Displaying publications 1021 - 1040 of 3507 in total

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  1. Soil bacterial community structure in five tropical forests in Malaysia and one temperate forest in Japan revealed by pyrosequencing analyses of 16S rRNA gene sequence variation
    Miyashita NT, Iwanaga H, Charles S, Diway B, Sabang J, Chong L
    Genes Genet Syst, 2013;88(2):93-103.
    PMID: 23832301
    Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.
    Matched MeSH terms: DNA, Bacterial/genetics*; Sequence Analysis, DNA
  2. Fulltext Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber
    Heinrichs J, Scheben A, Bechteler J, Lee GE, Schäfer-Verwimp A, Hedenäs L, et al.
    PLoS One, 2016;11(5):e0156301.
    PMID: 27244582 DOI: 10.1371/journal.pone.0156301
    Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea). We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae.
    Matched MeSH terms: DNA, Plant/genetics; DNA, Plant/history
  3. Forensic timber identification: a case study of a CITES listed species, Gonystylus bancanus (Thymelaeaceae)
    Ng KKS, Lee SL, Tnah LH, Nurul-Farhanah Z, Ng CH, Lee CT, et al.
    Forensic Sci Int Genet, 2016 07;23:197-209.
    PMID: 27213560 DOI: 10.1016/j.fsigen.2016.05.002
    Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA (trnH-psbA and trnL) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring (K=2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently for random match probability estimation within respective regions. The reliability of the databases was further determined by independent self-assignment tests based on the likelihood of each individual's multilocus genotype occurring in each identified population, genetic cluster and region with an average percentage of correctly assigned individuals of 54.80%, 99.60% and 100% respectively. Thus, after appropriate validation, the genetic identification databases developed for G. bancanus in this study could support forensic applications and help safeguard this valuable species into the future.
    Matched MeSH terms: DNA Fingerprinting*; DNA Barcoding, Taxonomic
  4. The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae)
    Froufe E, Gan HM, Lee YP, Carneiro J, Varandas S, Teixeira A, et al.
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3571-2.
    PMID: 27158872 DOI: 10.3109/19401736.2015.1074223
    Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Mitochondrial/isolation & purification
  5. Fulltext Genetic Relatedness of Salmonella Serovars Isolated from Catfish (Clarias gariepinus) and Tilapia (Tilapia mossambica) Obtained from Wet Markets and Ponds in Penang, Malaysia
    Budiati T, Rusul G, Wan-Abdullah WN, Chuah LO, Ahmad R, Thong KL
    J Food Prot, 2016 Apr;79(4):659-65.
    PMID: 27052872 DOI: 10.4315/0362-028X.JFP-15-372
    A total of 43 Salmonella enterica isolates belonging to different serovars (Salmonella Albany, Salmonella Agona, Salmonella Corvallis, Salmonella Stanley, Salmonella Typhimurium, Salmonella Mikawasima, and Salmonella Bovismorbificans) were isolated from catfish (Clarias gariepinus) and tilapia (Tilapia mossambica) obtained from nine wet markets and eight ponds in Penang, Malaysia. Thirteen, 19, and 11 isolates were isolated from 9 of 32 catfish, 14 of 32 tilapia, and 11 of 44 water samples, respectively. Fish reared in ponds were fed chicken offal, spoiled eggs, and commercial fish feed. The genetic relatedness of these Salmonella isolates was determined by random amplified polymorphic DNA PCR (RAPD-PCR) using primer OPC2, repetitive extragenic palindromic PCR (REP-PCR), and pulsed-field gel electrophoresis (PFGE). Composite analysis of the RAPD-PCR, REP-PCR, and PFGE results showed that the Salmonella serovars could be differentiated into six clusters and 15 singletons. RAPD-PCR differentiated the Salmonella isolates into 11 clusters and 10 singletons, while REP-PCR differentiated them into 4 clusters and 1 singleton. PFGE differentiated the Salmonella isolates into seven clusters and seven singletons. The close genetic relationship of Salmonella isolates from catfish or tilapia obtained from different ponds, irrespective of the type of feed given, may be caused by several factors, such as the quality of the water, density of fish, and size of ponds.
    Matched MeSH terms: DNA Primers/genetics; Random Amplified Polymorphic DNA Technique
  6. Fulltext Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications
    Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, et al.
    BMC Genomics, 2016 Feb 17;17:118.
