Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 332.718
Filtrar
1.
Adv Exp Med Biol ; 1232: 299-306, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31893424

RESUMO

Hypoxic ischemic encephalopathy (HIE) is a significant cause of death and neurological disability in newborns. Therapeutic hypothermia at 33.5 °C is one of the most common treatments in HIE and generally improves outcome; however 45-55% of injuries still result in death or severe neurodevelopmental disability. We have developed a systems biology model of cerebral oxygen transport and metabolism to model the impact of hypothermia on the piglet brain (the neonatal preclinical animal model) tissue physiology. This computational model is an extension of the BrainSignals model of the adult brain. The model predicts that during hypothermia there is a 5.1% decrease in cerebral metabolism, 1.1% decrease in blood flow and 2.3% increase in cerebral tissue oxygenation saturation. The model can be used to simulate effects of hypothermia on the brain and to help interpret bedside recordings.


Assuntos
Circulação Cerebrovascular , Cérebro , Hipotermia , Modelos Biológicos , Animais , Animais Recém-Nascidos , Circulação Cerebrovascular/fisiologia , Cérebro/metabolismo , Simulação por Computador , Humanos , Hipotermia Induzida , Hipóxia-Isquemia Encefálica , Suínos
2.
Ecol Lett ; 23(1): 2-15, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31707763

RESUMO

Changing conditions may lead to sudden shifts in the state of ecosystems when critical thresholds are passed. Some well-studied drivers of such transitions lead to predictable outcomes such as a turbid lake or a degraded landscape. Many ecosystems are, however, complex systems of many interacting species. While detecting upcoming transitions in such systems is challenging, predicting what comes after a critical transition is terra incognita altogether. The problem is that complex ecosystems may shift to many different, alternative states. Whether an impending transition has minor, positive or catastrophic effects is thus unclear. Some systems may, however, behave more predictably than others. The dynamics of mutualistic communities can be expected to be relatively simple, because delayed negative feedbacks leading to oscillatory or other complex dynamics are weak. Here, we address the question of whether this relative simplicity allows us to foresee a community's future state. As a case study, we use a model of a bipartite mutualistic network and show that a network's post-transition state is indicated by the way in which a system recovers from minor disturbances. Similar results obtained with a unipartite model of facilitation suggest that our results are of relevance to a wide range of mutualistic systems.


Assuntos
Ecossistema , Modelos Biológicos , Previsões , Características de Residência , Simbiose
3.
Food Microbiol ; 85: 103285, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500704

RESUMO

The objective of this study was to determine the kinetic parameters and apply Markov Chain Monte Carlo (MCMC) simulation to predict the growth of Clostridium perfringens from spores in cooked ground chicken meat during dynamic cooling. Inoculated samples were exposed to various cooling conditions to observe dynamic growth. A combination of 4 cooling profiles was used in one-step inverse analysis with the Baranyi model as the primary model and the cardinal parameters model as the secondary model. Six kinetic parameters of the Baranyi model and the cardinal parameters model, including Q0, Ymax, µopt, Tmin, Topt, and Tmax, were estimated. The estimated Tmin, Topt, and Tmax were 14.8, 42.9, and 50.5 °C, respectively, with a µopt of 5.25 h-1 and maximum cell density of 8.4 log CFU/g. Correlation analysis showed that both Q0 and Ymax are weakly correlated to other parameters, while the remaining parameters are mostly mildly to strongly correlated with each other. Although it may be difficult to estimate highly correlated parameters using a single temperature profile, one-step analysis with multiple different temperature profiles helped estimate them successfully. The estimated parameters were used as the prior information to construct the posterior distribution for Bayesian analysis. MCMC simulation was used to predict the bacterial growth using different dynamic temperature profiles for validation of the accuracy of the predictive models. The MCMC simulation results showed that the Bayesian analysis produced more accurate predictions of bacterial growth during cooling than the deterministic method. With Bayesian analysis, the root-mean-square-error (RMSE) of prediction was only 0.1 log CFU/g with all residual errors within ±0.25 log CFU/g. Therefore, Bayesian analysis is recommended for predicting the growth of C. perfringens in cooked meat during cooling.


