochastic treatment). At the end of the treatment we analyzed the cell proliferation and cell death dynamics of small intestinal crypts in these animals. In addition, we measured organ masses and lengths, hydrolytic digestive enzyme activities, and energy output from feces. Finally, in order to explore the metabolic changes generated by these dietary conditions we assessed the catabolic activity (i.e., enzymes) of the liver. Our results show that individuals acclimated to a continuous and 60% regimen presented longer intestines in comparison to the other treatments. Indeed, their intestines grew with a rate of 0.22 cm/day, generating a significant caloric reduction in the content of their feces. Besides, both mass and intestinal lengths were predicted strongly by the stabilization coefficient of BrdU+ proliferating cells per crypt, the latter correlating positively with the activity of n-aminopeptidases. Interestingly, by using pharmacological inhibition of the kinase mammalian target of rapamycin complex 1 (mTORC1) by Rapamycin, we were able to recapitulate similar changes in the proliferation dynamics of intestinal stem cells. Based on our results, we propose that the impact of caloric restriction on macroscopic variation in morphology and functional changes in digestive n-aminopeptidases occurs through synchronization in the proliferation rate of stem and/or progenitor cells located in the small intestinal crypts and requires mTORC1 as a key mediator. Hence, we suggest that an excessive stem and progenitor activity could result in increased crypts branching and might therefore underlie the reported intestinal tissue expansion in response to short-term caloric restriction. Summarizing, we demonstrate for the first time that short-term caloric restriction induces changes in the level of cell proliferation dynamics explaining in part digestive tract plasticity in adaptive performance.

Opposing mechanisms affect taxonomic convergence between tree assemblages during tropical forest succession.

Whether successional forests converge towards an equilibrium in species composition remains an elusive question, hampered by high idiosyncrasy in successional dynamics. Based on long-term tree monitoring in second-growth (SG) and old-growth (OG) forests in Costa Rica, we show that patterns of convergence between pairs of forest stands depend upon the relative abundance of species exhibiting distinct responses to the successional gradient. For instance, forest generalists contributed to convergence between SG and OG forests, whereas rare species and old-growth specialists were a source of divergence. Overall, opposing trends in taxonomic similarity among different subsets of species nullified each other, producing a net outcome of stasis over time. Our results offer an explanation for the limited convergence observed between pairwise communities and suggest that rare species and old-growth specialists may be prone to dispersal limitation, while the dynamics of generalists and second-growth specialists are more predictable, enhancing resilience in tropical secondary forests.

Evaluating multiple spatial scales to understand the distribution of anuran beta diversity in the Brazilian Atlantic Forest.

We partitioned the total beta diversity in the species composition of anuran tadpoles to evaluate if species replacement and nestedness components are congruent at different spatial resolutions in the Brazilian Atlantic Forest. We alternated the sampling grain and extent of the study area (among ponds at a site, among ponds within regions, among sites within regions, and among sites within regions pooled together) to assess the importance of anuran beta diversity components. We then performed variation partitioning to evaluate the congruence of environmental descriptors and geographical distance in explaining the spatial distribution of the species replacement and nestedness components. We found that species replacement was the main component of beta diversity, independent of the sampling grain and extent. Furthermore, when considering the same sampling grain and increasing the extent, the values of species replacement increased. On the other hand, when considering the same extent and increasing the sampling grain, the values of species replacement decreased. At the smallest sampling grain and extent, the environmental descriptors and geographic distance were not congruent and alternated in the percentage of variation explaining the spatial distribution of species replacement and nestedness. At the largest spatial scales (SSs), the biogeographical regions showed higher values of the percentage explaining the variation in the beta diversity components. We found high values of species replacement independently of the spatial resolution, but the processes driving community assembly seem to be dependent on the SS. At small scales, both stochastic and deterministic factors might be important processes structuring anuran tadpole assemblages. On the other hand, at a large spatial grain and extent, the processes restricting species distributions might be more effective for drawing inferences regarding the variation in anuran beta diversity in different regions of the Brazilian Atlantic Forest.

An impulsive fishery model with environmental stochasticity. Feasibility.

An environmental random-effect over a deterministic population model of a resource (e.g., a fish stock) is introduced. It is assumed that the harvest activity is concentrated at a non-predetermined sequence of instants, at which the abundance reaches a certain predetermined level, then falls abruptly by a constant capture quota (pulse harvesting). So, the abundance is modeled by a stochastic impulsive type differential equation, incorporating a standard Brownian motion in the per capita rate of growth. With this random effect, the pulse times are "stopping times" of the stochastic process. The proof of the finite expectation of the next access time, i.e., the feasibility of regulation, is the main result.

Protein Synthesis Driven by Dynamical Stochastic Transcription.

