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Increased genome size is caused by heterochromatin addition in two non-related bat species, Hesperoptenus doriae and Philetor brachypterus (Vespertilionidae, Chiroptera, Mammalia). Chromosoma 2023; 132:269-288. [PMID: 37322170 DOI: 10.1007/s00412-023-00802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
The average genome size (GS) of bats, which are the only mammals capable of powered flight, is approximately 18% smaller than that of closely related mammalian orders. The low nuclear DNA content of Chiroptera is comparable to that of birds, which are also characterized by a high metabolic rate. Only a few chiropteran taxa possess notable amounts of constitutive heterochromatin. Here, we studied the karyotypes of two non-related vesper bat species with unusually high amounts of constitutive heterochromatin: Hesperoptenus doriae and Philetor brachypterus. Conventional staining methods and whole-chromosome painting with probes derived from Myotis myotis (2n = 44), showing a karyotype close to that of the presumed ancestor of Vespertilionidae, revealed Robertsonian fusions as the main type of rearrangement leading to the exceptionally reduced diploid chromosome number of 2n = 26 in both species. Moreover, both karyotypes are characterized by large blocks of pericentromeric heterochromatin composed of CMA-positive and DA-DAPI-positive segments. In H. doriae, the heterochromatin accumulation has resulted in a genome size of 3.22 pg (1C), which is 40% greater than the mean genome size for the family. For P. brachypterus, a genome size of 2.94 pg was determined, representing an increase of about 28%. Most notably, in H. doriae, the presence of additional constitutive heterochromatin correlates with an extended mitotic cell cycle duration in vitro. A reduction in diploid chromosome number to 30 or lower is discussed as a possible cause of the accumulation of pericentromeric heterochromatin in Vespertilionidae.
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Rapid Single-Step Immunochromatographic Assay for Angiostrongylus cantonensis Specific Antigen Detection. Pathogens 2023; 12:762. [PMID: 37375452 DOI: 10.3390/pathogens12060762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Angiostrongylus cantonensis is the major etiological nematode parasite causing eosinophilic meningitis and/or eosinophilic meningoencephalitis in humans. The rapid global spread of Angiostrongylus cantonensis and the emerging occurrence of the infection have exposed the shortcomings of traditional/conventional diagnostics. This has spurred efforts to develop faster, simpler and more scalable platforms that can be decentralized for point-of-need laboratory testing. By far, the point-of-care immunoassays such as the lateral flow assay (LFA) are the best-placed. In this work, a LFA in the form of an immunochromatographic test device (designated AcAgQuickDx), based on the detection of a circulating Angiostrongylus cantonensis-derived antigen, was established using anti-31 kDa Angiostrongylus cantonensis antibody as the capture reagent and anti-Angiostrongylus cantonensis polyclonal antibody as the indicator reagent. The AcAgQuickDx was evaluated for its diagnostic potential with a total of 20 cerebrospinal fluids (CSF) and 105 serum samples from patients with angiostrongyliasis and other clinically related parasitic diseases, as well as serum samples from normal healthy subjects. Three of the ten CSF samples from serologically confirmed angiostrongyliasis cases and two of the five suspected cases with negative anti-Angiostrongylus cantonensis antibodies showed a positive AcAgQuickDx reaction. Likewise, the AcAgQuickDx was able to detect Angiostrongylus cantonensis specific antigens in four serum samples of the 27 serologically confirmed angiostrongyliasis cases. No positive reaction by AcAgQuickDx was observed in any of the CSF (n = 5) and serum (n = 43) samples with other parasitic infections, or the normal healthy controls (n = 35). The AcAgQuickDx enabled the rapid detection of active/acute Angiostrongylus cantonensis infection. It is easy to use, can be transported at room temperature and does not require refrigeration for long-term stability over a wide range of climate. It can supplement existing diagnostic tests for neuroangiostrongyliasis under clinical or field environments, particularly in remote and resource-poor areas.
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Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae. REVISTA BRASILEIRA DE BOTANICA : BRAZILIAN JOURNAL OF BOTANY 2022; 45:1209-1222. [PMID: 36320930 PMCID: PMC9607705 DOI: 10.1007/s40415-022-00845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/15/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40415-022-00845-w.
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Core members and differential abundance of chrysomelid microbiota in the life stages of Podontiaaffinis (Galerucinae) and adult Silanafarinosa(Cassidinae, Coleoptera). Biodivers Data J 2022; 10:e87459. [PMID: 36761655 PMCID: PMC9836631 DOI: 10.3897/bdj.10.e87459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/12/2022] Open
Abstract
The chrysomelid beetlesPodontiaaffinis and Silanafarinosa are members of the subfamilies Galerucinae and Cassidinae, respectively. This study, based on 16S rRNA gene-targeted metagenomics sequencing, reports the core members and differential abundance of bacterial communities in the larvae and adult beetles of P.affinis and the adult S.farinosa. Cyanobacteria/Melainabacteria group was the predominant phylum in the larvae of P.affinis, while Proteobacteria was the predominant phylum in adult P.affinis and S.farinosa. The number of Order, Family, Genus and Species OTUs in the adult stage of P.affinis was higher than that in the larval stage. The bacterial species richness of adult P.affinis was significantly higher than that of adult S.farinosa. Betaproteobacteria was the predominant class in adult P.affinis, Cyanobacteria in the larvae of P.affinis and Gammaproteobacteria in S.farinosa. The larvae and adult beetles of P.affinis and adult S.farinosahad a low number of unique and shared bacterial OTUs (> 5% relative abundance). The differences in the microbiota indicate possible differences in nutrient assimilation, host taxonomy and other stochastic processes. These findings provide new information to our understanding of the bacteria associated with specialist phytophagous chrysomelid beetles and beetles in general.
