Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning

1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae, In our cladogram, the genera in Leuciscinae were divided into two groups that have no direct relationship. The genera in Leuciscinae distributed in Europe, Sibera and North America, including Leuciscus, Rutilus, Phoxinus, N. crysole, Opsopoeodus emilae, form a monophyletic group. And the Leuciscinae in southern China including Ctenopharyngodon idellus, Mylopharyngodon piceus, Squalibarbus and Ochetobius elongatus have a common origination.

来自易变山羊草抗禾谷孢囊线虫基因的克隆与序列分析

禾谷孢囊线虫（Heterodera avenae）是严重危害禾谷类作物的病原线虫之一,它广泛分布于澳大利亚、欧洲、北美、印度和中国等世界主要小麦产区,使作物严重减产,造成巨大的经济损失。目前最有效的防治措施之一是将外源抗性基因导入栽培小麦(Triticum aestivum L.)，培育抗禾谷孢囊线虫的新品种。但迄今为止抗禾谷孢囊线虫基因克隆研究的相关报道却很少。 本实验根据此前从抗禾谷孢囊线虫材料E-10扩增得到的与来自节节麦（Aegilops tauschii）的抗禾谷孢囊线虫基因Cre3高度同源的序列Rccn4,设计出三条嵌套引物,采用SON-PCR(single oligonucleotide nested PCR)方法,从E-10基因组DNA中得到一个长为1264 bp的扩增产物(命名为Rccn-L),测序比对结果显示,这一序列将Rccn4的3’端延伸了1209 bp,与抗禾谷孢囊线虫Cre3基因核苷酸同源性为86﹪，核苷酸编码区长1026 bp，含一个不完整的开放阅读框,一个终止密码子，没有起始密码子和内含子结构,编码一个342个氨基酸残基的蛋白质。该蛋白质等电点为5.19，分子量为38112.6Da。从序列的第113位开始到第332位是NBS-LRR类抗病性基因LRR区,呈现XXLXXLXXL重复。LRR编码区内亮氨酸残基的含量达17﹪，与抗禾谷孢囊线虫Cre3基因LRR编码区的核苷酸和氨基酸同源性分别为89﹪和78﹪。本实验首次将SON-PCR成功地运用于植物基因克隆，为植物基因克隆提供了又一有效方法。 此外,还根据Cre3基因及其他的NBS-LRR类植物抗性基因的NBS和LRR区保守序列设计了两对特异性引物，从禾谷孢囊线虫抗性材料易变山羊草基因组DNA中扩增到两个相应的目标条带。测序分析结果表明，它们的长度分别为532bp和1175bp，构成了一个有32bp的共同序列的NBS-LRR编码区。其序列总长为1675bp（命名为RCCN），含有一个不完整的开放阅读框，没有起始密码子、终止密码子和内含子结构。其中编码序列为1673bp，可编码一个557个氨基酸的蛋白质，等电点（pI）为5.39，分子量为63537.5Da。与Cre3的核苷酸和氨基酸同源性分别为87.8﹪和77﹪。RCCN氨基酸序列中含有已知抗病基因NBS区域的几个保守模体：kinase2区的ILDD、kinase3的（ⅰ）ESKILVTTRSK，（ⅱ）KGSPLAARTVGG，（ⅲ）RRCFAYCS及EGF。RCCN NBS区与Cre3 NBS区的核苷酸和氨基酸的同源性分别为96.4﹪和94﹪。从氨基酸序列的274位到548位为LRR保守区，呈现不规则的aXXLXXLXXL（其中a代表I，V，L，F或M）重复，其中亮氨酸的含量为15.6﹪。该区域与Cre3的LRR区的核苷酸和氨基酸同源性分别为80.8﹪和74﹪。推测该序列可能为一个抗禾谷孢囊线虫的新基因。 本文对抗禾谷孢囊线虫基因的克隆研究，为进一步克隆基因全序列，探索其结构与功能，和研究该基因表达与调控提供了关键信息。同时也为通过基因工程途径将抗性基因向优良小麦品种高效、定向转移，最终培育出小麦抗禾谷孢囊线虫新品种奠定了基础。 Cereal cyst nematode (CCN) is a damaging pathogen of broad acre cereal crops in Australia, Europe, North America, India and China. It affects wheat, barley, oat and triticale and causes yield loss of up to 80%. At present, Transferring resistance genes against CCN into wheat cultivars and breeding varieties are considered one of the most effective methods for controlling the CCN. However, there are very limited reports concerning the cloning studies of resistance genes against the cereal cyst nematode. According to the sequence of Rccn4 which had high similarity to the nucleotide binding site (NBS) coding region of