Filipa Alves - Academia.edu (original) (raw)

Papers by Filipa Alves

Research paper thumbnail of Additive and non‐additive effects of day and night temperatures on thermally plastic traits in a model for adaptive seasonal plasticity

Evolution

Developmental plasticity can match organismal phenotypes to ecological conditions, helping popula... more Developmental plasticity can match organismal phenotypes to ecological conditions, helping populations to deal with the environmental heterogeneity of alternating seasons. In contrast to natural situations, experimental studies of plasticity often use environmental conditions that are held constant during development. To explore potential interactions between day and night temperatures, we tested effects of circadian temperature fluctuations on thermally plastic traits in a seasonally plastic butterfly, Bicyclus anynana. Comparing phenotypes for four treatments corresponding to a full‐factorial analysis of cooler and warmer temperatures, we found evidence of significant interaction effects between day and night temperatures. We then focused on comparing phenotypes between individuals reared under two types of temperature fluctuations (warmer days with cooler nights, and cooler days with warmer nights) and individuals reared under a constant temperature of the same daily mean. We found evidence of additive‐like effects (for body size), and different types of dominance‐like effects, with one particular period of the light cycle (for development time) or one particular extreme temperature (for eyespot size) having a larger impact on phenotype. Differences between thermally plastic traits, which together underlie alternative seasonal strategies for survival and reproduction, revealed their independent responses to temperature. This study underscores the value of studying how organisms integrate complex environmental information toward a complete understanding of natural phenotypic variation and of the impact of environmental change thereon.

Research paper thumbnail of Many ways to make darker flies: Intra- and inter-specific variation in Drosophila body pigmentation components

ABSTRACTBody pigmentation is an evolutionarily diversified and ecologically relevant trait that s... more ABSTRACTBody pigmentation is an evolutionarily diversified and ecologically relevant trait that shows variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution and its ecological and genetic bases. Yet, while pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, its study frequently focuses on one single aspect. Here, we develop a method to quantify color and color pattern in Drosophila body pigmentation, decomposing thorax and abdominal pigmentation into distinct measurable traits, and we quantify different sources of variation in those traits. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate the two body parts. By focusing on two standard D. melanoga...

Research paper thumbnail of Complex effects of day and night temperature fluctuations on thermally plastic traits in a seasonal plasticity model

BackgroundChanges in development in response to seasonally variable environments can produce phen... more BackgroundChanges in development in response to seasonally variable environments can produce phenotypes adjusted to fluctuating seasonal conditions and help organisms cope with temporal heterogeneity. In contrast to what happens in natural situations, experimental studies of developmental plasticity typically use environmental factors held constant during development, precluding assessment of potential environment-by-environment interaction effects.ResultsWe tested effects of circadian fluctuations in temperature on a series of thermally plastic traits in a model of adaptive seasonal plasticity, the butterfly Bicyclus anynana. Comparing phenotypes from individuals reared under two types of fluctuations (warmer days with cooler nights, and cooler days with warmer nights) and those reared under a constant temperature of the same daily average allowed us to identify complex patterns of response to day and night temperatures. We found evidence of additive-like effects (for body size), b...

Research paper thumbnail of Pattern Formation and Wound Healing : Experimental and Theoretical Approaches

Patterning and wound healing are intricately connected mechanisms in organism development and of ... more Patterning and wound healing are intricately connected mechanisms in organism development and of significant importance for biomedicine. These mechanisms can be studied both experimentally and theoretically using butterfly wing patterns. Butterfly wings are nearly two-dimensional structures, covered by a single layer of overlapping monochromatic scales. Many colors and kinds of scales generate highly diverse mosaics. This extraordinary variation makes butterfly wing patterns an excellent model to study the role of positional information in cell fate determination both in “normal” patterns and in patterns induce by damage. In this thesis, mathematical modelling is used to describe pattern formation. The model takes into account positional information via signalling molecules and activation of spatially defined expression patterns of transcription factors. The simplest gene regulatory network found to be compatible with experimental results is proposed to describe pattern formation in...

