脊椎动物的起源与演化研究进展

脊椎动物的起源与演化历来是进化生命科学的核心命题。近年脊椎动物的起源与演化有重大突破。云南澄江寒武纪化石群中的后口类“皇冠西大动物” ,半索动物“云南虫”和“海口虫” ,尾索动物“始祖长江海鞘” ,头索动物“海口华夏鱼”和“中间型中新鱼” ,脊椎动物“凤姣昆明鱼”和“海口鱼” ,论证了普通无脊椎动物向脊椎动物演化过渡的各种中间类型 ,勾勒出一幅较为完整的早期生命演化谱系。西北大学早期生命研究所舒德干教授基于对靠近脊椎动物“源头”时段软躯体后口动物化石系列的研究以及新的发现提出脊椎动物起源分“五步走”的新假说 ,即在脊椎动物的起源的“四步走”前还有更为原始的“一步” :云南澄江出土的古虫动物门化石很可能代表了原口动物和后口动物间的过渡类型。本文即综述了普通无脊椎动物向脊椎动物演化的研究进展。     

脊椎动物的起源与演化研究进展(图版Ⅷ,Ⅸ)

脊椎动物的起源与演化历来是进化生命科学的核心命题。近年脊椎动物的起源与演化有重大突破。云南澄江寒武纪化石群中的后口类“皇冠西大动物”,半索动物“云南虫”和“海口虫”,尾索动物“始祖长江海鞘”,头索动物“海口华夏鱼”和“中间型中新鱼”,脊椎动物“凤姣昆明鱼”和“海口鱼”,论证了普通无脊椎动物向脊椎动物演化过渡的各种中间类型,勾勒出一幅较为完整的早期生命演化谱系。西北大学早期生命研究所舒德干教授基于对靠近脊椎动物“源头”时段软躯体后口动物化石系列的研究以及新的发现提出脊椎动物起源分“五步走”的新假说,即在脊椎动物的起源的“四步走”前还有更为原始的“一步”：云南澄江出土的古虫动物门化石很可能代表了原口动物和后口动物间的过渡类型。本文即综述了普通无脊椎动物向脊椎动物演化的研究进展。     

以斑马鱼为模式动物研究器官的发育与再生

斑马鱼因其受精卵体外发育、胚胎透明、具有较强的再生能力以及适于大规模遗传筛选的优势, 成为研究脊椎动物器官发育与再生的新兴模式动物。通过数十年的探索, 科研工作者已经在斑马鱼中建立了一套成熟的研究方法, 并对斑马鱼胚胎发育早期的细胞命运决定和分化、组织器官的形态建成以及受损后的再生过程有了初步的认识。近年来, 随着遗传筛选技术的大规模开展和活体成像技术在斑马鱼中的深入应用, 许多在小鼠等模式动物中悬而未决的问题开始得到充分解答。随着研究的不断深化和技术的不断更新, 以斑马鱼为模式动物, 对脊椎动物器官发育与再生的研究将会更加深入, 相关的调控机制也会被逐步探明, 从而为临床相关疾病的防治提供富有价值的参考。文章通过对近年来发表的文章进行回顾, 总结了斑马鱼作为模式动物研究中枢神经系统、肝脏和胰腺、血液细胞和血管等重要器官早期发育过程及其调控机制的进展, 并阐述了以斑马鱼研究尾鳍、心脏、肝脏等器官再生的优势和初步发现。     

基因倍增和脊椎动物起源

有机体基因复制导致基因复杂性增加及其和脊椎动物起源的关系已经成为进化生物学研究的热点。20世纪70年代由Ohno提出后经Holland等修正的原始脊索动物经两轮基因组复制产生脊椎动物的假设目前已被广泛接受。脊椎动物起源和进化过程中发生过两轮基因组复制的主要证据有三点：（1）据估计脊椎动物基因组内编码基因数目大约相当于果蝇、海鞘等无脊椎动物的4倍;原口动物如果蝇和后口动物如头索动物文昌鱼的基因组大都只有单拷贝的基因,而脊椎动物的基因组则通常有4个同属于一个家族的基因。（2）无脊椎动物如节肢动物、海胆和头索动物文昌鱼都只有一个Hox基因簇,而脊椎动物除鱼类外,有7个具有Hox基因簇,其余都具有4个Hox基因簇。（3）基因作图证明,不但在鱼类和哺乳动物染色体广大片段上基因顺序相似,而且有证据显示哺乳动物基因组不同染色体之间存在相似性。据认为第一次基因倍增发生在脊椎动物与头索动物分开之后,第二次基因倍增发生在有颌类脊椎动物和无颌类脊椎动物分开以后。但是,基因是逐个发生倍增,还是通过基因组内某些DNA片段抑或整个基因组的加倍而实现的,目前还颇有争议。     

