Displaying publications 81 - 100 of 166 in total

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  1. The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2123-4.
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  2. Haplotype data of mitochondrial DNA coding region encompassing nucleotide positions 11,719-12,184 and evaluate the importance of these positions for forensic genetic purposes in Iraq
    Hameed IH, Jebor MA, Ommer AJ, Abdulzahra AI, Yoke C
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1324-7.
    PMID: 25090379 DOI: 10.3109/19401736.2014.945576
    Samples of 100 random healthy unrelated Iraqi male persons from the Arab ethnic group of Iraqi population were collected for mtDNA coding region sequencing by using the Sanger technique and to establish the degree of variation characteristic of a fragment. Portion of coding region encompassing positions 11,719-12,184 was amplified in accordance with the Anderson reference sequence. PCR products were purified by EZ-10 spin column then sequenced and detected by using the ABI 3130xL DNA Analyzer. This is to intend the detection of polymorphisms of mtDNA. Four new polymorphic positions 11,741, 11,756, 11,878, and 12,133 are described which may be suitable in the future to be the sources for human identification purpose in Iraq. The obtained data can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants. The calculated value GD = 0.95 and RMP = 0.048 of the genetic diversity should be understood as high in the context of coding function of the analysed DNA fragment. The relatively high gene diversity and a relatively low random match probability were observed in this study.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  3. The complete mitogenome of the marine bivalve Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae)
    Gan HM, Tan MH, Thai BT, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):335-6.
    PMID: 24617474 DOI: 10.3109/19401736.2014.892104
    The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  4. The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea
    Gan HM, Tan MH, Eprilurahman R, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):337-8.
    PMID: 24617471 DOI: 10.3109/19401736.2014.892105
    The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  5. The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae)
    Gan HM, Tan MH, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):385-6.
    PMID: 24617485 DOI: 10.3109/19401736.2014.895997
    The commercial freshwater crayfish Cherax quadricarinatus complete mitochondrial genome was recovered from partial genome sequencing using the MiSeq Personal Sequencer. The mitogenome has 15,869 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of C. quadricarinatus is 32.16% for T, 23.39% for C, 33.26% for A, and 11.19% for G, with an AT bias of 65.42%.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  6. The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae)
    Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):826-7.
    PMID: 24845437 DOI: 10.3109/19401736.2014.919460
    The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  7. 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: DNA, Mitochondrial/genetics*
  8. 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
  9. DNA barcoding of shrimps from a mangrove biodiversity hotspot
    Jamaluddin JAF, Mohammed Akib NA, Ahmad SZ, Abdul Halim SAA, Abdul Hamid NK, Mohd Nor SA
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 05;30(4):618-625.
    PMID: 31012766 DOI: 10.1080/24701394.2019.1597073
    A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  10. Variations in mitochondrial DNA control region among Malay and Chinese subpopulations (sequence 16000-16200)
    Ishar SM, Parameswaran K, Masduki NS, Rus Din RD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 12;30(8):843-847.
    PMID: 31709874 DOI: 10.1080/24701394.2019.1687693
    DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000-16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  11. Next generation sequencing yields the complete mitochondrial genome of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae)
    Shen KN, Chang CW, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4118-4119.
    PMID: 25600747
    In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  12. The complete mitochondrial genome of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae)
    Shen KN, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4122-4123.
    PMID: 25585497
    In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  13. Tracking the southern river terrapin (Batagur affinis) through environmental DNA: prospects and challenges
    Wilson JJ, Sing KW, Chen PN, Zieritz A
    Mitochondrial DNA A DNA Mapp Seq Anal, 2018 08;29(6):862-866.
    PMID: 28885060 DOI: 10.1080/24701394.2017.1373109
    Environmental DNA detection has emerged as a powerful tool to monitor aquatic species without the need for capture or visual identification and is particularly useful for rare or elusive species. Our objective was to develop an eDNA approach for detecting the southern river terrapin (Batagur affinis) in Malaysia. We designed species-specific primers for a fragment of B. affinis mtDNA and evaluated their effectiveness in silico, in vitro and in situ. The primers amplified 110 bp of the cytochrome b mtDNA sequence of B. affinis from aquarium water samples housing nine juvenile B. affinis. We also successfully detected B. affinis eDNA from river samples taken from a site where turtles were known to be in the vicinity. Prospects and challenges of using an eDNA approach to help determine the distribution of B. affinis, essential information for an effective conservation plan, are discussed.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  14. Complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi (Sauria, Gekkota, Gekkonidae)
    Yan J, Tian C, Zhou J, Bauer AM, Lee Grismer L, Zhou K
    Mitochondrial DNA, 2014 Jun;25(3):181-2.
    PMID: 23631365 DOI: 10.3109/19401736.2013.792066
    We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  15. Old World screwworm fly, Chrysomya bezziana, occurs as two geographical races
    Hall MJ, Edge W, Testa JM, Adams ZJ, Ready PD
    Med Vet Entomol, 2001 Dec;15(4):393-402.
    PMID: 11776458
