Displaying publications 1041 - 1060 of 3446 in total

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  1. 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: DNA, Ribosomal/genetics; DNA Primers
  2. Fulltext A phylogeny of the family Poritidae (Cnidaria, Scleractinia) based on molecular and morphological analyses
    Kitano YF, Benzoni F, Arrigoni R, Shirayama Y, Wallace CC, Fukami H
    PLoS One, 2014;9(5):e98406.
    PMID: 24871224 DOI: 10.1371/journal.pone.0098406
    The family Poritidae formerly included 6 genera: Alveopora, Goniopora, Machadoporites, Porites, Poritipora, and Stylaraea. Morphologically, the genera can be differentiated based on the number of tentacles, the number of septa and their arrangement, the length of the polyp column, and the diameter of the corallites. However, the phylogenetic relationships within and between the genera are unknown or contentious. On the one hand, Alveopora has been transferred to the Acroporidae recently because it was shown to be more closely related to this family than to the Poritidae by previous molecular studies. On the other hand, Goniopora is morphologically similar to 2 recently described genera, Machadoporites and Poritipora, particularly with regard to the number of septa (approximately 24), but they have not yet been investigated at the molecular level. In this study, we analyzed 93 samples from all 5 poritid genera and Alveopora using 2 genetic markers (the barcoding region of the mitochondrial COI and the ITS region of the nuclear rDNA) to investigate their phylogenetic relationships and to revise their taxonomy. The reconstructed molecular trees confirmed that Alveopora is genetically distant from all poritid genera but closely related to the family Acroporidae, whereas the other genera are genetically closely related. The molecular trees also revealed that Machadoporites and Poritipora were indistinguishable from Goniopora. However, Goniopora stutchburyi was genetically isolated from the other congeneric species and formed a sister group to Goniopora together with Porites and Stylaraea, thus suggesting that 24 septa could be an ancestral feature in the Poritidae. Based on these data, we move G. stutchburyi into a new genus, Bernardpora gen. nov., whereas Machadoporites and Poritipora are merged with Goniopora.
    Matched MeSH terms: Sequence Analysis, DNA; DNA, Ribosomal Spacer/genetics
  3. Synthesis, crystal structures and characterization of late first row transition metal complexes derived from benzothiazole core: anti-tuberculosis activity and special emphasis on DNA binding and cleavage property
    Netalkar PP, Netalkar SP, Budagumpi S, Revankar VK
    Eur J Med Chem, 2014 May 22;79:47-56.
    PMID: 24721314 DOI: 10.1016/j.ejmech.2014.03.083
    Air and moisture stable coordination compounds of late first row transition metals, viz. Co(II), Ni(II), Cu(II) and Zn(II), with a newly designed ligand, 2-(2-benzo[d]thiazol-2-yl)hydrazono)propan-1-ol (LH), were prepared and successfully characterized using various spectro-analytical techniques. The molecular structures of the ligand and nickel complex were unambiguously determined by single-crystal X-ray diffraction method. The [Ni(LH)2]Cl2.3H2O complex is stabilized by intermolecular CH⋯π stacking interactions between the methyl hydrogen and the C18 atom of the phenyl ring (C11-H11B⋯C18) forming 1D zig-zag chain structure. Both, the ligand and its copper complex, were electrochemically active in the working potential range, showing quasi-reversible redox system. The interactions of all the compounds with calf thymus DNA have been comprehensively investigated using electronic absorption spectroscopy, viscosity, electrochemistry and thermal denaturation studies. The cleavage reaction on pBR322 DNA has been monitored by agarose gel electrophoresis. The results showed that the ligand can bind to CT-DNA through partial intercalation, whereas the complexes bind electrostatically. Further, [Ni(LH)2]Cl2.3H2O and [CuLCl(H2O)2] complexes in the series have high binding and cleavage affinity towards pBR322 DNA. Additionally, all the compounds were screened for anti-tuberculosis activity. All the complexes revealed an MIC value of 0.8 μg/mL, which is almost 8 times active than standard used (Streptomycin, 6.25 μg/mL).
    Matched MeSH terms: DNA/chemistry*; DNA Cleavage
  4. Distribution and haplotype associations of XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln polymorphisms with nasopharyngeal carcinoma in the Malaysian population
    Visuvanathan S, Chong PP, Yap YY, Lim CC, Tan MK, Lye MS
    Asian Pac J Cancer Prev, 2014;15(6):2747-51.
