Classification of jinjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis

The jinjiang oyster Crassostrea rivularis [Gould, 1861. Descriptions of Shells collected in the North Pacific Exploring Expedition under Captains Ringgold and Rodgers. Proc. Boston Soc. Nat. Hist. 8 (April) 33-40] is one of the most important and best-known oysters in China. Based on the color of its flesh, two forms of C rivularis are recognized and referred to as the "white meat" and 11 red meat" oysters. The classification of white and red forms of this species has been a subject of confusion and debate in China. To clarify the taxonomic status of the two forms of C. rivularis, we collected and analyzed oysters from five locations along China's coast using both morphological characters and DNA sequences from mitochondrial 16S rRNA and cytochrome oxidase 1, and the nuclear 28S rRNA genes. Oysters were classified as white or red forms according to their morphological characteristics and then subjected to DNA sequencing. Both morphological and DNA sequence data suggest that the red and white oysters are two separate species. Phylogenetic analysis of DNA sequences obtained in this study and existing sequences of reference species show that the red oyster is the same species as C. ariakensis Wakiya [1929. Japanese food oysters. Jpn. J. Zool. 2, 359-367.], albeit the red oysters from north and south China are genetically distinctive. The white oyster is the same species as a newly described species from Hong Kong, C. hongkongensis Lam and Morton [2003. Mitochondrial DNA and identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aqua. 228, 1-13]. Although the name C. rivularis has seniority over C. ariakensis and C. hongkongensis, the original description of Ostrea rivularis by Gould [1861] does not fit shell characteristics of either the red or the white oysters. We propose that the name of C. rivularis Gould [1861] should be suspended, the red oyster should take the name C. ariakensis, and the white oyster should take the name C. hongkongensis. (C) 2004 Elsevier B.V. All rights reserved.

Sequence of mitochondrial DNA cytochrome oxidase II in Cryptopygus nanjiensis and phylogeny of apterygota

The mitochondrial cytochrome oxidase II (Co II) from four different apterygotens Cryptopygus nanjiensis (Collembola), Neanura latior (Collembola), Gracilentulus maijiawensis (Protura) and Lepidocampa weberi (Diplura) were sequenced. Their A+T content, number of nucleotide substitutions, TV/TV ratio; and Tamura-Nei's distance were calculated. A series of phylogenetic trees were constructed by parsimony and distance methods using a crustacean Artemia franciscana as outgroup, Finally the evolutionary trend A+T content of CO II genetic divergence and phylogenetic relationship of apterygotan groups were discussed.

Mitochondrial Cytochrome b Sequence Variations and Population Structure of Siberian Chipmunk (Tamias sibiricus) in Northeastern Asia and Population Substructure in South Korea

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we

Classification of common oysters from North China

Oysters are commonly found on rocky shores along China's northern coast, although there is considerable confusion as to what species they are. To determine the taxonomic status of these oysters, we collected specimens from nine locations north of the Yangtze River and conducted genetic identification using DNA sequences. Fragments from three genes, mitochondrial 165 rRNA, mitochondria! cytochrome oxidase I (COI), and nuclear 285 rRNA, were sequenced in six oysters from each of the nine sites. Phylogenetic analysis of all three gene fragments clearly demonstrated that the small oysters commonly found on intertidal rocks in north China are Crassostrea gigas (Thunberg, 1793), not C. plicatula (the zhe oyster) as widely assumed. Their small size and irregular shell characteristics are reflections of the stressful intertidal environment they live in and not reliable characters for classification. Our study confirms that the oysters from Weifang, referred to as Jinjiang oysters or C. rivularis (Gould, 1861), are C. ariakensis (Wakiya, 1929). We found no evidence for the existence of C. talienwhanensis (Crosse, 1862) and other Crassostrea species in north China. Our study highlights the need for reclassifying oysters of China with molecular data.

