Dot-Blot Hybridization for Detection of Five Cucurbit Viruses by Digoxigenin-Labelled cDNA Probes

Dot-blot hybridization was applied in this paper to detect five viruses infecting cucurbitaceous crops, Zuccini yellow mosaic virus （ZYMV）, Watermelon mosaic virus （WMV）, Cucumber mosaic virus （CMV）, Papaya ringspot viruswatermelon strain （PRSV-W） and Squash mosaic virus （SqMV）, as a good alternative assay in seed health test and epidemiological and transgenic research. Digoxigenin-labelled cDNA probes of the five viruses were synthesized by PCR with the specific primers and applied in dot-blot hybridization to detect five viruses in crude extraction of the infected leaves. And three SqMV probes of different lengths （0.55, 1.6, and 2.7 kb, respectively） were designed to investigate the effect of hybridization. The results showed that the sensitivity for detecting the crude extraction of infected leaves by ZYMV, WMV, CMV, PRSV-W, and SqMV was down to 1：160, 1：160, 1：320, 1：160, and 1：320, respectively. Three SqMV probes of different length showed no differences on the sensitivity and specificity. The digoxigenin-labelled probes prepared by PCR could be used for accurate and rapid identification of 5 viruses infecting cucurbitaceous crops with good stabilities, sensitivities, specificity, and reproducibilifies.

The Distribution of Repetitive DNAs Along Chromosomes in Plants Revealed by Self-genomic in situ Hybridization

The distribution of repetitive DNAs along chromosomes is one of the crucial elements for understanding the organization and the evolution of plant genomes. Using a modified genomic in situ hybridization （GISH） procedure, fluorescence in situ hybridization （FISH） with genomic DNA to their own chromosomes （called self-genomic in situ hybridization, self-GISH） was carried out in six selected plant species with different genome size and amount of repetitive DNA. Nonuniform distribution of the fluorescent labeled probe DNA was observed on the chromosomes of all the species that were tested. The signal patterns varied among species and were related to the genome size. The chromosomes of the small Arabidopsis genome were labeled almost only in the pericentromeric regions and the nucleolus organizer regions （NORs）. The signals in the relatively small genomes, rice, sorghum, and Brassica oleracea var. capitata L., were dispersed along the chromosome lengths, with a predominant distribution in the pericentromeric or proximal regions and some heterochromatic arms. All chromosomes of the large genomes, maize and barley, were densely labeled with strongly labeled regions and weakly labeled or unlabeled regions being arranged alternatively throughout the lengths. In addition, enhanced signal bands were shown in all pericentromeres and the NORs in B. oleracea var. capitata, and in all pericentromeric regions and certain intercalary sites in barley. The enhanced signal band pattern in barley was found consistent with the N-banding pattern of this species. The GISH with self-genomic DNA was compared with FISH with Cot-1 DNA in rice, and their signal patterns are found to be basically consistent. Our results showed that the self-GISH signals actually reflected the hybridization of genomic repetitive DNAs to the chromosomes, thus the self-GISH technique would be useful for revealing the distribution of the regions where repetitive DNAs concentrate along chromosomes and some chromatin differentiation associated with repetitive DNAs in plants.

Detection of hepatitis B virus DNA by real-time PCR using TaqMan-MGB probe technology

AIM: To develop a real-time PCR for detecting hepatitis B virus-(HBV) DNA based on TaqMan technology using a new MGB probe.METHODS: Plasmid containing the sequence of X gene (1414-1744 nt) was constructed as HBV-DNA standard for quantitative analysis. A TaqMan-MGB probe between primers for amplification was designed to detect PCR products. The interested sequence contained in the plasmid and in clinical specimens was quantitatively measured.RESULTS: The detection limit of the assay for HBV DNA was 1 genome equivalent per reaction. A linear standard curve was obtained between 100 and 109 DNA copies/reaction (r＞0.990). None of the negative control samples showed false-positive reactions in duplicate. HBV DNA was detected in 100% (50/50) of HBV patients with HbeAg, and in 72.0% (36/50) with HBsAg, HBeAb and HBcAb. The coefficient of variation for both intra- and inter-experimental variability demonstrated high reproducibility and accuracy.CONCLUSION: Real-time PCR based on TaqMan-MGB probe technology is an excellent method for detection of HBV DNA.

