细胞信号网络功能鲁棒的简并性拓扑特征

细胞信号网络对于外界环境的干扰表现出优良的鲁棒性,但是其维持功能鲁棒的内在机制尚未明确,本文研究了细胞信号网络功能鲁棒性的拓扑特征。选择布尔网络模型模拟细胞网络的动态行为,利用网络节点状态的扰动模拟外界环境干扰。基于演化策略探寻不同网络拓扑的功能并分析其在干扰环境下的鲁棒性,采用埃德尔曼提出的基于信息论的计算方法评估网络拓扑的简并度、冗余度和复杂度等拓扑属性,对比分析它们与功能鲁棒度的相关性及作用机理。结果显示,在网络模型的演化过程中,其拓扑简并度与功能鲁棒度显著正相关,相关性水平高于拓扑冗余度与鲁棒度的相关性。并且,随着鲁棒度的提升,网络的节点数和复杂度也随之升高,同样简并度与网络的节点数和复杂度的相关性高于拓扑冗余度与网络的节点数和复杂度的相关性。这说明增加的网络节点以简并的方式同时提高了网络拓扑的鲁棒度和复杂度。因此,细胞网络功能鲁棒性的拓扑特征是简并而不是冗余,简并为解决生物系统的复杂问题提供了有效手段,为人工系统的可靠性设计提供有益的借鉴。     

Roles of positive and negative feedback in biological systems

We discuss the influence of positive and negative feedback on the stability of a system, which is not clear-cut, and involves complex, mathematical problems. We show in particular that positive feedback can have a stabilising effect on some systems. We also point out the role that positive feedback plays in the digital treatment of signals required by cellular signalling, drawing on analogies from electronics, and the role that negative feedback plays in making a system robust against alteration of its parameters. Both positive and negative feedback can be seen as important enhancers of the properties of biological systems.     

Robustness of G1/S checkpoint pathways in cell cycle regulation based on probability of DNA-damaged cells passing as healthy cells

We investigate the robustness and the behaviours of the critical proteins under parameter perturbations of G1/S checkpoint pathways with different levels of DNA-damage, based on a mathematical model of the pathways. We identify the peak times (PTs) of two key proteins as the in silico biomarkers based on the currently established biology, and the results from the local and global sensitivity analyses show the significant kinetic parameters that are associated with the key proteins. The robustness of the G1/S checkpoint pathways with or without DNA-damage is defined based on the probability (β) of DNA-damaged cells passing as healthy cells under the given perturbation regimes. The results from the global sensitivity analyses based on four defined levels of parameter range reveal that we can accurately distinguish healthy cells from the defective cells when parameter variations are within a range of ±10%. However, the probability of wrongly identifying damaged cells as healthy cells became very large (more than 0.43) when the level of change of parameters exceeds ±30%. Provided that there are probably millions of cells that are oncogenically primed at any given time, these dangerous cells are disposed through apoptosis and cellular senescence. However, the very recent experimental findings state that this irreversible process happens not in the pre-tumoral stage but in the pre-malignant tissue where a non-invasive tumor is formed. This points out that a large number of damaged cells undergo proliferation without being caught at DNA-damage checkpoints. Our simulation results, in terms of percentage of damaged cells that pass G1/S checkpoint agree with this possibility.     

Phylogeny of Leavenworthia S-alleles suggests unidirectional mating system evolution and enhanced positive selection following an ancient population bottleneck

The adoption of self-fertilization from an ancestral outcrossing state is one of the most common evolutionary transitions in the flowering plants. In the mustard family, outcrossing is typically enforced by sporophytic self-incompatibility (SI), but there are also many self-compatible species. The genus Leavenworthia contains taxa that either possess or lack SI. Here, we present data showing that SI is associated with strict outcrossing and that there is widespread trans-specific sequence polymorphism at the locus involved in the recognition of self-pollen (the S-locus). This ancestral polymorphism is consistent with the presence of an outcrossing mating system in the common ancestor of Leavenworthia species, and suggests that there have been several independent losses of SI in the group. When compared with other mustard species, the bulk of Leavenworthia S-allele sequences are highly diverged from those found in other Brassicaceae and show relatively low levels of nucleotide diversity, a pattern that suggests the common ancestor of the genus likely underwent a strong population bottleneck. The hypothesis of postbottleneck S-locus rediversification is supported by tests showing stronger positive selection acting on S-alleles from Leavenworthia than those found in other Brassicaceae.     

