A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes

Mapping Drosophila mutations with molecularly defined P element insertions

The isolation of chemically induced mutations in forward genetic screens is one of the hallmarks of Drosophila genetics. However, mapping the corresponding loci and identifying the molecular lesions associated with these mutations are often difficult and labor-intensive. Two mapping methods are most often used in flies: meiotic recombination mapping with marked chromosomes and deficiency mapping. The availability of the fly genome sequence allows the establishment and usage of molecular markers. Single-nucleotide polymorphisms have therefore recently been used to map several genes. Here we show that thousands of molecularly mapped P element insertions in fly strains that are publicly available provide a powerful alternative method to single-nucleotide polymorphism mapping. We present a strategy that allows mapping of lethal mutations, as well as viable mutations with visible phenotypes, with minimal resources. The most important unknown in using recombination rates to map at high resolution is how accurately recombination data correlate with molecular maps in small intervals. We therefore surveyed distortions of recombination rates in intervals <500 kb. We document the extent of distortions between the recombination and molecular maps and describe the required steps to map with an accuracy of <50 kb. Finally, we describe a recently developed method to determine molecular lesions in 50-kb intervals by using a heteroduplex DNA mutation detection system. Our data show that this mapping approach is inexpensive, efficient, and precise, and that it significantly broadens the application of P elements in Drosophila.

Subtraction hybridization in microplates: an improved method to generate strain-specific PCR primers

An improved subtraction hybridization technique was developed and evaluated. The hybridization is performed in a microplate with the subtractor-DNA immobilized in the plate while the probe-DNA is in solution. After hybridization the probe-specific DNA can easily be removed from the microwell and submitted to further analysis. This new technique has been successfully applied to generate several strain-specific PCR-primers for Lactococcus lactis subsp. lactis, Pediococcus spec., Saccharomyces spec. and Listeria monocytogenes.

Predicting crossover generation in DNA shuffling

We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model the annealing process. Statistics obtained for the annealing events then are combined with a reassembly algorithm to infer crossover allocation in the reassembled sequences. The fraction of reassembled sequences containing zero, one, two, or more crossovers and the probability that a given nucleotide position in a reassembled sequence is the site of a crossover event are estimated. Comparisons of the predictions against experimental data for five example systems demonstrate good agreement despite the fact that no adjustable parameters are used. An in silico case study of a set of 12 subtilases examines the effect of fragmentation length, annealing temperature, sequence identity and number of shuffled sequences on the number, type, and distribution of crossovers. A computational verification of crossover aggregation in regions of near-perfect sequence identity and the presence of synergistic reassembly in family DNA shuffling is obtained.

Rapid Single-Tube Screening of the C282Y Hemochromatosis Mutation by Real-Time Multiplex Allele-specific PCR without Fluorescent Probes

Background: An accurate determination of the major HFE mutation (C282Y), which is associated with hereditary hemochromatosis, is important in diagnosis and risk assessment for this disease. We report a single-tube high-throughput PCR method for the detection of C282Y.

Methods: We combined three previously described principles: allele-specific PCR, mutagenically separated PCR, and amplicon identification by specific dissociation curves. PCR amplification was performed with fluorescence detection or conventional thermocycler using the same primers, reactant constituents, and cycling protocol. Primer cross-reactions were prevented by deliberate primer:primer and primer:template mismatches.

Results: PCR products were identified by their characteristic melting temperatures based on SYBR Green I fluorescence. For each of the 256 random and 17 known HFE C282Y samples, mutant homozygous, wild-type, and heterozygous samples were unequivocally distinguished.

Conclusions: This homogeneous assay is rapid, reproducible, does not require fluorescent oligonucleotide probes, and correctly identifies HFE genotypes.

A flagellar calmodulin gene of Naegleria, coexpressed during differentiation with flagellar tubulin genes, shares DNA, RNA, and encoded protein sequence elements

Two calmodulins are synthesized during differentiation of Naegleria gruberi from amoebae to flagellates; one remains in the cell body and the other becomes localized in the flagella. The single, intronless, expressed gene for flagellar calmodulin has been cloned and sequenced. The encoded protein is a typical calmodulin with four putative calcium-binding domains, but it has an amino-terminal extension of 10 divergent amino acids preceding conserved calmodulin residue 4. The transcripts encoding flagellar calmodulin and flagellate cell body calmodulin are clearly divergent. Expression of the flagellar calmodulin gene is differentiation-specific; its mRNA appears and then disappears concurrently with those encoding flagellar alpha- and beta-tubulin. Three provocative sequence elements are shared among these unrelated coexpressed genes: (i) a palindromic DNA sequence element is found in duplicate or triplicate upstream to each transcribed region; (ii) a perfect 12-nucleotide match is found near the AUG start codon of flagellar calmodulin and alpha-tubulin; and (iii) the novel amino-terminal extension of flagellar calmodulin contains a 5-amino-acid element similar to the amino terminus of flagellar alpha-tubulin. These shared sequence elements are proposed to have roles in differentiation, possibly in regulation of transcription, mRNA stability, and localization of these proteins to flagella.

Immediate-early gene expression and gene mapping comparisons among isolates of bovine herpesvirus 1 and 5

Bovine herpesviruses (BHV) are associated with a variety of clinical syndromes. Bovine herpesvirus 1 isolates were placed into three genome subtypes based on restriction endonuclease analyses, which were loosely associated by clinical manifestation as BHV1.1 (respiratory), BHV1.2 (genital), and BHV1.3 (encephalitic). More recently the encephalitic isolate has been classified BHV5. A comparison of the cytopathic effect (CPE) in fetal bovine lung cell cultures in the presence of cycloheximide showed that BHV1.1 and 1.2 isolates produced elongated, spindle-shaped CPE, whereas BHV5 produced more syncytial-like CPE. Each BHV-1 subtype synthesized four immediate-early transcripts. The sizes in kb were: 1.6, 3.4, 5.8, 7.5 (BHV1.1); 1.8, 3.6, 5.8, 7.5 (BHV1.2); and 1.8, 3.6, 5.8, 8.6 (BHV5). These transcripts were mapped to the inverted repeat region of each isolate by Southern blot hybridization using cDNA prepared from cycloheximide-treated BHV1-infected cellular polyA RNA. A possible unique immediate-early RNA may be produced by the BHV5 encephalitic isolate from an area of the internal repeat region unique to this isolate. Hybridization analysis using BHV1.1 cloned probes of the immediate-early protein gene, thymidine kinase gene, DNA binding/DNA polymerase gene, and glycoprotein III gene provided information for mapping of these genes to the BHV5 encephalitic isolate.