Identification of Crassostrea ariakensis and related oysters by multiplex species-specific PCR

Genetic markers are needed for rapid and reliable identification of oysters. In this study, we developed multiplex genus- and species-specific PCR markers for the identification of oysters from China. We used the mitochondrial cytochrome oxidase I (COI) and nuclear 28S ribosomal RNA genes for marker development. DNA sequences from different species were obtained from GenBank or by direct sequencing. Sequences were aligned, and genus- and species-specific nucleotides were identified. Primers were designed for genus/species-specific amplification to generate fragments of different sizes. A multiplex set of genus- and species-specific primers from the 28S gene was able to separate C. ariakensis and C. hongkongensis from other species and assign oysters to four genera. A set of species-specific COI primers provided positive identification of all five Crassostrea species from China, C. ariakensis, C. hongkongensis, C. angulata, C. gigas, and C. sikamea in a single PCR. The multiplex PCR assays do not require fluorescence-labeling or post-PCR enzyme digestion, providing a simple, fast and reliable method for the identification of oysters from China.

Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japon

A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda : Penaeidae) based on mitochondrial dna sequences of selected species from the Indo-West Pacific

Phylogenetic relationships within Metapenaeopsis remain largely unknown. The modern revision of the genus suggests that the shape of the petasma, followed by the presence of a stidulating organ, are the most important distinguishing taxonomic features. In the present study, phylogenetic relationships were studied among seven Metapenaeopsis species from the Indo-West Pacific based on partial sequences of mitochondrial 16S rRNA and cytochrome c oxidase I (COI) genes. Mean sequence divergence was 6.4% for 16S and 15.8% for COI. A strikingly large nucleotide distance (10.0% for 16S and 16.9% for COI) was recorded between M. commensalis, the only Indo-West Pacific species with a one-valved petasma, and the other species with a two-valved petasma. Phylogenetic analyses using neighbor-joining, maximum parsimony, and maximum likelihood generated mostly identical tree topologies in which M. commensalis is distantly related to the other species. Two clades were resolved for the remaining species, one with and the other without a stridulating organ, supporting the main groupings of the recent taxonomic revision. Results of the present study also indicate that the deep-water forms represent a relatively recent radiation in Metapenaeopsis.

Structural determinants of steroids for cytochrome P450 3A4-mediated metabolism

Cytochrome P450 3A4 (CYP3A4), a major member of cytochrome P450 isoenzymes, metabolizes the majority of steroids in 6beta-position. For the purpose of determining requisite structural features of a series of structurally related steroids for CYP3A4-mediated metabolism, three-dimensional pharmacophore modeling as well as electrotopological state map were conducted for 15 steroids. Though prior studies speculated that the chemical reactivity of the allylic 6beta-position might have a greater influence on CYP3A4 selective 6-hydroxylation than steric constraints in the enzyme, our results reveal that for CYP3A4 steroidal substrates, it is not the chemical reactivity of atoms at 6beta-site, but the pharmacophoric features, i.e. the two hydrophobic rings together with two H-bond donors, that act as the key factors responsible for detemining the CYP3A4 selective 6-hydroxylation of steroids. (C) 2004 Elsevier B.V. All rights reserved.

MITOCHONDRIAL-DNA POLYMORPHISM IN NATURAL-POPULATIONS OF DROSOPHILA-ALBOMICANS(I)

The technique of mtDNA restriction fragments length polymorphism (RFLP) was used to survey the population structure of D. albomicans. Remarkable mtDNA polymorphism has been observed in D. albomicans populations. A total of 34 nucleomorphs were detected from 82 isofemale lines assayed by only 8 restriction enzymes. The cause and the effect of this phenomenon were discussed. As a result, it is suggested that a mechanism which maintains mtDNA diversity exists in this fly, and that the high intra-populational polymorphism could numerically conceal the extent of differentiation between populations. In addition, on the base of restriction maps, it was found that the mtDNA molecule of D. albomicans might be impacted by the selection pressure during its evolution process both on the nucleotide composition and on the functional regions.

