Browse publications by year: 2016

  1. Gan HM, Tan MH, Thai BT, Austin CM
    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.
    MeSH terms: Animals; Base Composition; DNA, Mitochondrial/analysis; DNA, Mitochondrial/genetics; RNA, Transfer/genetics; Gene Order; Bivalvia/genetics*; Genome, Mitochondrial*
  2. Gan HM, Tan MH, Austin CM
    PMID: 24617484 DOI: 10.3109/19401736.2014.895996
    The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
    MeSH terms: Animals; Perches/genetics*; Perciformes/genetics; RNA, Ribosomal/genetics; RNA, Transfer/genetics; Gene Order; Fish Proteins/genetics; Genes, Mitochondrial; Genome, Mitochondrial*
  3. Gan HM, Tan MH, Austin CM
    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%.
    MeSH terms: Animals; Base Sequence; Astacoidea/genetics*; DNA, Mitochondrial/genetics; Fresh Water; Molecular Sequence Data; Shellfish; Sequence Analysis, DNA/veterinary; Genome, Mitochondrial*
  4. Wong YL, Dali AZ, Mohamed Rose I, Jamal R, Mokhtar NM
    Asia Pac J Clin Oncol, 2016 Jun;12(2):e259-68.
    PMID: 24673814 DOI: 10.1111/ajco.12182
    Ovarian cancer is the deadliest of all gynecologic cancers because of its late diagnosis and poor treatment outcomes. This study aimed to identify potential molecular signatures associated with biological processes that are implicated in epithelial ovarian cancer (EOC).
  5. Lim HC, Ahmad AT, Nuruddin AA, Mohd Nor SA
    Mitochondrial DNA, 2016;27(1):575-84.
    PMID: 24724977 DOI: 10.3109/19401736.2014.908354
    We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p < 0.05, FSC = 0.00, p > 0.05 and FCT = 0.07, p < 0.05) attributed to the Kuala Besar population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.
  6. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM
    Mitochondrial DNA, 2016;27(1):595-6.
    PMID: 24730605 DOI: 10.3109/19401736.2014.908361
    The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
    MeSH terms: Animals; Base Composition; Base Sequence; Astacoidea; Fresh Water; RNA, Transfer; Gene Order; Genome, Mitochondrial; Ribosome Subunits
  7. Austin CM, Tan MH, Lee YP, Croft LJ, Gan HM
    Mitochondrial DNA, 2016;27(1):729-30.
    PMID: 24779601 DOI: 10.3109/19401736.2014.913162
    The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442 bp (58% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 768 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Maccullochella, and the fourth for the family Percichthyidae.
  8. Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Pierce SJ, et al.
    Mitochondrial DNA, 2016;27(1):694-5.
    PMID: 24779605 DOI: 10.3109/19401736.2014.913147
    The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384 bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.
  9. Zainal Abidin DH, Mustaffa S, Rahim MA, Nair DM, Md Naim D, Mohd Nor SA
    Mitochondrial DNA, 2016;27(1):647-58.
    PMID: 24786018 DOI: 10.3109/19401736.2014.913137
    Mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to assess the population genetics of the commercially important black scar oyster, Crassostrea iredalei among 11 populations throughout the west and east coasts Peninsular Malaysia and Sabah (Malaysian Borneo). Overall, populations of C. iredalei demonstrated low nucleotide diversity π (0.000-0.004) and low-to-high haplotype diversity h (0.000-0.795) levels. Genetic structuring was detected between the Peninsular Malaysia and Sabah populations as revealed by the FST analysis. However, the COI gene analyses showed minimal and non-significant (p > 0.05) population differentiation within the east and west coasts Peninsular Malaysia and Sabah regions. This was attributed to both high larval dispersal along the east and west coasts and human-driven spat translocation between the two coastlines due to C. iredalei cultivation practices. Phylogeographic relationships inferences were also conducted to further support these hypotheses. The neutrality and mismatch distribution analyses suggested that C. iredalei had experienced a/several bottleneck event(s), followed by population expansion. The molecular information obtained from this study could be incorporated in a pragmatic aquaculture management strategy of wild broodstock and the hatchery lines of C. iredalei in Malaysia.
  10. Dawe K, Montgomery A, McGee H, Panagopoulou E, Morgan K, Hackshaw L, et al.
    J Health Psychol, 2016 05;21(5):607-18.
    PMID: 24829376 DOI: 10.1177/1359105314532970
    We synthesised evidence on biological correlates of psychological stress in hospital-based healthcare professionals, and examined whether there was evidence of consistent biological changes. Electronic databases were searched for empirical studies; 16 articles (0.6%) met the inclusion criteria. Evidence of a relationship between indices of psychological stress and biological parameters was limited and inconsistent. There was some evidence of a consistent relationship between natural killer cells and lymphocyte subpopulations. Considerable heterogeneity in the methods used was seen. Future prospective studies examining the relationship between indices of psychological stress and natural killer cells, including lymphocyte subsets, is required.
    MeSH terms: Humans; Occupational Diseases/immunology; Occupational Diseases/physiopathology*; Occupational Diseases/psychology; Perception; Personnel, Hospital/psychology*; Stress, Psychological/immunology; Stress, Psychological/physiopathology*; Stress, Psychological/psychology
  11. Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM
    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.
    MeSH terms: Animals; Australia; Base Composition; Base Sequence; Astacoidea/genetics*; DNA, Mitochondrial/genetics*; Phylogeny; Sequence Analysis, DNA/veterinary; Gene Order; Genome, Mitochondrial*
  12. Phing Lau WC, Latif MA, Y Rafii M, Ismail MR, Puteh A
    Crit Rev Biotechnol, 2016;36(1):87-98.
    PMID: 24937109 DOI: 10.3109/07388551.2014.923987
    The eating and cooking qualities of rice are heavily emphasized in breeding programs because they determine market values and they are the appealing attributes sought by consumers. Conventional breeding has developed traditional varieties with improved eating and cooking qualities. Recently, intensive genetic studies have pinpointed the genes that control eating and cooking quality traits. Advances in genetic studies have developed molecular techniques, thereby allowing marker-assisted breeding (MAB) for improved eating and cooking qualities in rice. MAB has gained the attention of rice breeders for the advantages it can offer that conventional breeding cannot. There have been successful cases of using MAB to improve the eating and cooking qualities in rice over the years. Nevertheless, MAB should be applied cautiously given the intensive effort needed for genotyping. Perspectives from conventional breeding to marker-assisted breeding will be discussed in this review for the advancement of the eating and cooking qualities of fragrance, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) in rice. These four parameters are associated with eating and cooking qualities in rice. The genetic basis of these four parameters is also included in this review. MAB is another approach to rice variety improvement and development in addition to being an alternative to genetic engineering. The MAB approach shortens the varietal development time, and is therefore able to deliver improved rice varieties to farmers within a shorter period of time.
