Pathogenicity of diatraea saccharalis densovirus to host insets and characterization of its viral genome

Pathogenicity of the Diatraea saccharalis densovirus (DsDNV) was tested on its host larvae.The results showed that up to 4 days after inoculation,no larvae mortality was observed and the infected larvae started to exhibit the infection symptoms from the fourth day.After 5 days of infection,the cumulative mortality of infected larvae increased significantly and reached 60% after 12 days and 100% after 21 days of infection,whereas that of the control group was only 10% and 20%,respectively,after same periods of infection,suggesting that the high mortality of infected larvae groups was due to the high pathogenicity of DsDNV.The size of the DsDNA was determined by Electron microscopy visualization of viral DNA molecules and gel electrophoresis of both native and endonuclease digested DNA fragments.The total length of the native DsDNA was about 5.95 kb.The DsDNV DNA was digested with 16 restriction enzymes and a restriction map of those enzymes was constructed with 41 restriction sites.Comparison of the restriction map of the DsDNV genome with those of the genomes ofJunonia coenia densovirus (JcDNV) and Galleria mellonella densovirus (GmDNV) indicated that the three densovirus genomes were found to share many identical restriction sites.Thus,most of the restriction sites of the following endonucleases Bam H Ⅰ,Hha Ⅰ,Xba Ⅰ,Cla Ⅰ,Asp 700,Spe Ⅰ,Nco Ⅰ and Bcl Ⅰ,were found to be conserved among the three densovirus genomes.Symmetrical cleavage sites mapped at the both ends of the genome suggested the presence of inverted terminal repeats (ITRs) whose size was estimated to be about 500 bp.The similar genome size,almost identical restriction sites and presence of an ITR of about 500 bp for these three densoviruses suggested that they belong to the same group of ambisense densoviruses.     

浓核病毒分子生物学特性研究进展

浓核病毒是只感染无脊椎动物的细小病毒.该病毒颗粒直径为19～24 nm,无囊膜包裹,呈二十面体对称.病毒基因组为4～6 kb的单链线性DNA,基因组末端是与DNA复制相关的反向重复序列.浓核病毒的基因组包含编码非结构蛋白和衣壳蛋白的基因.对近年来关于浓核病毒分子生物学方面的研究取得的新进展进行了综述,介绍了浓核病毒基因组结构的分类和单双义浓核病毒的表达策略,以及浓核病毒在作为表达载体和生物防治方面的潜在应用能力.     

Analysis of Aleutian disease virus infection in vitro and in vivo: demonstration of Aleutian disease virus DNA in tissues of infected mink.

Aleutian disease virus (ADV) infection was analyzed in vivo and in vitro to compare virus replication in cell culture and in mink. Initial experiments compared cultures of Crandell feline kidney (CRFK) cells infected with the avirulent ADV-G strain or the highly virulent Utah I ADV. The number of ADV-infected cells was estimated by calculating the percentage of cells displaying ADV antigen by immunofluorescence (IFA), and several parameters of infection were determined. Infected cells contained large quantities of viral DNA (more than 10(5) genomes per infected cell) as estimated by dot-blot DNA-DNA hybridization, and much of the viral DNA, when analyzed by Southern blot hybridization, was found to be of a 4.8-kilobase-pair duplex monomeric replicative form (DM DNA). Furthermore, the cultures contained 7 to 67 fluorescence-forming units (FFU) per infected cell, and the ADV genome per FFU ratio ranged between 2 X 10(3) and 164 X 10(3). Finally, the pattern of viral antigen detected by IFA was characteristically nuclear, although cytoplasmic fluorescence was often found in the same cells. Because no difference was noted between the two virus strains when cultures containing similar numbers of infected cells were compared, it seemed that both viruses behaved similarly in infected cell culture. These data were used as a basis for the analysis of infection of mink by virulent Utah I ADV. Ten days after infection, the highest levels of viral DNA were detected in spleen (373 genomes per cell), mesenteric lymph node (MLN; 750 genomes per cell), and liver (373 genomes per cell). In marked contrast to infected CRFK cells, the predominant species of ADV DNA in all tissues was single-stranded virion DNA; however, 4.8-kilobase-pair DM DNA was found in MLN and spleen. This observation suggested that MLN and spleen were sites of virus replication, but that the DNA found in liver reflected sequestration of virus produced elsewhere. A final set of experiments examined MLN taken from nine mink 10 days after Utah I ADV infection. All of the nodes contained ADV DNA (46 to 750 genomes per cell), and although single-stranded virion DNA was always the most abundant species, DM DNA was observed. All of the lymph nodes contained virus infectious for CRFK cells, but when the genome per FFU ratio was calculated, virus from the lymph nodes required almost 1,000 times more genomes to produce an FFU than did virus prepared from infected cell cultures.(ABSTRACT TRUNCATED AT 400 WORDS)     

