Petri net modelling of biological networks

Mathematical modelling is increasingly used to get insights into the functioning of complex biological networks. In this context, Petri nets (PNs) have recently emerged as a promising tool among the various methods employed for the modelling and analysis of molecular networks. PNs come with a series of extensions, which allow different abstraction levels, from purely qualitative to more complex quantitative models. Noteworthily, each of these models preserves the underlying graph, which depicts the interactions between the biological components. This article intends to present the basics of the approach and to foster the potential role PNs could play in the development of the computational systems biology.     

腾格里沙漠东南缘不同生物土壤结皮细菌多样性及其季节动态特征

微生物多样性对于生物土壤结皮在沙漠生态系统中改善局部环境以及提升生态功能具有重要作用。本研究对腾格里沙漠东南缘沙坡头地区藻结皮、藓结皮及其下层的四季样品进行了16S rDNA高通量测序, 以期阐明细菌多样性及其在生物土壤结皮演替过程中的季节变化规律。结果表明4种类型样品的细菌丰富度在夏季显著低于其他3个季节。4种类型样品中主要的细菌类群为变形菌门、放线菌门、绿弯菌门、酸杆菌门、蓝细菌门等, 其中变形菌门和放线菌门为优势类群, 夏季时变形菌门的相对多度显著高于春季、秋季、冬季, 且在结皮层中相对多度显著高于结皮下层。放线菌门的相对多度在春季、夏季显著高于秋季、冬季, 且结皮下层相对多度高于结皮层。生物土壤结皮演替过程中细菌多样性及其相对多度季节动态变化表明其对沙漠土壤局部环境的变化作出了响应, 这为深入理解生物土壤结皮在沙漠生态系统中的生态功能提供了微生物多样性数据。     

Protein structure dynamics by crosslinking mass spectrometry

Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.     

高寒沙区生物土壤结皮覆盖土壤碳释放动态

生物土壤结皮广泛分布于荒漠生态系统,能够通过自身的呼吸作用影响土壤碳释放以及区域碳循环过程。本研究在具有典型高寒沙区气候特征的青藏高原东北部（青海共和盆地）,以广泛分布于人工植被恢复区的藻类和藓类结皮为研究对象,裸地为对照,观测了裸地与两种类型生物土壤结皮去除和覆盖土壤碳释放速率的日动态和生长季动态规律,探讨生物土壤结皮对土壤碳释放量的影响。结果表明：生物土壤结皮去除和覆盖土壤碳释放速率日动态和生长季动态特征与裸地一致,均呈“单峰”曲线。生物土壤结皮覆盖土壤的日最大碳释放速率出现于13:00左右,裸地与去除结皮土壤的日峰值均出现于15:00左右,生物土壤结皮的存在使土壤碳释放速率的日峰值出现时间提前2h左右,各观测类型生长季内碳释放速率最大值均出现在8月。在相对干旱年份（2017）,藻类和苔藓结皮覆盖导致土壤碳释放量分别增加了22.07%和85.61%,其中,藻类和苔藓结皮层碳释放量占增加量的67.60%和25.76%;而在相对湿润年份（2018）,藻类和苔藓结皮覆盖导致土壤碳释放量分别增加了139.37%和290.53%,二者结皮层碳释放量分别占增加量的69.09%和45.59%,生物土壤结皮发育促进了土壤的碳释放。温度对土壤碳释放变化的贡献率为48.89%,是高寒沙区土壤碳释放日动态变化的关键驱动因子。因此,在核算荒漠生态系统碳交换过程中,应充分考虑各区域不同类型生物土壤结皮对土壤碳释放产生的影响。     

An integrated,spatio‐temporal modelling framework for analysing biological invasions

Aim

We develop a novel modelling framework for analysing the spatio‐temporal spread of biological invasions. The framework integrates different invasion drivers and disentangles their roles in determining observed invasion patterns by fitting models to historical distribution data. As a case study application, we analyse the spread of common ragweed (Ambrosia artemisiifolia).

Location

Central Europe.