    MeSH terms: Farmers; Amylose; Attention; Breeding; Cooking; Food; Genetic Engineering; Genotype; Humans; Phenotype; Oryza; Temperature
  13. Krzeminska U, Wilson R, Rahman S, Song BK, Gan HM, Tan MH, et al.
    PMID: 24938087 DOI: 10.3109/19401736.2014.926512
    The complete mitochondrial genome of the invasive house crow (Corvus splendens) was sequenced (GenBank accession number: KJ766304) using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitochondrial genome is 16,962 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes and a non-coding control region. The mitogenome structural organization is identical to that of the other Corvus species and related genera. The overall base composition of C. splendens is 30.65% for A, 29.71% for C, 14.84% for G and 24.80% for T, with an AT content of 55.45%. We propose to use full mitochondrial genome to address taxonomic issues and to study the population genetics of crows.
  14. Gan HM, Tan MH, Austin CM
    PMID: 24938115 DOI: 10.3109/19401736.2014.926490
    The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 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 E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
    MeSH terms: Animals; Australia; Base Composition; Astacoidea; Molecular Conformation; RNA, Transfer; Base Pairing; Gene Order; Genome, Mitochondrial; Ribosome Subunits
  15. Kasapila W, Shaarani SM
    Crit Rev Food Sci Nutr, 2016;56(1):56-64.
    PMID: 24987986 DOI: 10.1080/10408398.2012.710277
    The need for accurate nutrition labeling on food products has never been greater. Obesity has assumed near-epidemic levels in both industrialized and emerging nations in recent years, and governments and consumer groups around the world are looking for ways to improve the nutritional choices for their citizenry while simultaneously balancing their freedom of choice through the use of nutrition labeling. Despite increasingly aggressive efforts by government and industry organizations to raise consumer awareness, though, many consumers either do not consult nutrition labels or they are not in a position to interpret the information on these labels accurately. To gain some fresh insights into nutrition labeling practices worldwide, this paper provides a review of the relevant peer-reviewed, scholarly, and government literature to describe regulations enacted to date, evolving and future trends, and the likely impact of food product labels. In this regard, the paper highlights similarities and discrepancies that exist, identifies gaps, and gives directions for the future.
    MeSH terms: Humans; Health Knowledge, Attitudes, Practice; Legislation, Food; Nutritive Value*; Patient Compliance
  16. Kelly B, Hebden L, King L, Xiao Y, Yu Y, He G, et al.
    Health Promot Int, 2016 Mar;31(1):144-52.
    PMID: 24997194 DOI: 10.1093/heapro/dau055
    There is an established link between food promotions and children's food purchase and consumption. Children in developing countries may be more vulnerable to food promotions given the relative novelty of advertising in these markets. This study aimed to determine the scope of television food advertising to children across the Asia-Pacific to inform policies to restrict this marketing. Six sites were sampled, including from China, Indonesia, Malaysia and South Korea. At each site, 192 h of television were recorded (4 days, 16 h/day, three channels) from May to October 2012. Advertised foods were categorized as core/healthy, non-core/unhealthy or miscellaneous, and by product type. Twenty-seven percent of advertisements were for food/beverages, and the most frequently advertised product was sugar-sweetened drinks. Rates of non-core food advertising were highest during viewing times most popular with children, when between 3 (South Korea) and 15 (Indonesia) non-core food advertisements were broadcast each hour. Children in the Asia-Pacific are exposed to high volumes of unhealthy food/beverage television advertising. Different policy arrangements for food advertising are likely to contribute to regional variations in advertising patterns. Cities with the lowest advertising rates can be identified as exemplars of good policy practice.
    MeSH terms: Advertising as Topic; Asia; Beverages; Child; China; Cities; Developing Countries; Humans; Indonesia; Malaysia; Sweetening Agents; Television; Republic of Korea
  17. Raj DV, Abuzar M, Borromeo GL
    Gerodontology, 2016 Mar;33(1):135-43.
    PMID: 25039439 DOI: 10.1111/ger.12141
    OBJECTIVE: General medical and dental practitioner and pharmacists all encounter patients on bisphosphonates and as such require adequate knowledge regarding osteonecrosis of the jaw, a potential complication associated with its use. The cross-sectional study investigated perceived implications of and attitudes towards bisphosphonate use in oral health among general medical and dental practitioners and pharmacists.
    MATERIALS AND METHODS: Medical and dental practitioners and pharmacists registered in Victoria, Australia, completed an online survey (SurveyMonkey©). Data analysis consisted of chi-square tests with significance as p < 0.05.
    RESULTS: One hundred and thirty six doctors (general medical practitioners, GMPs), 283 dentists (GDPs) and 26 pharmacists (PHs) participated. 70, 38 and 80%, respectively, reviewed patients prescribed bisphosphonates (BPs). GMPs (88%), GDPs (76%) and PHs (85%) were aware of osteonecrosis of the jaws (ONJ). GMPs (76%) and PHs (100%) advised patients to inform dentists. GMPs (45%) referred patients for dental assessments prior to commencing BPs with 71.9% of GDPs received such referrals. In terms of available information on oral health and BPs, GMPs (56%), GDPs (50%) and PH (53.8%) were either unsure any existed or reported receiving sufficient information.
    CONCLUSIONS: Discrepancies exist amongst different healthcare professionals in terms of BP use and oral health, and common consensus guidelines are warranted.
    KEYWORDS: bisphosphonates; clinical guidelines; drug therapy; oral health; osteonecrosis.
    MeSH terms: Adult; Attitude of Health Personnel*; Australia; Cross-Sectional Studies; Delivery of Health Care*; Dentists/psychology; Diphosphonates/adverse effects; Diphosphonates/therapeutic use*; Education, Dental; Female; Humans; Male; Middle Aged; Oral Health*; Osteonecrosis/drug therapy; Osteonecrosis/prevention & control; Osteoporosis/drug therapy; Osteoporosis/prevention & control; Pharmacists/psychology; Surveys and Questionnaires; Referral and Consultation; Chi-Square Distribution; Practice Patterns, Dentists'; Guideline Adherence/statistics & numerical data; General Practitioners/psychology; Bisphosphonate-Associated Osteonecrosis of the Jaw/prevention & control
  18. Kumaresan R, Cugati N, Chandrasekaran B, Karthikeyan P
    J Investig Clin Dent, 2016 Feb;7(1):102-9.
    PMID: 25048008 DOI: 10.1111/jicd.12116
    OBJECTIVE: To evaluate the reliability and validity of Demirjian's, Willems, Nolla's, Haavikko's, and Cameriere's radiographic methods of dental-age estimation in a population of Malaysian children.

