Papers by Alexandre Ramos
In this manuscript we use an exactly solvable stochastic binary model for regulation of gene expr... more In this manuscript we use an exactly solvable stochastic binary model for regulation of gene expression to analyse the dynamics of response to a treatment aiming to modulate the number of transcripts of RKIP gene. We demonstrate the usefulness of our method simulating three treatment scenarios aiming to reestablish RKIP gene expression dynamics towards pre-cancerous state: i. to increase the promoter’s ON state duration; ii. to increase the mRNAs’ synthesis rate; iii. to increase both rates. We show that the pre-treatment kinetic rates of ON and OFF promoter switching speeds and mRNA synthesis and degradation will affect the heterogeneity and time for treatment response. Hence, we present a strategy for reducing drug dosage by simultaneously targeting multiple kinetic rates. That enables a reduction of treatment response time and heterogeneity which in principle diminishes the chances of emergence of resistance to treatment. This approach may be useful for inferring kinetic constant...
Entropy, 2020
The promoter state of a gene and its expression levels are modulated by the amounts of transcript... more The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter of a gene (the source) is communicated by the amounts of transcription factors that it expresses (the message) to modulate the state of the promoter and expression levels of another gene (the receptor). The reliability of the gene network dynamics can be quantified by Shannon’s entropy of the message and the mutual information between the message and the promoter state. Here we consider a stochastic model for a binary gene and use its exact steady state solutions to calculate the entropy and mutual information. We show that a slow switching promoter with long and equally standing ON and OFF states maximizes the mutual information and reduces entropy. That is a binary gene expression regime generating a high variance message governed by ...
Mathematical Biosciences and Engineering, 2020
This manuscript presents a comparison of noise properties exhibited by two stochastic binary mode... more This manuscript presents a comparison of noise properties exhibited by two stochastic binary models for: (i) a self-repressing gene; (ii) a repressed or activated externally regulating one. The stochastic models describe the dynamics of probability distributions governing two random variables, namely, protein numbers and the gene state as ON or OFF. In a previous work, we quantify noise in protein numbers by means of its Fano factor and write this quantity as a function of the covariance between the two random variables. Then we show that distributions governing the number of gene products can be super-Fano, Fano or sub-Fano if the covariance is, respectively, positive, null or negative. The latter condition is exclusive for the self-repressing gene and our analysis shows the conditions for which the Fano factor is a sufficient classifier of fluctuations in gene expression. In this work, we present the conditions for which the noise on the number of gene products generated from a self-repressing gene or an externally regulating one are quantitatively similar. That is important for inference of gene regulation from noise in gene expression quantitative data. Our results contribute to a classification of noise function in biological systems by theoretically demonstrating the mechanisms underpinning the higher precision in expression of a self-repressing gene in comparison with an externally regulated one.
Contact inhibition is a central feature orchestrating cell proliferation in culture experiments; ... more Contact inhibition is a central feature orchestrating cell proliferation in culture experiments; its loss is associated with malignant transformation and tumorigenesis. We performed a co-culture experiment with human metastatic melanoma cell line (SK-MEL-147) and immortalized keratinocyte cells (HaCaT). After 8 days a spatial pattern was detected, characterized by the formation of clusters of melanoma cells surrounded by keratinocytes constraining their proliferation. In addition, we observed that the proportion of melanoma cells within the total population has increased. To explain our results we propose a spatial stochastic model (following a philosophy of the Widom-Rowlinson model from Statistical Physics and Molecular Chemistry) which considers cell proliferation, death, migration, and cell-to-cell interaction through contact inhibition. Our numerical simulations demonstrate that loss of contact inhibition is a sufficient mechanism, appropriate for an explanation of the increase...
Randomness is an unavoidable feature of inner cellular environment and its effects propagate to h... more Randomness is an unavoidable feature of inner cellular environment and its effects propagate to higher levels of living matter organization such as cells, tissues, and organisms. Approaching those systems experimentally to understand their dynamics is a complex task because of the plethora of compounds interacting in a web that combines intra and inter level elements such that a coordinate behavior come up. Such a characteristic points to the necessity of establishing principles that help on the description, categorization, classification, and the prediction of the behavior of biological systems. The theoretical machinery already available, or the ones to be discovered motivated by biological problems, can play an important role on that quest. Here we exemplify the applicability 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 dis...
