Displaying publications 1 - 20 of 922 in total

  1. Teo WF, Wee WY, Choo SW, Tan GY
    Mar Genomics, 2015 Apr;20:11-2.
    PMID: 25554669 DOI: 10.1016/j.margen.2014.12.006
    The bacterium strain SE31, a member of the genus Sciscionella, was isolated from intertidal sediments collected from Cape Rachado, Malaysia. The high quality draft genome sequence of Sciscionella strain SE31 with a genome size of approximately 7.4 Mbp is reported. Preliminary analysis revealed 46 putative gene clusters involved in the biosynthesis of secondary metabolites and 113 putative genes that are associated with bacterial virulence, disease and defense. Availability of the genome sequence of Sciscionella SE31 will contribute to a better understanding of the genus Sciscionella.
    Matched MeSH terms: Molecular Sequence Data
  2. Fikáček M, Maruyama M, Vondráček D, Short AE
    Zootaxa, 2013;3716:277-88.
    PMID: 26106776
    Anew hydrophilid genus Chimaerocyon gen. nov. containing two species, C. shimadai sp. nov. (Malaysia: Pahang) and C. sumatranus sp. nov. (Indonesia: Sumatra), is described. Specimens of C. shimadai were collected from brood cells in anest of Pheidole singaporensis Özdikmen, 2010. The biology of C. sumatranus remains unknown. A molecular phylogeny based on four genes (cox1, cox2, 18S and 28S) supports the placement of the genus as deeply nested within the Cercyon-group of the tribe Megasternini. This position is supported by the subdistal position of the median spur in the hind wing (unique to Megasternini) and the presence of sucking disc on male maxilla (unique for Megastemini+Sphaeridiini). The remaining external morphology differs substantially from other representatives of Megasternini. The hypothesis that the aberrant morphology of Chimaerocyon gen. nov. is a consequence of myrmecophily is discussed.
    Matched MeSH terms: Molecular Sequence Data
  3. Hong KW, Thinagaran Da, Gan HM, Yin WF, Chan KG
    J. Bacteriol., 2012 Nov;194(22):6324.
    PMID: 23115161 DOI: 10.1128/JB.01608-12
    Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.
    Matched MeSH terms: Molecular Sequence Data
  4. Hong KW, Koh CL, Sam CK, Yin WF, Chan KG
    J. Bacteriol., 2012 Nov;194(22):6317.
    PMID: 23105060 DOI: 10.1128/JB.01578-12
    Burkholderia sp. strain GG4, isolated from the ginger rhizosphere, possesses a unique N-acylhomoserine lactone (AHL)-modifying activity that reduces 3-oxo-AHLs to 3-hydroxy-AHLs. To the best of our knowledge, this is the first sequenced genome from a bacterium of the genus Burkholderia that shows both quorum-sensing and signaling confusion activities.
    Matched MeSH terms: Molecular Sequence Data
  5. Rosli MK, Zakaria SS, Syed-Shabthar SM, Zainal ZZ, Shukor MN, Mahani MC, et al.
    Genet. Mol. Res., 2011;10(1):482-93.
    PMID: 21476194 DOI: 10.4238/vol10-1gmr1002
    The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
    Matched MeSH terms: Molecular Sequence Data
  6. Wan KL, Chong SP, Ng ST, Shirley MW, Tomley FM, Jangi MS
    Int. J. Parasitol., 1999 Dec;29(12):1885-92.
    PMID: 10961844
    A study of about 500 expressed sequence tags (ESTs), derived from a merozoite cDNA library, was initiated as an approach to generate a larger pool of gene information on Eimeria tenella. Of the ESTs, 47.7% had matches with entries in the databases, including ribosomal proteins, metabolic enzymes and proteins with other functions, of which 14.3% represented previously known E. tenella genes. Thus over 50% of the ESTs had no significant database matches. The E. tenella EST dataset contained a range of highly abundant genes comparable with that found in the EST dataset of T. gondii and may thus reflect the importance of such molecules in the biology of the apicomplexan organisms. However, comparison of the two datasets revealed very few homologies between sequences of apical organelle molecules, and provides evidence for sequence divergence between these closely-related parasites. The data presented underpin the potential value of the EST strategy for the discovery of novel genes and may allow for a more rapid increase in the knowledge and understanding of gene expression in the merozoite life cycle stage of Eimeria spp.
    Matched MeSH terms: Molecular Sequence Data
  7. Rota PA, Liffick S, Rosenthal S, Heriyanto B, Chua KB
    Lancet, 2000 Apr 29;355(9214):1557-8.
    PMID: 10801203 DOI: 10.1016/S0140-6736(05)74612-2
    Matched MeSH terms: Molecular Sequence Data
  8. Khoo AS, Balraj P, Rachedi A, Chin CN, Volpi L
    Hum. Mutat., 1999 Nov;14(5):448.
