Nematode transmissibility of pseudo-recombinant isolates of tomato black ring virus

Pseudo-recombinant isolates of tomato black ring virus (TBRV), containing RNA-i of the potato bouquet serotype and RNA-2 of the beet ring-spot serotype, were transmitted by the nematode Longidorus elongatus, which also transmits the beet ringspot serotype but not the potato bouquet serotype. Transmissibility by L. elongatus was correlated with antigenic specificity of the virus particles, providing further evidence that nematode transmissibility depends on the structure of the virus coat protein. The distribution of genetic determinants for biological properties between the RNA-1 and RNA-2 of TBRV resembles that for raspberry ringspot virus.     

Identification of Tomato black ring virus from tomato plants grown in greenhouses in Saudi Arabia

A survey was conducted in Al-Kharj governorate, Riyadh region to identify viruses causing variety of virus-like symptoms on tomato plants. A total of 135 samples were collected from symptomatic tomato plants. Symptoms included mottling, deformation, necrosis of leaves and fruits. Eighteen viruses were tested by DAS-ELISA. Tomato black ring virus (TBRV) was the virus of concern as it was not detected in Saudi Arabia before and was detected in 52.6% of the collected samples in this study. RT-PCR was used to confirm detection of TBRV and to sequence the amplified products to determine molecular characteristics of this virus. In the host range test study that was performed using a purified isolate of TBRV, sixteen out of the twenty two tested plants showed symptoms. Brassica oleracea was not infected by this virus. Gel electrophoreses (2% agarose) yielded fragments of 978 bp of coat protein gene of TBRV. Nucleotide sequences of purified RT-PCR products for three TBRV Saudi isolates were deposited in the GenBank with the following accession numbers MT274656, MT274657, and MT274658. These isolates of TBRV indicated a close Phylogenetic relationship of (99–100%) among themselves and with five isolates from Poland (95–98%) but a distant relationship of 85% with isolates from England and Lithuania deposited in the GenBank. This is the first report for detection and molecular characterization of TBRV infecting tomato plants in Saudi Arabia.     

Restriction pattern analysis of genomic DNA ofFrankia isolates

Summary Total genomic DNAs ofFrankia isolates were subjected to restriction enzyme digestion and subsequent agarose gel electrophoresis. Restriction fragment banding patterns were unique for each isolate and may therefore be used as a method to distinguish between isolates which may be morphologically indistinguishable. This method might be useful for practical purposes such as tracing specificFrankia strains during field studies.     

Biological and Molecular Characterization of Polish Isolates of Tomato torrado virus*

Three isolates of Tomato torrado virus (ToTV) were found in Poland. The isolates were characterized on the basis of their symptomatology on plant species, serological reactions, electron microscopy, and nucleotide and amino acid sequence analyses of coat protein subunit genes. In comparative tests, the Polish ToTV isolates were shown to be closely related to each other and also to the isolate from Spain.     

Analyses of genetic and pathogenic variability among Botrytis cinerea isolates

Seventy nine isolates of Botrytis cinerea were collected from different host plants and different locations of India and Nepal. All the isolates were identified as B. cinerea based on morphological features and were confirmed using B. cinerea specific primers. Differentiation among the isolates was assessed using morphological, genetic and biochemical approaches. To analyze morphological variability, differences in conidial size, presence or absence of sclerotia and their arrangement were observed. Genetic variability was characterized using RAPD analysis, presence or absence of transposons and mating type genes. Cluster analysis based on RAPD markers was used for defining groups on the basis of geographical region and host. The biochemical approach included determining differences in concentration of oxalic acid and activity of lytic enzymes. All the isolates were categorized into different pathogenic groups on the basis their variable reaction towards chickpea plants. Isolates with higher concentration of oxalic acid and greater activity of lytic enzymes were generally more pathogenic. Pathogenicity was also correlated to transposons. Isolates containing transposa group showed some degree of correlation with pathogenic behavior. However, isolates could not be grouped on the basis of a single approach which provides evidence of their wide diversity and high evolution potential. Sensitivity of sampled isolates was also tested against five botryticides. Most of the isolates from same region were inhibited by a particular fungicide. This feature provided interesting cues and would assist in devising novel and more effective measures for managing the disease.     

