Displaying publications 161 - 180 of 867 in total

Abstract:
Sort:
  1. Novel black yeast-like species in chaetothyriales with ant-associated life styles
    Quan Y, Ahmed SA, Menezes da Silva N, Al-Hatmi AMS, Mayer VE, Deng S, et al.
    Fungal Biol, 2021 Apr;125(4):276-284.
    PMID: 33766306 DOI: 10.1016/j.funbio.2020.11.006
    Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.
    Matched MeSH terms: Sequence Analysis, DNA
  2. A description of Joostella sp. strain CR20 with potential biotechnological applications
    Zakaria MR, Vodovnik M, Zorec M, Liew KJ, Tokiman L, Chong CS
    Antonie Van Leeuwenhoek, 2024 Nov 29;118(1):38.
    PMID: 39613983 DOI: 10.1007/s10482-024-02045-w
    The underexplored halophilic genus Joostella within the Flavobacteriaceae family consists of only two species, both of which have received little attention for their potential biotechnological applications. In this study, we report the isolation and characterisation of a novel halophilic bacterium, strain CR20, using a genomic approach to investigate its biotechnological potential. Analysis of the 16S rRNA gene revealed that strain CR20 shares 97.5% and 96.2% sequence similarity with Joostella marina DSM 19592 T and Joostella atrarenae M1-2 T, respectively. Strain CR20 exhibited average nucleotide identity and digital DNA-DNA hybridisation values of 76.8-79.1% and 20.8-22.8%, respectively, with Joostella spp., which fall below the species delineation thresholds. Additionally, strain CR20 demonstrated average amino acid identity and percentage of conserved proteins values of 81.3-84.0% and 71.7-75.3%, respectively, with Joostella spp., above the genus delineation thresholds. Meanwhile, the average amino acid identity and percentage of conserved proteins values of strain CR20 against Galbibacter spp. are 73.9-80.0% and 61.3-72.3%, respectively, also above the genus delineation thresholds. These findings indicated strain CR20 has a close relationship with both genera. Chemotaxonomic analysis of strain CR20 identified predominant fatty acids, including iso-C17:0 3OH (25.3%), iso-C15:0 (14%), and C16:1 ω6c/C16:1 ω7c (12.2%). The assembled genome comprises 62 contigs, with a size of approximately 3,168,727 bp and a G + C content of 35.1%. Among 2,804 predicted genes, 2,559 were classified into 25 COG functional groups. A total of 68 genes with potential industrial applications were identified, including 1 β-mannanase, 2 β-xylosidases, 1 polysaccharide deacetylase, 4 other hemicellulases, 6 β-glucosidases, 25 proteases, and 29 phosphate-solubilising enzymes. Hydrolytic assays confirmed that strain CR20 produces these enzymes extracellularly. These findings highlight strain CR20 has potential for industrial applications.
    Matched MeSH terms: Sequence Analysis, DNA
  3. The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae)
    Austin CM, Tan MH, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4176-4177.
    PMID: 25630729
    Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  4. Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region
    Lee NK, Fong PK, Abdullah MT
    Biomed Mater Eng, 2014;24(6):3807-14.
    PMID: 25227097 DOI: 10.3233/BME-141210
    Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  5. Colorimetric detection of DNA hybridization based on a dual platform of gold nanoparticles and graphene oxide
    Thavanathan J, Huang NM, Thong KL
    Biosens Bioelectron, 2014 May 15;55:91-8.
    PMID: 24368225 DOI: 10.1016/j.bios.2013.11.072
    The unique property of gold nanoparticles (Au NP) to induce colour change and the versatility of graphene oxides (GO) in surface modification makes them ideal in the application of colorimetric biosensor. Thus we developed a label free optical method to detect DNA hybridization through a visually observed colour change. The Au NP is conjugated to a DNA probe and is allowed to hybridize with the DNA target to the GO thus causing a change in colour from pinkish-red to purplish blue. Spectrophometry analysis gave a wavelength shift of 22 nm with 1 µM of DNA target. Sensitivity testing using serially diluted DNA conjugated GO showed that the optimum detection was at 63 nM of DNA target with the limit at 8 nM. This proves the possibility for the detection of DNA hybridization through the use of dual nanoparticle system by visual observation.
