系统生物学与细胞发生系统动力学

系统生物学是系统理论和实验生物技术、计算机数学模型等方法整合的生物系统研究,系统遗传学研究基因组的稳态与进化、功能基因组和生物性状等复杂系统的结构、动态与发生演变等。合成生物学是系统生物学的工程应用,采用工程学方法、基因工程和计算机辅助设计等研究人工生物系统的生物技术。系统与合成生物学的结构理论,序列标志片段显示分析与微流控生物芯片,广泛用于研究细胞代谢、繁殖和应激的自组织进化、生物体形态发生等细胞分子生物系统原理等。     

Monotone and near-monotone biochemical networks

Monotone subsystems have appealing properties as components of larger networks, since they exhibit robust dynamical stability and predictability of responses to perturbations. This suggests that natural biological systems may have evolved to be, if not monotone, at least close to monotone in the sense of being decomposable into a “small” number of monotone components, In addition, recent research has shown that much insight can be attained from decomposing networks into monotone subsystems and the analysis of the resulting interconnections using tools from control theory. This paper provides an expository introduction to monotone systems and their interconnections, describing the basic concepts and some of the main mathematical results in a largely informal fashion. Supported in part by NSF Grants DMS-0504557 and DMS-0614371.     

Virtual special issue: Social-ecological systems research in tropical ecosystems

Biodiversity is declining globally, primarily due to anthropogenic threats. Therefore, effective conservation efforts must integrate human and environmental components. Social-ecological systems research is increasingly being adopted as a means of studying complex relationships between people and the environment. I assess how researchers are employing social-ecological systems approaches or frameworks to the study of tropical ecosystems. I reviewed articles published in Biotropica from 2010 through 2022 searching for research on social-ecological systems. A broad keyword search revealed only 2 articles using a variation of social-ecological systems, human-environment systems, or coupled human and natural systems. This contrasts with a growing number of articles published with these search terms in other conservation-related journals, primarily led by environmental scientists. After reviewing titles for all 1298 research articles published during this period, I selected 12 articles for inclusion in the virtual special issue “Social-Ecological Systems Research in Topical Ecosystems”. These articles cover a broad range of geographical locations, ecosystem types, species, and conservation themes. Social-ecological systems frameworks offer an integrated way to study complex relationships between humans and nature, yet this type of research appears under-utilized by authors in Biotropica. I offer seven guidelines for authors interested in pursuing this research such as developing collaborations between social and environmental scientists.     

Beyond the Food Web Connections to a Deeper Industrial Ecology

Industrial ecology is a school of thought based, in part, upon a simple analogy between industrial systems and ecological systems in terms of their material and energy flows. This article argues for a more sophisticated connection between these diverse systems based on the fact that they are all complex self-organizing systems, operating far from thermodynamic equilibrium. As such, industrial and ecological systems have in common certain constraints and dynamic properties that move beyond the central metaphor of industrial ecology and could align these systems under a more comprehensive analytical framework. If incorporated at a fundamental level, the complex systems framework could add depth and sophistication to the field of industrial ecology.     

DDS: Dynamics of Developmental Systems

Abstract. The acronym Developmental systems theory (DST) has been introduced into the literature on development in at least three different contexts in recent years – twice for DST, and before that, for Dynamical Systems Theory – and in all cases, to designate a new perspective for understanding development. Subtle but significant differences in argument and aims distinguish these uses, and confound the difficulty of saying just what DST is. My aim in this paper is to disambiguate these different terms – both to call attention to the difference of perspectives, and to carve out a conceptual space for the concrete issues at stake.     

Social groupings in 18 species of butterflyfish and pair bond weakening during the nonreproductive season

I surveyed social groupings in 18 butterflyfish species of genus Chaetodon, focusing on how many individuals usually swim together in the reproductive season. Social groupings in 4 of the 18 species were first reported. Six of the 18 species were also observed in the nonreproductive seasons. Three species, of which 2 species were found to be monogamous, spent less time swimming with their partner during the nonreproductive season than the reproductive season. This observation is consistent with the hypothesis that the function of pair swimming is to increase the egg production of the female.     

A cellular mechanism for multi-robot construction via evolutionary multi-objective optimization of a gene regulatory network

A major research challenge of multi-robot systems is to predict the emerging behaviors from the local interactions of the individual agents. Biological systems can generate robust and complex behaviors through relatively simple local interactions in a world characterized by rapid changes, high uncertainty, infinite richness, and limited availability of information. Gene Regulatory Networks (GRNs) play a central role in understanding natural evolution and development of biological organisms from cells. In this paper, inspired by biological organisms, we propose a distributed GRN-based algorithm for a multi-robot construction task. Through this algorithm, multiple robots can self-organize autonomously into different predefined shapes, and self-reorganize adaptively under dynamic environments. This developmental process is evolved using a multi-objective optimization algorithm to achieve a shorter travel distance and less convergence time. Furthermore, a theoretical proof of the system's convergence is also provided. Various case studies have been conducted in the simulation, and the results show the efficiency and convergence of the proposed method.     