Design and Fabrication of AlGaN-Based Resonant-Cavity-Enhanced p-i-n UV PDs

AlGaN-based resonant-cavity-enhanced (RCE) p-i-n photodetectors (PDs) for operating at the wavelength of 330 nm were designed and fabricated. A 20.5-pair AlN/Al0.3Ga0.7N distributed Bragg reflector (DBR) was used as the back mirror and a 3-pair AlN/Al0.3Ga0.7N DBR as the front one. In the cavity is a p-GaN/i-GaN/n-Al0.3Ga0.7N structure. The optical absorption of the RCE PD structure is at most 59.8% deduced from reflectance measurement. Selectively enhanced by the cavity effect, a response peak of 0.128 A/W at 330 nm with a half-peak breadth of 5.5 nm was obtained under zero bias. The peak wavelength shifted 15 nm with the incident angle of light increasing from 0 degrees to 60 degrees.

Using the ribosomal internal transcribed spacer (ITS) as a complement marker for species identification of red macroalgae

Barcodes based on mitochondrial cytochrome oxidase (mtDNA CO1) sequences are being used for broad taxonomic groups of animals with demonstrated success in species identification and cryptic species discovery, but it has become clear that complementation by a nuclear marker system is necessary, in particular for the barcoding of plants. Here, we propose the nuclear internal transcribed spacer (ITS) as a potentially usable and complementary marker for species identification of red macroalgae, as well as present a primary workflow for species barcoding. Data show that for most red macroalgal genera (except members of the family Delesseriaceae), the size of ITS region ranges from 600 to 1200 bp, and contains enough variation to generate unique identifiers at either the species or genus levels. Consistent with previous studies, we found that the ITS sequence can resolve closely related species with the same fidelity as mtDNA CO1. Significantly, we confirmed that length polymorphism in the ITS region (including 5.8S rRNA gene) can be utilized as a character to discriminate red macroalgal species. As a complementary marker, the verifiable nuclear ITS region can speed routine identification and the detection of species, advance ecological and taxonomic inquiry, and permit rapid and accurate analysis of red macroalgae.

假根羽藻细胞色素b6f蛋白复合体中α-胡萝卜素的结构与功能

细胞色素b6f蛋白复合体（Cyt b6f）是光合链中连接两个光系统（PSII 和PSI）的中间电子载体蛋白复合物，其主要的生理功能是催化电子传递和质子跨膜转移，形成跨膜质子电化学梯度，为ATP的合成提供能量，在光合作用光能转化过程中占有很重要的地位。细菌和莱茵衣藻Cyt b6f的晶体结构已于2003年底获得了近原子水平的解析，但有关该复合物中两种色素（Chl a和β-Car）的生理功能及其机理尚无明确的解释。预计它们将成为今后几年的研究热点,因为揭示Cyt b6f蛋白复合体中Chl a和β-Car分子的生理功能对于进一步阐明光合作用高效转能及其调控的分子机理具十分重要的意义。鉴于目前尚未见到海洋绿藻Cyt b6f的报道，本文以海洋绿藻—假根羽藻（Bryopsis corticulans）类囊体膜上的Cyt b6f蛋白复合体为对象，对其中的类胡萝卜素的分子结构与生理功能进行了比较系统地研究。 首先，我们改进了原用于菠菜类囊体膜Cyt b6f的分离、纯化流程，在原流程的基础上增加了一次2 mol/L NaBr洗膜，彻底地去除了膜表面的杂蛋白;还调整了第二次硫酸铵分级沉淀时的饱和度，并将38-45%饱和度下的沉淀物确定为需要收集的Cyt b6f制剂。采用此改进的流程，我们首次从假根羽藻类囊体膜中分离纯化了高活性、高纯度的Cyt b6f制剂。SDS-PAGE分析的结果显示该制剂的4个多肽亚基 （Cytf 、Cyt b6 、Rieske[Fe-s]及亚基IV）的表观分子量分别为34.8、24.0、18.7和16.7 kD;Cyt b6 / f 比值接近2.0， 其纯度值为9.9 nmol cyt f/mg;其催化电子传递的活性 （C10-PQH2→PC）为73 e/s。HPLC 和共振拉曼光谱分析表明，假根羽藻Cyt b6f中的类胡萝卜素为α-胡萝卜素分子，它是一种在Cyt b6f中尚未报道过的类胡萝卜素。定量分析表明，每个假根羽藻Cyt b6f单体中全反式(all-trans)和9顺式（9-cis）α-胡萝卜素的含量分别为0.2和0.7个分子，另外还含有1.2分子的Chl a。CD光谱分析表明该9-cis-α-胡萝卜素处在一个不对称的蛋白环境中。TLC分析表明该制剂是一种缺脂的Cyt b6f蛋白复合体。 采用稳态荧光激发光谱，时间分辨吸收光谱及Chl a的光破坏实验对假根羽藻Cyt b6f中α-胡萝卜素的功能进行了研究。结果表明，Cyt b6f中α-胡萝卜素可以将它吸收的光能传递给Chl a，其能量传递效率为62.4%，提出α-胡萝卜素分子与Chl a分子之间的单线态能量传递是遵从Föster 机制进行的;α-胡萝卜素分子对Chl a分子有一定的光保护作用，这种保护作用是通过清除单线态氧来实现的。另外还发现Cyt b6f中的Chl a分子可能与其周围的氨基酸残基存在相互作用，认为这是其进行自我光保护的一种方式。 此外，还采用HPLC研究了光和暗交替对假根羽藻Cyt b6f中α-胡萝卜素构型的影响，并对假根羽藻Cyt b6f选择结合α-胡萝卜素的原因进行了初步的分析。