Methods

A lattice system represents actual landscapes with environmental heterogeneity. Modelling covers the spatio‐temporal invasion sequence in this grid and integrates the effects of environmental conditions on local invasion suitability, the role of invaded cells and spatially implicit “background” introductions as propagule sources, within‐cell invasion level bulk‐up and multiple dispersal means. A modular framework design facilitates flexible numerical representation of the modelled invasion processes and customization of the model complexity. We used the framework to build and contrast increasingly complex models, and fitted them using a Bayesian inference approach with parameters estimated by Markov chain Monte Carlo (MCMC).

Results

All modelled invasion drivers codetermined the A. artemisiifolia invasion pattern. Inferences about individual drivers depended on which processes were modelled concurrently, and hence changed both quantitatively and qualitatively between models. Among others, the roles of environmental variables were assessed substantially differently subject to whether models included explicit source‐recipient cell relationships, spatio‐temporal variability in source cell strength and human‐mediated dispersal means. The largest fit improvements were found by integrating filtering effects of the environment and spatio‐temporal availability of propagule sources.

Main conclusions

Our modelling framework provides a straightforward means to build integrated invasion models and address hypotheses about the roles and mutual relationships of different putative invasion drivers. Its statistical nature and generic design make it suitable for studying many observed invasions. For efficient invasion modelling, it is important to represent changes in spatio‐temporal propagule supply by explicitly tracking the species’ colonization sequence and establishment of new populations.

     

A framework for multidimensional modelling of activity and structure of multispecies biofilms

Concepts from previous biofilm models were integrated to create a framework for the implementation of multidimensional (2D and 3D) multispecies biofilm models. The framework is here described at three levels: (i) mathematical representation of the processes involved in biofilm formation, (ii) numerical implementation into a computer program (freely available from our website http://www.biofilms.bt.tudelft.nl/frameworkMaterial) and (iii) using the program for the creation of biofilm models with multiple bacterial and solute species. An improved version of the individual-based modelling (IbM) that allows structured biomass was used. In this approach biomass composition may be discriminated into any number of particulate species, including extracellular polymeric substances (EPS) for which specific functionality was included. Detachment is also included, described as occurring at the biofilm surface with variable local rates derived from functions of state variables. The application of this modelling framework to a multispecies system with structured biomass is illustrated in a case study where the competition between an organism capable of accumulating polyhydroxybutyrate (PHB, an internal storage compound) and an EPS-producing organism in a two-species biofilm is analysed. Results illustrate that biofilms enriched in PHB-producing organisms may be obtained by supplying substrate intermittently in feast/famine cycles.     

Wind modelling for wind erosion research by open source computational fluid dynamics

The open source computational fluid dynamics (CFD) wind model (CFD-WEM) for wind erosion research in the Xilingele grassland in Inner Mongolia (autonomous region, China) is compared with two open source CFD models Gerris and OpenFOAM. The evaluation of these models was made according to software technology, implemented methods, handling, accuracy and calculation speed. All models were applied to the same wind tunnel data set. Results show that the simplest CFD-WEM has the highest calculation speed with acceptable accuracy, and the most powerful OpenFOAM produces the simulation with highest accuracy and the lowest calculation speed. Gerris is between CFD-WEM and OpenFOAM. It calculates faster than OpenFOAM, and it is capable to solve different CFD problems. CFD-WEM is the optimal model to be further developed for wind erosion research in Inner Mongolia grassland considering its efficiency and the uncertainties of other input data. However, for other applications using CFD technology, Gerris and OpenFOAM can be good choices. This paper shows the powerful capability of open source CFD software in wind erosion study, and advocates more involvement of open source technology in wind erosion and related ecological researches.     

科尔沁沙质草地沙漠化过程中土壤生物活性的变化

选择相邻地段的固定沙丘、半固定沙丘和流动沙丘为对象,研究了科尔沁西部沙质草地沙漠化过程中土壤微生物量、土壤酶活性和土壤养分的变化特征以及三者之间的相关关系.结果表明:土壤养分含量、土壤酶活性和微生物量均随土壤深度的增加而逐渐降低;沙漠化过程中土壤养分严重丧失,土壤微生物量碳、氮、磷,以及土壤脲酶、蛋白酶、蔗糖酶、磷酸单酯酶、脱氢酶、多酚氧化酶和硝酸还原酶的活性均随沙漠化程度的加剧而大幅度下降;土壤生物活性对土壤沙漠化比较敏感,在固定沙丘到半固定沙丘的转化过程中土壤生物活性下降最快;土壤微生物量、土壤酶活性以及土壤养分之间均存在显著的相关关系.     

