Displaying publications 1761 - 1780 of 1878 in total

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  1. Morphological and molecular characterization, sexual reproduction, and pathogenicity of Setosphaeria rostrata isolates from rice leaf spot
    Kusai NA, Azmi MM, Zainudin NA, Yusof MT, Razak AA
    Mycologia, 2016 09;108(5):905-914.
    PMID: 27474518
    Setosphaeria rostrata, a common plant pathogen causing leaf spot disease, affects a wide range of plant species, mainly grasses. Fungi were isolated from brown spots on rice leaves throughout Peninsular Malaysia, and 45 isolates were identified as Setosphaeria rostrata The isolates were then characterized using morphological and molecular approaches. The mating type was determined using PCR amplification of the mating type alleles, and isolates of opposite mating types were crossed to examine sexual reproduction. Based on nuclear ribosomal DNA ITS1-5.8S-ITS2 region (ITS) and beta-tubulin (BT2) sequences, two phylogenetic trees were constructed using the maximum likelihood method; S. rostrata was clustered in one well-supported clade. Pathogenicity tests showed that S. rostrata isolates are pathogenic, suggesting that it is the cause of the symptoms. Mating-type analyses indicated that three isolates carried the MAT1-1 allele, and the other 42 isolates carried MAT1-2 After isolates with opposite mating types were crossed on Sach's medium and incubated for 3 wk, six crosses produced pseudothecia that contained eight mature ascospores, and 12 other crosses produced numerous pseudothecia with no ascospores. To our knowledge, this is the first report on S. rostrata isolated from leaf spots on rice.
    Matched MeSH terms: Phylogeny
  2. Fulltext Phosphorylated and Nonphosphorylated PfMAP2 Are Localized in the Nucleus, Dependent on the Stage of Plasmodium falciparum Asexual Maturation
    Dahalan FA, Sidek HM, Murtey MD, Embi MN, Ibrahim J, Fei Tieng L, et al.
    Biomed Res Int, 2016;2016:1645097.
    PMID: 27525262 DOI: 10.1155/2016/1645097
    Plasmodium falciparum mitogen-activated protein (MAP) kinases, a family of enzymes central to signal transduction processes including inflammatory responses, are a promising target for antimalarial drug development. Our study shows for the first time that the P. falciparum specific MAP kinase 2 (PfMAP2) is colocalized in the nucleus of all of the asexual erythrocytic stages of P. falciparum and is particularly elevated in its phosphorylated form. It was also discovered that PfMAP2 is expressed in its highest quantity during the early trophozoite (ring form) stage and significantly reduced in the mature trophozoite and schizont stages. Although the phosphorylated form of the kinase is always more prevalent, its ratio relative to the nonphosphorylated form remained constant irrespective of the parasites' developmental stage. We have also shown that the TSH motif specifically renders PfMAP2 genetically divergent from the other plasmodial MAP kinase activation sites using Neighbour Joining analysis. Furthermore, TSH motif-specific designed antibody is crucial in determining the location of the expression of the PfMAP2 protein. However, by using immunoelectron microscopy, PPfMAP2 were detected ubiquitously in the parasitized erythrocytes. In summary, PfMAP2 may play a far more important role than previously thought and is a worthy candidate for research as an antimalarial.
    Matched MeSH terms: Phylogeny
  3. Fulltext High diversity of picornaviruses in rats from different continents revealed by deep sequencing
    Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, et al.
    Emerg Microbes Infect, 2016 Aug 17;5(8):e90.
    PMID: 27530749 DOI: 10.1038/emi.2016.90
    Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
    Matched MeSH terms: Phylogeny
  4. In silico identification and validation of a novel hypothetical protein in Cryptosporidium hominis and virtual screening of inhibitors as therapeutics