Research paper thumbnail of Modeling segmental patterning in Drosophila: Maternal and gap genes

Journal of Theoretical Biology, 2006

We propose a new mathematical model describing the establishment of maternal and gap proteins seg... more We propose a new mathematical model describing the establishment of maternal and gap proteins segmental patterning along the antero-posterior axis of the Drosophila early embryo. This model is based on experimental data and, without recurring to pre-defined activation thresholds, predicts qualitatively and quantitatively the expression patterns of the maternal and gap proteins, as well as the expression patterns of proteins resulting from mRNA ectopic expression and from some loss-of-function mutations. We conclude that the gap genes segmental patterning and consequent spatial organization of the embryo is determined by three main factors: (1) the initial positioning of the maternal bicoid and torso mRNA inside the egg, and subsequent diffusion of the corresponding proteins; (2) the structure of the genetic regulatory network; (3) the role of conservation laws in the establishment of steady and non-uniform spatial distributions of non-diffusing proteins. r

Research paper thumbnail of A Software Tool to Model Genetic Regulatory Networks: Applications to Segmental Patterning in Drosophila

BIOMAT 2005 - Proceedings of the International Symposium on Mathematical and Computational Biology, 2006

Based on the bimolecular mass action law and the derived mass conservation laws, we have proposed... more Based on the bimolecular mass action law and the derived mass conservation laws, we have proposed a mathematical framework in order to describe the regulation of gene expression in prokaryotes (F. Alves, R. Dilão, C. R. Biologies 328 ). Within this framework, a genetic regulatory network is described by a system of ordinary differential equations. As the number of equations increases exponentially with the number of genes and interactions in the network, we have developed a software package to write symbolically the associated system of differential equations. With this software package, GeNetSim, it is possible to follow in time the concentration of proteins and genes of the network. We show some applications of GeNetSim to the modeling of a genetic regulatory network involved in the segmentation of the embryo of Drosophila.

Research paper thumbnail of A simple framework to describe the regulation of gene expression in prokaryotes

Comptes Rendus Biologies, 2005

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mat... more Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments. To cite this article: F. Alves, R. Dilão, C. R. Biologies 328 (2005).  2005 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Research paper thumbnail of The role of ion fluxes in polarized cell growth and morphogenesis: the pollen tube as an experimental paradigm

International Journal of Developmental Biology, 2009

In order to cope with reproduction in a dry environment without any sort of motility, plants have... more In order to cope with reproduction in a dry environment without any sort of motility, plants have developed a very specialized and unique sexual system. Of special notice, the two sperm cells that will perform the double fertilization typical of higher plants are carried by one of the fastest growing cells in nature, the pollen tube. This tube develops from the vegetative cell of the pollen grain upon germination on the female tissues. While it cannot be considered as a canonical excitable cell, pollen tubes depend for most of their fundamental functional features on a close regulation of ion dynamics, namely in terms of polarization of extracellular fluxes and formation of standing cytosolic free ion gradients, namely of calcium (Ca 2+ ) and protons (H + ). In turn, these imply that plasma membrane transporters are polarized, or polarly regulated, and that internal signaling cascades transduce this spatial information into the basic features of growth and morphogenesis needed for pollen tubes to target correctly the ovules and discharge the sperm cells. Because of the singularity of this organization, and the ease with which pollen tubes can be experimentally handled, recent years have witnessed an accumulation of data at many levels, from basic biophysical and cell biology characterization, to gene assignment and transcriptomic description of pollen development. In this review we aim to organize this information in terms of the basic biophysical features of membrane function and integrate it into conceptual testable hypotheses on how the dynamics of ion regulation may underlie fundamental properties of cell development.

Research paper thumbnail of A simple framework to describe the regulation of gene expression in prokaryotes

Comptes Rendus Biologies, 2005

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mat... more Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments. To cite this article: F. Alves, R. Dilão, C. R. Biologies 328 (2005).  2005 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Research paper thumbnail of Modeling segmental patterning in Drosophila: Maternal and gap genes

Journal of Theoretical Biology, 2006

We propose a new mathematical model describing the establishment of maternal and gap proteins seg... more We propose a new mathematical model describing the establishment of maternal and gap proteins segmental patterning along the antero-posterior axis of the Drosophila early embryo. This model is based on experimental data and, without recurring to pre-defined activation thresholds, predicts qualitatively and quantitatively the expression patterns of the maternal and gap proteins, as well as the expression patterns of proteins resulting from mRNA ectopic expression and from some loss-of-function mutations. We conclude that the gap genes segmental patterning and consequent spatial organization of the embryo is determined by three main factors: (1) the initial positioning of the maternal bicoid and torso mRNA inside the egg, and subsequent diffusion of the corresponding proteins; (2) the structure of the genetic regulatory network; (3) the role of conservation laws in the establishment of steady and non-uniform spatial distributions of non-diffusing proteins. r

