三叶因子在结直肠癌组织中的表达与临床关系及三叶因子-2在大肠杆菌中的重组表达和活性研究

癌症是世界发达国家和许多发展中国家人口的疾病主要死亡原因之一，其中，每年结直肠癌的新增病例和死亡病例排在癌症的第三位。在我国，北京、上海等地的统计资料显示，结直肠癌的发病上升很快 ，已排在癌症的第二位。结直肠癌的发生发展过程涉及一系列细胞和分子事件的改变，包括基因结构的异常和基因表达谱的异常。三叶因子（trefoil factor, TFF）是在上世纪80年代末到90初初由不同研究小组先后发现的含特殊的三叶因子结构域的蛋白多肽，其结构域的特征是含38-40个氨基酸残基的肽段中，有6保守的个半胱氨酸残基以1—5、2—4、3—6的方式形成二硫键，从而形成紧密的三叶结构域。在哺乳动物体内目前发现的三叶因子有三种，由粘膜组织内不同细胞合成并分泌到粘膜表面，对粘膜起保护作用。在粘膜损伤时，可通过多种途径促进上皮细胞迁移和抑制细胞凋亡，并促进血管形成，参与粘膜损伤的修复和重建。三叶因子在肿瘤组织中表达，则可能对癌症的发展起促进作用。研究资料显示，三叶因子在肿瘤中的表达异常与多种肿瘤的发生和发展过程有关。我们通过DNA测序检测结直肠癌组织中TFF1和TFF3基因各外显子的核苷酸序列，以确定是否存在基因突变。并用QRT-PCR和免疫组织化学的方法检测结直肠癌组织中TFF1和TFF3的mRNA和蛋白质的表达水平，分析其表达与结直肠癌的临床和病理特征之间的关系。同时，用ELISA方法检测结直肠癌患者血清中TFF1和TFF3的含量，以分析其与临床的关系，并逐步研究这两种三叶因子有否可能作为结直肠癌有用的血清分子标记。 目前得到以下研究结果：①在TFF1基因5`-端非翻译区位于起始密码上游—2bp处有一高频率的（C→T）突变位点,频率为40%，在其他非编码区也发现若干个较低频率的突变位点。未发现TFF3的基因突变；②TFF1和TFF3的mRNA水平在不同患者结直肠癌组织中的表达水平差异很大。与临床病理关系由于样品例数较少，未作统计学出理。结直肠癌组织中TFF1和TFF3蛋白表达检出阳性率分别为90%和94%。TFF1的表达与结直肠癌临床及病理类型未发现统计学意义，TFF3的表达上调与肿瘤淋巴结转移有关；③结直肠癌患者血清中TFF1的含量为（78.6575±53.300ng/ml），比健康人群血清TFF1含量（19.6457±5.3880ng/ml），增高约4倍，这一结果属首次报道。结直肠癌患者血清中TFF3的含量为（27.96±21.985ng/ml），比正常人群血清TFF3含量（9.0875±2.0315ng/ml）增高约3 1 倍。TFF1和TFF3能否作为结直肠癌的血清分子标志，尚需完善相关资料和作进一步研究。 TFF1和TFF3分别含一个三叶结构域，在靠近C-末端有一个游离的半胱氨酸巯基，TFF1和TFF3通过此二硫键形成同源二聚体，是其活性的主要形式。TFF2含两个三叶结构域，在三叶结构域外其靠近N-端和C-端各有一个半胱氨酸，两者以二硫键相连，形成紧密的结构。我们用pET系统克隆和表达人TFF2(hTFF2)，以及TFF2三叶结构域外二硫键解开的突变型TFF2(MhTFF2)，并测定细胞迁移活性。结果获得高效表达的hTFF2和MhTFF2，占细胞质总蛋白量的40%以上，经亲和层析后得到样品纯度在95%以上。对HCT116细胞株的划痕试验表明，hTFF2和MhTFF2对HCT116细胞具有迁移作用，细胞迁移数约为对照BSA的1.5倍。 结论:①结直肠癌组织中三叶因子-1和三叶因子-3基因突变不是三叶因子表达异常的主要原因；②TFF1和TFF3的转录水平在不同结直肠癌组织中有很多差异，TFF3蛋白的高表达与结直肠癌淋巴转移有关；③血清中TFF1和TFF3的含量检测可能会成为结直肠癌有用的血清分子标志；④pET质粒系统可高效表达可溶性三叶因子-2，并可表达获得有细胞迁移活性的重组融合蛋白TFF2；⑤TFF2的三叶结构域外的二硫键对TFF2的细胞迁移活性不是必须的。