    PMID: 26884275 DOI: 10.1186/s12864-016-2448-1
    In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB).
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  7. Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium
    Yong D, Ee R, Lim YL, Yu CY, Ang GY, How KY, et al.
    J Biotechnol, 2016 Jan 10;217:51-2.
    PMID: 26603120 DOI: 10.1016/j.jbiotec.2015.11.009
    Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.
    Matched MeSH terms: DNA, Bacterial/genetics; Sequence Analysis, DNA
  8. TaqMan probe real-time polymerase chain reaction assay for the quantification of canine DNA in chicken nugget
    Rahman MM, Hamid SB, Basirun WJ, Bhassu S, Rashid NR, Mustafa S, et al.
    Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2016;33(1):10-8.
    PMID: 26458055 DOI: 10.1080/19440049.2015.1104558
    This paper describes a short-amplicon-based TaqMan probe quantitative real-time PCR (qPCR) assay for the quantitative detection of canine meat in chicken nuggets, which are very popular across the world, including Malaysia. The assay targeted a 100-bp fragment of canine cytb gene using a canine-specific primer and TaqMan probe. Specificity against 10 different animals and plants species demonstrated threshold cycles (Ct) of 16.13 ± 0.12 to 16.25 ± 0.23 for canine DNA and negative results for the others in a 40-cycle reaction. The assay was tested for the quantification of up to 0.01% canine meat in deliberately spiked chicken nuggets with 99.7% PCR efficiency and 0.995 correlation coefficient. The analysis of the actual and qPCR predicted values showed a high recovery rate (from 87% ± 28% to 112% ± 19%) with a linear regression close to unity (R(2) = 0.999). Finally, samples of three halal-branded commercial chicken nuggets collected from different Malaysian outlets were screened for canine meat, but no contamination was demonstrated.
    Matched MeSH terms: DNA/analysis*; DNA/genetics
  9. Cytogenetic and Molecular Evidence of Additional Cryptic Diversity in High Elevation Black fly Simulium feuerborni (Diptera: Simuliidae) Populations in Southeast Asia
    Pramual P, Thaijarern J, Sofian-Azirun M, Ya'cob Z, Hadi UK, Takaoka H
    J Med Entomol, 2015 Sep;52(5):829-36.
    PMID: 26336220 DOI: 10.1093/jme/tjv080
    Simulium feuerborni Edwards is geographically widespread in Southeast Asia. Previous cytogenetic study in Thailand revealed that this species is a species complex composed of two cytoforms (A and B). In this study, we cytologically examined specimens obtained from the Cameron Highlands, Malaysia, and Puncak, Java, Indonesia. The results revealed two additional cytoforms (C and D) of S. feuerborni. Specimens from Malaysia represent cytoform C, differentiated from other cytoforms by a fixed chromosome inversion on the long arm of chromosome III (IIIL-5). High frequencies of the B chromosome (33-83%) were also observed in this cytoform. Specimens from Indonesia represent the cytoform D. This cytoform is differentiated from others by a fixed chromosome inversion difference on the long arm of chromosome II (IIL-4). Mitochondrial DNA sequences support genetic differentiation among cytoforms A, B, and C. The pairwise F(ST) values among these cytoforms were highly significantly consistent with the divergent lineages of the cytoforms in a median-joining haplotype network. However, a lack of the sympatric populations prevented us from testing the species status of the cytoforms.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; DNA, Mitochondrial/metabolism
  10. Lab-on-a-chip-based PCR-RFLP assay for the confirmed detection of short-length feline DNA in food
    Ali ME, Al Amin M, Hamid SB, Hossain MA, Mustafa S
    Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2015;32(9):1373-83.
    PMID: 26208950 DOI: 10.1080/19440049.2015.1075068
    Wider availability but lack of legal market trades has given feline meat a high potential for use as an adulterant in common meat and meat products. However, mixing of feline meat or its derivatives in food is a sensitive issue, since it is a taboo in most countries and prohibited in certain religions such as Islam and Judaism. Cat meat also has potential for contamination with of severe acute respiratory syndrome, anthrax and hepatitis, and its consumption might lead to an allergic reaction. We developed a very short-amplicon-length (69 bp) PCR assay, authenticated the amplified PCR products by AluI-restriction digestion followed by its separation and detection on a lab-on-a-chip-based automated electrophoretic system, and proved its superiority over the existing long-amplicon-based assays. Although it has been assumed that longer DNA targets are susceptible to breakdown under compromised states, scientific evidence for this hypothesis has been rarely documented. Strong evidence showed that shorter targets are more stable than the longer ones. We confirmed feline-specificity by cross-challenging the primers against 10 different species of terrestrial, aquatic and plant origins in the presence of a 141-bp site of an 18S rRNA gene as a universal eukaryotic control. RFLP analysis separated 43- and 26-bp fragments of AluI-digest in both the gel-image and electropherograms, confirming the original products. The tested detection limit was 0.01% (w/w) feline meat in binary and ternary admixed as well as meatball matrices. Shorter target, better stability and higher sensitivity mean such an assay would be valid for feline identification even in degraded specimens.