We chemically characterize the symmetries underlying the exact solutions of a stochastic negative... more We chemically characterize the symmetries underlying the exact solutions of a stochastic negatively self-regulating gene. The breaking of symmetry at low molecular number causes three effects. Two branches of the solution exist, having high and low switching rates, such that the low switching rate branch approaches deterministic behavior and the high switching rate branch exhibits sub-Fano behavior. Average protein number differs from the deterministically expected value. Bimodal probability distributions appear as the protein number becomes a readout of the ON/OFF state of the gene.
The Journal of Chemical Physics, 2019
We chemically characterize the symmetries underlying the exact solutions of a stochastic negative... more We chemically characterize the symmetries underlying the exact solutions of a stochastic negatively self-regulating gene. The breaking of symmetry at a low molecular number causes three effects. Two branches of the solution exist, having high and low switching rates, such that the low switching rate branch approaches deterministic behavior and the high switching rate branch exhibits sub-Fano behavior. The average protein number differs from the deterministically expected value. Bimodal probability distributions appear as the protein number becomes a readout of the ON/OFF state of the gene.
BMC systems biology, Jan 29, 2017
Models that incorporate specific chemical mechanisms have been successful in describing the activ... more Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite this, the minimum set of mechanisms required to reconstruct an enhancer from its constituent parts is not known. Synthetic biology offers the potential to test the sufficiency of known mechanisms to describe the activity of enhancers, as well as to uncover constraints on the number, order, and spacing of motifs. Using a functional model and in silico compensatory evolution, we generated putative synthetic even-skipped stripe 2 enhancers with varying degrees of similarity to the natural enhancer. These elements represent the evolutionary trajectories of the natural stripe 2 enhancer towards two synthetic enhancers designed ab initio. In the first trajectory, spatially regulated expression was maintained, even after more than a third of binding sites were lost. In the second, ...
PLoS Genetics, 2013
Rearrangements of about 2.5 kilobases of regulatory DNA located 59 of the transcription start sit... more Rearrangements of about 2.5 kilobases of regulatory DNA located 59 of the transcription start site of the Drosophila evenskipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small ''spacer'' segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2-3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cisregulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein-DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory ''elements'' are not elementary objects.
eLife, 2021
Metastasis suppression by high-dose, multi-drug targeting is unsuccessful due to network heteroge... more Metastasis suppression by high-dose, multi-drug targeting is unsuccessful due to network heterogeneity and compensatory network activation. Here, we show that targeting driver network signaling capacity by limited inhibition of core pathways is a more effective anti-metastatic strategy. This principle underlies the action of a physiological metastasis suppressor, Raf Kinase Inhibitory Protein (RKIP), that moderately decreases stress-regulated MAP kinase network activity, reducing output to transcription factors such as pro-metastastic BACH1 and motility-related target genes. We developed a low-dose four-drug mimic that blocks metastatic colonization in mouse breast cancer models and increases survival. Experiments and network flow modeling show limited inhibition of multiple pathways is required to overcome variation in MAPK network topology and suppress signaling output across heterogeneous tumor cells. Restricting inhibition of individual kinases dissipates surplus signal, prevent...
The Journal of Supercomputing, 2022
Communication latency has become one of the determining factors for the performance of parallel c... more Communication latency has become one of the determining factors for the performance of parallel clusters. To design low-latency network topologies for high-performance computing clusters, we optimize the diameters, mean path lengths, and bisection widths of circulant topologies. We obtain a series of optimal circulant topologies of size 2 5 through 2 10 and compare them with torus and hypercube of the same sizes and degrees. We further benchmark on a broad variety of applications including effective bandwidth, FFTE, Graph 500 and NAS parallel benchmarks to compare the optimal circulant topologies and Cartesian products of optimal circulant topologies and fully connected topologies with corresponding torus and hypercube. Simulation results demonstrate superior potentials of the optimal circulant topologies for communication-intensive applications. We also find the 1
ABSTRACTObjectiveTo present Motiro, an unified framework for non-supervised statistical analysis ... more ABSTRACTObjectiveTo present Motiro, an unified framework for non-supervised statistical analysis endomicroscopy videos of the colorectal mucosa.Materials and MethodsWe wrote an open-source Python wrapper using ImageJ software with OpenCV, Seaborn and NumPy libraries. It generates a mosaic from the video of the mucosa, evaluates morphometric properties of the crypts, their distribution, and return their statistics. Shannon entropy (and Hellinger distance) are used for quantifying variability (and comparing different mucosa).ResultsThe segmentation process applied to normal mucosa of pre(post)- neoadjuvant patient is presented along with the corresponding statistical analysis of morphometric parameters.DiscussionOur analysis provides estimation of morphometric parameters consistent with available methods, is faster, and, additionally, provides statistical characterization of the mucosa morphometry. Motiro enables the analysis of large amounts of endomicroscopy videos for building a no...