From computational modelling of the intrinsic apoptosis pathway to a systems-based analysis of chemotherapy resistance: achievements,perspectives and challenges in systems medicine

Our understanding of the mitochondrial or intrinsic apoptosis pathway and its role in chemotherapy resistance has increased significantly in recent years by a combination of experimental studies and mathematical modelling. This combined approach enhanced the quantitative and kinetic understanding of apoptosis signal transduction, but also provided new insights that systems-emanating functions (i.e., functions that cannot be attributed to individual network components but that are instead established by multi-component interplay) are crucial determinants of cell fate decisions. Among these features are molecular thresholds, cooperative protein functions, feedback loops and functional redundancies that provide systems robustness, and signalling topologies that allow ultrasensitivity or switch-like responses. The successful development of kinetic systems models that recapitulate biological signal transduction observed in living cells have now led to the first translational studies, which have exploited and validated such models in a clinical context. Bottom-up strategies that use pathway models in combination with higher-level modelling at the tissue, organ and whole body-level therefore carry great potential to eventually deliver a new generation of systems-based diagnostic tools that may contribute to the development of personalised and predictive medicine approaches. Here we review major achievements in the systems biology of intrinsic apoptosis signalling, discuss challenges for further model development, perspectives for higher-level integration of apoptosis models and finally discuss requirements for the development of systems medical solutions in the coming years.     

三江平原沼泽湿地水系统研究浅析

综述了沼泽湿地水文研究进展,对其水系统研究的地位和作用进行讨论,并综合分析了其主要内容和研究系统,同时对沼泽湿地水系统研究前景提出了展望。     

Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group

Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.     

一类离散双线性生态系统的正规化控制

双线性系统能对非线性系统很好的近似,可对生态、生物等过程中的许多现象进行描述,对双线性系统研究具有一定的实际价值与理论意义.本文研究了一类离散双线性生态系统的全局渐近稳定问题.针对该系统,给出了一种简单的正规化反馈控制律.运用Lyapunov稳定性理论证明了在此控制律下的闭环系统是全局渐近稳定的.     

Mean Lifetime and First-Passage Time of the Enzyme Species Involved in an Enzyme Reaction. Application to Unstable Enzyme Systems

Taking as starting point the complete analysis of mean residence times in linear compartmental systems performed by Garcia-Meseguer et al. (Bull. Math. Biol. 65:279–308, 2003) as well as the fact that enzyme systems, in which the interconversions between the different enzyme species involved are of first or pseudofirst order, act as linear compartmental systems, we hereby carry out a complete analysis of the mean lifetime that the enzyme molecules spend as part of the enzyme species, forms, or groups involved in an enzyme reaction mechanism. The formulas to evaluate these times are given as a function of the individual rate constants and the initial concentrations of the involved species at the onset of the reaction. We apply the results to unstable enzyme systems and support the results by using a concrete example of such systems. The practicality of obtaining the mean times and their possible application in a kinetic data analysis is discussed.     

Concentration oscillations in three-component reaction systems

Based on the sufficient conditions for the existence of oscillation modes in the mathematical models of biological systems, simple three-component schemes of chemical reactions with oscillatory behavior including only mono- and bimolecular steps are suggested.     

Stability regions and transition phenomena for harvested predator-prey systems

Summary We analyze the global behaviour of a predator-prey system under constant-rate predator harvesting, showing how to classify the possibilities and determine the region of asymptotic stability by a combination of relatively elementary theoretical methods and computer simulations.Research sponsored in part by the National Research Council of Canada. Grant No. A-3138     

Analysis of protein folding and function using backbone modified proteins

With the recent development of chemical and biological methods to introduce backbone modifications into the polypeptide chains of proteins, there have been a growing number of site-directed mutagenesis experiments focused on understanding the role of the polypeptide backbone in protein folding and function. The substitution of a main chain amide bond with an ester bond is now a popular mutation to investigate the role of the polypeptide backbone in ligand, binding, enzyme catalysis, and protein folding. Here we review the results of studies on some 25 ester-bond containing analogues from nine different protein systems. The structural, thermodynamic, and functional consequences of introducing backbone amide- to ester-bond mutations into these protein systems are discussed.     