哺乳动物生长激素/泌乳刺激素基因超家族的分子进化研究

生长激素（Growthhormone，GH）和泌乳刺激素（Prolactin，PRL）基因具有相似的结构和功能，它们和其他一些相关基因组成了GH/PRL基因超家族。在大部分哺乳动物基因组中，GH和PRL都是单拷贝基因。但在灵长目动物中，PRL是单拷贝基因，GH基因却发生了串联重复事件，形成一个基因家族。而在啮齿目中则相反，GH是单拷贝的，PRL却发生了串联重复事件形成一个基因家族。用PCR、克隆、测序的方法，我们从7种灵长目动物中得到了35条GH－类似基因。系统发育分析的结果显示所有旧大陆猴／人猿超科（OWM/H）的GH一类似基因和所有新大陆猴（NWM）的GH-类似基因分别形成两个单系，提示新大陆猴的GH基因家族和旧大陆猴／人猿超科GH基因家族起源于独立的基因重复事件。我们的分析结果还提示在。H基因家族的进化历程中发生了多次基因重复和基因转换事件。此外，不同GH基因家族成员的进化速率和所受到的选择压力存在显著差异。GHN基因在人猿超科和旧大陆猴中进化速率都比较慢，且受到了很强的纯化选择的作用；而CSH基因在两个世系中进化速率都比较快而且可能受到近中性选择的作用；GHV的进化速率和选择压力在旧大陆猴和人猿超科之间存在显著差异。对于新大陆猴GH基因家族，我们发现3个主要的功能基因簇，有趣的是这3个基因簇分别受到了纯化选择、近中性选择和正选择3种不同类型的选择压力。进一步分析的结果显示GH基因家族的进化符合所谓"生一和一灭（Birth-and-death）"的进化模式，该模式以频繁的基因重复和假基因化为主要特征。啮齿目泌乳刺激素基因家族由多个结构相似、在染色体上串联排列的基因组成，创门主要在生殖过程中协调作用。我们利用生物信息学手段在大鼠中得到了两个新的家族成员。结合系统发育、基因转换分析及染色体相对位置的比较，我们认为啮齿目PRL基因家族中的PL-I和PL-II基因亚家族是在大、小鼠分歧之后由物种特异的基因重复事件形成的。此外，啮齿目PRL基因家族的进化历程较复杂，因为除了通常的5-外显子结构的基因外，该家族还包含6-外显子结构的基因，后者在前者的第2和第3外显子之间获得了一个额外的外显子。本研究中我们意外地发现这个外显子在两个基因簇中的起源方式并不相同。在groupA中，它来源于一段外源DNA的插入，而在groupB中则来源于原先的非编码序列。对同义替换和异义替换速率比较的结果显示，在这些获得额外外显子的基－因中纯化选择压力得到了放松。激素蛋白必须与其受体结合经过信号传导才能发挥其生物学功能，因此，研究激素和受体的协同进化就显得尤为重要。我们对哺乳动物泌乳刺激素基因和其受体（PRLR）基因进行了协同进化分析，结果发现哺乳动物PRLR的膜外区和膜内区显示出和PRL一致的"插曲"式的进化模式。皮耳森相关系数计算的结果说明PRLR的膜外区和PRL基因发生了协同进化，同时PRLR的两个功能区域：膜外区和膜内区之间也发生了协同进化。此外，我们还发现灵长目PRL基因也发生了和GH基因类似的"插曲"式的进化，而且快速进化可能是选择压力放松的结果。