Revised selection criteria for candidate restriction enzymes in genome walking

A new method to improve the efficiency of flanking sequence identification by genome walking was developed based on an expanded, sequential list of criteria for selecting candidate enzymes, plus several other optimization steps. These criteria include: step (1) initially choosing the most appropriate restriction enzyme according to the average fragment size produced by each enzyme determined using in silico digestion of genomic DNA, step (2) evaluating the in silico frequency of fragment size distribution between individual chromosomes, step (3) selecting those enzymes that generate fragments with the majority between 100 bp and 3,000 bp, step (4) weighing the advantages and disadvantages of blunt-end sites vs. cohesive-end sites, step (5) elimination of methylation sensitive enzymes with methylation-insensitive isoschizomers, and step (6) elimination of enzymes with recognition sites within the binary vector sequence (T-DNA and plasmid backbone). Step (7) includes the selection of a second restriction enzyme with highest number of recognition sites within regions not covered by the first restriction enzyme. Step (8) considers primer and adapter sequence optimization, selecting the best adapter-primer pairs according to their hairpin/dimers and secondary structure. In step (9), the efficiency of genomic library development was improved by column-filtration of digested DNA to remove restriction enzyme and phosphatase enzyme, and most important, to remove small genomic fragments (<100 bp) lacking the T-DNA insertion, hence improving the chance of ligation between adapters and fragments harbouring a T-DNA. Two enzymes, NsiI and NdeI, fit these criteria for the Arabidopsis thaliana genome. Their efficiency was assessed using 54 T(3) lines from an Arabidopsis SK enhancer population. Over 70% success rate was achieved in amplifying the flanking sequences of these lines. This strategy was also tested with Brachypodium distachyon to demonstrate its applicability to other larger genomes.     

Tandem repeats within the inverted terminal repetition of vaccinia virus DNA

A tandemly repeated sequence within the genome of vaccinia virus is cut to fragments of approximately 70 bp by Hinf I, Taq I or Mbo II. The 70 bp repetition was localized within the much larger (10,300 bp) inverted terminal repetition by restriction analysis of cloned DNA fragments and by hybridization of the purified 70 bp repeat to vaccinia virus DNA restriction fragments. The molar abundance of the 70 bp fragment corresponds to a 30 fold repetition at each end of the genome. The repeating restriction endonuclease sites were mapped by agarose gel electrophoresis of partial Hinf I digests of the terminally labeled cloned DNA fragment. The first of 13 repetitive Hinf I sites occurred approximately 150 bp from the end of the cloned DNA. After an intervening sequence of approximately 435 bp, a second series of 17 repetitive Hinf I sites occurred. The DNA between the two blocks of repetitions has a unique sequence containing single Dde I, Alu I and Sau 3A sites. Tandem repeats within the inverted terminal repetition could serve to accelerate self-annealing of single strands of DNA to form circular structures during replication.     

