Restriction Endonuclease Cleavage Patterns Research Articles

Contagious caprine pleuropneumonia in an organised goat farm of Tamil Nadu

A detailed systematic approach on the disease dynamics, differential diagnosis and control measures adopted in an outbreak of contagious caprine pleuropneumonia (CCPP) in an organised goat farm located at Kattupakkam (Tamil Nadu) has been reported. The outbreak occurred during April to June 2014 among 60 newly purchased adult non-descript goats. The clinical signs were profuse bilateral mucous discharge, respiratory distress with abnormal respiratory sounds. On post-mortem gross lesions were fibrinous pleurobronchopneumonia with extensiveness of the lesions involving all lobes of either one or both lungs, thickened interlobular septae. The samples were found negative for peste des petitis ruminants virus by polymerase chain reaction. Mycoplasma capricolum subsp. capripneumoniae or F-38 was isolated from clinical (n=20) and necropsy samples (n=25) of goats. The characteristic restriction enzyme cleavage pattern of M. capripneumoniae, differentiated it from the other members of M. mycoides cluster. The disease outbreak of caprine mycoplasmosis was contained soon after identification of the etiological agent by adopting proper control and preventive measures.

Molecular discrimination of Hyalomma tick species serving as reservoirs and vectors for Crimean-Congo hemorrhagic fever virus in sub-Saharan Africa

The species identification of tick vectors of Crimean-Congo hemorrhagic fever virus (CCHFV), especially Hyalomma (H.) species, is a prerequisite to understand the eco-epidemiology of this disease and to reveal vector and virus reservoir species. However, the morphologic species discrimination can be difficult for damaged or blood-fed ticks and in case of species intercrosses. Therefore, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and restriction fragment length polymorphism (RFLP) analysis to distinguish the most common Hyalomma species from sub-Saharan Africa (H. truncatum, H. rufipes and H. dromedarii). Within the last years, MALDI-TOF MS analysis based on tick leg proteins has been shown to be a reliable method to distinguish several tick species. For this purpose, a reference spectral library of several European, American and African tick species was established. In this study, six different Hyalomma species were tested, all of which were all clearly distinguishable by mass spectrometric analyses. Moreover, MALDI TOF- MS was able to confirm morphologic findings where sequencing provided ambiguous results. In addition, a polymerase chain reaction (PCR) based on the CO1 gene amplification of ticks has been developed for the unequivocal species identification by amplicon sequencing and specific restriction endonuclease cleavage pattern analysis. RFLP proved to be a feasible auxiliary discrimination tool for selected Hyalomma species when access to sequencing methods is not available, as for instance during field studies.

Molecular epidemiology of an outbreak of clinical mastitis in sheep caused by Mannheimia haemolytica

The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep and grain producing property in south east Australia during drought conditions in 2009. Milk samples were collected aseptically from all affected ewes and plated on sheep blood agar for bacterial identification. M. haemolytica was isolated from 80% of the samples that yielded cultivable microorganisms and thus was the main microorganism responsible for the outbreak. Analysis of the restriction endonuclease cleavage patterns of the isolates using pulsed field gel electrophoresis revealed some evidence of clonality, suggesting the possibility of horizontal transmission, but there was also considerable diversity between the clusters of closely related isolates. Multilocus sequence typing of the M. haemolytica isolates revealed most of the isolates belonged to ST1 with no association between the PFGE and MLST fingerprints of the isolates. Resistance to neomycin, streptomycin and sulphafurazole was detected in some of the isolates, but they were all susceptible to penicillin, ampicillin, ceftiofur, amoxycillin/clavulanic acid, ciprofloxacin, tetracycline, erythromycin and trimethoprim. This is the first published record of a comparison of the strains of M. haemolytica involved in a clinical mastitis outbreak in sheep and demonstrates the importance of this pathogen in sheep production systems, particularly during adverse climatic conditions and increased stocking rate.

The upper respiratory tract is a natural reservoir of haemolytic Mannheimia species associated with ovine mastitis

Lamb suckling has been suggested to be an important way of infecting a ewe's udder with different bacteria, including Mannheimia haemolytica. To test the potential role of lambs in transferring Mannheimia species to the ewe’s udder, the restriction endonuclease cleavage patterns of isolates obtained from nasopharyngeal swabs were compared with those obtained from cases of mastitis. Sterile cotton swabs were used to collect nasopharyngeal samples from 50 ewes and 36 lambs from three flocks. M. haemolytica and Mannheimia glucosida as well as haemolytic Mannheimia ruminalis-like organisms were detected in the upper respiratory tract of lambs and ewes. Comparison of the restriction endonuclease cleavage patterns of the isolates suggested that the M. haemolytica isolates obtained from different milk samples from ewes with mastitis were more clonal than those obtained from the nasal swabs. However, some nasal isolates within both Mannheimia species had restriction endonuclease cleavage patterns identical to those obtained from milk samples from ewes with mastitis, indicating that lambs may have a role in transferring these organisms to the udder. More clonality was observed between the M. glucosida isolates than between M. haemolytica isolates.

