共查询到20条相似文献,搜索用时 15 毫秒
1.
Tenazinha N Vinga S 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2011,8(4):943-958
Understanding how cellular systems build up integrated responses to their dynamically changing environment is one of the open questions in Systems Biology. Despite their intertwinement, signaling networks, gene regulation and metabolism have been frequently modeled independently in the context of well-defined subsystems. For this purpose, several mathematical formalisms have been developed according to the features of each particular network under study. Nonetheless, a deeper understanding of cellular behavior requires the integration of these various systems into a model capable of capturing how they operate as an ensemble. With the recent advances in the "omics" technologies, more data is becoming available and, thus, recent efforts have been driven toward this integrated modeling approach. We herein review and discuss methodological frameworks currently available for modeling and analyzing integrated biological networks, in particular metabolic, gene regulatory and signaling networks. These include network-based methods and Chemical Organization Theory, Flux-Balance Analysis and its extensions, logical discrete modeling, Petri Nets, traditional kinetic modeling, Hybrid Systems and stochastic models. Comparisons are also established regarding data requirements, scalability with network size and computational burden. The methods are illustrated with successful case studies in large-scale genome models and in particular subsystems of various organisms. 相似文献
2.
Jing Wui Yeoh Sudhaghar S/O Jayaraman Sean Guo‐Dong Tan Premkumar Jayaraman Maciej B. Holowko Jingyun Zhang Chang‐Wei Kang Hwa Liang Leo Chueh Loo Poh 《Biotechnology and bioengineering》2021,118(1):305-318
Due to sustainability concerns, bio‐based production capitalizing on microbes as cell factories is in demand to synthesize valuable products. Nevertheless, the nonhomogenous variations of the extracellular environment in bioprocesses often challenge the biomass growth and the bioproduction yield. To enable a more rational bioprocess optimization, we have established a model‐driven approach that systematically integrates experiments with modeling, executed from flask to bioreactor scale, and using ferulic acid to vanillin bioconversion as a case study. The impacts of mass transfer and aeration on the biomass growth and bioproduction performances were examined using minimal small‐scale experiments. An integrated model coupling the cell factory kinetics with the three‐dimensional computational hydrodynamics of bioreactor was developed to better capture the spatiotemporal distributions of bioproduction. Full‐factorial predictions were then performed to identify the desired operating conditions. A bioconversion yield of 94% was achieved, which is one of the highest for recombinant Escherichia coli using ferulic acid as the precursor. 相似文献
3.
Catabolism of hydroxyacids and biotechnological production of lactones by Yarrowia lipolytica 总被引:6,自引:0,他引:6
The gamma- and delta-lactones of less than 12 carbons constitute a group of compounds of great interest to the flavour industry. It is possible to produce some of these lactones through biotechnology. For instance, gamma-decalactone can be obtained by biotransformation of methyl ricinoleate. Among the organisms used for this bioproduction, Yarrowia lipolytica is a yeast of choice. It is well adapted to growth on hydrophobic substrates, thanks to its efficient and numerous lipases, cytochrome P450, acyl-CoA oxidases and its ability to produce biosurfactants. Furthermore, genetic tools have been developed for its study. This review deals with the production of lactones by Y. lipolytica with special emphasis on the biotransformation of methyl ricinoleate to gamma-decalactone. When appropriate, information from the lipid metabolism of other yeast species is presented. 相似文献
4.
《Biophysical journal》2022,121(10):1919-1930
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria, metabolic activity may be guided by universal principles. The constrained optimization of evolutionarily motivated objective functions, such as the growth rate, has emerged as the key theoretical assumption for the study of bacterial metabolism. While conceptually and practically useful in many situations, the idea that certain functions are optimized is hard to validate in data. Moreover, it is not always clear how optimality can be reconciled with the high degree of single-cell variability observed in experiments within microbial populations. To shed light on these issues, we develop an inverse modeling framework that connects the fitness of a population of cells (represented by the mean single-cell growth rate) to the underlying metabolic variability through the maximum entropy inference of the distribution of metabolic phenotypes from data. While no clear objective function emerges, we find that, as the medium gets richer, the fitness and inferred variability for Escherichia coli populations follow and slowly approach the theoretically optimal bound defined by minimal reduction of variability at given fitness. These results suggest that bacterial metabolism may be crucially shaped by a population-level trade-off between growth and heterogeneity. 相似文献
5.
Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories. 相似文献
6.
Neufeld TP 《Mechanisms of development》2003,120(11):1283-1296
Growth of organisms and their constituent parts responds to both intrinsic and extrinsic cues during development: organisms of a given species generally grow at a predictable rate and to a specific body size, but individuals can modify this program during development in response to environmental conditions. Recent experiments, using gene knockouts and targeted overexpression, have revealed the central role of a signaling network controlled by the PI3K and TOR kinases in this regulation. These signaling molecules control growth by coordinately regulating a large number of cell biological processes. This review focuses on the cellular activities regulated by PI3K and TOR during development, and discusses how changes in different aspects of cellular metabolism may interact to regulate growth. 相似文献
7.
Although developmental biology has been dominated by the genetic analysis of embryonic development, in recent years genetic tools have been combined with new approaches such as imaging of live processes, automated and quantitative image analysis, mechanical perturbation and mathematical modeling, to study the principles underlying the formation of organisms. Here we focus on recent work carried out on Dorsal Closure, a morphogenetic process during Drosophila embryogenesis, to illustrate how this multidisciplinary approach is yielding new and unexpected insights into how cells organize themselves through the activity of their molecular components to give rise to the stereotyped and macroscopic movements observed during development. 相似文献
8.
《Trends in plant science》2023,28(5):519-526
Infectious plant diseases are a major threat to global agricultural productivity, economic development, and ecological integrity. There is widespread concern that these social and natural disasters caused by infectious plant diseases may escalate with climate change and computer modeling offers a unique opportunity to address this concern. Here, we analyze the intrinsic problems associated with current modeling strategies and highlight the need to integrate evolutionary principles into polytrophic, eco-evolutionary frameworks to improve predictions. We particularly discuss how evolutionary shifts in functional trade-offs, relative adaptability between plants and pathogens, ecosystems, and climate preferences induced by climate change may feedback to future plant disease epidemics and how technological advances can facilitate the generation and integration of this relevant knowledge for better modeling predictions. 相似文献
9.
Adaptive laboratory evolution and reverse engineering enhances autotrophic growth in Pichia pastoris
Synthetic biology offers several routes for CO2 conversion into biomass or bio-chemicals, helping to avoid unsustainable use of organic feedstocks, which negatively contribute to climate change. The use of well-known industrial organisms, such as the methylotrophic yeast Pichia pastoris (Komagataella phaffii), for the establishment of novel C1-based bioproduction platforms could wean biotechnology from feedstocks with alternative use in food production. Recently, the central carbon metabolism of P. pastoris was re-wired following a rational engineering approach, allowing the resulting strains to grow autotrophically with a μmax of 0.008 h−1, which was further improved to 0.018 h−1 by adaptive laboratory evolution. Using reverse genetic engineering of single-nucleotide (SNPs) polymorphisms occurring in the genes encoding for phosphoribulokinase and nicotinic acid mononucleotide adenylyltransferase after evolution, we verified their influence on the improved autotrophic phenotypes. The reverse engineered SNPs lead to lower enzyme activities in putative branching point reactions and in reactions involved in energy balancing. Beyond this, we show how further evolution facilitates peroxisomal import and increases growth under autotrophic conditions. The engineered P. pastoris strains are a basis for the development of a platform technology, which uses CO2 for production of value-added products, such as cellular biomass, technical enzymes and chemicals and which further avoids consumption of organic feedstocks with alternative use in food production. Further, the identification and verification of three pivotal steps may facilitate the integration of heterologous CBB cycles or similar pathways into heterotrophic organisms. 相似文献
10.