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Genetic diversity and identity of Ascaris worms from human and pig hosts in Thailand. Vet Parasitol Reg Stud Reports 2022; 33:100752. [PMID: 35820723 DOI: 10.1016/j.vprsr.2022.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Ascaris roundworms are of public health and socio-economic importance worldwide. They are conventionally attributed to two taxa - A. lumbricoides infecting principally human and A. suum infecting principally pig. Phylogenomic analysis has revealed that Ascaris worms from both human and pig are represented in Clades A and B. A recent study indicates that the Ascaris worms from human and pig in Thailand belong to Clade A. We examined adult Ascaris worms from human and pig in Thailand by means of the partial sequences of three mitochondrial genes (cox1, cox2 and nad1) and concatenation of these genes. Phylogenomic analysis indicates that two isolates (H1,H2) of A. lumbricoides from human belonged to Clade B; one isolate (H3) belonged to Clade A (based on cox1, cox2 and concatenated sequences) or as an outlier to Clades A and B (based on nad1 sequences). All the eight isolates of A. suum from pig clustered in Clade A. The partial nad1 and the concatenated sequences revealed two lineages of A. suum isolates which were distinct from the two A. lumbricoides isolates of Clade B. It is evident that greater genetic diversity, and a more robust phylogeny, could be uncovered by the application of multiple genes. In sum, the present study reveals the presence in Thailand of A. lumbricoides from human in Clades A and B which necessitates appropriate treatment and control measures; Clades A and B have been reported to contain haplotypes of Ascaris worms from both human and pig in other parts of the world. A country wide study is needed to elucidate the identity, distribution, prevalence, cross transmission, genetic diversity and phylogeny of the Ascaris worms in Thailand.
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Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina. Antonie van Leeuwenhoek 2022; 115:995-1007. [DOI: 10.1007/s10482-022-01750-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
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Cytogenetic Analyses Detect Cryptic Diversity in Megaderma spasma from Malaysia. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2021.23.2.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Complete mitochondrial genome of Dacus vijaysegarani and phylogenetic relationships with congeners and other tephritid fruit flies (Insecta: Diptera). Mol Biol Rep 2021; 48:6047-6056. [PMID: 34357549 PMCID: PMC8342272 DOI: 10.1007/s11033-021-06608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022]
Abstract
Background Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank. Methods and results In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific. Conclusions Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06608-2.
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Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea). Sci Rep 2021; 11:10680. [PMID: 34021208 PMCID: PMC8139964 DOI: 10.1038/s41598-021-90162-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.
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Mitochondrial Genome of Rattus tiomanicus (Rodentia: Muridae) and Molecular Phylogeny of Murinae. SAINS MALAYS 2021. [DOI: 10.17576/jsm-2021-5004-07] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rattus tiomanicus is a murid rodent of considerable agricultural and public health importance in Southeast Asia. The whole mitochondrial genome of R. tiomanicus was sequenced by the Ion Torrent PGM platform. It had a total length of 16,309 bp, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and two non-coding regions (L-strand replication origin and control region). Only TAA and incomplete T-stop codons were represented in the protein-coding genes. Of the tRNAs, tryptophan (W) had ACU anticodon. The cloverleaf structure for serine S1 (AGN) tRNA lacked the entire D-arm, while in lysine (K) tRNA, the DHU arm lacked the D-loop. Molecular phylogeny based on 15 mt-genes indicated R. tiomanicus having closest genetic affinity to R. rattus complex (R. rattus, R. tanezumi). There were two major clades for the Murinae subfamily namely the Rattini tribe and the Apodemini, Murini and Hydromyini tribes. The whole mitogenome of R. tiomanicus will serve as a useful dataset for studying the systematics and phylogenetic relationships of the murid rodents.
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Sandwich dot-immunogold filtration assay (DIGFA) for specific immunodiagnosis of active neuroangiostrongyliasis. Parasitology 2021; 148:234-239. [PMID: 33004092 PMCID: PMC11010216 DOI: 10.1017/s0031182020001894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 11/06/2022]
Abstract
Serological tests may yield false-negative results for specific antibodies detection before or at the early seroconversion phase. Tests that detect circulating antigens of Angiostrongylus cantonensis would therefore be of value in diagnosis to distinguish current or past infection. Here, a quick, easy to perform, portable and inexpensive diagnostic device for detection of 31-kDa A. cantonensis specific antigens had been developed. This sandwich dot-immunogold filtration assay (AcDIGFAAg), for detecting active angiostrongyliasis was produced using anti-A. cantonensis polyclonal antibody dotted on the nitrocellulose membrane as a capture agent and colloidal gold-labelled anti-31 kDa A. cantonensis antibody as a detection agent. A well-defined pink dot, indicating positivity, was seen readily by naked eye within 10-15 min. The AcDIGFAAg detected A. cantonensis-specific antigens in cerebrospinal fluid samples from 4 out of 10 serologically confirmed angiostrongyliasis cases and 2 out of 5 suspected cases with negative anti-A. cantonensis antibodies. Among the 19 patient sera with A. cantonensis infection, 2 showed positive reaction by AcDIGFAAg. No positive AcDIGFAAg reaction was observed in all the serum samples with other parasitic diseases, and the healthy controls. The present 'AcDIGFAAg' enables rapid qualitative detection of the specific 31-kDa antigens of A. cantonensis in clinical samples with potential for application even under resource-limited settings.
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Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae). Plasmid 2021; 114:102559. [PMID: 33476637 DOI: 10.1016/j.plasmid.2021.102559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022]
Abstract
The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.
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Genetic variation of NADH dehydrogenase subunit 1 (nad1) mitochondrial gene sequence in adult Necator americanus hookworms recovered from a female patient in Thailand. Trop Biomed 2020; 37:536-541. [PMID: 33612820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Two female and one male adult hookworms were recovered from a female patient in Thailand. Based on gross and microscopic morphology, the three hookworms are members of Necator americanus. Phylogenetic reconstruction based on partial NADH dehydrogenase subunit 1 (nad1) mitochondrial gene sequences shows that these hookworms belong to the same genetic lineage as N. americanus adult worm from Zhejiang, China. The male and female hookworms were genetically distinct, belonging to two different nad1-haplotypes. This is the first report targeting the nad1 gene on the identification and genetic characterization of the human hookworms originated from infected patient. The nad1 gene marker is useful for species and higher taxa differentiation of hookworms.
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Cytogenetic Investigations in Emballonuroidea. I. Taphozoinae and Emballonurinae Karyotypes Evolve at Different Rates and Share No Derived Chromosomal Characters. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia. Mol Biol Rep 2019; 46:3765-3776. [PMID: 31012029 DOI: 10.1007/s11033-019-04818-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/12/2019] [Indexed: 12/29/2022]
Abstract
Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla-Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria-were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.