哺乳动物适应性进化的分子机制探讨——若味受体基因和犁鼻器受体1基因的研究

动物的适应进化是生物学研究的最基本的问题之一。虽然，人们早从形态学上研究了动物的适应现象，但是对适应的遗传学机制知之甚少。动物感觉系统对周围环境的适应是动物适应进化中的一个关键问题。因此，我们选取了动物感觉系统中苦味受体基因家族（T2R）和犁鼻器受体1基因家族（VIR）为研究对象，对哺乳动物适应性进化的分子机制进行探讨。通过生物信息学和分子生物学手段相结合，我们在哺乳动物6个目共16个物种中获得了157个的苦味味觉受体基因，并对这些TZR基因的系统发育关系进行分析，结果显示哺乳动物的TZR基因家族经历了"生一和一灭"的进化模式，即频繁的基因重复和假基因化。另外，结果还显示这些基因可以被分为3个主要类群，分别命名为A，B和C。有趣的是，B和C类群的基因在所研究的物种间普遍是一对一的直系同源的，而A类群基因则显示了种属或世系特异性。有可能B和C类群的基因是识别哺乳动物共同的苦味物质所必需的，而A类群基因则是用于识别具有种属特异性的苦味物质。这个分析还揭示了在系统发育关系上近相关的基因在它们的染色体位置上也是靠近的，这证明了串联重复是新的TZR基因产生的主要方式。此外，通过核昔酸的异义替换数和同义替换数的比较显示不同物种新近产生的基因所编码的受体蛋白在膜外区的异义替换数显著地大于同义替换数，提示着这些通过基因重复产生的新基因受到了正选择的作用。在自然界中，许多的天然有毒物质一般都是苦的，因此，我们推测哺乳动物TZR基因的分"化选择是为了使其在探索新的生活环境和寻找新食物时能够辨别出更多不同的有毒物质，更好地适应新环境。此外，我们还研究了苦味受体基因和甜味／鲜味受体基因的进化途径。结果显示苦味受体基因和甜味／鲜味受体基因在进化上具有远相关，并具有不同的进化途径，提示着这可能是导致了这些受体基因具有不同功能，传导不同味觉的原因。犁鼻受体噬因家族（VIR）是哺乳动物的信息素受体。应用生物信息学手，我们从大鼠和小鼠的基因组中分别得到了152和115个VIR基因。大鼠VIR基因家族包含11个亚家族，其中10个是与小鼠共享的，而M家族是大鼠特有的；另夕卜大鼠缺少了H和I亚家族，而这两个亚家族存在于小鼠的基因组中。系统发育关系分析发现，"生一和一灭"进化模式也在V1R基因的进化过程中占了主导地位。所有检测到的亚家族都出现于啮齿目和灵长目分歧之后，这说明V1R基因的多样性反映了这一基因家族在啮齿目内基因重复、丢失，基因漂变及自然选择等作用的动态过程。我们的分析还表明大部分不同亚家族下的基因簇爆发的时间接近于大、小鼠分歧的时间。此外，用最大似然法分析的结果表明在这些基因簇中异义替换和同义替换的比值远大于1，揭示了正选择在这些基因的分化过程的作用。一般认为V1R在动物识别信息素过程中起重要的作用，因此我们推测V1R基因的适应性进化是为了使不同的哺乳动物能够识别不同的、复杂的信息素。

