Genome organization and phylogenetic tree analysis of Garlic virus E, a new member of genus Allexivirus

The complete sequence of an Allexivirus isolated from garlic plants in Yuhang City, Zhejiang Province, China had been determined. The single-strand, positive RNA genome was 8451 nucleotides in length excluding poly(A) tail. The genome organization of this virus was similar to that of the other Allexiviruses but only with 62.8%-64.8% nucleotide acid identities. The amino acid sequences of proteins encoded by ORF1-6 shared 67.6%-78.5%, 55.4%-66.2%, 56.7%- 66.4%, 40.3%-55.6%, 66.3%-79.7% and 52.2%- 68.8% identities with those of the others respectively. The homology range between it and the other Allexiviruses was similar to that between the other distinct species in this genus. A more comprehensive comparison using all available CP amino acid sequences showed that it shared only 63.9%- 79.8% amino acids identical with the others. Therefore, it had been considered as a new member of the genus, named as garlic virus E (GarV-E). Phylogenetic analysis confirmed GarV-E as a distinct member and the correct names and classification of some members of genus Allexivirus were also discussed.     

Southern rice black-streaked dwarf virus: A new proposed <Emphasis Type="Italic">Fijivirus</Emphasis> species in the family <Emphasis Type="Italic">Reoviridae</Emphasis>

For the past several years, a novel dwarf disease has been observed on rice （Oryza sativa） in some regions of Guangdong Province and Hainan Province, southern China. Infected plants showed stunting, dark leaf and small enations on stem and leaf back. Typical Fijivirus viroplasma containing crystalline arrayed spherical virons approximately 70--75 nm in diameter and tubular structures were detected in ultrathin sections by an electron microscope in parenchyma phloem cells of the infected plants. The virus was transmitted to rice seedlings by white-backed planthoppers, Sogatella furcifera （Hemiptera： Delphacidae）, collected in the diseased fields. Analysis of dsRNA extracts from infected plants revealed ten linear segments, which were similar to the electrophoretic profile of Rice black-streaked dwarf virus （RBSDV）. RT-PCR with a single primer which matched to a linker sequence ligated to both 3＇ ends of the viral genomic dsRNAs resulted in amplification of genome segments 9 （S9） and 10 （S10） cDNA products. The complete nucleotide sequences of S9 and S10 were obtained from clones of the RT-PCR amplicon exhibited characteristic properties of Fijivirus including low GC content （34.5% and 35.6%）, genus conserved 5＇ and 3＇ termini sequences and similar genome organization. Blast searches indicated that the sequences of S9 and S10 shared 68.8%--74.9% and 67.1% --77.4% nucleotide identities with those of viruses in the Fijivirus group 2, respectively. These values were similar to those among other viruses in the Fijivirus group 2 and considerably lower than those among RBSDV isolates. Phylogenetic trees based on S9 and S10 nucleotide sequences and their putative amino acid sequences showed that this virus represented a separate branch among other Fijiviruses. The virus was also detected by a nested RT-PCR assay in corn （Zea mays）, barnyard grass （Echinochloa crusgalll）, Juncellus serotinus and flaccidgrass （Pennisetum flaccidum） in and/or adjacent to the infected rice fields. I     

Analysis of components of conserved “backbone sequences” among genomes of<Emphasis Type="Italic">Shigella</Emphasis> spp. strains

Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora- or strain-specific genes, those floras with closer relationship in the evolution also have conserved “backbone sequences”, which reveal the marks of their origin and evolution, and these “backbone sequences” are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and SG01 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%–22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common “backbone sequences”. Advanced analysis indicated that the “backbone sequences” are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore, only 20% SGO1-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains. the first two authours made equal contribution to this work.     

Identification of a novel DNA molecule associated with Tobacco leaf curl virus

A circular DNA molecule, designated as DNAβ, was identified in tobacco plants infected with Tobacco leaf curl virus (TLCV) isolates Y5 and Y8 by PCR using primers based on the conserved region of the two reported DNAβ sequences of whitefly-transmitted geminiviruses (WTGs). The complete nucleotide sequences of DNAβ of Y5 and Y8 (TLCV DNAβ) were determined. Y5 DNAβ comprises 1333 nucleotides encoding 8 predicted ORFs with 4 ORFs in virion-sense DNA and 4 ORFs in complementary-sense DNA; Y8 DNAβ consists of 1338 nucleotides encoding 7 predicted ORFs with 4 ORFs in virion-sense DNA and 3 ORFs in complementary-sense DNA. TLCV DNAβ has little sequence homology to DNA-A of TLCV., except that it shares conserved TAATATTAC loop sequence with TLCV DNA-A. Sequence comparison showed that Y5 DNAβ shared 85% sequence homology with Y8 DNAβ, and both Y5 DNAβ and Y8 DNAβ had relatively low sequence identity (51%–65%) with the reported DNAβ molecules associated with Ageratum yellow vein virus and Cotton leaf curl virus. The immunotrapping PCR and whitefly transmission tests showed that DNAβ molecule could be encapsidated in virus particle and transmitted by Bemisia tabaci. This is the first report of DNAβ associated with WTGs in China.     