Effects of body size and temperature on population growth 总被引:1,自引:0,他引:1
For at least 200 years, since the time of Malthus, population growth has been recognized as providing a critical link between the performance of individual organisms and the ecology and evolution of species. We present a theory that shows how the intrinsic rate of exponential population growth, rmax, and the carrying capacity, K, depend on individual metabolic rate and resource supply rate. To do this, we construct equations for the metabolic rates of entire populations by summing over individuals, and then we combine these population-level equations with Malthusian growth. Thus, the theory makes explicit the relationship between rates of resource supply in the environment and rates of production of new biomass and individuals. These individual-level and population-level processes are inextricably linked because metabolism sets both the demand for environmental resources and the resource allocation to survival, growth, and reproduction. We use the theory to make explicit how and why rmax exhibits its characteristic dependence on body size and temperature. Data for aerobic eukaryotes, including algae, protists, insects, zooplankton, fishes, and mammals, support these predicted scalings for rmax. The metabolic flux of energy and materials also dictates that the carrying capacity or equilibrium density of populations should decrease with increasing body size and increasing temperature. Finally, we argue that body mass and body temperature, through their effects on metabolic rate, can explain most of the variation in fecundity and mortality rates. Data for marine fishes in the field support these predictions for instantaneous rates of mortality. This theory links the rates of metabolism and resource use of individuals to life-history attributes and population dynamics for a broad assortment of organisms, from unicellular organisms to mammals. 相似文献
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12.
Tatsumi Imada Chiaki Yamamoto Masakazu Toyoshima Yoshihiro Toya Hiroshi Shimizu 《Biotechnology progress》2023,39(3):e3326
In nature, photosynthetic organisms are exposed to fluctuating light, and their physiological systems must adapt to this fluctuation. To maintain homeostasis, these organisms have a light fluctuation photoprotective mechanism, which functions in both photosystems and metabolism. Although the photoprotective mechanisms functioning in the photosystem have been studied, it is unclear how metabolism responds to light fluctuations within a few seconds. In the present study, we investigated the metabolic response of Synechocystis sp. PCC 6803 to light fluctuations using 13C-metabolic flux analysis. The light intensity and duty ratio were adjusted such that the total number of photons or the light intensity during the low-light phase was equal. Light fluctuations affected cell growth and photosynthetic activity under the experimental conditions. However, metabolic flux distributions and cofactor production rates were not affected by the light fluctuations. Furthermore, the estimated ATP and NADPH production rates in the photosystems suggest that NADPH-consuming electron dissipation occurs under fluctuating light conditions. Although we focused on the water–water cycle as the electron dissipation path, no growth effect was observed in an flv3-disrupted strain under fluctuating light, suggesting that another path contributes to electron dissipation under these conditions. 相似文献
13.
Monnat RJ 《DNA Repair》2007,6(9):1386-1390
Two recent reports provide new information on how DNA damage may generate progeroid changes at the cell and organismal level by suppressing growth hormone (GH)/insulin-like growth factor 1 (IGF1) endocrine signaling. This endocrine signaling pathway is of particular interest as it is a key regulator of metabolism and longevity in many organisms. 相似文献
14.
15.
Eva Darko Parisa Heydarizadeh Beno?t Schoefs Mohammad R. Sabzalian 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2014,369(1640)
Providing an adequate quantity and quality of food for the escalating human population under changing climatic conditions is currently a great challenge. In outdoor cultures, sunlight provides energy (through photosynthesis) for photosynthetic organisms. They also use light quality to sense and respond to their environment. To increase the production capacity, controlled growing systems using artificial lighting have been taken into consideration. Recent development of light-emitting diode (LED) technologies presents an enormous potential for improving plant growth and making systems more sustainable. This review uses selected examples to show how LED can mimic natural light to ensure the growth and development of photosynthetic organisms, and how changes in intensity and wavelength can manipulate the plant metabolism with the aim to produce functionalized foods. 相似文献
16.
Julia Van Etten Luiz Felipe Benites Timothy G. Stephens Hwan Su Yoon Debashish Bhattacharya 《Journal of phycology》2023,59(2):293-300
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as “algae obscura.” The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems. 相似文献
17.