Detection of H.pylori DNA in gastric epithelial cells by in situ hybridization

AIM: To investigate the presence of H.pylori DNA within gastric epithelial cells in patients with H.pylori infection and its possible carcinogenic mechanism. METHODS: Total 112 patients, with pathologically confirmed chronic superficial gastritis, chronic atrophic gastritis, intestinal metaplasia, atypical hyperplasia or gastric cancer were studied. Among them, 28 were H.pylori negative and 84 H.pylori positive. H.pylori DNA in gastric epithelial cells was detected by GenPoint catalyzed signal amplification system for in situ hybridization. RESULTS: In the H.pylori positive group, zero out of 24 chronic superficial gastritis (0.0%), four out of 25 precancerous changes (16.0%) and thirteen out of 35 gastric cancers (37.1%) showed H.pylori DNA in the nucleus of gastric epithelial cells, the positive rates of H.pylori DNA in the nucleus of gastric epithelial cells were progressively increased in chronic superficial gastritis, precancerous changes and gastric cancer groups (chi(2)=12.56, P=0.002); One out of 24 chronic superficial gastritis (4.2%), eleven out of 25 precancerous changes (44.0%) and thirteen out of 35 gastric cancers (37.1%) showed H.pylori DNA in the cytoplasm of gastric epithelial cells (chi(2)=10.86, P=0.004). In the H.pylori negative group, only one patient with gastric cancer was found H.pylori DNA in the nucleus of gastric epithelial cells; Only two patients, one patient with precancerous changes and another with gastric cancer, showed H.pylori DNA in the cytoplasm of gastric epithelial cells. Furthermore, H.pylori DNA must have been in the cytoplasm as long as it existed in the nucleus of gastric epithelial cells. CONCLUSION: H.pylori DNA exists both in the nucleus and the cytoplasm of gastric epithelial cells in patients with H.pylori infections. The pathological progression from chronic superficial gastritis, precancerous changes to gastric cancer is associated with higher positive rates of H.pylori DNA presence in the nucleus of gastric epithelial cells.

Development of taxonomic rRNA-targeted probes of two harmful algae: Prorocentrum minimum and Karenia mikimotoi by fluorescence in situ hybridization

Harmful algal blooms recently have been under the spotlight throughout the world, because of their nega- tive impact on the marine environment, aquaculture, fisheries as well as public health. The development of methods for rapid and precise identification and quantification of causative species is essential for the warning and monitoring of blooms, among which the techniques based on taxonomic probes are the most favored. In this study, two harmful algae, i.e., Prorocentrum minimum and Karenia mikimotoi were tak- en into consideration. The partial large subunit rDNA （D1-D2） of both species were firstly PCR-amplified, cloned and sequenced. The obtained sequences were then introduced to carry out alignment analysis for gene specific regions. Three respective candidate probes for each species were designed and used to screen the optimal probe by performing fluorescence in situ hybridization （FISH） tests. The results showed that the probes Pmin0443 and Kmik0602 displayed the best hybridization for P. minimum and K.. mikimotoi, respectively. Both the specific （taxonomic） （Pmin0443 and Kmik0602） and the control probes （UniC0512 and UniR0499） were used for cross-reactivity tests with other microalgae in our laboratory. The probes Pmin0443 and Kmik0602 are specific and could be served as taxonomic probes introduced into the tech- niques targeting rRNA, such as FISH, sandwich hybridization, and DNA-microarray assay of P minimum and K. mikimotoi in the future. Finally, FISH analyses with both probes were performed on the simulated field samples. The probes could hybridize exclusively with the target cells well, and no significant differ- ence （p 〉0.05） was observed in the cell densities of the samples determined by FISH and light microscopy （LM）. All suggest that the probes are specific and could be introduced into FISH for the monitoring of both harmful algae.

