基于软件网络的软件系统演化规律验证和模拟

演化是计算机软件的固有特性.了解演化规律,可以改进软件演化过程,提高软件质量,降低维护成本.本文定义类依赖图,将软件系统描述为软件网络,基于网络度量验证软件演化规律,并讨论软件演化建模的可行性.首先针对Lehman的8项演化定律,设计3个方面的网络度量:网络规模、网络质量、以及结构控制.然后基于四个开源软件系统构建软件网络,统计网络度量;实证研究表明:支持Lehman的4项演化定律,否定另外3项,即复杂度提升、持续增长、以及质量折旧定律.最后分别采用E-R模型和模块依附模型模拟软件系统的演化过程,所生成的随机网络同软件网络的比较结果说明,软件演化存在客观规律,能够通过建模来重现甚至优化.     

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Reggies (flotillins) are detergent-resistant microdomains involved in the scaffolding of large heteromeric complexes that signal across the plasma membrane. Based on the presence of an evolutionarily widespread motif, reggies/flotillins have been included within the SPFH (stomatin-prohibitin-flotillin-HflC/K) protein superfamily. To better understand the origin and evolution of reggie/flotillin structure and function, we searched databases for reggie/flotillin and SPFH-like proteins in organisms at the base and beyond the animal kingdom, and used the resulting dataset to compare their structural and functional domains. Our analysis shows that the SPFH grouping has little phylogenetic support, probably due to convergent evolution of its members. We also find that reggie/flotillin homologues are highly conserved among metazoans but are absent in plants, fungi and bacteria, where only proteins with ‘reggie-like’ domains can be found. However, despite their low sequence similarities, reggie/flotillin and ‘reggie-like’ domains appear to subserve related functions, suggesting that their basic biological role was acquired independently during evolution. Received 21 September 2005; received after revision 14 November 2005; accepted 21 November 2005     

Structure, function and evolution of antifreeze proteins

Antifreeze proteins bind to ice crystals and modify their growth. These proteins show great diversity in structure, and they have been found in a variety of organisms. The ice-binding mechanisms of antifreeze proteins are not completely understood. Recent findings on the evolution of antifreeze proteins and on their structures and mechanisms of action have provided new understanding of these proteins in different contexts. The purpose of this review is to present the developments in contrasting research areas and unite them in order to gain further insight into the structure and function of the antifreeze proteins. Received 2 September 1998; received after revision 21 October 1998; accepted 2 November 1998     

SET domain proteins modulate chromatin domains in eu- and heterochromatin

The SET domain is a 130-amino acid, evolutionarily conserved sequence motif present in chromosomal proteins that function in modulating gene activities from yeast to mammals. Initially identified as members of the Polycomb- and trithorax-group (Pc-G and trx-G) gene families, which are required to maintain expression boundaries of homeotic selector (HOM-C) genes, SET domain proteins are also involved in position-effect-variegation (PEV), telomeric and centromeric gene silencing, and possibly in determining chromosome architecture. These observations implicate SET domain proteins as multifunctional chromatin regulators with activities in both eu- and heterochromatin – a role consistent with their modular structure, which combines the SET domain with additional sequence motifs of either a cysteine-rich region/zinc-finger type or the chromo domain. Multiple functions for chromatin regulators are not restricted to the SET protein family, since many trx-G (but only very few Pc-G) genes are also modifiers of PEV. Together, these data establish a model in which the modulation of chromatin domains is mechanistically linked with the regulation of key developmental loci (e.g. HOM-C).     

The HERC proteins: functional and evolutionary insights

HERC proteins are defined as containing both HECT and RCC1-like domains in their amino acid sequences. Six HERC genes have turned up in the human genome which encode two different sorts of polypeptides: while the small HERC proteins possess little more than the two aforementioned domains, the large ones are giant proteins with a plethora of potentially important regions. It is now almost 10 years since the discovery of the first family member and information is starting to accumulate pointing to a general role for these proteins as ubiquitin ligases involved in membrane-trafficking events. In this review, the available data on these six members are discussed, together with an account of their evolution.Received 16 March 2005; received after revision 13 April 2005; accepted 28 April 2005     

Function and molecular evolution of multicopper blue proteins

Multicopper blue proteins (MCBPs) are multidomain proteins that utilize the distinctive redox ability of copper ions. There are a variety of MCBPs that have been roughly classified into three different groups, based on their domain organization and functions: (i) nitrite reductase-type with two domains, (ii) laccase-type with three domains, and (iii) ceruloplasmin-type with six domains. Together, the second and third group are often commonly called multicopper oxidases (MCOs). The rapid accumulation of genome sequence information in recent years has revealed several new types of proteins containing MCBP domains, mainly from bacteria. In this review, the recent research on the functions and structures of MCBPs is summarized, mainly focusing on the new types. The latter half of this review focusses on the twodomain MCBPs, which we propose as the evolutionary intermediate of the MCBP family.Received 25 February 2005; received after revision 23 May 2005; accepted 31 May 2005     

