Optimality in evolution: new insights from synthetic biology

1. Download : Download high-res image (164KB)
2. Download : Download full-size image

     

Plant systems biology: insights,advances and challenges

Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this  review, we discuss the basics of systems biology including the various ‘omics’ approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.     

Comparative physiology and molecular evolution of carbonic anhydrase in the erythrocytes of early vertebrates

The different isozymes of carbonic anhydrase (CA) have been the subject of intensive study in mammals, but there is still much to be learned about the early evolution of this enzyme in vertebrates. Erythrocyte CA plays an essential role in the respiratory processes of most vertebrates and is probably the most well studied CA isozyme. The available evidence indicates that there has been a progressive increase in the efficiency of erythrocyte CA during the early evolution of vertebrates. There also appears to be a substantial increase in erythrocyte CA activity during development in some species. At the present time, however, the selective pressures that may be influencing the properties of erythrocyte CA during vertebrate evolution and development have not been clearly determined. When the available molecular sequence information is examined, it is evident that the erythrocyte CAs of early vertebrates have active sites that are more similar to those of mammalian CA VII and II, rather than CA I. We can now also begin to examine the phylogenetic relationships between the different rbc CAs in vertebrates, but more CA sequence information is clearly required from different groups of vertebrates before we have a complete picture of the molecular evolution of erythrocyte CA.     

Origin of the Retiolitidae: insights from a new graptolite genus from the early Silurian of Arctic Canada

Isolated specimens of Hercograptus introversus n. gen., n. sp. show features characteristic of the Retiolitidae, such as partial periderm reduction, and extended ancora lists and a reticulum that are attached to the thecal margins, on a rhabdosome that, in most other respects, resembles Pseudorthograptus. This newly discovered graptolite provides support for the hypothesis that Pseudoretiolites is the first-evolved retiolitid, since they share a similar ancora type and unique thecal style. It is also clear that the suite of features that normally distinguish the Retiolitidae did not all evolve simultaneously. It is proposed that development of a complete thecal framework of lists, permitting complete periderm reduction, should be the character used to distinguish the Retiolidae from the Petalolithidae. Unusual apertural modifications, such as strong introversion, lateral lappets, and a short, free dorsal wall suggest that Hercograptus may be an offshoot of the lineage leading from Pseudorthograptus to Pseudoretiolites.     

Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish

Tripartite motif proteins (TRIM) constitute a large family of proteins containing a RING-Bbox-Coiled Coil motif followed by different C-terminal domains. Involved in ubiquitination, TRIM proteins participate in many cellular processes including antiviral immunity. The TRIM family is ancient and has been greatly diversified in vertebrates and especially in fish. We analyzed the complete sets of trim genes of the large zebrafish genome and of the compact pufferfish genome. Both contain three large multigene subsets--adding the hsl5/trim35-like genes (hltr) to the ftr and the btr that we previously described--all containing a B30.2 domain that evolved under positive selection. These subsets are conserved among teleosts. By contrast, most human trim genes of the other classes have only one or two orthologues in fish. Loss or gain of C-terminal exons generated proteins with different domain organizations; either by the deletion of the ancestral domain or, remarkably, by the acquisition of a new C-terminal domain. Our survey of fish trim genes in fish identifies subsets with different evolutionary dynamics. trims encoding RBCC-B30.2 proteins show the same evolutionary trends in fish and tetrapods: they evolve fast, often under positive selection, and they duplicate to create multigenic families. We could identify new combinations of domains, which epitomize how new trim classes appear by domain insertion or exon shuffling. Notably, we found that a cyclophilin-A domain replaces the B30.2 domain of a zebrafish fintrim gene, as reported in the macaque and owl monkey antiretroviral TRIM5α. Finally, trim genes encoding RBCC-B30.2 proteins are preferentially located in the vicinity of MHC or MHC gene paralogues, which suggests that such trim genes may have been part of the ancestral MHC.     

Hantaviruses: molecular biology, evolution and pathogenesis

Hantaviruses are tri-segmented negative sense single stranded RNA viruses that belong to the family Bunyaviridae. In nature, hantaviruses are exclusively maintained in the populations of their specific rodent hosts. In their natural host species, hantaviruses usually develop a persistent infection with prolonged virus shedding in excreta. Humans become infected by inhaling virus contaminated aerosol. Unlike asymptomatic infection in rodents, hantaviruses cause two acute febrile diseases in humans: hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). The mortality rate varies from 0.1% to 40% depending on the virus involved. Hantaviruses are distributed world wide, with over 150,000 HFRS and HPS cases being registered annually. In this review we summarize current knowledge on hantavirus molecular biology, epidemiology, genetic diversity and co-evolution with rodent hosts. In addition, special attention was given in this review to describing clinical manifestation of HFRS and HPS, and advances in our current understanding of the host immune response, treatment, and prevention.     

