一个基于基因表达谱的基因逻辑网络模型的建立与应用

基因之间除了线性关联作用关系外,还存在着非线性的逻辑关系.用这种逻辑关系构建的生物系统网络模型对研究细胞内的各种生物通路和细胞分子网络非常重要.首先,根据图着色原理确定了基因的低阶和高阶逻辑关系,然后应用结肠癌基因表达谱数据分析了51个癌基因和抑癌基因的逻辑关系,在此基础上构建了结肠癌基因表达的逻辑网络.通过这个网络模型发现了与KEGG数据库中结肠癌通路一致的转化生长因子信号通路,并分析了各生物通路成员之间错综复杂的关系.实验结果表明,基因逻辑网络模型在一定程度上揭示了结肠癌基因和抑癌基因之间并行、分叉等复杂的相互作用关系,反映了结肠癌发病的复杂分子机制,为分子生物医学家提供了一个参考模型.     

Network representation of protein interactions: Theory of graph description and analysis

A methodological framework is presented for the graph theoretical interpretation of NMR data of protein interactions. The proposed analysis generalizes the idea of network representations of protein structures by expanding it to protein interactions. This approach is based on regularization of residue‐resolved NMR relaxation times and chemical shift data and subsequent construction of an adjacency matrix that represents the underlying protein interaction as a graph or network. The network nodes represent protein residues. Two nodes are connected if two residues are functionally correlated during the protein interaction event. The analysis of the resulting network enables the quantification of the importance of each amino acid of a protein for its interactions. Furthermore, the determination of the pattern of correlations between residues yields insights into the functional architecture of an interaction. This is of special interest for intrinsically disordered proteins, since the structural (three‐dimensional) architecture of these proteins and their complexes is difficult to determine. The power of the proposed methodology is demonstrated at the example of the interaction between the intrinsically disordered protein osteopontin and its natural ligand heparin.     

Toward a Practical Ontology for Socioeconomic Metabolism

The complexity of data and methods in industrial ecology (IE) keeps growing, and the demand for comprehensive and interdisciplinary assessments increases. To keep up with this development, the field needs a data infrastructure that allows researchers to annotate, store, retrieve, combine, and exchange data at low cost, without loss of information, and across disciplines and model frameworks. A consensus‐building debate about how to describe the common object of study, socioeconomic metabolism (SEM), is necessary for the development of practical data structures and databases. We review the definitions of basic concepts to describe SEM in IE and related fields such as integrated assessment modeling. We find that many definitions are not compatible, are implicit, and are sometimes lacking. To resolve the conflicts and inconsistencies within the current definitions, we propose a hierarchical system of terms and definitions, a practical ontology, for describing objects, their properties, and events in SEM. We propose a typology of object properties and use sets to group objects into a hierarchical, mutually exclusive, and collectively exhaustive (H‐MECE) classification. This grouping leads to a general definition of stocks. We show that a MECE representation of events necessarily requires two complementary concepts: processes and flows, for which we propose general definitions based on sets. Using these definitions, we show that the system structure of any interdisciplinary model of SEM can be formulated as a directed graph. We propose guidelines for semantic data annotation and database design, which can help to turn the vision of a powerful data infrastructure for SEM research into reality.     

模糊图论在山西植被区划中的应用

本文用模糊图论的最大树方法对山西植被区划进行了数量分类研究,将山西植被分为2个植被地带,6个植被地区,17个植被小区。与在植物群落学中应用的模糊聚类分析和其它方法相比,模糊图论的最大树方法直接依模糊相似系数矩阵得到树状图,从而避免了相似系数矩阵复杂的合成运算,而分类结果不仅更具直观性,而且也是令人满意的。我们认为模糊图论应用于植被区划是合适的。     

基于CiteSpace分析铜绿假单胞菌耐药性研究热点与趋势

【背景】铜绿假单胞菌(Pseudomonas aeruginosa)是临床引发感染的主要病原菌之一,对多种抗菌药物均有耐药性,临床治疗难度大,对该病原菌耐药性的研究一直备受关注。【目的】基于CiteSpace可视化功能,探究铜绿假单胞菌耐药性研究现状、热点与发展趋势。【方法】利用文献计量分析法,以2014–2021年中国知网(CNKI)、万方数据库(Wanfang)、Web of Science (WoS)共8 996篇铜绿假单胞菌耐药性的中英文文献为分析样本,运用Citespace软件对文献发文量、作者合作网络、国家和机构合作网络、文献共被引及期刊分析、关键词聚类、突现等方面进行分析,以探究该研究主题的研究热点及趋势。【结果】英文文献发文量增长速度高于中文文献;我国文献发文量仅次于美国、印度,在该领域科研成果贡献度较高,国际学术影响力较大;中英文文献中均对院内感染疾病和耐碳青霉烯类铜绿假单胞菌持高关注度。然而,中文文献较关注铜绿假单胞菌耐药性的临床防治问题,英文文献则较关注铜绿假单胞菌耐药性的基础研究。【结论】国内外铜绿假单胞菌耐药性研究对院内感染疾病及新型耐药菌的产生与防治关注度最高,暗示以上研究主题是该领域的研究热点与趋势。     