    PMID: 24761895
    BACKGROUND: DNA repair pathways play a crucial role in maintaining the human genome. Previous studies associated DNA repair gene polymorphisms (XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln) with nasopharyngeal carcinoma. These non-synonymous polymorphisms may alter DNA repair capacity and thus increase or decrease susceptibility. The present study aimed to determine the genotype distribution of XPD codon 751, XRCC1 codon 280 and codon 399 polymorphisms and haplotype associations among NPC cases and controls in the Malaysian population.

    MATERIALS AND METHODS: We selected 157 NPC cases and 136 controls from two hospitals in Kuala Lumpur, Malaysia for this study. The polymorphisms studied were genotyped by PCR-RFLP assay and allele and genotype frequencies, haplotype and linkage disequilibrium were determined using SNPstat software.

    RESULTS: For the XPD Lys751Gln polymorphism, the frequency of the Lys allele was higher in cases than in controls (94.5% versus 85.0%). For the XRCC1 Arg280His polymorphism, the frequency of Arg allele was 90.0% and 89.0% in cases and controls, respectively and for XRCC1 Arg399Gln the frequency of the Arg allele was 72.0% and 72.8% in cases and controls respectively. All three polymorphisms were in linkage disequilibrium. The odds ratio from haplotype analysis for these three polymorphisms and their association with NPC was 1.93 (95%CI: 0.90-4.16) for haplotype CGC vs AGC allele combinations. The global haplotype association with NPC gave a p-value of 0.054.

    CONCLUSIONS: Our study provides an estimate of allele and genotype frequencies of XRCC1Arg280His, XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms in the Malaysian population and showed no association with nasopharyngeal cancer.

    Matched MeSH terms: DNA Repair; DNA-Binding Proteins/genetics*
  5. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment
    Lee LH, Azman AS, Zainal N, Eng SK, Fang CM, Hong K, et al.
    Int J Syst Evol Microbiol, 2014 Apr;64(Pt 4):1194-201.
    PMID: 24408529 DOI: 10.1099/ijs.0.059014-0
    A novel bacterium, strain MUSC 273(T), was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273(T) was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence of strain MUSC 273(T) showed the highest sequence similarity to those of Novosphingobium indicum H25(T) (96.8 %), N. naphthalenivorans TUT562(T) (96.4 %) and N. soli CC-TPE-1(T) (95.9 %) and lower sequence similarity to members of all other species of the genus Novosphingobium. Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273(T) formed a distinct cluster with members of the genus Novosphingobium. DNA-DNA relatedness of strain MUSC 273(T) to the type strains of the most closely related species, N. indicum MCCC 1A01080(T) and N. naphthalenivorans DSM 18518(T), was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were C18 : 1ω7c, C17 : 1ω6c, C16 : 0, C15 : 0 2-OH and C16 : 1ω7c. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273(T) represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium malaysiense sp. nov. is proposed. The type strain is MUSC 273(T) ( = DSM 27798(T) = MCCC 1A00645(T) = NBRC 109947(T)).
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  6. Fulltext Analyses of hypomethylated oil palm gene space
    Low ET, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, et al.
    PLoS One, 2014;9(1):e86728.
    PMID: 24497974 DOI: 10.1371/journal.pone.0086728
    Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
    Matched MeSH terms: Sequence Analysis, DNA; DNA Methylation*
  7. Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae
    Lee LH, Zainal N, Azman AS, Mutalib NA, Hong K, Chan KG
    Int J Syst Evol Microbiol, 2014 May;64(Pt 5):1461-1467.
    PMID: 24449791 DOI: 10.1099/ijs.0.058701-0
    A novel actinobacterial strain, designated MUSC 201T, was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201T represented a novel lineage within the class Actinobacteria. Strain MUSC 201T formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1%), Aeromicrobium (92.7-94.6%), Marmoricola (92.5-93.1%) and Kribbella (91.5-92.4%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3γ. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5:0.9:1.0:1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18:1ω9c (30.8%), C16:0 (24.1%), and 10-methyl C18:0 (13.9%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201T (=DSM 27763T=MCCC 1A00646T=NBRC 109973T).