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Evaluation of a user-friendly test device (AcQuickDx) for detection of specific antibodies to human angiostrongyliasis. ACTA ACUST UNITED AC 2019. [DOI: 10.25177/jfst.4.4.ra.520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mitogenome of Gymnothorax minor and Phylogenetic Relationship with Its Congeners and Related Genera (Anguilliformes: Muraenidae). SAINS MALAYS 2018. [DOI: 10.17576/jsm-2018-4710-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Molecular phylogeography and genetic diversity of Angiostrongylus cantonensis and A. malaysiensis (Nematoda: Angiostrongylidae) based on 66-kDa protein gene. Parasitol Int 2018; 68:24-30. [PMID: 30267903 DOI: 10.1016/j.parint.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/30/2018] [Accepted: 09/25/2018] [Indexed: 12/01/2022]
Abstract
Angiostrongylus cantonensis is the main causative agent of human angiostrongyliasis. A sibling species, A. malaysiensis has not been unequivocally incriminated to be involved in human infections. To date, there is only a single report on the application of the partial 66-kDa protein gene sequence for molecular differentiation and phylogeny of Angiostrongylus species. Nucleotide sequences of the 66-kDa protein gene of A. cantonensis and A. malaysiensis from Thailand, as well as those of the laboratory strains of A. cantonensis from Thailand and Hawaii, A. cantonensis from Japan and China, A. malaysiensis from Malaysia, and A. costaricensis from Costa Rica, were used for the reconstruction of phylogenetic tree by the maximum likelihood (ML) method and the haplotypes by the median joining (MJ) network. The ML phylogenetic tree contained two major clades with a full support bootstrap value - (1) A. cantonensis and A. malaysiensis, and (2) A. costaricensis. A. costaricensis was basal to A. cantonensis and A. malaysiensis. The genetic distance between A. cantonensis and A. malaysiensis ranged from p = .82% to p = 3.27%, that between A. cantonensis and A. costaricensis from p = 4.90% to p = 5.31%, and that between A. malaysiensis and A. costaricensis was p = 4.49% to p = 5.71%. Both A. cantonensis and A. malaysiensis possess high 66-kDa haplotype diversity. There was no clear separation of the conspecific taxa of A. cantonensis and A. malaysiensis from different geographical regions. A more intensive and extensive sampling with larger sample size may reveal greater haplotype diversity and a better resolved phylogeographical structure of A. cantonensis and A. malaysiensis.
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Genetic differentiation of Anisakis species (Nematoda: Anisakidae) in marine fish Priacanthus tayenus from Gulf of Thailand. Trop Biomed 2018; 35:669-677. [PMID: 33601754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Members of the genus Anisakis are parasitic nematodes of the family Anisakidae. They are potential zoonotic parasites, causing anisakiasis in humans who consume raw or undercooked seafood (fish or squid) infected with the larvae of this nematode. In the present study, anisakid nematodes collected from the marine fish Priacanthus tayenus (Purplespotted big-eye) caught from the Gulf of Thailand were examined morphologically and characterized genetically by DNA sequence analysis. Sequence data from the mitochondrial cytochrome c oxidase subunit II (mtDNA cox2) gene were used to identify these nematodes to species level and to evaluate the phylogenetic relationship among various taxa. All the 15 third-stage larvae of Anisakis nematodes investigated in this study belonged to the same genetic lineage as the A. typica species complex (named here as A. typica sp. T - T for Thailand). Eight mtDNA cox2 haplotypes were revealed in the 15 isolates of this Anisakis from Thailand. The mtDNA cox2 haplotypes of A. typica sp. T from Thailand were genetically distinct from those of the A. typica sensu stricto. Taxonomic description of this A. typica sp. T as a distinct species however awaits the availability of adult specimens.
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Immunochromatographic test for rapid serological diagnosis of human angiostrongyliasis. Int J Infect Dis 2018; 73:69-71. [DOI: 10.1016/j.ijid.2018.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 10/14/2022] Open
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Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene. PLoS One 2017; 12:e0189325. [PMID: 29216281 PMCID: PMC5720772 DOI: 10.1371/journal.pone.0189325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/23/2017] [Indexed: 01/19/2023] Open
Abstract
The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.
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Predominance of Wolbachia endosymbiont in the microbiota across life stages of Bactrocera latifrons (Insecta: Tephritidae). Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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23
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The Climate Range Expansion of Aedes albopictus (Diptera: Culicidae) in Asia Inferred From the Distribution of Albopictus Subgroup Species of Aedes (Stegomyia). JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:1615-1625. [PMID: 28968769 DOI: 10.1093/jme/tjx156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Indexed: 06/07/2023]
Abstract
We compared climatic distribution ranges between Aedes albopictus (Skuse) (Diptera: Culicidae) and the five wild (nondomesticated) species of Albopictus Subgroup of Scutellaris Group of Aedes (Stegomyia) in southern Asia. Distribution sites of the wild species concentrate in seasonal forest and savannah climate zones in India, Indochina, and southern China. The distribution of Ae. albopictus is broader than the wild species under 1) tropical rain-forest climate, 2) steppe and temperate savannah climate, and 3) continental climate with large seasonal temperature variation (hot summer and cold winter) at temperate lowlands (northernmost sites 40°N in Ae. albopictus vs 32°N in the wild species). However, the distribution of Ae. albopictus is more limited at tropical and subtropical highlands where the climate is cool but less continental (small seasonal variation, mild summer, and winter). We discuss a possibility that the broader climate ranges of Ae. albopictus are ecological or eco-evolutionary consequences of adaptation to human habitats. We also propose a general scenario for the origin, dispersal, and adaptation of Ae. albopictus in Asia as a hypothesis for future research.
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High Diversity of Bacterial Communities in Developmental Stages of Bactrocera carambolae (Insecta: Tephritidae) Revealed by Illumina MiSeq Sequencing of 16S rRNA Gene. Curr Microbiol 2017. [PMID: 28642971 DOI: 10.1007/s00284-017-1287-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bactrocera carambolae is a highly polyphagous fruit pest of agricultural importance. This study reports the bacterial communities associated with the developmental stages of B. carambolae. The microbiota of the developmental stages were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. At 97% similarity, there were 19 bacterial phyla and unassigned bacteria, comprising 39 classes, 86 orders, 159 families and 311 genera. The bacterial composition varied among the specimens of developmental stage and across developmental stages as well as exuviae. Four phyla of bacteria (with relative abundance of ≥1% in at least one specimen)-Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria-were recovered from the larva, pupa, adult stages and exuviae. Proteobacteria was the predominant phylum in all the developmental stages as well as the exuviae. Enterobacteriaceae (Proteobacteria) was the predominant family in the adult flies while the family [Weeksellaceae] (Bacteroidetes) was predominant in the larval and pupal stages. Among the genera occurring in more than one developmental stage of B. carambolae, Erwinia was more abundant in the larval stage, Halomonas more abundant in adult female, Stenotrophomonas more abundant in adult male, and Chryseobacterium more abundant in the larval and pupal stages. The results indicate transmission of bacteria OTUs from immatures to the newly emerged adults, and from exuviae to the environment.