    Matched MeSH terms: Sequence Analysis, DNA/instrumentation
  6. Detection and molecular characterization of infectious spleen and kidney necrosis virus from major ornamental fish breeding states in Peninsular Malaysia
    Subramaniam K, Shariff M, Omar AR, Hair-Bejo M, Ong BL
    J Fish Dis, 2014 Jul;37(7):609-18.
    PMID: 23952914 DOI: 10.1111/jfd.12152
    'Gold standard' OIE reference PCR assay was utilized to detect the presence of infectious spleen and kidney necrosis virus (ISKNV) in freshwater ornamental fish from Malaysia. From total of 210 ornamental fish samples representing 14 species, ISKNV was detected in 36 samples representing 5 fish species. All positive cases did not show any clinical signs of ISKNV. Three restriction enzymes analyses showed that the fish were infected by identical strains of the same virus species within Megalocytivirus genus. Major capsid protein (MCP) genes of 10 ISKNV strains were sequenced and compared with 9 other reference nucleotide sequences acquired from GenBank. Sequence analysis of MCP gene showed that all strains detected in this study were closely related to the reference ISKNV with nucleotide sequence identity that was ranging from 99.8% to 100%. In addition, phylogenetic analysis of MCP gene revealed that viruses from genus Megalocytivirus can be divided into three genotypes: genotype 1 include reference ISKNV and all other strains that were detected in this study, genotype 2 include viruses closely related to red sea bream iridovirus (RSIV), and genotype 3 include viruses closely related turbot reddish body iridovirus (TRBIV).
    Matched MeSH terms: Sequence Analysis, DNA/veterinary
  7. Fulltext Blood meal analysis of tabanid fly after it biting the rare Sumatran rhinoceros
    Rovie-Ryan JJ, Zainuddin ZZ, Marni W, Ahmad AH, Ambu LN, Payne J
    Asian Pac J Trop Biomed, 2013 Feb;3(2):95-9.
    PMID: 23593586 DOI: 10.1016/S2221-1691(13)60031-3
    To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly.
    Matched MeSH terms: Sequence Analysis, DNA/veterinary
  8. 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: Sequence Analysis, DNA/methods
  9. Fulltext Genetic characterization of Japanese encephalitis virus genotype II strains isolated from 1951 to 1978
    Schuh AJ, Tesh RB, Barrett AD
    J Gen Virol, 2011 Mar;92(Pt 3):516-27.
    PMID: 21123550 DOI: 10.1099/vir.0.027110-0
    Japanese encephalitis virus (JEV), the prototype member of the JEV serocomplex, genus Flavivirus, family Flaviviridae, is the most significant arthropod-borne encephalitis worldwide in terms of morbidity and mortality. At least four genotypes (GI-GIV) of the virus have been identified; however, to date, the genomic nucleotide sequence of only one GII virus has been determined (FU strain, Australia, 1995). This study sequenced three additional GII strains of JEV isolated between 1951 and 1978 in Korea, Malaysia and Indonesia, respectively, and compared them with the FU strain, as well as with virus strains representing the other three genotypes. Based on nucleotide and amino acid composition, the genotype II strains were the most similar to GI strains; however, these two genotypes are epidemiologically distinct. Selection analyses revealed that the strains utilized in this study are under predominantly purifying selection, and evidence of positive selection was detected at aa 24 of the NS4B protein, a protein that functions as an alpha/beta interferon signalling inhibitor.
    Matched MeSH terms: Sequence Analysis, DNA*
  10. Sequence analysis and characterization of vacuolar-type H+ -ATPase proteolipid transcript from Acanthus ebracteatus Vah1
    Ho CL, Nguyen PD, Harikrishna JA, Rahim RA
    DNA Seq., 2008 Feb;19(1):73-7.
    PMID: 17852357
    The vacuolar-type H+ -ATPase (V-ATPase) is a multimeric enzyme with diverse functions in plants such as nutrient transport, flowering, stress tolerance, guard cell movement and development. A partial sequence of V-ATPase proteolipid was identified among the expressed sequence tags (ESTs) generated from Acanthus ebracteatus, and selected for full-length sequencing. The 876-nucleotide cDNA consists of an open reading frame of 165 amino acids. The deduced amino acid sequence displays high similarity (81%) with its homologs from Arabidopsis thaliana, Avecinnia marina and Gossypium hirsutum with the four transmembrane domains characteristics of the 16 kDa proteolipid subunit c of V-ATPase well conserved in this protein. Southern analysis revealed the existence of several members of proteolipid subunit c of V-ATPase in A. ebracteatus. The mRNA of this gene was detected in leaf, floral, stem and root tissues, however, the expression level was lower in stem and root tissues.