Automated analysis of courtship suppression learning and memory in Drosophila melanogaster

Study of the fruit fly, Drosophila melanogaster, has yielded important insights into the underlying molecular mechanisms of learning and memory. Courtship conditioning is a well-established behavioral assay used to study Drosophila learning and memory. Here, we describe the development of software to analyze courtship suppression assay data that correctly identifies normal or abnormal learning and memory traits of individual flies. Development of this automated analysis software will significantly enhance our ability to use this assay in large-scale genetic screens and disease modeling. The software increases the consistency, objectivity, and types of data generated.     

Source apportionment of pollution in groundwater source area using factor analysis and positive matrix factorization methods

By means of factor analysis (FA) and positive matrix factorization (PMF) methods, groundwater pollution sources were identified in the Jinji groundwater source area, which is beside the Yellow River and is the only urban water supply source for the city of Wuzhong in Northwestern China. The sources of groundwater were quantified based on 16 samples of shallow groundwater from the source area. The source apportionment with the PMF model identified three dominant groundwater pollution sources. These were anthropogenic activities of agricultural and industrial pollution with a pollution contribution of 53.0%, water–rock interaction of 24.6%, and evaporation and concentration of 22.4%. The source apportionment with the FA model identified four sources which were evaporation and concentration, with the largest contribution (42.6%), followed by anthropogenic activities (29.2%), mineral dissolution and industrial pollution (22.4%), and natural effects (5.8%). Specific attention should be paid to these natural (fluoride, TH, etc.) and anthropogenic sources (NH₄⁺, NO₂^?, turbidity, total bacterial count, etc.), and pertinent measures should be taken to control local groundwater pollution. The most significant trait of the PMF is its scientific interpretation and physical explanation of the results, depending on non-negative restriction of the pollution source profiles and contributions.     

A kinematic analysis of tepal growth in Lilium longiflorum

Time-lapse marking experiments indicate that the growth of tepals in Lilium longiforum Thunb. from 3.7 mm to maturity is triphasic. Phase I (tepal lengths 3.7–10 mm) is characterized by spatial and temporal variation in growth rate and, in the epidermis, a random distribution of mitoses with an acropetal increase in cell area. During phase II (10–90 mm) cell elongation and (later) cell division is restricted largely to basal regions. Cell division ceases when tepals are less than one-third of their mature length of 155 mm. Phase III (90–155 mm) is characterized by the gradual transition from basal to apical growth, and a modification of epidermal cell shape. A sharp peak in growth at the extreme tip of the tepal coincides with anthesis.Abbreviations LRGR local relative growth rate - RER relative elemental rate of growth     

辽宁省朝阳市农业生态经济系统能值分析

应用能值分析的方法,研究了以辽宁省朝阳市为代表的辽西半干旱区农业生态经济系统的能值投入及产出结构,并通过计算、对比能值评价指标,分析了朝阳市农业生态经济系统的发展现状。结果表明,对自然资源的过度利用造成了当地生态环境条件的恶化,由此产生不可更新自然资源的流失以及产出能值的损失;对可更新有机能的不充分利用也是造成当地资源浪费和环境破坏的重要原因。     

The impact of calmodulin on the cell cycle analyzed in a novel human cellular genetic system