    Shrivastava AK, Kumar S, Sahu PS, Mahapatra RK
    Parasitol Res, 2017 May;116(5):1533-1544.
    PMID: 28389892 DOI: 10.1007/s00436-017-5430-1
    Computational approaches to predict structure/function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are ineffective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical protein (TU502HP) in the C. hominis genome from the CryptoDB database. A three-dimensional model of the protein was generated using the Iterative Threading ASSEmbly Refinement server through an iterative threading method. Functional annotation and phylogenetic study of TU502HP protein revealed similarity with human transportin 3. The model is further subjected to a virtual screening study form the ZINC database compound library using the Dock Blaster server. A docking study through AutoDock software reported N-(3-chlorobenzyl)ethane-1,2-diamine as the best inhibitor in terms of docking score and binding energy. The reliability of the binding mode of the inhibitor is confirmed by a complex molecular dynamics simulation study using GROMACS software for 10 ns in the water environment. Furthermore, antigenic determinants of the protein were determined with the help of DNASTAR software. Our findings report a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for treatment and prophylaxis of cryptosporidiosis among humans and animals.
    Matched MeSH terms: Phylogeny
  5. Population dynamics, antibiotics resistance and biofilm formation of Aeromonas and Vibrio species isolated from aquatic sources in Northern Malaysia
    Odeyemi OA, Ahmad A
    Microb Pathog, 2017 Feb;103:178-185.
    PMID: 28062284 DOI: 10.1016/j.micpath.2017.01.007
    This study aimed to compare population dynamics, antibiotic resistance and biofilm formation of Aeromonas and Vibrio species from seawater and sediment collected from Northern Malaysia. Isolates with different colony morphology were characterized using both biochemical and molecular methods before testing for antibiotic resistance and biofilm formation. Results obtained from this study showed that in Kedah, the population of Aeromonas isolated from sediment was highest in Pantai Merdeka (8.22 log CFU/ml), Pulau Bunting recorded the highest population of Aeromonas from sediment (8.43 log CFU/g). It was observed that Vibrio species isolated from seawater and sediment were highest in Kuala Sanglang (9.21 log CFU/ml). In Kuala Perlis, the population of Aeromonas isolated from seawater was highest in Jeti (7.94 log CFU/ml). Highest population of Aeromonas from sediment was recorded in Kampong Tanah Baru (7.99 log CFU/g). It was observed that Vibrio species isolated from seawater was highest in Padang Benta (8.42 log CFU/g) while Jeti Kuala Perlis had highest population of Vibrio isolated from sediment. It was observed that location does not influence population of Aeromonas. The results of the independent t - test revealed that there was no significant relationship between location and population of Vibrio (df = 10, t = 1.144, p > 0.05). The occurrence of biofilm formation and prevalence of antibiotic resistant Aeromonas and Vibrio species in seawater and sediment pose danger to human and aquatic animals' health.
    Matched MeSH terms: Phylogeny
  6. Fulltext Antigenic Variation of East/Central/South African and Asian Chikungunya Virus Genotypes in Neutralization by Immune Sera
    Chua CL, Sam IC, Merits A, Chan YF
    PLoS Negl Trop Dis, 2016 08;10(8):e0004960.
    PMID: 27571254 DOI: 10.1371/journal.pntd.0004960
    BACKGROUND: Chikungunya virus (CHIKV) is a re-emerging mosquito-borne virus which causes epidemics of fever, severe joint pain and rash. Between 2005 and 2010, the East/Central/South African (ECSA) genotype was responsible for global explosive outbreaks across India, the Indian Ocean and Southeast Asia. From late 2013, Asian genotype CHIKV has caused outbreaks in the Americas. The characteristics of cross-antibody efficacy and epitopes are poorly understood.