鹅细小病毒CHv强毒株VP3基因克隆及遗传进化

根据Genbank中的鹅细小病毒(GPV)B株全基因序列,设计合成一对引物,应用PCR技术扩增了GPV强毒株CHv的VP3基因片段,将扩增后的VP3基因重组到pMD18-T质粒载体上,并对插入片段进行序列测定,将测序结果及由该结果推导的氨基酸序列与国内外分离的GPV、MDPV、PPV和CPV等不同宿主的细小病毒的VP3进行比对分析。结果表明:中国四川分离的GPV CHv株VP3基因长1 605 bp,编码534个氨基酸,与国内外10株GPV的VP3基因进行比较,核苷酸同源性为93.4%~99.8%,氨基酸同源性为96.5%~99.3%,其变异较小,是GPV保持一个血清型的分子基础。与番鸭细小病毒的核苷酸和氨基酸同源性分别为79.6%和89.9%,而与其他种属的细小病毒同源性均在30%以下,表明它们与GPV CHv株亲缘关系较远。     

Molecular cloning of a fulllength cDNA for ECBP21 from Angelica dahurica

ECBP21 is an extracellular calmodulin-binding protein which was first detected and purified from extracellular extracts of suspension-cultured cells of Angelica dahurica. The purified protein was electroblotted onto PVDF membrane and the amino acid sequences from 1 to 20 were determined. Using degenerate oligonucleotides of the sequence, a full-length cDNA coding for ECBP21 was isolated by a combination of RT-PCR and 5′-RACE cloning. The cDNA contains 947 nucleotides and codes for a precursor protein of 216 amino acids. The N-terminal 1–25 amino acid sequence is a predicted signal peptide and the other 26–216 amino acid sequence is a mature peptide. The 26–45 amino acid sequence shows identity with the N-terminal amino acid sequence of purified ECBP21 from Angelica dahurica. The fragment of encoding the mature protein was cloned into pET-28b(+) and transformed into E. coli BL21(DE3). A protein with relative molecular mass 21 ku was expressed in E. coli. Using a biotinylated-CaM gel overlay technique, the expression protein was tested for its ability to bind CaM. The results indicated that the expression protein is a Ca²⁺-dependent CaM-binding protein. Thus, these results further defined the cDNA clone for ECBP21. This work laid a foundation for elucidating biological functions of ECBP21 by using molecular biological means.     

Genome sequencing and characterization analysis of a Beijing isolate of chicken coronavirus infectious bronchitis virus

Avian infectious bronchitis virus (AIBV) is classified as a member of the genus coronavirus in the family coronaviridae. The enveloped virus has a positive-sense, single-stranded RNA genome of approximately 28 kilo-bases,which has a 5‘ cap structure and 3‘ polyadenylation tract.The complete genome sequence of infectious bronchitis virus (IBV), Beijing isolate, was determined by cloning sequencing and primer walking. The whole genome is 27733 nucleotides in length, has ten open reading frames:5′-orfla-orflab-s-3a-3b-e-m- 6a-6b-n-3′. Alignments of the genome sequence of IBV Beijing isolate with those of two AIBV strains and one SARS coronavirus were performed respectively. The genome sequence of IBV Beijing isolate compared with that of the IBV strain LX4 (uncompleted, 19440 bp in size) was 91.2% similarity. However, the full-length genome sequence of IBV Beijing isolate was 85.2% identity to that of IBV Strain Beaudette, and was only 50.8% homology to that of SARS coronavirus. The results showed that the genome of IBV has remarkable variation. And IBV Beijing isolate is not closely related to SARS coronavirus. Phylogenetic analyses based on the whole genome sequence, S protein, M protein and N protein, also showed that AIBV Bering isolate is lone virus in group Ⅲ and is distant from SARS coronavirus. In conclusion, this study will contribute to the studies of diagnosis and diseases control on IBV in China.     