Calmodulin (CaM) is the principle mediator of the Ca²⁺ signal in all eukaryotic cells. A huge variety of basic cellular processes including cell cycle control, proliferation, secretion and motility, among many others are governed by CaM, which regulates activities of myriads of target proteins. Mammalian CaM is encoded by three genes localized on different chromosomes all producing an identical protein. In this study, we have generated HeLa human cancer cells conditionally expressing CaM in a genetic background with all three genes inactivated by CRISPR/Cas9. We demonstrate that downregulation of ectopically expressed CaM is achieved after 120 h, when cells are arrested in the M phase of the cell cycle. We show for the first time that CaM downregulation in human cancer cells is followed by a multinucleated senescent state as indicated by expression of β-galactosidase as well as cell morphology typical for senescent cells. Our newly generated genetic system may be useful for the analysis of other CaM regulated processes in eukaryotic cells in the absence of endogenous CaM genes.     

The development of the plasma membrane reticular system in the fat body of an insect

Several insect tissues have plasma membranes that are folded inwards to make a subsurface reticulum on faces that are exposed to hemolymph. The infolds have been called plasma membrane reticular systems (RSs) to distinguish them from the somewhat similar structures found in transporting epithelia. They are characterized by having negative charges on the plasma membranes of the entranceways and by the concentration of some hemolymph proteins in their lymph spaces. Their formation and loss in the fat body has been studied by scanning electron microscopy during the fifth stadium of Calpodes ethlius (Lepidoptera, Hesperiidae). Fat body cells begin the fifth stadium arranged in ribbons with the cells linked together by a fringe of processes. In the first stage many more processes form. These partially fuse together in the second stage, leaving a subsurface reticulum connected by narrow entrances to the lateral cell faces and the face below the basal lamina. Both the cell processes and the reticular systems that they enclose are usually axially orientated. The completed RS persists for the second half of the intermoult devoted to larval syntheses when the concentration of hemolymph proteins rises. After protein sequestration prior to pupation the RS is lost and the fat body returns to being a tissue of rounded cells linked by a few enmeshed processes.     

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis

The linker histone H1 has a fundamental role in DNA compaction. Although models for H1 binding generally involve the H1 C‐terminal tail and sites S1 and S2 within the H1 globular domain, there is debate about the importance of these binding regions and almost nothing is known about how they work together. Using a novel fluorescence recovery after photobleaching (FRAP) procedure, we have measured the affinities of these regions individually, in pairs, and in the full molecule to demonstrate for the first time that binding among several combinations is cooperative in live cells. Our analysis reveals two preferred H1 binding pathways and we find evidence for a novel conformational change required by both. These results paint a complex, highly dynamic picture of H1–chromatin binding, with a significant fraction of H1 molecules only partially bound in metastable states that can be readily competed against. We anticipate the methods we have developed here will be broadly applicable, particularly for deciphering the binding kinetics of other nuclear proteins that, similar to H1, interact with and modify chromatin.     

The cellular parameters of leaf development in tobacco: a clonal analysis

The cellular parameters of leaf development in tobacco (Nicotiana tabacum L.) have been characterized using clonal analysis, an approach that provides unequivocal evidence of cell lineage. Our results indicate that the tobacco leaf arises from a group of around 100 cells in the shoot apical meristem. Each of these cells contributes to a unique longitudinal section of the axis and transverse section of the lamina. This pattern of cell lincage indicates that primordial cells contribute more or less equally to the growth of the axis, in contrast to the more traditional view of leaf development in which the leaf is pictured as arising from a group of apical initials. Clones induced prior to the initiation of the lamina demonstrate that the subepidermal layer of the lamina arises from at least six files of cells. Submarginal cells usually divide with their spindles parallel to the margin, and therefore contribute relatively little to the transverse expansion of the lamina. During the expansion of the lamina the orientation and frequency of cell division are highly regulated, as is the duration of meristematic growth. Initially, cell division is polarized so as to produce lineages that are at an oblique angle to the midrib; later cell division is in alternating perpendicular planes. The distribution of clones generated by irradiation at various stages of development indicates that cell division ceases at the tip of the leaf when the leaf is about one tenth its final size, and then ceases in progressively more basal regions of the lamina. Variation in the mutation frequency within the lamina reflects variation in the frequency of mitosis. Prior to the mergence of the leaf the frequency of mutation is maximal near the tip of the leaf and extremely low at its base; after emergence, the frequency of mutation increases at the base of the leaf. In any given region of the lamina the frequency of mutation is highest in interveinal regions, and is relatively low near the margin. Thus, both the orientation and frequency of cell division at the leaf margin indicate that this region plays a minor role in the growth of the lamina.Abbreviation MF mutation frequency     

Comparative analysis of two-component signal transduction system in two streptomycete genomes

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.     