胆型螺旋杆菌(Helicobacter bilis)的分离、鉴定与序列分析

鉴定分离到的微需氧菌为螺旋杆菌,并对该菌进行分型。小鼠皮下或肌肉注射地塞米松使其免疫抑制,取小鼠肠内容物培养,对分离到的细菌,经油镜,电镜观察,然后提取细菌DNA,用根据螺旋杆菌（Helicobacter sp.)rRNA保守区设计的引物P7/P8进行扩增,并对扩增产物分别用MboI,HhaI,XspI内切酶酶切,酶切产物用10%PAGE分析。再用根据螺旋杆菌胆型（H.bilis)rRNA设计特异引物P7/Pb扩增,将扩增产物测序分析。最后。将该细菌在Scid小鼠上作动物感染。细菌在油镜下呈鸟翼状,电镜下观察到双极鞭毛。无周质纤毛。引物P7/P8扩增出374bp的特异带,此片段能分别被MboI,HhaI,Zsp内切酶酶切,引物P7/Pb扩增出364bp的条带,测得的DNA序列中存在MboI,HhaI,Xsp内切酶酶切。引物P7/Pb扩增出364bp的条带,测得的DNA序列中存在MboI,HhaI,XspI的内切位点,与文献中H.bilis序列比较,同源性为97.5%。动物感染试验符合Koch准则。分离到的细菌确为胆型螺旋杆菌。     

Genome size of Myxococcus xanthus determined by pulsed-field gel electrophoresis.

Genomic DNA of the myxobacterium Myxococcus xanthus was digested with the rare cutting restriction endonuclease AseI or SpeI, and the restriction products were separated by pulsed-field gel electrophoresis. Transposons Tn5-132 and Tn5 lac, which contain AseI restriction sites, were used to determine the number of restriction fragments in each band. The size of the genome was determined by adding the molecular sizes of the restriction products. The genomes of strains DK101, MD2, and DZF1 have identical restriction patterns and were estimated to be 9,454 +/- 101 kilobase pairs from the AseI digestions and 9,453 +/- 106 kilobase pairs from the SpeI digestions. DK1622, which was derived from DK101 by treatment with UV light, has suffered a 220- to 222-kilobase-pair deletion that removed an AseI and an SpeI restriction site. The deleted DNA may consist exclusively of Mx alpha-associated sequences.     

Infection and pathogenicity of the mosquito densoviruses AeDNV, HeDNV, and APeDNV in Aedes aegypti mosquitoes (Diptera: Culicidae)

These studies compared three genetically distinct mosquito densoviruses Aedes aegypti (AeDNV), Hemagogus equinus (HeDNV), and Aedes Peruvian (APeDNV) densoviruses in a laboratory investigation to begin to evaluate their potential as mosquito control agents. A real-time polymerase chain reaction (PCR) assay for quantification of viral genomes and a standardized mosquito infection protocol were developed. Mortality associated with exposure to AeDNV increased in a dose-dependent manner, with the maximum mortality of 75.1% occurring in those organisms exposed to the highest dose of virus. The majority of death occurred as larvae. Similar results were observed with AeDNV produced from ground larvae and AeDNV produced from cell culture. Exposure of mosquitoes to HeDNV and APeDNV resulted in lower mortality, with values peaking at 33.5% for HeDNV and 27.8% for APeDNV. AeDNV-exposed larvae develop at a slower rate than nonexposed and HeDNV- and APeDNV-exposed larvae. Decreased virulence does not reflect a decrease in virus replication. PCR analysis of infectivity rates and titers in adults revealed reproduction of all three viruses, with an average viral titer of approximately 10 logs/mosquito after exposure to the highest dose of each virus. Accumulation of virus in the larval-rearing water was also observed with values approaching 10-11 logs/ml for each virus. These data indicate that there are dramatic differences in the pathogenicity among mosquito densoviruses.     

鳞翅目基因组IIB型内切酶位点的统计分析

IIB型限制内切酶能够识别并切割特异酶切位点两端特定距离的DNA,形成粘性末端的30 bp左右的等长DNA片段。利用其特性与限制性酶切位点关联测序技术(RAD)相结合发展出2b-RAD简化基因组测序技术,应用于遗传图谱构建、种群遗传结构分析、性状定位以及细菌分型等多种研究领域。构建2b-RAD测序文库之前,需要对基因组中的IIB型限制内切酶位点进行预测与统计分析,制定有效的测序文库构建方案。本文利用Python语言构建分析基因组中IIB型限制内切酶位点的流程,预测并统计6个鳞翅目代表物种基因组含有的8个商业化IIB型限制内切酶的酶切位点,比较了各个基因组与IIB型限制内切酶之间含有的酶切位点总量、重复序列数量以及酶切间隔长度的关系,为在昆虫基因组中进一步试行2b-RAD研究提供了参考。     

Detection and mapping of homologous, repeated and amplified DNA sequences by DNA renaturation in agarose gels.