In this manuscript, we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations, while the dynamics of protein density is governed by a random differential equation. The coupling between the two processes is given by a stochastic perturbation whose statistics satisfies the master equations. In this approach, from the knowledge of the analytical time-dependent distribution of mRNA number, we are able to calculate the dynamics of the probability density of the protein population.

Experimental evolution of bet hedging under manipulated environmental uncertainty in Neurospora crassa.

All organisms are faced with environmental uncertainty. Bet-hedging theory expects unpredictable selection to result in the evolution of traits that maximize the geometric-mean fitness even though such traits appear to be detrimental over the shorter term. Despite the centrality of fitness measures to evolutionary analysis, no direct test of the geometric-mean fitness principle exists. Here, we directly distinguish between predictions of competing fitness maximization principles by testing Cohen's 1966 classic bet-hedging model using the fungus Neurospora crassa. The simple prediction is that propagule dormancy will evolve in proportion to the frequency of 'bad' years, whereas the prediction of the alternative arithmetic-mean principle is the evolution of zero dormancy as long as the expectation of a bad year is less than 0.5. Ascospore dormancy fraction in N. crassa was allowed to evolve under five experimental selection regimes that differed in the frequency of unpredictable 'bad years'. Results were consistent with bet-hedging theory: final dormancy fraction in 12 genetic lineages across 88 independently evolving samples was proportional to the frequency of bad years, and evolved both upwards and downwards as predicted from a range of starting dormancy fractions. These findings suggest that selection results in adaptation to variable rather than to expected environments.

Evidências do efeito Moran na sincronia populacional: uma demonstração em microcosmo experimental / Evidences of Moran effect in the population synchrony: a demonstration in experimental microcosm

São propostas três causas principais para sincronia de populações: fatores exógenos, dispersão e interações interespecíficas. O presente trabalho teve por objetivo testar a influência dos fatores exógenos na sincronia de populações de Sitophilus zeamais (Mots.) (Coleoptera: Curculionidae), isoladas espacialmente (sem dispersão), em microcosmos com diferentes condições ambientais (umidade e temperatura). Doze populações com 20 indivíduos cada, foram divididas, aleatoriamente, em dois tratamentos: com lâmpada e sem lâmpada. O censo dos indivíduos adultos foi realizado semanalmente, durante sete meses. A tendência de crescimento da abundância ao longo do tempo foi eliminada através do ajuste de modelos autoregressivos. A sincronia entre as populações, detectada por meio dos coeficientes de correlação de Pearson e Spearman, foi maior dentro do que entre tratamentos, embora as populações mantidas sem lâmpada tenham sido mais sincrônicas do que as populações com lâmpada. Além de evidenciarem a influência do ambiente nas flutuações populacionais, esses resultados sugerem que o metabolismo e as interações intraespecíficas são fatores importantes na dinâmica populacional. Organismos em ambientes desfavoráveis podem apresentar taxas metabólicas anormais, contribuindo pouco para o crescimento populacional. Logo, populações pequenas sofrem maior influência da estocasticidade demográfica, reduzindo a probabilidade de sincronia entre elas. Nos ambientes mais favoráveis, espera-se que os indivíduos desenvolvam funções metabólicas normais, levando as populações a apresentar taxas de crescimento mais elevadas. Nesse caso, a estocasticidade demográfica tem menor influência, levando as populações sem lâmpada a flutuar de forma mais sincrônica.

Three main causes to population synchrony are proposed: exogenous factors, dispersal and inter-specific interactions. This paper had as main goal to test the influence of the exogenous factors in the synchrony in spatially isolated (i.e., no dispersal) populations of Sitophilus zeamais (Mots.) (Coleoptera: Curculionidae), in microcosms with different environmental conditions (humidity, temperature and light intensity). Twelve populations of 20 individuals each, were randomly assigned between two treatment conditions: with or without light. Population size and environmental factors (temperature and relative humidity) were weekly assessed for seven months. Temporal trend in populations increase was eliminated adjusting autoregressive models. Population synchrony, detected by means of Pearson’s and Spearman’s correlation coefficients, was higher within than between treatments, although the populations kept without lamp were more synchronized than populations with lamp. Besides demonstrating the influence of environment on population fluctuations, these results suggest that metabolism and intra-specific interactions are important factors in population dynamic. Organisms exposed to unsuitable environmental conditions may have abnormal metabolic rates, which negatively influences the population grow. Thus, small populations are more likely to suffer from demographic stochasticity, decreasing the probability of the synchrony among populations. On the other hand, in more suitable environments, individuals are expected to have normal metabolic functions, and so, to achieve higher rates of population grow. In this case, the demographic stochasticity has smaller influence, leading populations without lamp to fluctuate synchronously.