鳜传染性脾肾坏死病毒ICR489基因序列分析

报道了鳜鱼传染性脾肾坏死病毒 (ISKNV)的ICR489基因结构及其序列分析。对ISKNVDNAKpnⅠB酶切片段的序列分析结果发现该序列中含有完整的ICR489基因。ISKNVICR489基因完整读码框为 10 11bp ,GC含量为 5 6 97% ,等电点为 6 82 ,编码一个长为 337aa、相对分子质量为 382 70的推定蛋白。结构分析发现该基因起始密码子上游具有启动子元件TATAbox,有反向重复序列可形成茎环 ,并有一段回文序列。ISKNV与其它 3种虹彩病毒 (FV3、RRV和LCDV_1)的ICR489基因氨基酸序列具有一定的同源性 ,但ISKNV与它们的同源性不高 ,序列比较和系统树分析发现ISKNV与蛙病毒属和淋巴囊肿病毒属的病毒都不尽相同     

A practical artificial diet for the diamondback moth

A new artificial diet for the diamondback moth,Plutella Xylostella (L), had been selected out successfully. The diet contained the following constituents: soybean powder, wheat germ, wheat bran powder, brewer's yeast and other constituents. So far, the diamondback moth had been reared on this artificial diet for 25 generations and still mantained its normal biological characteristics. Under 25±1 C and 60%–75%RH with 12 h PH, the results of rearing the diamondback moth on the diet as follows: egg hatch, 81.3%–94.7%; survival from eggs to pupae, 55.0%–76.7%; pupal survival, 79.7%–100%; adult emergence, 80%–100%; fecundity 94.7–144. 4 eggs/♀; pupal weight, 90.4–110.8 mg/20 pupae; average days to adult: ♀, 10.2; ♂ 13.1. The diet is not only simpler on the constituents but also have better rearing results and more rearing generations. Li Guanghong: born in June 1965, Ph.D. graduate student. Current research interest is in entomo logical physiology Supported by the State Eighth Five-Year-Plan     

Regenerating plants from cryopreserved adventitious buds of haploids in rice

A large number of adventitious buds were induced fromin vitro cultured young inflorescences of haploids of rice. Having been subcultured on solidified subculture media at 26°C for 7 days, the adventitious buds were loaded into 1.8 mL plastic cryotubes with cryoprotectant and kept on ice for 45–60 min. After cooled at a rate of 1.0°C/min down to −40°C, the samples, were kept in liquid nitrogen. The adventitious buds which have been cryopreserved for about 30 days were thawed rapidly in 38–40°C water and then plated on solidified MS medium containing 3% sucrose, 0.5 mg/L NAA and 2.0 mg/L kinetin. After plated, 23%–32% of adventitious buds resumed growth and 15%–22% regenerated plantlets. The results of this work indicated that the adventitious buds derived fromin vitro cultured young inflorescences is a critical factor for the success and subculturing adventitious buds on MS medium containing 3% sucrose and 4% sorbitol or 20% potato extract is essential to the procedure. The effective cryoprotectant is 10% DMSO (dimethyl sulfoximide)+0.5 mol/L sorbitol. Supported by the Natural Science Foundation of Hubei Province Zhang Zhihong: born in 1963, Lecturer     

A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

Severe Acute Respiratory Syndrome (SARS) is a newly identified infectious disease[1—5]. The global outbreak of SARS has been threatening the health of people worldwide and has killed 353 people and infected more than 5462 in 27 countries, as reported by WHO on April 29, 2003 (http://www.who.int/csr/sarscountry/en). Although it has been recognized that a variant of virus from the family of coronavirus might be the candidate pathogen of SARS[1—5], its identity as the unique pathogen sti…     

Rapid classification ofBacillus isolates using RAPD technique

This paper describes the typing of selectedBacillus strains from environmental origin and ATCC type strains. The objective of the study was to evaluate the usefulness of PCR-fingerprinting using Randomly Amplified Polymorphic DNA (RAPD) as a method for classifying members of the genusbacillus. Our experiments show that the levels of similarity of 69%∼90%, 40%∼60% were observed between the members of the same species and among the species of genusBacillus, respectively. In a dendrogram showing the positions of 28 strains, these strains were clearly seperated into distinct species, 13 of which are corresponding to type strains used in this study. These results suggest that RAPD analyses is a simple and powerful method for species identification and delimitation. Supported by the National Natural Science Foundation of China Yi Qingming: born in Apt. 1938, Professor     

The taxonomic status ofMoschus moschiferus anhuiensis

Since the musk deer distributed in the Dabie Mountains, Anhui was defined asMoschus moschiferus anhuiensis, its status has been disputed based on researches of morphology and ecology. This study further probed into its taxonomic status with principal components analysis (PCA) on skull measurements and mtDNA cytochrome b sequences (367 bp) analysis so as to clear its status. It is concluded that the figure and skull in Anhui musk deer are different from other species, and DNA divergence between it and other species is 6.24%–7.90%, which belongs to inter-specific difference. Thus, the study defines this musk deer as one distinct species,Moschus anhuiensis (Wang, Huet al.)     