DNA methylation modification in heterosis initiation through analyzing rice hybrid contemporary seeds

Heterosis is an important biological phenomenon and widely applied in agriculture.Although many studies have been performed by using vegetative organs of F_(1) hybrid plants,how heterosis (or hybrid vigor) is initiated and formed,particularly the underlying molecular mechanism,remain elusive.Hybrid contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA methylation.Genes,especially those relate to hormones function and transcriptional regulation present non-additive methylation.Previously identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds,suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F_(1) hybrid vegetative tissues after germination,demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F_(1) hybrid plants.Notably,a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids,suggesting that endosperm might also contribute to heterosis.

Prediction of the Best Three-Breed Hybridized Combination of Imported Meat Sheep Using Genetic Polymorphism of Microsatellite DNA

The allelic frequency, the polymorphic information contents （PIC）, the number of effective alleles, the heterozygosity, and the genetic distances were studied in three imported meat sheep （Suffolk, Dorset, Texel） and their F1 crossbred obtained from those crossed with indigenous Small Tail Hun Sheep （Suffolk♂× Small Tail Hun Sheep, SH; Dorset ♂× Small Tail Han Sheep♂, DH; Texel♂× Small Tail Hart Sheep ♀, TH） using six microsatellite DNA loci. The perpormences of three-breed crossbred （Suffolk ♂× DH ♀, Suffolk ♂× TH ♀, Texel ♂× SH ♀, Texel ♂× DH ♀, Dorset ♂× TH ♀, and Dorset ♂× SH ♀ ） were tested. The results indicated that there were genetic polymorphisms at six microsatellite loci in six sheep populations. Six microsatellite loci could be used for genetic diversity evaluation in sheep populations. The order of three-breed heterosis by the analysis of genetic relationship from large to small was Texel ♂× DH ♀, Suffolk ♂× DH ♀, Suffolki ♂× TH ♀, Texel ♂× SH ♀, Dorset ♂×TH ♀, and Dorset ♂× SH ♀, which was in accordance with the testing results on actual heterosis. These results showed that prediction of the best three-breed hybridized combination among sheep breeds by microsatellite DNA polymorphism was feasible, which will have an important value on the reasonable utilization of introduced meat sheep and sheep breeding in our country in the future.

Application of rRNA probes and fluorescence in situ hybridization for rapid detection of the toxic dinoflagellate Alexandrium minutum

The dinoflagellate Alexandrium minutum is often associated with harmful algal blooms (HABs). This species consists of many strains that differ in their ability to produce toxins but have similar morphology, making identification difficult. In this study, species-specific rRNA probes were designed for whole-cell fluorescence in situ hybridization (FISH) to distinguish A. minutum from two phylogenetic clades. We acquired the complete SSU to LSU rDNA sequences (GenBank accession numbers JF906989-JF906999) of 11 Alexandrium strains and used these to design rRNA targeted oligonucleotide probes. Three ribotype-specific probes, M-GC-1, M-PC-2, and M-PC-3, were designed. The former is specific for the GC clade ("Global clade") of A. minutum, the majority of which have been found non-toxic, and the latter two are specific for the PSP (paralytic shellfish poisoning)-producing PC clade ("Pacific clade"). The specificity of these three probes was confirmed by FISH. All cells in observed fields of view were fluorescently labeled when probes and target species were incubated under optimized FISH conditions. However, the accessibility of rRNA molecules in ribosomes varied among the probe binding positions. Thus, there was variation in the distribution of positive signals in labeled cells within nucleolus and cytosol (M-GC-1, M-PC-3), or just nucleolus (M-PC-2). Our results provide a methodological basis for studying the biogeography and population dynamics of A. minutum, and providing an early warning of toxic HABs.

