Displaying publications 61 - 80 of 262 in total

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  1. Fulltext Role of mitochondrial DNA mutations in brain tumors: A mini-review
    Mohamed Yusoff AA
    J Cancer Res Ther, 2015 Jul-Sep;11(3):535-44.
    PMID: 26458578 DOI: 10.4103/0973-1482.161925
    Brain tumor is molecularly a heterogeneous group of diseases, and genetic factors seem to play a crucial role in its genesis. Even though multiple alterations in the nuclear-encoded genes such as tumor suppressor and oncogenes are believed to play a key role in brain tumorigenesis, the involvement of the mitochondrial genome to this event remains controversial to date. Mitochondrial DNA (mtDNA) has been suspected to be associated with the carcinogenesis because of its high sensitivity to mutations and inefficient repair mechanisms in comparison to nuclear DNA. Thus, defects in mtDNA could also lead to the development of brain tumor. By virtue of their clonal nature and high copy number, mtDNA mutations may provide a new effective molecular biomarker for the cancer detection. It has been suggested that establishing mtDNA defective pattern might be useful in cancer diagnostics and detection, the prognosis of cancer outcome, and/or the response to certain treatments. This mini-review gives a brief overview on the several aspects of mtDNA, with a particular focus on its role in tumorigenesis and progression of brain tumor. Understanding the role of mitochondria and brain tumor development could potentially translate into therapeutic strategies for patients with these tumors.
    Matched MeSH terms: DNA, Mitochondrial
  2. Fulltext Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data
    Aketarawong N, Isasawin S, Sojikul P, Thanaphum S
    Zookeys, 2015.
    PMID: 26798262 DOI: 10.3897/zookeys.540.10058
    The Carambola fruit fly, Bactrocera carambolae, is an invasive pest in Southeast Asia. It has been introduced into areas in South America such as Suriname and Brazil. Bactrocera carambolae belongs to the Bactrocera dorsalis species complex, and seems to be separated from Bactrocera dorsalis based on morphological and multilocus phylogenetic studies. Even though the Carambola fruit fly is an important quarantine species and has an impact on international trade, knowledge of the molecular ecology of Bactrocera carambolae, concerning species status and pest management aspects, is lacking. Seven populations sampled from the known geographical areas of Bactrocera carambolae including Southeast Asia (i.e., Indonesia, Malaysia, Thailand) and South America (i.e., Suriname), were genotyped using eight microsatellite DNA markers. Genetic variation, genetic structure, and genetic network among populations illustrated that the Suriname samples were genetically differentiated from Southeast Asian populations. The genetic network revealed that samples from West Sumatra (Pekanbaru, PK) and Java (Jakarta, JK) were presumably the source populations of Bactrocera carambolae in Suriname, which was congruent with human migration records between the two continents. Additionally, three populations of Bactrocera dorsalis were included to better understand the species boundary. The genetic structure between the two species was significantly separated and approximately 11% of total individuals were detected as admixed (0.100 ≤ Q ≤ 0.900). The genetic network showed connections between Bactrocera carambolae and Bactrocera dorsalis groups throughout Depok (DP), JK, and Nakhon Sri Thammarat (NT) populations. These data supported the hypothesis that the reproductive isolation between the two species may be leaky. Although the morphology and monophyly of nuclear and mitochondrial DNA sequences in previous studies showed discrete entities, the hypothesis of semipermeable boundaries may not be rejected. Alleles at microsatellite loci could be introgressed rather than other nuclear and mitochondrial DNA. Bactrocera carambolae may be an incipient rather than a distinct species of Bactrocera dorsalis. Regarding the pest management aspect, the genetic sexing Salaya5 strain (SY5) was included for comparison with wild populations. The SY5 strain was genetically assigned to the Bactrocera carambolae cluster. Likewise, the genetic network showed that the strain shared greatest genetic similarity to JK, suggesting that SY5 did not divert away from its original genetic makeup. Under laboratory conditions, at least 12 generations apart, selection did not strongly affect genetic compatibility between the strain and wild populations. This knowledge further confirms the potential utilization of the Salaya5 strain in regional programs of area-wide integrated pest management using SIT.
