Investigation of diversity and isotypes of the beta-tubulin cDNA in several small strongyle (Cyathostominae) species

The diversity of the beta-tubulin cDNAs of the cyathostominae and the occurrence of further isotypes were examined in adult worms isolated from an anthelmintic-na?ve horse. cDNAs encoding beta-tubulin from Cyathostomum catinatum, Cylicocyclus nassatus, Cylicocyclus insigne, Cylicocyclus radiatus, Cylicocyclus elongatus, Cyathostomum coronatum, and Cyathostomum pateratum were characterized using specific primers developed from the cDNA sequence of Cc. nassatus. The cDNA sequences span 1,429 bp and show identities ranging from 95.6 to 100%. The deduced protein sequences span 448 amino acids and were 98-100% identical. The amino acid sequences of the 7 species varied within and between species at 10 positions. A 3' Rapid Amplification of cDNA ends using a degenerate forward primer was carried out with cDNA from Cy. pateratum, Cy. coronatum, Cy. catinatum, and Cc. nassatus to investigate the occurrence of further beta-tubulin isotypes. The expected polymerase chain reaction (PCR) product of 400 bp, including 306 bp of coding sequence, was amplified, as was an additional fragment of 600 nucleotides in the case of Cy. pateratum, Cy. coronatum, and Cy. catinatum. Sequencing of the PCR products revealed no evidence for the existence of a second beta-tubulin isotype in cyathostomes. The variation in size was caused by a length polymorphism within the 3' untranslated region, and 2 functional mRNAs seem to be transcribed from the same gene.     

Beta-tubulin complementary DNA sequence variations observed between cyathostomins from benzimidazole-susceptible and -resistant populations

The molecular mechanism of benzimidazole (BZ) resistance in cyathostomins of horses is still unclear. Previous studies revealed that the TTC or TAC polymorphism in codon 200 of the beta-tubulin isotype 1 gene is not as strictly correlated with BZ resistance as in trichostrongyles in sheep. To identify further sites of polymorphism within the beta-tubulin gene related to BZ resistance, complete complementary DNAs (cDNAs) encoding beta-tubulin of adult worms of Cylicocyclus nassatus, Cyathostomum pateratum, Cyathostomum coronatum, Cyathostomum catinatum, Cylicostephanus longibursatus, and Cylicostephanus goldi of a BZ-resistant cyathostomin population were characterized using specific primers. The cDNA sequence of each species spans 1,429 bp, encoding a protein of 448 amino acids. The interspecific identities are 95.2-99.6% at the nucleotide and 98.7-100.0% at the peptide level. The comparison of the amino acid sequences of individuals isolated from the BZ-resistant cyathostomin population with those from individuals of Cc. nassatus, Cy. coronatum, Cy. pateratum, and Cy. catinatum of a BZ-susceptible one showed differing amino acids in 11 positions. The commonness of a phenylalanine to tyrosine mutation at position 167 in all the 6 cyathostomin species isolated from a BZ-resistant population suggests its involvement in the molecular mechanism in BZ resistance.     

Prevalence and abundance of equine strongyles (Nematoda: Strongyloidea) in tropical Australia

A postmortem survey of 57 horses in tropical northern Queensland revealed 41 (89%) infected with intestinal strongyles. Thirty-five strongyle species (8 large strongyles and 27 small strongyles [Cyathostominae]) were recorded of which 9 species are reported from Australia for the first time. The 14 most prevalent small strongyles were Cyathostomum catinatum (in 76% of horses), Cyathostomum coronatum (65%), Cyathostomum pateratum (33%), Cyathostomum labiatum (30%), Cylicostephanus calicatus (70%), Cylicostephanus longibursatus (67%), Cylicostephanus goldi (43%), Cylicostephanus minutus (26%), Cylicocylus nassatus (67%), Cylicocyclus leptostomus (41%), Cylicocylus insigne (41%), Cylicocyclus radiatus (33%), Cylicocyclus brevicapsulates (22%), and Poteriostomum imperidentum (24%). The remaining cyathostomes were each found in less than 15% of horses. The 4 most common large strongyles were Triodontophorus serratus (30%), Strongylus vulgaris (28%), Strongylus equinus, and Strongylus edentatus (both 22%). The number of species of small strongyles per horse showed a marked variation (mean 10.3, range 2-21) but bore no relationship to either the total number of strongyles per horse, age, sex, and breed of horse, or season. Total number of strongyles per horse (mean 15,890, range 20-165,000) was less than in recent surveys in Europe and the U.S.A. Most horses had low worm burdens, whereas a very small number were heavily infected. Ninety-seven per cent of the total strongyle counts were small strongyles. Strongylus species contributed just over 1%. Small numbers of large strongyles per horse were usual with T. serratus (mean 570), S. vulgaris (mean 330), and S. equinus (mean 330) the most numerous.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evidence of p-glycoprotein sequence diversity in cyathostomins

