Sequence analysis of the ITS region and 5.8S rDNA of Porphyra haitanensis

The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli(NB,PT and ST) were amplified,sequenced and analyzed.In addition,the phylogenic relationships of the sequences identified in this study with those of other Porphyra retrieved from GenBank were evaluated.The results are as follows:the sequences of the ITS and 5.8S rDNA were essentially identical among the three strains.The sequences of ITS1 were 331 bp to 334 bp,while those of the 5.8S rDNA were 158 bp and the sequences of ITS2 ranged from 673 bp to 681 bp.The sequences of the ITS had a high level of homology(up to 99.5%) with that of P.haitanensis(DQ662228) retrieved from GenBank,but were only approximately 50% homologous with those of other species of Porphyra.The results obtained when a phylogenetic tree was constructed coincided with the results of the homology analysis.These results suggest that the three cultivated strains of P.haitanensis evolved conservatively and that the ITS showed evolutionary consistency.However,the sequences of the ITS and 5.8S rDNA of different Porphyra species showed great variations.Therefore,the relationship of Porphyra interspecies phyletic evolution could be judged,which provides the proof for Porphyra identification study.However,proper classifications of the subspecies and the populations of Porphyra should be determined through the use of other molecular techniques to determine the genetic variability and rational phylogenetic relationships.

Sequence Difference of Mitochondrial DNA Control Region and Genetic Differentiation of Cervinae in China

[Objective] The study aimed at analyzing Genetic Differentiation of Cervinae. [Method] The complete mitochondrial DNA control region of five species of Cervinae was determined by direct DNA sequencing. Homologous sequences of others Cervinae were gained from GenBank, and then analyzed through biology software. [Result] The lengths of their control region were 921-1 072 bp, the nucleotide content of T, A, C, and G was 32.1%, 30.2%, 22.7% and 15.0% separately. Genetic distance of each species ranged from 0.062-0.106, which belonged to level of inter-genus. The molecular phylogenetic tree indicated that red deer, skia deer and White-lipped Deer had close relationship, and they constituted one branch with sambar deer. Eld＇s deer and elk deer constituted the second branch, and hog deer constituted the third branch alone. [Conclusion] Hog deer and fallow deer should be incorporated in Cervus, divergence time is about 1.55-2.60 million years among Cervinae in China.

Sequence Analysis of Mitochondrial DNA D-loop Region in Xinjiang Goose

[Objective] The sequences of mitochondrial DNA D-loop region of Xinjiang Goose with three different colors of plumage were analyzed in order to study the genetic diversity of Xinjiang Goose, as well as the phylogeny and evolution. [Method] Ten geese were selected randomly from the core populations of grey-, mosaic- and white-plumaged Xinjiang Goose respectively with a total number of thirty as experi- mental materials, of which the blood samples were collected from the largest vein under the wing （brachial vein） for DNA extraction. Sequences of mitochondrial DNA D-loop regions were determined using DNA sequencing technology to analyze the polymorphism. In addition, the genetic distances among different populations were estimated through the comparison with the reference sequences. [Resull] The con- tents of A, G, C and T nucleotides in the D-loop region of Xinjiang Goose were 28.85%, 17.05%, 25.38% and 28.72%, respectively. The average haplotype diversity and nucleotide diversity of Xinjiang Goose were 0.583 and 0.056. Xinjiang Goose and Greylag Goose were clustered into the same group. [Conclusion] The results showed that Xinjiang Geese with three different colors of plumage all descend from Greylag Goose （Anser anser）.

