Functional characterization of a ficolin-mediated complement pathway in amphioxus

The ficolin-mediated complement pathway plays an important role in vertebrate immunity, but it is not clear whether this pathway exists in invertebrates. Here we identified homologs of ficolin pathway components from the cephalochordate amphioxus and investigated whether they had been co-opted into a functional ficolin pathway. Four of these homologs, ficolin FCN1, serine protease MASP1 and MASP3, and complement component C3, were highly expressed in mucosal tissues and gonads, and were significantly up-regulated following bacterial infection. Recombinant FCN1 could induce hemagglutination, discriminate among sugar components, and specifically recognize and aggregate several bacteria (especially gram-positive strains) without showing bactericidal activity. This suggested that FCN1 is a dedicated pattern-recognition receptor. Recombinant serine protease MASP1/3 formed complexes with recombinant FCN1 and facilitated the activation of native C3 protein in amphioxus humoral fluid, in which C3 acted as an immune effector. We conclude that amphioxus have developed a functional ficolin-complement pathway. Because ficolin pathway components have not been reported in non-chordate species, our findings supported the idea that this pathway may represent a chordate-specific innovation in the evolution of the complement system.     

Identification and expression analysis of BMP signaling inhibitors genes of the DAN family in amphioxus

Bone morphogenetic proteins (BMPs) are members of the Transforming Growth Factor-β (TGF-β) family implicated in many developmental processes in metazoans such as embryo axes specification. Their wide variety of actions is in part controlled by inhibitors that impede the interaction of BMPs with their specific receptors. Here, we focused our attention on the Differential screening-selected gene Aberrative in Neuroblastoma (DAN) family of inhibitors. Although they are well-characterized in vertebrates, few data are available for this family in other metazoan species. In order to understand the evolution of potential developmental roles of these inhibitors in chordates, we identified the members of this family in the cephalochordate amphioxus, and characterized their expression patterns during embryonic development. Our data suggest that the function of Cerberus/Dand5 subfamily genes is conserved among chordates, whereas Gremlin1/2 and NBL1 subfamily genes seem to have acquired divergent expression patterns in each chordate lineage. On the other hand, the expression of Gremlin in the amphioxus neural plate border during early neurulation strengthens the hypothesis of a conserved neural plate border gene network in chordates.     

EST analysis of mRNAs expressed in neurula of Chinese amphioxus

Amphioxus, a cephalochordate, is the closest living relative to the vertebrates. In order to investigate the molecular mechanisms of the early embryogenesis of amphioxus, we constructed a neurula embryo cDNA library of Chinese amphioxus (Branchiostoma belcheri tsingtauense) and generated 5235 expressed sequenced tags in the present study. The initial ESTs consisted of 638 clusters and 1855 singletons, which revealed approximately 2493 unique genes in the data set. Of these sequences, 35.52% ESTs matched to known genes, 12.76% matched to other ESTs, and 51.71% had no match to any known sequences in GenBank. Interestingly we found homologous genes related to neural development and human disease. Bioinformatic analysis showed the direct evidence that the gene homologue found only in vertebrates in previous studies also exists in the amphioxus genome. This study provides a preliminary view of the gene information involved in the development of neurula embryos of Chinese amphioxus and helps our understanding of vertebrate evolution at gene level.     

Formation of the chordamesoderm in the amphioxus embryo: Analysis with Brachyury and fork head/HNF-3 genes

 The embryonic development of amphioxus (cephalochordates) has much in common with that of vertebrates, suggesting a close phylogenetic relationship between the two chordate groups. To gain insight into alterations in the genetic cascade that accompanied the evolution of vertebrate embryogenesis, we investigated the formation of the chordamesoderm in amphioxus embryos using the genes Brachyury and fork head/HNF-3 as probes. Am(Bb)Bra1 and Am(Bb)Bra2 are homologues of the mouse Brachyury gene isolated from Branchiostoma belcheri. Molecular phylogenetic analysis suggests that the genes are independently duplicated in the amphioxus lineage. Both genes are initially expressed in the involuting mesoderm of the gastrula, then in the differentiating somites of neurulae, followed by the differentiating notochord and finally in the tail bud of ten-somite stage embryos. On the other hand, Am(Bb)fkh/HNF3-1, an amphioxus (B. belcheri) homologue of the fork head/HNF-3 gene, is initially expressed in the invaginating endoderm and mesoderm, then later in the differentiating notochord and in the tail bud. With respect to these two types of genes, the formation of the notochord and tail bud in amphioxus embryos shows similarity and dissimilarity with that of the notochord and tail bud in vertebrate embryos. Received: 21 November 1996 / Accepted: 24 January 1997     