Restriction endonuclease fingerprinting analysis of Canadian isolates of Aeromonas salmonicida

Restriction endonuclease fingerprinting (REF) analysis was used to examine total cellular DNA prepared from 56 independent field isolates of the fish pathogen, Aeromonas salmonicida. DNA was digested singly with the restriction enzymes EcoRI and HindIII, and the resulting fragments separated by polyacrylamide gel electrophoresis and visualized by silver staining. The REF patterns of typical isolates of A. salmonicida subsp. salmonicida were distinct from those of A. hydrophila, A. salmonicida subsp. achromogenes, A. salmonicida subsp. masoucida, and atypical isolates of A. salmonicida subsp. salmonicida. Differences between strains of typical A. salmonicida subsp. salmonicida could also be distinguished. Canadian isolates examined could be assigned to 1 of 12 different groups (REF groups), with the majority of the isolates belonging to REF groups 1 and 5. REF group 1 strains were isolated from British Columbia and New Brunswick while REF group 5 isolates were found in Ontario. None of the European strains examined had REF patterns identical to those of Canadian isolates. Based on REF analysis, there was little genetic heterogeneity detected among 23 isolates from two short-term studies of naturally occurring infections. Several different REF groups were seen among A. salmonicida collected over a 10-year period from coho salmon from the Credit River. Consistent with earlier biochemical and hybridization studies, the REF data suggest that A. salmonicida is a clonal pathogen. REF analysis can, however, permit the identification of subgroups, which may be useful in epidemiological studies.     

Examination of the genetic variability among biofilm-forming Candida albicans clinical isolates

Biofilms are microbial communities encased in a self-produced polymeric matrix and represent a common mode of microbial growth. Candida albicans is able to colonize the surface of catheters, prostheses, and epithelia, forming biofilms that are highly resistant to antimicrobial drugs. The objective of this study was the genotypic characterization of biofilm-forming C. albicans clinical isolates using RAPD (Random Amplified Polymorphic DNA). We have studied 25 clinical isolates of C. albicans from oral cavities, blood, skin, nail, stool, oesophagus biopsy and vaginal fluids from patients suffering from candidiasis. For each strain biofilm formation was analysed by measuring the ability to adhere to and grow on polystyrene plastic surfaces using XTT [2,3-bis(2-methoxi-4nitro-5sulfophenil)-2H tetrazolium-5carboxanilide] reduction assay. The similarity coefficients generated by RAPD using four different primers varied from 49 to 91%, indicating a high degree of genetic variability between the clinical isolates. The dendrogram clustered the isolates in four related groups, all groups included strains with very different abilities to form biofilms. The isolates with similar genotypes often showed very different biofilm formation abilities. Strains were grouped into clusters independently of their clinical sources. Our results suggested that a direct correlation does not exist between the biofilm-forming ability of natural populations of C. albicans and the genotype as determined by RAPD.     

Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients

To define further the genetic variability of the human AIDS retrovirus, we have cloned and sequenced the complete genomes of two isolates obtained from Zairian patients. Their genetic organization is identical with that of isolates from Europe and North America, confirming a common evolutionary origin. However, the comparison of homologous proteins from these different isolates reveals a much greater extent of genetic polymorphism than previously observed. It is nevertheless possible to define conserved domains in the viral proteins, especially in the envelope, that could be of interest for the understanding of the molecular mechanisms of viral pathogenicity and for the development of diagnostic and therapeutic reagents.     

Restriction analysis of conserved and variable regions of VP2 gene of Indian isolates of bluetongue virus serotype 1

Bluetongue virus (BTV) is a member of Orbivirus genus in family Reoviridae. The virus genome is composed of 10 double-stranded RNA segments. The RNA segment L2 encodes an outer capsid viral protein VP2, which is the main determinant of neutralization and serotype-specific immune response. BTV serotype 1 (BTV-1) specific novel primer pair was designed using VP2 gene sequences available in GenBank to amplify 1240-1844 bp region because two hypervariable and three conserved regions have been reported within these 604 nucleotides. This primer pair successfully amplified cell culture adapted six Indian isolates of BTV-1 from different geographical regions of the country. The 604 bp PCR product of VP2 gene of all six BTV-1 yielded two fragments of 273 and 331 bp when digested with Taq1 restriction enzyme. This indicated that there is only one TaqI site at 1513 bp (within 1240-1844 bp region) of VP2 gene of BTV-1 Indian isolates. The in silico restriction analysis revealed that in BTV-1 South African isolate (BTV-1SA) there is no TaqI site while in BTV-1 Australian isolates (BTV-1AUS), there are two TaqI sites (at 1513 and 1567 bp) within 1240-1844 bp region of VP2 gene. The earlier reported VP2 gene based primer pair for BTV-1 was used in the present study to amplify 2242-2933 bp region of six BTV-1 Indian isolates as three conserved regions have been reported within these 691 nucleotides. The digestion of 691 bp PCR products with XmnI yielded three fragments of 364, 173 and 154 bp with all the six Indian isolates of BTV-1 suggesting that there are two XmnI sites within 2242-2933 bp region of VP2 gene. A single XmnI site was observed in silico in BTV-1AUS and BTV-1SA isolates at different positions within this region. The in vitro and in silico restriction profile analyses of partial VP2 gene sequences using TaqI and XmnI restriction enzymes indicated a close relationship of Indian isolates of BTV-1 with BTV-1AUS isolates but not with BTV-1SA isolate.     

