Displaying publications 21 - 40 of 79 in total

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  1. Fulltext Examination of Sarcocystis spp. of giant snakes from Australia and Southeast Asia confirms presence of a known pathogen - Sarcocystis nesbitti
    Wassermann M, Raisch L, Lyons JA, Natusch DJD, Richter S, Wirth M, et al.
    PLoS One, 2017;12(11):e0187984.
    PMID: 29131856 DOI: 10.1371/journal.pone.0187984
    We examined Sarcocystis spp. in giant snakes from the Indo-Australian Archipelago and Australia using a combination of morphological (size of sporocyst) and molecular analyses. We amplified by PCR nuclear 18S rDNA from single sporocysts in order to detect mixed infections and unequivocally assign the retrieved sequences to the corresponding parasite stage. Sarcocystis infection was generally high across the study area, with 78 (68%) of 115 examined pythons being infected by one or more Sarcocystis spp. Among 18 randomly chosen, sporocyst-positive samples (11 from Southeast Asia, 7 from Northern Australia) the only Sarcocystis species detected in Southeast Asian snakes was S. singaporensis (in reticulated pythons), which was absent from all Australian samples. We distinguished three different Sarcocystis spp. in the Australian sample set; two were excreted by scrub pythons and one by the spotted python. The sequence of the latter is an undescribed species phylogenetically related to S. lacertae. Of the two Sarcocystis species found in scrub pythons, one showed an 18S rRNA gene sequence similar to S. zamani, which is described from Australia for the first time. The second sequence was identical/similar to that of S. nesbitti, a known human pathogen that was held responsible for outbreaks of disease among tourists in Malaysia. The potential presence of S. nesbitti in Australia challenges the current hypothesis of a snake-primate life cycle, and would have implications for human health in the region. Further molecular and biological characterizations are required to confirm species identity and determine whether or not the Australian isolate has the same zoonotic potential as its Malaysian counterpart. Finally, the absence of S. nesbitti in samples from reticulated pythons (which were reported to be definitive hosts), coupled with our phylogenetic analyses, suggest that alternative snake hosts may be responsible for transmitting this parasite in Malaysia.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  2. Identification of microbial agents in culture-negative brain abscess samples by 16S/18S rRNA gene PCR and sequencing
    John DV, Aryalakshmi B, Deora H, Purushottam M, Raju R, Mahadevan A, et al.
    Trop Biomed, 2022 Dec 01;39(4):489-498.
    PMID: 36602206 DOI: 10.47665/tb.39.4.002
    Despite clinical suspicion of an infection, brain abscess samples are often culture-negative in routine microbiological testing. Direct PCR of such samples enables the identification of microbes that may be fastidious, non-viable, or unculturable. Brain abscess samples (n = 217) from neurosurgical patients were subjected to broad range 16S rRNA gene PCR and sequencing for bacteria. All these samples and seven formalin-fixed paraffin-embedded tissue (FFPE) samples were subjected to species-specific 18S rRNA PCR for neurotropic free-living amoeba that harbour pathogenic bacteria. The concordance between smear and/or culture and PCR was 69%. One-third of the samples were smear- and culture-negative for bacterial agents. However, 88% of these culture-negative samples showed the presence of bacterial 16S rRNA by PCR. Sanger sequencing of 27 selected samples showed anaerobic/fastidious gram negative bacteria (GNB, 38%), facultative Streptococci (35%), and aerobic GNB (27%). Targeted metagenomics sequencing of three samples showed multiple bacterial species, including anaerobic and non-culturable bacteria. One FFPE tissue revealed the presence of Acanthamoeba 18S rRNA. None of the frozen brain abscess samples tested was positive for 18S rRNA of Acanthamoeba or Balamuthia mandrillaris. The microbial 16/18S rRNA PCR and sequencing outperformed culture in detecting anaerobes, facultative Streptococci and FLA in brain abscess samples. Genetic analyses of 16S/18S sequences, either through Sanger or metagenomic sequencing, will be an essential diagnostic technology to be included for diagnosing culture-negative brain abscess samples. Characterizing the microbiome of culture-negative brain abscess samples by molecular methods could enable detection and/or treatment of the source of infection.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  3. Assessment of pan-Leishmania detection by recombinase polymerase amplification assay
    Louizi C, Khan MAA, Faisal K, Chowdhury R, Ghosh P, Hossain F, et al.