    METHODOLOGY/PRINCIPAL FINDINGS: We characterized human immune sera collected during two independent outbreaks in Malaysia of the Asian genotype in 2006 and the ECSA genotype in 2008-2010. Neutralizing capacity was analyzed against representative clinical isolates as well as viruses rescued from infectious clones of ECSA and Asian CHIKV. Using whole virus antigen and recombinant E1 and E2 envelope glycoproteins, we further investigated antibody binding sites, epitopes, and antibody titers. Both ECSA and Asian sera demonstrated stronger neutralizing capacity against the ECSA genotype, which corresponded to strong epitope-antibody interaction. ECSA serum targeted conformational epitope sites in the E1-E2 glycoprotein, and E1-E211K, E2-I2T, E2-H5N, E2-G118S and E2-S194G are key amino acids that enhance cross-neutralizing efficacy. As for Asian serum, the antibodies targeting E2 glycoprotein correlated with neutralizing efficacy, and I2T, H5N, G118S and S194G altered and improved the neutralization profile. Rabbit polyclonal antibody against the N-terminal linear neutralizing epitope from the ECSA sequence has reduced binding capacity and neutralization efficacy against Asian CHIKV. These findings imply that the choice of vaccine strain may impact cross-protection against different genotypes.

    CONCLUSION/SIGNIFICANCE: Immune serum from humans infected with CHIKV of either ECSA or Asian genotypes showed differences in binding and neutralization characteristics. These findings have implications for the continued outbreaks of co-circulating CHIKV genotypes and effective design of vaccines and diagnostic serological assays.

    Matched MeSH terms: Phylogeny
  7. The genetic characteristics and evolution of Tembusu virus
    Lei W, Guo X, Fu S, Feng Y, Tao X, Gao X, et al.
    Vet Microbiol, 2017 Mar;201:32-41.
    PMID: 28284620 DOI: 10.1016/j.vetmic.2017.01.003
    BACKGROUND: Since the turn of the 21st century, there have been several epidemic outbreaks of poultry diseases caused by Tembusu virus (TMUV). Although multiple mosquito and poultry-derived strains of TMUV have been isolated, no data exist about their comparative study, origin, evolution, and dissemination.

    METHODOLOGY: Parallel virology was used to investigate the phenotypes of duck and mosquito-derived isolates of TMUV. Molecular biology and bioinformatics methods were employed to investigate the genetic characteristics and evolution of TMUV.

    PRINCIPAL FINDINGS: The plaque diameter of duck-derived isolates of TMUV was larger than that of mosquito-derived isolates. The cytopathic effect (CPE) in mammalian cells occurred more rapidly induced by duck-derived isolates than by mosquito-derived isolates. Furthermore, duck-derived isolates required less time to reach maximum titer, and exhibited higher viral titer. These findings suggested that poultry-derived TMUV isolates were more invasive and had greater expansion capability than the mosquito-derived isolates in mammalian cells. Variations in amino acid loci in TMUV E gene sequence revealed two mutated amino acid loci in strains isolated from Malaysia, Thailand, and Chinese mainland compared with the prototypical strain of the virus (MM1775). Furthermore, TMUV isolates from the Chinese mainland had six common variations in the E gene loci that differed from the Southeast Asian strains. Phylogenetic analysis indicated that TMUV did not exhibit a species barrier in avian species and consisted of two lineages: the Southeast Asian and the Chinese mainland lineages. Molecular traceability studies revealed that the recent common evolutionary ancestor of TMUV might have appeared before 1934 and that Malaysia, Thailand and Shandong Province of China represent the three main sources related to TMUV spread.

    CONCLUSIONS: The current broad distribution of TMUV strains in Southeast Asia and Chinese mainland exhibited longer-range diffusion and larger-scale propagation. Therefore, in addition to China, other Asian and European countries linked to Asia have used improved measures to detect and monitor TMUV related diseases to prevent epidemics in poultry.