Conservation of salivary glycoprotein-interacting and human immunoglobulin G-cross-reactive domains of antigen I/II in oral streptococci

In this study we localized more precisely the salivary glycoprotein-interacting and the human immunoglobulin G (hIgG)-cross-reacting domains on the SR molecule, an antigen I/II-related protein from S. mutans serotype f. Mapping of the SR molecule with polypeptides expressed by subclones covering the entire molecule and with synthetic peptides demonstrates that the salivary glycoprotein-binding domain is located in the N-terminal alanine-rich repeats of the SR molecule. In order to investigate the degree of conservation of both regions in various oral streptococci, we tested the reactivity of 8 representative strains of the mutans group and 11 nonmutans oral Streptococcus strains (S. anginosus, S. milleri, S. constellatus, S. intermedius, S. mitis, S. sanguis, S. gordonii, S. salivarius, and S. mitis strains) with antipeptide antibodies in a whole-cell enzyme linked immunosorbent assay together with colony hybridization analysis using DNA probes designed to map these two regions. All the mutans group strains except S. rattus and the 11 nonmutans streptococcal strains showed a high conservation of the C-terminal part of the SR molecule, especially the hIgG-cross-reacting domain, and less homology for the N-terminal salivary glycoprotein-binding region. Almost all of the sera from patients with rheumatic disease reacted strongly with SR from S. mutans serotype f, P1 from S. mutans serotype c, and four peptides located in the hIgG-cross-reacting region and not with peptides located at the C and N termini and in the proline-rich repeats. These results confirm that epitopes located within this region are immunogenic in humans and could lead to the synthesis of natural anti-IgG antibodies.

Physical mapping of buzura suppressaria nuclear polyhedrosis virus genome

A physical map of the genome of buzura suppressaria singly-enveloped nuclear polyhedrosis virus (BsSNPV) was determined using six restriction endonucleases (RE), singly or in pairs, and Southern hybridizations of cloned or gel-purified DNA fragments. The maps of the genomes of BsSNPV and autographa californica multiply-enveloped nuclear polyhedrosis virus (AcMNPV) were different.

Molecular analysis of the 3,6-dideoxyhexose pathway genes of Yersinia pseudotuberculosis serogroup IIA

Salmonella enterica and Yersinia pseudotuberculosis are the only examples in nature known to use a variety of 3,6-dideoxyhexose derivatives as O antigen constituents. To allow a comparison of the responsible biosynthetic genes of the two organisms, we have sequenced a section of the Y. pseudotuberculosis serogroup IIA rfb region that contained the genes for the abequose biosynthetic pathway. Comparison of the identified genes with the rfb region of S. enterica LT2 showed that the two dideoxyhexose pathway gene clusters are related. The arrangement of the genes was largely conserved, and the G + C compositions of the two DNA regions were strikingly similar; however, the degree of conservation of nucleotide and protein sequences suggested that the two gene clusters have been evolving independently for considerable time. Hybridization experiments showed that the dideoxyhexose pathway genes are widespread throughout the various serogroups of Y. pseudotuberculosis.

Physical mapping and homology studies of egg drop syndrome (EDS-76) adenovirus DNA

Homologous sequences between EDS-76 adenovirus strain 127 DNA and bovine adenovirus DNA were found by the Southern blotting technique and no homology with CELO virus DNA could be detected. These data suggest a genetic similarity between EDS-76 virus and bovine adenoviruses. The fragments generated form EDS-76 adenovirus DNA by eight restriction endonucleases were physically mapped.

Applications of genetic engineering technology in feline medicine

Genetic engineering technology is a rapidly developing field that has almost unlimited potential for the production of safer and more effective vaccines, therapeutic proteins, and more specific and sensitive diagnostic reagents. Although applications in veterinary medicine of genetically engineered products are presently limited by availability of species-specific reagents, the use of recombinant DNA products is increasing. Because of the recent discovery of FIV and the relevance of FIV as an animal model for the study of human immunodeficiency virus, feline genetic research is gaining in importance. Research using FIV as a human AIDS model ideally will yield many new species-specific feline recombinant DNA products that have important applications in feline medicine and research.

The genomes of simian varicella virus and varicella zoster virus are colinear

Simian varicella virus (SVV) causes an exanthematous disease in non-human primates which is clinically similar to varicella zoster virus (VZV) infection of humans. In this study, the genetic relatedness of SVV and VZV was confirmed and the location of SVV DNA sequences homologous to VZV restriction endonuclease (RE) fragments and viral genes was determined. VZV DNA RE fragments representing 98.3% of the VZV genome were 32P-labeled and hybridized to RE digested, immobilized SVV DNA. Homologous sequences were located throughout the viral DNAs in similar map positions, indicating a colinear relationship between the VZV and SVV genomes. 32P-labeled VZV glycoprotein (gp I, II, III, and IV) and gene 62 DNA probes also hybridized to SVV DNA in a colinear manner. The results suggest that the location of specific SVV genes may be predicted from the known map positions of homologous VZV genes. This study provides further support for SVV infection of non-human primates as a model for VZV infection of humans.

