Displaying publications 941 - 960 of 8276 in total

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  1. Mapping of the quantitative trait locus (QTL) conferring partial resistance to rice leaf blast disease
    Ashkani S, Rafii MY, Rahim HA, Latif MA
    Biotechnol Lett, 2013 May;35(5):799-810.
    PMID: 23315158 DOI: 10.1007/s10529-012-1130-1
    Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F3 families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F3 population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects.
    Matched MeSH terms: Oryza/genetics*; Genes, Plant/genetics*; Plant Leaves/genetics; Microsatellite Repeats/genetics
  2. Isolation and characterisation of a partial peptide synthetase gene from Trichoderma asperellum
    Chutrakul C, Peberdy JF
    FEMS Microbiol Lett, 2005 Nov 15;252(2):257-65.
    PMID: 16214297
    Many species of Trichoderma have attracted interest as agents for the biological control of soil borne fungal pathogens of a range of crop plants. Research on the biochemical mechanisms associated with this application has focused on the ability of these fungi to produce enzymes which lyse fungal cell walls, and antifungal antibiotics. An important group of the latter are the non-ribosomal peptides called peptaibols. In this study Trichoderma asperellum, a strain used in biological control in Malaysia, was found to produce the peptaibol, trichotoxin. This type of peptide molecule is synthesised by a peptide synthetase (PES) enzyme template encoded by a peptide synthetase (pes) gene. Using nucleotide sequences amplified from adenylation (A-) domains as probes, to hybridise against a lambda FIXII genomic library from T. asperellum, 25 clones were recovered. These were subsequently identified as representative of four groups based on their encoding properties for specific amino acid incorporation modules in a PES. This was based on analysis of their amino acid sequences which showed up to 86% identity to other PESs including TEX 1.
    Matched MeSH terms: DNA, Fungal/genetics; Fungal Proteins/genetics; Peptide Synthases/genetics*; Trichoderma/genetics
  3. Frequencies of A(TA)7TAA, G71R, and G493R mutations of the UGT1A1 gene in the Malaysian population
    Yusoff S, Van Rostenberghe H, Yusoff NM, Talib NA, Ramli N, Ismail NZ, et al.
    Biol. Neonate, 2006;89(3):171-6.
    PMID: 16210851
    Gilbert syndrome is caused by defects in the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene. These mutations differ among different populations and many of them have been found to be genetic risk factors for the development of neonatal jaundice.
    Matched MeSH terms: Gilbert Disease/genetics; Promoter Regions, Genetic/genetics; Glucuronosyltransferase/genetics*; Hyperbilirubinemia, Neonatal/genetics
  4. Molecular subtyping of clinical isolates of Candida albicans and identification of Candida dubliniensis Malaysia
    Tay ST, Chai HC, Na SL, Ng KP
    Mycopathologia, 2005 Apr;159(3):325-9.
    PMID: 15883714
    The genotypes of 221 recent isolates of Candida albicans from various clinical specimens of 213 patients admitted to the University Malaya Medical Centre, Malaysia was determined based on the amplification of a transposable intron region in the 25 S rRNA gene. The analyses of 178 C. albicans isolated from nonsterile clinical specimens showed that they could be classified into three genotypes: genotype A (138 isolates), genotype B (38 isolates) and genotype C (2 isolates). The genotyping of 43 clinical isolates from sterile specimens showed that they belonged to genotype A (29 isolates), genotype B (10 isolates), genotype C (2 isolates) and genotype D (2 isolates). The overall distribution of C. albicans genotypes in sterile and nonsterile specimens appeared similar, with genotype A being the most predominant type. This study reported the identification of C. dubliniensis (genotype D) in 2 HIV-negative patients with systemic candidiasis, which were missed by the routine mycological procedure. The study demonstrated the genetic diversity of clinical isolates of C. albicans in Malaysia.
    Matched MeSH terms: Candida albicans/genetics*; DNA, Fungal/genetics; RNA, Fungal/genetics; RNA, Ribosomal/genetics
  5. Fulltext Characterisation of beta-globin gene mutations in Malaysian children: a strategy for the control of beta-thalassaemia in a developing country
    Thong MK, Tan JA, Tan KL, Yap SF
    J Trop Pediatr, 2005 Dec;51(6):328-33.
    PMID: 15967770 DOI: 10.1093/tropej/fmi052
    beta-thalassaemia major, an autosomal recessive hemoglobinopathy, is one of the most common single gene disorders in multi-racial Malaysia. The control of beta-thalassaemia major requires a multi-disciplinary approach that includes population screening, genetic counselling, prenatal diagnosis and the option of termination of affected pregnancies. To achieve this objective, the molecular characterisation of the spectrum of beta-globin gene mutations in each of the affected ethnic groups is required. We studied 88 consecutive unrelated individuals and their respective families with beta-thalassaemia (74 beta-thalassaemia major, 12 HbE-beta-thalassaemia, 2 with HbE homozygotes) and four individuals with beta-thalassaemia trait that contributed a total 180 alleles for study. Using a 2-step molecular diagnostic strategy consisting of amplification refractory mutation system (ARMS) to identify the 8 most common mutations followed by other DNA-based diagnostic techniques, a total of 177 (98.3 per cent) of the 180 beta-thalassaemia alleles were characterised. One out of 91 (1 per cent) of the Chinese alleles, one out of 46 (2.2 per cent) Malay alleles and one out of two Indian alleles remained unknown. A 100 per cent success rate was achieved in studying the Kadazandusun community in this study. A strategy to identify beta-globin gene mutations in Malaysians with beta-thalassaemia is proposed based on this outcome.