Assuntos
Clostridium perfringens/crescimento & desenvolvimento , Culinária , Manipulação de Alimentos , Produtos da Carne/microbiologia , Temperatura Ambiente , Animais , Teorema de Bayes , Galinhas , Contagem de Colônia Microbiana , Simulação por Computador , Cinética , Cadeias de Markov , Modelos Biológicos , Método de Monte Carlo , Esporos Bacterianos/crescimento & desenvolvimento
4.
Adv Exp Med Biol ; 1174: 401-440, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31713207

RESUMO

The human body can be viewed as an organism consisting of a variety of cellular and non-cellular materials interacting in a highly ordered manner. Its complex and hierarchical nature inspires the multi-level recapitulation of the human body in order to gain insights into the inner workings of life. While traditional cell culture models have led to new insights into the cellular microenvironment and biological control in vivo, deeper understanding of biological systems and human pathophysiology requires the development of novel model systems that allow for analysis of complex internal and external interactions within the cellular microenvironment in a more relevant organ context. Engineering organ-on-chip systems offers an unprecedented opportunity to unravel the complex and hierarchical nature of human organs. In this chapter, we first highlight the advances in microfluidic platforms that enable engineering of the cellular microenvironment and the transition from cells-on-chips to organs-on-chips. Then, we introduce the key features of the emerging organs-on-chips and their proof-of-concept applications in biomedical research. We also discuss the challenges and future outlooks of this state-of-the-art technology.


Assuntos
Microfluídica , Engenharia Tecidual , Microambiente Celular , Humanos , Microfluídica/tendências , Modelos Biológicos , Técnicas de Cultura de Órgãos/tendências , Fisiologia/tendências , Engenharia Tecidual/tendências
5.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1901-1913, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668037

RESUMO

To quickly and efficiently understand the intracellular metabolic characteristics of industrial microorganisms, and to find potential metabolic engineering targets, genome-scale metabolic network models (GSMMs) as a systems biology tool, are attracting more and more attention. We review here the 20-year history of metabolic network model, analyze the research status and development of GSMMs, summarize the methods for model construction and analysis, and emphasize the applications of metabolic network model for analyzing intracellular metabolic activity of microorganisms from cellular phenotypes, and metabolic engineering. Furthermore, we indicate future development trend of metabolic network model.


Assuntos
Microbiologia Industrial , Engenharia Metabólica , Redes e Vias Metabólicas , Modelos Biológicos , Biologia de Sistemas , Redes e Vias Metabólicas/genética
6.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1914-1924, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668038

RESUMO

Genome-scale metabolic network models have been successfully applied to guide metabolic engineering. However, the conventional flux balance analysis only considers stoichiometry and reaction direction constraints, and the simulation results cannot accurately describe certain phenomena such as overflow metabolism and diauxie growth on two substrates. Recently, researchers proposed new constraint-based methods to simulate the cellular behavior under different conditions more precisely by introducing new constraints such as limited enzyme content and thermodynamics feasibility. Here we review several enzyme-constrained models, giving a comprehensive introduction on the biological basis and mathematical representation for the enzyme constraint, the optimization function, the impact on the calculated flux distribution and their application in identification of metabolic engineering targets. The main problems in these existing methods and the perspectives on this emerging research field are also discussed. By introducing new constraints, metabolic network models can simulate and predict cellular behavior under various environmental and genetic perturbations more accurately, and thus can provide more reliable guidance to strain engineering.


Assuntos
Enzimas/metabolismo , Engenharia Metabólica , Redes e Vias Metabólicas , Modelos Biológicos , Genoma/genética , Redes e Vias Metabólicas/genética , Termodinâmica
7.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1974-1985, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668042

RESUMO

Industrial fermentation is the basic operation unit of industrial biotechnology in large-scale production. Mathematical simulation of microbial cells and their reactors will help deepen the understanding of microorganisms and fermentation processes, and will also provide solutions for the construction of new synthetic organisms. In this paper, the characteristics of industrial fermentation system, the development of mathematical simulation, the classification, characteristics and functions of mathematical models are described in depth, and the development trend of whole fermentation system simulation is prospected.