    Diagn Microbiol Infect Dis, 2023 Feb;105(2):115862.
    PMID: 36493571 DOI: 10.1016/j.diagmicrobio.2022.115862
    The spread of vector habitats along with increasing human mobility can introduce atypical Leishmania species and hence can challenge existing diagnostic practices for rapid detection of active infection with species outside the narrow target range. Here we assessed the pan-Leishmania detection ability of isothermal recombinase polymerase amplification (RPA) assays targeting 18S rRNA gene, cathepsin L-like cysteine proteinase B (Cpb) gene, and kinetoplast minicircle DNA (kDNA) regions. While the lowest limit of detection of the 18S rRNA-RPA and Cpb-RPA assays were estimated as 12 and 17 standard DNA molecules, respectively, both assays could amplify genomic DNA of 7 pathogenic Leishmania species. Evaluation of 18S rRNA-RPA and our previously developed kDNA-RPA assays on 70 real-time PCR-positive leishmaniasis samples of varying pathologies resulted in sensitivity rates of 35.71% and 88.57%, respectively, while the combined sensitivity was 98.57%. Combinatorial application of 18S rRNA-RPA and kDNA-RPA assays can be recommended for further diagnostic assessments.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  4. Phylogenetics and systematics of Angiostrongylus lungworms and related taxa (Nematoda: Metastrongyloidea) inferred from the nuclear small subunit (SSU) ribosomal DNA sequences
    Eamsobhana P, Lim PE, Yong HS
    J Helminthol, 2015 May;89(3):317-25.
    PMID: 24622302 DOI: 10.1017/S0022149X14000108
    The Angiostrongylus lungworms are of public health and veterinary concern in many countries. At the family level, the Angiostrongylus lungworms have been included in the family Angiostrongylidae or the family Metastrongylidae. The present study was undertaken to determine the usefulness and suitability of the nuclear 18S (small subunit, SSU) rDNA sequences for differentiating various taxa of the genus Angiostrongylus, as well as to determine the systematics and phylogenetic relationship of Angiostrongylus species and other metastrongyloid taxa. This study revealed six 18S (SSU) haplotypes in A. cantonensis, indicating considerable genetic diversity. The uncorrected pairwise 'p' distances among A. cantonensis ranged from 0 to 0.86%. The 18S (SSU) rDNA sequences unequivocally distinguished the five Angiostrongylus species, confirmed the close relationship of A. cantonensis and A. malaysiensis and that of A. costaricensis and A. dujardini, and were consistent with the family status of Angiostrongylidae and Metastrongylidae. In all cases, the congeneric metastrongyloid species clustered together. There was no supporting evidence to include the genus Skrjabingylus as a member of Metastrongylidae. The genera Aelurostrongylus and Didelphostrongylus were not recovered with Angiostrongylus, indicating polyphyly of the Angiostrongylidae. Of the currently recognized families of Metastrongyloidea, only Crenosomatidae appeared to be monophyletic. In view of the unsettled questions regarding the phylogenetic relationships of various taxa of the metastrongyloid worms, further analyses using more markers and more taxa are warranted.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  5. Fulltext Seasonal Filarial Infections and Their Black Fly Vectors in Chiang Mai Province, Northern Thailand
    Aupalee K, Saeung A, Srisuka W, Fukuda M, Streit A, Takaoka H
    Pathogens, 2020 Jun 25;9(6).
    PMID: 32630410 DOI: 10.3390/pathogens9060512
    The transmission of zoonotic filarial parasites by black flies has so far been reported in the Chiang Mai and Tak provinces, Thailand, and the bites of these infected black flies can cause a rare disease-human zoonotic onchocerciasis. However, species identification of the filarial parasites and their black fly vectors in the Chiang Mai province were previously only based on a morphotaxonomic analysis. In this study, a combined approach of morphotaxonomic and molecular analyses (mitochondrial cox1, 12S rRNA, and nuclear 18S rRNA (SSU HVR-I) genes) was used to clarify the natural filarial infections in female black flies collected by using human and swine baits from two study areas (Ban Lek and Ban Pang Dang) in the Chiang Mai province from March 2018 to January 2019. A total of 805 and 4597 adult females, belonging to seven and nine black fly taxa, were collected from Ban Lek and Ban Pang Dang, respectively. At Ban Lek, four of the 309 adult females of Simulium nigrogilvum were positive for Onchocerca species type I in the hot and rainy seasons. At Ban Pang Dang, five unknown filarial larvae (belonging to the same new species) were detected in Simulium sp. in the S. varicorne species-group and in three species in the S. asakoae species-group in all seasons, and three non-filarial larvae of three different taxa were also found in three females of the S. asakoae species-group. This study is the first to molecularly identify new filarial species and their vector black fly species in Thailand.