    Matched MeSH terms: Phylogeny
  8. Fulltext Evolutionary study of Yersinia genomes deciphers emergence of human pathogenic species
    Tan SY, Tan IK, Tan MF, Dutta A, Choo SW
    Sci Rep, 2016 10 31;6:36116.
    PMID: 27796355 DOI: 10.1038/srep36116
    On record, there are 17 species in the Yersinia genus, of which three are known to be pathogenic to human. While the chromosomal and pYV (or pCD1) plasmid-borne virulence genes as well as pathogenesis of these three species are well studied, their genomic evolution is poorly understood. Our study aims to predict the key evolutionary events that led to the emergence of pathogenic Yersinia species by analyzing gene gain-and-loss, virulence genes, and "Clustered regularly-interspaced short palindromic repeats". Our results suggest that the most recent ancestor shared by the human pathogenic Yersinia was most probably an environmental species that had adapted to the human body. This might have led to ecological specialization that diverged Yersinia into ecotypes and distinct lineages based on differential gene gain-and-loss in different niches. Our data also suggest that Y. pseudotuberculosis group might be the donor of the ail virulence gene to Y. enterocolitica. Hence, we postulate that evolution of human pathogenic Yersinia might not be totally in parallel, but instead, there were lateral gene transfer events. Furthermore, the presence of virulence genes seems to be important for the positive selection of virulence plasmid. Our studies provide better insights into the evolutionary biology of these bacteria.
    Matched MeSH terms: Phylogeny
  9. Fulltext Clinical manifestations of dengue in relation to dengue serotype and genotype in Malaysia: A retrospective observational study
    Suppiah J, Ching SM, Amin-Nordin S, Mat-Nor LA, Ahmad-Najimudin NA, Low GK, et al.
    PLoS Negl Trop Dis, 2018 09;12(9):e0006817.
    PMID: 30226880 DOI: 10.1371/journal.pntd.0006817
    BACKGROUND: Malaysia experienced an unprecedented dengue outbreak from the year 2014 to 2016 that resulted in an enormous increase in the number of cases and mortality as compared to previous years. The causes that attribute to a dengue outbreak can be multifactorial. Viral factors, such as dengue serotype and genotype, are the components of interest in this study. Although only a small number of studies investigated the association between the serotype of dengue virus and clinical manifestations, none of these studies included analyses on dengue genotypes. The present study aims to investigate dengue serotype and genotype-specific clinical characteristics among dengue fever and severe dengue cases from two Malaysian tertiary hospitals between 2014 and mid-2017.

    METHODOLOGY AND PRINCIPAL FINDINGS: A total of 120 retrospective dengue serum specimens were subjected to serotyping and genotyping by Taqman Real-Time RT-PCR, sequencing and phylogenetic analysis. Subsequently, the dengue serotype and genotype data were statistically analyzed for 101 of 120 corresponding patients' clinical manifestations to generate a descriptive relation between the genetic components and clinical outcomes of dengue infected patients. During the study period, predominant dengue serotype and genotype were found to be DENV 1 genotype I. Additionally, non-severe clinical manifestations were commonly observed in patients infected with DENV 1 and DENV 3. Meanwhile, patients with DENV 2 infection showed significant warning signs and developed severe dengue (p = 0.007). Cases infected with DENV 2 were also commonly presented with persistent vomiting (p = 0.010), epigastric pain (p = 0.018), plasma leakage (p = 0.004) and shock (p = 0.038). Moreover, myalgia and arthralgia were highly prevalent among DENV 3 infection (p = 0.015; p = 0.014). The comparison of genotype-specific clinical manifestations showed that DENV 2 Cosmopolitan was significantly common among severe dengue patients. An association was also found between genotype I of DENV 3 and myalgia. In a similar vein, genotype III of DENV 3 was significantly common among patients with arthralgia.

    CONCLUSION: The current data contended that different dengue serotype and genotype had caused distinct clinical characteristics in infected patients.