A new molecular hybridization approach to the analysis of complex genomes has been developed. Tracer and driver DNAs were digested with the same restriction enzyme(s), and tracer DNA was labeled with 32P using T4 DNA polymerase. Tracer DNA was mixed with an excess amount of driver, and the mixture was electrophoresed in an agarose gel. Following electrophoresis, DNA was alkali-denatured in situ and allowed to reanneal in the gel, so that tracer DNA fragments could hybridize to the driver only when homologous driver DNA sequences were present at the same place in the gel, i.e. within a restriction fragment of the same size. After reannealing, unhybridized single-stranded DNA was digested in situ with S1 nuclease. The hybridized tracer DNA was detected by autoradiography. The general applicability of this technique was demonstrated in the following experiments. The common EcoRI restriction fragments were identified in the genomes of E. coli and four other species of bacteria. Two of these fragments are conserved in all Enterobacteriaceae. In other experiments, repeated EcoRI fragments of eukaryotic DNA were visualized as bands of various intensity after reassociation of a total genomic restriction digest in the gel. The situation of gene amplification was modeled by the addition of varying amounts of lambda phage DNA to eukaryotic DNA prior to restriction enzyme digestion. Restriction fragments of lambda DNA were detectable at a ratio of 15 copies per chicken genome and 30 copies per human genome. This approach was used to detect amplified DNA fragments in methotrexate (MTX)-resistant mouse cells and to identify commonly amplified fragments in two independently derived MTX-resistant lines.     

Molecular cloning of unintegrated visna viral DNA and characterization of frequent deletions in the 3' terminus

Visna viral DNA, like other retroviral DNA, exists in two circular forms in infected cells. The larger probably contains two copies of the LTR, the smaller, one copy. Recombinant DNA techniques were used to clone unintegrated circular visna viral DNA in the lambda WES . lambda B vector. Circular visna viral DNA was digested with the restriction enzyme SstI, which yields a 9.2-kb viral DNA fragment containing 90% of the viral genome colinear with the restriction map of linear viral DNA. This fragment extends from a site about 900 bp from the left (5') end of the viral DNA molecule, through the 3' region, including U3 and R sequences at its right (3') end. The recombinant clones isolated contain visna viral DNA inserts which range in size from 3.1 kb to 9.2 kb. All the clones contain the 5' region intact, but most had sustained deletions of varying lengths in the 3' terminal region of the cloned fragment.     

Determination of Gardnerella vaginalis Genome Size by Pulsed-Field Gel Electrophoresis

The chromosomal DNA of four strains of Gardnerella vaginaliswere digested with rare cutting restriction enzymes and analyzedby pulsed-field gel electrophoresis (PFGE). The four strainsstudied were two clinical isolates (GVP 004 & GVP 007) andtwo American Type Culture Collection strains (ATCC 14018 &ATCC 14019). The restriction enzyme SfiI generated two DNA fragmentsof about 0.6 Mb and 1.1 Mb in all four strains giving a G. vaginalisgenome size of about 1.7 Mb. A similar genome size was calculatedutilizing two more GC-rich sequence specific restriction endonucleases,NotI and AscI. When digested with AscI, the chromosomal DNAof all four strains gave rise to 11 to 12 DNA fragments rangingbetween 0.01 Mb to 0.43 Mb. DNA from the two clinical isolateswere digested by NotI (yielding 7 to 9 fragments), while theDNA from the two ATCC strains were resistant to NotI digestion.In contrast to the clinical isolates, DNA from the two ATCCstrains gave an identical profile for all restriction endonucleasestested. From double digestion experiments, the two SfiI sitescould be localized on two AscI fragments. From these PFGE studies,it is concluded that the G. vaginalis genome is a circular DNAthat ranges between 1.67 Mb and 1.72 Mb in size.     