皖贝母内生真菌的初步研究

采用平板分离法从皖贝母新鲜鳞茎、茎杆和叶中分离出2种内生真菌（A1和B1）,通过菌落形态和ITS序列确定内生菌的种属,通过DNAMAN软件多重序列比对确定与其他真菌的同源关系。结果表明,A1归为被孢霉属,与Mortierella elon-gata的ITS序列同源性高达99.44%;另一种归为青霉属,与Penicillium janthinellum的ITS序列同源性高达98.65%。     

新疆白蒜洋葱黄矮病毒的分子鉴定

从新疆吉木萨尔县采集具有条纹花叶、畸形等症状的大蒜叶片提取总RNA,利用洋葱黄矮病毒的特异性引物进行RT-PCR扩增,可得到大小为1402bp片段。将获得的片段克隆到PMD18-T载体进行序列测定和同源性比较,结果表明,OYDV新疆吉木萨尔分离物为1402个核苷酸,可编码467个氨基酸,与GeneBank中的12个OYDV核苷酸序列相比,序列同源性为80%～99%,由此推导的氨基酸序列同源性为88%～99%。     

The model of hydrocarbon generation and evolution for coal and macerals in the Tuha Basin

By means of Py-GC,¹³c NMR and fluorescent analysis, the properties of hydrocarbon generation of rnacerals are determined, and the evolution model of hydrocarbon generation is established for macerals and coal of the Tuha Basin. There are two stages of oil generation for the coal of the Tuha Basin, whoseR° values are 0.40 %–0.80 % and 0.90 %–1.20 % respectively.     

Medical image compression by applying 3D DWT in PACS

The process of image compression in a practical Picture Archiving and Communication System (PACS) was discussed with detail. To fully reduce the inter-slice correlation existing in the volumetric image sets generated by CT and MR, 3D Discrete Wavelet Transformation (DWT) was introduced in our application. Instead of using a fixed quantizer of lossless low frequency and distinct loss of high frequency, an adaptive quantizer was devised taking MSE as the performance index. In the low frequency subband, DPCM was replaced withS+P transform to facilitate coding computation. Compared with JPEG or 2D DWT, our method is 20%–50% more efficient. Furthermore, preliminary tests showed that 33 dB may be the maximal distortion threshold for CT images. Biography: WANG Si-xian(1944-), male, Associate professor. Research direction: image processing.     

A competitive dual-label time-resolved fluoroimmunoassay for the simultaneous determination of chloramphenicol and ractopamine in swine tissue

A novel dual-label time-resolved fluoroimmunoassay method was developed for the simultaneous determination of chloramphenicol (CAP) and ractopamine (RAC) residues in 18 swine tissue samples, using anti-CAP and anti-RAC monoclonal antibodies labeled with europium (Eu³⁺) and samarium (Sm³⁺), respectively. The detection limits for CAP and RAC were 0.06 and 0.25 ng/g. The recovery from swine muscle samples was 102%–121% for CAP at spiking levels of 0.1–5 ng/g, and 69.8%–85.8% for RAC at spiking levels of 1–10 ng/g. The results obtained from the swine tissue samples using this method showed good agreement with those obtained using ELISA and GC-MS, with correlation coefficients (R) between 0.92–0.98.     

Tobacco curly shoot virus isolated in Yunnan is a distinct species of Begomovirus

Virus isolate Y1 was obtained from tobacco showing curly shoot symptoms in Baoshan, Yunnan Province. Whitefly transmission test and virion morphology observation showed that it is a begomovirus. In reactions with 14 monoclonal antibodies raised against begomoviruses, Y1 was readily differentiated from begomoviruses reported in China, Pakistan and India. The complete nucleotide sequence of DNA-A was determined, it contains 2746 nucleotides, with two ORFs in virion-sense DNA and four ORFs in complementary-sense DNA. Comparisons with total DNA-A, intergenic region and deduced amino acid sequences of individual ORFs showed that Yl is a distinct Begomovirus species, for which the name Tobacco curly shoot virus (TCSV) is proposed. The total DNA-A of TCSV is most closely related to that of Tomato leaf curl virus from India (85% sequence identity). In contrast, the deduced coat protein of TCSV is most like that of Cotton leaf curl virus 72b isolate from Pakistan (98% amino acid sequence identity).