Research paper thumbnail of Additive and non‐additive effects of day and night temperatures on thermally plastic traits in a model for adaptive seasonal plasticity

Evolution

Developmental plasticity can match organismal phenotypes to ecological conditions, helping popula... more Developmental plasticity can match organismal phenotypes to ecological conditions, helping populations to deal with the environmental heterogeneity of alternating seasons. In contrast to natural situations, experimental studies of plasticity often use environmental conditions that are held constant during development. To explore potential interactions between day and night temperatures, we tested effects of circadian temperature fluctuations on thermally plastic traits in a seasonally plastic butterfly, Bicyclus anynana. Comparing phenotypes for four treatments corresponding to a full‐factorial analysis of cooler and warmer temperatures, we found evidence of significant interaction effects between day and night temperatures. We then focused on comparing phenotypes between individuals reared under two types of temperature fluctuations (warmer days with cooler nights, and cooler days with warmer nights) and individuals reared under a constant temperature of the same daily mean. We found evidence of additive‐like effects (for body size), and different types of dominance‐like effects, with one particular period of the light cycle (for development time) or one particular extreme temperature (for eyespot size) having a larger impact on phenotype. Differences between thermally plastic traits, which together underlie alternative seasonal strategies for survival and reproduction, revealed their independent responses to temperature. This study underscores the value of studying how organisms integrate complex environmental information toward a complete understanding of natural phenotypic variation and of the impact of environmental change thereon.

Research paper thumbnail of Many ways to make darker flies: Intra- and inter-specific variation in Drosophila body pigmentation components

ABSTRACTBody pigmentation is an evolutionarily diversified and ecologically relevant trait that s... more ABSTRACTBody pigmentation is an evolutionarily diversified and ecologically relevant trait that shows variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution and its ecological and genetic bases. Yet, while pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, its study frequently focuses on one single aspect. Here, we develop a method to quantify color and color pattern in Drosophila body pigmentation, decomposing thorax and abdominal pigmentation into distinct measurable traits, and we quantify different sources of variation in those traits. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate the two body parts. By focusing on two standard D. melanoga...

Research paper thumbnail of Complex effects of day and night temperature fluctuations on thermally plastic traits in a seasonal plasticity model

BackgroundChanges in development in response to seasonally variable environments can produce phen... more BackgroundChanges in development in response to seasonally variable environments can produce phenotypes adjusted to fluctuating seasonal conditions and help organisms cope with temporal heterogeneity. In contrast to what happens in natural situations, experimental studies of developmental plasticity typically use environmental factors held constant during development, precluding assessment of potential environment-by-environment interaction effects.ResultsWe tested effects of circadian fluctuations in temperature on a series of thermally plastic traits in a model of adaptive seasonal plasticity, the butterfly Bicyclus anynana. Comparing phenotypes from individuals reared under two types of fluctuations (warmer days with cooler nights, and cooler days with warmer nights) and those reared under a constant temperature of the same daily average allowed us to identify complex patterns of response to day and night temperatures. We found evidence of additive-like effects (for body size), b...

Research paper thumbnail of Pattern Formation and Wound Healing : Experimental and Theoretical Approaches

Patterning and wound healing are intricately connected mechanisms in organism development and of ... more Patterning and wound healing are intricately connected mechanisms in organism development and of significant importance for biomedicine. These mechanisms can be studied both experimentally and theoretically using butterfly wing patterns. Butterfly wings are nearly two-dimensional structures, covered by a single layer of overlapping monochromatic scales. Many colors and kinds of scales generate highly diverse mosaics. This extraordinary variation makes butterfly wing patterns an excellent model to study the role of positional information in cell fate determination both in “normal” patterns and in patterns induce by damage. In this thesis, mathematical modelling is used to describe pattern formation. The model takes into account positional information via signalling molecules and activation of spatially defined expression patterns of transcription factors. The simplest gene regulatory network found to be compatible with experimental results is proposed to describe pattern formation in...