    Matched MeSH terms: DNA/analysis*; DNA/genetics*
  11. The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex
    Fuchs J, Ericson PG, Bonillo C, Couloux A, Pasquet E
    Mol Ecol, 2015 Nov;24(21):5460-74.
    PMID: 26224534 DOI: 10.1111/mec.13337
    The Indo-Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such that their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from Sundaland with sequential divergence of taxa from southwest to northeast characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a ring species model driven by geographic isolation. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo-Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo-Malaya.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA
  12. Graphene-Based Materials as Solid Phase Extraction Sorbent for Trace Metal Ions, Organic Compounds, and Biological Sample Preparation
    Ibrahim WA, Nodeh HR, Sanagi MM
    Crit Rev Anal Chem, 2016 Jul 03;46(4):267-83.
    PMID: 26186420 DOI: 10.1080/10408347.2015.1034354
    Graphene is a new carbon-based material that is of interest in separation science. Graphene has extraordinary properties including nano size, high surface area, thermal and chemical stability, and excellent adsorption affinity to pollutants. Its adsorption mechanisms are through non-covalent interactions (π-π stacking, electrostatic interactions, and H-bonding) for organic compounds and covalent interactions for metal ions. These properties have led to graphene-based material becoming a desirable adsorbent in a popular sample preparation technique known as solid phase extraction (SPE). Numerous studies have been published on graphene applications in recent years, but few review papers have focused on its applications in analytical chemistry. This article focuses on recent preconcentration of trace elements, organic compounds, and biological species using SPE-based graphene, graphene oxide, and their modified forms. Solid phase microextraction and micro SPE (µSPE) methods based on graphene are discussed.
    Matched MeSH terms: DNA/isolation & purification*; DNA/chemistry
  13. Fulltext Colorimetric detection of SARS-CoV-2 by uracil-DNA glycosylase (UDG) reverse transcription loop-mediated isothermal amplification (RT-LAMP)
    Lai MY, Bukhari FDM, Zulkefli NZ, Ismail I, Mustapa NI, Soh TST, et al.
    Int J Infect Dis, 2022 Jul;120:132-134.
    PMID: 35472524 DOI: 10.1016/j.ijid.2022.04.036
    OBJECTIVES: Preventing reverse transcription loop-mediated isothermal amplification (RT-LAMP) carryover contamination could be solved by adding deoxyuridine triphosphate (dUTP) and uracil-DNA glycosylase (UDG) into the reaction master mix.

    METHODS: RNA was extracted from nasopharyngeal swab samples by a simple RNA extraction method.

    RESULTS: Testing of 77 samples demonstrated 91.2% sensitivity (95% confidence interval [CI]: 78-98.2%) and 100% specificity (95% confidence interval: 92-100%) using UDG RT-LAMP.

    CONCLUSION: This colorimetric UDG RT-LAMP is a simple-to-use, fast, and easy-to-interpret method, which could serve as an alternative for diagnosis of SARS-CoV-2 infection, especially in remote hospitals and laboratories with under-equipped medical facilities.

    Matched MeSH terms: Uracil-DNA Glycosidase/genetics; Uracil-DNA Glycosidase/metabolism
  14. Fulltext Deciphering the structural consequences of R83 and R152 methylation on DNA polymerase β using molecular modeling
    Srivastava A, Idriss H, Das G, Abedrabbo S, Shamsir MS, Homouz D
    PLoS One, 2025;20(3):e0318614.