Human adenovirus type identification.

Dear editor The published paper in your journal entitling “Human adenovirus type 8 epidemic keratoconjunctivitis with large corneal epithelial full-layer detachment: an endemic outbreak with uncommon manifestations” has come into our attention.1 The article provides interesting clinical presentation of corneal epithelial layer detachment among 25% (4 out of 16 human adenovirus [HAdV]-positive cases) of patients diagnosed with epidemic keratoconjunctivitis (EKC). However, we have some opinions about the article that are stated below: First, we have noticed that the authors have used the combination of hexon gene sequence and BLASTN for the typing of HAdV. Due to the appearance of many recombinant types of HAdVs, especially the EKC causing ones, for the last few years, many isolates were wrongly diagnosed as HAdV-8 by serological method. For example, type HAdV-54 was diagnosed as HAdV-8 due to cross reaction in neutralization test.2 Even this was described as genome type HAdV-8I due to its misidentification as HAdV-8.3,4 Nowadays, HAdV-54 has become the major agent of EKC in Japan, although a few HAdV-8 is still being isolated in some places.5–9 Another EKC causing recombinant type HAdV-53 carries the fiber gene of HAdV-8, penton of HAdV-37, and the hexon of HAdV-22.9 Therefore, current recommended type identification method of HAdV is sequencing of the penton (P)-hexon (H)-fiber (F) genes (molecular typing) or whole genome sequence.10 Second, the authors used the term HAdV-8 genotype on the basis of HAdV-8 hexon sequence followed by BLASTN. Now a days, PCR amplification and sequencing of variable regions within the hexon, penton base, and fiber genes is designated as molecular typing method. The term genotype is used for the recognition of a new type by full genome sequence. A genotype number is assigned where sequence data reveal that either i) the virus isolate encodes novel hexon (loops 1 and 2), penton base (hypervariable region), and fiber (knob) sequences, or ii) is a recombinant with one or two of these regions derived from previously designated genotypes, or iii) is a recombinant that has a unique combination of these three regions derived from previously recognized genotypes.10 Third, in the discussion, the authors described HAdV-8C–H genome types as genotypes. Traditionally, genome types of HAdV are designated by the restriction endonuclease cleavage pattern analysis of viral DNA.11 We hope the authors will perform the currently recommended methods to confirm the identity of their EKC causing HAdVs.

ISOLATION AND CHARACTERIZATION OF A NOVEL HERPESVIRUS FROM A FREE-RANGING EASTERN GREY KANGAROO (MACROPUS GIGANTEUS)

We isolated a macropodid herpesvirus from a free-ranging eastern grey kangaroo (Macropus giganteous) displaying clinical signs of respiratory disease and possibly neurologic disease. Sequence analysis of the herpesvirus glycoprotein G (gG) and glycoprotein B (gB) genes revealed that the virus was an alphaherpesvirus most closely related to macropodid herpesvirus 2 (MaHV-2) with 82.7% gG and 94.6% gB amino acid sequence identity. Serologic analyses showed similar cross-neutralization patterns to those of MaHV-2. The two viruses had different growth characteristics in cell culture. Most notably, this virus formed significantly larger plaques and extensive syncytia when compared with MaHV-2. No syncytia were observed for MaHV-2. Restriction endonuclease analysis of whole viral genomes demonstrated distinct restriction endonuclease cleavage patterns for all three macropodid herpesviruses. These studies suggest that a distinct macropodid alphaherpesvirus may be capable of infecting and causing disease in eastern grey kangaroos.