不同植物群落下铜尾矿废弃地生物结皮中真菌群落结构的比较

分布于铜尾矿废弃地的裸地表面及维管植物群落中的生物土壤结皮在尾矿废弃地生态恢复过程中扮演重要角色。利用分子生物学技术探讨了不同维管植物下以及不同演替阶段的生物土壤结皮中真菌的多样性及其群落结构的变化。结果表明:生物土壤结皮中的真菌主要包括子囊菌门(Ascomycota)、担子菌门(Basidiomycota)和壶菌门(Chytridiomycota),其中子囊菌门占绝对优势,其相对丰度为55.12%—87.73%,其次为担子菌门相对丰度为12.27%—43.86%;不同样本真菌群落结构在门、纲、目以及属的水平存在显著差异;生物土壤结皮中真菌群落结构和多样性的差异与维管植物群落类型以及演替阶段不同的生物土壤结皮的类型有关,与基质化学性质之间无显著的相关性。     

生物土壤结皮对荒漠土壤线虫群落的影响

在干旱的沙漠生态系统中,生物土壤结皮对于沙丘的固定和土壤生物的维持起着相当重要的作用.土壤线虫能敏感的指示土壤的恢复程度,是衡量沙区生态恢复与健康的重要生物学属性,而目前关于生物土壤结皮与土壤线虫的关系研究很少.为探明生物土壤结皮对土壤线虫的影响,以腾格里沙漠东南缘的人工植被固沙区藻结皮和藓类结皮覆盖的沙丘土壤为研究对象,根据固沙年限的不同将样地分为4个不同的区进行采样(1956、1964、1981和1991年固沙区),以流沙区作为对照;同时,在不同季度(4、7、9和12月)分别采集腾格里沙漠东南缘的人工植被固沙区藻结皮和藓类结皮覆盖下不同土层(0-10、10-20和20-30 cm)的沙丘土壤,以沙坡头地区的红卫天然植被区为对照,分析生物土壤结皮下土壤线虫的时空变化.采用改良的Baermann漏斗法进行分离线虫,用光学显微镜鉴定并统计.研究表明:1956、1964、1981和1991年人工植被固沙区的藻结皮和藓类结皮均可显著提高其下土壤线虫多度、属的丰富度、Shannon-Weaver多样性指数、富集指数和结构指数(P＜0.05),这可能是因为生物土壤结皮的存在为土壤线虫提供了重要的食物来源和适宜的生存环境;固沙年限与结皮下土壤线虫多度、属的丰富度、Shannon-Weaver多样性指数、富集指数和结构指数存在显著的正相关关系(P＜0.05),这说明固沙年限越久,越有利于土壤线虫的生存和繁衍;结皮类型显著影响土壤线虫群落,相对于藻结皮而言,藓类结皮下土壤线虫多度与属的丰富度更高(P＜0.05),这说明演替后期的藓类结皮比演替早期的藻结皮更有利于土壤线虫的生存和繁衍.此外,藻结皮和藓类结皮均可显著增加其下0-10、10-20和20-30 cm土层线虫多度和属的丰富度(P＜0.05),但随着土壤深度的增加,这种影响逐渐减弱,表明生物土壤结皮更有利于表层土壤线虫的生存;而且,随着季节的变化,藻结皮和藓类结皮下土壤线虫多度基本表现为秋季＞夏季＞春季＞冬季,这些反映了生物土壤结皮的生物量、盖度和种类组成随着季节变化而变化.因此,腾格里沙漠东南缘的人工植被固沙区生物土壤结皮的存在与演替有利于土壤线虫的生存和繁衍,增加了线虫数量、种类和多样性,这指示了生物土壤结皮有利于该区土壤及其相应生态系统的恢复.     