    A morphological and molecular analysis was undertaken with the objective of identifying markers for geographical populations of Old World screwworm flies, Chrysomya bezziana Villeneuve (Diptera: Calliphoridae). The morphological analysis involved 192 adult flies from 14 countries, and the molecular analysis involved 45 larvae or adults from 14 populations in 11 countries. Principal components and cluster analysis of 10 morphological characters indicated that flies from Papua New Guinea (PNG) were a distinct group and most similar to flies from nearby Asian islands (Java, Sabah). There was poor resolution of other geographical regions, but some support for clustering of flies from Africa or India. Cladistic analysis of mitochondrial DNA sequences gave strong support for recognizing two races of Old World screwworm, one from sub-Saharan Africa and the other from the Gulf region and Asia. This latter race could be further divided into two lineages, i.e. one from mainland Asia (from Iraq to the Malay Peninsula) and the other from two islands of PNG.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  16. Mitochondrial diversity of Musca domestica housefly populations in the Asian and western Pacific biogeographical regions
    Marquez JG, Bangs MJ, Krafsur ES
    Med Vet Entomol, 2003 Dec;17(4):429-35.
    PMID: 14651658
    Houseflies (Musca domestica L., Diptera: Muscidae) are cosmopolitan, colonizing, and eusynanthropic. Their distribution in the Malaysian archipelago provides an opportunity to study successive waves of colonization and extinction during the Pleistocene and Recent epochs. We scored single-strand conformation polymorphisms (SSCPs) at 16S2 and COII mitochondrial loci in 47 housefly samples from the Australian, Austro-Malayan, Indo-Malayan, Manchurian and Indo-Chinese subregions of Wallace's zoogeographical classification. We discuss the results in light of the Pleistocene vs. post-Pleistocene dispersal and faunal exchange in the Asia-Pacific area. Fourteen haplotypes were detected, of which 10 were confined to a single subregion. No haplotype was ubiquitous and only one was found in four subregions. Population diversity, HS, was greatest in the Indo-Malayan (0.36) and heterogeneous among subregions. The mean subregional diversity was 0.21 +/- 0.03, representing the probability that two randomly chosen flies, from any subregion, had different haplotypes. The hierarchical partition of diversity indicated restricted maternal gene flow among subregions (GRT = 0.60, Nm approximately 0.32). These results suggest long-standing genetic isolation of houseflies in the Malaysian archipelago and support the hypothesis that they dispersed widely during the Pleistocene. Haplotypes common among mainland populations but shared with island groups in low frequencies (<1%) indicate surprisingly little recent gene flow.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  17. Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia
    Low VL, Lim PE, Chen CD, Lim YA, Tan TK, Norma-Rashid Y, et al.
    Med Vet Entomol, 2014 Jun;28(2):157-68.
    PMID: 23848279 DOI: 10.1111/mve.12022
    The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  18. Fulltext A simple, high-throughput, colourimetric, field applicable loop-mediated isothermal amplification (HtLAMP) assay for malaria elimination
    Britton S, Cheng Q, Sutherland CJ, McCarthy JS
    Malar J, 2015;14:335.
    PMID: 26315027 DOI: 10.1186/s12936-015-0848-3
    To detect all malaria infections in elimination settings sensitive, high throughput and field deployable diagnostic tools are required. Loop-mediated isothermal amplification (LAMP) represents a possible field-applicable molecular diagnostic tool. However, current LAMP platforms are limited by their capacity for high throughput.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  19. Sequence polymorphism of the mitochondrial DNA hypervariable regions I and II in 205 Singapore Malays
    Wong HY, Tang JS, Budowle B, Allard MW, Syn CK, Tan-Siew WF, et al.
    Leg Med (Tokyo), 2007 Jan;9(1):33-7.
    PMID: 17150401
    Mitochondrial DNA sequences of the hypervariable regions HV1 and HV2 were analyzed in 205 unrelated ethnic Malays residing in Singapore as an initial effort to generate a database for forensic identification purposes. Sequence polymorphism was detected using PCR and direct sequencing analysis. A total of 152 haplotypes was found containing 152 polymorphisms. Out of the 152 haplotypes, 115 were observed only once and 37 types were seen in multiple individuals. The most common haplotype (16223T, 16295T, 16362C, 73G, 146C, 199C, 263G, and 315.1C) was shared by 7 (3.41%) individuals, two haplotypes were shared by 4 individuals, seven haplotypes were shared by 3 individuals, and 27 haplotypes by 2 individuals. Haplotype diversity and random match probability were estimated to be 0.9961% and 0.87%, respectively.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  20. Fulltext Prevalence of mitochondrial DNA common deletion in patients with gliomas and meningiomas: A first report from a Malaysian study group
    Mohamed Yusoff AA, Mohd Khair SZN, Abd Radzak SM, Idris Z, Lee HC
    J Chin Med Assoc, 2020 Sep;83(9):838-844.
    PMID: 32732530 DOI: 10.1097/JCMA.0000000000000401
    BACKGROUND: The 4977-bp common deletion (mtDNA) is a well-established mitochondrial genome alteration that has been described in various types of human cancers. However, to date, no studies on mtDNA in brain tumors have been reported. The present study aimed to determine mtDNA prevalence in common brain tumors, specifically, low- and high-grade gliomas (LGGs and HGGs), and meningiomas in Malaysian cases. Its correlation with clinicopathological parameters was also evaluated.

    METHODS: A total of 50 patients with pathologically confirmed brain tumors (13 LGGs, 20 HGGs, and 17 meningiomas) were enrolled in this study. mtDNA was detected by using polymerase chain reaction (PCR) technique and later confirmed via Sanger DNA sequencing.

    RESULTS: Overall, mtDNA was observed in 16 (32%) patients and it was significantly correlated with the type of tumor group and sex, being more common in the HGG group and in male patients.

    CONCLUSION: The prevalence of mtDNA in Malaysian glioma and meningioma cases has been described for the first time and it was, indeed, comparable with previously published studies. This study provides initial insights into mtDNA in brain tumor and these findings can serve as new data for the global mitochondrial DNA mutations database.

    Matched MeSH terms: DNA, Mitochondrial/genetics*
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