Morphology and General Characteristics of Bacteriophages Infectious to Robinia pseudoacacia Mesorhizobia

Four phages infectious to Mesorhizobium strains were identified in soil samples taken from local Robinia pseudoacacia stands. Based on their polyhedral heads and short noncontractile tails, three of the phages, Mlo30, Mam12, and Mam20, were assigned to group C of Bradley's classification, the Podoviridae family, while phage Mlo1, with its elongated hexagonal head and a long flexible tail represented subgroup B2 bacteriophages, the Siphoviridae family. The phages were homogeneous in respect of their virulence, as they only lysed Mesorhizobium strains, but did not affect strains of Rhizobium or Bradyrhizobium. On the basis of one-step growth experiments, the average virus yield was calculated as approximately 10-25 phage particles for phages Mlo30, Mam12 and Mam20, and as many as 100-120 for phage Mlo1. The rate of phage adsorption to heat-treated cells showed differences in the nature of their receptors, which seemed to be thermal sensitive, thermal resistant, or a combination of the two. Only the receptor for phage Mlo30 was likely to be an LPS molecule, which was supported by a neutralization test. The smooth LPS with O-antigenic chains of the phage-sensitive M. loti strain completely reduced the bactericidal activity of virions at a concentration of 1 μg/ml. The molecular weights of phage DNAs estimated from restriction endonuclease cleavage patterns were in the range from approximately 39 kb for group C phages to approximately 80 kb for B2.

Rapid pathotyping of recent H5N1 highly pathogenic avian influenza viruses and of H5 viruses with low pathogenicity by RT-PCR and restriction enzyme cleavage pattern (RECP)

Rapid and accurate diagnosis of avian influenza virus infections of poultry and humans comprises detection, subtyping, and, in case of subtypes H5 and H7, pathotyping of such viruses. Reliable methods for pathotyping of H5 avian influenza viruses (AIV) are based on determination of the intravenous pathogenicity index (IVPI) in specific pathogen free (SPF) chickens and on characterization of the hemagglutinin (HA) gene cleavage site by sequencing. The number of basic amino acids (arginine and lysine) at the cleavage site is an important indicator of pathogenicity. In this paper, a new rapid method for pathotyping of H5 subtype avian influenza viruses is described which is based on RT-PCR and restriction enzyme cleavage pattern (RECP) assay using the MboII restriction enzyme. Validation of the method using 28 H5 subtype reference isolates from different animal species revealed good performance characteristics regarding sensitivity and specificity, especially when targeting recent highly pathogenic AIV (HPAIV) of subtype H5N1 and Asian origin. In addition, RECP results were validated by testing 47 field samples from different sources and by sequencing of their RT-PCR products. This approach for H5 AIV pathotyping proved to be fast, reliable, and comparatively sensitive and is suitable especially for laboratories lacking sequencing or in vivo pathotyping facilities.

Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-19), was completely sequenced and shown to comprise 132,565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-19 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-19 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-19 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group II NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group II had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60 % of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

PCR-RFLP of mitochondrial DNA of swamp buffaloes in breeding station

Methods have been devised for detecting polymorphisms in the D-loop regions using the PCR followed by restriction enzyme digestion to reveal restriction fragment length polymorphism. Total DNA were extracted from the white blood cell of swamp buffaloes. Restriction endonuclease cleavage patterns of mitochondrial DNA (mtDNA) of local swamp buffalo from Lamphayaklang Livestock Research and Breeding Station in Thailand were analyzed using three enzymes (Ava lI, Bam H I and Hae III) which recognize 4 and 6 nucleotides. Among the 49 animals were analyzed, Ava II, BamH I and Hae III revealed different polymorphisms. Ava II showed two types of cleavage pattern. BamH I showed two type of cleavage pattern. And Hae III showed four types of cleavage pattern. The polymorphic fragments patterns for these three restriction endonuclease (Ava II- BamH I- Hae III) revealed five types of D-loop mtDNA in all the animals examined.These preliminary results indicated that polymorphism in the D-loop region of swamp buffalo mtDNA can be revealed by PCR and restriction enzyme analysis. And these enzymes would be able to show the genetic difference among the swamp buffaloes.These preliminary results indicated that polymorphism in the D-loop region of swamp buffalo mtDNA can be revealed by PCR and restriction enzyme analysis. And these enzymes would be able to show the genetic difference among the swamp buffaloes.

Rapid characterization of avian reoviruses using phylogenetic analysis, reverse transcription-polymerase chain reaction and restriction enzyme fragment length polymorphism

