Backward stochastic differential equation approach to modeling of gene expression

In this article, we introduce a novel backward method to model stochastic gene expression and protein level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of endpoint ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models. Numerical simulations show that the BSDE method is able to correctly infer the protein level distributions that preceded a known final condition, obtained originally from the forward SSA. This makes the BSDE method a powerful systems biology tool for time reversed simulations, allowing, for example, the assessment of the biological conditions (e.g. protein concentrations) that preceded an experimentally measured event of interest (e.g. mitosis, apoptosis, etc.).Comment: Accepted in Physical Review

On the bursting of gene products

In this article we demonstrate that the so-called bursting production of molecular species during gene expression may be an artifact caused by low time resolution in experimental data collection and not an actual burst in production. We reach this conclusion through an analysis of a two-stage and binary model for gene expression, and demonstrate that in the limit when mRNA degradation is much faster than protein degradation they are equivalent. The negative binomial distribution is shown to be a limiting case of the binary model for fast "on to off" state transitions and high values of the ratio between protein synthesis and degradation rates. The gene products population increases by unity but multiple times in a time interval orders of magnitude smaller than protein half-life or the precision of the experimental apparatus employed in its detection. This rare-and-fast one-by-one protein synthesis has been interpreted as bursting.Comment: 13 page

Lessons and perspectives for applications of stochastic models in biological and cancer research

The effects of randomness, an unavoidable feature of intracellular environments, are observed at higher hierarchical levels of living matter organization, such as cells, tissues, and organisms. Additionally, the many compounds interacting as a well-orchestrated network of reactions increase the difficulties of assessing these systems using only experiments. This limitation indicates that elucidation of the dynamics of biological systems is a complex task that will benefit from the establishment of principles to help describe, categorize, and predict the behavior of these systems. The theoretical machinery already available, or ones to be discovered to help solve biological problems, might play an important role in these processes. Here, we demonstrate the application of theoretical tools by discussing some biological problems that we have approached mathematically: fluctuations in gene expression and cell proliferation in the context of loss of contact inhibition. We discuss the methods that have been employed to provide the reader with a biologically motivated phenomenological perspective of the use of theoretical methods. Finally, we end this review with a discussion of new research perspectives motivated by our results

Diclidophora luscae (Monogenea: Diclidophoridae) in pouting, Trisopterus luscus (Linnaeus, 1758) from the northeast Atlantic; epidemiology, morphology, molecular and phylogenetic analysis

Diclidophora (Monogenea) species are gill parasites with a stenoxenic specifcity occurring only in Gadiformes. Epidemiologi‑cal, morphological, molecular and phylogenetic studies were performed on 594 Diclidophora specimens collected from 213 Trisopterus luscus captured in the northeast Atlantic of the Portuguese coast during 2012, 2013 and 2020. Prevalence, parasite abundance and infection intensity were determined. Positive correlation between fsh weight and length and infection intensity was observed. The efects of preservation on the parasite morphological features were studied, highlighting that specimen’s identifcation should be reinforced by molecular studies. A sequence of D. luscae capelanii from T. capelanus captured in the Mediterranean Sea included in the 28S rDNA molecular analysis was nested within a robust D. luscae clade. Data analysis suggested that this species is in fact D. luscae, which is compatible with T. luscus and T. capelanus. The identity of fsh hosts was confrmed by barcoding. For the frst time, data on the infection parameters is shown, highlighting the importance of including this parasite in the monitoring plans for a holistic approach with possible efects for the management of pouting resources aiming of attaining sustainable development and biodiversity conservation measures, according to the 14th objective of the 2030 agendainfo:eu-repo/semantics/publishedVersio

Representações da andropausa: um estudo de métodos mistos com mulheres portuguesas

