Diagnosis of rotavirus infection with cloned cDNA copies of viral genome segments.

The diagnostic potential of cloned cDNA copies of human rotavirus (strain WA) genome segments for the detection of rotavirus in clinical specimens has been determined. A hybridization assay in which a mixture of 32P-labeled cDNAs representing the 11 rotavirus segments was used as a probe compared favorably with three frequently used diagnostic tests for rotavirus in terms of both specificity and sensitivity. Significantly, clinical isolates could be readily distinguished when cloned cDNA copies of individual genome segments were used independently as a probe. In assays in which genome RNA from rotaviruses of known subgroups and serotypes were tested, cloned probes that encode nonstructural viral proteins hybridized efficiently to genome RNAs of all strains, whereas cloned probes corresponding to genome segments 6 and 9 exhibited the potential for differentiating strains of different subgroups and serotypes. Cloned cDNA copies of rotavirus genome segments therefore offer considerable potential for improved general diagnosis of rotavirus in clinical specimens, as well as for epidemiological studies in which virus isolates can be distinguished on the basis of nucleotide sequence homology of individual genome segments.     

Sequence diversity of human rotavirus strains investigated by northern blot hybridization analysis.

Rotavirus genomic RNAs, derived from a series of human isolates that exhibit variability in the pattern of migration of the double-stranded RNA on polyacrylamide gels, were transferred to diazobenzyloxymethyl paper, and their sequence diversity was investigated. Hybridization of cDNA probes prepared from the 11 segments of rotavirus RNA indicated that considerable sequence diversity exists among these viruses. Under conditions of both low and high stringency, hybridization analysis of virus collected between 1975 and 1980 suggested that the variation among rotavirus strains may have occurred by a process involving both "drift" and "shift" in the sequence of the rotavirus genomic segments.     

Identification of cognate genes among heterologous strains of group B rotavirus.

The genetic relatedness of group B rotavirus (GBR) strains has previously been documented by hybridization with probes derived from whole genomic sequences, but the relationship of individual genes of heterologous GBR strains has not been evaluated. Definition of cognate GBR genes would facilitate investigation of the determinants of group specificity, serotype identity, and neutralization epitopes. Therefore, we investigated the genetic relatedness of three GBR strains by means of Northern (RNA) blot hybridization with isotopically labeled probes prepared from each of the 11 genes of the IDIR strain of GBR. Under low-stringency conditions, hybridization between each of the IDIR gene probes and genomic RNA from the ADRV strain of GBR was observed. Genomic RNA obtained from a bovine strain of GBR hybridized with 9 of the 11 IDIR gene probes. In most cases, cognate genes of each of the GBR strains appeared to migrate to similar positions following polyacrylamide gel electrophoresis. However, the electropherotype positions of GBR genes 5, 6, and 7 were different for each of the three GBR strains. Identification of these genomic segments among GBR strains should prove helpful in future evaluations of GBR structure and function.     

Sequence relationships between the genome segments of human and animal rotavirus strains.

The sequence relationships of a range of cultivable and noncultivable human and animal rotaviruses were investigated by hybridization of rotavirus cDNA probes to genomic RNAs immobilized on diazobenzyloxymethyl paper. Under conditions of low stringency (34% base mismatch tolerated) most genome segments exhibited partial homology except for genes 4 and 5. In contrast, under more stringent conditions of hybridization in which no more than 8% base mismatch was tolerated, few segments exhibited homology. Generally the human and animal rotaviruses were found to possess distinct nucleic acid sequences that exhibit only a low order of sequence relatedness. These results are consistent with the notion that both cumulative changes in nucleic acid sequences and the interchange of segments may be involved in the evolution of distinct rotavirus strains.     

轮状病毒基因重配株血清型鉴定方法的研究

Ａ组轮状病毒中根据基因９的不同目前至少已发现有１３个不同Ｇ血清型,其中能引起人类致病的有Ｇ１－Ｇ４,Ｇ８,Ｇ９和Ｇ１２型。建立可靠的血清型鉴定技术对于轮状病毒疫苗的研制和分子流行病学的研究具有重要意义。本文首次报导了一种鉴定轮状病毒Ｇ血清型的新方法,利用已知有关轮状病毒ＶＰ７基因的序列资料,设计合成了一套鉴定轮状病毒Ｇ血清型的寡核苷酸探针,利用地高辛标记上述探针。待检品经反转录ＰＣＲ扩增后与上述一套寡核苷酸探针分别进行杂交得以确定其血清型。这一方法与目前常用的套式ＰＣＲ方法相比更适合于大量样品的操作而且结果可靠。用这一方法对本实验室组建的四株基因重配疫苗株进行实验,其结果与套式ＰＣＲ方法完全一致。     