A reverse transcription-polymerase chain reaction is described, which amplified the full-length sigmaC-encoding and sigmaNS-encoding genes of avian reovirus (ARV). DNA fragments of 1022 and 1152 base pairs were amplified among ARV isolates, respectively, indicating that there were no apparent deletions or insertions in these regions. Fragments amplified from vaccine strains and field isolates were digested with five different restriction enzymes Bcn I, Hae III, Taq I, Dde I, and Hinc II, respectively. Restriction fragment profiles observed on polyacrylamide gels showed heterogeneity between vaccine and Taiwanese isolates. All ARV isolates tested showed different restriction enzyme cleavage patterns and could be clearly distinguished. The strain-typing based on the cleavage sites in the sigmaC-encoding gene of ARV showed that viruses could be classified into four distinct groups. A phylogenetic tree based on the nucleotide sequences of the sigmaC-encoding gene revealed that Taiwanese ARV isolates were classified into four distinct groups, indicating that the genotyping is consistent with typing based on restriction enzyme fragment length polymorphism of the sigmaC-encoding gene of ARV. The results suggested that polymerase chain reaction followed by restriction enzyme analysis provided a simple and rapid approach for characterization of ARV isolates. Also, it is possible to determine whether a new variant strain has been introduced into a flock or a given virus strain has spread from one flock to another.

Comparison of virulence and restriction endonuclease cleavage patterns of infectious laryngotracheitis viruses isolated in Korea

Isolates of infectious laryngotracheitis virus (ILTV) obtained from field disease outbreaks in Korea from 1982 to 1998 were compared by virulence testing and by examining restriction endonuclease (REN) cleavage patterns of viral DNA. Based on pathogenicity tests, eight of 11 ILTV strains were classified as virulent, because these strains caused 40 to 80% mortality in specific pathogen free chickens, while three strains were classified as low virulence because these did not cause mortality. The REN cleavage patterns of the low virulence strains were identical with those of two reference vaccine strains, which were of chicken embryo origin. However, the DNA cleavage patterns of the virulent strains differed from those of both the low virulence and the vaccine strains. Furthermore, one virulent Korean strain N87278 had REN cleavage patterns that were clearly different from other virulent strains. In the present study, ILTV strains examined could be classified into two groups (virulent and low virulence strains) by pathogenicity testing, and three groups based on their REN cleavage patterns. These results suggest that most outbreaks of infectious laryngotracheitis were not likely to be associated with vaccine strains, but some were associated with viruses indistinguishable from commercial vaccine strains. At least three genetically distinct groupings of ILTV have been involved in outbreaks of infectious laryngotracheitis in Korea.

Characterization of a bovine herpesvirus type 4 isolated from the spinal cord of a cow with astasia.

A bovine herpesvirus (BHV) strain designated B11-41, was recently isolated from the spinal cord of a cow with astasia. By BHV type specific polymerase chain reaction (PCR), a BHV-4 specific fragment was amplified from the DNA of strain B11-41. The nucleotide sequence of the PCR product revealed high homologies (98.4% and 99.8%) with those of two BHV-4 strains (Movar 33/63 and 86-068). The BamHI restriction endonuclease cleavage patterns of the B11-41 were more similar to those of BHV-4 than those of other types of BHV. BHV-4 is divided into two groups, European and American. The EcoRI, and BamHI, and HindIII restriction endonuclease analysis demonstrated that strain B11-41 was closely related to the American type of BHV-4. It was concluded that B11-41 was identified as a BHV-4 that belongs to the American group. Additionally, the results of this study may indicate that the nervous system is one of the sites of viral latency in natural infection.

Molecular characterisation and differential diagnosis of a necrotic PVY isolate in tomato

SummaryA PVY isolate which causes strong necrotic lesions in tomato was isolated and characterised. It did not infect potato and did not react with antiserum specific to the N‐strain of PVY. Restriction endonuclease cleavage patterns of PCR products derived from the 5′‐end of the virus genome (Hinc II and Rsa I) clearly distinguished the tomato, pepper and potato strains. Additional sequence analysis indicated that the tomato and pepper isolates were closely related, while both markedly differed from the necrotic strains of potato. Hence, it was concluded that the necrotic tomato isolate is uniquely specific for tomato.

Partial characterization of a Brazilian strain of Aujeszky’s disease virus recovered from a pig with subclinical infection

One Brazilian strain of Aujeszky’s disease virus isolated from a piglet in which the disease had not been observed was studied as for its virulence in pigs. The genome of the virus was molecularly analysed as for their restriction endonuclease cleavage pattern. Fifty-day-old non-immune weanlings exposed to this strain showed no disease although the virus was present in their oropharyngeal area for at least three days. All animals developed moderate titers of neutralizing antibody. Based on number of bands and migration rate of restriction fragments the isolate was classified into Herrmann’s type I group. Latent infection was detected in all pigs by PCR. Some variations were detected in the cleavage pattern of the strain ASB Piau when compared to LA031 virulent Brazilian strain, that could be related to differences in the virulence.