Assuntos
Biotecnologia , Fermentação , Microbiologia Industrial , Modelos Biológicos
8.
Phys Rev Lett ; 123(13): 138101, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31697512

RESUMO

Multipartite viruses have a genome divided into different disconnected viral particles. A majority of multipartite viruses infect plants; very few target animals. To understand why, we use a simple, network-based susceptible-latent-infectious-recovered model. We show both analytically and numerically that, provided that the average degree of the contact network exceeds a critical value, even in the absence of an explicit microscopic advantage, multipartite viruses have a lower threshold to colonizing network-structured populations compared to a well-mixed population. We further corroborate this finding on two-dimensional lattice networks, which better represent the typical contact structures of plants.


Assuntos
Modelos Biológicos , Vírus de Plantas/fisiologia , Viroses/transmissão , Viroses/virologia , Genoma Viral , Doenças das Plantas/virologia , Vírus de Plantas/genética , Vírion/genética , Vírion/fisiologia
9.
Phys Rev Lett ; 123(13): 138003, 2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31697550

RESUMO

We study the orientation statistics of spheroidal, axisymmetric microswimmers, with shapes ranging from disks to rods, swimming in chaotic, moderately turbulent flows. Numerical simulations show that rodlike active particles preferentially align with the flow velocity. To explain the underlying mechanism, we solve a statistical model via the perturbation theory. We show that such an alignment is caused by correlations of fluid velocity and its gradients along particle paths combined with fore-aft symmetry breaking due to both swimming and particle nonsphericity. Remarkably, the discovered alignment is found to be a robust kinematical effect, independent of the underlying flow evolution. We discuss its possible relevance for aquatic ecology.


Assuntos
Modelos Teóricos , Fenômenos Fisiológicos Bacterianos , Fenômenos Biomecânicos , Hidrodinâmica , Modelos Biológicos , Movimento (Física) , Natação
10.
Phys Rev Lett ; 123(17): 178001, 2019 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-31702266

RESUMO

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations; thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cell numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature.


Assuntos
Bactérias/crescimento & desenvolvimento , Modelos Biológicos , Técnicas Bacteriológicas
11.
Phys Rev Lett ; 123(15): 158006, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31702312

RESUMO

Microswimmers in nature often experience spatial gradients of viscosity. In this Letter we develop theoretical results for the dynamics of active particles, biological or otherwise, swimming through viscosity gradients. We model the active particles using the squirmer model, and show how viscosity gradients lead to viscotaxis for squirmers, and how the effects of viscosity gradients depend on the swimming gait of the microswimmers. We also show how such gradients in viscosity can be used to control active particles and suggest a mechanism to sort them based on their swimming style.


Assuntos
Modelos Teóricos , Chlamydomonas/fisiologia , Escherichia coli/fisiologia , Modelos Biológicos , Modelos Químicos , Natação , Viscosidade
12.
Phys Rev Lett ; 123(15): 158101, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31702314

RESUMO

Microorganismal motility is often characterized by complex responses to environmental physico-chemical stimuli. Although the biological basis of these responses is often not well understood, their exploitation already promises novel avenues to directly control the motion of living active matter at both the individual and collective level. Here we leverage the phototactic ability of the model microalga Chlamydomonas reinhardtii to precisely control the timing and position of localized cell photoaccumulation, leading to the controlled development of isolated bioconvective plumes. This novel form of photobioconvection allows a precise, fast, and reconfigurable control of the spatiotemporal dynamics of the instability and the ensuing global recirculation, which can be activated and stopped in real time. A simple continuum model accounts for the phototactic response of the suspension and demonstrates how the spatiotemporal dynamics of the illumination field can be used as a simple external switch to produce efficient bio mixing.


Assuntos
Chlamydomonas reinhardtii/fisiologia , Modelos Biológicos , Fotobiologia , Processos Fototróficos
13.
Biochemistry (Mosc) ; 84(10): 1186-1196, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31694514

RESUMO

Studies of interactions between natural killer (NK) cells and trophoblasts and identification of conditions for the NK cells to perform their cytotoxic function are of fundamental and practical importance for understanding their role in the development of pathological processes and complications during pregnancy. In this study, we examined changes in the content of caspases and studied activation of these enzymes in Jeg-3 trophoblasts in various models of their coculturing with NK-92 cells and demonstrated the necessity of direct contact between these cell populations for the activation of caspase-8 and caspase-3 in the trophoblasts. Contact coculturing of the two cell lines resulted in the appearance of the cytotoxic protein granzyme B in Jeg-3 cells that was accompanied by a decrease in the content of this enzyme in NK-92 cells. Distant coculturing of NK-92 and Jeg-3 cells did not trigger initiator and effector caspases characteristic for the apoptosis development in Jeg-3 cells. The observed decrease in the content of procaspases in the trophoblasts may be associated with alternative non-apoptotic functions of these enzymes.