Discrimination Amongst Leishmania by Polymerase Chain Reaction and Hybridization with Small Subunit Ribosomal DNA Derived Oligonucleotides

ABSTRACT. A method for discriminating among Leishmania is described, based upon small subunit ribosomal DNA sequence differences. The method was to amplify the entire 2.2 kb small subunit rDNA by polymerase chain reaction using conserved primers specific for the 5' and 3' termini of the small subunit ribosomal RNA, and then hybridize the product dotted onto nylon membranes with labeled oligonucleotides. The design of the hybridization probes was based upon complete small subunit rDNA sequences from L. amazonensis, L. major and L. guyanensis and partial sequences of L. mexicana, L. braziliensis, L. tropica and L. chagasi. A high degree of sequence similarity (> 99%) among species was found. However, sufficient sequence divergence occurred to permit the design of internal oligonucleotide probes specific for species complexes. This procedure successfully discriminated amongst a wide range of Leishmania isolates. The method detected as few as 10 cultured organisms and detected parasites in tissue samples from experimentally infected animals. Non-radioactive labeling showed the same specificity and sensitivity as radioactive probes.     

光生物素标记DNA探针检测感染细胞的BHV—1 DNA

将七株从不同地区、不同牛种或不同部位分离出的牛Ⅰ型疱疹病毒(BHV-1)培养于MDBK细胞中,从感染的细胞中提取病毒并抽提其DNA将克隆的BHV-1LA株DNA的HindⅢ—Ⅰ片段(11.7Kb)用光生物素标记作为探针,检测上述七株感染细胞的BHV-1 DNA,其中有六株(均属IBR临床型)呈阳性反应,另一株(属IPP临床型)呈阴性反应,这一探针将作为一种有效的检疫工具在本病的防制中起重要作用.     

Protein G genes: structure and distribution of IgG-binding and albumin-binding domains

Protein G (also designated Fc receptor type III) is the IgG-binding protein of group C and G streptococci. Protein G has also been shown to bind human serum albumin but at a site that is structurally separated from the IgG-binding region. From the known gene sequence of protein G, two synthetic oligonucleotides were constructed for use as probes in DNA-hybridization experiments to study the structure and distribution of the albumin- and IgG-binding regions in bacterial strains belonging to different species. Thus, one of the probes corresponded to repeats within the IgG-binding region (I) and the other corresponded to repeats in the albumin-binding encoding region (II). Probe I showed strong hybridization to DNA isolated from 31 human group C and G strains, whereas hybridization to probe II was variable. With the three restriction endonucleases used, three restriction patterns were found in Southern blot experiments. No fundamental difference could be detected in hybridization experiments, either between strains of group C and G streptococci, or between isolates of different clinical origin. No hybridization to DNA from other bacterial species was found.     

检测A组轮状病毒的微阵列技术初探

采用荧光染料TAMRA标记上游引物,经RT semi nestedPCR扩增A组轮状病毒的保守区域,并将扩增产物与自行研制的玻片微阵列进行杂交。经杂交信号扫描分析,可简便快速地检出A组轮状病毒,并能达到高灵敏性,为下步进入临床打下了基础。     

Cloning of cDNA Derived from mRNA of the Electric Lobe of Torpedo marmorata and Selection of Putative Cholinergic-Specific Sequences

With the aim of selecting cDNA sequences expressed in neurons utilizing exclusively cholinergic synaptic transmission, cDNA derived from Torpedo electric lobe was cloned and screened by hybridization with probes originating from another brain region known for its low content of cholinergic neurons (cerebellum) and a nonneuronal tissue (muscle). This method led to the isolation of 18 clones among 3,200 showing no hybridization with probes other than those derived from electric lobe. These clones can therefore be considered to represent sequences involved in the expression of cholinergic function in neurons.     

Concentration and detection of hepatitis A virus and rotavirus from shellfish by hybridization tests.