Cloning and expression of a plasmid-linked pediocin determinant trait ofPediococcus acidilactici F

Plasmid DNA from Pediococcus acidilactici F was prepared by lysozyme-mutanolysin method and purified by cesium chloride-ethidium bromide (CsCl-EtBr) density gradient ultracentrifugation. Agarose gel electrophoresis of plasmid DNA and plasmid-curing experiments suggested that bacteriocin activity was harboured on a small plasmid of approximately 9.1 kb (kilobasepair) in Pediococcus acidilactici F. Plasmid encoding bacteriocin production in P. acidilactici F was examined for restriction enzyme cleavage patterns and its map has been constructed. An Escherichia coli strain transformed with the recombinant plasmid, pQE322, produced and, most probably, secreted pediocin F.

Cloning and expression of a plasmid‐linked pediocin determinant trait of Pediococcus acidilactici F

Plasmid DNA from Pediococcus acidilactici F was prepared by lysozyme-mutanolysin method and purified by cesium chloride-ethidium bromide (CsCl-EtBr) density gradient ultracentrifugation. Agarose gel electrophoresis of plasmid DNA and plasmid-curing experiments suggested that bacteriocin activity was harboured on a small plasmid of approximately 9.1 kb (kilobasepair) in Pediococcus acidilactici F. Plasmid encoding bacteriocin production in P. acidilactici F was examined for restriction enzyme cleavage patterns and its map has been constructed. An Escherichia coli strain transformed with the recombinant plasmid, pQE322, produced and, most probably, secreted pediocin F.

Detection of avian reovirus RNA and comparison of a portion of genome segment S3 by polymerase chain reaction and restriction enzyme fragment length polymorphism

A reverse transcription-polymerase chain reaction (RT-PCR) was established to amplify a 672-base pairs fragment on the segment S3 of avian reovirus (ARV). The amplified fragments were detected in nine strains of ARV as well as three tendon tissue specimens, indicating that the primer regions were well conserved. The RT-PCR was able to detect as low as 0· pg using an ethidium bromide stained gel. The detection limit could be enhanced further to 0·04 pg by hybridisation after southern transfer. The amplified DNA fragments from nine ARV strains and two tissue specimens showed different restriction enzyme cleavage patterns. Analysis of the data revealed that these 11 strains were classified into four groups. The results suggest that PCR followed by restriction enzyme analysis may provide a simple and rapid method for the characterisation of ARV isolates.

The Mycoplasma hominis P120 membrane protein contains a 216 amino acid hypervariable domain that is recognized by the human humoral immune response.

In the antigenically heterogeneous species Mycoplasma hominis a monoclonal antibody, mAb 26.7D, was previously found to recognize a 120 kDa polypeptide from M. hominis 7488. This antibody did not react with the type strain PG21. The homologous gene from M. hominis PG21 was cloned and sequenced and found to have a sequence identity of 91% with the gene of strain 7488. One hypervariable and two semivariable regions were detected. The epitope for mAb 26.7D was mapped to the hypervariable domain by expression of various parts of this domain in Escherichia coli using expression vector systems. A polyclonal antiserum (pAb 121) generated against the hypervariable region of P120 from PG21 identified the P120 homologue in M. hominis PG21. Fusion proteins of the hypervariable and constant parts of the proteins were constructed and tested for reactivity with 21 human sera. Twelve sera reacted with the 7488 hypervariable fusion protein, but only four reacted with PG21 hypervariable fusion protein. No reactivity was seen with a fusion protein containing part of the constant region of P120. Gene fragments amplified from 18 M. hominis isolates by PCR confirmed the heterogeneity of the hypervariable domain. Based on restriction endonuclease cleavage patterns of the hypervariable domain the 18 isolates could be divided into four cases. Reactivity with both mAb 26.7D and pAb 121 confirmed these classes. The hypervariable, but not the constant, part of P120 was recognized by the human humoral immune response. Such a variable domain may be important in evasion of the host's immune response, and thus aid survival of the micro-organism.

Polymorphism of mitochondrial DNAs of Yunnan domestic water buffaloes, Bubalus bubalis, in China, based on restriction endonuclease cleavage patterns.

Restriction endonuclease cleavage patterns of mitochondrial DNA(mtDNA) of three local types of Yunnan native water buffalo were analyzed using 18 enzymes which recognize six nucleotides. Among the 12 animals analyzed, 3 of 18 enzymes, BamHI, EcoRI, and Scal, revealed polymorphisms. Three mtDNA types were identified. The results indicate that a relatively low level of mtDNA variation exists in Yunnan domestic water buffaloes. The origin of Chinese buffalo derived from Yunnan province of China is discussed.