Large-scale Migration of Fluids toward Foreland Basins during Collisional Orogeny: Evidence from Triassic Anhydrock Sequences and Regional Alteration in the Middle-Lower Yangtze Area

The middle-lower Yangtze area underwent a series of complex tectonic evolution, such as Hercynian extensional rifting, Indosinian foreland basining, and Yanshanian transpression-transtension, resulting in a large distinctive Cu-Fe-Au metallogenic belt. In the tectonic evolution, large-scale migration and convergence of fluids toward foreland basins induced during the collisional orogeny of the Yangtze and North China continental blocks were of vital importance for the formation of the metallogenic belt. Through geological surveys of the middle-lower Yangtze area, three lines of evidence of large-scale fluid migration are proposed: (1) The extensive dolomitic and silicic alteration penetrating Cambrian-Triassic strata generally occurs in a region sandwiched between the metallogenic belt along the Yangtze River and the Dabie orogenic belt, and in the alteration domain alternately strong and weak alteration zones extend in a NW direction and are controlled by the fault system of the Dabie orogenic belt; it might record the locus of the activities of long-distance migrating fluids. (2) The textures and structures of very thick Middle-Lower Triassic anhydrock sequences in restricted basins along the river reveal the important contribution of the convergence of regional hot brine in restricted basins and the chemical deposition or their formation. (3) Early-Middle Triassic syndepositional iron carbonate sequences and Fe-Cu-Pb-Zn massive sulfide deposits alternate with anhydrock sequences or are separated from the latter, but all of them occur in the same stratigraphic horizon and are intimately associated with each other, being the product of syndeposition of high-salinity hot brine. According to the geological surveys, combined with previous data, the authors propose a conceptual model of fluid migration-convergence and mineralization during the Dabie collisional orogeny.

Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

Head smut of maize （Zea mays L.）, which was caused by Sporisorium reiliana, occurred in most of the maize growing areas of the world. The purpose of this study was to develop SCAR markers for map-based cloning of resistance genes and MAS. Two sets of BC3 progenies, one （BC3Q） derived from the cross Qi319 （resistance）×Huangzao 4 （susceptible）, the other （BC3M） from Mol7 （resistance）× Huangzao 4 （susceptible）, were generated. Huangzao 4 was the recurrent parent in both progenies. A combination of BSA （bulked segregant analysis） with AFLP （amplified fragment length polymorphism） method was applied to map the genes involving the resistance to S. reiliana, and corresponding resistant and susceptible bulks and their parental lines were used for screening polymorphic AFLP primer pairs. One fragment of PI3M61-152 was converted into SCAR （sequence charactered amplified fragment） marker S130. The marker was mapped at chromosome bin 2.09, the interval of a major QTL region previously reported to contribute to S. reiliana resistance. Furthermore, S130 was highly and facilitate map-based cloni associated with resistance to S. reiliana, and could be useful for marker-assisted selection ng of resistance genes.

The Hyperspace of the Regions Below of Continuous Maps from the Converging Sequence

Let S = {1,1/2,1/2^2,…,1/∞ = 0} and I = [0, 1] be the unit interval. We use ↓USC（S） and ↓C（S） to denote the families of the regions below of all upper semi-continuous maps and of the regions below of all continuous maps from S to I and ↓C0（S） = {↓f∈↓C（S） ： f（0） = 0}. ↓USC（S） endowed with the Vietoris topology is a topological space. A pair of topological spaces （X, Y） means that X is a topological space and Y is its subspace. Two pairs of topological spaces （X, Y） and （A, B） are called pair-homeomorphic （≈） if there exists a homeomorphism h ： X→A from X onto A such that h（Y） = B. It is proved that, （↓USC（S）,↓C0（S）） ≈（Q, s） and （↓USC（S）,↓C（S）／ ↓C0（S））≈（Q, c0）, where Q = [-1,1]^ω is the Hilbert cube and s = （-1,1）^ω,c0= {（xn）∈Q ： limn→∞= 0}. But we do not know what （↓USC（S）,↓C（S））is.

Rapid detection of self-biting disease of mink by specific sequence-characterized amplified regions

