恢复生态学焦点问题

就恢复生态学的概念、近期的发展趋势与前沿命题、传统生态学理论在生态恢复过程中的应用及恢复生态学的社会性等核心问题展开论述。恢复生态学是一门年轻的学科,迄今尚无统一的定义。代表性的有3方面的学术观点。第1种强调受损的生态系统要恢复到理想的状态;第2种强调其应用生态学过程;第3种强调生态整合性恢复。笔者认为,恢复生态学是研究生态系统退化的原因、退化生态系统恢复与重建的技术与方法、过程与机理的科学。从近年的国际恢复生态学大会来看,恢复生态学研究近期主要有3个方面的发展趋势。一是强调自然恢复与社会、人文的耦合。认为恢复生态是全球性的,不只是自然的过程,应有全社会的支持,包括政治、经济和人文的介入。二是强调无论是在地域上还是在理论上都要跨越边界。有效的生态恢复实践在地域上要求多地区甚至是多国家的合作,在理论上要求多学科的交叉与耦合。三是强调以生态系统为基点,在景观尺度表达。随着环境和经济问题的全球化,生态系统和景观尺度的恢复生态学研究引起了越来越多的关注。2004年第15届国际恢复生态学大会的会议主题已定为：恢复、景观与设计。在当前研究趋势的基础上,提出了恢复生态学当前研究的6个前沿命题：恢复生态学的学科理论框架研究、恢复生态系统的功益研究、生物多样性在生态恢复中的作用研究、生态恢复对全球变化的响应研究、生态恢复立法研究和生态恢复与社会、经济的整合性研究。退化生态系统的恢复与重建是一项十分复杂的系统工程,尤其需要生态学理论的指导。多数生态学理论已被应用于恢复生态学的研究与实践。结合实例,着重阐述了生态系统演替理论在生态恢复中的应用。恢复生态与全球变化间的相互作用研究越来越多的引起了人们的关注,但多数研究仍停滞在定性研究阶段。在广东的恢复生态学研究表明,广东省从1986年至1998年,植被覆盖从26％到51％,新造林绿化的植被每年可吸收、固定广东省年排放CO2量的一半。人类社会与自然环境的协调可持续发展,不仅要求实现生态环境的可持续,同时亦要求实现人类社会与经济的可持续发展。这就要求生态系统的恢复与重建必须同时实现生态、经济与社会效率的三重优化。中国科学院华南植物研究所生态中心在中国热带、南亚热带进行的退化生态系统的恢复与重建研究历时30余年,所产生的显著的经济和社会效益,在各个实验站点均已有所反映。     

T.H. Huxley's Criticism of German Cell Theory: An Epigenetic and Physiological Interpretation of Cell Structure

In 1853, the young Thomas Henry Huxley published a long review of German cell theory in which he roundly criticized the basic tenets of the Schleiden-Schwann model of the cell. Although historians of cytology have dismissed Huxley’s criticism as based on an erroneous interpretation of cell physiology, the review is better understood as a contribution to embryology. “The Cell-theory” presents Huxley’s “epigenetic” interpretation of histological organization emerging from changes in the protoplasm to replace the “preformationist” cell theory of Schleiden and Schwann (as modified by Albert vonKölliker), which posited the nucleus as the seat of organic vitality. Huxley’s views influenced a number of British biologists, who continued to oppose German cell theory well into the twentieth century. Yet Huxley was pivotal in introducing the new German program of “scientific zoology” to Britain in the early 1850s,championing its empiricist methodology as a means to enact broad disciplinary and institutional reforms in British natural history.     

基于质谱技术筛选差异表达蛋白的统计学策略研究进展

随着质谱技术的快速发展,蛋白质组学已成为继基因组学、转录组学之后的又一研究热点,寻找可靠的差异表达蛋白对于生物标记物的发现至关重要.因此,如何准确、灵敏地筛选出差异蛋白已成为基于质谱的定量蛋白质组学的主要研究内容之一.目前,针对该问题的研究方法众多,但这些方法策略的适用范围不尽相同.总体来说,基于质谱技术筛选差异蛋白的统计学策略可以分为3类:基于经典统计学派的策略、基于贝叶斯学派的统计检验策略和其他策略,这3类方法有各自的应用范围、特点及不足.此外,筛选过程还将产生部分假阳性结果,可以采用其他方法对差异表达蛋白的质量进行控制,以提高统计检验结果的可靠性.     