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  8. Fulltext Malaysian child infected with Plasmodium vivax via blood transfusion: a case report
    Anthony CN, Lau YL, Sum JS, Fong MY, Ariffin H, Zaw WL, et al.
    Malar J, 2013;12:308.
    PMID: 24007496 DOI: 10.1186/1475-2875-12-308
    Malaria may be a serious complication of blood transfusion due to the asymptomatic persistence of parasites in some donors. This case report highlights the transfusion-transmitted malaria of Plasmodium vivax in a child diagnosed with germ cell tumour. This child had received blood transfusion from three donors and a week later started developing malaria like symptoms. Nested PCR and sequencing confirmed that one of the three donors was infected with P. vivax and this was transmitted to the 12-year-old child. To the best of the authors' knowledge, this is the first reported transfusion-transmitted malaria case in Malaysia.
    Matched MeSH terms: DNA, Protozoan/genetics; Sequence Analysis, DNA
  9. Fulltext Mucosal genetic immunization through microsphere-based oral carriers
    Rosli R, Nograles N, Hanafi A, Nor Shamsudin M, Abdullah S
    Hum Vaccin Immunother, 2013 Oct;9(10):2222-7.
    PMID: 24051430 DOI: 10.4161/hv.25325
    Polymeric carriers in the form of cellulose acetate phthalate (CAP) and alginate (ALG) microspheres were used for encapsulation of plasmid DNA for oral mucosal immunization. Access into the intestinal mucosa by pVAX1 eukaryotic expression plasmid vectors carrying gene-coding sequences, either for the cholera enterotoxin B subunit (ctxB) immunostimulatory antigen or the green fluorescent protein (GFP), delivered from both types of microsphere carriers were examined in orally immunized BALB/c mice. Demonstration of transgene protein expression and IgA antibody responses at local mucosal sites suggest immunological response to a potential oral DNA vaccine formulated within the microsphere carriers.
    Matched MeSH terms: Vaccines, DNA/administration & dosage*; Vaccines, DNA/immunology
  10. Acinetobacter kookii sp. nov., isolated from soil
    Choi JY, Ko G, Jheong W, Huys G, Seifert H, Dijkshoorn L, et al.
    Int J Syst Evol Microbiol, 2013 Dec;63(Pt 12):4402-4406.
    PMID: 23950148 DOI: 10.1099/ijs.0.047969-0
    Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202(T) and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter. Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838(T) (97.9-98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963(T) and Acinetobacter bouvetii 4B02(T) (85.4-87.6 and 78.1-82.7 %, respectively). Strain 11-0202(T) displayed low DNA-DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter. The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter: summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3-27.2 %), C18 : 1ω9c (19.9-22.1 %), C16 : 0 (15.2-22.0 %) and C12 : 0 (9.2-14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202(T) ( = KCTC 32033(T) = JCM 18512(T)).
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  11. Fulltext A pentaplex PCR assay for the detection and differentiation of Shigella species
    Ojha SC, Yean Yean C, Ismail A, Singh KK
    Biomed Res Int, 2013;2013:412370.
    PMID: 23509722 DOI: 10.1155/2013/412370
    The magnitude of shigellosis in developing countries is largely unknown because an affordable detection method is not available. Current laboratory diagnosis of Shigella spp. is laborious and time consuming and has low sensitivity. Hence, in the present study, a molecular-based diagnostic assay which amplifies simultaneously four specific genes to identify invC for Shigella genus, rfc for S. flexneri, wbgZ for S. sonnei, and rfpB for S. dysenteriae, as well as one internal control (ompA) gene, was developed in a single reaction to detect and differentiate Shigella spp. Validation with 120 Shigella strains and 37 non-Shigella strains yielded 100% specificity. The sensitivity of the PCR was 100 pg of genomic DNA, 5.4 × 10(4) CFU/ml, or approximately 120 CFU per reaction mixture of bacteria. The sensitivity of the pentaplex PCR assay was further improved following preincubation of the stool samples in gram-negative broth. A preliminary study with 30 diarrhoeal specimens resulted in no cross-reaction with other non-Shigella strains tested. We conclude that the developed pentaplex PCR assay is robust and can provide information about the four target genes that are essential for the identification of the Shigella genus and the three Shigella species responsible for the majority of shigellosis cases.
