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.

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.

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt(Sharqia,Qalyubia and Garbia).In this study,RT-PCR,Single-Strand Conformation Polymorphism(SSCP)and nucleotide sequence analysis were used for four independent CTV genomic regions(p65,p18,p20,and p23)to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates.RTPCR products(650 bp)for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing.SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns.Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7%with T36 isolate from USA,Florida.Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate(T36 isolate group),suggesting that they may have originated from closely related ancestors.Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang,p18,p20 and p65,amplified from isolate A3,Sharqia governorate,revealed that the p18,p65,and p20 genes were related to the T3-KB isolate from South Africa with 99%–100%sequence homology.Phylogenetic relationship analysis for p65,p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group.The recombination analysis identified three of six isolates from Sharqia,and Garbia as potential recombinant for p23 gene.The isolates T36 and T3 were identified as major donors for recombination events in isolate A3.Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event.The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

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.

“88542”水平沟整地措施下土壤微生物群落空间分异特征

为探明宁夏黄土丘陵区“88542”水平沟整地措施下土壤微生物群落结构的空间分异特征,选取整地措施下形成的水平沟(FL)和上、下相邻水平沟间的隔坡地(GL)表层土壤为对象,通过高通量测序技术,研究整地措施下土壤微生物组成及多样性的变化及其影响环境因素。结果表明,在2种样地共检测到细菌30门、82纲和真菌13门、29纲的微生物。土壤中的主要细菌门为变形菌门、放线菌门和酸杆菌门,主要真菌门为子囊菌门、担子菌门和被孢霉门。2种样地下主要微生物类群的相对丰度存在明显差异,水平沟土壤中变形菌门和担子菌门的相对丰度分别高于隔坡地43.8%和79.6%,隔坡地土壤中放线菌门和子囊菌门的相对丰度分别高于水平沟28.1%和42.1%。α多样性显示,在2种样地间土壤细菌多样性指数无显著差异,但隔坡地上的土壤真菌Shannon、Simpson指数显著高于水平沟。此外,冗余分析显示,脲酶、微生物量碳、有机质以及全N是驱动土壤细菌和真菌群落变化的主要因子。研究结果可为黄土丘陵区整地措施后的生物地球化学过程和微生物变化机制提供理论依据和数据支撑。

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.

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.

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.

Small cell lung carcinoma with KIF5B-RET fusion partially responded to the 4^(th)-line therapy with anlotinib:A case report

BACKGROUND Small cell lung cancer(SCLC)exhibits a pronounced tendency for metastasis and relapse,and the acquisition of resistance to chemotherapy and radiotherapy,leading to complexity in treatment outcomes.It is crucial to tackle these challenges by advancing targeted therapeutic approaches in ongoing research endeavors.Variant RET fusions have been reported in several solid tumors,but are rarely reported in SCLC.CASE SUMMARY We present the first case of a KIF5B-RET fusion in a 65-year-old male patient with SCLC.To date,the patient has received the 4th line chemotherapy with anlotinib for one year and has shown a sustained favorable partial response.According to the results of next generation sequencing,this SCLC patient harbors the KIF5BRET fusion,suggesting that RET fusion could serve as a promising molecular target for SCLC treatment.Next-generation sequencing(NGS)plays a critical rolein comprehensively assessing the genotype and phenotype of cancer.CONCLUSION NGS can provide SCLC patients with personalized and targeted therapy options,thereby improving their likelihood of survival.

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.

The Reaction Sequence and Dielectric Properties of BaAl₂Ti₅O₁₄Ceramics

To investigate the correct reaction sequence of BaO-Al2O3-5TiO2 system, powders calcined at different temperatures are analyzed by x-ray diffraction. The results show that the source phase BaCO3 decomposes below 800°C, TiO2 and Al2O3 start to consume at 900 and 1100°C, respectively. BaTi4O9 phase appears at 1000°C while BaAl2Ti5O14 phase starts to reveal at 1200°C. As the temperature increases, the density, dielectric constant and quality factor of the BaAl2Ti5O14 ceramic increase and keep unchanged at 1350°C. The dielectric properties of BaAl2Ti5O14 ceramic sintered at 1350°C for 3h are: εr=35.8, Q×f=5130GHz, τf=-6.8ppm/°C.

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.