    PMID: 10533073
    Matched MeSH terms: Molecular Sequence Data
  9. Tan GC, Dibb N
    Malays J Pathol, 2015 Aug;37(2):73-81.
    PMID: 26277662 MyJurnal
    Since the inception of deep sequencing, isomiRs are consistently observed to be produced by most miRNA genes in a variety of cell types. IsomiRs appear as a variation in length from the canonical sequence annotated in miRBase, due to an addition or deletion of one or more nucleotides at the 5(') or 3(') ends or both. As the seed sequence is located at the 5(') end of the microRNA, the target mRNA will be theoretically different. Therefore, 5(')isomiRs might potentially target a new set mRNA compared to their canonical counterpart. This article gives an overview of investigations that explored the functional potential of isomiRs such as their ability to incorporate into Argonaute protein, the differential expression of isomiRs in various tissue types and cell lines, and the differences of mRNA targets between isomiR and its canonical microRNA. In addition, this article provides a brief introduction of RNA sponges as a potential way to inhibit isomiRs.
    Matched MeSH terms: Molecular Sequence Data
  10. Khor BY, Tye GJ, Lim TS, Choong YS
    PMID: 26338054 DOI: 10.1186/s12976-015-0014-1
    Protein structure prediction from amino acid sequence has been one of the most challenging aspects in computational structural biology despite significant progress in recent years showed by critical assessment of protein structure prediction (CASP) experiments. When experimentally determined structures are unavailable, the predictive structures may serve as starting points to study a protein. If the target protein consists of homologous region, high-resolution (typically <1.5 Å) model can be built via comparative modelling. However, when confronted with low sequence similarity of the target protein (also known as twilight-zone protein, sequence identity with available templates is less than 30%), the protein structure prediction has to be initiated from scratch. Traditionally, twilight-zone proteins can be predicted via threading or ab initio method. Based on the current trend, combination of different methods brings an improved success in the prediction of twilight-zone proteins. In this mini review, the methods, progresses and challenges for the prediction of twilight-zone proteins were discussed.
    Matched MeSH terms: Molecular Sequence Data
  11. Wu YH, Cheong LC, Meon S, Lau WH, Kong LL, Joseph H, et al.
    Arch. Virol., 2013 Jun;158(6):1407-10.
    PMID: 23397332 DOI: 10.1007/s00705-013-1624-8
    A 246-nt variant of Coconut cadang-cadang viroid (CCCVd) has been identified and described from oil palms with orange spotting symptoms in Malaysia. Compared with the 246-nt form of CCCVd from coconut, the oil palm variant substituted C(31)→U in the pathogenicity domain and G(70)→C in the central conserved domain. This is the first sequence reported for a 246-nt variant of CCCVd in oil palms expressing orange spotting symptoms.
    Matched MeSH terms: Molecular Sequence Data
  12. Chan GF, Gan HM, Ling HL, Rashid NA
    Eukaryotic Cell, 2012 Oct;11(10):1300-1.
    PMID: 23027839 DOI: 10.1128/EC.00229-12
    A draft genome sequence of Pichia kudriavzevii M12 is presented here. The genome reveals the presence of genes encoding enzymes involved in xylose utilization and the pentose phosphate pathway for bioethanol production. Strain M12 is also a potential producer of phytases, enzymes useful in food processing and agriculture.
    Matched MeSH terms: Molecular Sequence Data
  13. Grismer LL, Anuar S, Muin MA, Quah ES, Wood PL
    Zootaxa, 2013;3616:239-52.
    PMID: 24758805 DOI: 10.11646/zootaxa.3616.3.2
    Molecular and morphological analyses indicate that a new upland species of the Cyrtodactylus sworderi complex, C. tebuensis sp. nov. from Gunung Tebu, Terengganu, Malaysia is most closely related to C. sworderi and together they form the sister lineage to C. quadrivirgatus. Cyrtodactylus tebuensis sp. nov. is differentiated from all other species of Sundaland Cyrtodactylus on the basis of having the unique combination of large, conical, keeled body tubercles; tubercles present on top of head, occiput, nape, and limbs, and extending posteriorly beyond base of tail; 43-51 ventral scales; no transversely enlarged, median subcaudal scales; proximal, subdigital lamellae transversely expanded; 17-21 subdigital lamellae on fourth toe; an abrupt transition between posterior and ventral femoral scales; enlarged femoral scales; no femoral or precloacal pores; no precloacal groove; body bearing four wide, bold, dark brown stripes (lateral stripe on each flank and a pair of paravertebral stripes); and a pairwise sequence divergence of 13.0% from its closest relative C. sworderi based on the mitochondrial gene ND2. Cyrtodactylus tebuensis sp. nov. is the first endemic upland species of gekkonid from northeastern Peninsular Malaysia and underscores the necessity for additional field work in all upland systems.