Specific antiviral activities of the human alpha interferons are determined at the level of receptor (IFNAR) structure

Differences in activity among the family of human IFNs alpha are much reduced if these ligands are assayed on bovine cells. In particular, the activity of IFN alpha D is much higher on bovine than on human cells. To examine these differences, the bovine counterpart of the human IFNAR has been cloned and expressed in a human cell line. The transfected cell line now recognizes the human IFN alpha D as a high-specific-activity IFN subtype, indicating that the differences in sensitivity between the bovine and human cells to the human IFN alpha lie in the structure of the IFNAR chain rather than in the other components of the functional receptor.

Identification of bent DNA and ARS fragments in the genome of Choristoneura fumiferana nuclear polyhedrosis virus

We identified four CfMNPV DNA fragments with autonomously replicating sequences (ARS) functional in Saccharomyces cerevisiae. A 0.9-kb fragment which, mapped to 54.5 to 55.3 map units within EcoRI HI of the CfMNPV genome, showed the strongest ARS activity of the four. Sequence analysis of this 0.9-kb DNA segment revealed an A+T-rich region separated from a G+C-rich region by 320 bp. Although no sequence matched exactly the ARS core-consensus sequence, 13 near-matches differing by only one or two nucleotides from the core-consensus sequence, were identified. Ten near-matches were clustered within a 105-bp A+T-rich region, and were arranged as inverted repeats. A section of bent DNA structure was predicted within this region. The bent DNA, which showed temperature-dependent retardation during polyacrylamide gel electrophoresis, was unique as its sequence was arranged as a symmetrical 'tilde' (approximately) structure. The second (1.0 kb) and third (1.6 kb) ARS-bearing fragments mapped within EcoRI-E and -B fragments which contain homologous repeat sequences. The fourth (1.5 kb) fragment had the weakest ARS activity and mapped to the EcoRI-D or -B regions of the genome.

Detection of IL-2 at mRNA and protein levels in synovial infiltrates from inflammatory arthropathies using biotinylated oligonucleotide probes in situ

A non-radioactive in situ hybridization method for IL-2 mRNA detection based on the use of four biotinylated oligonucleotide probes, plus appropriate positive and negative control probes was developed and applied to synovial surgical and needle biopsies from rheumatoid arthritis (RA), spondyloarthropathy (SpA), psoriatic arthritis (PsA) and juvenile chronic arthritis (JCA) patients. In eight surgical biopsies (six RA, one SpA, one PsA) this non-radioactive system showed similar sensitivity to that of a previously described 32P-labelled probe system, and in addition detected IL-2 mRNA in five out of seven biopsies from SpA and PsA patients and in two out of two JCA needle biopsies. IL-2 mRNA was found in the absence of IL-2 protein in RA biopsies (six surgical, 12 needle), but variable amounts of IL-2 protein were detected in six out of seven needle biopsies from SpA, PsA and JCA patients, where CD3+ lymphoid infiltrates were present. These data suggest differences in IL-2 regulation and expression in RA and non-RA inflammatory arthropathies.

Conservation of the gene encoding streptococcal antigen I/II in oral streptococci

The spaP gene of Streptococcus mutans serotype c encodes a major cell surface protein, streptococcal antigen (SA) I/II, with an Mr of 185,000, that is thought to be involved in bacterial adhesion to teeth. Proteins with significant amino acid sequence homology to SA I/II have also been found in S. sobrinus and S. sanguis. The objectives of this study were to investigate the conservation of the spaP gene in the mutans groups of streptococci and to determine whether homologous genes were present in other species of alpha-hemolytic streptococci. DNA extracted from representative strains of 19 streptococcal species was examined by Southern hybridization and partial DNA sequence analysis. A series of five overlapping DNA probes from the spaP gene were amplified by the polymerase chain reaction and used in the Southern hybridizations. The entire gene was found to be well conserved in all strains of S. mutans serotypes c, e, and f investigated. A probe from the 3' region of the gene, which encodes residues 857 to 1207 of the SA I/II protein, hybridized with DNA from a number of mutans streptococci, as well as with DNA from nonmutans alpha-hemolytic streptococci. Conservation within this region was further demonstrated by sequencing gene fragments of two strains of S. intermedius and S. oralis. The results show that some regions of the spaP gene are highly conserved not only in the mutans group of streptococci but also in other nonmutans alpha-hemolytic streptococci. This suggests that a family of cell surface proteins which, by analogy with the 185,000-Mr SA I/II of S. mutans, could be involved in bacterial adhesion might exist.

Hybridization analysis of genomic variability among isolates of bovine viral diarrhoea virus using cDNA probes

Genomic variability among 28 cytopathic and 37 non-cytopathic isolates of BVDV was evaluated using hybridization analysis. Total RNA, isolated from cell cultures infected with BVDV, was probed with each of three plasmids containing cDNA derived from the cytopathic BVDV-NADL isolate. The three cDNA plasmid probes represented about 40% of the BVDV-NADL genome. The probes originated from the 5' end of the viral genome, the region of the genome coding for the p80 polypeptide and the 3' end of the genome. Three temperatures, 63 degrees C, 53 degrees C and 43 degrees C, were used for hybridization and washing and allowed approximately 29%, 36%, and 43% mismatch, respectively. Fifteen of the BVD viral isolates differed by less than 29% from BVDV-NADL in all three of the regions probed. Seventeen of the BVD viral isolates differed between 36% and 43% from BVDV-NADL in all three of the regions probed. Ten viral isolates differed by more than 43% from BVDV-NADL in all the regions probed. The remaining viral isolates exhibited different levels of similarity to BVDV-NADL in the three areas probed.