P-glycoproteins (Pgps) are adenosine triphosphate-binding transporter proteins thought to be associated with multi-drug resistance in mammals and protozoans and have been suggested to be involved in the mechanism of ivermectin (IVM) resistance in Haemonchus contortus. Until now, resistance to IVM has not been reported in cyathostomins in horses in spite of its widespread and frequent use. Reasons for this might be differences in the molecular mechanism of the development of resistance. Based on this hypothesis, the present study was carried out to find homologues of Pgp in cyathostomins. A 416-bp polymerase chain reaction (PCR) product was generated using complementary DNA (cDNA) of Cylicocyclus elongatus and Cylicocyclus insigne and degenerate primers, located in the conserved Pgp nucleotide-binding domains. Resulting PCR products showed interspecific nucleotide and amino acid sequence identities of 73.3 and 76.8%, respectively. Specific primers were designed based on the Cc. elongatus sequence, and a PCR product of 268-bp was amplified from cDNA of single adults of Cylicocyclus radiatus, Cc. insigne, Cylicocyclus nassatus, Cc. elongatus, Cylicostephanus hybridus (2 individuals), Cylicostephanus goldi, Cyathostomum pateratum, Cyathostomum coronatum, and Cyathostomum catinatum. Two clusters of sequences were found representing 2 different internucleotide-binding domains (IBDs). A further distinct IBD is represented by the 416-bp PCR product of Cc. insigne. Therefore, a total of 3 clearly different sequences of the IBD were cloned and sequenced, suggesting that at least 2 Pgp genes exist in cyathostomins.     

Molecular characterization of benzimidazole-resistant isolates of Cladosporium fulvum

The benzimidazole fungicide thiophanate-methyl is commonly applied to control leaf mould of tomato caused by Cladosporium fulvum in China. In this study, 32 isolates of C. fulvum were examined for their sensitivities to thiophanate-methyl, and two benzimidazole-resistant (BenR) phenotypes BenR1 and BenR2 were identified. The BenR1 isolates were resistant to thiophanate-methyl, but were more sensitive to the phenylcarbamate fungicide diethofencarb than the wild-type isolates. The BenR2 isolates resistant to thiophanate-methyl were insensitive to diethofencarb. All tested isolates were sensitive to the dicarboximide fungicide iprodione. The complete beta-tubulin gene was isolated from this fungus to study its potential role in benzimidazole resistance. Analysis of the DNA sequence of the beta-tubulin gene showed that the BenR1 isolates had a point mutation at codon 198, causing a substitution of glutamic acid to alanine. In the BenR2 isolates, a point mutation at codon 200 causing a substitution of phenylalanine to tyrosine was detected. Based on these point mutations, a multiplex allele-specific PCR method was developed successfully for the first time to detect two point mutations at the beta-tubulin gene simultaneously in single PCR amplifications.     