    Matched MeSH terms: DNA, Mitochondrial
  3. Assessing diet of the rufous-winged philentoma (philentoma pyrhoptera) in lowland tropical forest using next-generation sequencing
    Mohammad Saiful Mansor, Shukor Md. Nor, Rosli Ramli
    Sains Malaysiana, 2018;47:1045-1050.
    Dietary study provides understanding in predator-prey relationships, yet diet of tropical forest birds is poorly understood.
    In this study, a non-invasive method, next-generation sequencing (Illumina MiSeq platform) was used to identify prey in
    the faecal samples of the Rufous-winged Philentoma (Philentoma pyrhoptera). Dietary samples were collected in lowland
    tropical forest of central Peninsular Malaysia. A general invertebrate primer pair was used for the first time to assess
    diet of tropical birds. The USEARCH was used to cluster the COI mtDNA sequences into Operational Taxonomic Unit (OTU).
    OTU sequences were aligned and queried through the GenBank or Biodiversity of Life Database (BOLD). We identified
    26 distinct arthropod taxa from 31 OTUs. Of all OTUs, there was three that could be identified up to species level, 20 to
    genus level, three to family level and five could not assigned to any taxa (the BLAST hits were poor). All sequences were
    identified to class Insecta belonging to 18 families from four orders, where Lepidoptera representing major insect order
    consumed by study bird species. This non-invasive molecular approach provides a practical and rapid technique to
    understand of how energy flows across ecosystems. This technique could be very useful to screen for possible particular
    pest insects consumed by insectivores (e.g. birds and bats) in crop plantation. A comprehensive arthropod studies and
    local reference sequences need to be added to the database to improve the proportion of sequences that can be identified.
    Matched MeSH terms: DNA, Mitochondrial
  4. Fulltext Sequence variation data of the mitochondrial DNA D-loop region of the captive Malayan Gaur (Bos gaurus hubbacki)
    Md-Zain BM, Abdul-Aziz A, Aifat NR, Mohd-Yusof NS, Zulkifli NA, Japning JRR, et al.
    Data Brief, 2019 Jun;24:103532.
    PMID: 31193484 DOI: 10.1016/j.dib.2018.11.117
    This article contains data of the sequence variation in the mitochondrial DNA D-loop region of the Malayan gaur (Bos gaurus hubbacki), locally known as the seladang, from two captive centers. Thirty fecal samples of Malayan gaur were collected from Jenderak Selatan Wildlife Conservation Center (Pahang) and the Sungkai Wildlife Reserve (Perak) for DNA extraction and amplification with polymerase chain reactions. DNA sequences were then analyzed using neighbor joining (NJ) and maximum parsimony (MP) methods. Based on the 652 base pairs obtained, we found seven variable characters with a value of 1%. The genetic distance between the two captive centers was 0.001. Haplotype analyses detected only four haplotypes between these two captive centers. Both NJ and MP trees demonstrate that all individuals in the Jenderak and Sungkai captive centers are in the same clade. Genetic variation of the Malayan gaur in these centers is considered low, possibly because individuals share the same common parent. This sequence variation data are of paramount importance for designing a proper breeding and management program of the Malayan gaur in the future.
    Matched MeSH terms: DNA, Mitochondrial
  5. Fulltext Partial mtDNA sequencing data of vulnerable Cephalopachus bancanus from the Malaysian Borneo
    Zahidin MA, Jalil NA, Naharuddin NM, Abd Rahman MR, Gani M, Abdullah MT
    Data Brief, 2019 Aug;25:104133.
    PMID: 31321260 DOI: 10.1016/j.dib.2019.104133
    Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (Carlito syrichta), Sulawesi (Tarsius tarsier-complex) and Borneo (Cephalopachus bancanus). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of C. bancanus in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome b) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.