实时PCR和cycling probe技术检测母血浆游离胎儿DNA筛选重型β地中海贫血胎儿

目的通过检测孕妇外周血中的游离胎儿DNA来筛选重型β-地中海贫血胎儿。方法选择行产前基因诊断的夫妇6对,孕妇孕周23-26周。血液学检查:胎儿的父亲均为β-地中海贫血17M/N型,孕妇本人为携带除17M/N型之外的另一β-地中海贫血突变类型。针对CD17(A→T)无义突变,设计β-珠蛋白肽链上该等位基因的一对特异性引物和通过cycling probe法分别设计检测正常基因序列和基因突变位点的两条荧光探针,分别用FAM和HEX荧光标记。结合RT-PCR技术检测孕妇外周血中游离胎儿DNA,诊断胎儿是否遗传了其父亲的β地中海贫血17M/N碱基突变位点。同时与脐血血液学检查所诊断的胎儿地贫基因型对照。结果提取的6例孕妇血浆DNA模板中有3例同时显示FAM和HEX荧光信号值阳性结果,即这3例孕妇的胎儿遗传了父亲β-珠蛋白肽链上CD17位点的突变碱基(A→T)。另外3例孕妇血浆DNA模板的FAM信号值阳性,HEX信号值阴性,即所孕胎儿没有遗传父亲的CD17位点的突变碱基。结论利用RT-PCR和cycling probe技术检测孕妇外周血中的游离胎儿DNA可用来筛选患重型地中海贫血的胎儿。

Study on the Interaction of Mitomycin C with ct-DNA by Pd-Porphin Room Temperature Phosphorescence Probe

Anticancer drug Mitomycin C (MMC) quenches remarkably phosphorescence and reduces lifetime of phosphorescence probe, Pd-meso-tetrakis-(4-trimethylaminophenyl)porphin (Pd-TAPP), in the presence of calf thymus DNA. These results may be attributed to the site competition of MMC with the probe and electron transfer between MMC and probe. MMC also increases polarization degree of the probe by covalent drug-DNA or DNA-drug-DNA crosslinking.

Use of (Dig)-DNA Probe for the Epidemiological Survey of Plasmodium falciparum Malaria

The Plasmodtum falctparum DNA fragment was isolated from a cloned recombinant plasmid pPF14. labelled with Digoxigenin (Dig) and used as a probe (pPF14-F-Dig)to detect 274 blood samples from the eqdemic area population in Hainan Province by dot hybridization.The results showed that out of 274 blood specimens one was positive when using microscopic examination and the positivity rate was 0.36 percent. Fifteen samples showed to be positive (including one positive specimen examined by microscopy) when this probe was applied to detect the 274 samples and its positivity rate was 5.47 percent.The positive coincidence rate between pPF14-F-Dig and microscopic examination was 1/1 and the negative coincidence rate was 94.87 percent. Since a piece of nitrocellulose membrane with the size of 9 by 12 square centimetres can accommodate blots of 96 samples,this probe is fit for large-scale epidemiological surveys.

Comparison of the Two Chromosome Forms of Paragonimus Westermani Using DNA Restriction Fragment Size and DNA Hybridization

Restriction enzyme digestion of total genomic DNA of two chro-mosome type Paragonimus westermani showed the presence of homologus highlyrepeated DNA in diploid and triploid forms. Southern blot analysis providedfurther evidence that the distribution of restriction enzyme sites (with 3enzymes) on repeated DNA of both was similar. But with Pst Ⅰ、Dde Ⅰ、Hae Ⅲand Hpa Ⅱ. They revealed polymorphism which also occured individually ineach form tested separatedly with hybridization technique. Mutation of recog-nize sites by enzymes, which is resulted from the alternation of gene sequance,has occured during evolution. Additionally, it is probably possible, based on PstⅠand Dde Ⅰdigest pattern to distinguish between diploid and triploid Parag-onimus westermani and group the Paragonimus simply and rapidly.