蕨类植物的起源演化:对"古老"类群的重新审视

一般认为,蕨类植物是一群非常古老的植物,其演化历史可以追溯到4亿多年前。近十几年来,由于多种研究手段的应用,特别是分子系统学的异军突起,在蕨类植物起源演化方面取得了重要进展,使我们可以重新审视这一古老植物类群的演化历史。本文与传统观点相对比,简述了蕨类植物在分类范畴、起源演化及其重要类群间的系统演化关系方面的最新进展。     

Electroreception in early vertebrates: survey,evidence and new information

Electroreception is widespread in living vertebrates, and is often considered to be a primitive vertebrate character. However, the early evolution of electroreception remains unclear. A variety of structures in early vertebrate fossils have been put forward as potential electroreceptors, but these need to be reassessed in light of the now substantial literature on electroreceptors in living vertebrates. Here we review the evidence for all putative electroreceptors in early vertebrates, and provide new information from CT scans. In the jawless osteostracans, the pore canal system in the dermal skeleton and the lateral and dorsal fields do not resemble electroreceptors in living species. Nevertheless, the presence of a recurrent ramus of the anterior lateral line nerve in osteostracans suggests that electroreceptors were present, by comparison with lampreys. In placoderms, cutaneous sense organs on arthrodire cheek plates are possible electroreceptors. CT data shows that the orientation of these pits is anomalous for electroreceptors, and intimately associated with bone growth. A newly identified type of cheek pit, for which the term ‘Young's apparatus’ is introduced, is known from only two arthrodire specimens. It is closely associated with the underlying jaw joint, but its precise function is unknown. In osteichthyans, the ‘pore group’ clusters of early sarcopterygians may have housed electroreceptors. CT data from Devonian lungfish support this interpretation, showing internal morphology consistent with electroreceptors, and innervation via the rostral tubuli underlying the dermal bone of the snout. The early osteichthyan Ligulalepis has pit structures which may be electroreceptors, and were possibly innervated by lateral line nerves. Specialized electroreceptor systems, including elaborated ‘pore group’ pits in Devonian lungfish and rostral organs in the earliest coelacanths, show that electroreception may have had an important role in niche specialization in early vertebrates. Finally, fossil data does not support the hypothesis that vertebrate hard tissues initially evolved to shield electroreceptors.     

Gene duplication and divergence in the early evolution of vertebrates

The duplication-degeneration-complementation model of duplicate gene preservation by subfunctionalisation is currently the best explanation for the high level of retention of duplicate genes in early vertebrate evolution. But a direct test of the applicability of this model to such ancient evolutionary events may be difficult. More likely, recent duplications in other lineages will allow us to establish general principles concerning the fate of genes of different types that are duplicated in different ways. These principles may be then extrapolated to understanding the early evolution of the vertebrates.     

Tissue/planar cell polarity in vertebrates: new insights and new questions

This review focuses on the tissue/planar cell polarity (PCP) pathway and its role in generating spatial patterns in vertebrates. Current evidence suggests that PCP integrates both global and local signals to orient diverse structures with respect to the body axes. Interestingly, the system acts on both subcellular structures, such as hair bundles in auditory and vestibular sensory neurons, and multicellular structures, such as hair follicles. Recent work has shown that intriguing connections exist between the PCP-based orienting system and left-right asymmetry, as well as between the oriented cell movements required for neural tube closure and tubulogenesis. Studies in mice, frogs and zebrafish have revealed that similarities, as well as differences, exist between PCP in Drosophila and vertebrates.     

Technological advances in the molecular biology of Leptospira

Pathogenic members of the genus Leptospira have been refractory to genetic study due to lack of known mechanisms of genetic exchange. To bypass this limitation, several techniques have been useful for Leptospira gene discovery, including heterologous complementation of Escherichia coli mutants, screening of DNA libraries with probes, and random sequence analysis. Construction of combined physical and genetic maps revealed the presence of two circular chromosomal replicons. The organization of the L. interrogans genome is quite variable, with genetically similar strains differentiated by many rearrangements. These rearrangements likely occur through recombination between repetitive DNA elements found scattered throughout the genome. Analysis of intervening sequences and genes encoding LPS biosynthetic enzymes provide evidence of lateral transfer of DNA between Leptospira spp. We have also gained insight into the biology of these bacteria by analyzing genes encoding LPS and outer membrane proteins (OMPs). Some of these OMPs are differentially expressed. Characterization of mechanisms governing the expression of the OMP genes should provide insight into host-parasite interactions. Furthermore, recent advances in heterologous expression of leptospiral OMP genes are opening new avenues of vaccine development.     