一种单核苷酸多态性的单倍型分析技术

运用多步PCR和测序技术,完成基因组中相距较远的单核苷酸多态位点的单倍型构建。通过设计2条等位基因特异性引物,扩增大片段DNA(10kb左右),以此大片段DNA作为下一轮PCR反应的模板,再在该片段中设计待检测区域的PCR引物,进行第2轮PCR。对PCR产物进行测序分析,确定其多态位点处的等位基因。结合第1轮PCR中的等位基因特异性引物,即可确定该大片段DNA中不同单核苷酸多态性构成的单倍型。以脂蛋白脂酶基因为例,应用其启动子区以及第4外显子区的等位基因特异性引物扩增约16kb的DNA片段,然后检测位于该片段中第2、3外显子的多态性。在￡-尸￡-基因第2内含子中发现了 13557G→A多态性。经分析确定出-421G／ 13557G／ 15222A、-421A／ 13557G／ 15222A、-421G／ 13557G／ 15222G、-421G／ 13557A／ 15222A等4种单倍型。等位基因特异性PCR结合小片段测序是一种快捷高效的对相距较远的多个SNP进行单倍型构建的新策略。     

A PCR-ELISA for the identification of cyathostomin fourth-stage larvae from clinical cases of larval cyathostominosis

We report the use of six oligoprobes designed from intergenic spacer region sequences to identify fourth-stage larvae (L4) of the tribe Cyathostominae. Oligoprobes were designed for identification of the following species: Cylicocyclus ashworthi, Cylicocyclus nassatus, Cylicocyclus insigne, Cyathostomum catinatum, Cylicostephanus goldi, and Cylicostephanus longibursatus. A seventh probe was designed as a positive control to identify all these members of the Cyathostominae. The intergenic spacer region was amplified by PCR using conserved primers. Initially, three oligoprobes were used in Southern blot analysis. To facilitate high-throughput identification, these and a further four oligoprobes were developed for use in a PCR-ELISA. All probes were validated for their ability to detect cyathostomin PCR products in the PCR-ELISA, using DNA from morphologically identified adult parasites. Initially, 712 L4 were isolated from the diarrhoeic faeces from horses (n=17) with clinical larval cyathostominosis. PCR products from 522 of these L4 were subjected to analysis, with 413 L4 being identified as one of the aforementioned species. With reference to individual species analysis, 28.5% of the 522 L4 were identified as C. longibursatus, 25.7% as C. nassatus, 15.9% as C. ashworthi, 7.3% as C. goldi and 1.7% as C. catinatum. No L4 were identified as being C. insigne species. When L4 within faeces from individual horses were compared, no sample was found to comprise parasites of one species. The least number of species identified in a single sample was two. This study suggests that clinical larval cyathostominosis is predominantly caused by mixed-species infections.     

The beta-tubulin genes of two Strongyloides species

The World Health Organization is sponsoring major treatment programs with the aim of controlling helminth infection throughout the tropical world. Prominent among the anthelmintics recommended for use in these programs are drugs in the benzimidazole (BZ) class. Resistance to these drugs has been associated with polymorphisms in the beta-tubulin gene. We have cloned and sequenced the beta-tubulin genes of Strongyloides stercoralis and Strongyloides ratti and have proceeded to develop a protocol for genotyping single worms for polymorphisms in beta-tubulin. Our findings indicate that S. ratti has a single beta-tubulin gene, making DNA sequence analysis of a single larva PCR product a feasible means of studying BZ resistance in these species. Our genotyping test allows the identification of polymorphisms at codons 167, 198, and 200 in the Strongyloides beta-tubulin gene, thus enabling survey for BZ resistant genotypes.     

Prevalence and biodiversity of helminth parasites in donkeys from South Africa

Seven donkeys (Equus asinus) from North-West and Mpumalanga Provinces in South Africa were examined at necropsy. Quantitative samples were collected from the gastrointestinal tract for recovery of helminth parasites from the stomach, small intestine, cecum, ventral colon, dorsal colon, descending colon, and cranial mesenteric artery. Fifteen genera and 29 species of helminths were identified comprising 27 species of nematodes in the Ascarididae, Atractidae, Habronematidae, Onchocercidae, Oxyuridae, and Strongylidae; 1 species of cestode in the Anoplocephalidae; and 1 species of trematode in the Paramphistomatidae. In addition, 2 species of oestrid fly larvae in the Gastrophiliidae were identified. The most abundant group in number of species was the cyathostomes (small strongyles) and, of these, Cyathostomum montgomeryi, Cylicocyclus sp. (a), and Cylicostephanus minutus were the most numerous. The most prevalent cyathostomes were C. montgomeryi and Cylicocyclus sp. n. (a). Strongylus vulgaris was the most abundant and prevalent large strongyle species. The occurrence of small strongyle species and their prevalences in this study are compared with 3 other studies on donkeys in Africa.     

