Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes （Teleostei： Cyprinidae） inferred from cytochrome b sequences

We recovered the phylogenetic relationships among 23 species and subspecies of the highly special-ized grade schizothoracine fishes distributing at 36 geographical sites in the Tibetan Plateau and its surrounding regions by analyzing sequences of cytochrome b genes. Furthermore, we estimated the possible divergent times among lineages based on a historical geological isolation event in the Tibetan Plateau. The molecular data revealed that the highly specialized grade schizothoracine fishes were not a monophyletic group, but were the same as genera Gymnocypris and Schizogypsis. Our results indi-cated that the molecular phylogenetic relationships apparently reflected their geographical and historical associations with drainages, namely species from the same and adjacent drainages clustered together and had close relationships. The divergence times of different lineages were well consistent with the rapid uplift phases of the Tibetan Plateau in the late Cenozoic, suggesting that the origin and evolution of schizothoracine fishes were strongly influenced by environment changes resulting from the upheaval of the Tibetan Plateau.     

Molecular evolution of connective tissue growth factor in Cyprinidae （Teleostei： Cypriniformes）

Connective tissue growth factor （CTGF） plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining （NJ）, maximum parsimony （MP）, maximum likelihood （ML） and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution （dN/dS） for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 bp indel （insertion/deletion） was found at the 5＇ end of CTGF gene of Cyprinidae, and this 6 bp deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity.     

Molecular phylogeny of the specialized schizothoracine fishes （Teleostei： Cyprinidae）,with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd.integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gdo pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene(about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic.Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 m during the late Pliocene(about 2.6 MaBP).     

Pollutants in stormwater runoff in Shanghai （China）： Implications for management of urban runoff pollution

Runoff samples were collected from four functional areas (traffic, residential, commercial and industrial) and four roof types (old concrete,new concrete, old clay and new clay) in central Shanghai, China, during rain events. The event mean concentrations (EMCs) of three forms of nitrogen (NH4+―N,NO3-―N,NO2-―N) and the temporal variations of total phosphorus (TP) were then measured to evaluate the effects of runoff from different areas on water quality management. The results revealed that the TP levels varied significantly in the samples collected from different functional areas and roof types during rain events. In addition, although the NO3-―N and NO2-―N concentrations in runoff remained well below the fifth class values of the national surface water quality standards, the NH4+―N levels were 1.36, 1.17, 1.10 and 0.85 times higher than the standard value in samples collected from commercial, traffic, industrial,and residential areas, respectively. Similarly, the concentrations of NH4+―N in samples collected from old concrete, new concrete,old clay and new clay roofs exceeded the fifth class standard by 6.66, 5.72, 4.32 and 3.32 times, respectively. And the NO3-―N levels were 1.86 and 1.53 times higher than the standard values in runoff samples collected from new and old concrete roofs, respectively.     

Ionic iron（III） complex of aryloxo-linked bis（imidazolium） cations： efficient and recyclable catalyst for aryl Grignard cross-coupling of alkyl chlorides

A novel phenol-linked bis（imidazolium） salt, H3LCl2 （L = O-4-C（CH3）3-C6H2-2,6-di[CH2{C（NCHCH- NAr）}]2, Ar = 2,6-diisopropylphenyl, 1）, was designed and used to prepare an ionic iron（III） complex [H2L][FeCl4] （2）. Complex 2 was a highly efficient catalyst for aryl Grignard cross-coupling of alkyl chlorides bearing β-hydrogens. Furthermore, complex 2 was reusable and could be reused in at least eight times without significant loss in catalytic activity.     

Reconsideration of the phylogenetic positions of three stichotrichous genera Holosticha, Anteholosticha and Pseudokeronopsis （Spirotrichea： Ciliophora） inferred from complete SSU rRNA gene sequences

The small subunit rRNA (SSU rRNA) gene for six marine stichotrichs, Pseudokeronopsis carnea, P. flava, Holosticha heterofoissneri, H. diademata, H. bradburyae and Anteholosticha manca, was sequenced and characterized. Using this molecular information, the phylogenetic positions of three related genera, Pseudokeronopsis, Holosticha and Anteholosticha were determined. The results indicate that the family Urostylidae is clearly separated from the family Pseudokeronopsidae. The present phylogenetic analyses unambiguously placed Pseudokeronopsis close to Holosticha, and support the conclusion that these genera should be regarded as the members of the order Urostylidae within the stichotrich clade. Furthermore, the results of this study also support the monophyly of the genus Pseudokeronopsis,the redefinition of Holosticha s. str. and the placement of Anteholosticha in a clade separate from Holosticha.     