Self-biting disease occurred in most farmed fur animals in the world. The mechanism and rapid detection method of this disease has not been reported. We applied bulked sergeant analysis （BSA） in combination with RAPD method to analyze a molecular genetic marker linked with self-biting trait in mink group. The molecular marker was converted into sequence-characterized amplified regions （SCAR） marker for rapid detection of this disease. A single RAPD marker A8 amplified a specific band of 263bp in self-biting minks, which was designated as SRA8-250, and non-specific band of 315bp in both self-biting and healthy minks. The sequences of the bands exhibited 75% and 88% similarity to Canis familiarizes major histocompatibility complex （MHC） class II region and Macaca mulatta MHC class I region, respectively. A SCAR marker SCAR-A8 was designed for the specific fragment SRA8-250 and validated in 30 self-biting minks and 30 healthy minks. Positive amplification of SCAR-A8 was detected in 24 self-biting minks and 12 healthy minks. χ2 test showed significant difference （p〈0.01） in the detection rate between the two groups. This indicated that SRA8-250 can be used as a positive marker to detect self-biting disease in minks. Furthermore, the finding that self-biting disease links with MHC genes has significant implications for the mechanism of the disease.

Human Enterovirus 71 DNA Vaccine Constructs Containing 5’UTR with Complete Internal Ribosome Entry Site Sequence Stimulated Improved Anti-Human Enterovirus 71 Neutralizing Immune Responses

Recent improvement in the technologies for efficient delivery of DNA vaccines has renewed interest in the DNA-based vaccines. Several DNA-based vaccines against human enterovirus 71 (EV71), the causative agent for hand, foot and mouth disease (HFMD) have been developed. Here we examined the potential of improving the vaccines by inserting the EV71 5’ untranslated region (5’ UTR) containing the full length internal ribosome entry site (IRES) sequence to the EV71 VP1-based DNA vaccine constructs. Four vaccine constructs designated as 5’ UTR-VP1/EGFP, VP1/EGFP, 5’ UTR-VP1/pVAX and VP1/pVAX, were designed using the pEGFP-N1 and pVAX-1 expression vectors, respectively. Transfection of Vero cells with the vaccine constructs with the 5’-UTR (5’-UTR-VP1/EGFP and 5’ UTR-VP1/pVAX) resulted in higher percentages of cells expressing the recombinant protein in comparison to cells transfected with vectors without the 5’-UTR (67% and 57%, respectively). Higher IgG responses (29%) were obtained from mice immunized with the DNA vaccine construct with the full length 5’ UTR. The same group of mice when challenged with life EV71 produced significantly higher neutralizing antibody (NAb) titers (>5-fold). These results suggest that insertion of the EV71 5’ UTR sequence consisting of the full length IRES to the EV71 DNA vaccine constructs improved the efficacy of the constructs with enhanced elicitation of the neutralizing antibody responses.

Sequence variability of the 5, UTR in isolates of hepatitis C virus in China

Background: Hepatitis C virus infection is a great is- sue in China; however, there is very little informa- tion on genotyping investigations based on sequence variability in the 5' untranslated (5'UTR) reported. The present study was to define the sequence varia- bility based on the sequence divergences of the 5' UTR of the virus. Methods: Sequences of 91 isolates from patients with chronic hepatitis C from Yunnan, southwest China, were sequenced and genotypes were defined accord- ing to the sequence divergences of the 5' UTR of the virus. Results: Eighty-six isolates were classified into 3 clades (previously termed groups or major types) by the methods proposed by Chan et al in 1992 and phy- logenetic analysis based on nucleotide sequence diver- gences within the 5' UTR. Fifty-six percent of the i- solates were classified into clade 3, 35% into clade 1, and 34.9% into clade 2. New genotypes 1f, 2h, 3h and 3i were defined. In addition, 3 novel sequences were discovered, respectively with an 18-nt sequence deletion (corresponding to nucleotide position -173 to -156), a 28-nt sequence insertion, and a 40-nt se- quence insertion, between -56 and -55. Of these i- solates, 56% possessed a 'G' at position -66 in place of the 'T' that is present in all previously re- ported sequences. Conclusions: These HCV variants, evolved or re- mained in this area, may be of great significance in diagnosis and treatment of hepatitis C patients.