Parasitic helminths of the cecum and colon of equidae in Italy]

Intestinal helminths from coecum and colon were studied in 93 equidae including 40 horses, 36 donkeys and 17 mules. A total of 38 species, 36 nematodes and 2 cestodes, were identified as follows: 1) Triodontophorus serratus, 2) Triodontophorus brevicauda, 3) Strongylus equinus, 4) Strongylus edentatus, 5) Strongylus vulgaris, 6) Cyathostomum tetracanthum, 7) Cyathostomum coronatum, 8) Cyathostomum labiatum, 9) Cyathostomum labratum, 10) Cyathostomum alveatum, 11) Cyathostomum pateratum, 12) Cyathostomum catinatum, 13) Cyathostomum sagittatum, 14) Cylicodontophorus bicoronatus, 15) Cylicocyclus radiatus, 16) Cylicocyclus auriculatus, 17) Cylicocyclus elongatus, 18) Cylicocyclus nassatus, 19) Cylicocyclus insigne, 20) Cylicocyclus leptostomus, 21) Cylicostephanus calicatus, 22) Cylicostephanus poculatus, 23) Cylicostephanus minutus, 24) Cylicostephanus longibursatus, 25) Cylicostephanus hybridus, 26) Cylicostephanus goldi, 27) Cylicostephanus ornatus, 28) Cylicostephanus skrjabini, 29) Poteriostomum ratzii, 30) Gyalocephalus capitatus, 31) Parascaris equorum*, 32) Probstmayria vivipara, 33) Draschia megastoma*, 34) Habronema muscae*, 35) Habronema majus*, 36) Setaria equina*, 37) Anoplocephala perfoliata, 38) Paranoplocephala mamillana. The asterisked species are those not usually localized in the examined material. The most frequent parasites were found in all three hosts. Species 1, 4, 6, 9, 10, 12, 21, 22, 30 and 35 showed significant differences in prevalence between horses and donkeys, the mule generally having intermediate values. Multiple infections and total worm burden appear to decrease in older animals (> 15 years). Parasite associations occur mostly at random as expected from the values of the respective total prevalences. Some significant excesses on expected values were recorded but not significant deficits. The total worm burden increases with the number of parasite species and the increase appears to follow an exponential pattern.     

Nematode parasites from Burchell's zebras in South Africa

Twenty-five Burchell's zebras (Equus burchelli antiquorum) which were culled at monthly intervals in the Kruger National Park were examined for helminths. Twenty-nine species of nematodes belonging to the families Atractidae, Habronematidae, Onchocercidae, Oxyuridae, Strongylidae, Strongyloididae and Trichostrongylidae were recovered. The cyathostomes (small strongyles) most abundant were Cyathostomum tetracanthum, Cylicostephanus calicatus, Cylindropharynx sp. (? C. intermedia Theiler, 1923) and Cylicocyclus auriculatus. Cyathostomum alveatum, Cyathostomum montgomeryi, Cylicostephanus calicatus and Cylindropharynx sp. (? C. intermedia Theiler, 1923) were the most prevalent cyathostomes (small strongyles) while Craterostomum acuticaudatum was the most prevalent of the large strongyles. Of all the species recovered those most abundant were Crossocephalus viviparus and Probstmayria vivipara with intensities of 100 to 3,857,772 and 18,400 to 104,120,467, respectively. Four new species, two Triodontophorus spp. (Strongylidae) and two Habronema spp. (Habronematidae) were identified. Furthermore, this study furnishes a first report of Triodontophorus minor in zebras. The fourth stage cyathostomes as well as the adults of 11 of the 14 species were present in significantly greater intensities in autumn and winter.     