线粒体基因组的变异与哺乳动物高原适应性

青藏高原是世界上最大、最年轻的高原。大气氧分压低、太阳辐射强烈和 气候寒冷等自然特点使得生活在青藏高原上的动物在形态、生态、行为以及生 理机能上都受到深刻的影响，并在进化过程中对高原环境产生了特殊的适应性。 生活在高原上的动物分为世居动物和移居动物，它们处于高原适应过程中的不 同阶段，并且有着不同的高原适应性的特点。为了研究高原哺乳动物所拥有的 特殊高原适应性的遗传基础和进化历史，以及探讨处于不同高原适应阶段的哺 乳动物对高原的适应性在遗传基础上的异同，本研究首次测定和分析了高原世 居动物中的藏羚羊（Pantholops hodgsonii）和高原鼠兔（Ochotona curzoniae） 以及高原移居动物中的藏马（Equns caballus）这三种具有代表性的高原动物的 线粒体全基因组。 1. 藏羚羊线粒体DNA 中的变异及其进化史 在对线粒体上13 个基因进行了进化分析后，我们发现细胞色素氧化酶1 （COX1）基因在藏羚羊和牦牛中都有高的非同义突变的现象。COX1 基因编码 的蛋白是线粒体氧化呼吸链上复合物Ⅳ的一部分，它将电子传递给氧，进行有 氧呼吸并产生能量。考虑到藏羚羊与牦牛都是生活在相同的气候环境中，我们 猜想线粒体基因组编码的COX1 基因的进化可能对青藏高原世居动物适应高原 环境起到作用。藏羚羊的线粒体DNA 数据表明，藏羚羊与绵羊、山羊的亲缘 关系较近，而与羚羊属家族的动物则相对较远，同时我们估算了藏羚羊与绵羊 山羊的分化时间大约为220 万年左右。这一时间与一些学者所估计的青藏高原 隆起时间大致吻合。 2. 高原鼠兔线粒体DNA 中的变异及其进化史 对高原鼠兔线粒体基因组上的基因进行进化分析后发现，对于高原鼠兔这一 分枝上，COX1 基因也有高的非同义突变速率。这表明COX1 基因在高原鼠兔 适应青藏高原高寒缺氧的环境过程中也可能受到选择压力的作用，结合我们在 藏羚羊和牦牛中的分析结果，我们推测高原世居动物在COX1 基因的进化过程 中很多都表现出类似的受选择现象。3. 藏马线粒体DNA 中的变异及其进化史 我们测定了西藏那曲(4500m)、云南中甸(3300m)、云南德钦(3300m)地区共 三匹藏马线粒体全基因组序列。通过对线粒体蛋白编码区的分析发现，与藏羚 羊、高原鼠兔等高原世居动物表现出的COX1 基因受选择不同，在三匹藏马中 NADH6 基因均表现高的非同义突变现象。NDAH6 基因编码的蛋白是线粒体氧 化呼吸链上复合物Ⅰ的一部分，它催化电子从NADH 传递给辅酶Q。不同地区 藏马中NADH6 基因类似的进化方式表明NADH6 基因的进化可能与藏马对高 原极端环境的适应有关。藏马在线粒体基因进化上所表现出的与其它高原世居 动物的不同究竟是由于动物在适应高原的不同阶段其遗传基础和策略的不同所 造成的，还是由于物种间的差异所造成的我们尚不能确定。还需要进一步对高 原动物线粒体基因进行研究。此外，我们对藏马进化史的研究表明藏马可能为 多地区起源

Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates

Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemosensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantly with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolutionary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among primates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

Radiation effects on the immiscible polymer blend of nylon1010 and high-impact polystyrene (HIPS) I: Gel/dose curves, mathematical expectation theorem and thermal behaviour