    Matched MeSH terms: DNA, Mitochondrial
  6. Fulltext First record of Phyllorhiza sp. (Cnidaria: Scyphozoa) in a Chinese coastal aquaculture pond
    Dong Z, Morandini AC, Schiariti A, Wang L, Sun T
    PeerJ, 2019;7:e6191.
    PMID: 30643699 DOI: 10.7717/peerj.6191
    Background: It has been suggested that aquaculture ponds on the Chinese coast could act as breeding grounds for scyphozoans. Here, we present the first record of the scyphomedusa Phyllorhiza sp. in an aquaculture pond on the coast of the southern Yellow Sea, based on a combination of morphological characteristics and mitochondrial 16S DNA sequence data.

    Methods: A field survey was performed on June 29, 2017 in a pond used for culturing the shrimp Penaeus japonicus, located in the southern Yellow Sea, China. Jellyfish specimens were collected for morphological and genetic analysis. The morphological characters of the jellyfish specimens were compared to taxonomic literature. Additionally, phylogenetic analysis of the mitochondrial 16S fragments of these specimens were also conducted.

    Results: These specimens had the following morphological characters: hemispherical umbrella without scapulets; J-shaped oral arms; a single larger terminal club on each arm; bluish colored with a slightly expanded white tip; and mouthlets present only in the lower half to one-third of each arm. These morphological features of the medusae indicated that the specimens found in the shrimp culture ponds belong to the genus Phyllorhiza Agassiz, 1862, but did not match with the description of any of the known species of the genus Phyllorhiza. Phylogenetic analyses of the mtDNA 16S regions revealed that these specimens, together with Phyllorhiza sp. from Malaysian coastal waters, belong to a sister group of Phyllorhiza punctata. Juveniles and ephyrae of Phyllorhiza sp. were observed in the aquaculture pond. The mean density of Phyllorhiza sp. medusa in the surface water within the pond was estimated to be 0.05 individuals/m2.

    Discussion: Based on our observations of the gross morphology and molecular data, we state that the specimens collected in the aquaculture pond can be identified as Phyllorhiza sp. This is the first record of Phyllorhiza sp. in Chinese seas. Large scale dispersal through ballast water or the expansion of jellyfish aquarium exhibitions are possible pathways of invasion, but this needs to be confirmed in further studies.

    Matched MeSH terms: DNA, Mitochondrial
  7. Fulltext Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia
    Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, et al.
    Hum Genet, 2016 Apr;135(4):363-76.
    PMID: 26875094 DOI: 10.1007/s00439-016-1640-3
    There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
    Matched MeSH terms: DNA, Mitochondrial
  8. Fulltext Species-specific identification of porcine blood plasma in heat-treated chicken meatballs
    Shahimi S, Abd Mutalib S, Ismail N, Elias A, Hashim H, Kashim MIAM
    Saudi J Biol Sci, 2021 Apr;28(4):2447-2452.
    PMID: 33911957 DOI: 10.1016/j.sjbs.2021.01.043
    This study was conducted to detect the presence of chicken and porcine DNA in meatballs using mitochondria DNA (mtDNA) of cytochrome b (cyt b) and nuclear DNA (nDNA) short interspersed nuclear element (SINE) species-specific primers, respectively. While, the mtDNA primers targeted transfer RNA-ATP8 (tRNA-ATP8) gene was used for 1 and 5% (w/w) chicken meatball spiked with commercial porcine blood plasm. Chicken meatballs spiked with 1% and 5% (v/w) fresh and commercial porcine blood plasma, respectively were prepared and heat-treated using five (n = 5) cooking methods: boiling, pan-frying, roasting, microwaving and autoclaving. Two pairs of mtDNA and nDNA primers used, produced 129 and 161 bp amplicons, respectively. Whereas, tRNA-ATP8 primers produced 212 bp of amplicon. Electrophoresis analysis showed positive results for porcine DNA at 1% and 5% (w/w or v/v) for all of the different cooking techniques, either for fresh or commercial blood plasma using SINE primers but not for tRNA-ATP8 primers. The present study has highlighted the useful of species-specific primers of SINE primers in PCR analysis for detecting porcine DNA blood plasma in heat-treated chicken meatballs.