    Matched MeSH terms: Phylogeny
  10. Fulltext Hexon and fiber gene changes in an attenuated fowl adenovirus isolate from Malaysia in embryonated chicken eggs and its infectivity in chickens
    Sohaimi NM, Bejo MH, Omar AR, Ideris A, Isa NM
    J Vet Sci, 2018 Nov 30;19(6):759-770.
    PMID: 30173491 DOI: 10.4142/jvs.2018.19.6.759
    Fowl adenovirus (FAdV) is distributed worldwide and causes economic losses in the poultry industry. The objectives of this study were to determine the hexon and fiber gene changes in an attenuated FAdV isolate from Malaysia in specific pathogen-free chicken embryonated eggs (SPF CEE) and its infectivity in commercial broiler chickens. SPF CEE were inoculated with 0.1 mL FAdV inoculum via the chorioallantoic membrane (CAM) for 20 consecutive passages. The isolate at passage 20 (E20), with a virus titer of 108.7TCID50/mL (TCID50, 50% tissue culture infective dose), was inoculated (0.5 mL) into one-day-old commercial broiler chicks either via oral or intraperitoneal routes. The study demonstrated that 100% embryonic mortality was recorded from E2 to E20 with a delayed pattern at E17 onwards. The lesions were confined to the liver and CAM. Substitutions of amino acids in the L1 loop of hexon at positions 49 and 66, and in the knob of fiber at positions 318 and 322 were recorded in the E20 isolate. The isolate belongs to serotype 8b and is non-pathogenic to broiler chickens, but it is able to induce a FAdV antibody titer. It appears that molecular changes in the L1 loop of hexon and the knob of fiber are markers for FAdV infectivity.
    Matched MeSH terms: Phylogeny
  11. CTP synthase knockdown during early development distorts the nascent vertebral column and causes fluid retention in multiple tissues in zebrafish
    Dzaki N, Wahab W, Azlan A, Azzam G
    Biochem Biophys Res Commun, 2018 10 20;505(1):106-112.
    PMID: 30241946 DOI: 10.1016/j.bbrc.2018.09.074
    CTP Synthase (CTPS) is a metabolic enzyme that is recognized as a catalyst for nucleotide, phospholipid and sialoglycoprotein production. Though the structural characteristics and regulatory mechanisms of CTPS are well-understood, little is known regarding the extent of its involvement during the early developmental stages of vertebrates. Zebrafish carries two CTPS genes, annotated as ctps1a and ctps1b. Phylogenetic analyses show that both genes had diverged from homologues in the ancestral Actinopterygii, Oreochromis niloticus. Conservation of common CTPS-catalytic regions further establishes that both proteins are likely to be functionally similar to hsaCTPS. Here, we show that ctps1a is more critical throughout the initial period of embryonic development than ctps1b. The effects of concurrent partial knockdown are dependent on ctps1a vs ctps1b dosage ratios. When these are equally attenuated, abnormal phenotypes acquired prior to the pharyngula period disappear in hatchlings (48hpf); however, if either gene is more attenuated than the other, these only become more pronounced in advanced stages. Generally, disruption to normal ctps1a or ctps1b expression levels by morpholinos culminates in the distortion of the early spinal column as well as multiple-tissue oedema. Other effects include slower growth rates, increased mortality rates and impaired structural formation of the young fish's extremities. Embryos grown in DON, a glutamine-analogue drug and CTPS antagonist, also exhibit similar characteristics, thus strengthening the validity of the morpholino-induced phenotypes observed. Together, our results demonstrate the importance of CTPS for the development of zebrafish embryos, as well as a disparity in activity and overall importance amongst isozymes.
    Matched MeSH terms: Phylogeny
  12. Fulltext Henneguya (Cnidaria: Myxosporea: Myxobolidae) infections of cultured barramundi, Lates calcarifer (Perciformes: Latidae) in an estuarine wetlands system of Malaysia: description of Henneguya setiuensis n. sp., Henneguya voronini n. sp. and Henneguya calcarifer n. sp
    Borkhanuddin MH, Cech G, Molnár K, Shaharom-Harrison F, Khoa TND, Samshuri MA, et al.