    Matched MeSH terms: DNA, Bacterial/analysis; Sequence Analysis, DNA
  12. The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers
    Syed-Shabthar SM, Rosli MK, Mohd-Zin NA, Romaino SM, Fazly-Ann ZA, Mahani MC, et al.
    Mol Biol Rep, 2013 Aug;40(8):5165-76.
    PMID: 23686165 DOI: 10.1007/s11033-013-2619-y
    Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
    Matched MeSH terms: Sequence Analysis, DNA; DNA Primers/genetics
  13. Fulltext Identification of actinomycete communities in Antarctic soil from Barrientos Island using PCR-denaturing gradient gel electrophoresis
    Learn-Han L, Yoke-Kqueen C, Shiran MS, Vui-Ling CM, Nurul-Syakima AM, Son R, et al.
    Genet. Mol. Res., 2012;11(1):277-91.
    PMID: 22370930 DOI: 10.4238/2012.February.8.3
    The diversity of specific bacteria taxa, such as the actinomycetes, has not been reported from the Antarctic island of Barrientos. The diversity of actinomycetes was estimated with two different strategies that use PCR-denaturing gradient gel electrophoresis. First, a PCR was applied, using a group-specific primer that allows selective amplification of actinomycete sequences. Second, a nested-PCR approach was used that allows the estimation of the relative abundance of actinomycetes within the bacterial community. Molecular identification, which was based on 16S rDNA sequence analysis, revealed eight genera of actinomycetes, Actinobacterium, Actinomyces, an uncultured Actinomycete, Streptomyces, Leifsonia, Frankineae, Rhodococcus, and Mycobacterium. The uncultured Actinomyces sp and Rhodococcus sp appear to be the prominent genera of actinomycetes in Barrientos Island soil. PCR-denaturing gradient gel electrophoresis patterns were used to look for correlations between actinomycete abundance and environmental characteristics, such as type of rookery and vegetation. There was a significant positive correlation between type of rookery and abundance of actinomycetes; soil samples collected from active chinstrap penguin rookeries had the highest actinomycete abundance. Vegetation type, such as moss, which could provide a microhabitat for bacteria, did not correlate significantly with actinomycete abundance.
    Matched MeSH terms: DNA, Bacterial; DNA, Ribosomal/genetics
  14. First molecular characterization of Giardia duodenalis from goats in Malaysia
    Lim YA, Mahdy MA, Tan TK, Goh XT, Jex AR, Nolan MJ, et al.
    Mol Cell Probes, 2013 Feb;27(1):28-31.
    PMID: 22971518 DOI: 10.1016/j.mcp.2012.08.006
    In the present study, 310 faecal samples from goats from eight different farms in Malaysia were tested for the presence of Giardia using a PCR-coupled approach. The nested PCR for SSU amplified products of the expected size (∼200 bp) from 21 of 310 (6.8%) samples. Sixteen of these 21 products could be sequenced successfully and represented six distinct sequence types. Phylogenetic analysis of the SSU sequence data using Bayesian Inference (BI) identified Giardia assemblages A, B and E. The identification of the 'zoonotic' assemblages A and B suggests that Giardia-infected goats represent a possible reservoir for human giardiasis in Malaysia.
    Matched MeSH terms: DNA, Protozoan/genetics*; Sequence Analysis, DNA
  15. Fulltext N-acyl homoserine lactone production by Klebsiella pneumoniae isolated from human tongue surface
    Yin WF, Purmal K, Chin S, Chan XY, Koh CL, Sam CK, et al.
    Sensors (Basel), 2012;12(3):3472-83.