    Matched MeSH terms: RNA, Ribosomal, 18S
  6. Fulltext Microbiota of Palm Oil Mill Wastewater in Malaysia
    Bala JD, Lalung J, Al-Gheethi AAS, Hossain K, Ismail N
    Trop Life Sci Res, 2018 Jul;29(2):131-163.
    PMID: 30112146 MyJurnal DOI: 10.21315/tlsr2018.29.2.10
    This study was aimed at identifying indigenous microorganisms from palm oil mill effluent (POME) and to ascertain the microbial load. Isolation and identification of indigenous microorganisms was subjected to standard microbiological methods and sequencing of the 16S rRNA and 18S rRNA genes. Sequencing of the 16S rRNA and 18S rRNA genes for the microbial strains signifies that they were known as Micrococcus luteus 101PB, Stenotrophomonas maltophilia 102PB, Bacillus cereus 103PB, Providencia vermicola 104PB, Klebsiella pneumoniae 105PB, Bacillus subtilis 106PB, Aspergillus fumigatus 107PF, Aspergillus nomius 108PF, Aspergillus niger 109PF and Meyerozyma guilliermondii 110PF. Results revealed that the population of total heterotrophic bacteria (THB) ranged from 9.5 × 105 - 7.9 × 106 cfu/mL. The total heterotrophic fungi (THF) ranged from 2.1 × 104 - 6.4 × 104 cfu/mL. Total viable heterotrophic indigenous microbial population on CMC agar ranged from 8.2 × 105 - 9.1 × 106 cfu/mL and 1.4 × 103 - 3.4 × 103 cfu/mL for bacteria and fungi respectively. The microbial population of oil degrading bacteria (ODB) ranged from 6.4 × 105 - 4.8 × 106 cfu/mL and the oil degrading fungi (ODF) ranged from 2.8 × 103 - 4.7 × 104 cfu/mL. The findings revealed that microorganisms flourish well in POME. Therefore, this denotes that isolating native microorganisms from POME is imperative for effectual bioremediation, biotreatment and biodegradation of industrial wastewaters.
    Matched MeSH terms: RNA, Ribosomal, 18S
  7. Occurrence and molecular characterisation of Acanthamoeba isolated from recreational hot springs in Malaysia: evidence of pathogenic potential
    Mohd Hussain RH, Ishak AR, Abdul Ghani MK, Ahmed Khan N, Siddiqui R, Shahrul Anuar T
    J Water Health, 2019 Oct;17(5):813-825.
    PMID: 31638031 DOI: 10.2166/wh.2019.214
    This study aimed to identify the Acanthamoeba genotypes and their pathogenic potential in five recreational hot springs in Peninsular Malaysia. Fifty water samples were collected between April and September 2018. Physical parameters of water quality were measured in situ while chemical and microbiological analyses were performed in the laboratory. All samples were filtered through the nitrocellulose membrane and tested for Acanthamoeba using both cultivation and polymerase chain reaction (PCR) by targeting the 18S ribosomal RNA gene. The pathogenic potential of all positive isolates was identified using thermo- and osmotolerance tests. Thirty-eight (76.0%) samples were positive for Acanthamoeba. Water temperature (P = 0.035), chemical oxygen demand (P = 0.026), sulphate (P = 0.002) and Escherichia coli (P < 0.001) were found to be significantly correlated with the presence of Acanthamoeba. Phylogenetic analysis revealed that 24 samples belonged to genotype T4, nine (T15), two (T3) and one from each genotype T5, T11 and T17. Thermo- and osmotolerance tests showed that 6 (15.79%) of the Acanthamoeba strains were highly pathogenic. The existence of Acanthamoeba in recreational hot springs should be considered as a health threat among the public especially for high-risk people. Periodic surveillance of hot spring waters and posting warning signs by health authorities is recommended to prevent disease related to pathogenic Acanthamoeba.