    Parasitol Res, 2020 Jan;119(1):85-96.
    PMID: 31768684 DOI: 10.1007/s00436-019-06541-1
    Examination of 35 barramundi (Lates calcarifer) from aquaculture cages in Setiu Wetland, Malaysia, revealed a single fish infected with three Henneguya spp. (Cnidaria: Myxosporea). Characterization of the infections using tissue tropism, myxospore morphology and morphometry and 18S rDNA sequencing supported description of three new species: Henneguya setiuensis n. sp., Henneguya voronini n. sp. and H. calcarifer n. sp. Myxospores of all three species had typical Henneguya morphology, with two polar capsules in the plane of the suture, an oval spore body, smooth valve cell surfaces, and two caudal appendages. Spores were morphometrically similar, and many dimensions overlapped, but H. voronini n. sp. had shorter caudal appendages compared with H. calcarifer n. sp. and H. setiuensis n. sp. Gross tissue tropism distinguished the muscle parasite H. calcarifer n. sp. from gill parasites H. setiuensis n. sp. and H. voronini n. sp.; and these latter two species were further separable by fine-scale location of developing plasmodia, which were intra-lamellar for H. setiuensis n. sp. and basal to the filaments for H. voronini n. sp. small subunit ribosomal DNA sequences distinguished all three species: the two gill species H. setiuensis n. sp. and H voronini n. sp. were only 88% similar (over 1708 bp), whereas the muscle species H. calcarifer n. sp. was most similar to H. voronini n. sp. (98% over 1696 bp). None of the three novel species was more than 90% similar to any known myxosporean sequence in GenBank. Low infection prevalence of these myxosporeans and lack of obvious tissue pathology from developing plasmodia suggested none of these parasites are currently a problem for barramundi culture in Setiu Wetland; however additional surveys of fish, particularly at different times of the year, would be informative for better risk assessment.
    Matched MeSH terms: Phylogeny
  13. Fulltext PreS1 Mutations Alter the Large HBsAg Antigenicity of a Hepatitis B Virus Strain Isolated in Bangladesh
    Hossain MG, Mahmud MM, Nazir KHMNH, Ueda K
    Int J Mol Sci, 2020 Jan 15;21(2).
    PMID: 31952213 DOI: 10.3390/ijms21020546
    Mutations in the hepatitis B virus (HBV) genome can potentially lead to vaccination failure, diagnostic escape, and disease progression. However, there are no reports on viral gene expression and large hepatitis B surface antigen (HBsAg) antigenicity alterations due to mutations in HBV isolated from a Bangladeshi population. Here, we sequenced the full genome of the HBV isolated from a clinically infected patient in Bangladesh. The open reading frames (ORFs) (P, S, C, and X) of the isolated HBV strain were successfully amplified and cloned into a mammalian expression vector. The HBV isolate was identified as genotype C (sub-genotype C2), serotype adr, and evolutionarily related to strains isolated in Indonesia, Malaysia, and China. Clinically significant mutations, such as preS1 C2964A, reverse transcriptase domain I91L, and small HBsAg N3S, were identified. The viral P, S, C, and X genes were expressed in HEK-293T and HepG2 cells by transient transfection with a native subcellular distribution pattern analyzed by immunofluorescence assay. Western blotting of large HBsAg using preS1 antibody showed no staining, and preS1 ELISA showed a significant reduction in reactivity due to amino acid mutations. This mutated preS1 sequence has been identified in several Asian countries. To our knowledge, this is the first report investigating changes in large HBsAg antigenicity due to preS1 mutations.
    Matched MeSH terms: Phylogeny
  14. Fulltext Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential
    Law JW, Ser HL, Ab Mutalib NS, Saokaew S, Duangjai A, Khan TM, et al.
    Sci Rep, 2019 02 28;9(1):3056.
    PMID: 30816228 DOI: 10.1038/s41598-019-39592-6
    A new Streptomyces species discovered from Sarawak mangrove soil is described, with the proposed name - Streptomyces monashensis sp. nov. (strain MUSC 1JT). Taxonomy status of MUSC 1JT was determined via polyphasic approach. Phylogenetic and chemotaxonomic properties of strain MUSC 1JT were in accordance with those known for genus Streptomyces. Based on phylogenetic analyses, the strains closely related to MUSC 1JT were Streptomyces corchorusii DSM 40340T (98.7%), Streptomyces olivaceoviridis NBRC 13066T (98.7%), Streptomyces canarius NBRC 13431T (98.6%) and Streptomyces coacervatus AS-0823T (98.4%). Outcomes of DNA-DNA relatedness between strain MUSC 1JT and its closely related type strains covered from 19.7 ± 2.8% to 49.1 ± 4.3%. Strain MUSC 1JT has genome size of 10,254,857 bp with DNA G + C content of 71 mol%. MUSC 1JT extract exhibited strong antioxidative activity up to 83.80 ± 4.80% in the SOD assay, with significant cytotoxic effect against colon cancer cell lines HCT-116 and SW480. Streptomyces monashensis MUSC 1JT (=DSM 103626T = MCCC 1K03221T) could potentially be a producer of novel bioactive metabolites; hence discovery of this new species may be highly significant to the biopharmaceutical industry as it could lead to development of new and useful chemo-preventive drugs.
    Matched MeSH terms: Phylogeny
  15. Leuconostoc durionis sp. nov., a heterofermenter with no detectable gas production from glucose
    Leisner JJ, Vancanneyt M, Van der Meulen R, Lefebvre K, Engelbeen K, Hoste B, et al.
    Int J Syst Evol Microbiol, 2005 May;55(Pt 3):1267-1270.
    PMID: 15879266 DOI: 10.1099/ijs.0.63434-0
    Three lactic acid bacterial (LAB) strains obtained from a Malaysian acid-fermented condiment, tempoyak (made from pulp of the durian fruit), showed analogous but distinct patterns after screening by SDS-PAGE of whole-cell proteins and comparison with profiles of all recognized LAB species. 16S rRNA gene sequencing of one representative strain showed that the taxon belongs phylogenetically to the genus Leuconostoc, with its nearest neighbour being Leuconostoc fructosum (98 % sequence similarity). Biochemical characteristics and DNA-DNA hybridization experiments demonstrated that the strains differ from Leuconostoc fructosum and represent a single, novel Leuconostoc species for which the name Leuconostoc durionis sp. nov. is proposed. The type strain is LMG 22556(T) (= LAB 1679(T) = D-24(T) = CCUG 49949(T)).
    Matched MeSH terms: Phylogeny
  16. Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine
    Carlsohn MR, Groth I, Tan GYA, Schütze B, Saluz HP, Munder T, et al.
    Int J Syst Evol Microbiol, 2007 Jul;57(Pt 7):1640-1646.
    PMID: 17625209 DOI: 10.1099/ijs.0.64903-0
    Three actinomycetes isolated from the surfaces of rocks in a medieval slate mine were examined in a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics of the isolates were typical of strains of the genus Amycolatopsis. The isolates had identical 16S rRNA gene sequences and formed a distinct phyletic line towards the periphery of the Amycolatopsis mediterranei clade, being most closely related to Amycolatopsis rifamycinica. The organisms shared a wide range of genotypic and phenotypic markers that distinguished them from their closest phylogenetic neighbours. On the basis of these results, a novel species, Amycolatopsis saalfeldensis sp. nov., is proposed. The type strain is HKI 0457(T) (=DSM 44993(T)=NRRL B-24474(T)).
    Matched MeSH terms: Phylogeny
  17. Fulltext Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia  during 2018-2019
    Amit LN, Mori D, John JL, Chin AZ, Mosiun AK, Jeffree MS, et al.
    PLoS One, 2021;16(7):e0254784.
    PMID: 34320003 DOI: 10.1371/journal.pone.0254784
    Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.
    Matched MeSH terms: Phylogeny
  18. Fulltext Differential prevalence of Plasmodium infections and cryptic Plasmodium knowlesi malaria in humans in Thailand
    Putaporntip C, Hongsrimuang T, Seethamchai S, Kobasa T, Limkittikul K, Cui L, et al.
    J Infect Dis, 2009 Apr 15;199(8):1143-50.
    PMID: 19284284 DOI: 10.1086/597414
    BACKGROUND: A case of human infection with Plasmodium knowlesi has been recently discovered in Thailand. To investigate the prevalence of this malaria species, a molecular-based survey was performed.

    METHODS: Blood samples from 1874 patients were tested for Plasmodium species by microscopy and nested polymerase chain reaction. P. knowlesi was characterized by sequencing the merozoite surface protein 1 gene (msp-1).

    RESULTS: Of all Plasmodium species identified, P. falciparum, P. vivax, P. malariae, P. ovale, and P. knowlesi contributed 43.52%, 68.08%, 1.37%, 1.03%, and 0.57%, respectively. Mixed-species infections were more common in northwestern and southwestern regions bordering Myanmar (23%-24%) than in eastern and southern areas (3%-5%). In northwestern and southwestern regions, mixed-species infections had a significantly higher prevalence in dry than in rainy seasons (P < .001). P. knowlesi was found in 10 patients, mostly from southern and southwestern areas-9 were coinfected with either P. falciparum or P. vivax. Most of the P. knowlesi Thai isolates were more closely related to isolates from macaques than to isolates from Sarawak patients. The msp-1 sequences of isolates from the same area of endemicity differed and possessed novel sequences, indicating genetic polymorphism in P. knowlesi infecting humans.

    CONCLUSIONS: This survey highlights the widespread distribution of P. knowlesi in Thailand, albeit at low prevalence and mostly occurring as cryptic infections.

    Matched MeSH terms: Phylogeny
  19. The draft genome of tropical fruit durian (Durio zibethinus)
    Teh BT, Lim K, Yong CH, Ng CCY, Rao SR, Rajasegaran V, et al.
    Nat Genet, 2017 Nov;49(11):1633-1641.
    PMID: 28991254 DOI: 10.1038/ng.3972
    Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced. Single-molecule sequencing and chromosome contact maps enabled assembly of the highly heterozygous durian genome at chromosome-scale resolution. Transcriptomic analysis showed upregulation of sulfur-, ethylene-, and lipid-related pathways in durian fruits. We observed paleopolyploidization events shared by durian and cotton and durian-specific gene expansions in MGL (methionine γ-lyase), associated with production of volatile sulfur compounds (VSCs). MGL and the ethylene-related gene ACS (aminocyclopropane-1-carboxylic acid synthase) were upregulated in fruits concomitantly with their downstream metabolites (VSCs and ethylene), suggesting a potential association between ethylene biosynthesis and methionine regeneration via the Yang cycle. The durian genome provides a resource for tropical fruit biology and agronomy.
    Matched MeSH terms: Phylogeny
  20. Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing
    Suhaimi NSM, Goh SY, Ajam N, Othman RY, Chan KG, Thong KL
    World J Microbiol Biotechnol, 2017 Aug 21;33(9):168.
    PMID: 28828756 DOI: 10.1007/s11274-017-2336-0
    Banana is one of the most important fruits cultivated in Malaysia, and it provides many health benefits. However, bacterial wilt disease, which attacks bananas, inflicts major losses on the banana industry in Malaysia. To understand the complex interactions of the microbiota of bacterial wilt-diseased banana plants, we first determined the bacterial communities residing in the pseudostems of infected (symptomatic) and diseased-free (non-symptomatic) banana plants. We characterized the associated microorganisms using the targeted 16S rRNA metagenomics sequencing on the Illumina MiSeq platform. Taxonomic classifications revealed 17 and nine known bacterial phyla in the tissues of non-symptomatic and symptomatic plants, respectively. Cyanobacteria and Proteobacteria (accounted for more than 99% of the 16S rRNA gene fragments) were the two most abundant phyla in both plants. The five major genera found in both plant samples were Ralstonia, Sphingomonas, Methylobacterium, Flavobacterium, and Pseudomonas. Ralstonia was more abundant in symptomatic plant (59% out of the entire genera) as compared to those in the non-symptomatic plant (only 36%). Our data revealed that 102 bacterial genera were only assigned to the non-symptomatic plant. Overall, this study indicated that more diverse and abundant microbiota were associated with the non-symptomatic bacterial wilt-diseased banana plant as compared to the symptomatic plant. The higher diversity of endophytic microbiota in the non-symptomatic banana plant could be an indication of pathogen suppression which delayed or prevented the disease expression. This comparative study of the microbiota in the two plant conditions might provide caveats for potential biological control strategies.
    Matched MeSH terms: Phylogeny
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