    Matched MeSH terms: DNA, Mitochondrial
  9. Mitochondrial Genetic Diversity of the Freshwater Snail Melanoides tuberculata
    Chiu YW, Gan YC, Kuo PH, Hsu KC, Tan MS, Ju YM, et al.
    Biochem Genet, 2018 Oct 26.
    PMID: 30367289 DOI: 10.1007/s10528-018-9892-3
    According to geological history, Peninsular Malaysia and Borneo formed at different times and were once connected during Quaternary glaciations. To determine how this history has influenced phylogeography, our study examined the population genetic structure of the tropical freshwater gastropod Melanoides tuberculata across Peninsular Malaysia and Borneo using the sequences from mitochondrial DNA 16S rRNA and cytochrome oxidase subunit I genes (1168 bp). In total, 104 specimens were collected from seventeen populations. All mtDNA haplotypes were identified as belonging to two highly divergent lineages, and these lineages were almost allopatric in their distributions. Our study found that the freshwater fauna in Malaysia might be divided into four regions: northeast Peninsular Malaysia, northwest Peninsular Malaysia, south Peninsular Malaysia, and Borneo. The phylogeography of M. tuberculata in Malaysia was shaped by the landforms of Peninsular Malaysia and by the paleo-river systems in the Sunda continental shelf. In addition, our study found that these two lineages in Malaysia have invaded the globe. These results suggest that Malaysia is located in important shipping lanes throughout the world, and the populations of M. tuberculate might be widely distributed throughout the world by shipping.
    Matched MeSH terms: DNA, Mitochondrial
  10. POPULATION GENETICS OF LONGTAIL TUNA (Thunnus tonggol) (BLEEKER, 1851) FROM EAST MALAYSIA BASED ON MITOCHONDRIAL DNA D-LOOP MARKER
    NURUL AZLIANA MOHD YASIN, NOORHANI SYAHIDA KASIM, TUN NURUL AIMI MAT JAAFAR, RUMEAIDA MAT PIAH, WAHIDAH MOHD ARSHAAD, SITI AZIZAH MOHD NOR, et al.
    UMT Journal of Undergraduate Research, 2020;2(2):49-56.
    MyJurnal
    Present study investigates the genetic diversity and genetic distribution of the longtail tuna Thunnus tonggol collected from east Malaysia (Borneo states of Sabah and Sarawak) based on mitochondrial DNA D-loop sequence analysis. 58 fish samples were obtained, specifically from Kota Kinabalu, KK (n = 22), Miri, MR (n=20) and Bintulu, BT (n = 17). DNA template was isolated using the salt extraction method. Final length of 404 base pair (bp) D-loop sequences revealed 52 haplotypes that comprise of 77 variable sites (38 of parsimony informative and 39 singleton). A total of 20 haplotypes were found in KK, 19 haplotypes in MR and 16 haplotypes in BT. Molecular diversity indices revealed high haplotype diversity and low nucleotide diversity in all populations; KK (h = 0.9913 ± 0.0165, π = 0.00239 ± 0.0127), MR (h = 0.9942 ± 0.0193, π = 0.0226 ± 0.0121) and BT (h = 0.9926 ± 0.0230, π = 0.0196 ± 0.0171). Population comparison pairwise FST show that KK and BT were significantly genetically differentiated. The result from this study will be beneficial for fisheries management and also to provide information on the population genetics of T. tonggol in East Malaysian waters.
    Matched MeSH terms: DNA, Mitochondrial
  11. Fulltext Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand
    Supmee V, Songrak A, Suppapan J, Sangthong P
    Trop Life Sci Res, 2021 Mar;32(1):63-82.
    PMID: 33936551 DOI: 10.21315/tlsr2021.32.1.4
    Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F
    ST
    , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
    Matched MeSH terms: DNA, Mitochondrial
  12. Fulltext Halal analysis of raw materials, ingredients and finished bakery products using PCR and gene chip southern-hybridization for detection of porcine DNA
    Norrakiah, A.S., Shahrul Azim, M. G., Sahilah, A.M., Abdul Salam, B.