cereal cyst nematode resistance gene, Cre3， We designed three 3’ nested primers. Using single oligonucleotide nested PCR (SON-PCR) we successfully amplified one band, Rccn-L, of 1264bp from E-10 which is the wheat-Ae.variabilis translocation line containing the cereal cyst nematode resistance gene of Ae.variabilis. We found that this band of interesting is the 3’ flanking sequence of 1209bp in size of Rccn4. The coding region was 1026bp, which contained an incomplete open reading frame and a terminator codon, without initiation codon and intron, encoding a peptide of 342 amino acid residues, and shared 86﹪nucleotide sequence identity with Cre3. This peptide had a conserved LRR domain, containing the imperfect repeats,XXLXXLXXL, which contains 17﹪ leucine residues and shares, respectively, 89﹪ nucleotide sequence and 78﹪ amino acid sequence identity with the LRR sequence of Cre3 locus. This research firstly used SON-PCR in the research of plant genome successfully, which indicated that SON-PCR is another method of cloning plant gene. At the same time, According to the conversed motif of NBS and LRR region of cereal cyst nematode resistance gene Cre3 from wild wheat (Triticum tauschlii L.) and the known NBS-LRR group resistance genes, we designed two pairs of specific primers for NBS and LRR region respectively. One band of approximately 530bp was amplified using the specific primers for conversed NBS region and one band of approximately 1200bp was amplified with the specific primers for conversed LRR region. After sequencing, we found that these two sequences included 32bp common nucleotide sequence and have 1675 bp in total, which was registered as RCCN in the Genbank. RCCN contained a NBS-LRR domain and an incomplete open reading frame without initiation codon, terminator codon and inxon. Its exon encodes a peptide of 557 amino acid residues. The molecular weight of the protein from the amino acid was 63.537 KDa. The amino acid sequence of RCCN contained conserved motif: ILDD, ESKILVTTRSK, KGSPLAARTVGG, RRCFAYCS, EGF，LRR. RCCN shares 87.8﹪ nucleotide sequence and 77﹪ amino acid sequence identity with cereal cyst nematode gene Cre3. It might be a novel cereal cyst nematode resistance gene. These research results of cloning the resistance genes against cereal cyst nematode bring a great promise for transferring resistance genes into wheat cultivars and breeding new wheat varieties against cereal cyst nematode by gene engineering. And these results also lay the hard foundation for the expressing researches of these genes.