EST analysis in barley defines a unigene set comprising 4,000 genes

We report the generation of 13,109 EST (Expressed Sequence Tag) sequences from barley as a first step towards the generation of a unigene set for this organism. Sequences were generated from three libraries encompassing 7,568 cDNA clones. Comparisons to nucleic acid and protein sequence databases enabled the assignment of putative functions to the mRNAs. The results of the searches against protein databases were parsed and built into a regularly updated database, available over the World Wide Web. The Stack_Pack clustering system has been applied to survey the level of redundancy, which was calculated to amount to 69%, thus we identified 4,000 different barley genes. To prove the usability of the results of the clustering process for further experiments, we subjected alignments with sequences similar to elongation factor 1 alpha to additional analysis. These sequences represented the largest group with identical putative functions (228 members) and clustering based on the analysis of 3′ sequences subdivided the group into five different assemblies. Alignments of the consensus sequences facilitated the development of PCR assays suitable for genetic mapping of four of the different gene-family members, which reside on chromosomes 2H, 4H and 5H, thus demonstrating the suitability of the cluster-results as a basis for in-depth analyses of barley gene families. Received: 15 March 2001 / Accepted: 18 April 2001     

内毒素诱发鸡多脏器损伤及其对肝TLR4 mRNA表达影响

选取20日龄肉仔鸡随机分为四组,实验组A（灌服LPS100EU／Kg）、B（灌服LPS200EU／Kg）、C（灌服LPS300EU／Kg）和对照组D（灌服生理盐水）。检测不同剂量的LPS在不同时间对鸡多脏器损伤以及内毒素识别因子肝脏Toll样受体4mRNA表达的影响,为进一步揭示禽内毒素血症的发病机理提供依据。实验表明：12～24h是LPS诱发多脏器损伤并引起TLR4表达异常的敏感期,12h肝组织TLR4mRNA的表达水平降至最低,24h后开始回升且随着LPS攻毒剂量的增加,TLR4表达水平回升的速度递减,至48h仍无法达到正常表达水平,这可能与肝细胞作为腺上皮细胞参与TLR4表达调节或机体对抗过度炎症反应而产生的一种保护性反馈引起。     

Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae)

The ParaHox cluster is the evolutionary sister to the Hox cluster. Like the Hox cluster, the ParaHox cluster displays spatial and temporal regulation of the component genes along the anterior/posterior axis in a manner that correlates with the gene positions within the cluster (a feature called collinearity). The ParaHox cluster is however a simpler system to study because it is composed of only three genes. We provide a detailed analysis of the amphioxus ParaHox cluster and, for the first time in a single species, examine the regulation of the cluster in response to a single developmental signalling molecule, retinoic acid (RA). Embryos treated with either RA or RA antagonist display altered ParaHox gene expression: AmphiGsx expression shifts in the neural tube, and the endodermal boundary between AmphiXlox and AmphiCdx shifts its anterior/posterior position. We identified several putative retinoic acid response elements and in vitro assays suggest some may participate in RA regulation of the ParaHox genes. By comparison to vertebrate ParaHox gene regulation we explore the evolutionary implications. This work highlights how insights into the regulation and evolution of more complex vertebrate arrangements can be obtained through studies of a simpler, unduplicated amphioxus gene cluster.     

Cloning and phylogenetic analysis of an amphioxus myogenic bHLH gene AmphiMDF

In this study, a member of the MyoD gene family, AmphiMDF, was isolated from the embryos of amphioxus by degenerate PCR, followed by rapid amplification of cDNA ends (RACE). Southern blot analysis confirmed that only a single myogenic bHLH gene was present in the genome of amphioxus Branchiostoma belcheri tsingtauense. Sequence and phylogenetic analyses indicated that AmphiMDF falls at the base of its vertebrate homologs. The amino acid sequence of AmphiMDF was almost equally similar to those of the four clusters of the vertebrate MyoD family. This suggests that AmphiMDF is not only the sister but also the archetype of the vertebrate myogenic bHLH genes. The scenarios to explain the origin of the vertebrate MyoD gene family from the ancestral myogenic bHLH gene like AmphiMDF are also discussed.     