Three nuclear genes for phylogenetic, SNP and population genetic studies of molluscs and other invertebrates

The study reports new primers capable of amplifying fragments from three nuclear protein-coding genes in a variety of deep-sea molluscs and annelids - adenine nucleotide translocase (Ant), calmodulin (Cal) and cyclophilin A (CycA). The Ant primers appear to be restricted to bivalve molluscs, whereas the Cal and CycA primers also amplified appropriate gene fragments from Lepetodrilus gastropod molluscs and Osedax polychaete worms. The amplified fragment of Cal contains an intron in the molluscs, but no intron was detected in the Ant and CycA fragments from any of the tested animals. DNA sequences generated by the three primer sets exhibited one to 15 single nucleotide polymorphism sites in deep-sea vesicomyid clams and Osedax boneworms. The observed levels of polymorphism indicate that the genes are likely to be useful in both population genetic and phylogenetic analyses of different invertebrate taxa.     

应用特异等位PCR快速鉴定灰霉病菌抗苯莱特与乙霉威菌株*

根据灰霉病菌Botrytis cinerea对苯并咪唑类（苯莱特）及N－苯氨基甲酸酯类（乙霉威）杀菌剂的抗性与其β－微管蛋白的198和200位密码子的单碱基突变紧密相关的原理,建立了一种同时检测灰霉病菌对这两类杀菌剂抗性表型的特异等位聚合酶链式反应（ASP,Allele-specific Polymerase Chain Reaction）方法,即将突变的单碱基作为正引物的3'末端,与之对应的未突变的单碱基作为负引物的3'末端, 自行设计了LP4～LP8等五个等位点特异性引物,应用包括这五个引物在内的七组引物,对生测为BenSNPCR、BenHRNPCS和BenHRNPCR菌株进行了ASP扩增,结果表明：该方法可以检测出相应抗药表型的菌株,并能有效地检测田间灰霉病菌的抗药性,从而该方法克服了生物检测方法费时和准确性差等缺点。该方法还能鉴定出生测法确定为同一表型如BenHRNPCR 中的BenSNPCR异核菌丝,或灰霉病菌侵染寄主后所产生的回复突变,因此其方法的灵敏度极高,可应用于灰霉病菌抗药性分子生态学机理研究和田间抗性菌株的快速鉴定。由于未发现BenMRNPCR型菌株,其适用性有待进一步验证。     

芒果炭疽病菌β-微管蛋白基因的克隆及其与多菌灵抗药性发生的关系

参照豆科合萌属 (Aeschynomene)作物炭疽病菌的tub1和tub2基因序列设计了 2对引物 ,分别从芒果 (Man gifera)炭疽病菌对多菌灵 (MBC)田间抗药性 (MBCR)和敏感 (MBCS)的菌株中扩增 β_微管蛋白基因。结果只有以tub2为参照设计的引物扩增到了特异片段。进一步对全基因进行了克隆和测序。该基因序列全长 1344bp ,编码4 4 7aa ,其核苷酸和氨基酸序列与豆科合萌属炭疽病菌的tub2基因高度同源。对芒果炭疽病菌抗、感菌株 β_微管蛋白氨基酸序列进行比较分析 ,发现第 181、2 37和 36 3位氨基酸发生了突变 ,而其它位置 (如第 198位或 2 0 0位 )均不变     

Identification and characterization of benzimidazole resistance in Monilinia fructicola from stone fruit orchards in California

Low and high levels of resistance to the benzimidazole fungicides benomyl and thiophanate-methyl were observed in field isolates of Monilinia fructicola, which is the causative agent of brown rot of stone fruit. Isolates that had low levels of resistance (hereafter referred to as LR isolates) and high levels of resistance (hereafter referred to as HR isolates) were also cold and heat sensitive, respectively. Results from microsatellite DNA fingerprints showed that genetic identities among the populations of sensitive (S), LR, and HR isolates were very high (>0.96). Analysis of DNA sequences of the beta-tubulin gene showed that the LR isolates had a point mutation at codon 6, causing a replacement of the amino acid histidine by tyrosine. Codon 198, which encodes a glutamic acid in S and LR isolates, was converted to a codon for alanine in HR isolates. Based on these point mutations in the beta-tubulin gene, allele-specific PCR assays were developed for rapid detection of benzimidazole-resistant isolates of M. fructicola from stone fruit.     

Rapid and direct detection of the most frequent Mediterranean beta-thalassemic mutations by multiplex allele-specific enzymatic amplification.