Solid/Liquid Cluster Recognition in Heterogeneous Systems

Abstract

Criteria are presented which enable the differentiation between the extent of solid-like and liquid-like character in a heterogeneous system on a per atom basis. Such criteria are developed for two different interatomic potentials, the Stillinger-Weber model for group IV semiconductors and the Lennard-Jones model for insulators. For the Stillinger-Weber potential model, three criteria are presented: one based on the coordination number of nearest neighbors, one based on the three-body energy, and one based on the angular positions (spatial arrangements) of neighbors. For the Lennard-Jones model an angular criterion is used. The difficulties associated with the assignation of interfacial atoms (those with partial solid and partial liquid character) are discussed. The effectiveness of these criteria for both models is tested by application to the identification of solid-like nuclei in the melt.     

Apical antennal sensilla in nymphs of Libellula depressa (Odonata: Libellulidae)

Abstract. In an ultrastructural study of the apical antenna of the last nymphal stages of Libellula depressa (Odonata: Libellulidae), we found long sensilla trichodea, 2 sensory pegs, and a coeloconic sensillum on the last article of the flagellum (the distal part of the antenna). The long sensilla trichodea are mechanoreceptors, almost identical to the long filiform hairs of some terrestrial insects and the first sensilla of this kind to be described in aquatic insects. Particular attention was given to the complex coeloconic sensillum, a compound sensillum innervated by 2 groups of 3 neurons wrapped in a dendritic sheath. A cuticular sleeve envelops the distal portion of the outer dendritic segment. The cuticle of the coeloconic sensillum shows wide channels and is contiguous to the underlying granular and fibrillar layer. Similar structures on the antennae of the adults of other dragonflies were identified as chemoreceptors in previous studies. We hypothesize that this larval coeloconic sensillum might likewise have a chemosensory function, responding to molecules that diffuse through the cuticle and the underlying granular and fibrillar layer, as no clear pore or pore-tubule system is visible. Alternative functions are also explored on the basis of morphological details.     

Bioactivity of phytochemicals in some lesser-known plants and their effects and potential applications in livestock and aquaculture production systems

Livestock and aquaculture production is under political and social pressure, especially in the European Union (EU), to decrease pollution and environmental damage arising due to animal agriculture. The EU has banned the use of antibiotics and other chemicals, which have been shown to be effective in promoting growth and reducing environment pollutants because of the risk caused to humans by chemical residues in food and by antibiotic resistance being passed on to human pathogens. As a result of this, scientists have intensified efforts in exploiting plants, plant extracts or natural plant compounds as potential natural alternatives for enhancing the livestock productivity. This paper discusses work on the effects of various phytochemicals and plant secondary metabolites in ruminant and fish species. The focus is on (i) plants such as Ananas comosus (pine apple), Momordica charantia (bitter gourd) and Azadirachta indica (neem) containing anthelmintic compounds and for their use for controlling internal parasites; (ii) plants containing polyphenols and their applications for protecting proteins from degradation in the rumen, increasing efficiency of microbial protein synthesis in rumen and decreasing methane emission; for using as antioxidants, antibacterial and antihelmintic agents; and for changing meat colour and for increasing n-3 fatty acids and conjugated linoleic acid in meat; (iii) saponin-rich plants such as quillaja, yucca and Sapindus saponaria for increasing the efficiency of rumen fermentation, decreasing methane emission and enhancing growth; for producing desired nutritional attributes such as lowering of cholesterol in monogastric animals; for increasing growth of fish (common carp and Nile tilapia) and for changing male to female ratio in tilapia; and for use as molluscicidal agents; (iv) Moringa oleifera leaves as a source of plant growth factor(s), antioxidants, beta-carotene, vitamin C, and various glucosinolates and their degraded products for possible use as antibacterial, antioxidant, anticarcinogenic and antipest agents; (v) Jatropha curcas toxic variety with high levels of various phytochemicals such as trypsin inhibitor, lectin, phytate and phorbol esters in seeds limiting the use of seed meal in fish and livestock diets; and the use of phorbol esters as bio-pesticidal agent; and (vi) lesser-known legumes such as Entada phaseoloides seeds containing high levels of trypsin inhibitor and saponins, Sesbania aculeate seeds rich in non-starch polysaccharides and Mucuna pruriens var. utilis seeds rich in l-3,4-dihydroxyphenylalanine and their potential as fish feed; Cassia fistula seeds as a source of antioxidants; and the use of Canavalia ensiformis, C. gladiata and C. virosa seeds containing high levels of trypsin inhinitor, lectins and canavanine. The paper also presents some challenges and future areas of work in this field.