Since psychosocial factors have some impact on andropause, and this phenomenon can affect conjugal relationships (and women tend to be health information seekers) it becomes important to study the representations of andropause using the Common-Sense Model – a model used to understand the representations of menopause. This research aimed to assess Portuguese women’s representations of andropause, the suitability of the Common-Sense Model in explaining those representations, and to explore differences among participants with different characteristics (e.g., level of education), regarding andropause representations. Interviews to 30 women were analysed (directed qualitative content analysis). A multiple correspondence analysis explored the association between the emergent categories. Mann-Whitney U tests were performed to test differences regarding the frequency of emergent categories. Undefined identity was the most frequently mentioned feature regarding andropause Identity, whereas Sexual Function was the most mentioned Negative Consequence; few Positive Consequences were mentioned, being the Absence of positives consequences and the Lack of information the most frequent ones. Two bidimensional models were found - one for Identity of andropause: (1) Aging related changes, and (2) Sexual changes/lack of information; the other for Negative Consequences: (1) Symptoms/health problems, and (2) Depression/lack of information. No differences were found in the frequency of andropause representations between women with different characteristics (e.g., with a romantic relationship vs. without a romantic relationship). The suitability of the Common-Sense Model to explain these women’s andropause representations did not differ among participants with distinctive characteristics. This research may help healthcare professionals to develop comprehensive interventions (based on this theoretical model) in order to help couples to better understand and cope with andropause.info:eu-repo/semantics/publishedVersio

Directives for Sustainability Management in the Amazon Forest Economy

This paper presents drivers to promote sustainable management in the forest economy in Rondocirc;nia, as an alternative to the traditional economic approach to forest resources. Therefore, the study questions how the forest management in the State of Rondocirc;nia can contribute as an alternative to the predatory use of the forest, mitigating the impact on the Amazonian socio-biodiversity. The general objective is to generate knowledge about the exploitation of timber and non-timber resources in Rondocirc;nia, and has as specific goals to promote the survey of the theme, as indicated in theory and according to practices carried out in the State of Rondocirc;nia / Brazil (1); to discuss the main characteristics of forest management with sustainability, promoting its multifaceted characterization in the face of commercial and intercropping (2); and finally, to address the alternative uses of Forest Management, indicating drivers and adaptive the spatial conditions of the Amazon region, specifically Rondocirc;nia (3). This research is characterized as qualitative with the method of content analysis; involved the raising of theoretical bases that describe the scenario of study and consultation of specialists, to promote the proficient contextualization, analysis, and inference of the results. It was verified that the drivers for sustainable forest management are alternatives to the predatory use of natural resources, providing the use of multiple conservative mechanisms, interrelating profitability and sustainable development, in favor of the emergence and consolidation of an integrated forest production chain with diversified industrial systems. This work is of interest to the scientific community and rural managers and producers since it offers a contribution to the management of forest resources with sustainability

Impact of Euro-Atlantic blocking patterns in Iberia precipitation using a novel high resolution dataset

In this work we reassess the impacts of blocking patterns on precipitation regimes in the Iberian Peninsula, distinguishing between north Atlantic and European blocking. For this we take full advantage of the recently developed high-resolution datasets for the Iberian countries. Precipitation anomalies during blocking events obtained with this dataset allow a much finer regional characterization of the impacts in both average and extreme daily precipitation, particularly when compared to widely used low-resolution reanalysis datasets. Blocked patterns induce a negative-positive dipole of precipitation anomalies from northwest to southeast Iberia. Increases are widespread during Atlantic blocks and pronounced in southern and eastern areas of Iberia, while during European blocks they are more spatially restricted, with increases above 50 % in coastal Mediterranean areas, which represents a considerable fraction of the annual precipitation. Blocking impacts in precipitation are nearly opposite to those found during strong zonal flow situations, but there are also some asymmetries in the precipitation responses. A significant increase in cyclones and cut-off lows frequency southwards of blocking structures is related to precipitation excesses over southern and eastern areas, where dynamical factors and local processes play a crucial role. On the contrary, precipitation deficits in northwest Iberia during blocking episodes are better explained by a reduction in north Atlantic frontal activity and simultaneous decreases in large-scale moisture advection towards northern Iberia. We show that these anomalies during blocking result from changes in precipitation amount rather than from increases in rainy days, pointing to more extreme rainfall regimes, particularly in southeastern Iberia. Finally, an Extreme Value Analysis was performed, fitting Generalized Pareto Distributions to precipitation extremes. Results show that the different extreme precipitation regimes of northwest and Mediterranean regions are partially determined by opposite anomalies of the zonal flow. Thus, heavy precipitation events in Mediterranean areas are usually short-lived and frequently associated with blocking conditions, while in northwest Iberia the total accumulations during rainfall episodes are more important for triggering extreme events and they are mainly related to strong westerly flows.Peer reviewe