Theoretical study of overstretching DNA–RNA hybrid duplex

DNA–RNA hybrid(DRH) plays important roles in many biological processes. Here, we use a thermodynamic theory to analyze the free energy and unpeeling properties of the overstretching transition for the DRH molecule and compare the results with double-helix DNA. We report that the RNA strand of DRH is easier to get unpeeled than the DNA strand while the difficulty in unpeeling the double helix DNA lies in between. We also investigate the sequence effect, such as GC content and purine content, on the properties of unpeeling the DRH. Further, to study the temperature effect, the forcetemperature phase diagram of DRH and DNA are calculated and compared. Finally, using a kinetic model, we calculate the force–extension curves in the DRH stretching and relaxation process under different pulling rates and temperatures. Our results show that both pulling rate and temperature have important influences on the stretching and relaxation kinetics of unpeeling the DRH. Putting all these results together, our work provides a comprehensive view of both the thermodynamics and kinetics in DRH overstretching.

DETECTION OF STRAND BREAKS OF DNA IN HUMAN EARLY CHORIONIC VILLUS CELLS INDUCED BY DIAGNOSTIC ULTRASOUND USING ^(32)P-LABELED ALU HYBRIDIZATION

Objective To explore if strand breaks of DNA in human early chorionic villus cells in uterus were induced by diagnostic ultrasound and to evaluate the method used for detection of single-stranded breaks and double-stranded breaks in human DNA. Methods 60 normal pregnant women aged 20-30, who underwent artificial abortion during 6-8 weeks of gestation, were randomly divided into 2 experimental groups: All 30 cases were exposed to diagnostic ultrasound in uterus for 10 minutes, and 24 hours later chorionic villi were extracted; the other 30 cases were taken as the control group. Single-stranded DNA and double-stranded DNA in villus cells in all cases were isolated by the alkaline unwinding combined with hydroxylapatite chromatography, and were quantitatively detected using 32 P-labeled Alu probe for dot-blotting hybridization. Results There was no significant difference in quantity and percentage in single-stranded DNA and double-stranded DNA between 2 groups (P>0.05). 32 P-Alu probe could only hybridize with human DNA, and could detect DNA isolated from as few as 2.5×10 3 chorionic villus cells and 0.45ng DNA in human leukocytes. Conclusion The results suggested that there were no DNA strand damages in human chorionic villus cells when the uterus was exposed to diagnostic ultrasound for 10 minutes. The method,^(32)P-Alu probe for dot-blotting hybridization, was even more specific, sensitive and accurate than conventional approaches.

Screening of Species-specific DNA Probes for Identification of Fallopia multiflora

To screen species-specific DNA probes for identification of Fallopia muhiflora, the genomic DNA （gDNA） suppression subtraction hybridization （SSH） between F. muhiflora and F. muhiflora var. ciliinervis was firstly performed. The obtained differential gDNA fragments by SSH were then hybridized with gDNA ar- rays consisting of multiple whole genomes of several species （adulterants and/or closely related species of F. muhiflora） and four differential fragments were screened uniquely representing F. muhiflora, which could be used as F. muhiflora species-specific probes. The screened DNA probes were tested by reverse dot blot hybridization and the results demonstrated that these probes could be used reliably to identify F, muhiflora. The species-specific DNA probes obtained in this study exhibited broad application prospects in the preparation of gene chips for identifying Chinese traditional medicines and the authentication of germplasm re- sources and crude drugs of F. muhiflora.

Evaluation of a sulfonated DNA probe (sulfoprobe) for diagnosis of falciparum malaria

In this study,the DNA probe pPF14 was nonradioactively labelled by sulfo-modifica-tion,and used in a dot blot hybridization assay for detection of P.falciparum.The resultsshowed that the sulfoprobe successfully detected 25pg purified DNA and 0.001% parasitemia ofcultured P.falciparum,and did not react with human leukocyte DNA.In the study of 179clinical blood samples of malaria patients from Yunnan province,the DNA probe results corre-lated well with blood smear ones.Of 107 P.falciparum samples determined by microscope ex-amination,99 were positive by sulfoprobe (92.5%);Of 72 P.vivax samples,1 was crosslyreacted;no cross reactions were found with any of 48 normal blood samples.It is indicated thatsulfoprobe may be useful in specific diagnosis and epidemiological investigation of P.falciparuminfection.