    Matched MeSH terms: Sequence Analysis, DNA*
  11. Characterization of Malaysian velogenic NDV strain AF2240-I genomic sequence: a comparative study
    Murulitharan K, Yusoff K, Omar AR, Molouki A
    Virus Genes, 2013 Jun;46(3):431-40.
    PMID: 23306943 DOI: 10.1007/s11262-012-0874-y
    Newcastle disease virus (NDV) strain AF2240 is a viscerotropic velogenic strain that is used as a vaccine challenge virus in Malaysia. The identification of the full length genome will be a crucial platform for further studies of this isolate. In this study, we fully sequenced the genome of a derivative of this strain named AF2240-I. The 15,192 nt long genome contains a 55-nt leader sequence at the 3' whereas the trailer region consists of 114 nt at the 5'. The intergenic sequences between the NP-P, P-M, M-F, F-HN, and HN-L genes comprise 1, 1, 1, 31, and 47 nt, respectively. The acknowledged cleavage site of fusion protein showed amino acid sequence of 112-R-R-Q-K-R-F-117, which corresponds to those of virulent NDV strains. Phylogenetic analysis of the whole virus genome shows that the strain AF2240-I belongs to genotype VIII and is more closely related to velogenic strains QH1, QH4, Fontana, Largo, and Italienas compared to other strains of NDV. Differences are noticed in the hemagglutinin-neuraminidase (HN) and matrix (M) gene between AF2240 and its derivative AF2240-I. This is the first report of a complete genome sequence of an NDV strain isolated in Malaysia.
    Matched MeSH terms: Sequence Analysis, DNA*
  12. The complete mitochondrial genome of Bactrocera diaphora (Diptera: Tephtitidae)
    Zhang KJ, Liu L, Rong X, Zhang GH, Liu H, Liu YH
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4314-4315.
    PMID: 26462416
    We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  13. In vitro isolation and molecular identification of reptarenavirus in Malaysia
    Abba Y, Hassim H, Hamzah H, Ibrahim OE, Ilyasu Y, Bande F, et al.
    Virus Genes, 2016 Oct;52(5):640-50.
    PMID: 27142080 DOI: 10.1007/s11262-016-1345-7
    Boid inclusion body disease (BIBD) is a viral disease of boids caused by reptarenavirus. In this study, tissue from naturally infected boid snakes were homogenized and propagated in African Monkey kidney (Vero) and rat embryonic fibroblast (REF) cells. Virus replication was determined by the presence of cytopathic effect, while viral morphology was observed using transmission electron microscopy. Viral RNA was amplified using RT-PCR with primers specific for the L-segment of reptarenavirus; similarly, quantification of viral replication was done using qPCR at 24-144 h postinfection. Viral cytopathology was characterized by cell rounding and detachment in both Vero and REF cells. The viral morphology showed round-to-pleomorphic particles ranging from 105 to 150 nm which had sand-like granules. Sanger sequencing identified four closely associated reptarenavirus species from 15 (37.5 %) of the total samples tested, and these were named as follows: reptarenavirus UPM-MY 01, 02, 03, and 04. These isolates were phylogenetically closely related to the University Helsinki virus (UHV), Boa Arenavirus NL (ROUTV; BAV), and unidentified reptarenavirus L20 (URAV-L20). Comparison of deduced amino acid sequences further confirmed identities to L-protein of UHV, L-polymerase of BAV and RNA-dependent RNA polymerase of URAV-L20. Viral replication in Vero cells increased steadily from 24 to 72 h and peaked at 144 h. This is the first study in South East Asia to isolate and characterize reptarenavirus in boid snakes with BIBD.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  14. Complete sequence analyses of enterovirus 71 strains from fatal and non-fatal cases of the hand, foot and mouth disease outbreak in Singapore (2000)
    Singh S, Poh CL, Chow VT
    Microbiol. Immunol., 2002;46(11):801-8.
