Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.     

华癸中慢生根瘤菌7653R 3个脂质转运蛋白基因的克隆、突变及共生表型北大核心CSCD

【目的】脂类转移家族蛋白基因编码一类参与脂类转运及代谢的蛋白。本研究旨在构建华癸中慢生根瘤菌3个脂质转运家族蛋白基因的突变株,检测及分析突变体与紫云英共生条件下的表型及功能。【方法】利用生物信息学分析与预测转脂蛋白的结构特征及功能,采用荧光定量技术检测目标基因在自生和共生条件下的表达特性,通过插入突变技术构建目标基因突变株,并进行植物盆栽实验考察其共生表型。【结果】MCHK-5577、MCHK-2172和MCHK-2779基因编码蛋白属于START/RHO alpha_C/PITP/Bet_v1/Cox G/Cal C(SRPBCC)超家族,包含脂类转移结构域,参与脂类转运或代谢,与百脉根等中慢生根瘤菌相应基因的序列相似性达95%以上。这3个基因在共生条件下的表达水平都增高。分别构建了MCHK-5577、MCHK-2172和MCHK-2779基因突变菌株,与野生型菌株7653R相比,接种突变株MCHK-2172mut、MCHK-2779mut和MCHK-5577mut后的植株地上部分生物量和根瘤固氮酶活性显著降低。【结论】华癸中慢生根瘤菌脂质转移家族蛋白基因在共生互作过程中发挥重要作用,突变后明显影响共生固氮表型。本文的实验结果为深入研究脂类转移蛋白在共生固氮作用中的功能机制奠定了基础。     

丹霞地貌沟谷生态效应

以广东省丹霞山为研究实例,探讨丹霞地貌特殊的沟谷生态效应.结果表明,丹霞地貌的特殊沟谷生态效应体现在以下两个方面:第一是丹霞地貌演变过程中形成了众多石峰隆起和沟谷凹陷,特殊的地貌环境使得沟谷中的生态因子与其它非丹霞地貌开阔区域产生差异,小气候相对封闭,水湿条件极好,为喜高温高湿的热带物种提供了较好的生存环境;沟谷所处位置的地理环境,如四周崖壁的光滑程度会影响到太阳光反射到沟谷的光强,这些都会对沟谷中的温湿度产生影响.第二是丹霞地貌特殊的生态条件,为沟谷地带孕育出一批热带性较强的分类群提供了可能,与相近纬度的诸多植被相比,丹霞地貌植物区系热带性明显增强,热带分布区类型所占比重比同纬度区域要大10%以上,大多数沟谷中热带性物种分布现象比较明显,藤本分布较多,蕨类植物也较丰富,耐水湿的植物区系发育良好;这实际上造成了植物水平分布上的移位,使中亚热带区域中分布有南亚热带甚至热带区域的物种,出现了由于其特殊的沟谷地貌效应而形成的与其地貌条件保持协调和平衡的演替顶级群落类型,称为地貌顶级群落.     

果蝇程序化死亡基因5(PDCD5)同源cDNA的克隆和序列分析

 为了解人类白血病细胞凋亡相关新基因 TFAR1 9(PDCD5,programmed cell death5)在不同种属间的序列同源性 ,利用 EST(expression sequence tag)拼接、RT- PCR、DNA序列测定技术及计算机分析技术 ,首次成功地进行了果蝇 PDCD5同源 c DNA编码区基因克隆和序列分析 .发现果蝇与小鼠及果蝇与人 PDCD5在核苷酸水平上分别有 57.5%和 57.1 %的同源性 ,在氨基酸水平上分别有 46.8%和 46.4%的同源性 .功能区分析发现 ,果蝇 PDCD5c DNA编码 1 33个氨基酸 ,计算机预测可能是一种核蛋白 ,含 5个可能的酪蛋白激酶 (casein kinase )磷酸化位点 ,2个可能的 PKC磷酸化位点 ,与人 PDCD5的功能区类似 .因而果蝇 PDCD5是与人 PDCD5同源的新基因 ,可能都与细胞程序化死亡相关 .     

伯乐树种子不同条件贮藏下前后生理比较

对3个不同地区（浙江省遂昌县、福建省浦城县和浙江江山市）的伯乐树种子形态指标进行了测定。并分别设置3种贮藏方式（A为室内湿沙环境下贮藏;B为低温（4℃）湿沙下贮藏;C为低温（4℃）封口袋中贮藏）,对贮藏前后种子的发芽率、发芽势、含水量等生理指标进行了比较研究。结果表明,浦城县地区较另外二个地区的种子狭长而扁平,且质量较小。经130d的贮藏后,3个地区的种子内淀粉含量显著下降（P〈0．05）,含水量、蛋白酶活性、淀粉酶活性、蛋白含量和可溶性糖含量则均显著升高（P〈0．05）,从而使休眠得以解除。贮藏后的发芽率和发芽势显著提高（P〈0．05）,以湿沙低温下的发芽率和发芽势为最高。     