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Molecular identification of Gnathostoma spinigerum (Nematoda: Gnathostomatidae) as causative agent of human gnathostomiasis in Thailand. Trop Biomed 2017; 34:478-482. [PMID: 33593032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A 43-year-old male residing in Prachin Buri Province, Thailand, was admitted to the Siriraj University Hospital of Mahidol University, Thailand, in July 2014 with right eyelid swelling and serpiginous lesion for three weeks. A nematode specimen was accidentally recovered from his upper right eyelid area. The body of the worm was cylindrical and measured 11.0 × 1.4 mm. The head bulb had eight circles of transverse spines. Anterior half of the body was covered with rows of comb-like pointed spines. The tail part was rounded dorsally and flattened ventrally and no copulatory spicule was observed at the posterior end. It was morphologically identified as an immature female worm of gnathostome species. Sequence analysis for partial cytochrome c oxidase subunit I (COI) gene revealed this recovered nematode as Gnathostoma spinigerum.
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Complete mitochondrial genome of Eurema blanda and phylogenetic relationship with its congener E. hecabe and other pierid butterflies. Meta Gene 2017. [DOI: 10.1016/j.mgene.2016.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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27
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Complete mitochondrial genome of Orthetrum dragonflies and molecular phylogeny of Odonata. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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A multigene approach to determine the molecular phylogeography of Argiope mangal and Argiope dang (Araneae: Araneidae) and their genetic relationships with the Argiope aetherea species group. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Complete mitochondrial genome of Angiostrongylus malaysiensis lungworm and molecular phylogeny of Metastrongyloid nematodes. Acta Trop 2016; 161:33-40. [PMID: 27207134 DOI: 10.1016/j.actatropica.2016.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/29/2016] [Accepted: 05/06/2016] [Indexed: 11/29/2022]
Abstract
Angiostrongylus malaysiensis is a nematode parasite of various rat species. When first documented in Malaysia, it was referred to as A. cantonensis. Unlike A. cantonensis, the complete mitochondrial genome of A. malaysiensis has not been documented. We report here its complete mitogenome, its differentiation from A. cantonensis, and the phylogenetic relationships with its congeners and other Metastrongyloid taxa. The whole mitogenome of A. malaysiensis had a total length of 13,516bp, comprising 36 genes (12 PCGs, 2 rRNA and 22 tRNA genes) and a control region. It is longer than that of A. cantonensis (13,509bp). Its control region had a long poly T-stretch of 12bp which was not present in A. cantonensis. A. malaysiensis and A. cantonensis had identical start codon for the 12 PCGs, but four PCGs (atp6, cob, nad2, nad6) had different stop codon. The cloverleaf structure for the 22 tRNAs was similar in A. malaysiensis and A. cantonensis except the TΨC-arm was absent in trnV for A. malaysiensis but present in A. cantonensis. The Angiostrongylus genus was monophyletic, with A. malaysiensis and A. cantonensis forming a distinct lineage from that of A. costaricensis and A. vasorum. The genetic distance between A. malaysiensis and A. cantonensis was p=11.9% based on 12 PCGs, p=9.5% based on 2 rRNA genes, and p=11.6% based on 14 mt-genes. The mitogenome will prove useful for studies on phylogenetics and systematics of Angiostrongylus lungworms and other Metastrongyloid nematodes.
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Differentiating sibling species of Zeugodacus caudatus (Insecta: Tephritidae) by complete mitochondrial genome. Genetica 2016; 144:513-521. [PMID: 27502829 DOI: 10.1007/s10709-016-9919-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/02/2016] [Indexed: 11/29/2022]
Abstract
Zeugodacus caudatus is a pest of pumpkin flowers. It has a Palearctic and Oriental distribution. We report here the complete mitochondrial genome of the Malaysian and Indonesian samples of Z. caudatus determined by next-generation sequencing of genomic DNA and determine their taxonomic status as sibling species and phylogeny with other taxa of the genus Zeugodacus. The whole mitogenome of both samples possessed 37 genes (13 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region. The mitogenome of the Indonesian sample (15,885 bp) was longer than that of the Malaysian sample (15,866 bp). In both samples, TΨC-loop was absent in trnF and DHU-loop was absent in trnS1. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with the two samples of Z. caudatus forming a sister group and the genus Zeugodacus was monophyletic. The Malaysian and Indonesian samples of Z. caudatus have a genetic distance of p = 7.8 % based on 13 PCGs and p = 7.0 % based on 15 mitochondrial genes, indicating status of sibling species. They are proposed to be accorded specific status as members of a species complex.