Butterflies and ants: The communicative domain

Associations with ants, termed myrmecophily, are widespread in the butterfly family Lycaenidae and range from mere co-existence to more or less specific mutualistic or even parasitic interactions. Secretions of specialized epidermal glands are crucial for mediating the interactions. Transfer of nutrients (carbohydrates, amino acids) from butterfly larvae to ants plays a major role, but manipulative communication with the help of odour signals is also involved. By means of myrmecophily, lycaenid butterflies largely escape ant predation, and certain species gain protection through attendant ants or achieve developmental benefits from ant-attendance. Benefits to the ants range from minimal to substantial food rewards. While most lycaenid species maintain facultative relationships with a variety of ant genera, highly specific and obligatory associations have convergently evolved in a number of butterfly lineages. As a corollary, communication systems are largely unspecific in the former, but may be highly specialized in the latter. The sophisticated communication between obligate myrmecophiles and their host ants is tightly connected with the evolutionary rise of specialized life-cycles and thus is a source of augmenting diversity within the butterflies.     

The evolution, complex structures and function of septin proteins

The septin family is a conserved GTP-binding protein family and was originally discovered through genetic screening for budding yeast mutants. Septins are implicated in many cellular processes in fungi and metazoa. The function of septins usually depends on septin assembling into oligomeric complexes and highly ordered polymers. The expansion of the septin gene number in vertebrates increased the complex diversity of septins. In this review, we first discuss the evolution, structures and assembly of septin proteins in yeast and metazoa. Then, we review the function of septin proteins in cytokinesis, membrane remodeling and compartmentalization.     

The cephalopod heart: The evolution of a high-performance invertebrate pump

Cephalopods typically have high metabolic rates. They have blood in which the oxygen carrier is haemocyanin, a pigment that is found only in solution and which never seems to be present in concentrations that will transport more than 4–5 vols % of oxygen. Their hearts must in consequence have very high cardiac outputs. In this account the performance of the heart ofNautilus, the only surviving ectocochleate, is contrasted with the performance of the hearts of coleoids,Octopus which has a relatively low metabolic rate (for a coleoid) and squids which have very high oxygen uptakes by any standards. In all these animals, heartbeat frequency is temperature-dependent and the additional oxygen demand in exercise is met very largely by a 2–3-fold increase in stroke volume. With the exception ofNautilus, cephalopods tend to utilise nearly all of the oxygen transported in the blood even at rest; they show very limited factorial scopes. Specific power output has, however, increased dramatically from 2.7 mWg^–1 in an activeNautilus to 5.5 mWg^–1 inOctopus and up to 20 or 30 mWg^–1 in species ofLoligo. The increase is almost entirely due to a 10-fold increase in heartbeat frequency. It is argued that frequency cannot be used as a means of responding to extra demand in an animal that must also carry automatic compensation for changes in metabolic rate dependent upon the ambient temperature, and that the use of frequency in some squid may be associated with a reduced temperature tolerance. Cephalopod systemic hearts do not scale directly with body mass, like the hearts of fish and the higher vertebrates. Smaller cephalopods have relatively larger hearts (as Mass^0.9). A typical 100-g coleoid would have a heart mass of 0.15 g. Oegopsid squids appear to be exceptional with hearts twice as large.     

基于网络的可信软件大规模协同开发与演化

随着网络时代的来临,软件的开发模式、运行环境和提供方式发生了巨大变化.互联网作为一种开放的协同工作环境,其中孕育的大规模协同创作机理对软件开发和应用产生了深刻影响.如何将其与工业化可信软件生产相结合以提高软件生产效率和质量,是网络时代软件技术面临的新课题.本文提出汇聚群体智慧的可信软件开发新方法——群体化方法,该方法的核心是"群体协同、资源分享、运行监控、可信分析",支持创新软件作品向可信软件产品转化,支持软件的可信演化.提出一种基于证据的可信软件概念模型,将软件在开发阶段、分享阶段和应用阶段的基础数据作为软件的可信证据,并据此建立了软件演化过程模型;提出一种支持可信软件协同开发与演化的服务模型,支持软件创作与生产深度协同的可信软件社会化生产、开放有序的可信软件资源分享,以及基于海量数据分析的软件可信评估.最后以"十一五"国家高技术研究发展计划重点项目"高可信软件生产工具及集成环境"为背景,阐述了面向群体化方法的关键技术、开发环境和应用实践.     

Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation

The ubiquitin–proteasome pathway of protein degradation is one of the major mechanisms that are involved in the maintenance of the proper levels of cellular proteins. The regulation of proteasomal degradation thus ensures proper cell functions. The family of proteins containing ubiquitin-like (UbL) and ubiquitin-associated (UBA) domains has been implicated in proteasomal degradation. UbL–UBA domain containing proteins associate with substrates destined for degradation as well as with subunits of the proteasome, thus regulating the proper turnover of proteins.     