Grain-size Characteristics and Climate Variability in TMS5e Sequence of Tumen Section in Southern Tengger Desert,Northwestern China

The TMS5e sequence from the Tumen section, at the southern edge of Tengger Desert in the northwestern China, is synchronous with Marine Isotope Stage 5e （MIS5e）. It consists of 16 layers of aeolian dune sands, 11 layers of lacustrine loess-like facies, and 5 layers of lacustrine facies. The results of grain-size analysis shows that the pa- laeo-mobile dune sands, palaeo-fixed to semi-fixed dune sands and loess-like sandy loams are mainly composed of sands, ranging from 70% to 96%; their silt contents ranged from 4% to 20%, and their clay contents ranged from 1% to 5%; the climate under which the aeolian dune sands were deposited is similar to that under which modern mobile dune sands form, which is caused by the dominance of the cold, dry East Asian winter monsoon. In contrast, the lacustrine loess-like facies and lacustrine facies had a lower sand contents than those of the three aeolian dune sands, but have higher silt and clay contents, most of their sand content ranged from 30% to 60%, their silt contents ranged from 35% to 55%, and their clay contents ranged from 6% to 20%. The lacustrine loess-like facies and lacustrine facies formed under the influence of the warm, humid East Asian summer monsoon based on their similarity with modern sediments. The grain-size indicator Mz （mean grain diameter） and the SC/D value in the TMS5e sequence indicate climatic insta- bility at the southern edge of the Tengger Desert during MIS5e, with at least 14 fluctuations between a warm, humid climate and a cold, dry climate, divided into five stages： TMS5e5 （139 kyr to 129.3 kyr B.P.）, TMS5e4 （129.3 kyr to 124 kyr B.P.）, TMS5e3 （124 kyr to 119.5 kyr B.P.）, TMS5e2 （119.5 kyr to 116.5 kyr B.P.）, and TMS5el （116.5 kyr to 113.7 kyr B.P.）. These correspond roughly to MIS5e5, MIS5e4, MIS5e3, MIS5e2, and MIS5el, respectively, in the GRIP ice core data.

Panax ginseng-specific sequence characterized amplified region (SCAR) marker for testing medicinal products

To screen genetic polymorphisms of Panax ginseng, as well as those of Panax quinquefolium and Panax notoginseng, analysis of random amplified polymorphic DNA （RAPD） was performed using 120 random primers. Of the successful amplicons obtained, the Panax ginseng-specific RAPD marker C-12 was cloned into a TA vector and sequenced （Genl3ank access number KU553472）. Based on the sequence analysis results, a pair of primers specific to C-12 was designed. Finally, a SCAR marker-based identification system for Panax ginseng was developed after optimization of the reaction conditions. Using this method, two positive bands were stably observed at 300 bp and 130 bp in 33 batches of Panax ginseng samples tested, while negative results were obtained for another 101 batches of samples, including Panax quinquefolium, Panax notoginseng, adulterants, and other medicinal herbs. Thus, we successfully developed a PCR-based method for rapid and effective identification of Panax ginseng, which can be effectively used for the protection and utilization of germplasm resources and identification of the origins of Panax ginseng samples.

Effect of Impregnation Sequence on Propane Dehydrogenation Performance of PtSnNa/ZSM-5 Catalyst

The effects of the sequence for impregnation of metal precursors on the performance of PtSnNa/ZSM-5 catalyst for propane dehydrogenation to propene were studied in this paper.Some methods such as XRD,TPDA,BET,H2-TPR,XPS,ICP,TEM and hydrogen chemisorption were used to characterize the catalysts.The structure of ZSM-5 zeolite was not destroyed by the introduction of metal components.Meanwhile the different impregnation sequence of metal precursors could affect the behavior of Sn4+species entering the ZSM-5 channel,and the interaction between platinum and tin species,as well as the degree for reduction of Pt and Sn components.As a result,the prepared catalysts exhibited different reaction activity and selectivity.Compared with the co-impregnation treated catalyst,the catalysts prepared by the sequential impregnation method showed better catalytic activity in propane dehydrogenation,especially the one prepared through impregnation with tin precursor at first.Finally,a model for the effect of impregnation sequence on the distribution of Pt and Sn species in PtSnNa/ZSM-5 catalyst was proposed.