A rapid PCR method to discriminate between Tomato yellow leaf curl virus isolates

Tomato yellow leaf curl virus (TYLCV) was recently divided into two different species: Tomato yellow leaf curl virus‐Israel (TYLCV‐Is) and Tomato yellow leaf curl virus‐Sardinia (TYLCV‐Sar). There are no rapid methods by which TYLCV viruses may be assigned to either TYLCV‐Is or TYLCV‐Sar species. In the present work, using an extensive alignment of begomovirus sequences, TYLCV‐specific primers were designed and tested which allow the specific amplification of DNA fragments from any isolate of TYLCV. Also, a primer was designed and tested which allows the specific amplification of TYLCV‐Sar. Furthermore, a combination of these primers was selected to develop a duplex PCR method, which has the potential to detect either TYLCV‐Is or TYLCV‐Sar. The PCR methods were also highly effective with minimal sample preparation and allowed direct amplification of TYLCV from infected leaf extracts. This approach may be used in the laboratory as a tool for rapid, large‐scale diagnostics of TYLCV‐infected samples.     

Phylogenetic analysis of clinical herpes simplex virus type 1 isolates identified three genetic groups and recombinant viruses

Herpes simplex virus type 1 (HSV-1) is a ubiquitous human pathogen which establishes lifelong infections. In the present study, we determined the sequence diversity of the complete genes coding for glycoproteins G (gG), I (gI), and E (gE), comprising 2.3% of the HSV-1 genome and located within the unique short (US) region, for 28 clinical HSV-1 isolates inducing oral lesions, genital lesions, or encephalitis. Laboratory strains F and KOS321 were sequenced in parallel. Phylogenetic analysis, including analysis of laboratory strain 17 (GenBank), revealed that the sequences were separated into three genetic groups. The identification of different genogroups facilitated the detection of recombinant viruses by using specific nucleotide substitutions as recombination markers. Seven of the isolates and strain 17 displayed sequences consistent with intergenic recombination, and at least four isolates were intragenic recombinants. The observed frequency of recombination based on an analysis of a short stretch of the US region suggests that most full-length HSV-1 genomes consist of a mosaic of segments from different genetic groups. Polymorphic tandem repeat regions, consisting of two to eight blocks of 21 nucleotides in the gI gene and seven to eight repeats of 3 nucleotides in the gG gene, were also detected. Laboratory strain KOS321 displayed a frameshift mutation in the gI gene with a subsequent alteration of the deduced intracellular portion of the protein. The presence of polymorphic tandem repeat regions and the different genogroup identities can be used for molecular epidemiology studies and for further detection of recombination in the HSV-1 genome.     

The purification and some properties of cocoa necrosis virus, a serotype of tomato black ring virus