斑马鱼在再生医学研究中的应用及进展

组织器官的再生现象一直以来吸引着众多生物学家们的关注。再生能力在不同物种间差异很大, 与人及高等脊椎动物相比, 低等脊椎动物(如：斑马鱼)有着较高的再生能力。斑马鱼的鳍、心脏、视网膜、视神经、脊髓、肝脏及感觉毛细胞等都具有很强的再生能力。因此, 从斑马鱼再生过程的研究中将获得大量有用的信息, 促进对人类再生能力缺陷的认识, 进而推动再生医学的发展。文章就斑马鱼在心脏、神经系统、肝脏、鳍再生医学研究中的进展及应用做一综述。     

心肌再生相关分子的调控机制

心脏是脊椎动物的中心器官,其适当大小及功能在整个生命周期都是至关重要的。由于心肌损伤造成的心肌梗死、心力衰竭等疾病在全世界范围内的发病率和死亡率逐年上升,目前依然没有找到好的治疗方法。已经发现在新生哺乳动物以及低等脊椎动物中存在多种进化保守的心脏再生机制,然而不幸的是,成年哺乳动物的心脏再生能力极其有限。近年来人们对心肌再生的研究越来越多,有证据表明成年哺乳动物可以产生新的心肌细胞。了解心脏再生的能力,并且掌握其中的原理是心血管方向研究的重要目标。本文主要综述了心肌再生相关分子及信号通路,如转录因子GATA4、微小RNA(microRNA)、Hippo信号通路、ERBB2和Notch通路以及一些炎症因子等发挥的调控作用及其机制。     

植物生长的一些特性

生物个体在细胞、组织、器官和整体水平上量的不可逆的增加称为生长。种子植物的生长一般具有以下几个特点:无限性、局部性、不可逆性、相关性、向性和全能性。无限性植物有三种分生组织,特别在其茎端和根端存在着能始终保持胚性活动的具有无限分生能力的顶端分生组织。这就使植物在其一生中不断产生新组织、形成新器官,一直持续到个体死亡。局部性动物(特别是脊椎动物)出生后基本上已具备了成体的一切器官,以后的生长仅是身体各部分体积的增大。因此,动物的成体及其幼体在体形上保持“相似形”关系。植物则完全不同,其生长仅限于存在分生组织的某些特定部位,并非整体生长。如在根、茎顶端及其侧方周围以及某些器官的基部。这就使植物与其幼苗相比显得面目全非了。     

泽蛙早期胚胎头部再生现象的观察

本文报道通过对泽蛙早期胚胎进行截头再生实验的观察,结果发现泽蛙尾芽期、肌肉感应期、孵化期及角膜透明期等不同发育时期的胚胎对截断头部的反应都有着基本相同的方式,即不同程度地出现完全再生、不完全再生及不出现再生的现象。泽蛙胚胎发育早期能再生出头的事实,充分证明某些脊椎动物也和某些无脊椎动物一样是具有头部再生能力的。     

编者按

<正>组织器官再生是指由于生理或病理原因导致生物体组织器官损伤后,在损伤部位又生长出与原有组织具有相同形态和功能的结构的过程。再生在低等动物中比较常见,蝾螈等能够再生出整个前肢,甚至是几乎整个个体。但动物界内不同物种的组织器官的再生能力具有明显的差异。以心脏再生为例,脊椎动物如斑马鱼具有一定的心脏再生能力;哺乳动物小鼠等出生7天前心脏具有再生能力,而7天后心脏再生能力丧失;     

斑马鱼尾鳍——理想的再生研究模型

脊椎动物组织和器官的发育与再生,与许多疾病的发生发展密切相关。不同物种间其再生能力差异很大,与哺乳动物相比,低等脊椎动物斑马鱼有着较强的再生能力。斑马鱼的多个组织器官如鳍、心脏、视网膜、脊髓、肝脏等都具有再生能力,对斑马鱼组织器官再生过程的研究将使我们获得大量有用的信息,能更好的理解脊椎动物再生功能,我们将以斑马鱼胚胎为实验材料,细致观察其尾鳍再生过程。     

Regeneration in vertebrates

One way or another, all species possess the ability to regenerate damaged tissues. The degree of regeneration, however, varies considerably among tissues within a body and among species, with urodeles being the most spectacular. Such differences in regenerative capacity are indicative of specific mechanisms that control the different types of regeneration. In this review the different types of regeneration in vertebrates and their basic characteristics are presented. The major cellular events, such as dedifferentiation and transdifferentiation, which allow complex organ and body part regeneration, are discussed and common molecular mechanisms are pinpointed.     