From Basin Black Shales to Platform Carbonate Rocks:A Study on Sequence Stratigraphy for the Lower Cambrian of the Upper-Yangtze Region in South China

In the Upper-Yangtze region, especially in Guizhou Province and its adjacent areas, the Lower Cambrian is well developed and is marked by a succession from black shales of the basin facies to carbonate rocks of the platform facies. The drowning event of the platform occurring at the turn from Sinian to Cambrian resulted in a set of black shales, i.e. the Niutitang Formation, which makes up the bottom part of the Lower Cambrian. With the shoaling of the sedimentary environment, a set of carbonate rocks, i.e. the Qingxudong Formation, was formed in the top part of the Lower Cambrian. Thus, the Lower Cambrian in the study area makes up one second-order sequence that can be further subdivided into five third-order sequences, and forms a regularly cyclic succession of transgression-regression. There is a regularly vertical stacking pattern for the third-order sequences in the second-order sequence. From bottom to top, the succession of the ＂CS （condensed section） ＋HST （high-stand system tract）＂ of the third-order sequences is changed into the succession of the ＂TST （transgressive system tract）＋CS＋HST＂. Correspondingly, the drowning-type sequence boundary is changed into the exposure-type one. Therefore, both the second-order and the third-order sequences have similar sedimentary-facies architectures. A concomitant with these temporal changes, the Lower Cambrian with a thickness of 1000 m that contains five third-order sequences is changed into a condensed succession that cannot identify third-order sequences toward the southeast with the deepening of the sedimentary environment. According to the elementary features of the third-order sequences, i.e. the regularity o sedimentary-facies successions in space and the synchronism of sedimentary-environment changes in time, the detailed division of the third-order sequences at main logged sections in different paleogeographical background becomes the basis to establish the sequence-stratigraphic framework that can demonstrate two types of facies-changing surface and two types of diachronism in the stratigraphic records. This sequence-stratigraphic framework shows a growing process of the carbonate platform from the base of the condensed succession formed by black shales of basin facies. Resulting from the rapid transgression at the turn from Sinian to Cambrian the ecological space became open, which formed the antecedent condition of paleogeographical setting for ＂the Cambrian Biological Explosion＂. Ultimately, the genetic relationship between the depositional events and the biological-diversity events is very complex and there remain lots of problems that need further research in the future.

The Late Triassic Sequence-Stratigraphic Framework of the Upper Yangtze Region,South China

In the transitional period between the Middle and the Late Triassic, the Indochina orogeny caused two tectonic events in South China：（1） the formation and uplift of the Qinling-Dabie orogenic belt along the northern margin of the South China Plate, due to its collision with the North China Plate; and 2） the development of a 1300-km-wide intra-continental orogen in the southeastern part of the South China Plate, which led to a northwestward movement of the foreland thrust-fold zone. These tectonic events resulted in the ending of the Yangtze Platform, and were a stable paleogeographic factor from the Eidacaran to the end of the Middle Triassic. This platform was characterized by the widespread development of shallow-water carbonates. After the end of the Yangtze Platform, the upper Yangtze foreland basin（or Sichuan foreland basin） was formed during the Late Triassic and became a accumulation site of fluvial deposits that are composed of related strata of the Xujiahe Formation. In western Sichuan Province, the Xujiahe Formation overlies the Maantang Formation shallow-water carbonate rocks of the Xiaotangzi Formation siliciclastic rocks（from shelf shales to littoral facies）. The sequence-stratigraphic framework of the Upper Triassic in the upper Yangtze foreland basin indicates a particular alluvial architecture, characterized by sequences composed of（1） successions of low-energy fluvial deposits of high-accommodation phases, including coal seams, and（2） high-energy fluvial deposits of low-accommodation phases, including amalgamated river-channel sandstones. The spatial distribution of these fluvial deposits belonging to the Xujiahe Formation and its relative strata is characterized by gradual thinning-out, overlapping, and pinching-out toward both the east and south. This sedimentary record therefore expresses a particular sequence-stratigraphic succession of fluvial deposits within the filling succession of the foreland basin. The sequence-stratigraphic framework for the Upper Triassic in the Upper Yangtze region provides a record of the end of the Yangtze Platform and the formation of the upper Yangtze foreland basin.