短时高温对烟蚜生长发育、繁殖和取食行为的影响

【目的】烟蚜Myzus persicae是一种世界性的重要农业害虫,本研究测定了短时高温对烟蚜生长发育、繁殖和取食行为的影响。【方法】测定初产若蚜每天在30, 35和40℃下处理1, 2和4 h的发育历期及成蚜在相同处理下的繁殖力,应用刺吸电位技术（electronic penetration graph, EPG）测定成蚜在30和35℃下处理1和2 h后以及在25, 28, 30和35℃恒温下的取食行为。【结果】短时高温（30~35℃）对各龄若蚜发育历期影响较小,但40℃下处理2 h后其发育历期显著增加（P<0.05）;若蚜存活率、成蚜寿命及其繁殖历期随温度和处理时间的增加而降低;在25~35℃下,随温度和处理时间的增加,成蚜繁殖率变化较小,但40℃下处理2和4 h后,其繁殖率显著降低（P< 0.01）;短时高温对烟蚜的取食行为影响显著,随温度和处理时间的增加,非刺探波np数量（P<0.05）及其持续时间（P<0.01）显著减少,而韧皮部刺吸波E持续时间显著增加（P<0.05）;但持续高温下,随温度升高,np波数量及其持续时间先减少后增加,而E波则相反。【结论】短时高温对烟蚜若蚜发育速率影响较小,但使若蚜存活率、成蚜寿命及其繁殖历期显著降低,且对成蚜繁殖有一定的抑制作用,而对成蚜的取食有一定的促进作用。研究结果有助于了解烟蚜不同年份间夏季种群数量的变化机制。     

Towards predicting Ca2+‐binding sites with different coordination numbers in proteins with atomic resolution

Ca²⁺‐binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally‐diverse set of biological functions. Although the highly‐conserved EF‐Hand motif has been studied extensively, non‐EF‐Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca²⁺‐binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca²⁺‐binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca²⁺‐binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca²⁺ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca²⁺ positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca²⁺‐binding sites in three datasets of highly‐diversified protein structures with 0.22 to 0.49 Å accuracy. All multiple‐binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low‐coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor‐coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low‐coordination and cofactor‐coordinating Ca²⁺‐binding sites. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Recombination and lineage‐specific gene loss in the aflatoxin gene cluster of Aspergillus flavus

Aflatoxins produced by Aspergillus flavus are potent carcinogens that contaminate agricultural crops. Recent efforts to reduce aflatoxin concentrations in crops have focused on biological control using nonaflatoxigenic A. flavus strains AF36 (=NRRL 18543) and NRRL 21882 (the active component of afla‐guard^®). However, the evolutionary potential of these strains to remain nonaflatoxigenic in nature is unknown. To elucidate the underlying population processes that influence aflatoxigenicity, we examined patterns of linkage disequilibrium (LD) spanning 21 regions in the aflatoxin gene cluster of A. flavus. We show that recombination events are unevenly distributed across the cluster in A. flavus. Six distinct LD blocks separate late pathway genes aflE, aflM, aflN, aflG, aflL, aflI and aflO, and there is no discernable evidence of recombination among early pathway genes aflA, aflB, aflC, aflD, aflR and aflS. The discordance in phylogenies inferred for the aflW/aflX intergenic region and two noncluster regions, tryptophan synthase and acetamidase, is indicative of trans‐species evolution in the cluster. Additionally, polymorphisms in aflW/aflX divide A. flavus strains into two distinct clades, each harbouring only one of the two approved biocontrol strains. The clade with AF36 includes both aflatoxigenic and nonaflatoxigenic strains, whereas the clade with NRRL 21882 comprises only nonaflatoxigenic strains and includes all strains of A. flavus missing the entire gene cluster or with partial gene clusters. Our detection of LD blocks in partial clusters indicates that recombination may have played an important role in cluster disassembly, and multilocus coalescent analyses of cluster and noncluster regions indicate lineage‐specific gene loss in A. flavus. These results have important implications in assessing the stability of biocontrol strains in nature.     

Predicting epidemics on directed contact networks

Contact network epidemiology is an approach to modeling the spread of infectious diseases that explicitly considers patterns of person-to-person contacts within a community. Contacts can be asymmetric, with a person more likely to infect one of their contacts than to become infected by that contact. This is true for some sexually transmitted diseases that are more easily caught by women than men during heterosexual encounters; and for severe infectious diseases that cause an average person to seek medical attention and thereby potentially infect health care workers (HCWs) who would not, in turn, have an opportunity to infect that average person. Here we use methods from percolation theory to develop a mathematical framework for predicting disease transmission through semi-directed contact networks in which some contacts are undirected-the probability of transmission is symmetric between individuals-and others are directed-transmission is possible only in one direction. We find that the probability of an epidemic and the expected fraction of a population infected during an epidemic can be different in semi-directed networks, in contrast to the routine assumption that these two quantities are equal. We furthermore demonstrate that these methods more accurately predict the vulnerability of HCWs and the efficacy of various hospital-based containment strategies during outbreaks of severe respiratory diseases.     

Directed graphs of DNA sequences and their numerical characterization

In this paper we (1) introduce a directed graphical representation of DNA primary sequences; (2) describe a scheme that transforms the directed graph of a DNA sequence into an upper triangular matrix; (3) investigate whether or not the existing matrix-based invariants of DNA sequences are compatible for the upper triangular matrix representation. The utility of our method is illustrated by an examination of the similarity between human and other seven species.