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BACKGROUND: Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. RESULTS: Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. CONCLUSIONS: Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.
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Escherichia coli , Redes Reguladoras de Genes , Forma Celular , Simulação por Computador , Escherichia coli/genética , Biologia SintéticaRESUMO
BACKGROUND: During range expansion in spatially distributed habitats, organisms differ from one another in terms of their patterns of localization versus propagation. To exploit locations or explore the landscape? This is the competition-colonization trade-off, a dichotomy at the core of ecological succession. In bacterial communities, this trade-off is a fundamental mechanism towards understanding spatio-temporal fluxes in microbiome composition. RESULTS: Using microfluidics devices as structured bacterial habitats, we show that, in a synthetic two-species community of motile strains, Escherichia coli is a fugitive species, whereas Pseudomonas aeruginosa is a slower colonizer but superior competitor. We provide evidence highlighting the role of succession and the relevance of this trade-off in the community assembly of bacteria in spatially distributed patchy landscapes. Furthermore, aggregation-dependent priority effects enhance coexistence which is not possible in well-mixed environments. CONCLUSIONS: Our findings underscore the interplay between micron-scale landscape structure and dispersal in shaping biodiversity patterns in microbial ecosystems. Understanding this interplay is key to unleash the technological revolution of microbiome applications.
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Infecções por Escherichia coli , Microbiota , Humanos , Biodiversidade , Escherichia coli , Pseudomonas aeruginosaRESUMO
Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil.
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Cancer is a singular cellular state, the emergence of which destabilises the homeostasis reached through the evolution to multicellularity. We present the idea that the onset of the cellular disobedience to the metazoan functional and structural architecture, known as the cancer phenotype, is triggered by changes in the cell's external environment that occur with ageing: what ensues is a breach of the social contract of multicellular life characteristic of metazoans. By integrating old ideas with new evidence, we propose that with ageing the environmental information that maintains a multicellular organisation is eroded, rewiring internal processes of the cell, and resulting in an internal shift towards an ancestral condition resulting in the pseudo-multicellular cancer phenotype. Once that phenotype emerges, a new local social contract is built, different from the homeostatic one, leading to tumour formation and the foundation of a novel local ecosystem.
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Evolução Biológica , Neoplasias , Envelhecimento , Animais , Ecossistema , Humanos , Neoplasias/genética , FenótipoRESUMO
We aim to understand general consequences of niche construction on metapopulation dynamics in ephemeral landscapes. To this effect, a contact process-like stochastic spatial model is introduced where local populations colonize and go extinct on a dynamic landscape of habitable and destroyed patches. In contrast to previous models, where the extinction threshold is a consequence of available niche rendered by global rates of patch destruction/renewal, here we investigate how the metapopulation persists when they are the sole generators of their own niche. Niche construction is full-filled by localized populations through the transformation of destroyed patches in their neighborhood to viable habitat for future colonization. With this theoretical framework we are able to address the dual nature of niche construction by investigating the ephemerality of the landscape (destruction rate) and the continuum of population level strategies, where construction comes at a cost to colonization. Using mean field theory and Monte Carlo simulations of the model, we are able to quantify optimal population level strategies in a wide range of ephemeral landscapes. Interestingly, we observe qualitative differences at the extinction threshold between analytic and numeric results. Investigating this discrepancy further, we find that increasing niche construction neighborhood in the spatial model leads to two interrelated effects i) an increased rate in range expansion ii) a loss in resiliency and return of the discontinuous transition at the extinction threshold. Furthermore, in the discontinuous regime of the model, spatial clustering prior to a critical transition disappears. This is a significant finding as spatial clustering has been considered to be an early warning signal before ecosystems reach their 'tipping point'. In addition to maintaining stability, we find local niche construction strategies have an advantage when in scramble competition with an exploiter strategy because of their ability to monopolize the constructed niche due to spatial adjacency. As the niche construction neighborhood expands this advantage disappears and the exploiter strategy out-competes the niche constructor. In some cases the exploiter pushes the niche constructor to extinction, thus a tragedy of the commons ensues leading to 'ecological suicide' and a collapse of the niche.
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The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.
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Biologia/educação , Engenharia Biomédica/métodos , Imagem Óptica/instrumentação , Pesquisa Biomédica , Linhagem Celular , Desenho de Equipamento , Equipamentos e Provisões/economia , Escherichia coli/crescimento & desenvolvimentoRESUMO
Desde que en 1955 Björn y Engströn introducen la ventilación mecánica (VM) en pacientes con insuficiencia respiratoria post operatoria, han exitido cambios importantes en los tipos y modos de ventilación. Para minimizar las complicaciones de la ventilación mecánica convencional, se desarrolló la ventilación de alta frecuencia (HFV), la que utiliza volumenes corrientes (Vc) bajos y frecuencias respiratorias elevadas. Esta se define como un método de VM con frecuencias superiores a 100 ciclos por minutos y Vc menor o igual al volumen de espacio muerto. Se han desarrollado diferentes sistemas de ventilación de alta frecuencia. Este trabajo revisa la aplicación clínica de la ventilación oscilatoria de alta frecuencia (HFOV), basada en la experiencia como grupo de trabajo de servicio de Terapia Ventilatoria desde el año 1995. Este tipo de ventilación mecánica no convencional se ha usado en las unidades de Neonatología y Pediatría ya que el equipo utilizado (Sensor Medics 3100A) está diseñado para pacientes hasta 20 kilos, que presentan: hipertensión pulmonar, cortocircuito intrapulmonar, Sindrome de distress respiratorio (SDR) o barotrauma. Los mecanismo de acción HFOV son. Aumento longitudinal del gas transportado y aumento de la dispersión. Ventilación alveolar directa. Efecto pendular intra alveolar. Efecto de dispersión convectiva por perfiles asismétrico de velocidad. Se revisan los criterios de conexión, programación y control del funcionamiento de la HFOV y se analizan los pricipales problemas a que se ve enfrentado el equipo de salud
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Humanos , Respiração Artificial/métodos , Síndrome do Desconforto Respiratório do Recém-Nascido/terapia , Respiração Artificial/classificação , Respiração Artificial/instrumentação , Ventilação de Alta Frequência/métodosRESUMO
La helio-oxígeno terapia es un método terapéutico relativamente nuevo en Chile, sin embargo, su utilización se conoce ya desde 1934 por los estudios de Barach et.al. El helio (He) es un gas inerte que, por sus características de muy baja densidad (1/8 de la densidad del nitrógeno), al mezclarlo con oxígeno dísminuye la densidad de éste. La utilidad de la mezcla helio-oxígeno o Heliox radica en su capacidad de disminuir la resistencia al paso del flujo gaseoso permitiendo su difusión a través de espacios aéreos estrechos; es por ello que en enfermedades como obstrucción de la vía aérea alta, asma y enfermedades pulmonares obstructivas crónicas, su administración ha resultado en mejorías de la relación VIQ, disminución de P a CO, y menor trabajo respiratorio, proyectándose como herramienta segura y sin efectos deletéreos para los pacientes