    International Food Research Journal, 2015;22(5):1883-1887.
    MyJurnal
    This study was conducted to investigate the sensitivity and detection of porcine DNA in raw materials, ingredients and finished bakery products by polymerase chain reaction (PCR) - southern hybridization on chip analysis. A total of 20 samples (n=20* 3) with three replicates for each samples were obtained from a bakery factory located in Bangi, Selangor from January to December 2012. The sensitivity level of PCR-southern hybridization on chip was 0.001 ng. The species-specific oligonucleotide primers used in PCR-southern hybridization were targeted on the mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence, namely cty b biotin-labeled oligonucleotide primers. The amplicon from PCR amplification was 276 bp in size. None of the raw materials, ingredients and finished bakery product samples was positive towards porcine DNA, except for the positive control. The results in the present study demonstrated that the PCR- southern-hybridization technique on the gene chip (OliproTM Porcine gene chip) is a sensitive tool for monitoring the porcine component in highly processed ingredients and finished bakery products.
    Matched MeSH terms: DNA, Mitochondrial
  13. Unusually high genetic diversity in the Bornean Limnonectes kuhlii-like fanged frogs (Anura: Dicroglossidae)
    Matsui M, Kuraishi N, Eto K, Hamidy A, Nishikawa K, Shimada T, et al.
    Mol Phylogenet Evol, 2016 09;102:305-19.
    PMID: 27374495 DOI: 10.1016/j.ympev.2016.06.009
    A fanged frog Limnonectes kuhlii was once thought to be wide-ranging in Southeast Asia, but is now confined to its type locality Java through recent phylogenetic studies, which clarified heterospecific status of non-Javanese populations, and monophyly of Bornean populations. However, large genetic differences among Bornean populations suggest occurrence of cryptic species, which we test using dense geographic sampling. We estimated the phylogenetic relationships among samples of Bornean populations together with their putative relatives from the continental Southeast Asia, using 2517bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA, and 2367bp sequences of the NCX1, POMC, and RAG1 of nuclear genes. In the mtDNA trees, Bornean L. kuhlii-like frogs formed a monophyletic group split into 18 species lineages including L. hikidai, with the deepest phylogenetic split separating L. cintalubang from the remaining species. Almost all of these lineages co-occur geographically, and two to three lineages were found syntopically in each locality. Co-occurrence of more than one lineage may be maintained by differential morphology and microhabitat selection. These syntopic lineages should be regarded as distinct species. Our results clearly indicate that taxonomic revision is urgent to clarify many evolutionary problems of Bornean L. kuhlii-like frogs.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Mitochondrial/metabolism; DNA, Mitochondrial/chemistry
  14. Fulltext Mitochondrial DNA Mutations in Grade II and III Glioma Cell Lines Are Associated with Significant Mitochondrial Dysfunction and Higher Oxidative Stress
    Soon BH, Abdul Murad NA, Then SM, Abu Bakar A, Fadzil F, Thanabalan J, et al.
    Front Physiol, 2017;8:231.