The M5.0 Suining-Tongnan （China） earthquake of 31 January 2010： A destructive earthquake occurring in sedimentary cover

Usually, only crystalline basement is strong enough to store the massive strain energy that can be released in a damaging earthquake. By contrast, sedimentary cover is weak, because of its relatively high porosity and fluids. Therefore, it generally cannot accumulate enough energy for strong earthquakes. On January 31, 2010, a M5.0 earthquake occurred near the border of Suining and Tongnan in China. It excited strong short-period Rayleigh waves Rg, indicative of its shallow focal depth. The focal depth is constrained to less than 4 km, most probably in the range of 1-3 km, by modeling amplitude dependence on the frequency and waveforms of teleseismic depth phases (pP, sP). Because the local Mesozoic sedimentary cover is about 6 km thick, this earthquake should have occurred in the sedimentary cover. Though some shallow earthquakes with magnitudes up to M4 occur in Paleozoic sediments, this earthquake is the first M5 event studied in Mesozoic sedimentary cover. This event provides a rare opportunity to study seismogenic processes of damaging earthquakes in sedimentary basins.     

Construction of habitat suitability models （HSMs） for benthic macroinvertebrate and their applications to instream environmental flows： A case study in Xiangxi River of Three Gorges Reservior region, China

Based on a long-term ecological monitoring,the present study chose the most dominant benthic macroinvertebrate(Baetis spp.)as tar-get organisms in Xiangxi River,built the habitat suitability models(HSMs)for water depth,current velocity and substrate,respectively,which is the first aquatic organisms model for habitat suitability in the Chinese Mainland with a long-term consecutive in situ measurement.In order to protect the biointegrity and function of the river ecosystem,the theory system of instream environmental flow should be categorized into three hierarchies, namely minimum required instream flow(hydrological level),minimum instream environmental flow(bio-species level),and optimum instream environmental flow(ecosystem level).These three hierarchies of instream environmental flow models were then constructed with the hydropogical and seighted usable area(WUA)method.The results show that the minimum required instream flow of Yiangxi River calculated by the Tennant method(10% of the mean annual flow)was 0.615m3s-1;the minimum instream environmental flow accounted for 19.22% of the mean annual flow(namely 1.182m3s-1),which was the damaged river channel flow in the dry season;and 42.91% of the mean annual flow(namely 2.639m3s-1)should be viewed as the optimum instream environmental flow in order to protect the health of the river ecosystem,maintain the instream biodiversity,and reduce the impact of small hydropower stations nearby the Xiangxi River.We recommend that the hydrological and biological methods can help establish better instream environmental flow models and design best management practices for use in the small hydropower station project.     

The R- and AR-indices： Complementing the h-index

Based on the foundation laid by the h-index we introduce and study the R- and AR-indices. These new indices eliminate some of the disadvantages of the h-index, especially when they are used in combina-tion with the h-index. The R-index measures the h-core’s citation intensity, while AR goes one step further and takes the age of publications into account. This allows for an index that can actually in-crease and decrease over time. We propose the pair (h, AR) as a meaningful indicator for research evaluation. We further prove a relation characterizing the h-index in the power law model.     

Asymmetric epoxidation of <Emphasis Type="Italic">α</Emphasis>,<Emphasis Type="Italic">β</Emphasis>-unsaturated ketones using <Emphasis Type="Italic">α</Emphasis>,<Emphasis Type="Italic">α</Emphasis>-diarylprolinols as catalysts

Asymmetric epoxidation of α,β-unsaturated ketones has been extensively studied and several important procedures have been developed in the last decade. This review addresses the most significant advances in asymmetric epoxidation of α,β-unsaturated ketones using proline-derived α,α-diarylprolinols as catalysts. Special attention has been paid to the enantioselective epoxidation of chalcones, α,β-unsaturated trifluoromethyl, trichloromethyl ketones and β,γ-unsaturated α-keto esters based on the reseach of our group.     

Transpositional behaviour of the Ds element in the Ac/Ds system in rice

Insertional mutagenesis based on maize Activator/Dissociator (Ac/Ds) transposons is becoming a ma- jor approach used to produce a saturated mutant collection in rice. In this research, Ds-T-DNA trans- formed homozygotes were crossed with Ac-T-DNA transformed homozygotes in order to establish an Ac/Ds transposon system in rice. The successive investigation of Ds transposition from F1 to F5 gen- erations indicated that the frequencies of germinal transposition increased over successive genera- tions and reached 54.2% in F3 generation. The Ds transposition pattern revealed that a Ds transposition induced an approximately 170-bp deletion of T-DNA sequence and another Ds transposition carried a 272-bp T-DNA sequence. Using thermal asymmetric interlaced PCR (TAIL-PCR), some flanking se- quences of the Ds element were amplified. Analyses of 17 Ds-flanking sequences showed that five Ds were inserted into gene regions. The Ds could transpose not only to the linked sites but also to the unlinked sites. The frequency of inter-chromosomal transposition of Ds was 33.3%.     