Molecular diagnosis of alcelaphine herpesvirus (malignant catarrhal fever) infections by nested amplification of viral DNA in bovine blood buffy coat specimens

A fragment of alcelaphine herpesvirus-1 (AHV-1; malignant catarrhal fever) DNA was subcloned into pUC 18 and sequenced. The subclone hybridized strongly to AHV-1 DNA, weakly to alcelaphine herpesvirus-2 (AHV-2) DNA, and not at all to DNA from bovine herpesvirus-1 (BHV-1; infectious bovine rhinotracheitis [IBR] virus), bovine herpesvirus-2 (BHV-2; bovine herpes mamillitis [BHM] virus), and bovine herpesvirus-4 (BHV-4; isolate DN599). A 2-stage (nested) polymerase chain reaction (PCR) diagnostic test was devised based on a portion of the subcloned AHV-1 DNA sequence. First and second stage amplified AHV-1 DNA targets were 487 and 172 base pairs (bp) in length, respectively. Unique Pvu II and Stu I restriction endonuclease cleavage sites confirmed the identity of amplified AHV-1 DNA. Five AHV-1 and 2 AHV-2 isolates were identically and specifically PCR positive. BHV-1, BHV-2, and BHV-4 viruses were negative by the same procedure. As little as 0.01 TCID50 AHV-1 was detected using the nested amplification procedure. Simple methods of buffy coat isolation from bovine blood were employed to prepare specimens for PCR. An AHV-1-infected calf was PCR positive from 3 to 77 days postinoculation (PI), with rising seroconversion first noted 14 days PI. The AHV-1 DNA sequence was 62% homologous to a portion of the Epstein-Barr virus genome. The nested PCR procedure may improve the viral diagnosis of clinical and subclinical alcelaphine herpesvirus infections.

Heterologous gene expression on the linear DNA killer plasmid from Kluyveromyces lactis

Linear hybrid plasmids based on the killer plasmid pGKL1 from Kluyveromyces lactis were obtained by in vivo recombination in Saccharomyces cerevisiae. Like pGKL1, the hybrids are located in the cytoplasm, have terminal inverted repeats (TIR) and possess covalently linked proteins at their 5' ends. The construction of cytoplasmic hybrid plasmids is based on the use of a pGKL1 promoter to control the marker gene used for recombination. Nuclear promoters are not recognised in the cytoplasm.

Differentiation of pestiviruses by a hog cholera virus-specific genetic probe

A hog cholera virus (HCV)-specific genetic probe has been generated after cloning of the genomic viral RNA. This probe distinguished between HCV and the closely related bovine viral diarrhoea virus (BVDV). Furthermore, it detected a broad spectrum of HCV strains and isolates which differ in their phenotype such as virulence.

In situ hybridization of immunoglobulin light chain mRNA in paraffin sections using biotinylated or hapten-labelled oligonucleotide probes

An in situ hybridization technique has been developed for the detection of immunoglobulin light chain mRNA in routine pathology specimens. The method detects kappa or lambda constant region sequences using a cocktail of synthetic oligonucleotide probes labelled with biotin or fluorescein 5-isothiocyanate (FITC) reporter molecules. The probes were labelled at flanking sites chemically by primary amine directed acylation and by 'homopolymer tailing' with terminal deoxynucleotidyl transferase using non-radioactive nucleotide analogues. The mRNA was unmasked in the formalin-fixed tissue sections by digestion with varying concentrations of proteinase K, and the hybrids were demonstrated using alkaline phosphatase with either a streptavidin/biotin based four-stage system or an anti-FITC antibody based detection system. Alkaline phosphatase was visualized using a Fast Red naphthol-capture method and the sections were counterstained with haematoxylin. The results confirm that the method is specific for kappa or lambda mRNA and show that specific mRNAs can be detected in routine formalin-fixed sections using non-radioactive techniques with retention of good morphology. The method reliably detects light chain mRNA in cells expressing secretory immunoglobulin. The protocol can also be applied to tissue rich in endogenous biotin by using hapten-labelled probes.

Discrimination of closely homologous HPV types by nonisotopic in situ hybridization: definition and derivation of tissue melting temperatures

It is generally assumed that nucleic acid association during in situ hybridization reactions is similar to that of nucleic acid association in solution. This assumption has been investigated by detecting closely homologous human papillomavirus types 6 and 11 by in situ hybridization as a model for the evaluation of stringency conditions in clinical biopsies. By examining matched and mismatched, labelled and target sequences under various stringency conditions, empirical DNA-DNA stability curves and their derivative equations for tissue melting temperatures (Tmt) were derived. The corresponding values for Tmt are 10-20 degrees C higher than their solution equivalents. These data, supported by polymerase chain reaction experiments, demonstrate that closely homologous viral DNAs cross linked in tissue by formaldehyde fixation do not interact with the corresponding labelled probes as predicted from solution kinetic equations. This not only has theoretical implications but is also relevant to the accuracy of clinical diagnostic testing.

Phylogenetic distribution of the novel avian endogenous provirus family EAV-0

A new family of related endogenous proviruses, existing at 50 to 100 copies per haploid genome and distinguishable by remarkably short long terminal repeats, has been described for domestic chickens (Gallus gallus subsp domesticus). In this communication, by using Southern blot analysis and probes derived from both internal viral sequences and locus-specific, cellular flanking sequences, we studied the genetic distribution of this family of moderately repetitive avian endogenous retroviruses within the genomes of four Gallus species. Eight inbred lines of domestic chickens, the evolutionary progenitor to the domestic chicken (red jungle fowl), and two more distantly related species (grey and green jungle fowl) were studied. All Gallus species harbored this class of elements, although the different lines of domestic chickens and different species of jungle fowl bore distinguishable complements of the proviral loci. Jungle fowl appeared to have fewer copies than domestic chickens. For three randomly isolated proviral loci, domestic chickens (G. gallus subsp. domesticus) and red jungle fowl (G. gallus subsp. gallus) showed only a proviral state, whereas the most primitive and divergent of the jungle fowl, the green jungle fowl (G. varius), consistently demonstrated only preintegration states or disparate alleles. The presence of this family in all Gallus species and of related sequences in other genera suggests that a primordial founding integration event occurred prior to the evolutionary separation of Gallus species and possibly related genera. Additionally, at least one proviral locus has been acquired subsequent to speciation, indicating that this family was actively infectious after the primary founding event. This conserved, repetitive proviral family appears to represent the vestigial remnant of an avian retrovirus class related to and evolutionarily more ancient than the Rous-associated virus-0 family of avian endogenous retroviruses.