2,4-二氯苯酚在土壤与河流底泥中降解动力学

以南京化学工业园内四柳河沿岸土壤与河流底泥为研究对象,通过土壤灭菌、温度与污染物初始浓度调控,研究了2,4-二氯苯酚在土壤与河流底泥中降解动力学及其影响因子。结果表明:微生物对2,4-二氯苯酚降解起主导作用,在45d内,非灭菌土壤和河流底泥的降解率分别是灭菌条件下的1.5～3倍、1.4～2.8倍,土壤和河流底泥中的2,4-二氯苯酚微生物降解量分别为0.128～0.599和0.113～0.718mg·kg-1,非灭菌处理半衰期时间短于灭菌处理;(10±1)℃～(30±1)℃范围内,随着温度的增高,2,4-二氯苯酚降解加快,在(30±1)℃土壤与河流底泥中残留量最小,分别为0.305和0.203mg·kg-1,半衰期也最短;土壤与河流底泥中的2,4-二氯苯酚均在其浓度为0.5mg·kg-1时降解最快,随着初始浓度的增加,2,4-二氯苯酚降解速度呈现递减趋势,半衰期增长。     

蚯蚓对土壤微生物及生物肥力的影响研究进展

蚯蚓被称为“生态系统工程师”,可以通过改善微生境(排粪、作穴、搅动)、提高有机物的表面积、直接取食、携带传播微生物等方式影响土壤微生物结构、组成和功能.蚯蚓活动形成的大孔隙(洞穴)、中、微空隙(排泄物)可以增加土壤孔隙度和通气性,有助于改善微生物微环境,促进其生长和繁殖.蚯蚓还通过取食、粉碎、混合等活动使复杂有机质转变为微生物可利用的形式,增加土壤微生物与有机质的接触面积,促进微生物对有机质的矿化作用,对土壤中碳、氮、磷养分循环等关键过程产生影响,最终促进土壤养分循环和周转速率,提高土壤生物肥力.     

An object-oriented modelling framework for the arterial wall

An object-oriented modelling framework for the arterial wall is presented. The novelty of the framework is the possibility to generate customisable artery models, taking advantage of imaging technology. In our knowledge, this is the first object-oriented modelling framework for the arterial wall. Existing models do not allow close structural mapping with arterial microstructure as in the object-oriented framework. In the implemented model, passive behaviour of the arterial wall was considered and the tunica adventitia was the objective system. As verification, a model of an arterial segment was generated. In order to simulate its deformation, a matrix structural mechanics simulator was implemented. Two simulations were conducted, one for an axial loading test and other for a pressure–volume test. Each simulation began with a sensitivity analysis in order to determinate the best parameter combination and to compare the results with analogue controls. In both cases, the simulated results closely reproduced qualitatively and quantitatively the analogue control plots.     

生物结构上的“反应点阵”

细胞膜和各种细胞器膜表面均结合和分布着具有不同生物活性的生物大分子,能引起各种反应,可以看作是一些反应点。进化使这些反应点组合,排列,构成特异的反应点序列,可称为"反应点阵"。     

冻融条件下生物结皮覆盖对土壤饱和导水率的影响

生物结皮(BSC)是广泛分布的地被物,每逢冬春季节,受冻融交替作用影响,结皮土壤的理化性质和水文学特征明显改变且与裸土差异显著,从而影响该地区土壤可蚀性评估和土壤侵蚀防治。采用室内模拟实验,以蓝藻结皮土壤为对象,研究不同冻融交替次数和初始含水量下,土壤三相对温度变化的响应特征并定量分析结皮覆盖土壤在此条件下饱和导水率(Ks)的变化趋势和突变点。结果表明:初始含水量对Ks无显著影响(P>0.05),冻融交替次数对Ks有极显著影响(P<0.01),冻融条件下裸土的平均Ks为1.941 mm/min,结皮覆盖土壤平均Ks为0.325 mm/min,两者具有极显著差异(P<0.01),且随交替次数增加,Ks差异逐渐增大,并在10次时达到最大值为10.13倍。不同冻融含水量下的结皮土壤的Ks在冻融10—20次时趋近,平均值为0.219mm/min。冻融作用显著改变土壤结构,且在冻融7次时土壤结构变化较明显,冻融过程中<0.1 mm的土壤颗粒显著变化。试验条件下,Ks受因子影响程度大小为:冻融交替次数>土壤结构>结皮厚度>结皮容重>下层土壤容重>...     

