徐闻西岸造礁石珊瑚的组成及空间分布

2008年5-6月在徐闻西岸设置了25个站点,运用截线样带法调查了造礁石珊瑚的种类多样性和空间分布.本次研究共发现造礁石珊瑚57种,每个站位的种类数均不超过30种.Shannon-Wiener多样性指数和Pielou均匀度指数均值分别为1.79和0.42.二异角孔珊瑚(Goniopora duofasciata)、盾形...     

过氧化氢驱动的细胞色素P450酶研究进展

细胞色素P450酶在自然界中广泛存在,能催化多种类型的氧化反应,在有机合成和生物化工方面具有重要的应用潜力。尽管大多数P450酶通常需要辅酶和复杂的电子传递体系协助活化氧分子,一些P450酶也可以利用过氧化氢作为末端氧化剂,这极大地简化了催化循环,为P450酶的合成应用提供了一条新的简便途径。本文系统地介绍了几类过氧化氢驱动的P450酶催化体系,包括脂肪酸羟化酶P450SPα和P450BSβ、脂肪酸脱羧酶P450OleTJE、人工改造的羟化酶P450BM3和P450cam突变体、以及基于底物误识别策略的P450-H2O2体系。通过分析催化反应机制,本文探讨了P450-H2O2催化体系在目前存在的挑战和可能的解决途径,并对其进一步应用前景进行了展望。     

Expression and Assembly Mechanism of the Capsid Proteins of a Satellite Virus （XSV） Associated with Macrobrachium rosenbergii Nodavirus

The extra small virus （XSV） is a satellite virus associated with Macrobrachium rosenbergii nodavirus （MrNV） and its genome consists of two overlapping ORFs, CP17 and CP16. Here we demonstrate that CP16 is expressed from the second AUG of the CP17 gene and is not a proteinase cleavage result of CP17. We further expressed CP17 and several truncated CP17s （in which the N-or C-terminus or both was deleted）, respectively, in Escherichia coli. Except for the recombinant plasmid CP17^AC10, all recombinant plasmids expressed soluble protein which assembled into virus-like particles （VLPs）, suggesting that the C-terminus is important for VLP formation.     

How Do Variable Substitution Rates Influence Ka and Ks Calculations？

The ratio of nonsynonymous substitution rate (Ka) to synonymous substitution rate (Ks) is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new γ-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and ...     

Dancing to the rhythms of geological time: the biorhythm capabilities of Polychaeta in a geological context

Summary

Errant polychaete worms in the Orders Eunicida (family Eunicidae) and Phyllodocida (families Nereidae and Polynoidae) exhibit a highly developed biorhythmic capability. The Pacific palolo worms are well known for a precisely timed annual breeding event in which mass spawning occurs at a particular time of day, on one day per year, that day having a fixed relationship to the lunar period. Nereidae and Polynoidae exhibit photoperiodic responses that determine the breeding season by regulation of oocyte growth. Nereis virens shows short-term cycles of foraging activity; automated recording of these patterns has revealed four distinct behaviour rhythm phenotypes: circadian, tidal, lunidian and arrhythmic, the last phenotype being expressed during the photoperiod induced growth diapause. The Eunicids and Phyllodocids are represented in the fossil record by scolecodonts, their fossilised jaws. There was a major radiation of these polychaetes during the Ordovician and the earliest suggested polychaete fossils are from the Cambrian. The simultaneous expression of tidal and circadian rhythmicity is characteristic of intertidal animals and it is likely that this complex behavioural repertoire was found in the ancestors of modern terrestrial forms, such as tetrapods and arthropods, prior to their emergence onto land during the Carboniferous and Silurian periods at least 400 Ma. The period of the earth's rotation, and hence day length and tidal period, has long been known to be increasing, and additionally the moon to be retreating from the earth, due to the phenomenon of tidal friction caused by the gravitational interactions between the moon and the earth. These changes are significant over a geological time scale. Consequently, the length of day was substantially less (and the number of days in a year more) than at present in the Cambrian and Ordovician periods. Recent theoretical analysis of the period of the earth's rotation suggests that the day length prior to a critical period (t _crit ) around 1800 Ma may have been stable, with a length of only 4 h. At that time a period of more rapid change in the dynamics of the rotation was initiated. The implications of this theory for the evolution of the biological clock are discussed.     