Nucleic acid probe characterizes Leptospira interrogans serovars by restriction fragment length polymorphisms

Restriction endonuclease analysis (REA) of genomic DNA can discriminate between many Leptospira interrogans serovars. However, several serovars have similar restriction endonuclease digestion patterns which prohibits accurate identification. This investigation expands previous REA studies of L. interrogans to include serovars in serogroup Tarassovi. Most serovars in this serogroup had characteristic digestion patterns by which they could be identified. However, four of the serovars in this serogroup had similar digestion patterns, thus preventing serovar identification by REA alone. To discriminate between these serovars REA was supplemented with Southern blot analysis. The DNA from each serovar showed similar but unique patterns when hybridized with a probe synthesized from a repetitive sequence element cloned from L. interrogans serovar hardjo type hardjo-bovis. The applicability of this technique to characterize other serogroups was assessed. One hundred sixty six of 190 serovars screened by Southern blot analysis contained sequences which hybridized with the repetitive element probe under conditions of relaxed stringency. These results suggest that Southern blot analysis using this probe will be a valuable supplement for typing L. interrogans.

Applications of nucleic acid probes in veterinary infectious diseases

Nucleic acid probe technology is increasingly being used in basic research in veterinary microbiology and in diagnosis of infectious diseases of veterinary importance. This review presents an overview of nucleic acid probe methodology and its applications in veterinary infectious diseases. The major applications of nucleic acid probes include detection of pathogens in clinical samples, especially those organisms which are fastidious and difficult to cultivate, differentiation of virulent from avirulent organisms and vaccine strains from wild type isolates, typing of microorganisms, mapping genes, screening libraries of cloned DNA for specific genes, detection of latently infected or carrier animals, study of mechanisms of pathogenesis, epidemiological studies and food safety.

Restriction endonuclease analysis of alcelaphine herpesvirus 1 DNA and molecular cloning of virus genomic DNA for potential diagnostic use

Alcelaphine herpesvirus 1 (AHV-1) genomic DNA was analyzed using restriction enzymes having recognition sequences both low in guanine-cytosine content (BamHI, KpnI, HindIII) and high in guanine-cytosine content (SmaI, AvaI, ApaI). The results from the restriction enzyme analyses along with exonuclease treatment demonstrated that the termini of AHV-1 DNA are likely composed of polyrepetitive sequences high in guanine-cytosine content similar to those found in Herpesvirus saimiri DNA. Cleaving AHV-1 DNA with the restriction enzyme SmaI produced polyrepetitive sequences that appeared as low molecular weight supermolar bands less than 1 kilobase pairs (kb) in size. Analysis of AHV-1 DNA cleaved with HindIII indicated that the polyrepetitive sequences are approximately 29.5 kb in size. The total molecular weight for AHV-1 DNA was determined to be approximately 118 kb. Seventy-five percent of the AHV-1 genome was cloned into the plasmids pAT153 and pBR322. Cloned DNA fragments representing unique sequences of the AHV-1 genome hybridized with AHV-1 genomic DNA but showed no appreciable hybridization with AHV-2 DNA or bovine herpesvirus 1, 2, or 4 DNA.

The detection and differentiation of foot-and-mouth disease viruses using solid-phase nucleic acid hybridization

Thirteen complementary DNA (cDNA) probes were used to detect the presence of foot-and-mouth disease virus (FMDV) RNA extracted from cell cultures. When labelled with 32P, these probes enabled the detection of 1 pg of FMDV-RNA, or 1 virus copy per cell. Two FMDV A12 probes that coded for the leader, structural protein VP1 region and part of the polymerase gene respectively, showed no hybridization with other closely related picornaviruses. Differentiation between FMDV serotypes A, O and C was possible, using cDNA probes from individual serotypes that corresponded to structural protein VP1.

Molecular cloning of a type D retrovirus from human cells (PMFV) and its homology to simian acquired immunodeficiency type D retroviruses

Unintegrated circular proviral DNA of a type D retrovirus (PMFV) isolated from a permanent human cell line was molecularly cloned in the bacteriophage vector L47.1 and subcloned in the plasmid vector pGEM-2. A restriction endonuclease map of PMFV DNA was established using 10 different enzymes for single and multiple digestions of closed circular and cloned DNA molecules. By restriction endonuclease analysis cloned PMFV DNA represented full-length viral DNA with one long terminal repeat (LTR). The comparison of the physical map of cloned PMFV to those of other cloned type D retroviruses revealed closest homology to the map of retrovirus D/New England (pD398) and SAIDS retrovirus type 1 (SRV-1). The relatedness of PMFV to further type D retroviruses (Mason-Pfizer monkey virus, MPMV; SAIDS retrovirus type 2, SRV-2) was also demonstrated by cross-hybridization of cloned DNAs under different stringencies (i) using full-length genomic probes of PMFV, MPMV, and SRV-2 and (ii) by DNA sequence analysis of regions of the group specific antigen (gag) protease (prt), polymerase (pol), and envelope (env) genes.