A study on the focal parameters of Shidian M=5.9 earthquake sequences in 2001

On the basis of about 300 earthquake wave forms observed in the Shidian MS=5.9 sequences on April 12, 2001 recorded in Kunming Digital Seismic Network, the spectra of shear wave have been used to estimate the focal parameters of these earthquake sequences. The results show that within the magnitude range of 1.5~5.3, the seis-mic moments are 1010~1016 N?m, the corner frequencies are 0.2~0.8 Hz, radii of the focal rupture are 200~2 500 m and the stress drops are 0.1×105~20×105Pa. Through the statistical analyses of variation of corner frequency fc and stress drop ?σ with time, it is discovered that the average corner frequency of the foreshock sequences is obviously lower than that of the aftershock sequences. Contrarily, the average stress drops ?σ of the foreshock sequences are clearly higher than that of the aftershocks. It is considered that these variation characteristics of av-erage corner frequency and stress drops before and after the main shock have index significance to the precursory information before a strong earthquake. The higher stress drops for the foreshock sequences show that the higher shear stresses have been stored in the area of main shock. After the main shock, most of the stresses have been released, so the aftershock sequences show a rupture process of lower stresses.

Research on Outcrop Sequence Stratigraphy of Permian in Middle-Lower Yangtze Region

According to the latest International Chronostratigraphic Scheme (ICS, 2000), the Permian in the Middle Lower Yangtze region of South China can be divided into three series and nine stages relevant to the traditional six stages of South China. From Assellian to Changxingian of Permian, 44 Ma in age range, the strata are composed of 14 third order sequences, each of which is 3.14 Ma in average age range. There is one third order sequence of Zisongian, equivalent to middle and upper Chuanshan Formation or equal to Asselian and two thirds of Sakmarian. There are two third order sequences, corresponding to Liang shan Formation or Zhenjiang Formation and upper Chuanshan Formation, which are assigned to Longlingian, coinciding with Artinskian and one third of Sakmarian. In addition, three third order sequences, equal to Qixia Formation, are attributed to Chihsian, corresponding to Kubergandian and one third of Roadian. Four third order sequences, comprising Gufeng, Maokou, Yanqiao, Yinping and Wuxue formations, are assigned to Maokouan, equivalent to two thirds of Roadian, Wordian and Capitanian. Two third order sequences, equal to Longtan Formation or Wujiaping Formation, are included in Wuchiapingian. Other two third order sequences, corresponding to Changxing Formation or Dalong Formation, are assigned to Changhsingian. In brief, these above third order sequences can be incorporated into 4 sequences sets.

Comparative Analysis of Mitochondrial Control Region Sequence from Three Flatfish Species(Pleuronectidae)

The 5’-end of the mitochondrial control region sequences of three flatfishes (Pleuronectiformes: Pleuronectidae) were amplified and sequenced. These sequences were compared with those of other three Pleuronectids species retrieved from GenBank. A phylogenetic tree was constructed based on the partial control region sequences. The results of phyloge- netic analysis are consistent with those of conventional systematics. Compared to previous studies, the structure of the 5’-end of mitochondrial control region was analyzed. The terminal associated sequence motif and its complementary motif were i- dentified at the 5’-end of the sequences. A conserved sequence block, named as CM5’d, was identified in the 5’-end of con- trol region sequences in all Pleuronectids. Another central conserved sequence block, named as CSB-F, was detected in the central conserved blocks.

Identification of the interactive region by the homology of the sequence spectrum

The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.

THE ABNORMAL EXPRESSION OF CLONED REPEATED SEQUENCE DNA, L5B-4, IN RAT HEPATOMA BERH-2

A repeated sequence DNA fragment, L5B-4, was cloned from the 5 kb BamHI DNA fragments of rat genomic DNA. The expressions of the L5B-4 DNA fragment are different in liver and hepatoma cells. The amounts of transcripts in hepatoma cells are lower in nucleus and higher in cytoplasm, especially in polysomal RNA, as compared with that in liver cells. The alteration shown in polysomal RNA of hepatoma cells seems to be specific. These results are discussed with respect to the possible function of this repeated DNA and its variation in hepatoma cells.