沙漠化对沙地土壤呼吸的影响及其对环境变化的响应

为了了解沙漠化过程中土壤呼吸速率变化及其对环境因素变化的响应,于2005年在科尔沁沙地研究了固定、半固定和流动沙地的土壤呼吸日变化和生长季动态及其与环境变化的关系,得出以下结论:(1)3种沙地土壤呼吸日变化在春季和秋季呈单峰曲线,夏季呈多峰曲线;(2)3种沙地土壤呼吸速率从春季到秋季的季节动态均呈双峰曲线,峰值分别出现在6月下旬和8月下旬;(3)固定和半固定沙地的土壤呼吸的日变化幅度明显大于流动沙地,季节变化幅度也是固定沙地半固定沙地流动沙地;(4)随着沙漠化的发展,土壤呼吸平均速率明显下降,生长季平均土壤呼吸速率从固定沙地的2.32μmolCO2/(m·2s)降为半固定的1.65μmolCO2/(m·2s)和流动沙地的1.06μmolCO2/(m·2s);(5)3种沙地土壤呼吸速率日变化均与土壤温度呈正相关,与空气湿度呈负相关,在季节尺度上3种沙地土壤呼吸速率与土壤温度、土壤水分和大气湿度均呈正相关,但只有固定沙地的相关性达到了显著水平;(6)沙漠化过程中,虽然土壤温度、土壤有机碳含量和植物根系碳含量都是导致沙地土壤呼吸发生改变的重要因子,但制约其变化的关键因子还是土壤水分和空气湿度。     

The Pendulum Model for Genome Compositional Dynamics:from the Four Nucleotides to the Twenty Amino Acids

The genetic code serves as one of the natural links for life’s two conceptual frameworks-the informational and operational tracks- bridging the nucleotide sequence of DNA and RNA to the amino acid sequence of protein and thus its structure and function.On the informational track,DNA and its four building blocks have four basic variables:order,length,GC and purine contents;the latter two exhibit unique characteristics in prokaryotic genomes where protein-coding sequences dominate.Bridging the two tracks,tRNAs and their aminoacyl tRNA synthases that interpret each codon-nucleotide triplet,together with ribosomes,form a complex machinery that translates genetic information encoded on the messenger RNAs into proteins.On the operational track,proteins are selected in a context of cellular and organismal functions constantly.The principle of such a functional selection is to minimize the damage caused by sequence alteration in a seemingly random fashion at the nucleotide level and its function-altering consequence at the protein level;the principle also suggests that there must be complex yet sophisticated mechanisms to protect molecular interactions and cellular processes for cells and organisms from the damage in addition to both immediate or short-term eliminations and long-term selections.The twocentury study of selection at species and population levels has been leading a way to understand rules of inheritance and evolution at molecular levels along the informational track,while ribogenomics,epigenomics and other operationally-defined omics(such as the metabolite-centric metabolomics) have been ushering biologists into the new millennium along the operational track.     

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition

Although strand-biased gene distribution(SGD) was described some two decades ago,the underlying molecular mechanisms and their relationship remain elusive.Its facets include,but are not limited to,the degree of biases,the strand-preference of genes,and the influence of background nucleotide composition variations.Using a dataset composed of 364 non-redundant bacterial genomes,we sought to illustrate our current understanding of SGD.First,when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy,the SGD of the polC group stood out more significantly than that of the non-polC group.Second,when examining horizontal gene transfer,coupled with gene functional conservation(essentiality) and expressivity(level of expression),we realized that they all contributed to SGD.Third,we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance(both G and A) on the leading strand of the polC group.We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands,and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.     

介形类系统分类与起源演化的形态、分子和化石证据

介形类(Ostracoda)因其丰富的化石记录和广布的海陆现生代表类群,而被认为是进化生物学中研究生物多样性产生机制和演变历程的颇具潜力的重要模式生物。介形类在甲壳亚门中的谱系发生位置、起源及其内部各类群间的系统关系还存在诸多争议。基于其体制构造的形态学特征,介形类被归入甲壳亚门下的颚足纲(Maxillopoda),但来自18S rDNA序列数据分析却显示Maxillopoda不是单系群。基于化石记录和壳体形态特征,高肌虫(Bradoriida)长期以来被认为是介形类的一个祖先类群,但保存有软躯体的早寒武世化石的研究表明,Bradoriida不是介形类甚至可能也不属于甲壳类。不同的研究者所强调的壳体和肢体形态特征各异,导致介形类最大的现生类群速足目(Podocopida)的四个超科之间的关系也存在诸多推测。壳体和肢体特征在系统演化意义上的不兼容,需要分子生物学等证据的介入。分子、形态和化石证据的积累及各种信息整合是系统演化研究的必然趋势。     

禾本科针茅族(Stipeae)7种花粉形态比较研究

利用光学显微镜(LM)和扫描电子显微镜(SEM)观察了针茅族7种花粉形态.观察显示,花粉形态均为近球形,具远极单孔,并有萌发孔盖(Operculum).LM观察到花粉外壁纹饰具粗细不一的颗粒状结构,SEM则可辨不同种类的颗粒或瘤状结构的大小及其形成图案的差异,其中芨芨草属(Achnatherum)花粉外壁纹饰的种间差异...