    Matched MeSH terms: Molecular Sequence Data
  14. Grismer LL, Wood PL, Mohamed M, Chan KO, Heinz HM, Sumarli AS, et al.
    Zootaxa, 2013;3746:463-72.
    PMID: 25113489 DOI: 10.11646/zootaxa.3746.3.5
    A new species of karst-adapted gekkonid lizard of the genus Cnemaspis Strauch is described from Gua Gunting and Gua Goyang in a karst region of Merapoh, Pahang, Peninsular Malaysia whose unique limestone formations are in immediate danger of being quarried. The new species differs from all other species of Cnemaspis based on its unique suite of morphological and color pattern characters. Its discovery underscores the unique biodiversity endemic to karst regions and adds to a growing list of karst-adapted reptiles from Peninsular Malaysia. We posit that new karst-adapted species endemic to limestone forests will continue to be discovered and these regions will harbor a significant percentage of Peninsular Malaysia's biodiversity and thusly should be conserved rather than quarried.
    Matched MeSH terms: Molecular Sequence Data
  15. Manjeri G, Muhamad R, Faridah QZ, Tan SG
    J. Genet., 2012 Nov 22;91(3):e92-6.
    PMID: 23257301
    Matched MeSH terms: Molecular Sequence Data
  16. Chan XY, Chua KH, Puthucheary SD, Yin WF, Chan KG
    J. Bacteriol., 2012 Nov;194(22):6350.
    PMID: 23105081 DOI: 10.1128/JB.01642-12
    Aeromonas is a pathogenic organism that is often found to infect humans. Here we report the draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain 159, which shows N-acylhomoserine lactone production. In the draft genome of strain 159, luxI and luxR homologue genes were found to be located at contig 47, and these genes are believed to be important for the quorum-sensing system present in this pathogen.
    Matched MeSH terms: Molecular Sequence Data
  17. Hong KW, Koh CL, Sam CK, Yin WF, Chan KG
    J. Bacteriol., 2012 Nov;194(22):6318.
    PMID: 23105061 DOI: 10.1128/JB.01579-12
    Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium.
    Matched MeSH terms: Molecular Sequence Data
  18. Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, Ainuddin AN, et al.
    Microb. Ecol., 2012 Apr;63(3):674-81.
    PMID: 21990015 DOI: 10.1007/s00248-011-9953-1
    Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.
    Matched MeSH terms: Molecular Sequence Data
  19. Ong SY, Pratap CB, Wan X, Hou S, Abdul Rahman AY, Saito JA, et al.
    J. Bacteriol., 2012 Apr;194(8):2115-6.
    PMID: 22461552 DOI: 10.1128/JB.00121-12
    We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.
    Matched MeSH terms: Molecular Sequence Data
  20. Ithoi I, Ahmad AF, Nissapatorn V, Lau YL, Mahmud R, Mak JW
    PLoS ONE, 2011;6(9):e24327.
    PMID: 21915311 DOI: 10.1371/journal.pone.0024327
    BACKGROUND: In Malaysia, researchers and medical practitioners are unfamiliar with Naegleria infections. Thus little is known about the existence of pathogenic Naegleria fowleri, and the resultant primary amoebic meningoencephalitis (PAM) is seldom included in the differential diagnosis of central nervous system infections. This study was conducted to detect the presence of Naegleria species in various environmental samples.

    METHODS/FINDINGS: A total of 41 Naegleria-like isolates were isolated from water and dust samples. All these isolates were subjected to PCR using two primer sets designed from the ITS1-ITS2 regions. The N. fowleri species-specific primer set failed to produce the expected amplicon. The Naegleria genus-specific primers produced amplicons of 408 bp (35), 450 bp (2), 457 bp (2) or 381 bp (2) from all 41 isolates isolated from aquatic (33) and dust (8) samples. Analysis of the sequences from 10 representative isolates revealed that amplicons with fragments 408, 450 and 457 bp showed homology with non-pathogenic Naegleria species, and 381 bp showed homology with Vahlkampfia species. These results concurred with the morphological observation that all 39 isolates which exhibited flagella were Naegleria, while 2 isolates (AC7, JN034055 and AC8, JN034056) that did not exhibit flagella were Vahlkampfia species.

    CONCLUSION: To date, pathogenic species of N. fowleri have not been isolated from Malaysia. All 39 isolates that produced amplicons (408, 450 and 457 bp) from the genus-specific primers were identified as being similar to nonpathogenic Naegleria. Amplicon 408 bp from 5 representative isolates showed 100% and 99.7% identity to Naegleria philippinensis isolate RJTM (AM167890) and is thus believed to be the most common species in our environment. Amplicons 450 bp and 457 bp were respectively believed to be from 2 new species of Naegleria, since representative isolates showed lower homology and had a longer base pair length when compared to the reference species in the Genbank, Naegleria schusteri (AJ566626) and Naegleria laresi (AJ566630), respectively.

    Matched MeSH terms: Molecular Sequence Data
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