Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup

Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during huma

The testis-specific apoptosis related gene TTL.6 underwent adaptive evolution in the lineage leading to humans

The TTL.6 gene is a member of the tubulin-tyrosine ligase (TTL) family involved in apoptosis and preferentially expressed in the testis. We sequenced the coding region and part of the introns of TTL.6 in world wide human populations and five representativ

Evolutionary trends of the mitochondrial lineage differentiation in species of genera Martes and Mustela

We compared partial sequences (402 bp) of the mitochondrial cytochrome b gene in 68 individuals of martens (Martes), weasels (Mustela) and their relatives from the Northern Hemisphere to identify the modes of geographic differentiation in each species. We then compared complete sequences (1140 bp) of the gene in 17 species of the family Mustelidae to know the spatial and temporal modes of speciation, constructing linearized trees with transversional substitutions for deeper lineage divergences and with transversions and transitions for younger lineages. Our data suggested that these lineages of Martes and Mustela differentiated in a stepwise fashion with five radiation stages from the generic divergences (stage I) to the intraspecific divergences (stage V), during the last 10 or 20 million years as the fossil evidence suggests. In the lineage of Martes, the first offshoots are of Martes flavigula, M. pennanti, and Gulo gulo (stage II), the second is M. foina (stage III), and the third are M. americana, M. martes, M. melampus, and M. zibellina (stage IV). The divergence of the lineages of Mustela is likely to have taken place concurrently with the radiations of the Martes. These divergence processes are attributable in part to the geographic allocation along the two continents, North America and Eurasia, as well as among peripheral insular domains, such as Taiwan and the Japanese Islands. In addition, the Eurasian continent itself was shown to have been involved in the species diversification in the martens and weasels.

A NEW SPECIES FROM SOUTHWESTERN CHINA IN THE AFRO-PALEARCTIC LINEAGE OF THE HORSESHOE BATS (RHINOLOPHUS)

A new species of horseshoe bat (Chiroptera: Rhinolophidae) is described from southwestern China. The presence of a wedge-shaped sella and pointed connecting process of the nose leaf aligns the new species to the landeri group in the Afro-Palearctic lineag

Formal specification and refinement of a safe train control function

Motivated by the design and development challenges of the BART case study, an approach for developing and analyzing a formal model for reactive systems is presented. The approach makes use of a domain specific language for specifying control algorithms able to satisfy competing properties such as safety and optimality. The domain language, called SPC, offers several key abstractions such as the state, the profile, and the constraint to facilitate problem specification. Using a high-level program transformation system such as HATS being developed at the University of Nebraska at Omaha, specifications in this modelling language can be transformed to ML code. The resulting executable specification can be further refined by applying generic transformations to the abstractions provided by the domain language. Problem dependent transformations utilizing the domain specific knowledge and properties may also be applied. The result is a significantly more efficient implementation which can be used for simulation and gaining deeper insight into design decisions and various control policies. The correctness of transformations can be established using a rewrite-rule based induction theorem prover Rewrite Rule Laboratory developed at the University of New Mexico.

facilitating formal specification acquisition by using recursive functions on context-free languages

Although formal specification techniques are very useful in software development, the acquisition of formal specifications is a difficult task. This paper presents the formal specification language LFC, which is designed to facilitate the acquisition and validation of formal specifications. LFC uses context-free languages for syntactic aspect and relies on a new kind of recursive functions, i.e. recursive functions on context-free languages, for semantic aspect of specifications. Construction and validation of LFC specifications are machine-aided. The basic ideas behind LFC, the main aspects of LFC, and the use of LFC and illustrative examples are described.

Formalization and specification for controlling process modularity in mobile computing

新的计算模式，普适计算和全局计算，正在作为高度分布式和移动计算的计算模式展现出来。这篇论文探讨了在抽象层面上支持这些新型计算模式的适合的形式化基础，关注在进程移动单位上的控制, 以便在分布式与移动计算环境下更好地协调进程的移动性。 论文的第一部分概述了针对分布式、移动计算的现有进程演算模型中的进程移动单元，并且设计了一种在此方面更优、更具弹性的进程框架。为了表示这种进程框架，我们提出了一种新的、针对移动和分布式系统的进程演算,这种进程演算的优点是动态、弹性的控制进程的移动单元；具体的思路就是扩展π- calculus以及其支持分布式和移动性的变体。我们把这种新的演算叫做Modular π-calculus。我们通过这种演算的提出来说明进程框架提供了一种针对移动进程更为合适的协调机制以及编程模型，例如移动的代理和动态组件载入的支持。之后，我们通过讨论互模拟的几种提法来具体说明能够反映演算设计的进程描述的关键，之后我们讨论了它们的具体性质。 本文的第二部分提出了一个对进程模型的行为和性质进行推理的规约框架。首先，提出了一个对Modularπ-calculus中进程的系统性质进行规约的模态逻辑。为了更好的理解该逻辑，文中对由这个逻辑推出的进程等价的特征进行了研究，并且证明了该逻辑的区分能力介于互模拟和结构一致之间。接下来关于这个规约框架的自动化，本文针对该逻辑和Modular π-calculus的有限控制子集，提出了模型检测算法，并且给出了算法正确性的证明。同时文中贯穿了一些实际且直观的例子，以展现本文提出的一组框架即演算、逻辑和模型算法的有效性。

Haematopoietic lineage cell-specific protein 1 (HS1) promotes actin-related protein (Arp) 2/3 complex-mediated actin polymerization

HS1 (haematopoietic lineage cell-specific gene protein 1), a prominent substrate of intracellular protein tyrosine kinases in haematopoietic cells, is implicated in the immune response to extracellular stimuli and in cell differentiation induced by cytokines. Although HS1 contains a 37-amino acid tandem repeat motif and a C-terminal Src homology 3 domain and is closely related to the cortical-actin-associated protein cortactin, it lacks the fourth repeat that has been shown to be essential for cortactin binding to filamentous actin (F-actin). In this study, we examined the possible role of HS1 in the regulation of the actin cytoskeleton. Immunofluorescent staining demonstrated that HS1 co-localizes in the cytoplasm of cells with actin-related protein (Arp) 2/3 complex, the primary component of the cellular machinery responsible for de novo actin assembly. Furthermore, recombinant HS1 binds directly to Arp2/3 complex with an equilibrium dissociation constant (K-d) of 880 nM. Although HS1 is a modest F-actin-binding protein with a Kd of 400 nM, it increases the rate of the actin assembly mediated by Arp2/3 complex, and promotes the formation of branched actin filaments induced by Arp2/3 complex and a constitutively activated peptide of N-WASP (neural Wiskott-Aldrich syndrome protein). Our data suggest that HS1, like cortactin, plays an important role in the modulation of actin assembly.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.