Plant cell biology in the new millennium: new tools and new insights

The highly regulated structural components of the plant cell form the basis of its function. It is becoming increasingly recognized that cellular components are ordered into regulatory units ranging from the multienzyme complexes that allow metabolic channeling during primary metabolism to the "transducon" complexes of signal transduction elements that allow for the highly efficient transfer of information within the cell. Against this structural background the highly dynamic processes regulating cell function are played out. Recent technological advances in three areas have driven our understanding of the complexities of the structural and functional dynamics of the plant cell. First, microscope and digital camera technology has seen not only improvements in the resolution of the optics and sensitivity of detectors, but also the development of novel microscopy applications such as confocal and multiphoton microscopy. These technologies are allowing cell biologists to image the dynamics of living cells with unparalleled three-dimensional resolution. The second advance has been in the availability of increasingly powerful and affordable computers. The computer control/analysis required for many of the new microscopy techniques was simply unavailable until recently. Third, there have been dramatic advances in the available probes to use with these new microscopy approaches. Thus the plant cell biologist now has available a vast array of fluorescent probes that will report cell parameters as diverse as the pH of the cytosol, the oxygen level in a tissue, or the dynamics of the cytoskeleton. The combination of these new approaches has led to an increasingly detailed picture of how plant cells regulate their activities.     

文昌鱼—研究脊柱动物起源和进化的模式动物

长久以来,文昌鱼一直被认为和生活在约5亿年前的脊椎动物的直接祖先相似。由于文昌鱼在进化上的重要性,它在动物学研究史上发挥着关键作用,近100多年来,文昌鱼作为研究对象曾数次受到动物学界青睐或冷落,大约10年前,随着分子生物学技术应用于文昌鱼研究,又激发了动物学家对文昌鱼的研究兴趣,又一次出现在文昌鱼研究的高潮,并且一直持续至今,分子生物学研究结果表明,文昌鱼样生物可能是环节动物样动物和最早的脊椎动物之间的进化中间体,因此,文昌鱼在动物学研究史上好像绕了个大圈又回到了原处,在被忽视一段时间之后,又重新占据脊椎动物起源和进化研究中心舞台的位置,成为研究脊椎动物起源和进化的模式动物。     

Application in clinical epidemiology of new advances in immunology and molecular biology of malaria

The first purpose was to study the sensitivity of a spot hybridization assay for P. falciparum with a DNA probe. This assay was compared with light microscopy for the detection of low-grade parasitemia. The second purpose was to study in clinically immune individuals the seroreactivity, against a newly identified P. falciparum antigen, deposited in the erythrocyte membrane during merozoite invasion (Perlmann et al., 1984). This antigen is considered to be a potential component in a future vaccine against the blood stage of the parasite. In a holoendemic village in Yekepa area, Northern Liberia, 28 adult men with a high degree of protective immunity against malaria, were shown to have repeatedly low-grade parasitemias of varying density. The spot hybridization assay with the DNA probe was highly sensitive in detecting parasitic infection. The sensitivity was comparable to that of the examination of a blood film for about 15 min by an experienced microscopist. The seroreactivity against Pf 155 antigen varied between a high positive titer to negativity in different subjects, but the reactivity was constant over a period of 15 months for each subject despite numerous new infections and comparable protective immunity against malaria infection.     

新基因起源：从自然进化到人工设计

生命体系历经40多亿年的自然进化,创造了无数丰富多彩的功能基因,保障了生命体系的传承与繁荣。然而生命体系的自然进化历程极其缓慢,新的功能基因产生需要数百万年时间,无法满足快速发展的工业生产需求。利用合成生物学技术,研究人员可以依据已知的酶催化机理和蛋白质结构进行全新的基因设计与合成,按照工业生产需求快速创造全新的蛋白质催化剂,实现各种自然界生物无法催化的生物化学反应。尽管新基因设计技术展现了激动人心的应用前景,但是目前该技术还存在设计成功率不高、酶催化活性较低、合成成本较高等科技挑战。未来随着合成生物学技术的快速发展,设计、改造、合成和筛选等技术将融合为一体,为新基因设计与创建带来全新的发展机遇。