Analysis of ascidian <Emphasis Type="Italic">Not</Emphasis> genes highlights their evolutionarily conserved and derived features of structure and expression in development

The ascidian larva is often regarded as an organism close to the ancestral form of chordates, while it is generally accepted that the Spemanns organizer is absent from ascidian embryos. Not is one of the genes expressed in the organizer to execute functions in vertebrate embryos. To address the extent of conservation of Not gene expression among ascidians and vertebrates, we examined the structure and developmental expression of Not of the two distantly related ascidian species, Halocynthia and Ciona. Putative ascidian Not proteins were noted by the absence of one of the two motifs conserved among Not proteins of sea urchin and vertebrates. Analysis by in situ hybridization revealed that Not gene expression of ascidians could be categorized into three types: expression likely to be conserved between ascidians and vertebrates, that probably unique to ascidians, and that specific to ascidian species. Expression of ascidian Not in the posterior end of the tail as well as the notochord and a small part of the anterior neural tube at the tailbud stage is reminiscent of the expression of the vertebrate counterparts in the tailbud, which is regarded as a continuation of the organizer and the pineal gland, respectively. The expression of Not in the epidermis precursors during cleavage stage may be unique to ascidians. In the light of the present findings, evolutionary aspects of Not genes are discussed.Electronic Supplementary Material Supplementary material is available for this article at Edited by N. Satoh     

The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans

BACKGROUND INFORMATION: Caspases are cysteine proteases that mediate apoptosis (programmed cell death) initiation and execution. Apoptosis is a conserved mechanism shared by all metazoans, although its physiological function and complexity show considerable taxon-dependent variations. To gain insight into the caspase repertoire of putative ancestors to vertebrates, we performed exhaustive genomic searches in urochordates, a sister taxon to vertebrates in which ascidians and appendicularians display chordate characters at early stages of their development. RESULTS: We identified the complete caspase families of two ascidians (Ciona intestinalis and C. savignyi) and one larvacean (Oikopleura dioica). We found in ascidian species an extremely high number of caspase genes (17 for C. intestinalis and 22 for C. savignyi), deriving from five founder gene orthologues to human pro-inflammatory, initiator and executioner caspases. Although considered to be sibling species, C. intestinalis and C. savignyi only share 11 orthologues, most of the additional genes resulting from recent mass duplications. A sharply contrasted picture was found in O. dioica, which displayed only three caspase genes deriving from a single founder gene distantly related to caspase 3/7. The difference between ascidian and larvacean caspase repertoires is discussed in the light of their developmental patterns and life cycles. CONCLUSIONS: The identification of caspase members in two ascidian species delineates five founder genes that bridge the gap between vertebrates and Ecdysozoa (arthropods and nematodes). Given the amazing diversity among urochordates, determination and comparison of the caspase repertoires in species from orders additional to Enterogona (ascidians) and Oikopleuridae might be highly informative on the evolution of caspase-dependent physiological processes.     

Evolution and the origin of the visual retinoid cycle in vertebrates

Absorption of a photon by visual pigments induces isomerization of 11-cis-retinaldehyde (RAL) chromophore to all-trans-RAL. Since the opsins lacking 11-cis-RAL lose light sensitivity, sustained vision requires continuous regeneration of 11-cis-RAL via the process called ‘visual cycle’. Protostomes and vertebrates use essentially different machinery of visual pigment regeneration, and the origin and early evolution of the vertebrate visual cycle is an unsolved mystery. Here we compare visual retinoid cycles between different photoreceptors of vertebrates, including rods, cones and non-visual photoreceptors, as well as between vertebrates and invertebrates. The visual cycle systems in ascidians, the closest living relatives of vertebrates, show an intermediate state between vertebrates and non-chordate invertebrates. The ascidian larva may use retinochrome-like opsin as the major isomerase. The entire process of the visual cycle can occur inside the photoreceptor cells with distinct subcellular compartmentalization, although the visual cycle components are also present in surrounding non-photoreceptor cells. The adult ascidian probably uses RPE65 isomerase, and trans-to-cis isomerization may occur in distinct cellular compartments, which is similar to the vertebrate situation. The complete transition to the sophisticated retinoid cycle of vertebrates may have required acquisition of new genes, such as interphotoreceptor retinoid-binding protein, and functional evolution of the visual cycle genes.     