Genetic variation of fish parasite populations in historically connected habitats: undetected habitat fragmentation effect on populations of the nematode Procamallanus fulvidraconis in the catfish Pelteobagrus fulvidraco

Habitat fragmentation may have some significant effects on population genetic structure because geographic distance and physical barriers may impede gene flow between populations. In this study, we investigated whether recent habitat fragmentation affected genetic structure and diversity of populations of the nematode Procamallanus fulvidraconis in the yellowhead catfish, Pelteobagrus fin't4draco. The nematode was collected from 12 localities in 7 floodplain lakes of the Yangtze River. Using I I intersirnple sequence repeat markers, analysis of molecular variance showed that genetic diversity occurred mainly within populations (70.26%). Expected heterozygosity (He) of P. fulvidraconis was barely different between connected (0.2105) and unconnected lakes (0.2083). Population subdivision (Fst) between connected lakes (0.2177) was higher than in unconnected lakes (0. 1676). However, the connected and unconnected lakes did not Cluster into 2 clades. A Mantel test revealed significant positive correlation between genetic and geographic distances (R = 0.5335, P < 0.01). These results suggest that habitat fragmentation did not cause genetic differentiation among populations or a reduction of diversity in isolated populations of P. fulvidraconis. At least 2 factors may increase the dispersal range of the nematode, i.e., flash flooding in summer and other species of fish that may serve as the definitive hosts. Moreover, lake fragmentation is probably a recent process; population size of the nematode in these lakes is large enough to maintain Population structure.

Preparation and AFM characterization of self-ordered porous alumina films on semi-insulated gaas substrate

Self-ordered porous alumina films on a semi-insulated GaAs substrate were prepared in oxalic acid aqueous solutions by three-step anodization. The I-t curve of anodization process was recorded to observe time effects of anodization. Atomic force microscopy was used to investigate structure and morphology of alumina films. It was revealed that the case of oxalic acid resulted in a self-ordered porous structure, with the pore diameters of 60-70 nm, the pore density of the order of about 10(10) pore cm(-2), and interpore distances of 95-100nm. At the same time the pore size and shape change with the pore widening time. Field-enhanced dissolution model and theory of deformation relaxation combined were brought forward to be the cause of self-ordered pore structure according to I-t curve of anodization and structure characteristics of porous alumina films. (c) 2006 Elsevier Ltd. All rights reserved.