This paper studies the radiation properties of the immiscible blend of nylon1010 and HIPS. The gel fraction increased with increasing radiation dose. The network was found mostly in nylon1010, the networks were also found in both nylon1010 and HIPS when the dose reaches 0.85 MGy or more. We used the Charleby-Pinner equation and the modified Zhang-Sun-Qian equation to simulate the relationship with the dose and the sol fraction. The latter equation fits well with these polymer blends and the relationship used by it showed better linearity than the one by the Charleby-Pinner equation. We also studied the conditions of formation of the network by the mathematical expectation theorem for the binary system. Thermal properties of polymer blend were observed by DSC curves. The crystallization temperature decreases with increasing dose because the cross-linking reaction inhibited the crystallization procession and destroyed the crystals. The melting temperature also reduced with increasing radiation dose. The dual melting peak gradually shifted to single peak and the high melting peak disappeared at high radiation dose. However, the radiation-induced crystallization was observed by the heat of fusion increasing at low radiation dose. On the other hand, the crystal will be damaged by radiation. A similar conclusion may be drawn by the DSC traces when the polymer blends were crystallized. When the radiation dose increases, the heat of fusion reduces dramatically and so does the heat of crystallization. (C) 1999 Elsevier Science Ltd. All rights reserved.

The immune responses in Chinese mitten crab Eriocheir sinensis challenged with double-stranded RNA

Double-stranded RNA (dsRNA) is a virus-associated molecular pattern which induces antiviral innate immune responses and RNA interference (RNAi) in mammals. In invertebrates, RNAi phenomenon has been widely studied, but dsRNA-induced innate immune response is seldom reported. In the present study, two different dsRNAs specific for green fluorescent protein (GFP) and the putative D1 protein of photosystem II (NoPSD) from Nannochloropsis oculata, were employed to challenge Chinese mitten crab Eriocheir sinensis. The temporal changes of phenoloxidase (PO), acid phosphatase (ACP), superoxide dismutase (SOD) and malondialdehyde (MDA) content, as well as the mRNA expression of some immune-related genes were examined in order to estimate the effect of dsRNAs on the innate immunity of E. sinensis. The activities of PO, ACP and SOD significantly increased after dsRNA treatment, whereas malondialdehyde (MDA) content did not change significantly. Among the examined genes, only the mRNA expression of EsALF, an antibacterial peptide in E. sinensis, was significantly up-regulated (about 5 fold, P < 0.05) at 12 h after dsRNA treatment, while no significant expression changes were observed among the other immune genes. The increase of PO, ACP and SOD activities, and mRNA expression level of EsALF after dsRNA stimulation indicate that phenoloxidase, hydrolytic enzyme, antioxidation and EsALF were involved in dsRNA-induced innate immunity, suggesting that broad-spectrum immune responses could be induced by dsRNA in E. sinensis. (C) 2009 Elsevier Ltd. All rights reserved.

Characterization of an ETS transcription factor in the sea scallop Chlamys farreri

We have cloned and characterized a cDNA encoding a putative ETS transcription factor, designated Cf-ets. The Cf-ets encodes a 406 amino acid protein containing a conserved ETS domain and a Pointed domain. Phylogenetic analysis revealed that Cf-ets belongs to the ESE group of ETS transcription factor family. Real-time PCR analysis of Cf-ets expression in adult sea scallop tissues revealed that Cf-ets was expressed mainly in gill and hemocytes, in a constitutive manner. Cf-ets mRNA level in hemocytes increased drastically after microbial challenge indicated its indispensable role in the anti-infection process. Simultaneously, the circulating hemocyte number decreased. In mammals, most ETS transcription factors play indispensable roles in blood cell differentiation and linage commitment during hematopoisis. Cf-ets is therefore likely to be a potential biomarker for hematopoiesis studies in scallops. (C) 2009 Elsevier Ltd. All rights reserved.

Identification of an Atlantic salmon IFN multigene cluster encoding three IFN subtypes with very different expression properties