Identification of <Emphasis Type="Italic">Fallopia</Emphasis> species based on the chloroplast <Emphasis Type="Italic">mat</Emphasis>K gene sequences

In order to develop an efficient identification method for Fallopia plants and drugs, molecular analysis of the partial matK gene sequences was performed on 6 Fallopia species. Based on the matK sequences, a phylogenetic tree was constructed, which showed that different populations of inter- and intra-species could be specified and distinguished. The matK gene sequences of the 6 Fallopia species were all found to be of 1 271 bp in length, with some nucleotide variations throughout the entire sequences. The nucleotide difference at position 1 041 could distinguish F. denticulata from others, while specific nucleotide at position 1 154 became identification markers for F. aubertii. Moreover, four specific marker sites for F. multiflora var. ciliinerve at positions 216, 224, 1 060 and 1 179, seven for F. convolvulus at 318, 765, 772, 874, 936, 952 and 1 036, and seven for F. dentate alata at 111, 192, 366, 450, 457, 1 032 and 1 074 were also observed. By detecting the marker nucleotides and analyzing the phylogenetic relationship, the botanical origins of five inspected drugs were determined, suggesting that matK sequences can be used for authenticating Fallopia plants and drugs.     

Developmental sequence of Cambrian embryo Markuelia

Based on more exquisitely preserved specimens of Markuelia hunanensis recently recovered from Middle and Upper Cambrian in western Hunan and in the light of Synchrotron radiation X-ray tomo-graphic microscopy, the developmental sequence from cleavage through organogenesis to the pre-hatching of Cambrian embryo Markuelia, especially the developmental sequence during the pre-hatching stage, i.e. from the earliest period when the scalids and tail spines only took shape to the latest period (just about hatching), is established. This developmental sequence provides a pattern of embryonic development during the pre-hatching stage, which has not been established in the living scalidophorans (priapulids, loriciferans and kinorhynchs). Thus, it not only enriches our knowledge on the embryonic development of the extant descendants of Markuelia, but also opens a new window to the evolution and development of the animal.     

Genetic and physical mapping of AvrPi7, a novel avirulence gene of Magnaporthe oryzae using physical position-ready markers

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating crop diseases worldwide. The avirulence gene corresponding to rice blast resistance gene Pi7 in field isolate CHL346 was inherited as a single gene, designated AvrPi7, in a segregating population consisting of 189 ascospore progenies derived from a cross between field isolates CHL346 and CHL42. In order to determine the chromosomal location of the AvrPi7 locus, a total of 121 simple sequence repeat (SSR) markers were developed based on the whole-genome sequence of reference isolate 70-15 of M. oryzae. Linkage analysis of the locus with these SSR markers showed that eight SSR markers on chromosome 1 were linked to the locus, among which the closest flanking markers MS1-9 and MS1-15 were 3.2 and 16.4 cM from the locus, respectively. For fine mapping, additional PCR-based makers including eight SSR markers and three candidate avirulence gene (CAG) markers were developed in the region flanking both markers. The AvrPi7 locus was genetically delimited within a 1.6-cM region flanked by markers MS1-21 and MS1-22, and co-segregated with the marker CAG2. To construct a physical map of the AvrPi7 locus, molecular markers linked to the Avr gene were mapped on the supercontigs of the ref-erence isolate 70-15 through bioinformation analysis (BIA). Consequently, the AvrPi7 locus was delim-ited to a 75-kb interval flanked by markers MS1-21 and MS1-22 based on the reference sequence. Merodiploids observed in this study are also discussed.     

dr1127： A novel gene of Deinococcus radiodurans responsible for oxidative stress

The functional analysis of dr1127,a novel gene in Deinococcus radiodurans was performed in this pa-per. The dr1127 gene was found occasionally in our microarray and 2-DE gel experiments. Mutation of the dr1127 gene decreased the γ-radiation and H2O2 resistance of D. radiodurans,and weakened the scavenging abilities of cell extracts for free radicals (superoxide anion,hydrogen peroxide,and hy-droxyl radical). Further oxidative damage assays demonstrated that the purified DR1127 protein of D. radiodurans could bind to double stranded DNA in vitro and protect DNA from oxidative damage in this way. These results suggest that the dr1127 gene is an important gene that can maintain γ-radiation and oxidative resistance in D. radiodurans and may take part in the oxidative stress process.