Cellular and molecular processes of regeneration, with special emphasis on fish fins

The phenomenon of 'epimorphic regeneration', a complete reformation of lost tissues and organs from adult differentiated cells, has been fascinating many biologists for many years. While most vertebrate species including humans do not have a remarkable ability for regeneration, the lower vertebrates such as urodeles and fish have exceptionally high regeneration abilities. In particular, the teleost fish has a high ability to regenerate a variety of tissues and organs including scales, muscles, spinal cord and heart among vertebrate species. Hence, an understanding of the regeneration mechanism in teleosts will provide an essential knowledge base for rational approaches to tissue and organ regeneration in mammals. In the last decade, small teleost fish such as the zebrafish and medaka have emerged as powerful animal models in which a variety of developmental, genetic and molecular approaches are applicable. In addition, rapid progress in the development of genome resources such as expressed sequence tags and genome sequences has accelerated the speed of the molecular analysis of regeneration. This review summarizes the current status of our understanding of the cellular and molecular basis of regeneration, particularly that regarding fish fins.     

Decoding cis-regulatory systems in ascidians

Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.     

Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates

The evolutionary history of the diverse lifestyles adopted by urochordates has attracted intense interest because it may effect the evolutionary history of vertebrates. Here, we report the complete mitochondrial (mt) DNA sequence of the pelagic thaliacean doliolid Doliolum nationalis. The doliolid mt genome shares the unusual tRNAs of trnM(uau) and trnG(ucu) with other ascidians, such as Halocynthia and Ciona. On the other hand, the gene order of the doliolid mt genome is significantly different from that of any ascidian species or vertebrate reported to date. Phylogenetic analyses of the amino acid sequences of 12 protein-coding genes strongly support the sister-grouping of doliolids and the Phlebobranch ascidian Ciona, with the Stolidobranch ascidian alocynthia as the outgroup, thereby providing strong support for the paraphyly of ascidians, as has been suggested by 18S rDNA studies. Given the paraphyletic nature of ascidians, it seems likely that the common ancestor of ascidians and thaliaceans was sessile, as are the present-day ascidians, and that the thaliaceans subsequently evolved a pelagic lifestyle.     

Evidence for the Heparin-Binding Ability of the Ascidian Xlink Domain and Insight into the Evolution of the Xlink Domain in Chordates

The vertebrate Xlink domain is found in two types of genes: lecticans and their associated hyaluronan-and-proteoglycan-binding-link-proteins (HAPLNs), which are components of the extracellular matrix, and those represented by CD44 and stabilins, which are expressed on the surface of lymphocytes. In both types of genes, Xlink functions as a hyaluronan binding domain. We have already reported that protochordate ascidians possess only the latter type of gene. The present analysis of the expression of ascidian Xlink domain genes revealed that these genes function in blood cell migration and apoptosis. While the Xlink domain is found in various metazoans, including ascidians and nematodes, hyaluronan is believed to be specific for vertebrates. In comprehensive genome surveys for hyaluronan synthase (HAS), we found no HAS gene in ascidians. We also established that hyaluronan is absent from the ascidian body biochemically. Therefore, ascidians possess the Xlink domain, but they lack HA. We recovered one ascidian Xlink domain gene that encoded a heparin-binding protein, although it shows no affinity for hyaluronan. Based on these findings, we conclude that in invertebrates, the Xlink domain serves as heparin-binding protein domain and functions in blood cell migration and apoptosis. Its binding affinity for HA might have been acquired in the vertebrate lineage.     

Developmental aspects of spinal cord and limb regeneration

The ability of birds and mammals to regenerate tissues is limited. By contrast, urodele amphibians can regenerate a variety of injured tissues such as intestine, cardiac muscle, lens and neural retina, as well as entire structures such as limbs, tail and lower jaw. This regenerative capacity is associated with the ability to form masses of mesenchyme cells (blastemas) that differentiate into the missing tissues or parts. Understanding the mechanisms that underlie blastema formation in urodeles will provide valuable tools with which to achieve the goal of stimulating regeneration in mammalian tissues that do not naturally regenerate. Here we discuss an example of tissue regeneration (spinal cord) and an example of epimorphic appendage regeneration (limb) in the axolotl Ambystoma mexicanum , emphasizing analysis of the processes that produce the regeneration blastema and of the tissue interactions and blastemal products that contribute to the regeneration-promoting environment.