The Journal of Supercomputing, 2020
We propose that clusters interconnected with network topologies having minimal mean path length w... more We propose that clusters interconnected with network topologies having minimal mean path length will increase their overall performance for a variety of applications. We approach our heuristic by constructing clusters of up to 36 nodes having Dragonfly, torus, ring, Chvatal, Wagner, Bidiakis and several other topologies with minimal mean path lengths and by simulating the performance of 256-node clusters with the same network topologies. The optimal (or sub-optimal) low-latency network topologies are found by minimizing the mean path length of regular graphs. The selected topologies are benchmarked using pingpong messaging, the MPI collective communications, and the standard parallel applications including effective bandwidth, FFTE, Graph 500 and NAS parallel benchmarks. We established strong correlations between the clusters' performances and the network topologies, especially the mean path lengths, for a wide range of applications. In communication-intensive benchmarks, clusters with optimal network topologies out-perform those with mainstream topologies by several folds. It is striking that a mere adjustment of the network topology suffices to reclaim performance from the same computing hardware.
The promoter state of a gene and its expression levels are modulated by the amounts of transcript... more The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter of a gene (the source) is communicated by the amounts of transcription factors that it expresses (the message) to modulate the state of the promoter and expression levels of another gene (the receptor). The reliability of the gene network dynamics can be quantified by the Shannon’s entropy of the message and the mutual information between the message and the promoter state. Here we consider a stochastic model for a binary gene and use its exact steady state solutions to calculate the entropy and mutual information. We show that a slow switching promoter having long and equally standing ON and OFF states maximizes the mutual information and reduces entropy. That is a bursty regime generating a high variance message governed by a bimodal ...
Clinics, 2018
The effects of randomness, an unavoidable feature of intracellular environments, are observed at ... more 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.
Recent experimental data on the transcription dynamics of eve gene stripe two formation of Drosop... more Recent experimental data on the transcription dynamics of eve gene stripe two formation of Drosophila melanogaster embryos occurs in bursts of multiple sizes and durations. That has motivated the proposition of a transcription model having multiple ON states for the promoter of the eve gene each of them characterized by different synthesis rate. To understand the role of multiple ON states on gene transcription we approach the exact solutions for a two state stochastic model for gene transcription in D. melanogaster embryos and derive its bursting limit. Simulations based on the Gillespie algorithm at the bursting limit show the occurrence of bursts of multiple sizes and durations. Based on our theoretical approach, we interpret the aforementioned experimental data as a demonstration of the intrinsic stochasticity of the transcriptional processes in fruit fly embryos. Then, we conceive the experimental arrangement to determine when gene transcription has multiple ON promoter state i...
Physical Review E, 2016
We examine immunostaining experimental data for the formation of the strip 2 of even-skipped tran... more We examine immunostaining experimental data for the formation of the strip 2 of even-skipped transcripts on D. melanogaster embryos. An estimate of the factor converting immunofluorescence intensity units into molecular numbers is given. The analysis of the eve dynamics at the region of the stripe 2 suggests that the promoter site of the gene has two distinct regimes: an earlier phase when it is predominantly activated until a critical time when it becomes mainly repressed. That suggests proposing a stochastic binary model for gene transcription on D. melanogaster embryos. Our model has two random variables: the transcripts number and the state of the source of mRNAs given as active or repressed. We are able to reproduce available experimental data for the average number of transcripts. An analysis of the random fluctuations on the number of eve and their consequences on the spatial precision of the stripe 2 is presented. We show that the position of the anterior/posterior borders fluctuate around their average position by ∼ 1% of the embryo length which is similar to what is found experimentally. The fitting of data by such a simple model suggests that it can be useful to understand the functions of randomness during developmental processes.