The Compact Pulsed Hadron Source: A Design Perspective

During the past. decades, large-scale national neutron sources have been developed in Asia, Europe, and North America. Complementing such efforts, compact hadron beam complexes and neutron sources intended to serve primarily universities and industrial institutes have been proposed, and some have recently been established. Responding to the demand in China for pulsed neutron/proton-beam platforms that are dedicated to fundamental and applied research for users in multiple disciplines from materials characterization to hadron therapy and radiography to accelerator-driven sub-critical reactor systems (ADS) for nuclear waste transmutation, we have initiated the construction of a compact, yet expandable, accelerator complex-the Compact Pulsed Hadron Source (CPHS). It consists of an accelerator front-end (a high-intensity ion source, a 3-MeV radio-frequency quadrupole linac (RFQ), and a 13-MeV drift-tube linac (DTL)), a neutron target station (a beryllium target with solid methane and room-temperature water moderators/reflector), and experimental stations for neutron imaging/radiography, small-angle scattering, and proton irradiation. In the future, the CPHS may also serve as an injector to a ring for proton therapy and radiography or as the front end to an ADS test facility. In this paper, we describe the design of the CPHS technical systems and its intended operation.

长白山森林生态系统中的稀有和濒危多孔菌

In last 10 years,extensive field inventories were carried out to investigate Polypore species, the major wood decaying fungi in the Changbaishan Nature Reserve of Northeastern China. The following 27 species were treated as rare or threathened species: Amylocystis lapponica (Romell) Singer, Anomoporia albolutescens (Romell) Pouzar, Anomoporia bombycina (Fr.) Pouzar, Anomoporia vesiculosa Y.C. Dai & Niemel, Antrodia carbonica (Overh.) Ryvarden & Gilb., Antrodia crassa (P. Karst.) Ryvarden, Antrodiella citrinella Niemel & Ryvarden, Diplomitoporus flavescens (Bres.) Dománski, Donkioporia expansa (Desm.) Kotl. & Pouzar, Gloeophyllum carbonarium (Berk. & M.A. Curtis) Ryvarden, Haploporus odorus (Sommerf.) Bondartsev & Singer, Inonotopsis subiculosa (Peck) Parmasto, Nigroporus ussuriensis (Bondartsev & Ljub.) Y.C. Dai & Niemela, Oxyporus sinensis X.L. Zeng, Parmastomyces taxi (Bondartsev) Y.C. Dai & Niemela, Phellinidium sulphurascens (Pilat) Y.C. Dai, Phellinus vaninii Ljub., Polyporus vassilievae Thorn, Pycnoporellus fulgens (Fr.) Donk, Skeletocutis brevispora Niemela, Skeletocutis ochroalba Niemela, Skeletocutis perennis Ryvarden, Trechispora candidissima (Schwein.) Bondartsev & Singer, Wolfiporia dilatohypha Ryvarden & Gilb., Wolfiporia curvispora Y.C. Dai, Wrightoporia avellanea (Bres.) Pouzar and Wrightoporia lenta (Oveh. & J. Lowe) Pouzar. Polypores are richer in East Asia than in Europe and North America, not only because of destructive galciations and fewer hosts in the latters, but also because of the geography. NE Asia is a link between Europe and North America. Changbaishan Nature Reserve is very rich in polypores, and over 260 species were recorded in the reserve. Some rare species in North America and Europe, for instance, Anomoporia albolutescens, Antrodia crassa, Diplomitoporus flavescens, Inonotopsis subiculosa and Skeletocutis ochroalba etc. were found in Changbaishan Nature Reserve as well, and these species are in fact rare in the earth. Most of the 27 species occurred on fallen trunks or rotten wood in the reserve, but some of them grew on living trees. 18 species occured on substrate of gymnosperms, and 9 species grew on wood of angiosperm.Among the 27 species, 7 species caused a brown rot,and 20 species produced a white rot. The morphology, substrate and ecology of each species were briefly discussed. The most important tool for polypore conservation is the conservation of their habitats, and it is necessary to study the ecology of the rare and threathened species of polypores in the Changbaishan Nature Reserve. Because most of polypores live on the substrate of fallen trunks and rotten wood, it is very important to keep such substrate in the ecosystem.

Ten Years of the Relative Risk Model and Regional Scale Ecological Risk Assessment

It has been 10 years since the publication of the relative risk model (RRM) for regional scale ecological risk assessment. The approach has since been used successfully for a variety of freshwater, marine, and terrestrial environments in North America, South America, and Australia. During this period the types of stressors have been expanded to include more than contaminants. Invasive species, habitat loss, stream alteration and blockage, temperature, change in land use, and climate have been incorporated into the assessments. Major developments in the RRM have included the extensive use of geographical information systems, uncertainty analysis using Monte Carlo techniques, and its application to retrospective assessments to determine causation. The future uses of the RRM include assessments for forestry and conservation management, an increasing use in invasive species evaluation, and in sustainability. Developments in risk communication, the use of Bayesian approaches, and in uncertainty analyses are on the horizon.

Development of expressed sequence tags from the bay scallop, Argopecten irradians irradians

The bay scallop, Argopecten irradians irradians, introduced from North America, has become one of the most important aquaculture species in China. Inan effort to identify scallop genes involved in host defense, a high-quality cDNA library was constructed from whole body tissues of the bay scallop. A total of 5828 successful sequencing reactions yielded 4995 expressed sequence tags (ESTs) longer than 100 bp. Cluster and assembly analyses of the ESTs identified 637 contigs (consisting of 2853 sequences) and 2142 singletons, totaling 2779 unique sequences. Basic Local Alignment Search Tool (BLAST) analysis showed that the majority (73%) of the unique sequences had no significant homology (E-value >= 0.005) to sequences in GenBank. Among the 748 sequences with significant GenBank matches, 160 (21.4%) were for genes related to metabolism, 131 (17.5%) for cell/organism defense, 124 (16.6%) for gene/protein expression, 83 (11.1%) for cell structure/motility, 70 (9.4%) for cell signaling/communication, 17 (2.3%) for cell division, and 163 (21.8%) matched to genes of unknown functions. The list of host-defense genes included many genes with known and important roles in innate defense such as lectins, defensins, proteases, protease inhibitors, heat shock proteins, antioxidants, and Toll-like receptors. The study provides a significant number of ESTs for gene discovery and candidate genes for studying host defense in scallops and other molluscs.