A modified polyethylene glycol precipitation method for concentration of virus followed by a new method to recover nucleic acid was used to detect hepatitis A virus (HAV) and rotavirus (SA11) in shellfish (oysters and hard-shell clams) by hybridization tests. Infectious virus, seeded into relatively large quantities of shellfish, was recovered consistently, with greater than 90% efficiency as measured by either in situ hybridization (HAV) or plaque assay (rotavirus SA11). Viral nucleic acid for dot blot hybridization assays was extracted and purified from virus-containing polyethylene glycol concentrates. Separation of shellfish polysaccharides from nucleic acid was necessary before viral RNA could be detected by dot blot hybridization. Removal of shellfish polysaccharides was accomplished by using the cationic detergent cetyltrimethylammonium bromide (CTAB). Use of CTAB reduced background interference with hybridization signals, which resulted in increased hybridization test sensitivity. After polysaccharide removal, dot blot hybridization assays could detect approximately 10(6) physical particles (corresponding to approximately 10(3) infectious particles) of HAV and 10(4) PFU of SA11 rotavirus present in 20-g samples of oyster and clam meats. These studies show continuing promise for the development of uniform methods to directly detect human viral pathogens in different types of shellfish. However, practical applications of such methods to detect noncultivatable human viral pathogens of public health interest will require additional improvements in test sensitivity.     

Concentration and detection of hepatitis A virus and rotavirus from shellfish by hybridization tests.

A modified polyethylene glycol precipitation method for concentration of virus followed by a new method to recover nucleic acid was used to detect hepatitis A virus (HAV) and rotavirus (SA11) in shellfish (oysters and hard-shell clams) by hybridization tests. Infectious virus, seeded into relatively large quantities of shellfish, was recovered consistently, with greater than 90% efficiency as measured by either in situ hybridization (HAV) or plaque assay (rotavirus SA11). Viral nucleic acid for dot blot hybridization assays was extracted and purified from virus-containing polyethylene glycol concentrates. Separation of shellfish polysaccharides from nucleic acid was necessary before viral RNA could be detected by dot blot hybridization. Removal of shellfish polysaccharides was accomplished by using the cationic detergent cetyltrimethylammonium bromide (CTAB). Use of CTAB reduced background interference with hybridization signals, which resulted in increased hybridization test sensitivity. After polysaccharide removal, dot blot hybridization assays could detect approximately 10(6) physical particles (corresponding to approximately 10(3) infectious particles) of HAV and 10(4) PFU of SA11 rotavirus present in 20-g samples of oyster and clam meats. These studies show continuing promise for the development of uniform methods to directly detect human viral pathogens in different types of shellfish. However, practical applications of such methods to detect noncultivatable human viral pathogens of public health interest will require additional improvements in test sensitivity.     

Deletion mapping of the testis determining locus with DNA probes in 46,XX males and in 46,XY and 46,X,dic(Y) females.

Eleven Y-specific DNA probes hybridizing with DNA from one or more 46,XX males were isolated from a recombinant phage DNA library constructed from flow sorted human Y chromosomes. Two probes hybridized with DNA from nine out of eleven, i.e. greater than 80% of these 46,XX males. The relative frequency of hybridization of the probes in the 46,XX males and in a 46,X,dic(Y) female, together with in situ hybridization data, allowed mapping of the probes on Yp in relation to a putative testis determining locus. Several of those probes were also absent in a 46,XY female, further refining a model for ordering the probes on Yp. The DNA of one XX male hybridized both with probes from Yp and probes from proximal Yq (excluding the pericentral region). This suggests that complex translocations may occur into the DNA of 46,XX males that involve not only parts of Yp but also parts of Yq.     

Precise karyotyping of carrot mitotic chromosomes using multicolour-FISH with repetitive DNA

Carrot (Daucus carota L.) chromosomes are small and uniform in shape and length. Here, mitotic chromosomes were subjected to multicolour fluorescence in situ hybridization (mFISH) with probes derived from conserved plant repetitive DNA (18-25S and 5S rDNA, telomeres), a carrot-specific centromeric repeat (Cent-Dc), carrot-specific repetitive elements (DCREs), and miniature inverted-repeat transposable elements (MITEs). A set of major chromosomal landmarks comprising rDNA and telomeric and centromeric sequences in combination with chromosomal measurements enabled discrimination of carrot chromosomes. In addition, reproducible and unique FISH patterns generated by three carrot genome-specific repeats (DCRE22, DCRE16, and DCRE9) and two transposon families (DcSto and Krak) in combination with telomeric and centromeric reference probes allowed identification of chromosome pairs and construction of detailed carrot karyotypes. Hybridization patterns for DCREs were observed as pericentromeric and interstitial dotted tracks (DCRE22), signals in pericentromeric regions (DCRE16), or scattered signals (DCRE9) along chromosomes similar to those observed for both MITE families.     