Alcelaphine herpesviruses 1 and 2 SDS-PAGE analysis of virion polypeptides, restriction endonuclease analysis of genomic DNA and virus replication restriction in different cell types

Herpesviruses have been isolated from white-tailed, white-bearded and blue wildebeest, as well as from Jimela topi and Cape hartebeest. These animals are members of the sub-family Alcelaphinae of the family Bovidae. Viruses isolated from wildebeest cause malignant catarrhal fever (MCF) in susceptible ruminant species. Alcelaphine herpesviruses (AHV) isolated from wildebeest replicate in both fetal aoudad sheep kidney (FAK) cells and bovine embryonic lung (BEL) cells. However, virus isolates from topi and hartebeest, which have not been linked to clinical MCF, replicate only in FAK cells. Buoyant density analysis by analytical ultracentrifugation, restriction endonuclease analysis and blot hybridization of virus genomic DNA from both alcelaphine herpesviruses as well as from bovine herpesviruses 1, 2, and 4 demonstrate that there are two types of alcelaphine herpesviruses, each distinct and different from the other bovine herpesviruses. Genomic size of both alcelaphine herpesviruses, estimated from DNA restriction fragments, is approximately 110 kilobase pairs. Alcelaphine herpesvirus DNA resembles Herpesvirus saimiri DNA during equilibrium sedimentation in that the majority of the DNA bands as a light (L) fraction with a minor heavy (H) component. Polyacrylamide gel analysis of virion proteins indicates that both viruses have distinct patterns, each consisting of 36 polypeptides ranging in molecular weight from 12,000 to 275,000. Virus isolates from wildebeest have been designated AHV-1, while viruses isolated from topi and hartebeest have been designated AHV-2.

Sequence divergence yet conserved physical characteristics among the E4 proteins of cutaneous human papillomaviruses

Human papillomavirus (HPV) types 1, 2, and 4 together comprise the major cause of cutaneous papillomas in the general population. We have aligned the genomes of these three viruses by partial sequence analysis, and have sequenced the E4 open reading frames (ORFs) of HPV 2 and HPV 4. After expression as beta-gal fusion proteins in bacteria, antibodies raised to the putative E4 gene-products of both virus types were used to identify the native E4 proteins in naturally occurring tumors. At the primary amino acid sequence level, the E4 protein of HPV 2 was found to be most homologous with those of HPV 6 and 11 and was not closely related to those of HPV 1 or 4. Although the E4 ORF represents a region of weak homology amongst papillomaviruses, the E4 encoded proteins showed significant conservation in their physical characteristics. Like those of HPV 1, the E4 proteins of both HPV 2 and HPV 4 were found to be composed of a major low-molecular-weight doublet (16.5/18K for HPV 2, 20/21K for HPV 4, c.f. 16/17K for HPV 1) along with minor high-molecular-weight species, which probably represent dimers of the smaller proteins, (33K for HPV 2, 40K for HPV 4, c.f. 32/34K for HPV 1). The E4 products of all three virus types were multiply charged, and exhibited a characteristic migration pattern following alkaline urea gel electrophoresis. Although the levels of E4 expression in tumors induced by the different virus types was very different, this was found to correlate closely with the level of virus production characteristic of each virus type. In all three cases, E4 proteins were found to be primarily cytoplasmic, and to be associated with the distinctive cytoplasmic inclusion granules characteristic of each virus type. The poor sequence conservation between the E4 protein of HPVs 1, 2, and 4, taken alongside the ability of these viruses to infect similar histological sites, suggests that E4 may not be involved in determining tissue specificity. Our results suggest conserved physical characteristics (acidic, multiply charged, ability to form dimers) and similar site of expression may be the important factors for E4 function.

Selective conservation of GAP-43 structure in vertebrate evolution

GAP-43 (a.k.a. B-50, F1, pp46, or neuromodulin) is a major growth cone membrane protein whose expression is widely correlated with successful axon elongation, but whose function remains unknown. To distinguish the structural features of GAP-43 most relevant to its cellular functions, we have determined features of the protein that are most highly conserved in vertebrate evolution. Comparison of fish and mammalian GAP-43 distinguishes two domains of the protein. A strictly conserved amino-terminal domain contains the putative site for fatty acylation and membrane attachment, a calmodulin binding domain, and a proposed phosphorylation site. In the much larger carboxy-terminal domain, amino acid composition is strongly conserved without extensive sequence conservation. This amino acid composition predicts an extended, negatively charged rod conformation with some similarity to the side arms of neurofilaments. The results suggest that the biological roles of GAP-43 may depend on an ability to form a dynamic membrane-cytoskeleton-calmodulin complex.

The linear mitochondrial plasmid pClK1 of the phytopathogenic fungus Claviceps purpurea may code for a DNA polymerase and an RNA polymerase

Plasmid pClK1, a linear mitochondrial plasmid of Claviceps purpurea, was completely sequenced. The sequence contains two long open reading frames (ORF1, 3291 bp; ORF2, 2910 bp), and at least four smaller ORFs. The potential polypeptide derived from ORF1 shows homology to the family B type DNA polymerases. The product of ORF2 has significant homology to the mitochondrial RNA polymerase of yeast and RNA polymerases from bacteriophages. ORF1 and ORF2 show homology to URF3 and URF1 of the maize plasmids S1 and S2, respectively. No homology to any published protein sequence was found for the smaller ORFs. The origin of the terminal protein attached to the 5' ends of pClK1 remains open; several alternatives for its origin are discussed. The sequence data as a whole confirm the virus-like character of pClK1 already postulated from structural properties. Thus pClK1 together with S plasmids of maize and several other linear plasmids make up a distinct class of DNA species of plants and fungi probably derived from a common virus-like ancestor.

Molecular characterization of a surface protein antigen gene from serotype c Streptococcus mutans, implicated in dental caries

The complete nucleotide sequence of the gene for a cell-surface protein antigen (PAc) of Streptococcus mutans MT8148 (serotype c) was determined. The pac gene consisted of 4695 bp and coded for a 170773D protein. The pac gene product contained a putative 38 amino acid signal peptide, resulting in a 166817D mature protein. A potential promoter sequence and a putative Shine-Dalgarno sequence preceded the open reading frame. Two internal repeating amino acid sequences were present in the PAc. One repeating region located in the N-terminal region was rich in alanine, and the other located in the central region was rich in proline. Southern blot analysis under the less stringent condition (allowing up to 35% base mismatch) revealed that the probe covering the proline-rich region hybridized to DNA preparations from strains of Streptococcus cricetus, Streptococcus sobrinus and Streptococcus downei as well as Streptococcus mutans.