    Matched MeSH terms: RNA, Ribosomal, 18S
  8. Molecular identification of Eimeria hestermani and Eimeria prionotemni from a red-necked wallaby (Macropodidae; Macropus rufogriseus) in Japan
    Ekawasti F, Kitagawa K, Domae H, Wardhana AH, Shibahara T, Uni S, et al.
    Parasitol Res, 2020 Apr;119(4):1271-1279.
    PMID: 32072327 DOI: 10.1007/s00436-020-06618-2
    To date, more than 50 Eimeria spp. have been isolated from marsupials of the family Macropodidae. Although 18 species of Eimeria have been previously detected from multiple animal species belonging to the genus Macropus of the family, limited genetic analyses of the parasites are available, and their pathogenicity remains unclear. Here, we report the isolation of Eimeria spp. from a zoo specimen of red-necked wallaby (Macropodidae; Macropus rufogriseus). Specifically, two distinct types of Eimeria oocysts were recovered, one from the feces before treatment with an anthelmintic and the second from the intestinal contents after death of the animal. The oocysts obtained from the two sources were morphologically identified as E. hestermani and E. prionotemni, respectively. We successfully determined partial gene sequences from the two isolates, including segments of the 18S rRNA genes, and for the first time have used phylogenetic analyses of these sequences to assign the species to distinct clades. In combination with further genetic data, these results are expected to help elucidate the pathogenicity and host ranges of Eimeria spp. within the respective family and genus.
    Matched MeSH terms: RNA, Ribosomal, 18S
  9. Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA
    Ng YH, Fong MY, Subramaniam V, Shahari S, Lau YL
    Res Vet Sci, 2015 Dec;103:201-4.
    PMID: 26679818 DOI: 10.1016/j.rvsc.2015.10.009
    Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population.
    Matched MeSH terms: RNA, Ribosomal, 18S
  10. Fulltext Acanthamoeba-mediated cytopathic effect correlates with MBP and AhLBP mRNA expression
    Ng SL, Nordin A, Abd Ghafar N, Suboh Y, Ab Rahim N, Chua KH
    Parasit Vectors, 2017 12 28;10(1):625.
    PMID: 29282148 DOI: 10.1186/s13071-017-2547-0
    BACKGROUND: In recent years, the concern of Acanthamoeba keratitis has increased since the infection is often associated with contact lens use. Partial 18S rRNA genotypic identification of Acanthamoeba isolates is important to correlate with pathophysiological properties in order to evaluate the degree of virulence. This is the first report of genotypic identification for clinical isolates of Acanthamoeba from corneal scrapings of keratitis in Malaysia. This study is also the first to correlate the mRNA expression of MBP and AhLBP as virulent markers for axenic strains of Acanthamoeba.

    RESULTS: In this study, ten clinical isolates were obtained from corneal scrapings. Rns genotype and intra-genotypic variation at the DF3 region of the isolates were identified. Results revealed that all clinical isolates belonged to the T4 genotype, with T4/6 (4 isolates), T4/2 (3 isolates), T4/16 (2 isolates) and one new genotype T4 sequence (T4/36), being determined. The axenic clinical isolates were cytopathogenic to rabbit corneal fibroblasts. MBP and AhLBP mRNA expression are directly correlated to Acanthamoeba cytopathic effect.

    CONCLUSIONS: All ten Malaysian clinical isolates were identified as genotype T4 which is predominantly associated with AK. Measuring the mRNA expression of Acanthamoeba virulent markers could be useful in the understanding of the pathogenesis of Acanthamoeba keratitis.

    Matched MeSH terms: RNA, Ribosomal, 18S
  11. Fulltext Detection and molecular identification of blood parasites in rodents captured from urban areas of southern Sarawak, Malaysian Borneo
    Perison PWD, Amran NS, Adrus M, Anwarali Khan FA
    Vet Med Sci, 2022 Sep;8(5):2059-2066.