    PMID: 22737019 DOI: 10.3390/s120303472
    Bacteria communicate by producing quorum sensing molecules called autoinducers, which include autoinducer-1, an N-hexanoyl homoserine lactone (AHL), and autoinducer-2. Bacteria present in the human oral cavity have been shown to produce autoinducer-2, but not AHL. Here, we report the isolation of two AHL-producing Klebsiella pneumoniae strains from the posterior dorsal surface of the tongue of a healthy individual. Spent culture supernatant extracts from K. pneumoniae activated the biosensors Agrobacterium tumefaciens NTL4(pZLR4) and Escherichia coli [pSB401], suggesting the presence of both long and short chain AHLs. High resolution mass spectrometry analyses of these extracts confirmed that both K. pneumoniae isolates produced N-octanoylhomoserine lactone and N-3-dodecanoyl-L-homoserine lactone. To the best of our knowledge, this is the first report of the isolation of K. pneumoniae from the posterior dorsal surface of the human tongue and the production of these AHLs by this bacterium.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Ribosomal/metabolism
  16. Fulltext Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome
    Amiruddin N, Lee XW, Blake DP, Suzuki Y, Tay YL, Lim LS, et al.
    BMC Genomics, 2012 Jan 13;13:21.
    PMID: 22244352 DOI: 10.1186/1471-2164-13-21
    BACKGROUND: Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a high priority, especially in chickens raised for meat. Prophylactic chemotherapy has been the primary method used for the control of coccidiosis. However, drug efficacy can be compromised by drug-resistant parasites and the lack of new drugs highlights demands for alternative control strategies including vaccination. In the long term, sustainable control of coccidiosis will most likely be achieved through integrated drug and vaccination programmes. Characterisation of the E. tenella transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis.

    RESULTS: More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs). Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the E. tenella complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis.

    CONCLUSIONS: This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence.

    Matched MeSH terms: Sequence Analysis, DNA; DNA, Complementary/chemistry*
  17. Barcoding of Giardia duodenalis isolates and derived lines from an established cryobank by a mutation scanning-based approach
    Nolan MJ, Jex AR, Upcroft JA, Upcroft P, Gasser RB
    Electrophoresis, 2011 Aug;32(16):2075-90.
    PMID: 23479788
    We barcoded 25 in vitro isolates (representing 92 samples) of Giardia duodenalis from humans and other animals, which have been assembled by the Upcroft team at the Queensland Institute of Medical Research over a period of almost three decades. We used mutation scanning-coupled sequencing of loci in the triosephosphate isomerase, glutamate dehydrogenase and β-giardin genes, combined with phylogenetic analysis, to genetically characterise them. Specifically, the isolates (n514) of G. duodenalis from humans from Australia (AD113; BRIS/83/HEPU/106; BRIS/87/HEPU/713; BRIS/89/HEPU/1003; BRIS/92/HEPU/1541; BRIS/92/HEPU/1590; BRIS/92/HEPU/2443; BRIS/93/HEPU/1706), Malaysia (KL/92/IMR/1106) and Afghanistan (WB), a cat from Australia (BAC2), a sheep from Canada (OAS1) and a sulphur-crested cockatoo from Australia (BRIS/95/HEPU/2041) represented assemblage A (sub-assemblage AI-1, AI-2 or AII-2); isolates (n510) from humans from Australia (BRIS/91/HEPU/1279; BRIS/92/HEPU/2342; BRIS/92/HEPU/2348; BRIS/93/HEPU/1638; BRIS/93/HEPU/1653; BRIS/93/HEPU/1705; BRIS/93/HEPU/1718; BRIS/93/HEPU/1727), Papua New Guinea (BRIS/92/HEPU/1487) and Canada (H7) represented assemblage B (sub-assemblage BIV) and an isolate from cattle from Australia (BRIS/92/HEPU/1709) had a match to assemblage E. Isolate BRIS/90/HEPU/1229 from a human from Australia was shown to represent a mixed population of assemblages A and B. These barcoded isolates (including stocks and derived lines) now allow direct comparisons of experimental data among laboratories and represent a massive resource for transcriptomic, proteomic, metabolic and functional genomic studies using advanced molecular technologies.
    Matched MeSH terms: DNA Fingerprinting; Sequence Analysis, DNA/methods
  18. Fulltext Prevalence of human papillomavirus in abnormal cervical smears in Malaysian patients
    Sharifah NA, Seeni A, Nurismah MI, Clarence-Ko CH, Hatta AZ, Ho NP, et al.
    Asian Pac J Cancer Prev, 2009 Apr-Jun;10(2):303-6.