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Complete mitochondrial genome and phylogeny of Microhyla butleri (Amphibia: Anura: Microhylidae). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Geographical distribution and incidence of Angiostrongylus lungworms (Nematoda: Angiostrongylidae) and their rodent hosts in Thailand. Trop Biomed 2016; 33:35-44. [PMID: 33579139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The rat lungworm Angiostrongylus cantonensis, a zoonotic parasite, is known to be responsible for eosinophilic meningitis and meningoencephalitis in humans in many countries worldwide. Another congener A. malaysiensis is a potential pathogen. Rodents as natural definitive host of the parasites are abundant and globally widespread. In this study, the prevalence of Angiostrongylus infection in wild rats was investigated in twenty-four provinces of Thailand during the period December 2011 to June 2014. Of the 669 wild rats sampled, 46 (6.88%) were infected with Angiostrongylus lungworms. The rodents harbouring A. cantonensis worms included Bandicota indica, Bandicota savilei, Rattus exulans, Rattus norvegicus, Rattus rattus complex and Rattus tiomanicus, and those harbouring A. malaysiensis were B. savilei, Rattus losea, R. norvegicus and R. rattus complex. No parasite was recovered from Maxomys surifer (n=11), Mus musculus (n=1), Niviventer fulvescens (n=2), Rattus argentiventer (n=4), Rattus nitidus (n=3) and Sundamys muelleri (n=3). In positive rats, the incidence of infection with Angiostrongylus lungworms was variable among host species and provinces. There were also considerable variation in the proportion of male and female worms among rodent hosts and localities. Two hundred and thirty-five of the collected worms were male and 282 were female. The mean worm burden in the positive rats was 11.24 and ranged from 1 to 61. 81.82% (423/517) of the adult worms were morphologically identified as A. cantonensis, and 18.18% (94/517) were A malaysiensis. One R. rattus from Prachuap Khiri Khan had mixed infection of A. cantonensis and A. malaysiensis (10 worms of each species). The overall number of male (202) and female (221) A. cantonensis worms was not significantly different (χ2 = 0.86, 0.50 > P > 0.30). However, the overall number of male (33) and female (61) A. malaysiensis worms was significantly different (χ2 = 8.34, P < 0.01). The present study added one new definitive host (R. tiomanicus) for A. cantonensis and two new definitive hosts (B. savilei and R. losea) for A. malaysiensis in Thailand. Our data update and contribute significantly to existing knowledge of the geographical distribution of A. cantonensis in wild rats in Thailand and confirm the occurrence of A. malaysiensis throughout the country.
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Complete Mitochondrial Genome of Three Bactrocera Fruit Flies of Subgenus Bactrocera (Diptera: Tephritidae) and Their Phylogenetic Implications. PLoS One 2016; 11:e0148201. [PMID: 26840430 PMCID: PMC4739531 DOI: 10.1371/journal.pone.0148201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/14/2016] [Indexed: 12/27/2022] Open
Abstract
Bactrocera latifrons is a serious pest of solanaceous fruits and Bactrocera umbrosa is a pest of Artocarpus fruits, while Bactrocera melastomatos infests the fruit of Melastomataceae. They are members of the subgenus Bactrocera. We report here the complete mitochondrial genome of these fruit flies determined by next-generation sequencing and their phylogeny with other taxa of the subgenus Bactrocera. The whole mitogenomes of these three species possessed 37 genes namely, 13 protein-coding genes (PCGs), 2 rRNA and 22 tRNA genes. The mitogenome of B. latifrons (15,977 bp) was longer than those of B. melastomatos (15,954 bp) and B. umbrosa (15,898 bp). This difference can be attributed to the size of the intergenic spacers (283 bp in B. latifrons, 261 bp in B. melastomatos, and 211 bp in B. umbrosa). Most of the PCGs in the three species have an identical start codon, except for atp8 (adenosine triphosphate synthase protein 8), which had an ATG instead of GTG in B. umbrosa, whilst the nad3 (NADH dehydrogenase subunit 3) and nad6 (NADH dehydrogenase subunit 6) genes were characterized by an ATC instead of ATT in B. melastomatos. The three species had identical stop codon for the respective PCGs. In B. latifrons and B. melastomatos, the TΨC (thymidine-pseudouridine-cytidine)-loop was absent in trnF (phenylalanine) and DHU (dihydrouracil)-loop was absent in trnS1 (serine S1). In B. umbrosa, trnN (asparagine), trnC (cysteine) and trnF lacked the TψC-loop, while trnS1 lacked the DHU-stem. Molecular phylogeny based on 13 PCGs was in general concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with B. latifrons and B. umbrosa forming a sister group basal to the other species of the subgenus Bactrocera which was monophyletic. The whole mitogenomes will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
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Complete mitochondrial genome reveals genetic diversity of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae). Acta Trop 2015; 152:157-164. [PMID: 26348256 DOI: 10.1016/j.actatropica.2015.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022]
Abstract
Angiostrongylus cantonensis is a zoonotic parasite that causes eosinophilic meningitis in humans. Earlier work on its mitochondrial genome was based on long polymerase chain reaction method. To date, only the mitogenome of the isolates from China has been studied. We report here the complete mitogenome of the Thailand isolate based on next generation sequencing and compare the genetic diversity with other isolates. The mitogenome of the Thailand isolate (13,519bp) is longer than those of the China isolates (13,497-13,502bp). Five protein-coding genes (atp6, cox1, cox2, cob, nad2) show variations in length among the isolates. The stop codon of the Thailand isolate differs from the China and Taiwan isolates in 4 genes (atp6, cob, nad2, nad6). Additionally, the Thailand isolate has 4 incomplete T stop codon compared to 3 in the China and Taiwan isolates. The control region is longer in the Thailand isolate (258bp) than the China (230-236bp) and Taiwan (237bp) isolates. The intergenic sequence between nad4 and cox1 genes in the Thailand isolate lacks 2bp (indels) at the 5'-end of the sequence as well as differs at 7 other sites compared to the China and Taiwan isolates. In the Thailand isolate, 18 tRNAs lack the entire TΨC-arm, compared to 17 in the China isolate and 16 in the Taiwan isolate. Phylogenetic analyses based on 36 mt-genes, 12 PCGs, 2 rRNA genes, 22 tRNA genes and control region all indicate closer genetic affinity between the China and Taiwan isolates compared to the Thailand isolate. Based on 36 mt-genes, the inter-isolate genetic distance varies from p=3.2% between China and Taiwan isolates to p=11.6% between Thailand and China isolates. The mitogenome will be useful for population, phylogenetics and phylogeography studies.