电离层行进式扰动的GPS台网监测研究

In this dissertation, we investigated two types of traveling ionospheric disturbances (TIDs)/gravity waves (GWs) triggered separately by auroral energy input during super geomagnetic storms and solar terminator (ST) under quiet geomagnetic conditions (kp<3+) using TEC measurements from the global network of GPS receivers. Research into the generation and propagation of TIDs/GWs during storms greatly enhance our understandings on the evolution processes of energy transportation from the high-latitude’s magnetosphere to the low-latitude ionosphere and the conjugated effect of TIDs propagation between the northern and southern hemispheres. Our results revealed that the conjugacy of propagation direction between the northern and southern hemispheres was subject to the influence of Coriolis force. We also figure out the evolution processes of ionospheric disturbances at the global scale. These are important topics that had not been well addressed previously. In addition, we also obtained thee wave structures of medium scale TIDs excited by the solar terminator (ST) moving over the northern America and physical mechanisms involved. Our observations confirm that the ST is a stable and repetitive source of ionospheric wave disturbances and the evidence of solar terminator generated disturbances has been demonstrated experimentally via the GPS TEC measurement. The main researches and results of this dissertation are as follows. First, the global traveling ionospheric disturbances (TIDs) during the drastic magnetic storms of October 29–31, 2003 were analyzed using the Global Position System (GPS) total electron content (TEC) data observed in the Asian-Australian, European and North American sectors. We collected the most comprehensive set of the TEC data from more than 900 GPS stations on the International GNSS Services (IGS) website and introduce here a strategy that combines polynomial fitting and multi-channel maximum entropy spectral analysis to obtain TID parameters. Moreover, in collaboration with my thesis advisor, I have developed an imaging technique of 2-dimensional map of TIDs structures to obtain spatial and temporal maps of large scale traveling ionospheric disturbances (LSTIDs). The clear structures of TEC perturbations map during the passage of TIDs were displayed. The results of our study are summarized as follows: (1) Large-scale TIDs (LSTIDs) and medium-scale TIDs (MSTIDs) were detected in all three sectors after the sudden commencement (SC) of the magnetic storm, and their features showed longitudinal and latitudinal dependences. The duration of TIDs was longer at higher latitudes than at middle latitudes, with a maximum of about 16 h. The TEC variation amplitude of LSTIDs was larger in the North American sector than in the two other sectors. At the lower latitudes, the ionospheric perturbations were more complicated, and their duration and amplitude were relatively longer and larger. (2) The periods and phase speeds of TIDs were different in these three sectors. In Europe, the TIDs propagated southward; in North America and Asia, the TIDs propagated southwestward; in the near-equator region, the disturbances propagated with the azimuth (the angle of the propagation direction of the LSTIDs measured clockwise from due north with 0°) of 210° showing the influence of Coriolis force; in the Southern Hemisphere, the LSTIDs propagated conjugatedly northwestward. Both the southwestward and northeastward propagating LSTIDs are found in the equatorial region. These results mean that the Coriolis effect cannot be ignored for the wave propagation of LSTIDs and that the propagation direction is correlated with the polar magnetic activity. (3) The day (day of year: 301) before the SC (sudden commencement) of magnetic storm, we observed a sudden TEC skip disturbances (±10 TECU). It should be a response for the high flux of proton during the solar flare event, but not the magnetic storms. Next, the most comprehensive and dense GPS network’s data from North-America region were used in this paper to analyze the medium scale traveling ionospheric disturbances (MSTIDs) which were generated by the moving solar terminator during the quiet days in 2005. We applied the multi-channel maximum entropy spectral analysis to calculated TID parameters, and found that the occurrence of ST-MSTIDs depends on the seasonal variations. The results of our study are summarized as follows: (1) MSTIDs stimulated by the moving ST (ST-MSTIDs) are detected at mid-latitudes after the passage of the solar terminator with the life time of 2～3 hours and the variation amplitude of 0.2～0.8 TECU. Spectral analysis indicated that the horizontal wavelength, average period, horizontal phase velocity of the MSTIDs are around 300±150 km，150±80 m/s and 25±15 min, respectively. In addition, ST-MSTIDs have wave fronts elongating the moving ST direction and almost parallel to ST. (2) The statistical results demonstrate that the dusk MSTIDs stimulated by ST is more obvious than the dawn MSTIDs in summer. On the contrary, the more-pronounced dawn MSTIDs occurs in winter. (3) Further analysis indicates that the seasonal variations of ST-MSTIDs occurrence frequency are most probably related to the seasonal differences of the variations of EUV flux in the ionosphere region and recombination process during sunrise and sunset period at mid-latitudes. Statistical study of occurrence characteristics of TIDs using the GPS network in North-American and European during solar maximum, In conclusion, statistical studies of the propagation characteristics of TIDs, which excited by the two common origins including geomagnetic storms and moving solar terminator, were involved with global GPS TEC databasein this thesis. We employed the multichannel maximum entropy spectral analysis method to diagnose the characteristics of propagation and evolvement of ionospheric disturbances, also, the characteristics of their regional distribution and climatological variations were revealed by the statistic analysis. The results of these studies can improve our knowledge about the energy transfer in the solar-terrestrial system and the coupling process between upper and lower atmosphere (thermosphere-ionosphere-mesosphere). On the other hand, our results of the investigation on TIDs generated by particular linear origin such as ST are important for developing ionospheric irregularity physics and modeling the transionosphere radio wave propagation. Besides, the GPS TEC representation of the ST-generated ionospheric structure suggests a better possibility for investigating this phenomenon. Subsequently, there are scientific meaning of the result of this dissertation to deeply discuss the energy transfer and coupling in the ionosphere, as well as realistic value to space weather forecast in the ionosphere region.