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays

Although oligonucleotide probes complementary to single nucleotide substitutions are commonly used in microarray-based screens for genetic variation, little is known about the hybridization properties of probes complementary to small insertions and deletions. It is necessary to define the hybridization properties of these latter probes in order to improve the specificity and sensitivity of oligonucleotide microarray-based mutational analysis of disease-related genes. Here, we compare and contrast the hybridization properties of oligonucleotide microarrays consisting of 25mer probes complementary to all possible single nucleotide substitutions and insertions, and one and two base deletions in the 9168 bp coding region of the ATM (ataxia telangiectasia mutated) gene. Over 68 different dye-labeled single-stranded nucleic acid targets representing all ATM coding exons were applied to these microarrays. We assess hybridization specificity by comparing the relative hybridization signals from probes perfectly matched to ATM sequences to those containing mismatches. Probes complementary to two base substitutions displayed the highest average specificity followed by those complementary to single base substitutions, single base deletions and single base insertions. In all the cases, hybridization specificity was strongly influenced by sequence context and possible intra- and intermolecular probe and/or target structure. Furthermore, single nucleotide substitution probes displayed the most consistent hybridization specificity data followed by single base deletions, two base deletions and single nucleotide insertions. Overall, these studies provide valuable empirical data that can be used to more accurately model the hybridization properties of insertion and deletion probes and improve the design and interpretation of oligonucleotide microarray-based resequencing and mutational analysis.     

Evaluation of a plasmid-based 16S-23S rDNA intergenic spacer region array for analysis of microbial diversity in industrial wastewater

A plasmid-based 16S-23S rDNA intergenic spacer region (ISR) array was developed and optimized for analysis of microbial diversity within complex environmental samples. Plasmid probes with 16S-23S rDNA ISR inserts (800-1500 bp) from industrial wastewater treatment plant (WWTP) microorganisms were arrayed onto glass slides. Hybridization of fluorescently labeled target sequences from two clones from the ISR WWTP library to arrayed probes showed that there was a good linear relationship between hybridization intensity and ISR similarity (r(2)=0.82). Hybridization was highly specific (average background from arrayed probes with less than 80% similarity in ISR sequence was less than 7%). Strong fluorescence intensity corresponded to near-perfect match clones (99% or greater similarity in ISR sequence). A majority of probes (79%) showed no background hybridization. However, weak background (less than 50% for arrayed probes with 90% and 95% similarity in the 16S rRNA genes) was observed from closely related microorganisms. Background fluorescence from the negative control (plasmid vector with no insert) was similar to water and dimethyl sulfoxide (DMSO)-negative controls. Hybridization using fluorescently labeled ISR sequences from a mixed community sample produced strong fluorescent signals with no background from negative controls. A Cy5-labeled reference standard, part of the vector and present in every spotted probe, was used to normalize hybridization values. These results indicate that arrayed plasmid containing ISR probe insert sequences provides specificity and sensitivity for microbial community analysis in a high-throughput array format.     

Direct electrochemical genosensing for multiple point mutation detection of Mycobacterium tuberculosis during the development of rifampin resistance

We present a robust and simple method for the direct detection of multiple point mutations in the Mycobacterium tuberculosis rpoB gene during the development of rifampin (RIF) resistance using an electrochemical genosensor. The device contained five different capture probes which are designed to hybridize with several sequence segments within the bacterial rpoB gene hotspot region. Point mutations were detected by monitoring the guanine oxidation with differential pulse voltammetry after hybridization between PCR amplicons and inosine modified capture probes at graphite surface. Changes in the peak voltage corresponding to guanine oxidation provide an electrochemical signal for hybridization that can be used to determine the presence of point mutations conferring rifampin resistance. The analytical parameters (sensitivity, selectivity and reproducibility) were evaluated. High selective discrimination against point mutation of bacteria at hot-spot region was observed. Several mutations were detected at several parts of the amplicon from 21 positive samples.     

The use of repetitive DNA in cytogenetic studies of plant sex chromosomes

The structure of sex chromosomes in plants was analyzed by fluorescent in situ hybridization (FISH) with repetitive DNAs. FISH probes were successfully obtained from DNA libraries that were amplified from microdissected sex chromosomes. Some probes hybridized to the subtelomeric regions, where many kinds of repetitive DNAs are located with intrachromosomal similarity of their repeat units rather than interchromosomal similarity. For example, FISH with the subtelomeric repetitive sequence can easily show the location of the pseudoautosomal region (PAR) on the X chromosome of Silene latifolia. The other probes were localized on the interstitial region of the sex chromosomes. The interstitial region contains chloroplast DNAs or neighboring sequences of the internal telomeres, suggesting insertion or translocation occurred during differentiation of the sex chromosome. These data are very informative for understanding the structure of the plant sex chromosomes and their evolutionary process.