    PMID: 12516778
    Enterovirus 71 (EV71) is a major aetiological agent of hand, foot and mouth disease (HFMD). In recent years, several outbreaks in East Asia were associated with neurological complications and numerous deaths. An outbreak in Singapore in October 2000 afflicted thousands of children, resulting in four fatal cases from three of whom EV71 was isolated. The genomes of two representative EV71 strains isolated from a fatal case and a surviving patient were completely sequenced, and their nucleotide and amino acid sequences compared with known EV71 strains. The two outbreak strains were classified under genogroup B, together with those previously isolated in Singapore, Malaysia and Japan. Comparative sequence analysis of the two Singapore strains revealed 99% nucleotide similarity, while their deduced amino acid sequences were almost identical except for residue 1506 in the 3A non-structural region. Given that the outbreak involved closely related genetic variants of EV71, the broad spectrum of disease severity may be attributed to critical factors such as varying viral inoculation doses or differing host immune responses following infection, but is less likely to be due to the emergence of EV71 strains with heightened virulence.
    Matched MeSH terms: Sequence Analysis, DNA*
  15. Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation
    Lau CH, Drinkwater RD, Yusoff K, Tan SG, Hetzel DJ, Barker JS
    Anim. Genet., 1998 Aug;29(4):253-64.
    PMID: 9745663
    Swamp and river buffalo mitochondrial DNA (mtDNA) was sequenced for 303 bp of the cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations. Only one cytochrome b haplotype was found in river buffalo. Of the four haplotypes identified in swamp buffalo, one found in all populations is apparently ancestral both to the other swamp haplotypes and to the river haplotype. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only, also support the evolution of domesticated swamp and river buffalo from an ancestral swamp-like animal, most likely represented today by the wild Asian buffalo (Bubalus arnee). The time of divergence of the swamp and river types, estimated from the D-loop data, is 28,000 to 87,000 years ago. We hypothesise that the species originated in mainland south-east Asia, and that it spread north to China and west to the Indian subcontinent, where the rive type evolved and was domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland south-east Asia and then to the western islands of Indonesia.
    Matched MeSH terms: Sequence Analysis, DNA/veterinary
  16. Fulltext Characterization and comparative sequence analysis of the DNA mismatch repair MSH2 and MSH7 genes from tomato
    Tam SM, Samipak S, Britt A, Chetelat RT
    Genetica, 2009 Dec;137(3):341-54.
    PMID: 19690966 DOI: 10.1007/s10709-009-9398-3
    DNA mismatch repair proteins play an essential role in maintaining genomic integrity during replication and genetic recombination. We successfully isolated a full length MSH2 and partial MSH7 cDNAs from tomato, based on sequence similarity between MutS and plant MSH homologues. Semi-quantitative RT-PCR reveals higher levels of mRNA expression of both genes in young leaves and floral buds. Genetic mapping placed MSH2 and MSH7 on chromosomes 6 and 7, respectively, and indicates that these genes exist as single copies in the tomato genome. Analysis of protein sequences and phylogeny of the plant MSH gene family show that these proteins are evolutionarily conserved, and follow the classical model of asymmetric protein evolution. Genetic manipulation of the expression of these MSH genes in tomato will provide a potentially useful tool for modifying genetic recombination and hybrid fertility between wide crosses.
    Matched MeSH terms: Sequence Analysis, DNA*
  17. Fulltext Whole Genome Sequencing-Based Molecular Epidemiologic Analysis of Autochthonous Dengue Virus Type 1 Strains Circulating in Japan in 2014
    Tajima S, Nakayama E, Kotaki A, Moi ML, Ikeda M, Yagasaki K, et al.
    Jpn J Infect Dis, 2017 Jan 24;70(1):45-49.
    PMID: 27169954 DOI: 10.7883/yoken.JJID.2016.086
    Cases of autochthonous infections of dengue virus type 1 (DENV-1) were detected in Japan after a 70-year period devoid of dengue outbreaks. We previously showed that E gene sequences are identical in 11 of the 12 DENV-1 strains autochthonous to Japan. However, the E sequence represents only 14% of the DENV-1 genome. In the present study, we have sequenced the entire genome of 6 autochthonous DENV-1 strains that were isolated from patients during the 2014 outbreak. Sequencing of 5 Yoyogi group strains with identical E sequences and 1 Shizuoka strain with a different E sequence revealed that the first Yoyogi group strain differed from the Shizuoka strain by 18 amino acid residues. Furthermore, 2 Yoyogi group strains had different genomic sequences while the other 3 had identical genomes. Phylogenetic analyses indicated that the Hyogo strain, a Yoyogi group strain, was the first to diverge from the other 4 Yoyogi group strains. The E gene sequence of the Yoyogi group strains exhibits the highest homology to those of the strains isolated in Malaysia and Singapore between 2013 and 2014. The patient infected with the Hyogo strain visited Malaysia before the onset of dengue fever, suggesting that this was a case of dengue infection imported from Malaysia.