A hybrid swarm population of Pinus densiflora × P. sylvestris inferred from sequence analysis of chloroplast DNA and morphological characters

To confirm a hybrid swarm population of Pinus densiflora × P. sylvestris in Jilin, China, we used needles and seeds from P. densiflora, P. sylvestris, and P. densiflora × P. sylvestris collected from natural stands or experimental stations to study whether shoot apex morphology of 4-year old seedlings can be correlated with the sequence of a chloroplast DNA simple sequence repeat marker （cpDNA SSRs）. Total genomic DNA was extracted and subjected to sequence analysis of the pine cpDNA SSR marker Pt15169. Results show that morphological characters from 4-year old seedlings did not correlate with sequence variants of this marker. Marker haplotypes from all P. sylvestris trees had a CTAT element that was absent from all sampled P. densiflora trees. However, both haplotype classes involving this insertion/deletion element were found in a P. densiflora × P. sylvestris population and its seedling progeny. It was concluded that the P. densiflora × P. sylvestris accessions sampled from Jilin, China resulted from bi-directional crosses, as evidenced by both species’ cpDNA haplotypes within the hybrid swarm population.

Interspecific Hybridization between <i>Arisaema sikokianum</i>and <i>A. serratum</i>(Araceae) Confirmed through Nuclear and Chloroplast DNA Comparisons

A morphologically intermediate plant between Arisaema sikokianum Franch. et Sav. and A. serratum (Thunb.) Schott has been newly found in Kochi Prefecture, Shikoku, Japan. The putative hybrid has the intermediate morphological characteristics of the parental species. Molecular analysis using PCR-RFLP of internal transcribed spacer (ITS) in nuclear DNA (nrDNA) indicates that the putative hybrid has a combined pattern of the two putative parent species. Moreover, the sequence result of chloroplast DNA (cpDNA) of the putative hybrid was identical to that of A. sikokianum. These results suggest that the putative hybrid is a hybrid between A. sikokianum and A. serratum and that it was formed by interactive gene exchanging via pollens from A. serratum to A. sikokianum. It is the first record of a hybrid between A. sikokianum and A. serratum.

Use of Ultrastructuke and DNA Hybridization to Detect Replication of the Nuclear Polyhedrosis Virus in Midgut Cells of Homologous Host

It was controversial issue if nuclear polyhedrosis virus(NPV) could replicate in midgut cells of host larvae from Lepidoptera by now.The replication of Mythimna separata NPV(MsNPV) in M.separata larvae midgut cells was studied by ultrastructural and DNA hybridized techniques.The paper demonstrated that the MsNPV could neither infect midgut cell nor replicate in midgut cell of homologous host.Therefore MsNPV virions released from the virial occlusion bodies were considered as direct penetration though the intercellular spaces of midgut cells to hemocoel of the host larvae.

A Simple Method of Detecting Chlamydia Trachomatis UsingEnzymatically Amplified DNA and Immobilized Probes onMicrotiter Plate

We have develoPed a simPle and economical method f0r Chlamydia trachomatisdetecting, called microtiter plate hybridization (PCR-MPH), which may replace stan-dard PCR. This method is similar to that of an ELISA. Brithe, the PCR productslabeled at the 5'termini with biotin were hybridized with probes immobilized on a mi-crotiter well, and the bound PCR products were detected by streptavidin-c0njugatedenzymes followed by color development. Two inprovements have been made in immobi-lizing the probe to the microtiter wells, in terms of increasing both immobility and hy-bridization deciency. One is that singleustranded (ss )DNA, without the complemen-tary strand, is used. The other is that instead of a single copy, a tandem array of theprobe is used for immobilization and hybridization. Using of ssDNA containing abouta 5O-rePeat array of a relevant sequence as an immobilized probe, the sensitivity in-creased 1O-fold over that of a single oligonucleotide unit. We also found that the hy-brldizatlon condltions such as time, temPerature, and solution composition could be simplthed. The advantages of this microtiter plate-hybridization method for routinepathogens detecting are a short time assay, easy processing of large numbers of sansples, and the potential for automation.