Neutral lipids in the form of triacylglycerol (TAG) have emerged as critical regulators of cellular energy balance, lipid homeostasis, growth, development and stress response in organisms ranging from plants to yeast. Although TAGs are mostly recognized as the main storage component in cytoplasmic lipid droplets (LDs), TAG-rich LDs with similar structural and functional characteristics to those found in the cytoplasm also exist in chloroplasts of microalgae and higher plants. Chloroplasts contain up to 70% of total lipids in photosynthetic cells, yet how organisms maintain chloroplast lipid homeostasis remains an under-investigated area of research. Here we summarize the current state of knowledge about the metabolism of TAG and its function in chloroplasts, with a focus on the enzymes catalyzing the final steps of TAG assembly and the role of TAG synthesis in protection against lipotoxicity. We also discuss emerging data regarding connections between cytoplasmic and chloroplast TAG metabolism and the role of autophagy in the degradation of chloroplast storage lipids. 相似文献
18.
Currently, the predominant microbially produced biofuel is starch- or sugar-derived ethanol. However, ethanol is not an ideal fuel molecule, and lignocellulosic feedstocks are considerably more abundant than both starch and sugar. Thus, many improvements in both the feedstock and the fuel have been proposed. In this paper, we examine the prospects for bioproduction of four second-generation biofuels (n-butanol, 2-butanol, terpenoids, or higher lipids) from four feedstocks (sugars and starches, lignocellulosics, syngas, and atmospheric carbon dioxide). The principal obstacle to commercial production of these fuels is that microbial catalysts of robust yields, productivities, and titers have yet to be developed. Suitable microbial hosts for biofuel production must tolerate process stresses such as end-product toxicity and tolerance to fermentation inhibitors in order to achieve high yields and titers. We tested seven fast-growing host organisms for tolerance to production stresses, and discuss several metabolic engineering strategies for the improvement of biofuels production. 相似文献
19.
Despite its toxicity for the majority of living matter on our planet, numerous microorganisms, both aerobic and anaerobic, can use carbon monoxide (CO) as a source of carbon and/or energy for growth. The capacity to employ carboxidotrophic energy metabolism anaerobically is found in phylogenetically diverse members of the Bacteria and the Archaea. The oxidation of CO is coupled to numerous respiratory processes, such as desulfurication, hydrogenogenesis, acetogenesis, and methanogenesis. Although as diverse as the organisms capable of it, any CO-dependent energy metabolism known depends on the presence of carbon monoxide dehydrogenase. This review summarizes recent insights into the CO-dependent physiology of anaerobic microorganisms with a focus on methanogenic archaea. Carboxidotrophic growth of Methanosarcina acetivorans, thought to strictly rely on the process of methanogenesis, also involves formation of methylated thiols, formate, and even acetogenesis, and, thus, exemplifies how the beneficial redox properties of CO can be exploited in unexpected ways by anaerobic microorganisms. 相似文献
20.
Metabolic engineering is the field of introducing genetic changes in organisms so as to modify their function towards synthesizing new products of high impact to society. However, engineered cells frequently have impaired growth rates thus seriously limiting the rate at which such products are made. The problem is attributable to inadequate understanding of how a metabolic network functions in a dynamic sense. Predictions of mutant strain behavior in the past have been based on steady state theories such as flux balance analysis (FBA), minimization of metabolic adjustment (MOMA), and regulatory on/off minimization (ROOM). Such predictions are restricted to product yields and cannot address productivity, which is of focal interest to applications. We demonstrate that our framework ( [Song and Ramkrishna, 2010] and [Song and Ramkrishna, 2011]), based on a “cybernetic” view of metabolic systems, makes predictions of the dynamic behavior of mutant strains of Escherichia coli from a limited amount of data obtained from the wild-type. Dynamic frameworks must necessarily address the issue of metabolic regulation, which the cybernetic approach does by postulating that metabolism is an optimal dynamic response of the organism to the environment in driving reactions towards ensuring survival. The predictions made in this paper are without parallel in the literature and lay the foundation for rational metabolic engineering. 相似文献