The lateral line of zebrafish: a model system for the analysis of morphogenesis and neural development in vertebrates

The lateral line of the zebrafish has many of the advantages that made the sensory organs of Drosophila a very productive model system: 1) it comprises a set of discrete sense organs (neuromasts) arranged in a defined, species-specific pattern, such that each organ can be individually recognized; 2) the neuromasts are superficial and easy to visualize, and the innervating neurons are easy to label; 3) the sensory projection is simple yet reproducibly organized. Here we describe some of the tools that can be used to investigate the development of this system, and we illustrate their usefulness with specific examples. We conclude that the lateral line is uniquely suited among vertebrate sensory systems for a molecular, cellular and genetic analysis of pattern formation and of neural development.     

基于GIS的秦岭山区聚落用地适宜性评价

利用自然地理、生态和社会经济方面共14个因子构建秦岭山区聚落建设用地适宜性评价指标体系,采用AHP法确定各评价因子的权重,在地理信息系统(GIS)和遥感(RS)技术支持下,利用适宜性评价模型定量评价聚落建设用地适宜性,将聚落建设用地适宜性分为五个等级,并结合已建设区进行空缺分析。结果表明:(1)秦岭山区最适宜聚落用地面积为3378.1 km2,占研究区总面积的5.87%,说明秦岭山区适宜聚落开发的土地相对较少。(2)最适宜聚落用地集中在秦岭北、南坡山麓和东部的山间河谷地带,山地型特征明显。(3)有9.15%已建成区分布在限制建设区内,存在生态安全风险。(4)可用适宜聚落建设用地为3192.27 km2,空间分布不平衡。研究结果可为该区域城镇体系布局与用地规模的核算提供科学依据。     

Existence of memory in membrane channels: analysis of ion current through a voltage‐dependent potassium single channel

Ion current fluctuation of voltage‐dependent potassium channel in LβT2 cells has been investigated by autocorrelation function and DFA (detrended fluctuation analysis) methods. The calculation of the autocorrelation function exponent and DFA exponent of the sample was based on the digital signals or the 0–1 series corresponding to closing and opening of channels after routine evolution, rather than the sequence of sojourn times. The persistent character of the correlation of the time series was evident from the slow decay of the autocorrelation function. DFA exponent α was significantly greater than 0.5. The main outcome has been the demonstration of the existence of memory in this ion channel. Thus, the ion channel current fluctuation provided information about the kinetics of the channel protein. The result suggests the correlation character of the ion channel protein non‐linear kinetics indicates whether the channel is open or not.     

Comparative analysis of 35S and lectin promoters in transgenic soybean tissue using an automated image acquisition system and image analysis

Expression of the green fluorescent protein (gfp) gene, under regulatory control of either the constitutive 35S promoter or the developmentally-regulated lectin promoter was monitored and quantified using a newly-developed automated tracking system. The automated system consisted of a computer-controlled two-dimensional robotics table and a programmable image acquisition system, which was used to semi-continuously monitor gfp gene expression during development of transgenic soybean [Glycine max (L.) Merrill] somatic embryos. Quantitative analysis of GFP expression showed that, during somatic embryo proliferation and early development, expression of lectin-GFP was not detected. During late embryo development, expression of lectin-GFP gradually increased until the levels were similar to those of 35S-GFP. The use of an automated image collection system and image analysis facilitated the frequent monitoring and quantification of gfp gene expression on a large number of samples over an extended period of time.Electronic Supplementary Material Supplementary material is available for this article at