Role of proline in the imprinting developed by dipeptides — in Tetrahymena Possible role in hormone evolution

The effects of proline and serine dipeptides containing phenylalanine, alanine and leucine on the behaviour of receptors of Tetrahymena were investigated. Only proline-containing dipeptides were able to develop positive imprinting, and the activity depended on which other amino acid was present in the dipeptide. In contrast to the positive imprinting effect of the dipeptides Pro-Phe and Pro-Ala, the dipeptide Pro-Pro and Pro-Leu caused negative imprinting. Serine dipeptides produced negative imprinting in all cases. The possible importance of proline in the evolution of hormone specificity is discussed.     

The BAG proteins: a ubiquitous family of chaperone regulators

The BAG (Bcl-2 associated athanogene) family is a multifunctional group of proteins that perform diverse functions ranging from apoptosis to tumorigenesis. An evolutionarily conserved group, these proteins are distinguished by a common conserved region known as the BAG domain. BAG genes have been found in yeasts, plants, and animals, and are believed to function as adapter proteins forming complexes with signaling molecules and molecular chaperones. In humans, a role for BAG proteins has been suggested in carcinogenesis, HIV infection, and Parkinson’s disease. These proteins are therefore potential therapeutic targets, and their expression in cells may serve as a predictive tool for such diseases. In plants, the Arabidopsis thaliana genome contains seven homologs of the BAG family, including four with domain organization similar to animal BAGs. Three members contain a calmodulin-binding domain possibly reflecting differences between plant and animal programmed cell death. This review summarizes current understanding of BAG proteins in both animals and plants. Received 21 November 2007; received after revision 17 December 2007; accepted 2 January 2008     

Metabolic iteration,evolution and cognition in cellular proliferation

Summary A model for cellular proliferation is described according to which proliferation ensues when metabolism evolves towards commitment to DNA synthesis, and inhibition of proliferation occurs when enzymic interactions are iterated within a few metabolic pathways, another limiting factor being the supply of metabolites. The model successfully describes cellular growth and division as a cognitive process based on interaction within enzymic elements and the genome, and affords an explanation in these terms of some empirical phenomena which have previously been understood only as isolated observations.     

Oxygen consumption and the evolution of order: negentropy criteria applied to the evolution of ants

Optimization of energy use by evolving organisms, predicted by theoretical extensions of the neo-Darwinian theory, i. contrasted with that of irreversible thermodynamics, which predicts an increase in orderliness and thus an increase in energy consumption per unit of biomass. We compared this index with estimates of social complexity among ant genera and species. Our results show that simple optimization models cannot explain experimental data, and that social complexity correlates differently with negentropy at different levels of analysis. Comparing the genera among Formicidae, workers (not colonies) from genera with highly social species are less negentropic than those of socially primitive ones. At the sub-generic level, social complexity correlated positively with negentropy among species, for major workers inAcromyrmex and for minor workers inAtta. The results illustrate the complexity of thermodynamic criteria in the study of evolution but also hint at their usefulness. In this case, they show that two different evolutionary routes to the complex Attini ant societies may exist.     

The accessory gland proteins in maleDrosophila: structural,reproductive, and evolutionary aspects

Recent results from biochemical and molecular genetic studies of the accessory gland proteins in maleDrosophila are reviewed. The most prominent feature is the species-specific variability. However, the analysis of the sex peptide inD. melanogaster shows that there is a strong homology in the molecular structure to the closely related sibling species, and that divergence increases with increasing phylogenetic distance. For this reason the sex peptide, after being transferred to the female genital tract during copulation, reduces receptivity and increases oviposition only in virgin females belonging to the same species group and subgroup. Even though studies were hitherto limited to a small number of the secretory components, it is evident that the accessory gland proteins play a key role in reproductive success of the fruit fly by changing female sexual behavior, supporting sperm transfer, storage and displacement. Thus, genes encoding the accessory gland proteins are apparently under strong evolutionary selection.     

A cryptic intermediate in the evolution of chameleon tongue projection

Summary An incipient form of tongue projection occurs inPhrynocephalus helioscopus, a generalized agamid lizard. We argue that this condition represents a functional intermediate between typical lingual prehension and chamaeleontid tongue projection, and that tongue projection evolved in chameleons by augmentation of ancestral mechanisms still operating in related, generalized lizards.     

Conserved eukaryotic transposable elements and the evolution of gene regulation

Multiple remnants of transposable elements preserved in cis-regulatory modules may represent a record of mutations that were critical to the evolution of gene regulation and speciation. Received 13 August 2007; received after revision 8 October 2007; accepted 23 October 2007