The organization and expression of a maize ribosomal protein gene family

We have isolated several Zea mays cDNAs encoding the 40S subunit ribosomal protein S14. In maize, this ribosomal protein is encoded by a small multigene family, at least three members of which are expressed. S14 transcript levels are highest in mitotically active tissues, such as seedling shoot, developing endosperm, and tassel primordia, and lowest in tissues with little cell division, such as mature leaf and root. Very little S14 RNA is present in pollen, suggesting that translation of pollen mRNAs during pollen germination uses preformed ribosomes. During kernel development, the highest levels of S14 transcripts in endosperm tissue are found at 10-12 days postpollination; S14 RNA levels decline continuously from this point onward. The period of maximal expression of the S14 ribosomal protein gene appears to precede the onset of storage protein synthesis and does not correlate with the reported times of increased nucleolar volume or genome amplification.

Cloning and organization of seven arginine biosynthesis genes from Neisseria gonorrhoeae

A genomic library for Neisseria gonorrhoeae, constructed in the lambda cloning vector EMBL4, was screened for clones carrying arginine biosynthesis genes by complementation of Escherichia coli mutants. Clones complementing defects in argA, argB, argE, argG, argIF, carA, and carB were isolated. An E. coli defective in the acetylornithine deacetylase gene (argE) was complemented by the ornithine acetyltransferase gene (argJ) from N. gonorrhoeae. This heterologous complementation is reported for the first time. The carAB operon from E. coli hybridized with the gonococcal clones that carried carA or carB genes under conditions of high stringency, detecting 80% or greater similarity and showing that the nucleotide sequence of the carbamoylphosphate synthetase genes is very similar in these two organisms. Under these conditions for hybridization, the gonococcal clones carrying argB or argF genes did not hybridize with plasmids containing the corresponding E. coli gene. Cocomplementation experiments established gene linkage between carA and carB. Clones complementing a gene defect in argE were also able to complement an argA mutation. This suggests that the enzyme ornithine acetyltransferase from N. gonorrhoeae (encoded by argJ) may be able to complement both argA and argE mutations in E. coli. The arginine biosynthesis genes in N. gonorrhoeae appear to be scattered as in members of the family Pseudomonadaceae.

Nucleic acid hybridization as a diagnostic tool for the detection of human papillomaviruses

At this time nucleic acid hybridization tests are the most sensitive and reproduceable methods for the detection and differentiation of HPV types in clinical samples. The hybridization method of choice depends on the information desired and the availability of the proper diagnostic nucleic acid probes. Assuming most of the HPV nucleic acid probes become readily available in the near future, then the most sensitive test for screening clinical specimens--albeit the most laborious--will be the Southern blot procedure. As more information covering the involvement of HPV infections with the progression of lesions from benign to malignant is compiled, the need to know the particular subtype or status of HPV integration may become more or less important in the screening of clinical samples. If this information becomes less important, or unnecessary for a simple screening procedure, then dot blot hybridization may prove to be a much easier method for obtaining the information desired. If the sensitivity of in-situ hybridization using non-radioactive probes increases, then this method would become the fastest, easiest, and cleanest technique for the screening of a large number of clinical samples where limited information is desired. The ideal test for the future would be automated. In order to automate a test for HPV infections, the test design must become much simpler, and in order to design a simpler test, more information will be needed concerning the biology of HPV infections, how they cause benign or malignant cellular proliferation, and how the host immune system responds to HPV infections.

Papillomavirus. Effects upon mother and child

Papillomaviruses are widespread, sexually transmitted agents with an increasing prevalence. They are associated with a significant risk of genital carcinoma in infected women. Because they can be transmitted to the fetus before or during birth, they are also a risk to the infant born to an infected woman. Laryngeal HPV infections, while presumably much less prevalent than genital tract infections, are associated with a high degree of morbidity and a significant degree of mortality when they cause laryngeal papillomas. Therefore, transmission of these viruses to the fetus is a major problem. Much more information regarding mode of transmission and possible cure for this infection is needed in order to reduce the risk of laryngeal papillomatosis in infants in the future.

The genomic DNA organisation and evolution of a retrovirus-transmissible family of mouse (VL30) genetic elements

The sequence organisation of endogenous VL30 elements in the mouse genome was investigated by using a cloned representative of a retrovirus-transmissible VL30 cDNA. The majority of dispersed VL30 sequences could be assigned to a proviral-like structure 5.2-5.3 kbp long and bounded by long terminal repeats (LTRs). The existence of a hierarchy of evolutionarily conserved elements was rather limited and sequence heterogeneity between different elements was randomly distributed. However, the retrovirus-transmissible class of VL30 element was found to represent a distinct minority subgroup distinguishable by restriction sites and size (4.6-4.9 kbp long). Analysis of sequence conservation showed that VL30 elements display a more rapid turnover than endogenous murine leukaemia virus-related proviral sequences, and that VL30 LTRs show the most limited evolutionary distribution. Although discrete subsets of VL30 unique sequence were conserved in different rodents, the location of conserved regions was found to be variable, arguing against the presence of a functionally conserved protein coding region. These observations support the hypothesis that high frequency recombination, probably occurring during reverse transcription and the accompanying processes of duplicative transposition and amplification, have been a major determinant in the mode of evolution of the VL30 gene family.

Mitochondrial DNA of the human malarial parasite Plasmodium falciparum

Covalently closed circular DNA molecules were isolated from Plasmodium falciparum total DNA by isopycnic centrifugation in CsCl gradients containing either ethidium bromide or 2',6-diamidino-2-phenylindole. The circular molecules had an average contour length of 11.1 +/- 0.5 micron, similar to the analogous molecules previously isolated from the simian malaria parasite P. knowlesi. Both circular molecules shared considerable sequence homology and conserved restriction sites. The nucleotide sequence of one 936 bp fragment of the P. falciparum molecule was determined and identified, by a data base homology search, as part of a mitochondrial small rRNA subunit, thus confirming the mitochondrial origin of the circular DNAs of both malarial species.