    METHODS: A total of 426 dental panoramic radiographs of 5-15-year-old Malaysian children were included in the study. The mean age error and absolute age error for all the methods were calculated and their usability analyzed.

    RESULTS: The Nolla, Willems. and Demirjian methods overestimated the dental age with a mean of 0.97, 0.54, and 0.54 years, respectively, while the Cameriere and Haavikko methods underestimated by 0.41 and 1.31 years, respectively. The Cameriere method was highly precise and accurate in the population of Malaysian children, whereas the Haavikko and Demirjian methods were the least precise and accurate.

    CONCLUSIONS: The Cameriere method of dental-age estimation is highly valid and reliable for Malaysian population, followed by the Willems and Nolla methods.

    MeSH terms: Age Determination by Teeth*; Child; Forensic Dentistry*; Humans; Malaysia; Radiography, Panoramic*; Reproducibility of Results; Radiography, Dental, Digital
  19. Hameed IH, Jebor MA, Ommer AJ, Abdulzahra AI, Yoke C
    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.
    MeSH terms: Base Sequence; DNA, Mitochondrial/genetics*; Haplotypes; Humans; Iraq; Male; Molecular Sequence Data; Open Reading Frames*; Polymorphism, Single Nucleotide*; Forensic Genetics/methods*
  20. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25090387 DOI: 10.3109/19401736.2014.945572
    The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
    MeSH terms: Animals; Base Composition; Base Sequence; Molecular Sequence Data; Decapoda (Crustacea)/genetics*; Genome, Mitochondrial*; Molecular Sequence Annotation
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