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Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe. Sci Rep 2015; 5:15155. [PMID: 26472633 PMCID: PMC4607999 DOI: 10.1038/srep15155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/15/2015] [Indexed: 11/09/2022] Open
Abstract
The whole mitochondrial genome of the pest fruit fly Bactrocera arecae was obtained from next-generation sequencing of genomic DNA. It had a total length of 15,900 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The control region (952 bp) was flanked by rrnS and trnI genes. The start codons included 6 ATG, 3 ATT and 1 each of ATA, ATC, GTG and TCG. Eight TAA, two TAG, one incomplete TA and two incomplete T stop codons were represented in the protein-coding genes. The cloverleaf structure for trnS1 lacked the D-loop, and that of trnN and trnF lacked the TΨC-loop. Molecular phylogeny based on 13 protein-coding genes was concordant with 37 mitochondrial genes, with B. arecae having closest genetic affinity to B. tryoni. The subgenus Bactrocera of Dacini tribe and the Dacinae subfamily (Dacini and Ceratitidini tribes) were monophyletic. The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
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Draft genome of neurotropic nematode parasite Angiostrongylus cantonensis, causative agent of human eosinophilic meningitis. Acta Trop 2015; 148:51-7. [PMID: 25910624 DOI: 10.1016/j.actatropica.2015.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
Abstract
Angiostrongylus cantonensis is a bursate nematode parasite that causes eosinophilic meningitis (or meningoencephalitis) in humans in many parts of the world. The genomic data from A. cantonensis will form a useful resource for comparative genomic and chemogenomic studies to aid the development of diagnostics and therapeutics. We have sequenced, assembled and annotated the genome of A. cantonensis. The genome size is estimated to be ∼260 Mb, with 17,280 genomic scaffolds, 91X coverage, 81.45% for complete and 93.95% for partial score based on CEGMA analysis of genome completeness. The number of predicted genes of ≥300 bp was 17,482. A total of 7737 predicted protein-coding genes of ≥50 amino acids were identified in the assembled genome. Among the proteins of known function, kinases are the most abundant followed by transferases. The draft genome contains 34 excretory-secretory proteins (ES), a minimum of 44 Nematode Astacin (NAS) metalloproteases, 12 Homeobox (HOX) genes, and 30 neurotransmitters. The assembled genome size (260 Mb) is larger than those of Pristionchus pacificus, Caenorhabditis elegans, Necator americanus, Caenorhabditis briggsae, Trichinella spiralis, Brugia malayi and Loa loa, but smaller than Haemonchus contortus and Ascaris suum. The repeat content (25%) is similar to H. contortus. The GC content (41.17%) is lower compared to P. pacificus (42.7%) and H. contortus (43.1%) but higher compared to C. briggsae (37.69%), A. suum (37.9%) and N. americanus (40.2%) while the scaffold N50 is 42,191. This draft genome will facilitate the understanding of many unresolved issues on the parasite and the disorder it causes.
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Molecular phylogeography of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae) and genetic relationships with congeners using cytochrome b gene marker. Acta Trop 2015; 148:66-71. [PMID: 25930187 DOI: 10.1016/j.actatropica.2015.04.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/17/2015] [Accepted: 04/19/2015] [Indexed: 02/05/2023]
Abstract
Angiostrongylus cantonensis is an important emerging zoonotic parasite causing human eosinophilic meningitis (or meningoencephalitis) in many parts of the world. To-date there is only a single study using mitochondrial cytochrome b (CYTB) gene to determine its genetic structure in eight geographical localities in Thailand. The present study examined the molecular phylogeography of this rat lungworm and its phylogenetic relationship with congeners using CYTB gene marker. A total of 15 CYTB haplotypes was found in 37 sequences from 14 geographical localities (covering north, west, east, central and south regions) in Thailand. These CYTB haplotypes were distinct from those of A. cantonensis for China and Hawaii. In Thailand, some CYTB haplotypes appeared to be confined to specific geographical localities. The partial CYTB DNA nucleotide sequences separated unequivocally the A. cantonensis isolates of Thailand, China and Hawaii as well as the congeners Angiostrongylus malaysiensis, A. costaricensis and Angiostrongylus vasorum, with A. malaysiensis grouped with A. cantonensis and A. costaricensis grouped with A. vasorum. Likewise the congeners of Metastrongylus and Onchocerca genera could also be clearly differentiated. The present study added two new definitive hosts (Bandicota savilei and Rattus losea) and three new localities (Mae Hong Son in the north, Tak in the west, and Phang Nga in the south) for A. malaysiensis in Thailand, indicating its wide occurrence in the country. Three CYTB haplotypes were found in the Thailand samples of A. malaysiensis. In addition to differentiation of congeners, CYTB gene marker could be used for determining the genetic diversity of a given population/taxon.
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Multigene Phylogeography of Bactrocera caudata (Insecta: Tephritidae): Distinct Genetic Lineages in Northern and Southern Hemispheres. PLoS One 2015; 10:e0129455. [PMID: 26090853 PMCID: PMC4474862 DOI: 10.1371/journal.pone.0129455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/09/2015] [Indexed: 12/05/2022] Open
Abstract
Bactrocera caudata is a pest of pumpkin flower. Specimens of B. caudata from the northern hemisphere (mainland Asia) and southern hemisphere (Indonesia) were analysed using the partial DNA sequences of the nuclear 28S rRNA and internal transcribed spacer region 2 (ITS-2) genes, and the mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and 16S rRNA genes. The COI, COII, 16S rDNA and concatenated COI+COII+16S and COI+COII+16S+28S+ITS-2 nucleotide sequences revealed that B. caudata from the northern hemisphere (Peninsular Malaysia, East Malaysia, Thailand) was distinctly different from the southern hemisphere (Indonesia: Java, Bali and Lombok), without common haplotype between them. Phylogenetic analysis revealed two distinct clades (northern and southern hemispheres), indicating distinct genetic lineage. The uncorrected ‘p’ distance for the concatenated COI+COII+16S nucleotide sequences between the taxa from the northern and southern hemispheres (‘p’ = 4.46-4.94%) was several folds higher than the ‘p’ distance for the taxa in the northern hemisphere (‘p’ = 0.00-0.77%) and the southern hemisphere (‘p’ = 0.00%). This distinct difference was also reflected by concatenated COI+COII+16S+28S+ITS-2 nucleotide sequences with an uncorrected 'p' distance of 2.34-2.69% between the taxa of northern and southern hemispheres. In accordance with the type locality the Indonesian taxa belong to the nominal species. Thus the taxa from the northern hemisphere, if they were to constitute a cryptic species of the B. caudata species complex based on molecular data, need to be formally described as a new species. The Thailand and Malaysian B. caudata populations in the northern hemisphere showed distinct genetic structure and phylogeographic pattern.