Yeast gene SRP1 (serine-rich protein). Intragenic repeat structure and identification of a family of SRP1-related DNA sequences

We have isolated and sequenced a yeast gene encoding a protein (Mr 24,875) very rich in serine (SRP) and alanine residues that accounted for 25% and 20% of the total amino acids, respectively. The SRP1 gene is highly expressed in culture conditions leading to glucose repression (Marguet & Lauquin, 1986), the amount of SRP1 mRNA representing about 1 to 2% of total poly(A)+ RNA. A repetitive structure of eight direct tandem repeats 36-base long, also reflected in the amino acid sequence, was found in the second half of the open reading frame. The consensus amino acid sequence of the repeat was Ser-Ser-Ser-Ala-Ala-Pro-Ser-Ser-Ser-Glu-Ala-Lys. Replacing the genomic copy of the cloned gene with a disrupted SRP1 gene indicated that the SRP1 gene was not essential for viability in yeast, but several SRP1-homologous sequences were found within the yeast genome, raising the possibility that the disrupted SRP1 gene is rescued by one of the other SRP-homologous sequences. Complete separation of yeast chromosomes by contour-clamped homogeneous field electrophoresis indicated that, apart from chromosome V, which carries the SRP1 gene, 12 chromosomes have SRP-related sequences with various degrees of homology. These sequences were located on chromosomes XV, VII and XI under stringent conditions of hybridization (tm -20 degrees C), and observed on chromosomes I, II, III, IV, VI, VIII, X, XI and XII, only under low-stringency conditions (tm -40 degrees C). Northern blot analysis of both the wild type and SRP1-disrupted strains indicated that along with SRP1 at least one more member of the SRP family was transcribed to a 0.7 kb (1 kb = 10(3) bases) polyadenylated RNA species clearly distinct from the SRP1-specific mRNA (1 kb long). Analyses of the SRP1 repeat domain suggested a model for the divergent evolution of the repeats in the SRP1 sequence.

Analysis of genome segments from six different isolates of bluetongue virus using RNA-RNA hybridisation: a generalised coding assignment for bluetongue viruses

Nucleic acid probes prepared directly from bluetongue virus (BTV) genomic double-stranded RNA (dsRNA) have been used to identify the functionally equivalent genome segments from six distinct isolates of BTV after their separation in both agarose and polyacrylamide gel electrophoresis systems. Variations in the rate, and in one case the order, of migration of the equivalent genome segments from different viruses was detected in the polyacrylamide gel system. However, the genomic dsRNA profiles of eleven BTV isolates were found to be identical when analysed by agarose gel electrophoresis. Functionally equivalent genome segments from the six viruses that were analysed were found to migrate in identical relative positions in this gel system. From these data we propose a modified version of the protein coding assignments published for BTV 1 South Africa (Mertens et al., 1984) in which the identification of the genome segments would be based upon their order of migration in the agarose rather than the polyacrylamide gel system. The modified coding assignments, unlike the original assignments, would be applicable to all of those viruses analysed and appear likely to be valid for all normal BTV isolates.

Genomic location of bovid herpesvirus type 2 nucleotide sequences homologous to five herpes simplex virus type 1 genes

The location of nucleotide sequences within the bovid herpesvirus 1 (BHV-2) genome homologous to herpes simplex virus 1 (HSV-1) DNA were investigated. BHV-2 DNA was digested with restriction endonucleases and blotted to nitrocellulose paper. The blots were then probed with plasmids containing HSV-1 genes for thymidine kinase (TK), the major DNA binding protein (ICP8), the major capsid protein (VP5) and genes for HSV-1 glycoproteins gB, gD, and gC. Except for HSV-1 gC, each HSV-1 gene tested hybridized to BHV-2 nucleotide sequences that were located either on both sides of a restriction endonuclease cleavage site, within a small restriction endonuclease fragment, or to an area common to two overlapping restriction fragments. Thus, we were able to localize BHV-2 nucleotide sequences homologous to the HSV-1 ICP8 gene between 0.38 and 0.41 map units (m.u.), and BHV-2 nucleotide sequences homologous to the HSV-1 VP5 gene between 0.24 and 0.27 m.u. In addition, BHV-2 nucleotide sequences homologous to HSV-1 genes for TK, gB and gD were found to lie on both sides of restriction endonuclease cleavage sites at 0.30, 0.35, and 0.94 m.u., respectively.

Evidence that the gene for herpes simplex virus type 1 DNA polymerase accounts for the capacity of an intertypic recombinant to spread from eye to central nervous system

HSV-1(17) replicates 100-fold more efficiently than HSV-2(186) within trigeminal ganglia following ocular infection. In order to identify the nucleotide sequences responsible for the differences in the capacity of the two HSV strains to grow within the peripheral nervous system, an intertypic recombinant was generated by infecting neuroblastoma cells with HSV-2(186) and a HSV strain possessing nucleotide sequences from HSV-1(17). The genome of the intertypic recombinant was composed entirely of HSV-2(186) DNA except for 2.0 kb of HSV-1(17) DNA positioned between m.u. 0.413 and 0.426. Following corneal infection of mice, the intertypic recombinant grew to higher titers in both ocular tissues and trigeminal ganglia than did the HSV-2 parent. Most significantly, the intertypic recombinant could spread into the brain from the trigeminal ganglion and kill the host whereas mice inoculated with the HSV-2(186) parent survived infection. The 2.0 kb of HSV-1(17) DNA inserted into the genome of the intertypic recombinant encodes the 5' terminus of the HSV-1 gene for DNA polymerase. Thus, the results suggest that the difference in the capacity of two HSV strains to replicate within the trigeminal ganglion of its host and to spread into the brain is determined by nucleotide sequences within the gene for DNA polymerase.