A rapid nonradioactive method for the diagnosis of the most frequent Mediterranean beta-thalassemic mutations is described based on a multiplex allele-specific polymerase chain reaction (PCR). This method allows direct detection of normal or mutated alleles on genomic DNA. We have used this approach to detect the most frequent Mediterranean mutations: IVS-1 nt 110 (G----A) and 39 nonsense (C----T). For each mutation three allele-specific oligonucleotides were used: one common upstream primer and two downstream primers differing in their terminal 3' nucleotide (one specific for the normal allele and one for the mutant allele). For each sample two PCR reactions were performed in parallel using in one case IVS-1 nt 110 and codon 39 normal primers and in the second case using the corresponding mutated primers. In both cases the different PCR fragments were visualized. After optimization these primers directed only amplification of their complementary allele. A single blind study was performed on the DNA of 18 individuals who were homozygous or heterozygous for these mutations. In comparison with a parallel investigation, using oligonucleotide probes, all the results were unambiguous. This diagnosis method, which is rapid, easy, direct, and inexpensive, allows the screening of a population group, including heterozygotes, which is required from an epidemiological and anthropological point of view. It could be extended to the large series screening of haplotypes before targeted diagnosis of various genetic diseases.     

Molecular sexing and sources of CHD1‐Z/W sequence variation in Hawaiian birds

Sequence information from 28 CHD1 gene fragments reveals that a primary source of variability in CHD1‐W genes is a variable intron microsatellite; a single‐codon deletion was found in the 3′ exon in one species. Sequence variation of CHD1‐Z genes was detected in males that altered polymerase chain reaction (PCR) fragment length. Three sets of CHD1‐based primers were evaluated for sex determination in 12 endemic and 8 alien Hawaiian species, including one of the last po’o‐uli. Combined, these primers provide a reliable means of sex determination in most species (including the po’o‐uli), and have produced a valuable reference database for future expanded population‐level studies.     

A molecular tool for species identification and benzimidazole resistance diagnosis in larval communities of small ruminant parasites

This report describes a molecular method for determining in a first step the generic composition of a nematode community and in a second step, the resistance of each species to benzimidazole (BZ). We first established a polymerase chain reaction (PCR) linked to a restriction fragment length polymorphism strategy using the isotype 1 beta-tubulin gene. This method overcame the limitations of morphological identification of larval stages of trichostrongylid nematode species. Geographically distant isolates from the three main gastrointestinal species in temperate zones, Teladorsagia circumcincta, Haemonchus contortus, and Trichostrongylus colubriformis, were distinguished using this method. We then used an allele-specific PCR (AS-PCR) to detect mutations of residue 200 of the beta-tubulin, which is implicated in BZ resistance. The sequences of several samples confirmed the BZ-resistance genotype determined by AS-PCR. The ability to process large numbers of samples simultaneously makes this PCR-based strategy particularly suitable for epidemiological studies. It may also be useful for monitoring the emergence of resistant alleles in nematode communities.     

Random Amplified Polymorphic DNA Analysis of Heterodera cruciferae and H. schachtii populations

Heterodera schachtii and H. cruciferae are sympatric in California and frequently occur in the same field upon the same host. We have investigated the use of polymerase chain reaction (PCR) amplification of nematode DNA sequences to differentiate H. schachtii and H. cruciferae and to assess genetic variability within each species. Single, random oligodeoxyribonucleotide primers were used to generate PCR-amplified fragments, termed RAPD (random amplified polymorphic DNA) markers, from genomic DNA of each species. Each of 19 different random primers yielded from 2 to 12 fragments whose size ranged from 200 to 1,500 bp. Reproducible differences in fragment patterns allowed differentiation of the two species with each primer. Similarities and differences among six different geographic populations of H. schachtii were detected. The potential application of RAPD analysis to relationships among nematode populations was assessed through cluster analysis of these six different populations, with 78 scorable markers from 10 different random primers. DNA from single cysts was successfully amplified, and genetic variability was revealed within geographic populations. The use of RAPD markers to assess genetic variability is a simple, reproducible technique that does not require radioisotopes. This powerful new technique can be used as a diagnostic tool and should have broad application in nematology.