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Surprising Genetic Diversity inRhinolophus luctus(Chiroptera: Rhinolophidae) from Peninsular Malaysia: Description of a New Species Based on Genetic and Morphological Characters. ACTA CHIROPTEROLOGICA 2015. [DOI: 10.3161/15081109acc2015.17.1.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Evaluation of dot immunogold filtration assay (DIGFA) for rapid serodiagnosis of eosinophilic meningitis due to Angio-strongylus cantonensis (Nematoda: Metastrongyloidea). Trop Biomed 2015; 32:121-125. [PMID: 25801261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Angiostrongylus cantonensis is the most frequent cause of eosinophilic meningitis in humans in Thailand and worldwide. Because of difficulty of recovering the Angiostrongylus larvae from infected patients, detection of parasite-specific antibodies is used to support clinical diagnosis. This study tested serum samples from eosinophilic meningitis patients and individuals at risk of infection with A. cantonensis to evaluate a recently developed simple and rapid dot-immunogold filtration assay (DIGFA) for detection of specific antibodies against A. cantonensis. Purified 31-kDa glycoprotein of A. cantonensis and protein A colloidal gold conjugate were employed to detect the 31-kDa anti-A. cantonensis antibody in patients sera from the parasite endemic areas of northeast Thailand. The results were compared with those obtained by dot-blot enzyme-linked immunosorbent assay (ELISA) with 31-kDa A. cantonensis antigen. The overall positivity rate of DIGFA and dot-blot ELISA for A. cantonensis infection in 98 clinically diagnosed cases from three highly endemic districts in Khon Kaen province were 39.79% and 37.75%, respectively. Among 86 sera of subjects at risk of infection with A. cantonensis, 24.41% were positive by DIGFA and 23.25% by dot-blot ELISA. There were good correlation between the visual grading of DIGFA and dot-blot ELISA in both groups of defined sera. DIGFA is as sensitive and specific as dot-blot ELISA for confirming eosinophilic meningitis due to A. cantonensis infection, with advantages of simplicity, rapidity and without the use of specific and expensive equipment, and can be used in field settings.
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Karyotype evolution in the horseshoe bat Rhinolophus sedulus by whole-arm reciprocal translocation (WART). Cytogenet Genome Res 2014; 143:241-50. [PMID: 25139053 DOI: 10.1159/000365824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 11/19/2022] Open
Abstract
Robertsonian (centric) fusion or fission is one of the predominant modes of chromosomal rearrangement in karyotype evolution among mammals. However, in karyotypes composed of only bi-armed chromosomes, creation of new chromosomal arm combinations in one step is possible only via whole-arm reciprocal translocation (WART). Although this type of rearrangement has often been proposed to play an important role in chromosomal evolution, direct observations of WARTs remained rare, and, in most cases, were found in hybrids of chromosomal races in the genera Mus and Sorex. For the first time, we present the karyotype of the horseshoe bat species Rhinolophus sedulus (2n = 28, FNa = 52), where a WART between 2 metacentric autosomes was detected by G-banding and confirmed by FISH with painting probes of the vespertilionid bat Myotis myotis. Among the 6 specimens analyzed, 2 showed the heterozygous condition of the WART, 1 showed the presumed ancestral, and 3 specimens showed the derived homozygous state. As the existence of a hybrid zone at the sampling locality is thought to be rather improbable, the WART may indicate ongoing karyotype evolution in this taxon.
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Accuracy of lung nodule volumetry in low-dose CT with iterative reconstruction: an anthropomorphic thoracic phantom study. Br J Radiol 2014; 87:20130644. [PMID: 25026866 DOI: 10.1259/bjr.20130644] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE The purpose of this study was to assess accuracy of lung nodule volumetry in low-dose CT with application of iterative reconstruction (IR) according to nodule size, nodule density and CT tube currents, using artificial lung nodules within an anthropomorphic thoracic phantom. METHODS Eight artificial nodules (four diameters: 5, 8, 10 and 12 mm; two CT densities: -630 HU that represents ground-glass nodule and +100 HU that represents solid nodule) were randomly placed inside a thoracic phantom. Scans were performed with tube current-time product to 10, 20, 30 and 50 mAs. Images were reconstructed with IR and filtered back projection (FBP). We compared volume estimates to a reference standard and calculated the absolute percentage error (APE). RESULTS The APE of all nodules was significantly lower when IR was used than with FBP (7.5 ± 4.7% compared with 9.0 ±6.9%; p < 0.001). The effect of IR was more pronounced for smaller nodules (p < 0.001). IR showed a significantly lower APE than FBP in ground-glass nodules (p < 0.0001), and the difference was more pronounced at the lowest tube current (11.8 ± 5.9% compared with 21.3 ± 6.1%; p < 0.0001). The effect of IR was most pronounced for ground-glass nodules in the lowest CT tube current. CONCLUSION Lung nodule volumetry in low-dose CT by application of IR showed reliable accuracy in a phantom study. Lung nodule volumetry can be reliably applicable to all lung nodules including small, ground-glass nodules even in ultra-low-dose CT with application of IR. ADVANCES IN KNOWLEDGE IR significantly improved the accuracy of lung nodule volumetry compared with FBP particularly for ground-glass (-630 HU) nodules. Volumetry in low-dose CT can be utilized in patient with lung nodule work-up, and IR has benefit for small, ground-glass lung nodules in low-dose CT.
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Workshop on research priorities for management and treatment of angiostrongyliasis(1). Emerg Infect Dis 2013; 18:e1. [PMID: 23171634 PMCID: PMC3557862 DOI: 10.3201/eid1812.120499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Paratracheal air cysts on thoracic multidetector CT: incidence, morphological characteristics and relevance to pulmonary emphysema. Br J Radiol 2013; 86:20120218. [PMID: 23255540 DOI: 10.1259/bjr.20120218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To determine the incidence, morphological characteristics and relevance of paratracheal air cysts (PTACs) with pulmonary emphysema, as seen on thoracic multidetector CT (MDCT). METHODS The CT images of 854 consecutive patients who underwent thoracic MDCT during a period of 2 months at our institution were reviewed. 538 of the patients were male and 316 were female. The incidence, size and shape of the PTACs and their relation to pulmonary emphysema were retrospectively analysed. RESULTS Among the 854 patients, 69 (8.1%) had PTACs. 37 (6.9%) of the 538 male patients and 32 (10.1%) of the 316 female patients had PTACs. The highest prevalence of PTACs (25 patients, 11.2%) was found in those who were in the sixth decade of life. 48 (69.6%) PTACs measured 3-10 mm at the longest diameter and 33 (47.8%) were elongated on the coronal section images. 12 (17.4%) patients with PTACs had underlying gross morphological emphysema. The relationship between the presence of PTACs and the presence of emphysema and the relationship between the presence of PTACs and the severity of emphysema were not statistically significant. The size of PTACs showed an inverse relation to the severity of emphysema. CONCLUSION The incidence of PTACs was estimated to be much higher than that of previous studies. There was a slight female predilection for PTACs, most commonly found in the sixth decade of life; PTACs mostly measured 3-10 mm and were elongated in shape. The relation of PTACs to gross morphological emphysema was low. ADVANCES IN KNOWLEDGE PTACs are not correlated with the presence of emphysema on MDCT.