    PMID: 35636429 DOI: 10.1002/vms3.849
    BACKGROUND: Rodent species are well known for their potential as hosts and reservoirs for various zoonotic diseases. Studies on blood parasite infection in small mammals focused on urban cities in Peninsular Malaysia and have been conducted over the years. In contrast, there are information gaps related to molecular detection of blood parasites in urban areas of Sarawak that are associated with veterinary importance and zoonotic spillover potential. Increasing prevalence and transmission of blood parasite diseases is the most crucial public health issue, particularly in developing urban areas of Sarawak. Therefore, molecular identification studies were performed to determine and identify the blood parasites infecting rodents.

    METHODS: A total of 40 rodent blood samples were analysed for blood parasite infection and a combined approach using polymerase chain reaction-based technique, and traditional microscopic examination (blood smear test) was conducted. 18s rRNA (Plasmodium spp.) and cytochrome b (Hepatocystis spp.) gene marker were used to identify the blood parasites.

    RESULTS: Note that 67.5% (n = 27) blood samples were tested negative for blood parasites, while 32.5% (n = 13) blood samples collected were infected with at least one protozoan parasite. Out of 13 samples, 69.2% (n = 9) were detected with Hepatocystis sp., while 15.4% (n = 2) were positive with Hepatozoon ophisauri. Two individuals had multiple infections from both species. No Plasmodium spp. have been detected throughout this study using universal primer (targeted Plasmodium spp.); however, different parasite species which were H. ophisauri were detected.

    CONCLUSION: Although there is no evidence of human infection from H. ophisauri and Hepatocystis sp. detected from the study, the data show the host species are heavily infected, and the information is essential for future prevention of zoonotic outbreaks and surveillance programmes. Therefore, it is suggested that the surveillance programmes should be incorporated in targeted areas with a high risk of disease emergence.

    Matched MeSH terms: RNA, Ribosomal, 18S
  12. Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh
    Terao M, Akter S, Yasin MG, Nakao R, Kato H, Alam MZ, et al.
    Infect Genet Evol, 2015 Apr;31:53-60.
    PMID: 25620376 DOI: 10.1016/j.meegid.2015.01.011
    Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  13. Isolation, screening, and identification of potential cellulolytic and xylanolytic producers for biodegradation of untreated oil palm trunk and its application in saccharification of lemongrass leaves
    Ang SK, Yahya A, Abd Aziz S, Md Salleh M
    Prep Biochem Biotechnol, 2015;45(3):279-305.
    PMID: 24960316 DOI: 10.1080/10826068.2014.923443
    This study presents the isolation and screening of fungi with excellent ability to degrade untreated oil palm trunk (OPT) in a solid-state fermentation system (SSF). Qualitative assay of cellulases and xylanase indicates notable secretion of both enzymes by 12 fungal strains from a laboratory collection and 5 strains isolated from a contaminated wooden board. High production of these enzymes was subsequently quantified in OPT in SSF. Aspergillus fumigates SK1 isolated from cow dung gives the highest xylanolytic activity (648.448 U g(-1)), generally high cellulolytic activities (CMCase: 48.006, FPase: 6.860, beta-glucosidase: 16.328 U g(-1)) and moderate lignin peroxidase activity (4.820 U/g), and highest xylanolytic activity. The xylanase encoding gene of Aspergillus fumigates SK1 was screened using polymerase chain reaction by a pair of degenerate primers. Through multiple alignment of the SK1 strain's xylanase nucleotide sequences with other published xylanases, it was confirmed that the gene belonged to the xylanase glycoside hydrolase family 11 (GH11) with a protein size of 24.49 kD. Saccharification of lemongrass leaves using crude cellulases and xylanase gives the maximum reducing sugars production of 6.84 g/L with glucose as the major end product and traces of phenylpropanic compounds (vanillic acid, p-coumaric acid, and ferulic acid).
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  14. Fulltext High proportion of knowlesi malaria in recent malaria cases in Malaysia
    Yusof R, Lau YL, Mahmud R, Fong MY, Jelip J, Ngian HU, et al.
    Malar J, 2014;13:168.