Characterization and expression of amphioxus ApoD gene encoding an archetype of vertebrate ApoD proteins

Here we report a homologue of the apolipoprotein D gene (AmphiApoD) in amphioxus, Branchiostoma belcheri tsingtauense, the first such finding in a basal chordate cephalochordate. The main features of the protein predicted from AmphiApoD are characteristic of the apolipoprotein D. Phylogenetic analysis places AmphiApoD at the base of the phylogenetic tree, suggesting that AmphiApoD is the archetype of the vertebrate ApoD genes. Both whole mount in situ hybridization and Northern blotting and RT-PCR as well as in situ hybridization histochemistry reveal that AmphiApoD is expressed in tissues derived from mesoderm and endoderm including notochord and hind-gut, which contrasts with the strong expression patterns of ApoD genes in the ectodermal derivatives in mammals and birds. The expression profiles of the ApoD gene may have been changed to be expressed in the endo-mesodermal derivatives in amphioxus after the vertebrate and cephalochordate lineages diverged; alternatively, the ApoD gene may first have been expressed in the endo-mesoderm during embryogenesis in the last common ancestor of all chordates, and subsequently came to be expressed in the ectodermal derivatives of vertebrates including mammals and birds.     

Genes expressed in the amphioxus notochord revealed by EST analysis

The notochord cell of the cephalochordate amphioxus adult is unique due to the occurrence of myofilaments in the cytoplasm. The present EST (expressed sequence tag) analysis targeted mRNAs of the amphioxus notochord to determine genes that are expressed there. Notochord cells were isolated from Branchiostoma belcheri adults, from which a cDNA library was constructed. Analysis of a set of 257 ESTs (both 5' and 3' ends) showed that about 11% of the cDNAs are related to muscle genes, while 9% of them are genes for extracellular matrix proteins associated with formation of the notochordal sheath. The muscle-related genes included actin, tropomyosin, troponin I, myosin regulatory light chain, myosin light chain kinase, myosin heavy chain, calmodulin, calponin, calcium vector protein, creatine kinase, muscle LIM protein, and SH3-binding glutamate-rich protein, suggesting that vertebrate skeletal and smooth muscle-type genes are simultaneously expressed in the amphioxus notochord. Nucleotide sequences of cDNAs for actin, tropomyosin, troponin I, and a few others were completely determined to substantiate the conclusions. The chordate muscle-type actin is distinguishable from the cytoplasmic-type actin by the usage of amino acid residues at 20 diagnostic positions. Interestingly, analysis of the usage of amino acid residues at these positions showed that the "amphioxus notochord actin" is a unique intermediate between muscle-type and cytoplasmic-type actins. These results strongly suggest that the notochord of adult amphioxus is a mechanical swimming organ and its role is quite different from the role of the vertebrate embryonic notochord, which functions as a source of signals required for body plan formation.     

球毛壳菌(Chaetomium globosum)EST生物信息分析数据库的建立

用基因本体论（Cene Ontology,GO）中的相关的规范术语和BLAST分析结果来对球毛壳菌EST及CONTIG序列信息进行注释,利用GO的语义模型构建不同物种数据库之间的语义联接,在此基础上建立球毛壳菌EST生物信息分析数据库,在概念和联系层面上有效地解决了不同物种生物信息的整合问题,实现了对球毛壳菌生物信息学数据智能化的多重、复合和交叉检索。为球毛壳菌生物信息学的进一步研究奠定了坚实的基础。文中详细论述了基于GO的球毛壳菌EST生物信息学数据库的研究背景、建立过程、查询功能及其维护。     

An amphioxus snail gene: Expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo

 Homologs of the Drosophila snail gene have been characterized in several vertebrates. In addition to being expressed in mesoderm during gastrulation, vertebrate snail genes are also expressed in presumptive neural crest and/or its derivatives. Given that neural crest is unique to vertebrates and is considered to be of fundamental importance in their evolution, we have cloned and characterized the expression of a snail gene from amphioxus, a cephalochordate widely accepted as the sister group of the vertebrates. We show that, at the amino acid sequence level, the amphioxus snail gene is a clear phylogenetic outgroup to all the characterized vertebrate snail genes. During embryogenesis snail expression initially becomes restricted to the paraxial or presomitic mesoderm of amphioxus. Later, snail is expressed at high levels in the lateral neural plate, where it persists during neurulation. Our results indicate that an ancestral function of snail genes in the lineage leading to vertebrates is to define the paraxial mesoderm. Furthermore, our results indicate that a cell population homologous to the vertebrate neural crest may be present in amphioxus, thus providing an important link in the evolution of this key vertebrate tissue. Received: 11 May 1998 / Accepted: 2 August 1998     