A cluster of 11 interferon (IFN) genes were identified in the Atlantic salmon genome linked to the growth hormone I gene. The genes encode three different IFN subtypes; IFNa (two genes), IFNb (four genes) and IFNc (five genes), which show 22-32% amino acid sequence identity. Expression of the fish IFNs were studied in head kidney, leukocytes or To cells after stimulation with the dsRNA poly I:C or the imidazoquinoline S-27609. In mammals, poly I:C induces IFN-beta through the RIG-I/MDA5 or the TLR3 pathway, both of which are dependent on NF-kappa B. In contrast, S-27609 induces mammalian IFN-alpha in plasmacytoid dendritic cells through the TLR7 pathway independent of NF-kappa B. The presence of an NF-kappa B site in their promoters and their strong up-regulation by poly I:C, suggest that salmon IFNa1/IFNa2 are induced through similar pathways as IFN-beta. In contrast, the apparent lack of NF-kappa B motif in the promoter and the strong upregulation by S-27609 in head kidney and leukocytes, suggest that IFNb genes are induced through a pathway similar to mammalian IFN-alpha. IFNc genes showed expression patterns different from both IFNa and IFNb. Taken together, salmon IFNa and IFNb are not orthologs of mammalian IFN-beta and IFN-alpha, respectively, but appear to utilize similar induction pathways. (C) 2008 Elsevier Ltd. All rights reserved.

VEGF gene silencing by cytomegalovirus promoter driven ShRNA expression vector results in vascular development defects in zebrafish

Zebrafish has been generally considered as an excellent model in case of drug screening, disease model establishment, and vertebrate embryonic development study. In this work, the ability of human cytomegalovirus immediate early promoter (CMV promoter)-driven short hairpin RNA (shRNA) expression vector to induce shRNA against VEGF gene in zebrafish was tested, and its effect on vascular development was assed, too. Using RT-qPCR, blood vessel staining, and in situ hybridization, we confirmed certain transcriptional activity and down regulation of gene expression by the vector. In situ hybridization analysis indicated selective inhibition of NRP1 expression in the VEGF gene loss of function model, which might imply in turn that VEGF could not only activate endothelial cells directly but also could contribute to stimulating angiogenesis in vivo by a mechanism that involved up-regulation of its cognate receptor expression in zebrafish. This contributed to a better understanding of molecular mechanisms of cardiovascular development. The system improved the success rate in making inducible knockdown and widened the possibilities for better therapeutic targets in zebrafish.

The cDNA cloning and mRNA expression of cytoplasmic Cu, Zn superoxide dismutase (SOD) gene in scallop Chlamys farreri

Cu, Zn superoxide dismutases (SODs) are rnetalloenzymes that represent one important line of defence against reactive oxygen species (ROS). A cytoplasmic Cu. Zn SOD cDNA sequence was cloned from scallop Chlamys farreri by the homology-based cloning technique. The full-length cDNA of scallop cytoplasmic Cu, Zn SOD (designated CfSOD) was 1022 bp with a 459 bp open reading frame encoding a polypeptide of 153 amino acids. The predicted amino acid sequence of CfSOD shared high identity with cytoplasmic Cu. Zn SOD in molluscs, insects, mammals and other animals, such as cytoplasmic Cu, Zn SOD in oyster Crassostrea sostrea gigas (CAD42722), mosquito Aedes aegypti (ABF18094), and cow Bos taurus (XP_584414). A quantitative reverse transcriptase real-time PCR (qRT-PCR) assay was developed to assess the mRNA expression of CfSOD in different tissues and the temporal expression of CfSOD in scallop challenged with Listonella anguillarum, Micrococcus luteus and Candida lipolytica respectively. Higher-level mRNA expression of CfSOD was detected in the tissues of haemocytes, gill filaments and kidney. The expression of CfSOD dropped in the first 8-16 h and then recovered after challenge with L. anguillarum and M. litteus, but no change was induced by the C. lipolytica challenge. The results indicated that CfSOD was a constitutive and inducible acute-phase protein, and could play an important role in the immune responses against L. anguillarum and M. luteus infection. (C) 2007 Elsevier Ltd. All rights reserved.