    PMID: 24886266 DOI: 10.1186/1475-2875-13-168
    Plasmodium knowlesi is a simian parasite that has been recognized as the fifth species causing human malaria. Naturally-acquired P. knowlesi infection is widespread among human populations in Southeast Asia. The aim of this epidemiological study was to determine the incidence and distribution of malaria parasites, with a particular focus on human P. knowlesi infection in Malaysia.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  15. Gold-nanoparticle based electrochemical DNA sensor for the detection of fish pathogen Aphanomyces invadans
    Kuan GC, Sheng LP, Rijiravanich P, Marimuthu K, Ravichandran M, Yin LS, et al.
    Talanta, 2013 Dec 15;117:312-7.
    PMID: 24209346 DOI: 10.1016/j.talanta.2013.09.016
    Epizootic ulcerative syndrome (EUS) is a devastating fish disease caused by the fungus, Aphanomyces invadans. Rapid diagnosis of EUS is needed to control and treat this highly invasive disease. The current diagnostic methods for EUS are labor intensive. We have developed a highly sensitive and specific electrochemical genosensor towards the 18S rRNA and internal transcribed spacer regions of A. invadans. Multiple layers of latex were synthesized with the help of polyelectrolytes, and labeled with gold nanoparticles to enhance sensitivity. The gold-latex spheres were functionalized with specific DNA probes. We describe here the novel application of this improved platform for detection of PCR product from real sample of A. invadans using a premix sandwich hybridization assay. The premix assay was easier, more specific and gave higher sensitivity of one log unit when compared to the conventional method of step-by-step hybridization. The limit of detection was 0.5 fM (4.99 zmol) of linear target DNA and 1 fM (10 amol) of PCR product. The binding positions of the probes to the PCR amplicons were optimized for efficient hybridization. Probes that hybridized close to the 5' or 3' terminus of the PCR amplicons gave the highest signal due to minimal steric hindrance for hybridization. The genosensor is highly suitable as a surveillance and diagnostic tool for EUS in the aquaculture industry.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics*
  16. Molecular identification of Aspergillus and Eurotium species isolated from rice and their toxin-producing ability
    Yazdani D, Zainal Abidin MA, Tan YH, Kamaruzaman S
    Mikrobiologiia, 2011 Sep-Oct;80(5):707-13.
    PMID: 22168015
    Thirty milled rice samples were collected from retailers in 4 provinces of Malaysia. These samples were evaluated for Aspergillus spp. infection by direct plating on malt extract salt agar (MESA). All Aspergillus holomorphs were isolated and identified using nucleotide sequences of ITS 1 and ITS 2 of rDNA. Five anamorphs (Aspergillus flavus, A. oryzae, A. tamarii, A. fumigatus and A. niger) and 5 teleomorphs (Eurotium rubrum, E. amstelodami, E. chevalieri, E. cristatum and E. tonophilum) were identified. The PCR-sequencing based technique for sequences of ITS 1 and ITS 2 is a fast technique for identification of Aspergillus and Eurotium species, although it doesn't work flawlessly for differentiation of Eurotium species. All Aspergillus and Eurotium isolates were screened for their ability to produce aflatoxin and ochratoxin A (OTA) by HPLC and TLC techniques. Only A. flavus isolate UPM 89 was able to produce aflatoxins B1 and B2.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  17. Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species
    Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T
    Cytogenet Genome Res, 2020;160(9):554-564.
    PMID: 33171461 DOI: 10.1159/000511119
    Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that Menolird18, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in Cucumis melo, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, Menolird18 was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of Menolird18 were found in centromeric and rDNA regions of mitotic chromosomes suggests that Menolird18 is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of Menolird18 in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (C. melo) and cucumber (C. sativus) genomes.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  18. Fulltext Myxozoan infections in fishes of the Tasik Kenyir Water Reservoir, Terengganu, Malaysia
    Székely C, Shaharom-Harrison F, Cech G, Ostoros G, Molnár K
    Dis Aquat Organ, 2009 Jan 28;83(1):37-48.