    PMID: 19537900
    Cervical cancer is the second most common female malignancy in Malaysia. Despite advances in treatment, the overall survival for this disease has not changed in the last decade. Infection by certain types of HPV is recognized as a causal and necessary factor for its development. This study was carried out to determine the prevalence of HPV infection in abnormal cervical smears in Malaysian patients using archival cervical smears retrieved from the Cytopathology Unit, Universiti Kebangsaan Malaysia Medical Centre (UKMMC) between the years 1992-1995. DNA was extracted from 38 abnormal smears comprising 25 intraepithelial lesions and 13 cervical carcinomas and 10 normal smears. Amplification of HPV genes was carried out using the polymerase chain reaction (PCR) technique. HPV genotypes were determined using direct sequencing and the results were compared to the database from Genebank. DNA was successfully extracted from all 48 cervical smears. High-risk HPV (HR-HPV) genotypes were detected in 95% of the abnormal smears. Eight high-risk oncogenic types were identified: 16, 18, 31, 51, 52, 56, 58 and 66. All (100%) cervical cancer smears showed presence of HR-HPV compared to 92% of the cervical intraepithelial lesions. Among the eight HR-HPV genotypes identified, HPV 16 and 52 were the commonest (23.7% each) HPV genotypes encountered and among the CIN lesions, HPV 16 (28%) was the most frequent. We conclude that HPV 16 is the most prevalent HPV genotype present in abnormal cervical smears in Malaysian patients, and that the use of archival material to assess the presence of HPV is potentially worthwhile, and can be utilized for longitudinal studies of HPV presence and persistence.
    Matched MeSH terms: DNA, Viral/analysis; DNA, Viral/genetics
  19. Phenotypic and genotypic characterisation of Blastocystis hominis isolates implicates subtype 3 as a subtype with pathogenic potential
    Tan TC, Suresh KG, Smith HV
    Parasitol Res, 2008 Dec;104(1):85-93.
    PMID: 18795333 DOI: 10.1007/s00436-008-1163-5
    Despite frequent reports on the presence of Blastocystis hominis in human intestinal tract, its pathogenicity remains a matter of intense debate. These discrepancies may be due to the varying pathogenic potential or virulence of the isolates studied. The present study represents the first to investigate both phenotypic and genotypic characteristics of B. hominis obtained from symptomatic and asymptomatic individuals. Symptomatic isolates had a significantly greater size range and lower growth rate in Jones' medium than asymptomatic isolates. The parasite cells of symptomatic isolates exhibited rougher surface topography and greater binding affinity to Canavalia ensiformis (ConA) and Helix pomatia (HPA). The present study also identifies further phenotypic characteristics, which aided in differentiating the pathogenic forms from the non-pathogenic forms of B. hominis. Blastocystis subtype 3 was found to be correlated well with the disease.
    Matched MeSH terms: DNA, Protozoan/analysis; DNA, Protozoan/genetics
  20. Molecular identification of Candida orthopsilosis isolated from blood culture
    Yong PV, Chong PP, Lau LY, Yeoh RS, Jamal F
    Mycopathologia, 2008 Feb;165(2):81-7.
    PMID: 18266075 DOI: 10.1007/s11046-007-9086-8
    The incidence of candidemia and invasive candidiasis have increased markedly due to the increasing number of immunocompromised patients. There are five major medically important species of Candida with their frequency of isolation in the diminishing order namely Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata and Candida krusei. In addition, there are numerous other species of Candida which differ in their genetic makeup, virulence properties, drug susceptibilities and sugar assimilation capabilities. In this report, an unusual Candida species was isolated from the blood of two leukaemic patients. Conventional culture and biochemical tests identified the Candida species as C. parapsilosis. Using fungal-specific oligonucleotide primers ITS1 and ITS4, we managed to amplify the ribosomal RNA gene and its internal transcribed spacer region from the genomic DNA of these isolates. The PCR products were then purified and subjected to automated DNA sequencing using BLAST and CLUSTAL sequence analysis identified these isolates to be Candida orthopsilosis. Candida orthopsilosis is a new species recently identified in 2005, being morphologically indistinguishable from C. parapsilosis and was previously classified as a subspecies of C. parapsilosis. This report highlights the importance of complementing traditional culture and biochemical-based identification methods with DNA-based molecular assays such as PCR as the latter is more superior in terms of its discriminatory power and speed.
    Matched MeSH terms: Sequence Analysis, DNA; DNA, Ribosomal Spacer/genetics
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