    PMID: 40073046 DOI: 10.1371/journal.pone.0318614
    DNA polymerase β, a member of the X-family of DNA polymerases, undergoes complex regulations both in vitro and in vivo through various posttranslational modifications, including phosphorylation and methylation. The impact of these modifications varies depending on the specific amino acid undergoing alterations. In vitro, methylation of DNA polymerase β with the enzyme protein arginine methyltransferase 6 (PRMT6) at R83 and R152 enhances polymerase activity by improving DNA binding and processivity. Although these studies have shown that methylation improves DNA binding, the underlying mechanism of enhancement of polymerase activity in terms of structure and dynamics remains poorly understood. To address this gap, we modeled the methylated enzyme/DNA complex and conducted a microsecond-long simulation in the presence of Mg ions. Our results revealed significant structural changes induced by methylating both R83 and R152 sites in the enzyme. Specifically, these changes caused the DNA fragment to move closer to the C- and N-subdomains, forming additional hydrogen bonds. Furthermore, the cross-correlation map demonstrated that methylation enhanced long-range correlations within the domains/subdomains of DNA polymerase β, along with an increase in the linear mutual information value between the domains/subdomains and DNA fragments. The graph connectivity network also illustrated that methylation modulates the information pathway and identifies residues exhibiting long-distance coupling with the methylated sites. Our results provide an atomic-level understanding of the structural transition induced by methylation, shedding light on the mechanisms underlying the methylation-induced enhancement of activity in DNA polymerase β.
    Matched MeSH terms: DNA/metabolism; DNA/chemistry
  15. RNomic identification and evaluation of npcTB_6715, a non-protein-coding RNA gene as a potential biomarker for the detection of Mycobacterium tuberculosis
    Kanniappan P, Ahmed SA, Rajasekaram G, Marimuthu C, Ch'ng ES, Lee LP, et al.
    J Cell Mol Med, 2017 10;21(10):2276-2283.
    PMID: 28756649 DOI: 10.1111/jcmm.13148
    Technological advances in RNA biology greatly improved transcriptome profiling during the last two decades. Besides the discovery of many small RNAs (sRNA) that are involved in the physiological and pathophysiological regulation of various cellular circuits, it becomes evident that the corresponding RNA genes might also serve as potential biomarkers to monitor the progression of disease and treatment. sRNA gene candidate npcTB_6715 was previously identified via experimental RNomic (unpublished data), and we report its application as potential biomarker for the detection of Mycobacterium tuberculosis (MTB) in patient samples. For proof of principle, we developed a multiplex PCR assay and report its validation with 500 clinical cultures, positive for Mycobacteria. The analysis revealed 98.9% sensitivity, 96.1% specificity, positive and negative predictive values of 98.6% and 96.8%, respectively. These results underscore the diagnostic value of the sRNA gene as diagnostic marker for the specific detection of MTB in clinical samples. Its successful application and the general ease of PCR-based detection compared to standard bacterial culture techniques might be the first step towards 'point-of-care' diagnostics of Mycobacteria. To the best of our knowledge, this is the first time for the design of diagnostic applications based on sRNA genes, in Mycobacteria.
    Matched MeSH terms: Sequence Analysis, DNA/methods; DNA, Complementary/genetics; DNA, Complementary/chemistry
  16. Molecular characterization of a Toxocara variant from cats in Kuala Lumpur, Malaysia
    Zhu XQ, Jacobs DE, Chilton NB, Sani RA, Cheng NA, Gasser RB
    Parasitology, 1998 Aug;117 ( Pt 2):155-64.
    PMID: 9778638
    The ascaridoid nematode of cats from Kuala Lumpur, Malaysia, previously identified morphologically as Toxocara canis, was characterized using a molecular approach. The nuclear ribosomal DNA (rDNA) region spanning the first internal transcribed spacer (ITS-1), the 5.8S gene and the second internal transcribed spacer (ITS-2) was amplified and sequenced. The sequences for the parasite from Malaysian cats were compared with those for T. canis and T. cati. The sequence data showed that this taxon was genetically more similar to T. cati than to T. canis in the ITS-1, 5.8S and ITS-2. Differences in the ITS-1 and ITS-2 sequences between the taxa (9.4-26.1%) were markedly higher than variation between samples within T. canis and T. cati (0-2.9%). The sequence data demonstrate that the parasite from Malaysian cats is neither T. canis nor T. cati and indicate that it is a distinct species. Based on these data, PCR-linked restriction fragment length polymorphism (RFLP) and single-strand conformation polymorphism (SSCP) methods were employed for the unequivocal differentiation of the Toxocara variant from T. canis and T. cati. These methods should provide valuable tools for studying the life-cycle, transmission pattern(s) and zoonotic potential of this parasite.