    Matched MeSH terms: Sequence Analysis, DNA*
  18. Fulltext The effects of daily fasting hours on shaping gut microbiota in mice
    Li L, Su Y, Li F, Wang Y, Ma Z, Li Z, et al.
    BMC Microbiol, 2020 03 24;20(1):65.
    PMID: 32209070 DOI: 10.1186/s12866-020-01754-2
    BACKGROUND: It has recently been reported that intermittent fasting shapes the gut microbiota to benefit health, but this effect may be influenced to the exact fasting protocols. The purpose of this study was to assess the effects of different daily fasting hours on shaping the gut microbiota in mice. Healthy C57BL/6 J male mice were subjected to 12, 16 or 20 h fasting per day for 1 month, and then fed ad libitum for an extended month. Gut microbiota was analyzed by 16S rRNA gene-based sequencing and food intake was recorded as well.

    RESULTS: We found that cumulative food intake was not changed in the group with 12 h daily fasting, but significantly decreased in the 16 and 20 h fasting groups. The composition of gut microbiota was altered by all these types of intermittent fasting. At genus level, 16 h fasting led to increased level of Akkermansia and decreased level of Alistipes, but these effects disappeared after the cessation of fasting. No taxonomic differences were identified in the other two groups.

    CONCLUSIONS: These data indicated that intermittent fasting shapes gut microbiota in healthy mice, and the length of daily fasting interval may influence the outcome of intermittent fasting.

    Matched MeSH terms: Sequence Analysis, DNA/methods*
  19. DNA sequence analysis of a small cryptic plasmid from Lactococcus lactis subsp. lactis M14
    Raha AR, Hooi WY, Mariana NS, Radu S, Varma NR, Yusoff K
    Plasmid, 2006 Jul;56(1):53-61.
    PMID: 16675013
    A small plasmid designated pAR141 was isolated from Lactococcus lactis subsp. lactis M14 and its complete 1,594 base pair nucleotide sequence was determined. Analysis of the sequence indicated that this plasmid does not carry any industrially important determinants besides the elements involved in plasmid replication and control. The transcriptional repressor CopG and replication initiation protein RepB appeared as a single operon. A small countertranscribed RNA (ctRNA) coding region was found between the copG and repB genes. The double strand origin (dso) and single strand origin (sso) of rolling circle replicating (RCR) plasmids were also identified in pAR141, suggesting that this plasmid replicates by rolling circle (RC) mode. This observation was supported by S1 nuclease and Southern hybridization analyses.
    Matched MeSH terms: Sequence Analysis, DNA*
  20. Prevalence and molecular study of G6PD deficiency in Malaysian Orang Asli
    Amini F, Ismail E, Zilfalil BA
    Intern Med J, 2011 Apr;41(4):351-3.
    PMID: 21507164 DOI: 10.1111/j.1445-5994.2011.02456.x
    This study aims to define the prevalence and the molecular basis of G6PD deficiency in the Negrito tribe of the Malaysian Orang Asli. Four hundred and eighty seven consenting Negrito volunteers were screened for G6PD deficiency through the use of a fluorescent spot test. DNA from deficient individuals underwent PCR-RFLP analysis using thirteen recognized G6PD mutations. In the instances when the mutation could not be identified by PCR-RFLP, the entire coding region of the G6PD gene was subjected to DNA sequencing. In total, 9% (44/486) of the sample were found to be G6PD-deficient. However, only 25 samples were subjected to PCR-RFLP and DNA sequencing. Of these, three were found to carry Viangchan, one Coimbra and 16, a combination of C1311T in exon 11 and IVS11 T93C. Mutation(s) for the five remaining samples are unknown. The mean G6PD enzyme activity ranged 5.7 IU/gHb in deficient individuals. Our results demonstrate that the frequency of G6PD deficiency is higher among the Negrito Orang Asli than other Malaysian races. The dual presence of C1311T and IVS11 T93C in 64% of the deficient individuals (16/44) could well be a result of genetic drift within this isolated group.
    Matched MeSH terms: Sequence Analysis, DNA/methods
Related Terms
Filters
Contact Us

Please provide feedback to Administrator ([email protected])

External Links