    PMID: 19301635 DOI: 10.3354/dao01991
    During a survey on fishes of the Tasik Kenyir Reservoir, Malaysia, 5 new Myxobolus spp. and 2 known Henneguya spp. were found. The specific locations for 2 Myxobolus spp. were the host's muscles, while 2 other Myxobolus spp. were found to develop in the host's kidney and gills, respectively. Of the species developing intracellularly in muscle cells, M. terengganuensis sp. nov. was described from Osteochilus hasselti and M. tasikkenyirensis sp. nov. from Osteochilus vittatus. M. csabai sp. nov. and M. osteochili sp. nov. were isolated from the kidney of Osteochilus hasselti, while M. dykovae sp. nov. was found in the gill lamellae of Barbonymus schwanenfeldii. Henneguya shaharini and Henneguya hemibagri plasmodia were found on the gills of Oxyeleotris marmoratus and Hemibagrus nemurus, respectively. Description of the new and known species was based on morphological characterization of spores, histological findings on locations of plasmodia and DNA sequence data.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  19. Hamatopeduncularia Yamaguti, 1953 (Monogenea: Ancylodiscoididae) from catfish off Peninsular Malaysia: Description of two new species and insights on the genus
    Soo OYM, Tan WB
    Parasitol Int, 2021 Apr;81:102282.
    PMID: 33444771 DOI: 10.1016/j.parint.2021.102282
    Hamatopeduncularia longiangusticirrata sp. nov. and H. petalumvaginata sp. nov. were collected from Arius maculatus and Nemapteryx caelata, respectively from Tanjung Karang, Peninsular Malaysia. Morphological and molecular investigations were carried out to ascertain the identity of the new species. The two new species differ from previously described Hamatopeduncularia species in the morphology of the male and female reproductive organs. Hamatopeduncularia longiangusticirrata sp. nov. possesses a long penis similar to H. elongata, H. longicopulatrix, H. brisbanensis, H. major and H. petalumvaginata sp. nov., but differs in having a thread-like tapering distal end and can be distinguished from H. brisbanensis and H. major in not having an accessory piece. Hamatopeduncularia longiangusticirrata sp. nov. is also unique in having an ornamented penis initial and a vaginal tube surrounded by fine hair-like structures. Hamatopeduncularia petalumvaginata sp. nov. possesses a simple penis without an accessory piece and a petaloid vaginal opening that resembles the arrangement of petals on a flower. Maximum likelihood trees were constructed from partial 28S and 18S rDNA sequences of the two new species and other ancylodiscoidids to reveal a strongly supported monophyletic branch consisting of the two new species for both markers. According to Lim's classification in 1996 of Hamatopeduncularia species penis type, H. petalumvaginata sp. nov. has been classified within the elegans-type and H. longiangusticirrata sp. nov. is proposed as the longiangusticirrata-type.
    Matched MeSH terms: RNA, Ribosomal, 18S/analysis
  20. Fulltext From 18S to 28S rRNA Gene: An Improved Targeted Sarcocystidae PCR Amplification, Species Identification with Long DNA Sequences
    Lee FCH, Muthu V
    Am J Trop Med Hyg, 2021 02 22;104(4):1388-1393.
    PMID: 33617472 DOI: 10.4269/ajtmh.20-0767
    Sarcocystosis outbreaks in Tioman and Pangkor islands of Malaysia between 2011 and 2014 have raised the need to improve Sarcocystis species detection from environmental samples. In-house works found that published primers amplifying the 18S rRNA gene of Sarcocystis either could not produce the target from environmental samples or produced Sarcocystis DNA sequence that was insufficient for species identification. Using the primer pair of 18S S5 F (published) and 28S R6 R (new), this study improved the PCR amplification of Sarcocystidae to overcome these two difficulties. The PCR product spanned from the 18S to 28S rRNA genes, providing more information for species identification. The long DNA sequence allowed comparison between the "Ident" and "Query Cover" sorting in GenBank identity matching. This revealed the ambiguity in identity matching caused by different lengths of reference DNA sequences, which is seldom discussed in the literature. Using the disparity index test, a measurement of homogeneity in nucleotide substitution pattern, it is shown that the internal transcribed spacer (ITS)1-5.8S-ITS2 and 28S genes are better than the 18S gene in indicating nucleotide variations, implying better potentials for species identification. The example given by the handful of Sarcocystidae long DNA sequences reported herein calls for the need to report DNA sequence from the 18S to the 28S rRNA genes for species identification, especially among emerging pathogens. DNA sequence reporting should include the hypervariable 5.8S and ITS2 regions where applicable, and not be limited to single gene, per the current general trend.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics*
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