Research paper thumbnail of Modeling segmental patterning in Drosophila: Maternal and gap genes

Journal of Theoretical Biology, 2006

We propose a new mathematical model describing the establishment of maternal and gap proteins seg... more We propose a new mathematical model describing the establishment of maternal and gap proteins segmental patterning along the antero-posterior axis of the Drosophila early embryo. This model is based on experimental data and, without recurring to pre-defined activation thresholds, predicts qualitatively and quantitatively the expression patterns of the maternal and gap proteins, as well as the expression patterns of proteins resulting from mRNA ectopic expression and from some loss-of-function mutations. We conclude that the gap genes segmental patterning and consequent spatial organization of the embryo is determined by three main factors: (1) the initial positioning of the maternal bicoid and torso mRNA inside the egg, and subsequent diffusion of the corresponding proteins; (2) the structure of the genetic regulatory network; (3) the role of conservation laws in the establishment of steady and non-uniform spatial distributions of non-diffusing proteins. r

Research paper thumbnail of A Software Tool to Model Genetic Regulatory Networks: Applications to Segmental Patterning in Drosophila

BIOMAT 2005 - Proceedings of the International Symposium on Mathematical and Computational Biology, 2006

Based on the bimolecular mass action law and the derived mass conservation laws, we have proposed... more Based on the bimolecular mass action law and the derived mass conservation laws, we have proposed a mathematical framework in order to describe the regulation of gene expression in prokaryotes (F. Alves, R. Dilão, C. R. Biologies 328 ). Within this framework, a genetic regulatory network is described by a system of ordinary differential equations. As the number of equations increases exponentially with the number of genes and interactions in the network, we have developed a software package to write symbolically the associated system of differential equations. With this software package, GeNetSim, it is possible to follow in time the concentration of proteins and genes of the network. We show some applications of GeNetSim to the modeling of a genetic regulatory network involved in the segmentation of the embryo of Drosophila.

Research paper thumbnail of A simple framework to describe the regulation of gene expression in prokaryotes

Comptes Rendus Biologies, 2005

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mat... more Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments. To cite this article: F. Alves, R. Dilão, C. R. Biologies 328 (2005).  2005 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Research paper thumbnail of The role of ion fluxes in polarized cell growth and morphogenesis: the pollen tube as an experimental paradigm

International Journal of Developmental Biology, 2009

In order to cope with reproduction in a dry environment without any sort of motility, plants have... more In order to cope with reproduction in a dry environment without any sort of motility, plants have developed a very specialized and unique sexual system. Of special notice, the two sperm cells that will perform the double fertilization typical of higher plants are carried by one of the fastest growing cells in nature, the pollen tube. This tube develops from the vegetative cell of the pollen grain upon germination on the female tissues. While it cannot be considered as a canonical excitable cell, pollen tubes depend for most of their fundamental functional features on a close regulation of ion dynamics, namely in terms of polarization of extracellular fluxes and formation of standing cytosolic free ion gradients, namely of calcium (Ca 2+ ) and protons (H + ). In turn, these imply that plasma membrane transporters are polarized, or polarly regulated, and that internal signaling cascades transduce this spatial information into the basic features of growth and morphogenesis needed for pollen tubes to target correctly the ovules and discharge the sperm cells. Because of the singularity of this organization, and the ease with which pollen tubes can be experimentally handled, recent years have witnessed an accumulation of data at many levels, from basic biophysical and cell biology characterization, to gene assignment and transcriptomic description of pollen development. In this review we aim to organize this information in terms of the basic biophysical features of membrane function and integrate it into conceptual testable hypotheses on how the dynamics of ion regulation may underlie fundamental properties of cell development.

Research paper thumbnail of A simple framework to describe the regulation of gene expression in prokaryotes

Comptes Rendus Biologies, 2005

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mat... more Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments. To cite this article: F. Alves, R. Dilão, C. R. Biologies 328 (2005).  2005 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Research paper thumbnail of Modeling segmental patterning in Drosophila: Maternal and gap genes

Journal of Theoretical Biology, 2006

We propose a new mathematical model describing the establishment of maternal and gap proteins seg... more We propose a new mathematical model describing the establishment of maternal and gap proteins segmental patterning along the antero-posterior axis of the Drosophila early embryo. This model is based on experimental data and, without recurring to pre-defined activation thresholds, predicts qualitatively and quantitatively the expression patterns of the maternal and gap proteins, as well as the expression patterns of proteins resulting from mRNA ectopic expression and from some loss-of-function mutations. We conclude that the gap genes segmental patterning and consequent spatial organization of the embryo is determined by three main factors: (1) the initial positioning of the maternal bicoid and torso mRNA inside the egg, and subsequent diffusion of the corresponding proteins; (2) the structure of the genetic regulatory network; (3) the role of conservation laws in the establishment of steady and non-uniform spatial distributions of non-diffusing proteins. r