5-Variable genome sequence of the LIVP vaccinia virus. A possible role for short direct repeats in the formation of deletions]

HindIII-O/N DNA fragments of vaccinia virus (VV) of the LIVP strain were mapped using thirteen restriction endonucleases. Nucleotide sequences of the HindIII-O fragment (1530 bp) as well as of a site of the HindIII-N genome fragment 353 bp in size were determined. Comparison of restriction maps and nucleotide sequences of VV strains (WR and LIVP) demonstrated that DNA of VV LIVP contained % deletions and 2 insertions. "Reliable" short direct repeats were localized and their possible role in formation of DNA deletions was shown. It was suggested that VV endonuclease and DNA-ligase participate in replication and repair processes. Mechanism of formation of variable sequences of viral genomes is discussed.     

Human cytomegalovirus DNA replicates after early circularization by concatemer formation, and inversion occurs within the concatemer.

To determine the replicative mechanism for human cytomegalovirus (HCMV) DNA, field inversion gel electrophoresis was used to separate HCMV replicative DNAs during lytic infection. Unit-length circular HCMV genomes lacking terminal restriction fragments were detected starting 4 h after infection even when cells were treated with aphidicolin, phosphonoacetic acid, or cycloheximide. Viral DNA synthesis began 24 h after infection and produced large amounts of high-molecular-weight replicative DNA that was a precursor of progeny genomes. Replicative DNA contained rare terminal restriction fragments, and long-arm termini were much less frequent than short-arm termini. Replicative DNA was not composed of unit-length circles because low-dose gamma irradiation of replicative DNA generated numerous random high-molecular-weight fragments rather than unit-length molecules. PacI digestion of replicative DNA from a recombinant HCMV with two closely spaced PacI sites revealed that replicative DNA is concatemeric and genome segment inversion occurs after concatemer synthesis. These results show that after circularization of the parental genome, DNA synthesis produces concatemers and genomic inversion occurs within concatemeric DNA. The results further suggest that concatemers acquire genomic termini during the cleavage/packaging process which preferentially inserts short-arm termini into empty capsids, causing a predominance of short-arm termini on the concatemer.     

Identification and characterization of a baculovirus from Lonomia obliqua (Lepidoptera: Saturniidae)

A baculovirus has been isolated from larvae of Lonomia obliqua, a Saturniidae of medical importance due to a potent toxin found in their spines. Electron Microscopy analysis of the occlusion body obtained from diseased larvae showed polyhedra of approximately 1 microm in diameter containing multiple nucleocapsids per envelope. This baculovirus was thus named Lonomia obliqua multicapsid nucleopolyhedrovirus (LoobMNPV). Restriction endonuclease profiles of viral DNA digested with three restriction enzymes were obtained and the genome size was estimated to be 95.52 +/- 2.3 kbp. The polyhedrin gene of LoobMNPV was identified and its DNA sequence was determined. Phylogenetic analysis of the polyhedrin gene showed that the LoobMNPV polyhedrin belongs to group I NPV and that it is closely related to the polyhedrin of the NPV of Amsacta albistriga.     

Analysis of cellular integration sites in avian sarcoma virus infected duck embryo cells.

The cellular sites of integration of avian sarcoma virus (ASV) have been examined in clones of duck embryo cells infected with the Bratislava 77 strain of ASV using restriction endonuclease digestion, agarose gel electrophoresis, Southern blotting, and hybridization with labeled ASV complementary DNA probes. DNA prepared from 11 clones of duck embryo cells infected with the Bratislava 77 strain of ASV was digested with the restriction enzymes HpaI, which cleaves once within the viral genome, and Hind III, which cleaves twice within the viral genome, and the virus-cell DNA juncture fragments were resolved by agarose gel electrophoresis. Analysis of the virus-cell junctures present in individual ASV-infected duck embryo clones revealed that all clones contain at least one copy of nondefective proviral DNA with some clones containing as many as 5 to 6 copies of proviral DNA. A comparison of the virus-cell juncture fragments present in different ASV-infected clones showed that each clone contains a unique set of virus-cell junctures. These data suggest that ASV DNA can integrate at multiple sites within the duck embryo cell genome and that these sites appear to be different as defined by digestion with the restriction enzymes HpaI and HindIII.     