Assuntos
Caspases/metabolismo , Técnicas de Cocultura , Células Matadoras Naturais/metabolismo , Modelos Biológicos , Trofoblastos/metabolismo , Linhagem Celular Tumoral , Humanos
14.
Plant Dis ; 103(12): 3117-3128, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31634034

RESUMO

Globodera pallida is a major nematode pest of potato (Solanum tuberosum) and is of great economic importance for the potato industry. Assessing potato yield loss caused by the Idaho G. pallida population under field conditions was not performed due to its quarantine status in Idaho, where it is prohibited by regulatory statutes to grow potato in any infested fields. The experimental data came from three trials that were conducted under greenhouse conditions. A predictive risk model analysis was performed to: (i) determine the effect of the Idaho population of G. pallida on potato yield; (ii) estimate reproduction rate from different initial nematode densities; and (iii) simulate potato yield losses in Idaho field conditions by integrating the coefficients of potato yield into the SUBSTOR-DSSAT crop simulation model. Experiments were conducted under greenhouse conditions using five initial G. pallida soil infestation levels (0, 10, 20, 40, and 80 eggs/g soil). The coefficients of potato yield achieved under each initial nematode density were integrated into the SUBSTOR-DSSAT potato growth simulation model. The model showed that tuber weight reached a maximum yield of 96 ton/ha in noninfested soil. Based on the greenhouse trials, the model predicted a minimum yield of 12 and 58 ton/ha in trial 1 and trial 2/3 respectively, when initial nematode density was 80 eggs/g soil. In trial 1, tuber weight was significantly reduced by 44% at 40 eggs/g soil and by 87% at 80 eggs/g soil, and 20% at 40 eggs/g soil and by 39% at 80 eggs/g soil in trial 2/3. The outputs of this study should facilitate common understanding between regulators, policymakers, and potato growers on the challenges and opportunities for controlling this economically important pest in Idaho.


Assuntos
Agricultura , Modelos Biológicos , Solo , Solanum tuberosum , Tylenchoidea , Agricultura/métodos , Animais , Idaho , Solo/parasitologia , Solanum tuberosum/parasitologia , Tylenchoidea/fisiologia
15.
Adv Exp Med Biol ; 1146: 1-11, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31612450

RESUMO

Collective cell migration plays key roles in various physiological and pathological processes in multicellular organisms, including embryonic development, wound healing, and formation of cancer metastases. Such collective migration involves complex crosstalk among cells and their environment at both biochemical and mechanical levels. Here, we review various computational modeling strategies that have been helpful in decoding the dynamics of collective cell migration. Most of such attempts have focused either aspect - mechanical or biochemical regulation of collective cell migration, and have yielded complementary insights. Finally, we suggest some possible ways to integrate these models to gain a more comprehensive understanding of collective cell migration.


Assuntos
Movimento Celular , Modelos Biológicos , Animais , Movimento Celular/fisiologia , Humanos , Cicatrização
16.
Adv Exp Med Biol ; 1146: 13-29, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31612451

RESUMO

The development of traction-force microscopy, in the past two decades, has created the unprecedented opportunity of performing direct mechanical measurements on living cells as they adhere or crawl on uniform or micro-patterned substrates. Simultaneously, this has created the demand for a theoretical framework able to decipher the experimental observations, shed light on the complex biomechanical processes that govern the interaction between the cell and the extracellular matrix and offer testable predictions. Contour models of cellular adhesion, represent one of the simplest and yet most insightful approach in this problem. Rooted in the paradigm of active matter, these models allow to explicitly determine the shape of the cell edge and calculate the traction forces experienced by the substrate, starting from the internal and peripheral contractile stresses as well as the passive restoring forces and bending moments arising within the actin cortex and the plasma membrane. In this chapter I provide a general overview of contour models of cellular adhesion and review the specific cases of cells equipped with isotropic and anisotropic actin cytoskeleton as well as the role of bending elasticity.