    PMID: 28484394 DOI: 10.3389/fphys.2017.00231
    The role of mitochondria in tumorigenesis has regained much attention as it could dysregulate cellular energetics, oxidative stress and apoptosis. However, the role of mitochondria in different grade gliomasis still unknown. This study aimed to identify mitochondrial DNA (mtDNA) sequence variations that could possibly affect the mitochondrial functions and also the oxidative stress status. Three different grades of human glioma cell lines and a normal human astrocyte cell line were cultured in-vitro and tested for oxidative stress biomarkers. Relative oxidative stress level, mitochondria activity, and mitochondrial mass were determined by live cell imaging with confocal laser scanning microscope using CM-H2DCFDA, MitoTracker Green, and MitoTracker Orange stains. The entire mitochondrial genome was sequenced using the AffymetrixGeneChip Human Mitochondrial Resequencing Array 2.0. The mitochondrial sequence variations were subjected to phylogenetic haplogroup assessment and pathogenicity of the mutations were predicted using pMUT and PolyPhen2. The Grade II astrocytoma cells showed increased oxidative stress wherea high level of 8-OHdG and oxidative stress indicator were observed. Simultaneously, Grade II and III glioma cells showed relatively poor mitochondria functions and increased number of mutations in the coding region of the mtDNA which could be due to high levels of oxidative stress in these cells. These non-synonymous mtDNA sequence variations were predicted to be pathogenic and could possibly lead to protein dysfunction, leading to oxidative phosphorylation (OXPHOS) impairment, mitochondria dysfunction and could create a vicious cycle of oxidative stress. The Grade IV cells had no missense mutation but preserved intact mitochondria and excellent antioxidant defense mechanisms thus ensuring better survival. In conclusion, Grade II and III glioma cells demonstrated coding region mtDNA mutations, leading to mitochondrial dysfunction and higher oxidative stress.
    Matched MeSH terms: DNA, Mitochondrial
  15. Restriction Fragment Length Polymorphisms (RFLPs) analysis of several freshwater fishes of Malaysia
    Japning, J.R.R., Esa, Y.B.
    Buletin Persatuan Genetik Malaysia, 2005;11(1):0-0.
    MyJurnal
    The need to detect genetic variation has fueled the development of novel marker systems in fisheries biology. In this study, a simple, fast and cost effective method was used to differentiate between species of freshwater fishes focusing on Malaysian freshwater fishes by employing
    Restriction Fragment Length Polymorphisms (RFLPs) analysis of a 470-bp cytochrome b mtDNA segment. RFLP analysis using six restriction enzymes (AluI, BamHI, BsuRI, Csp61, HpaII and SalI) found variations in the digestion profile among most of the fish samples analyzed. Diagnostic digestion profiles were observed among the Hampala fishes, especially between H. macrolepidota and the other Hampala species/forms (using BsuRI and Csp61). Diagnostic digestion profiles were also detected between H.
    bimaculata Type A and Type B (using AluI, BamHI, BsuRI and SalI), supporting their status as distinct species. Additionally, unique digestion profiles were observed in other species such as Leptobarbus hosii (Csp61), Osteocheilus hasseltii (Csp61), Osteocheilus sp. (Csp61), Puntioplites bulu (Csp61), Puntius bramoides (AluI), P. sealei (AluI) and Helostoma temmincki (AluI and Csp61), which can be used as genetic markers for discriminating these species. Overall, the RFLP analysis of the cytochrome
    b mtDNA segment has proven to be a considerably effective, fast and non-expensive technique to discriminate among several freshwater fish species in Malaysia.
    Matched MeSH terms: DNA, Mitochondrial
  16. Fulltext Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)
    Goulding TC, Khalil M, Tan SH, Dayrat B
    Zookeys, 2018.
    PMID: 29896045 DOI: 10.3897/zookeys.763.21252
    A new genus of onchidiid slugs, Wallaconchis Goulding & Dayrat, gen. n., is described, including ten species. Five species were previously described but known only from the type material: Wallaconchis ater (Lesson, 1830), W. graniferum (Semper, 1880), W. nangkauriense (Plate, 1893), W. buetschlii (Stantschinsky, 1907), and W. gracile (Stantschinsky, 1907), all of which were originally classified in Onchidium Buchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new: Wallaconchis achleitneri Goulding, sp. n., W. comendadori Goulding & Dayrat, sp. n., W. melanesiensis Goulding & Dayrat, sp. n., W. sinanui Goulding & Dayrat, sp. n., and W. uncinus Goulding & Dayrat, sp. n. Nine of the ten Wallaconchis species are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia). Wallaconchis is distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify all Wallaconchis species. The copulatory organs of Wallaconchis species are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed, nomina dubia are discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.