    Matched MeSH terms: DNA, Ribosomal/chemistry; Sequence Analysis, DNA; DNA, Helminth/chemistry*
  17. Molecular cloning and sequence analysis of a cDNA encoding ornithine decarboxylase cDNA from chilli (Capsicum annuum)
    Zainal Z, Sajari R, Ismail I
    J. Biochem. Mol. Biol. Biophys., 2002 Dec;6(6):415-9.
    PMID: 14972797
    Ornithine decarboxylase (ODC) is an enzyme of one of the two pathways of putrescine biosynthesis in plants. The genes encoding ODC have previously been cloned from Datura stramonium and human. Using differential screening, we isolated ODC cDNA clone from a cDNA library of ripening Capsicum annuum fruit. The cDNA clone designated CUKM10 contains an insert of 1523 bp. The longest open reading frame potentially encodes a peptide of 345 amino acids with an estimated molecular mass of 47 kDa and exhibit striking similarity to other ODCs. Expression analysis showed that the capODC hybridised to a single transcript with a size of 1.7 kb. The capODC transcript was first observed in early ripening and increased steadily until it reached fully ripening stage. From the observation it is suggested that capODC is developmentally regulated especially during later stage of ripening.
    Matched MeSH terms: Sequence Analysis, DNA/methods*; DNA, Complementary/genetics; DNA, Complementary/chemistry
  18. Distinctive bacterial communities in the rhizoplane of four tropical tree species
    Oh YM, Kim M, Lee-Cruz L, Lai-Hoe A, Go R, Ainuddin N, et al.
    Microb Ecol, 2012 Nov;64(4):1018-27.
    PMID: 22767122 DOI: 10.1007/s00248-012-0082-2
    It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.
    Matched MeSH terms: DNA, Bacterial/analysis; DNA, Bacterial/genetics; Sequence Analysis, DNA/methods
  19. Fulltext Co-administration of avian influenza virus H5 plasmid DNA with chicken IL-15 and IL-18 enhanced chickens immune responses
    Lim KL, Jazayeri SD, Yeap SK, Alitheen NB, Bejo MH, Ideris A, et al.
    BMC Vet Res, 2012;8:132.
    PMID: 22866758 DOI: 10.1186/1746-6148-8-132
    DNA vaccines offer several advantages over conventional vaccines in the development of effective vaccines against avian influenza virus (AIV). However, one of the limitations of the DNA vaccine in poultry is that it induces poor immune responses. In this study, chicken interleukin (IL) -15 and IL-18 were used as genetic adjuvants to improve the immune responses induced from the H5 DNA vaccination in chickens. The immunogenicity of the recombinant plasmid DNA was analyzed based on the antibody production, T cell responses and cytokine production, following inoculation in 1-day-old (Trial 1) and 14-day-old (Trial 2) specific-pathogen-free chickens. Hence, the purpose of the present study was to explore the role of chicken IL-15 and IL-18 as adjuvants following the vaccination of chickens with the H5 DNA vaccine.
    Matched MeSH terms: DNA, Viral/genetics; DNA, Viral/immunology*; Vaccines, DNA/immunology
  20. Fulltext Reduced susceptibility of Malaysian clinical isolates of Burkholderia pseudomallei to ciprofloxacin
    Liew FY, Tay ST, Puthucheary SD
    Trop Biomed, 2011 Dec;28(3):646-50.
    PMID: 22433895 MyJurnal
    Ciprofloxacin, a quinolone with good intracellular penetration may possibly be used for treatment of melioidosis caused by Burkholderia pseudomallei, but problems with resistance may be encountered. Amino acid substitutions in gyrA/gyrB have given rise to fluoroquinolone resistance in various microorganisms. Using published primers for gyrA and gyrB, PCR was performed on 11 isolates of B. pseudomallei with varying degrees of sensitivity to ciprofloxacin, followed by DNA sequencing to detect possible mutations. Results showed an absence of any point mutation in either gene. Local isolates have yet to develop full resistance to ciprofloxacin and probably other mechanisms of resistance may have been involved in the decreased sensitivity to ciprofloxacin.
    Matched MeSH terms: Sequence Analysis, DNA; DNA Primers/genetics; DNA Gyrase/genetics
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