Kolmogorov complexity of epithelial pattern formation: The role of regulatory network configuration

The tissues of multicellular organisms are made of differentiated cells arranged in organized patterns. This organization emerges during development from the coupling of dynamic intra- and intercellular regulatory networks. This work applies the methods of information theory to understand how regulatory network structure both within and between cells relates to the complexity of spatial patterns that emerge as a consequence of network operation. A computational study was performed in which undifferentiated cells were arranged in a two dimensional lattice, with gene expression in each cell regulated by identical intracellular randomly generated Boolean networks. Cell–cell contact signalling between embryonic cells is modeled as coupling among intracellular networks so that gene expression in one cell can influence the expression of genes in adjacent cells. In this system, the initially identical cells differentiate and form patterns of different cell types. The complexity of network structure, temporal dynamics and spatial organization is quantified through the Kolmogorov-based measures of normalized compression distance and set complexity. Results over sets of random networks that operate in the ordered, critical and chaotic domains demonstrate that: (1) ordered and critical networks tend to create the most information-rich patterns; (2) signalling configurations in which cell-to-cell communication is non-directional mostly produce simple patterns irrespective of the internal network domain; and (3) directional signalling configurations, similar to those that function in planar cell polarity, produce the most complex patterns, but only when the intracellular networks function in non-chaotic domains.     

Choosing between two conflicting scientific hypotheses: The orce dilemmas

How may we choose between conflicting hypotheses when doing a scientific test? Bayesian theory of decision offers a tool to analyse what choosing actually is, preventing us either from giving too much value to rational compounds or from putting aside the scientists’ personal interests and prejudices. Gieres’ cognitive approach to the problem defines the Minimally Open-Minded Scientist’s approach as the right one to dial with the choice dilemma. This approach is used here to give an opinion on the status of the “Orce Man”.     

Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures

A systematic in silico approach has been employed to generate sound, experimentally validated active-site models for galactose oxidase (GO) using a hybrid density functional, B(38HF)P86. GO displays three distinct oxidation states: oxidized [Cu(II)-Y*]; semireduced [Cu(II)-Y]; and reduced [Cu(I)-Y]. Only the [Cu(II)-Y*] and the [Cu(I)-Y] states are assumed to be involved in the catalytic cycle, but their structures have not yet been determined. We have developed several models (1-7) for the [Cu(II)-Y*] state that were evaluated by comparison of our computational results with experimental data. An extended model system (6) that includes solvent molecules and second coordination sphere residues (R330, Y405, and W290) is essential to obtain an experimentally correct electronic structure of the active site. The optimized structure of 6 resulted in a five-coordinate Cu site with a protein radical centered on the Tyr-Cys cofactor. We further validated our converged model with the largest model (7) that included additional outer-sphere residues (Q406, H334, Y329, G513, and T580) and water molecules. Adding these residues did not affect significantly the active site's electronic and geometric structures. Using both 6 and 7, we explored the redox dependence of the active-site structure. We obtained four- and three-coordinate Cu sites for [Cu(II)-Y] and [Cu(I)-Y] states, respectively, that corroborate well with the experimental data. The relative energies of these states were validated by a comparison with experimental redox potentials. Collectively, our computational GO models well reproduce the physicochemical characteristics of the individual states, including their redox behaviors.     

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.     

基于潜意识理论的青少年网络成瘾研究

本文综述了青少年网络成瘾的预防和戒除方法,坚持了"习惯说",保留了对"疾病说"的看法。基于潜意识理论,将网络成瘾视为心理亚健康状态,分析了青少年网络成瘾的发生机理、提出了其预防和戒除原则。青少年网络成瘾的成因是心理上的缺失感,与青少年自我防护意识差、自我控制能力小、心理弹性弱,以及潜意识具有反复影响才可改变的特点有关。戒除网络成瘾的原则是淡化评判试测的标准、分散注意力、培养成就感、增强自信心、坚持以心治心等。