文昌鱼胚胎的程序化冷冻保存

文昌鱼在进化和发育生物学中有重要科学研究价值,然而由于文昌鱼实验室繁殖受产卵季节等因素的限制,以其胚胎为材料的研究工作受到局限,胚胎冷冻保存是解决这一问题的有效途径之一。本文首次对文昌鱼(Branchiostoma japonicum)胚胎的程序化冷冻保存进行了研究,通过筛选合适的程序化抗冻液、适宜的胚胎发育阶段,以及比较不同平衡处理时间、植冰温度、保存温度和洗脱时间对文昌鱼胚胎冷冻保存的影响。结果表明:几种抗冻液中,A2的效果较好,对胚胎的毒性小;原肠中期胚胎较其它时期对抗冻液的耐受力更强,适宜进行冷冻保存;胚胎在抗冻液中的最佳平衡处理时间为40-50min;冷冻降温时,适宜的植冰温度为-7.0℃--10.0℃;植冰后进行程序化冷冻,目前能稳定得到存活胚胎的最低保存温度为-15℃;此外,不同的洗脱时间对胚胎的存活率无显著影响。根据优化后的条件,对文昌鱼胚胎进行程序化冷冻保存(-196℃)实验,获得1粒存活的胚胎,并孵化出膜,发育至两鳃裂时期,幼鱼共存活了8d,但形态畸形。结果提示文昌鱼胚胎冷冻保存的可行性,但需要进一步优化包括抗冻液在内的各种条件,以提高存活率。     

青岛文昌鱼精子运动特征及计算机辅助分析

青岛文昌鱼的精子在精浆中不运动,在与精浆等渗的生理溶液中也不运动,把精液稀释到过滤海水或人工海水后,精子运动被激活。文昌鱼新鲜精液中精子浓度为(9.4±1.6)×1010/ml;在人工海水中,运动精子占总精子数的85.8%±6.9%,精子运动持续的平均时间是22.7±2.6min。文昌鱼精子经人工海水激活0.5min后,可观察到四种运动方式:(1)向前直线运动,其平均速度93.6±23.7μm/s,这类精子所占的百分比为27.8%±3.1%;(2)弧形曲线运动,平均速度55.6±18.9μm/s,所占的百分比为44.3%±2.5%;(3)左右摆动,平均前进速度27.4±13.4μm/s,所占百分比为14.7%±1.8%;(4)运动速度小于5μm/s的精子,视为不运动的精子,所占百分比为13.2%±1.8%。随着激活时间的延长,文昌鱼精子的运动状态发生改变,向前直线运动和弧形曲线运动的精子逐渐减少,而左右摆动和不运动的精子逐渐增多。     

Demonstration of plasminogen-like protein in amphioxus with implications for the origin of vertebrate liver

Plasminogen, the proenzyme of serine protease plasmin, is a plasma glycoprotein synthesized primarily in the liver, and its evolutionary origin in chordates remains unclear. We demonstrated here that the humoral fluid in amphioxus is capable of cross‐reacting with anti‐human or anti‐mouse plasminogen antibodies, and the hepatic diverticulum in amphioxus is the site of plasminogen‐like protein synthesis. The presence of plasminogen‐like protein in amphioxus pushes the origin of plasminogen to before the last common ancestor of vertebrates. In addition, the localization of plasminogen‐like protein in the hepatic diverticulum suggests that the diverticulum in amphioxus is functionally homologous to the vertebrate liver in respect of plasminogen synthesis, supporting the hypothesis that the vertebrate liver evolved from the hepatic diverticulum of an amphioxus‐like ancestor during early chordate evolution.     

表达序列标签(EST)在基因组学研究中的应用

表达序列标签 (expressedsequencetags)是一种快捷、高效的揭示基因组信息的方法。本文对EST的产生、概念、技术原理及其在基因组研究中的广泛应用作一详细的介绍