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Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy. Mol Phylogenet Evol 2011; 61:167-76. [DOI: 10.1016/j.ympev.2011.05.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 11/28/2022]
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From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides. BMC Evol Biol 2011; 11:175. [PMID: 21689462 PMCID: PMC3141433 DOI: 10.1186/1471-2148-11-175] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/21/2011] [Indexed: 11/25/2022] Open
Abstract
Background Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some microhylid subfamilies, and therefore subfamilial affiliations of some genera are still unclear. To elucidate the phylogenetic positions of two mysterious Asian genera, Gastrophrynoides and Phrynella, and to better understand the trans-continental distributions of microhylid taxa, we performed molecular phylogenetic and dating analyses using the largest molecular dataset applied to these taxa to date. Results Six nuclear and two mitochondrial genes (approx. 8 kbp) were sequenced from 22 microhylid frog species representing eight subfamilies. The maximum likelihood and Bayesian analyses could not fully elucidate the subfamilial relationships, suggesting a rapid radiation of these taxa between 85 and 66 million years ago. In contrast, generic relationships of Asian microhylines were generally well resolved. Conclusion Our results clearly showed that one of two problematic Asian genera, Phrynella, was nested in the clade of the Asian subfamily Microhylinae. By contrast, Gastrophrynoides occupied the most basal position of the Australian-New Guinean subfamily Asterophryinae. The estimated divergence of Gastrophrynoides from other asterophryine was unexpectedly around 48 million years ago. Although a colonization scenario via Antarctica to the Australian-New Guinean landmass has been suggested for Asterophryinae, our finding suggested a novel colonization route via Indo-Eurasia.
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Abstract
The aim of this study was to evaluate the feasibility of dual localisation with hookwire and lipiodol before needlescopy-assisted resection for pulmonary nodule. Computed tomography-guided dual marking was performed on 36 pulmonary nodules of 32 patients and needlescopy-assisted resection was performed monitored by C-arm fluoroscopy. The mean age of the patients was 58 ± 12 (range 12-77) yrs. The mean size of the nodules was 7.5 ± 3.7 (3-17) mm. Their mean distance from the pleural surface was 7.3 ± 7.5 (0-35) mm. There were nine pure ground-glass opacity lesions, five semi-solid lesions and 22 solid lesions. The time of the dual localisation procedure was 13.1 ± 4.8 (7-23) min. Complications of the marking were pneumothorax in nine patients, and intrapulmonary bleeding in three. One hookwire dislodged during the operation. All nodules were successfully resected under needlescopy without conversion to a conventional thoracoscopy (5 mm or 10 mm thoracoscopy) or a minithoracotomy. There was no complication related to needlescopy-assisted resection. Dual marking with hookwire and lipiodol is a safe and none time consuming procedure, and needlescopy-assisted lung resection for small nodules is technically feasible and useful for histological diagnosis and treatment.
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Effect of Thai 'koi-hoi' food flavoring on the viability and infectivity of the third-stage larvae of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae). Acta Trop 2010; 113:245-7. [PMID: 19931504 DOI: 10.1016/j.actatropica.2009.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 11/16/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
The effect of the food flavoring of 'koi-hoi', a popular Thai snail dish, on the viability and infectivity of Angiostrongylus (=Parastrongylus) cantonensis third-stage larvae was assessed in a mouse model. Groups of 50 each of actively moving, non-motile coiled, and extended larvae were obtained from experimentally infected snail meat, after one-hour exposure to standard 'koi-hoi' flavoring. These larvae and groups of 50 unexposed moving larvae (control) were individually fed to each group of three experimental BALB/c mice. The effect on Angiostrongylus worm burden was measured after 3 weeks of infection. Infectivity of the motile larvae after exposure to 'koi-hoi' food flavoring was 38 + or - 5.29%. This was highly significantly lower than the infectivity (62 + or - 7.21%) of the control (unexposed) third-stage larvae (chi(2) = 17.28, P < 0.001). In the non-motile larvae resulting from exposure to the food flavoring, no adult worm was recovered from the extended larvae, indicating that they were no longer alive and unable to cause infection. A small proportion (3.33 + or - 2.31%) of the coiled larvae developed into young adult worms, indicating that mobility alone is not a definitive indicator of viability. The present study confirms that the food flavoring components of 'koi-hoi' dish adversely affect the viability and infectivity of A. cantonensis larvae. Exposure of the third-stage larvae to 'koi-hoi' food flavoring resulted in decreased viability and eventually death. Prolonged treatment with food flavoring to inactivate/immobilize and then kill the infective, third-stage larvae of A. cantonensis in snail meat prior to consumption may be one of the possible economical means of reducing human infection.
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Meiotic chromosomes and sex determination mechanism in Thailand and Hawaii isolates of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae). Trop Biomed 2009; 26:346-351. [PMID: 20237450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Angiostrongylus cantonensis, the nematode lungworm of rats, has a XX/X0 sex-determination mechanism. The chromosome constitution consists of 10 autosomes, with 2n=12, XX in the female and 2n=11, X0 in the male. Meiosis-I shows five bivalents and one univalent for the male worm, and six bivalents for the female worm. The chromosome constitution of the Thailand and Hawaii isolates of A. cantonensis is similar to those reported for the taxa from Japan, Egypt and mainland China.
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A new species of Leptolalax (Amphibia, Anura, Megophryidae) from Peninsular Malaysia. Zoolog Sci 2009; 26:243-7. [PMID: 19341347 DOI: 10.2108/zsj.26.243] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new megophryid species, Leptolalax kecil, is described from the Cameron Highlands of Peninsular Malaysia on the basis of acoustic and morphological characteristics. It has an advertisement call dissimilar to that of other, congeneric species, and is the smallest of the known Leptolalax. It is similar to L. pluvialis from Vietnam in small body size, but differs from it in ventral color, and in the size and color of the pectoral gland. The distributional pattern of the new species Is discussed.
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