The altered activity of complex III may contribute to the high penetrance of Leber's hereditary optic neuropathy in a Chinese family carrying the ND4 G11778A mutation

The ND4 G11778A mutation is the most common mitochondrial DNA mutation leading to Leber's hereditary optic neuropathy (LHON). Despite considerable clinical evidences, the modifier role of nuclear background and mitochondrial haplotypes in phenotypic manifestation of LHON remains poorly understood. We investigated the effect of these modifiers on bioenergetics in lymphoblastoid cell lines derived from five affected subjects of one Chinese family carrying the G11778A mutation and five Chinese controls. Significant reductions in the activities of complexes I and III were observed in mutant cell lines from the Chinese family, whereas the mutant cell lines from other families carrying the same mutation exhibited only reduced activity of complex I. The reduced activities of complexes I and III caused remarkably higher reductions of ATP synthesis in mutant cell lines from the Chinese family than those from other families. The deficient respiration increased generation of reactive oxygen species. The defect in complex III activity, likely resulting from the mitochondrial haplotype or nuclear gene alteration, worsens mitochondrial dysfunction caused by the G11778A mutation, thereby causing extremely high penetrance and expressivity of optic neuropathy in this Chinese family. Our data provide the first experimental evidence that altered activity of complex III modulates the phenotypic manifestation of LHON-associated G11778A mutation. Thus, our findings may provide new insights into the pathophysiology of LHON.     

The effects of Bacillus thuringiensis Cry6A on the survival, growth, reproduction, locomotion, and behavioral response of Caenorhabditis elegans

Several families of crystal proteins from Bacillus thuringiensis exhibit nematicidal activity. Cry5B protein, a pore-forming toxin, has been intensively studied yielding many insights into the mode of action of crystal protein at molecular level and pathogenesis of pore-forming toxins. However, little attention was paid to Cry6A, another representative nematicidal crystal protein. Cry6A shares very low homology with Cry5B at amino acid sequence and probably acts in a distinct pathway from Cry5B and even the other main commercial crystal proteins. In the current study, we comprehensively investigated the nematicidal properties of Cry6Aa2 against the free-living soil nematode Caenorhabditis elegans and examined the physical response of C. elegans to Cry6Aa2 attack. Our results indicate that Cry6Aa2 exhibits high lethal activity to C. elegans and could cause detrimental effects on C. elegans, including obviously suppressed growth, decreased brood size, and even abnormal motility. Meanwhile, our study additionally shows that C. elegans could defend against the Cry6Aa2 toxin harmful threat through behavioral defense responses, such as reduced oral uptake and physical avoidance. In general, this study suggests that Cry6Aa2 possesses diverse nematicidal properties, which strongly indicates that Cry6Aa2 is a promising potential candidate of nematicidal agent. Moreover, this study highlights the importance of behavioral responses in defense of C. elegans for survival and demonstrates the key role of crystal protein in the interaction of B. thuringiensis–C. elegans. These findings could shed light on understanding the interaction of C. elegans with B. thuringiensis and provide a perfect model to study the role of pathogenic factor in the interaction of pathogen–host.     

社会竞争失败病因学的抑郁症树鼩模型

抑郁症是一种常见精神疾病,主要表现为持续两周以上的情绪低落。世界卫生组织预测在2030年抑郁症的疾病负担将高居所有疾病、伤残总负担的榜首。抑郁症面临三大难题:1)发病机理不完全清楚,因而缺乏有效的预测预防途径和生物学诊断;2)现有单胺类抗抑郁症药物起效慢,也可能导致患者自杀风险增加;3)缺乏副作用小的非单胺类快速起效抗抑郁症药物。针对这三大难题,长期以来,应用抑郁症啮齿类模型的众多研究并未取得实质性进展,至少部分因素归咎于啮齿类与人类大脑功能的极大种属差异。树鼩是灵长类近亲,具有更接近于人类的大脑功能。本文针对抑郁症发病机理假说、临床表象和抗抑郁症药物疗效等内容,综述了社会竞争失败病因学的抑郁症树鼩模型可能会具有更好的疾病同源性、表象一致性和药物预见性。这一被长期忽视的抑郁症树鼩模型尽管还需要进一步完善,但对其进一步深入研究可能为解决抑郁症的三大难题提供了一条新途径。     

重庆市爬行动物物种多样性研究及保护

1996～2004年对重庆市35个县(区、市)进行野外调查采集,结合有关资料记载,重庆市共有爬行动物2目12科38属58种,其中龟鳖目4种,有鳞目蜥蜴亚目12种、蛇亚目42种(含重庆市蛇类新记录3属4种)。建议加强对该市爬行动物物种多样性及其生境的保护,合理利用爬行动物资源。