    Matched MeSH terms: DNA, Mitochondrial
  17. Fulltext DNA extraction from ghee and beef species identification using polymerase chain reaction (PCR) assay
    Nooratiny, I., Sahilah, A.M., Alif Alfie, A.R., Mohd. Farouk, M.Y.
    International Food Research Journal, 2013;20(5):2959-2961.
    MyJurnal
    A technique to isolate DNA from ghee was developed for the authentication of beef fat product. The method was based on pre-mixed ghee with phosphate buffer solution (PBS) prior to DNA extraction using Epicentre extraction method. The recovery of beef DNA was then analysed by polymerase chain reaction (PCR) using beef species-specific oligonucleotide primers which targeted the mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene. The amplicon was 274 bp in size. The developed ghee extraction method offers a high yield of DNA providing 100 ng per μl and useful for validating beef fat product.
    Matched MeSH terms: DNA, Mitochondrial
  18. Molecular phylogeny of holothuria (mertensiothuria) leucospilota (Brandt 1835) as inferred from cytochrome C oxidase I mitochondrial DNA gene sequences
    Hajar Fauzan Ahmad, Mohd Hanafi Anua, Mohd Yaman Idris, Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, et al.
    Sains Malaysiana, 2011;40.
    Holothuria (Mertensiothuria) leucospilota (Brandt 1835), white threads fish or locally known as bat puntil is currently considered as the most abundant sea cucumber species in Malaysia. This study aimed to generate the genetic profile of H. leucospilota from Malaysia and then to determine the phylogenetic relationship between H. leucospilota and other members of genus Holothuria using partial sequences of cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In this study, specimens of H. leucospilota were collected from Intan Besar Island, Langkawi, Kedah Darul Aman in the west coast of Peninsular Malaysia. Three main methods namely neighbour joining, maximum parsimony and maximum likelihood were used for the phylogenetic tree reconstruction. Tree topologies showed that H. leucospilota has its own monophyletic clade clearly distinct from the other species. The pairwise genetic distance calculated further supported these findings. In addition, the results also should that the COI mtDNA gene is capable to unravel the phylogenetic relationship of H. leucospilota.
    Matched MeSH terms: DNA, Mitochondrial
  19. Molecular Mitochondrial DNA and radiographic approaches for human archaeology identification
    Rus Dina Rus Din, Shahrul Hisham Zainal Ariffin, Sahidan Senafi, Rohaya Megat Abdul Wahab, Intan Zarina Zainol Abidin
    Sains Malaysiana, 2014;43:1523-1535.
    Ancient remains are considered very valuable artefacts, as they allow for the study of ancient cultures, phylogeny, evolution and the reconstruction of demographic history. To obtain all the information contained within remains, the investigation of such samples requires the expertise and various techniques from multiple fields of study. The present review focuses on the molecular biology and radiographic approaches used to identify ancient samples. Studies of ancient remains face various limitations; for example, the quality and quantity of the ancient samples can affect the difficulty of the investigations. Due to these limitations, new sophisticated techniques are being introduced to replace the earlier conventional techniques. A search was conducted using PubMed, Scopus, Science Direct and Science Finder to provide a new and timely review on the molecular mitochondrial DNA and radiographic analysis for human archaeology identification. The present review has determined that molecular biological approaches are very accurate and useful for the use in the ancestral determination of incomplete specimens, whereas observations of the dental pulp chamber are suitable for age at death estimations in both adults and children. However, these techniques are expensive and require expert personnel. Therefore, conventional approaches remain the favourite methods of most institutions, especially in Asia.
    Matched MeSH terms: DNA, Mitochondrial
  20. Phylogenetic relationships within the genus holothuria inferred from 16S mitochondiral rRNA gene sequences
    Kamarul Rahim Kamarudin, ‘Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, Maryam Mohamed Rehan
    Sains Malaysiana, 2016;45:1079-1087.
    This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida
    from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently
    to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined
    species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and
    Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and
    Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria
    taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and
    posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of
    subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative
    taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is
    indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest
    that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due
    to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of
    genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches
    may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.
    Matched MeSH terms: DNA, Mitochondrial
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