Assuntos
Adesão Celular , Modelos Biológicos , Citoesqueleto de Actina , Animais , Elasticidade
17.
Adv Exp Med Biol ; 1146: 45-66, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31612453

RESUMO

Collective cell migration plays a central role in tissue development, morphogenesis, wound repair and cancer progression. With the growing realization that physical forces mediate cell motility in development and physiology, a key biological question is how cells integrate molecular activities for force generation on multicellular scales. In this review we discuss recent advances in modeling collective cell migration using quantitative tools and approaches rooted in soft matter physics. We focus on theoretical models of cell aggregates as continuous active media, where the feedback between mechanical forces and regulatory biochemistry gives rise to rich collective dynamical behavior. This class of models provides a powerful predictive framework for the physiological dynamics that underlies many developmental processes, where cells need to collectively migrate like a viscous fluid to reach a target region, and then stiffen to support mechanical stresses and maintain tissue cohesion.


Assuntos
Fenômenos Biomecânicos , Movimento Celular , Modelos Biológicos , Movimento Celular/fisiologia , Morfogênese , Cicatrização
18.
BMC Bioinformatics ; 20(1): 499, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615420

RESUMO

BACKGROUND: Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to study fluxes through the reactions, or to relate the graph structure to environmental characteristics and phenotypes. About ten years ago, Takemoto et al. (2007) stated that the structure of prokaryotic metabolic networks represented as undirected graphs, is correlated to their living environment. Although metabolic networks are naturally directed graphs, they are still usually analysed as undirected graphs. RESULTS: We implemented a pipeline to reconstruct metabolic networks from genome data and confirmed some of the results of Takemoto et al. (2007) with today data using up-to-date databases. However, Takemoto et al. (2007) used only a fraction of all available enzymes from the genome and taking into account all the enzymes we fail to reproduce the main results. Therefore, we introduce three robust measures on directed representations of graphs, which lead to similar results regardless of the method of network reconstruction. We show that the size of the largest strongly connected component, the flow hierarchy and the Laplacian spectrum are strongly correlated to the environmental conditions. CONCLUSIONS: We found a significant negative correlation between the size of the largest strongly connected component (a cycle) and the optimal growth temperature of the considered prokaryotes. This relationship holds true for the spectrum, high temperature being associated with lower eigenvalues. The hierarchy flow shows a negative correlation with optimal growth temperature. This suggests that the dynamical properties of the network are dependant on environmental factors.


Assuntos
Bactérias/metabolismo , Biologia Computacional , Redes e Vias Metabólicas , Modelos Biológicos , Temperatura Ambiente , Enzimas
19.
Plant Mol Biol ; 101(4-5): 507-516, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31617145

RESUMO

KEY MESSAGE: MMDH2 gene negatively regulates Cd tolerance by modulating reactive oxygen species (ROS) levels and the ROS-mediated signaling, thus, affecting the expression of PDR8. The molecular mechanism by which plants respond to stress caused by cadmium (Cd), one of the most toxic heavy metals to plants, is not well understood. Here, we show that MMDH2, a gene encoding mitochondrial malate dehydrogenase, is involved in Cd stress tolerance in Arabidopsis. The expression of MMDH2 was repressed by Cd stress. The mmdh2 knockdown mutants showed enhanced Cd tolerance, while the MMDH2-overexpressing lines were sensitive to Cd. Under normal and Cd stress conditions, lower H2O2 levels were detected in mmdh2 mutant plants than in wild-type plants. In contrast, higher H2O2 levels were found in MMDH2-overexpressing lines, and they were negatively correlated with malondialdehyde levels. In addition, the expression of the PDR8, a gene encoding a Cd efflux pump, increased and decreased in the mmdh2 mutant and MMDH2-overexpressing lines, in association with lower and higher Cd concentrations, respectively. These results suggest that the MMDH2 gene negatively regulates Cd tolerance by modulating reactive oxygen species (ROS) levels and the ROS-mediated signaling, thus, affecting the expression of PDR8.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Cádmio/toxicidade , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos , Transportadores de Cassetes de Ligação de ATP/genética , Sequência de Aminoácidos , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Cádmio/metabolismo , Técnicas de Silenciamento de Genes , Peróxido de Hidrogênio/metabolismo , Modelos Biológicos , Espécies Reativas de Oxigênio/metabolismo , Alinhamento de Sequência , Estresse Fisiológico
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA