Displaying publications 901 - 920 of 1878 in total

Abstract:
Sort:
  1. Fulltext Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia
    Lee LH, Zainal N, Azman AS, Eng SK, Goh BH, Yin WF, et al.
    ScientificWorldJournal, 2014;2014:698178.
    PMID: 25162061 DOI: 10.1155/2014/698178
    The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.
    Matched MeSH terms: Phylogeny
  2. Fulltext Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates
    Hron T, Fábryová H, Pačes J, Elleder D
    Retrovirology, 2014;11:84.
    PMID: 25280529 DOI: 10.1186/s12977-014-0084-x
    A significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes.
    Matched MeSH terms: Phylogeny
  3. The genus Hormiops Fage, 1933 (Hormuridae, Scorpiones), a palaeoendemic of the South China Sea: systematics and biogeography
    Monod L
    C. R. Biol., 2014 Oct;337(10):596-608.
    PMID: 25282174 DOI: 10.1016/j.crvi.2014.07.009
    The monotypic genus Hormiops Fage, 1933 is so far only known from two groups of granitic islands off the coasts of Peninsular Malaysia and Vietnam. Examination of newly collected material from both archipelagos and of the type series of Hormiops davidovi Fage, 1933 reveals previously disregarded morphological differences sufficient to assign the Malaysian specimens to a distinct species, described here as Hormiops infulcra sp. nov. An updated diagnosis of the genus, as well as a dichotomic key enabling the determination of Hormiops from its close relatives, Hormurus Thorell, 1876 and Liocheles Sundevall, 1833 are also provided. The phylogenetic position, distribution pattern, and ecology of these insular scorpions suggest that they are palaeoendemics, remnants of a previously more widely distributed lineage. A biogeographical model is proposed for the genus based on these observations and on a synthesis of palaeogeographical and palaeoenvironmental data currently available for Sundaland.
    Matched MeSH terms: Phylogeny
  4. Beyond Moa's Ark and Wallace's Line: extralimital distribution of new species of Austronothrus (Acari, Oribatida, Crotoniidae) and the endemicity of the New Zealand oribatid mite fauna
    Colloff MJ, Cameron SL
    Zootaxa, 2014;3780:263-81.
    PMID: 24871836 DOI: 10.11646/zootaxa.3780.2.3
    The genus Austronothrus was previously known from three species recorded only from New Zealand. Austronothrus kinabalu sp. nov. is described from Sabah, Borneo and A. rostralis sp. nov. from Norfolk Island, south-west Pacific. A key to Austronothrus is included. These new species extend the distribution of Austronothrus beyond New Zealand and confirms that the subfamily Crotoniinae is not confined to former Gondwanan landmasses. The distribution pattern of Austronothrus spp., combining Oriental and Gondwanan localities, is indicative of a curved, linear track; consistent with the accretion of island arcs and volcanic terranes around the plate margins of the Pacific Ocean, with older taxa persisting on younger island though localised dispersal within island arc metapopulations. Phylogenetic analysis and an area cladogram are consistent with a broad ancestral distribution of Austronothrus in the Oriental region and on Gondwanan terranes, with subsequent divergence and distribution southward from the Sunda region to New Zealand. This pattern is more complex than might be expected if the New Zealand oribatid fauna was derived from dispersal following re-emergence of land after inundation during the Oligocene (25 mya), as well as if the fauna emanated from endemic, relictual taxa following separation of New Zealand from Gondwana during the Cretaceous (80 mya).
    Matched MeSH terms: Phylogeny
  5. The genus Cerithideopsis Thiele, 1929 (Gastropoda: Potamididae) in the Indo-West Pacific region
    Reid DG, Claremont M
    Zootaxa, 2014;3779:61-80.
    PMID: 24871714 DOI: 10.11646/zootaxa.3779.1.8
    The genus Cerithideopsis is most common in mangrove and salt marsh habitats of the New World tropics, but there is also a small radiation in the Indo-West Pacific region. Previously, these Indo-Pacific snails have generally been classified as Cerithidea largillierti (Philippi, 1848). Molecular phylogenetic analysis (partial sequences of mitochondrial COI and 16S rRNA, and nuclear 28S rRNA) of 15 specimens from 8 localities between Japan and Australia reveal three clades, among which there are small morphological differences and which show allopatric distributions. Cerithideopsis largillierti sensu stricto is restricted to Japan and China, while the two other species are described as new: C. australiensis occurs in tropical Australasia and C. malayensis is found from Malaysia to Java and the Philippines. All occur on mud and in pools with leaf litter, in the shaded landward and middle zones of mangrove forests, and do not climb the trees. The species accounts include full synonymies, detailed descriptions of shells based on 82 museum samples, descriptions of living animals, distribution records and maps, and notes on habitat and conservation status.
    Matched MeSH terms: Phylogeny
  6. Fulltext Phenotypic and molecular characterization of Colletotrichum species associated with anthracnose of banana (Musa spp) in Malaysia
    Intan Sakinah MA, Suzianti IV, Latiffah Z
    Genet. Mol. Res., 2014;13(2):3627-37.
    PMID: 24854442 DOI: 10.4238/2014.May.9.5
    Anthracnose caused by Colletotrichum species is a common postharvest disease of banana fruit. We investigated and identified Colletotrichum species associated with anthracnose in several local banana cultivars based on morphological characteristics and sequencing of ITS regions and of the β-tubulin gene. Thirty-eight Colletotrichum isolates were encountered in anthracnose lesions of five local banana cultivars, 'berangan', 'mas', 'awak', 'rastali', and 'nangka'. Based on morphological characteristics, 32 isolates were identified as Colletotrichum gloeosporioides and 6 isolates as C. musae. C. gloeosporioides isolates were divided into two morphotypes, with differences in colony color, shape of the conidia and growth rate. Based on ITS regions and β-tubulin sequences, 35 of the isolates were identified as C. gloeosporioides and only 3 isolates as C. musae; the percentage of similarity from BLAST ranged from 95-100% for ITS regions and 97-100% for β-tubulin. C. gloeosporioides isolates were more prevalent compared to C. musae. This is the first record of C. gloeosporioides associated with banana anthracnose in Malaysia. In a phylogenetic analysis of the combined dataset of ITS regions and β-tubulin using a maximum likelihood method, C. gloeosporioides and C. musae isolates were clearly separated into two groups. We concluded that C. gloeosporioides and C. musae isolates are associated with anthracnose in the local banana cultivars and that C. gloeosporioides is more prevalent than C. musae.
    Matched MeSH terms: Phylogeny
  7. A new species of karst forest-adapted Bent-toed Gecko (genus Cyrtodactylus Gray, 1827) belonging to the C. sworderi complex from a threatened karst forest in Perak, Peninsular Malaysia
    Grismer LL, Belabut DM, Quah ES, Onn CK, Wood PL
    Zootaxa, 2014;3755:434-46.
    PMID: 24869831 DOI: 10.11646/zootaxa.3755.5.3
    A new species of Bent-toed Gecko Cyrtodactylus guakanthanensis sp. nov. of the C. sworderi complex is described from a limestone forest in Perak, Peninsular Malaysia whose karst formations at the type locality are within an active quarry. Cyrtodactylus guakanthanensis sp. nov. can be distinguished from all other Sundaland species by having the following suite of character states: adult SVL 77.7-82.2 mm; moderately sized, conical, weakly keeled, body tubercles; tubercles present on occiput, nape, and limbs, and extend posteriorly beyond base of tail; 37-44 ventral scales; no transversely enlarged, median, subcaudal scales; proximal subdigital lamellae transversely expanded; 19-21 subdigital lamellae on fourth toe; abrupt transition between posterior and ventral femoral scales; enlarged femoral scales; no femoral or precloacal pores; precloacal groove absent; wide, dark postorbital stripes from each eye extending posteriorly to the anterior margin of the shoulder region thence forming a transverse band across the anterior margin of the shoulder region; and body bearing five (rarely four) wide, bold, dark bands. Destruction of the karst microhabitat and surrounding limestone forest will extirpate this new species from the type locality and perhaps drive it to complete extinction given that it appears to be restricted to the particular microhabitat structure of the type locality and is not widely distributed throughout the karst formations. As with plants and invertebrates, limestone forests are proving to be significant areas of high herpetological endemism and should be afforded special conservation status rather than turned into cement.
    Matched MeSH terms: Phylogeny
  8. Fulltext Rhodotorula mucilaginosa, a quorum quenching yeast exhibiting lactonase activity isolated from a tropical shoreline
    Ghani NA, Sulaiman J, Ismail Z, Chan XY, Yin WF, Chan KG
    Sensors (Basel), 2014;14(4):6463-73.
    PMID: 24721765 DOI: 10.3390/s140406463
    Two microbial isolates from a Malaysian shoreline were found to be capable of degrading N-acylhomoserine lactones. Both Matrix Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometry and 18S rDNA phylogenetic analyses confirmed that these isolates are Rhodotorula mucilaginosa. Quorum quenching activities were detected by a series of bioassays and rapid resolution liquid chromatography analysis. The isolates were able to degrade various quorum sensing molecules namely N-hexanoyl-L-homoserine lactone (C6-HSL), N-(3-oxo-hexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) and N-(3-hydroxyhexanoyl)-L-homoserine lactone (3-hydroxy-C6-HSL). Using a relactonisation assay to verify the quorum quenching mechanism, it is confirmed that Rh. mucilaginosa degrades the quorum sensing molecules via lactonase activity. To the best of our knowledge, this is the first documentation of the fact that Rh. mucilaginosa has activity against a broad range of AHLs namely C6-HSL, 3-oxo-C6-HSL and 3-hydroxy-C6-HSL.
    Matched MeSH terms: Phylogeny
  9. Growth kinetics of a diesel-degrading bacterial strain from petroleum-contaminated soil
    Dahalan SF, Yunus I, Johari WL, Shukor MY, Halmi MI, Shamaan NA, et al.
    J Environ Biol, 2014 Mar;35(2):399-406.
    PMID: 24665769
    A diesel-degrading bacterium was isolated from a diesel-contaminated site in Selangor, Malaysia. The isolate was tentatively identified as Acinetobacter sp. strain DRY12 based on partial 16S rDNA molecular phylogeny and Biolog GN microplate panels and Microlog database. Optimum growth occurred from 3 to 5% diesel and the strain was able to tolerate as high as 8% diesel. The optimal pH that supported growth of the bacterium was between pH 7.5 to 8.0. The isolate exhibited optimal growth in between 30 and 35 degrees C. The best nitrogen source was potassium nitrate (between 0.6 and 0.9% (w/v)) followed by ammonium chloride, sodium nitrite and ammonium sulphate in descending order. An almost complete removal of diesel components was seen from the reduction in hydrocarbon peaks observed using Solid Phase Microextraction Gas Chromatography analysis after 10 days of incubation. The best growth kinetic model to fit experimental data was the Haldane model of substrate inhibiting growth with a correlation coefficient value of 0.97. The maximum growth rate- micromax was 0.039 hr(-1) while the saturation constant or half velocity constant Ks and inhibition constant Ki, were 0.387% and 4.46%, respectively. MATH assays showed that 75% of the bacterium was found in the hexadecane phase indicating that the bacterium was hydrophobic. The characteristics of this bacterium make it useful for bioremediation works in the Tropics.
    Matched MeSH terms: Phylogeny
  10. Fulltext Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean
    Nguyen VX, Detcharoen M, Tuntiprapas P, Soe-Htun U, Sidik JB, Harah MZ, et al.
    BMC Evol. Biol., 2014 Apr 30;14:92.
    PMID: 24886000 DOI: 10.1186/1471-2148-14-92
    BACKGROUND: The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions.

    RESULTS: Phylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all samples collected from both sides of the Thai-Malay peninsula were clustered into two clades: Gulf of Thailand and Andaman Sea.

    CONCLUSIONS: Our study documented the new records of H. major for Malaysia and Myanmar. The study also revealed that the Thai-Malay peninsula is a geographic barrier between H. ovalis populations in the Western Pacific and the Eastern Indian Ocean.

    Matched MeSH terms: Phylogeny
  11. Fulltext Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost
    Lim YL, Ee R, Yin WF, Chan KG
    Sensors (Basel), 2014 Apr 22;14(4):7026-40.
    PMID: 24759107 DOI: 10.3390/s140407026
    Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.
    Matched MeSH terms: Phylogeny
  12. Morpho-molecular analysis as a prognostic model for repulsive feedback of the medicinal plant "Andrographis paniculata" to allogamy
    Valdiani A, Talei D, Javanmard A, Tan SG, Kadir MA, Maziah M
    Gene, 2014 Jun 1;542(2):156-67.
    PMID: 24680780 DOI: 10.1016/j.gene.2014.03.039
    Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharmaceutical properties, facing a low diversity in Malaysia. Cross-pollination of AP accessions leads to considerable rates of heterosis in the agro-morphological characteristics and anticancer phytochemicals of this eminent medicinal herb. However, the poor crossability of the plant at the interpopulation or intraspecific levels is an obstacle from the evolutionary and breeding points of view as an average of 4.56% crossability was recorded for AP in this study. Hence, this research aimed to elicit the impact of parental genetic distances (GDs) on the rate of crossability of AP using seven accessions in 21 possible cross combinations. To this end, a set of 55 randomly amplified polymorphic DNA (RAPD) primers and a total of 13 agro-morphological markers were employed to test the hypothesis. Twenty-two out of the 55 RAPD primers amplified a total of 257 bands of which 107 bands were found to be polymorphic. The principal component analysis (PCA) based on the RAPD markers revealed that the studied AP accessions were distributed to three distinct groups. Furthermore, it was noticed that even a minor increase in GD between two parents can cause a decline in their crossability. Unlike, the morphological-based GDs acted neutrally to crossability. This finding suggests that, despite the low genetic diversity among the Malaysian APs, a population prescreening using RAPD markers would be useful to enhance the rate of fruit set through selecting the genetically adjacent parents.
    Matched MeSH terms: Phylogeny
  13. The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae)
    Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):826-7.
    PMID: 24845437 DOI: 10.3109/19401736.2014.919460
    The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
    Matched MeSH terms: Phylogeny
  14. Fulltext Quorum sensing activity of Hafnia alvei isolated from packed food
    Tan JY, Yin WF, Chan KG
    Sensors (Basel), 2014 Apr 14;14(4):6788-96.
    PMID: 24736131 DOI: 10.3390/s140406788
    Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.
    Matched MeSH terms: Phylogeny
  15. Fulltext Development of chloroplast simple sequence repeats (cpSSRs) for the intraspecific study of Gracilaria tenuistipitata (Gracilariales, Rhodophyta) from different populations
    Song SL, Lim PE, Phang SM, Lee WW, Hong DD, Prathep A
    BMC Res Notes, 2014;7:77.
    PMID: 24490797 DOI: 10.1186/1756-0500-7-77
    Gracilaria tenuistipitata is an agarophyte with substantial economic potential because of its high growth rate and tolerance to a wide range of environment factors. This red seaweed is intensively cultured in China for the production of agar and fodder for abalone. Microsatellite markers were developed from the chloroplast genome of G. tenuistipitata var. liui to differentiate G. tenuistipitata obtained from six different localities: four from Peninsular Malaysia, one from Thailand and one from Vietnam. Eighty G. tenuistipitata specimens were analyzed using eight simple sequence repeat (SSR) primer-pairs that we developed for polymerase chain reaction (PCR) amplification.
    Matched MeSH terms: Phylogeny
  16. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment
    Rosly HA, Nor SA, Yahya K, Naim DM
    Mol Biol Rep, 2013 Nov;40(11):6407-18.
    PMID: 24062076 DOI: 10.1007/s11033-013-2755-4
    A primary factor in population management and wildlife conservation is the delineation of population units derived from descriptions of population genetic structure. Yet, predicting factors that influence the patterns of gene flow in a population particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the mud crab Scylla olivacea examined based on a 542 bp segment of the mitochondrial DNA cytochrome c oxidase I gene among 91 individuals from six localities in the west and east coast of Peninsular Malaysia. In total 55 unique haplotypes were distinguished with 45 private haplotypes and a single common haplotype shared among all populations studied. The other ten haplotypes were shared among various populations. The sharing of this haplotype reflects the connection of the mangrove areas between east and west coast of Peninsular Malaysia. High haplotype diversity (h = 0.968 ± 0.021; mean ± SD) and low nucleotide diversity (π = 0.120 ± 0.015; mean ± SD) were displayed, which may be indicative of genetic bottleneck events. No significant phylogenetic lineages were recognized using neighbour-joining and maximum parsimony methods. Hierarchical AMOVA analysis indicated that 99.33 % of the genetic variation was contained within populations and 0.67 % occurred among populations, suggesting no geographical patterning among populations studied, supported by F st test. Mismatch distribution analysis showed that the observed distribution of the pairwise mutation differences among haplotypes was multimodal, which is not concordant with a sudden range expansion scenario. However, neutrality tests showed non-significant negative values suggesting that the populations studied may have experienced past population growth, but the expansion may have been restricted to separate local areas that resulted in the non-significant negative Fu's Fs and Tajima's D value. Overall, this present preliminary study was able to be a reference on the phylogenetic relationships and assessment of genetic structure of Scylla sp. in Malaysia.
    Matched MeSH terms: Phylogeny
  17. Novel hepatitis B virus strain developing due to recombination between genotypes H and B strains isolated from a Japanese patient
    Uchida Y, Kouyama JI, Naiki K, Sugawara K, Inao M, Nakayama N, et al.
    Hepatology research : the official journal of the Japan Society of Hepatology, 2014 Oct;44(11):1130-1141.
    PMID: 24020990 DOI: 10.1111/hepr.12238
    AIM: In Japan, genotypes B and C are the predominant genotypes isolated from patients with chronic hepatitis B, while genotype A predominates in patients with acute hepatitis B. Globalization, however, appears to have changed the distribution of the hepatitis B virus (HBV) genotypes. Thus, the viral characteristics of HBV genotypes other than genotypes A, B and C were examined.

    METHODS: Screening of genotypes was performed by enzyme immunoassay and/or polymerase chain reaction INVADER method in 222 patients with HBV. The full-length nucleotide sequences of unusual strains were compared to those in the database, followed by construction of a phylogenetic tree.

    RESULTS: Unusual HBV strains were isolated from two patients: a 27-year-old Japanese bisexual man with acute hepatitis B with HIV co-infection and a 52-year-old Japanese man with chronic hepatitis B. The former strain was classified as genotype H, showing an overall identity of 99.8% to the Thailand strain (EU498228), while the nucleotide sequence of the latter strain showed similarity to the genotype B strains isolated in Malaysia (JQ027316) and Indonesia (JQ429079) between DR2 and DR1 in the X region, with identities of 96.9%. However, this strain was classified as genotype H by full-length sequence analysis, and the sequence between nt2023 and nt2262 showed no similarity to that in any previously reported strains.

    CONCLUSION: HBV strains showing recombination between genotype B and H strains were found even in chronic hepatitis patients in Japan. Globalization may yield HBV strains of possible novel genotypes containing novel nucleotide sequences in the precore/core region.

    Matched MeSH terms: Phylogeny
  18. Fulltext Genetic assemblage of Sarcocystis spp. in Malaysian snakes
    Lau YL, Chang PY, Subramaniam V, Ng YH, Mahmud R, Ahmad AF, et al.
    Parasit Vectors, 2013 Sep 09;6(1):257.
    PMID: 24010903 DOI: 10.1186/1756-3305-6-257
    BACKGROUND: Sarcocystis species are protozoan parasites with a wide host range including snakes. Although there were several reports of Sarcocytis species in snakes, their distribution and prevalence are still not fully explored.

    METHODS: In this study, fecal specimens of several snake species in Malaysia were examined for the presence of Sarcocystis by PCR of 18S rDNA sequence. Microscopy examination of the fecal specimens for sporocysts was not carried as it was difficult to determine the species of the infecting Sarcocystis.

    RESULTS: Of the 28 snake fecal specimens, 7 were positive by PCR. BLASTn and phylogenetic analyses of the amplified 18S rDNA sequences revealed the snakes were infected with either S. nesbitti, S. singaporensis, S. zuoi or undefined Sarcocystis species.

    CONCLUSION: This study is the first to report Sarcocystis infection in a cobra, and S. nesbitti in a reticulated python.

    Matched MeSH terms: Phylogeny
  19. Fulltext Evolutionary history of HIV-1 subtype B and CRF01_AE transmission clusters among men who have sex with men (MSM) in Kuala Lumpur, Malaysia
    Ng KT, Ong LY, Lim SH, Takebe Y, Kamarulzaman A, Tee KK
    PLoS One, 2013;8(6):e67286.
    PMID: 23840653 DOI: 10.1371/journal.pone.0067286
    HIV-1 epidemics among men who have sex with men (MSM) continue to expand in developed and developing countries. Although HIV infection in MSM is amongst the highest of the key affected populations in many countries in Southeast Asia, comprehensive molecular epidemiological study of HIV-1 among MSM remains inadequate in the region including in Malaysia. Here, we reported the phylodynamic profiles of HIV-1 genotypes circulating among MSM population in Kuala Lumpur, Malaysia. A total of n = 459 newly-diagnosed treatment-naïve consenting subjects were recruited between March 2006 and August 2012, of whom 87 (18.9%) were self-reported MSM. Transmitted drug resistance mutations were absent in these isolates. Cumulatively, phylogenetic reconstructions of the pro-rt gene (HXB2∶2253-3275) showed that HIV-1 subtype B and CRF01_AE were predominant and contributed to approximately 80% of the total HIV-1 infection among MSM. In addition to numerous unique transmission lineages within these genotypes, twelve monophyletic transmission clusters of different sizes (2-7 MSM sequences, supported by posterior probability value of 1) were identified in Malaysia. Bayesian coalescent analysis estimated that the divergence times for these clusters were mainly dated between 1995 and 2005 with four major transmission clusters radiating at least 12 years ago suggesting that active spread of multiple sub-epidemic clusters occurred during this period. The changes in effective population size of subtype B showed an exponential growth within 5 years between 1988 and 1993, while CRF01_AE lineage exhibited similar expansion between 1993 and 2003. Our study provides the first insight of the phylodynamic profile of HIV-1 subtype B and CRF01_AE circulating among MSM population in Kuala Lumpur, Malaysia, unravelling the importance of understanding transmission behaviours as well as evolutionary history of HIV-1 in assessing the risk of outbreak or epidemic expansion.
    Matched MeSH terms: Phylogeny
  20. Fulltext MabsBase: a Mycobacterium abscessus genome and annotation database
    Heydari H, Wee WY, Lokanathan N, Hari R, Mohamed Yusoff A, Beh CY, et al.
    PLoS One, 2013;8(4):e62443.
    PMID: 23658631 DOI: 10.1371/journal.pone.0062443
    Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.
    Matched MeSH terms: Phylogeny
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links