A novel protocol of energy optimisation for predicted protein structures built by homology modelling

Homology modelling was applied to predict the three-dimensional (3D) structures of six sets of lipase proteins. Sequence identities between the target and template were 34.6, 44.9, 57.4, 69.9, 79.0 and 86.2%, respectively. Then, eight different protocols including three optimising factors [periodically bounded cell (PBC) water, molecular dynamics (MD) simulation, ‘grade-unpacking’ strategy or ‘combinatorial’ strategy] were used to refine the initial model of each system. By comparing the energy-optimised models with the true 3D structure of the target protein in terms of all backbone atoms' root mean square deviation, we determined a novel but all-purpose protocol for model refinement. The protocol refined a homology model by adopting the ‘grade-unpacking’ strategy for energy minimisation while the model was solvated in PBC water. Furthermore, by comparing the influence of each single optimising factor on the accuracy of the refined structure, we found that introducing the MD simulation into the model refinement method would decrease the accuracy of the final protein structure while methods with either PBC water or the ‘grade-unpacking’ strategy would increase the accuracy of the final model.     

Predicting substrate selectivity between UGT1A9 and UGT1A10 using molecular modelling and molecular dynamics approach

Uridine 5′-diphospho-glucuronosyltransferase-1A9 (UGT1A9) expressed in the liver, shows good sequence identity with UGT1A10, expressed in the intestine. Both uridine 5′-diphospho-glucuronosyltransferase (UGT) isoforms show comprehensive overlapping substrate selectivity but there are differences in stereoselectivity, regiospecificity and rate of glucuronidation of the substrates. Multiple sequence alignment analyses of UGT1A9 and UGT1A10 showed that 13% of the residues in N-terminal domain (NTD) are non-identical between them. Herein, authors attempted homology modelling of UGT1A9 and UGT1A10 and validation using software tools and reported mutagenic studies. A molecular docking study of the known substrates is performed on UGT1A9 and UGT1A10 homology models. The non-identical N-terminal residues ranging from 111 to 117 in UGT1A9 and UGT1A10 were identified to play a central role in the substrate selectivity. However, substrate binding is performed by Ser111, Gly115 and Leu117 in UGT1A10 and Gly111, Asp115 and Phe117 in UGT1A9. This study reports new residues in NTD, showing interaction with uridine 5′-diphospho-glucuronic acid which binds with C-terminal domain. Further, molecular dynamics simulations were carried out to study the role of non-identical residues in substrate identification. The study demonstrates the folding of the UGT enzyme, particularly, helix-loop-helix transition and movement of Nα3-2 helix, in response to substrate and co-substrate binding.     

黄土丘陵区生物结皮对土壤可蚀性的影响

在采样分析生物结皮对土壤理化属性影响的基础上,采用EPIC模型估算与模拟降雨试验相结合的方法,研究了黄土丘陵区不同生物量、不同土壤质地和不同季节的生物结皮对土壤可蚀性(K值)的影响.结果表明： 生物结皮显著降低了土壤可蚀性,生物结皮层土壤可蚀性较下层土壤降低17%;土壤可蚀性随生物结皮生物量的增加呈降低趋势,藓结皮土壤可蚀性K值较藻结皮土壤降低21%;生物结皮土壤可蚀性在不同季节因其生物活性不同而存在差异,雨季中显著高于雨季前和雨季末;不同质地土壤上生物结皮对可蚀性的影响不同,可蚀性K值为砂壤>粉壤>砂土;模拟降雨条件下测定表明,生物结皮的发育使土壤可蚀性较对照（下层5~10 cm土壤）降低约90%.