Characterization of amphioxus GDF8/11 gene, an archetype of vertebrate MSTN and GDF11

MSTN, also known as growth and differentiation factor 8 (GDF8), and GDF11 are members of the transforming growth factor-beta (TGF-beta) subfamily. They have been thought to be derived from one ancestral gene. In the present study, we report the isolation and characterization of an invertebrate GDF8/11 homolog from the amphioxus (Branchiostoma belcheri tsingtauense). The amphioxus GDF8/11 gene consists of five exons flanked by four introns, which have two more exons and introns than that of other species. In intron III, a possible transposable element was identified. This suggested that this intron might be derived from transposon. The amphioxus GDF8/11 cDNA encodes a polypeptide of 419 amino acid residues. Phologenetic analysis shows that the GDF8/11 is at the base of vertebrate MSTNs and GDF11s. This result might prove that the GDF8/11 derived from one ancestral gene and the amphioxus GDF8/11 may be the common ancestral gene, and also the gene duplication event generating MSTN and GDF11 occurred before the divergence of vertebrates and after or at the divergence of amphioxus from vertebrates. Reverse transcriptase polymerase chain reaction results showed that the GDF8/11 gene was expressed in new fertilized cell, early gastrulation, and knife-shaped embryo, which was different from that in mammals. It suggested that the GDF8/11 gene might possess additional functions other than regulating muscle growth in amphioxus.

Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. They are endowed with important physiological functions but until now only few of them have been studied. Here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. Sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxification, in sulfide-dependent respiration and photosynthesis, and in heavy metal tolerance. It may also play a crucial role in mammals, including humans, because sulfide acts as a neurotransmitter in these organisms. We isolated and purified sulfide:quinone oxidoreductase from the native membranes of the hyperthermophilic bacterium Aquifex aeolicus. We studied the pure and solubilized enzyme by denaturing and non-denaturing polyacrylamide electrophoresis, size-exclusion chromatography, cross-linking, analytical ultracentrifugation, visible and ultraviolet spectroscopy, mass spectrometry and electron microscopy. Additionally, we report the characterization of its enzymatic activity before and after crystallization. Finally, we discuss the crystallization of sulfide:quinone oxidoreductase in respect to its membrane topology and we propose a classification of monotopic membrane protein crystal lattices. Our data support and complement an earlier description of the three-dimensional structure of A. aeolicus sulfide:quinone oxidoreductase (M. Marcia, U. Ermler, G. Peng, H. Michel, Proc Natl Acad Sci USA, 106 (2009) 9625-9630) and may serve as a reference for further studies on monotopic membrane proteins. (C) 2010 Elsevier B.V. All rights reserved.

Paleoceanographic records in the sedimentary cores from the middle Okinawa Trough

Two gravity piston cores (Cores 155 and 18) involved in this study were collected from the middle Okinawa Trough. Stratigraphy of the two cores was divided and classified based on the features of planktonic foraminifera oxygen isotope changes together with depositional sequence, millennium-scale climatic event comparison, carbonate cycles and AMS(14)C dating. Some paleoclimatic information contained in sediments of these cores was extracted to discuss the paleoclimatic change rules and the short-time scale events presented in interglacial period. Analysis on the variation of oxygen isotope values in stage two shows that the middle part of the Okinawa Trough may have been affected by fresh water from the Yellow River and the Yangtze River during the Last Glacial Maximum (LGM). The oxygen isotope value oscillating ranges of the cores have verified that the marginal sea has an amplifying effect on climate changes. The delta(13)C of benthic foraminifera Uvigerina was lighter in the glacial period than that in the interglacial period, which indicates that the Paleo-Kuroshio's main stream moved eastward and its influence area decreased. According to the temperature difference during the "YD" period existing in Core 180 and other data, we can reach the conclusion that the climatic changes in the middle Okinawa Trough area were controlled by global climatic changes, but some regional factors had also considerable influence on the climate changes. Some results in this paper support Fairbanks's point that the "YD" event was a brief stagnation of sea level rising during the global warming up procession. Moreover, the falling of sea level in the glacial period weakened the exchange between the bottom water of the Okinawa Trough and the deep water of the northwestern Pacific Ocean and resulted in low oxygen state of bottom water in this area. These procedures are the reasons for carbonate cycle in the Okinawa Trough area being consistent with the "Atlantic type" carbonate cycle.