Cocoa necrosis virus (CNV) was transmitted by sap inoculation to twelve of twenty-one species tested. It was propagated and assayed in Phaseolus vulgaris. Sap from P. vulgaris was infective after dilution to 10^-3but not 10^-4, after 10 min at 60 d?C but not 65 d?C, and after 4 but not 7 days at 20–24 d?C. Lyophilized sap from P. vulgaris was infective after 2 years in vacuo. Virus was prepared by extracting infected leaves of P. vulgaris with 0.1 M phosphate (pH 7.5) containing 0.05 M ethylene diamine tetra-acetate and 0.02 M thioglycollate. After clarification with n-butanol, virus was purified by precipitation with polyethylene glycol and several cycles of differential centrifugation. Such preparations were very infective and contained numerous particles, 24–26 nm in diameter with a hexagonal profile, which sedimented as two components with sedimentation coefficients (Sd?_20,w) of 101 S and 129 S. The absorption spectra of both components with maximum and minimum absorption at 259 and 240 nm respectively were typical of nucleoproteins (101 S component, A 260/280 = 1.63; A 260/240 = 1.40:129 S component, A260/280 = 1.78; A260/240 = 1.58) and indicated nucleic acid contents of ca. 35% for the 129 S component and ca. 20% for the 101 S component; values calculated from the sedimentation coefficients were 41 and 30% respectively. Only the 129 S component seemed to be infective and was not more so when mixed with 101 S component. Both components contained a single protein subunit weighing ca. 60000 daltons. Under certain conditions sap fractionated without butanol gave virus preparations containing empty protein shells (54 S) and small spherical particles (20–30 S) ca. 12 nm diameter. CNV is a serotype of tomato blackring virus and is distantly related to Hungarian chrome mosaic virus. The cryptogram of CNV is */*:*/(35–41):S/S:S/*.     

Entamoeba histolytica: the serine-rich gene polymorphism-based genetic variability of clinical isolates from Georgia

It is generally accepted that a majority of individuals infected by Entamoeba histolytica do not develop symptomatic disease. However, the parasite and the host factors contributing to the development of the disease, remain undetermined. It is also unclear why certain individuals develop extra-intestinal amebiasis without exhibiting apparent intestinal symptoms. An outbreak of amebic liver abscess in Tbilisi, Georgia in 1998-1999 suggested that the causative E. histolytica strain had an unusual propensity for extra-intestinal spread. To correlate the genetic differences with pathogenic potential of the parasite, we have examined the SREHP gene polymorphisms among Georgian E. histolytica isolates. Comparison of polymorphic patterns revealed the presence of several different genotypes of E. histolytica, thus preventing an association of a single genotype with hepatic disease, but supporting the previous finding of extensive genetic diversity among E. histolytica isolates from the same geographic origin.     

Microsatellite analysis of genetic variation in black bear populations

Measuring levels of genetic variation is an important aspect of conservation genetics The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations Low levels of variation were observed in a population from the Island of Newfoundland The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of θ= 4 N_eu.     

Fine‐scale spatial genetic structure analysis of the black truffle Tuber aestivum and its link to aroma variability

Truffles are symbiotic fungi in high demand by food connoisseurs. Improving yield and product quality requires a better understanding of truffle genetics and aroma biosynthesis. One aim here was to investigate the diversity and fine‐scale spatial genetic structure of the Burgundy truffle Tuber aestivum. The second aim was to assess how genetic structuring along with fruiting body maturation and geographical origin influenced single constituents of truffle aroma. A total of 39 Burgundy truffles collected in two orchards were characterized in terms of aroma profile (SPME‐GC/MS) and genotype (microsatellites). A moderate genetic differentiation was observed between the populations of the two orchards. An important seasonal and spatial genetic structuring was detected. Within one orchard, individuals belonging to the same genet were generally collected during a single season and in the close vicinity from each other. Maximum genet size nevertheless ranged from 46 to 92 m. Geographical origin or maturity only had minor effects on aroma profiles but genetic structuring, specifically clonal identity, had a pronounced influence on the concentrations of C₈‐ and C₄‐VOCs. Our results highlight a high seasonal genetic turnover and indicate that the aroma of Burgundy truffle is influenced by the identity of single clones/genets.     

Genome Characteristics,Phylogeny and Varying Host Specificity of Polish Kra and Ros Isolates of Tomato torrado virus

The genome sequences of two Polish Kra and Ros isolates of Tomato torrado virus (ToTV) were determined and compared with data of previously described ToTV isolates and other Torradovirus members. Whole‐genome sequence comparisons revealed 97.0–99.6% nucleotide sequence identities and close relatedness, with other known ToTV isolates. The high homology between Kra, Ros and Wal'03 ToTVs is likely responsible for the similar symptoms observed on infected plants. However, the symptoms differed in intensity and various host specificity. We report that Kra ToTV caused a milder expression of symptoms on Solanum tuberosum than Wal'03. We hypothesize this may be a result of the significant variability observed within the 3′‐UTR of RNA1 of Kra as well as of Ros ToTV isolates. In the light of this fact, potato may be considered an indicator plant for distinguishing Kra and Wal'03 ToTV isolates.