The Journal of chemical physics, Jan 14, 2015
Physical Review E, 2015
Here we characterize the low noise regime of a stochastic model for a negative self-regulating bi... more Here we characterize the low noise regime of a stochastic model for a negative self-regulating binary gene. The model has two stochastic variables, the protein number and the state of the gene. Each state of the gene behaves as a protein source governed by a Poisson process. The coupling between the the two gene states depends on protein number. This fact has a very important implication: there exist protein production regimes characterized by sub-Poissonian noise because of negative covariance between the two stochastic variables of the model. Hence the protein numbers obey a probability distribution that has a peak that is sharper than those of the two coupled Poisson processes that are combined to produce it. Biochemically, the noise reduction in protein number occurs when the switching of genetic state is more rapid than protein synthesis or degradation. We consider the chemical reaction rates necessary for Poisson and sub-Poisson processes in prokaryotes and eucaryotes. Our results suggest that the coupling of multiple stochastic processes in a negative covariance regime might be a widespread mechanism for noise reduction.
Physical Review E, 2011
The exact time-dependent solution for the stochastic equations governing the behavior of a binary... more The exact time-dependent solution for the stochastic equations governing the behavior of a binary selfregulating gene is presented. Using the generating function technique to rephrase the master equations in terms of partial differential equations, we show that the model is totally integrable and the analytical solutions are the celebrated confluent Heun functions. Self-regulation plays a major role in the control of gene expression, and it is remarkable that such a microscopic model is completely integrable in terms of well-known complex functions.
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Papers by Alexandre Ramos
ENERGIA NUCLEAR E PROTEÇÃO AMBIENTAL
A despeito de a energia nuclear contribuir com 11% da eletricidade produzida no planeta, sua aceitação pela opinião pública continua controversa. Um dos motivos para tal controvérsia decorre dos tópicos de física ou engenharia nuclear serem pouco compreendidos pela população em geral, incluindo-se tomadores de decisão. Essa vacância de conhecimento dificulta uma apreciação correta dos problemas, soluções e benefícios que a energia nuclear pode trazer à humanidade. Destarte, uma fração significativa da sociedade acaba por ficar à mercê de abordagens mistificadoras sobre tópico nuclear.
Nesse minicurso, realizaremos uma introdução à energia nuclear, com intuito de proporcionar uma visão geral sobre o tema. Iniciaremos apresentando conceitos básicos sobre a geração de eletricidade. Em seguida, mostraremos como transformar a energia nuclear em eletricidade utilizando reações de fusão ou fissão nuclear. Em particular, descreveremos a utilização da fissão em reatores nucleares de tipo BWR, PWR e RBMK.
A descrição desses reatores será importante para apresentarmos as causas e consequências dos dois grandes acidentes nucleares já registrados, ocorridos em Fukushima (2011) e Chernobyl (1986). A análise das consequências desses acidentes será apresentada de acordo com relatórios produzidos por equipes de cientistas atuando pela ONU e suas agências: por exemplo Agência Internacional de Energia Atômica e Organização Mundial da Saúde; e órgãos científicos dos governos da Rússia, Ucrânia e Bielorrússia.
Uma das vantagens do uso da energia nuclear é a alta densidade energética de seu combustível. Isso implica no uso de menores quantidades de combustível nuclear na geração de energia. Essa característica garante a redução do uso de minérios e de produção de rejeitos. Essa redução possibilita amenizar tanto os impactos de mineração quanto as demandas por armazenamento de rejeitos. A redução no consumo de minerais, adicionada à baixa emissão de gás carbônico na produção de eletricidade, tornam a matriz nuclear elemento importante na composição da cesta energética mundial e nacional.
Aplicações de energia nuclear em medicina e agricultura serão abordadas, com destaque para o uso de radiação no controle de vetores, como o Aedes aegypti. Quanto às perspectivas, mostraremos um painel acerca do status da pesquisa em fusão nuclear e como esses avanços podem contribuir no equacionamento da questão dos rejeitos de fissão.
Ao final desse minicurso, esperamos contribuir para desmistificação do assunto nuclear junto aos seus participantes.
Publico-alvo: estudantes e profissionais da área ambiental; público interessado nas questões energética e ambiental; público em geral.
Equipe:
Prof. Dr. Alexandre Ferreira Ramos (coordenador);
Miguel Vasconcelos
Sophia Vergueiro
Suzylaine Lima
Caroline Lucchi