Genome analysis of Clostridium botulinum type A by pulsed-field gel electrophoresis.

Genomic DNA from type A Clostridium botulinum was digested with restriction endonucleases that cut at rare sites, and the large fragments were separated by pulsed-field gel electrophoresis. Of 15 restriction enzymes tested, MluI, RsrII, SmaI, NruI, KspI, NaeI, and XhoI generated satisfactory digestion patterns of genomic DNA of various C. botulinum strains, enabling the use of the method for genomic fingerprinting. The genomes of four group I (type A) C. botulinum strains examined had similar restriction patterns. However, each strain had unique digestion patterns, reflecting genotypic differences. The genome size of C. botulinum strain 62A was estimated to be 4,039 +/- 40 kbp from the summation of restriction fragments from MluI, RsrII, and SmaI digestions. Genes encoding proteins involved in the toxinogenicity of C. botulinum, including neurotoxin, hemagglutinin A, and genes for a temperate phage, as well as various transposon Tn916 insertion sites in C. botulinum 62A, were mapped by pulsed-field gel electrophoresis. The genes encoding neurotoxin and hemagglutinin A-1, were located on the same fragment in several cases, indicating their probable physical linkage. The macrorestriction analysis established here should be useful for genetic and epidemiological studies of C. botulinum.     

Topographical distribution of 5-methylcytosine in animal and plant DNA.

The topographical distribution of 5-methylcytosine on animal and plant cell DNA has been examined with methyl-sensitive restriction enzymes and gel electrophoresis analysis. These DNAs digested with the enzyme HpaII have a partially bimodal size distribution, indicating the existence of clusters of methylated and unmethylated CCGG sites in the DNA. By analyzing the methylation state of all CG moieties in restricted DNA fractions, it was possible to show that these genomes are, in general, arranged as clusters of relatively highly methylated and undermethylated regions. Plant DNA also contains 5-methylcytosine in the prototype sequence C-X-G. Restriction of this DNA with EcoRII revealed that these methyl groups are also distributed in clusters, suggesting that this is a general phenomenon. The undermethylated areas may correspond to the active fraction of the genome.     

Structural organization and evolution of the plastid genome of Vaucheria sessilis (Xanthophyceae)

The plastid DNAs of 18 Vaucheria sessilis strains from various habitats in western Europe were digested with the restriction endonucleases Eco RI, Sal I, Bam HI and Pvu II. Their restriction patterns showed variable fragment divergencies. Two main groups of plastid genomes were recognized, which were substantiated by morphological features. The differences among the restriction patterns could be attributed to the loss or appearance of restriction sites and to minor size variations caused by deletions/insertions. The Sal I and Bam HI restriction sites which together discriminate six different plastid genomes were mapped on the circular molecule of 124 kilobase paris (kbp). The plastid genomes of several Vaucheria sessilis strains were shown to exist in two inversion isomers caused by intramolecular recombination within the inverted repeat segments.     

Identification of two families of satellite-like repetitive DNA sequences from the zebrafish (Brachydanio rerio).

To further our understanding of the structure and organization of the zebrafish genome, we have undertaken the analysis of highly and middle-repetitive DNA sequences. We have cloned and sequenced two families of tandemly repeated DNA fragments. The monomer units of the Type I satellite-like sequence are 186 bp long, A+T-rich (65%), and exhibit a high degree of sequence conservation. The Type I satellite-like sequence constitutes 8% of the zebrafish genome, or approximately 8 x 10(5) copies per haploid genome. Southern analysis of genomic DNA, digested with several restriction endonucleases, shows a ladder of hybridizing bands, consistent with a tandem array, and suggests longer range periodic variations in the sequence of the tandem repeats. The Type II satellite has a monomer length of 165 bp, is also A+T-rich (68%), and constitutes 0.2% of the zebrafish genome (22,000 copies per haploid genome). Southern analysis reveals a complex pattern rather than a ladder of regularly spaced hybridizing bands.