    Matched MeSH terms: DNA/genetics; Globins/genetics*; Mutation/genetics*; beta-Thalassemia/genetics*
  6. Fulltext Presence of allelic loss and PTEN mutations in malignant gliomas from Malay patients
    Zainuddin N, Jaafar H, Isa MN, Abdullah JM
    Med J Malaysia, 2004 Oct;59(4):468-79.
    PMID: 15779579
    Loss of heterozygosity (LOH) on several loci and mutations on PTEN tumor suppressor gene (10q23.3) occur frequently in sporadic gliomas. We have performed polymerase chain reaction (PCR)-LOH analysis using microsatellite markers and single-stranded conformational polymorphism (SSCP) analysis to determine the incidence of allelic losses on chromosome 10q, 9p, 17p and 13q and mutations of exons 5, 6 and 8 of the PTEN gene in malignant gliomas. Twelve of 23 (52.2%) malignant glioma cases showed allelic losses whereas 7 of 23, (30.4%) samples showed aberrant band patterns and mutations of the PTEN gene. Four of these cases showed LOH on 10q23 and mutations of the PTEN gene. The data on LOH indicated the involvement of different genes in gliomagenesis whereas mutations of the PTEN gene indicated the role of PTEN tumor suppressor gene in the progression of glioma in Malay population.
    Matched MeSH terms: Brain Neoplasms/genetics*; Glioma/genetics*; Phosphoric Monoester Hydrolases/genetics*; Tumor Suppressor Proteins/genetics*
  7. Fulltext Analysis of the survival motor neuron and neuronal apoptosis inhibitory protein genes in Malay patients with Spinal Muscular Atrophy
    Zilfalil BA, Zabidi-Hussin AMH, Watihayati MS, Rozainah MY, Naing L, Sutomo R, et al.
    Med J Malaysia, 2004 Oct;59(4):512-4.
    PMID: 15779584 MyJurnal
    In Malaysia, Spinal Muscular Atrophy (SMA) is diagnosed based on clinical observation with or without muscle biopsy. Molecular analyses of the SMA-related genes have not been available so far. In this preliminary study, we searched for homozygous deletion of Survival Motor Neuron (SMN1) and Neuronal Apoptosis Inhibitory Protein (NAIP) genes in Malay patients with SMA and found homozygous deletion of SMN1 exon 7 and 8 in all the patients while homozygous deletion of NAIP exon 5 was detected in only our type 1 patients but not in the type 3 patient. To the best of our knowledge, these are the first SMA cases diagnosed at the molecular level in Malaysia.
    Matched MeSH terms: Muscular Atrophy, Spinal/genetics*; Nerve Tissue Proteins/genetics*; RNA-Binding Proteins/genetics*; Cyclic AMP Response Element-Binding Protein/genetics*
  8. Fulltext Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma
    De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, et al.
    Cancer Res, 2016 Jan 15;76(2):319-28.
    PMID: 26554828 DOI: 10.1158/0008-5472.CAN-15-0751
    Malignant pleural mesothelioma (MPM) is an aggressive cancer that occurs more frequently in men, but is associated with longer survival in women. Insight into the survival advantage of female patients may advance the molecular understanding of MPM and identify therapeutic interventions that will improve the prognosis for all MPM patients. In this study, we performed whole-genome sequencing of tumor specimens from 10 MPM patients and matched control samples to identify potential driver mutations underlying MPM. We identified molecular differences associated with gender and histology. Specifically, single-nucleotide variants of BAP1 were observed in 21% of cases, with lower mutation rates observed in sarcomatoid MPM (P < 0.001). Chromosome 22q loss was more frequently associated with the epithelioid than that nonepitheliod histology (P = 0.037), whereas CDKN2A deletions occurred more frequently in nonepithelioid subtypes among men (P = 0.021) and were correlated with shorter overall survival for the entire cohort (P = 0.002) and for men (P = 0.012). Furthermore, women were more likely to harbor TP53 mutations (P = 0.004). Novel mutations were found in genes associated with the integrin-linked kinase pathway, including MYH9 and RHOA. Moreover, expression levels of BAP1, MYH9, and RHOA were significantly higher in nonepithelioid tumors, and were associated with significant reduction in survival of the entire cohort and across gender subgroups. Collectively, our findings indicate that diverse mechanisms highly related to gender and histology appear to drive MPM.
    Matched MeSH terms: Lung Neoplasms/genetics*; Mesothelioma/genetics*; Pleural Neoplasms/genetics*; Biomarkers, Tumor/genetics
  9. Genetic polymorphism in domain I of the apical membrane antigen-1 among Plasmodium knowlesi clinical isolates from Peninsular Malaysia
    Fong MY, Wong SS, Silva JR, Lau YL
    Acta Trop, 2015 Dec;152:145-150.
    PMID: 26384455 DOI: 10.1016/j.actatropica.2015.09.009
    The simian malaria parasite Plasmodium knowlesi is now recognized as a species that can cause human malaria. The first report of large scale human knowlesi malaria was in 2004 in Malaysia Borneo. Since then, hundreds of human knowlesi malaria cases have been reported in Southeast Asia. The present study investigates the genetic polymorphism of P. knowlesi DI domain of the apical membrane antigen-1 (AMA-1), a protein considered as a promising vaccine candidate for malaria. The DI domain of AMA-1 gene of P. knowlesi clinical isolates from Peninsular Malaysia was amplified by PCR, cloned into Escherichia coli, then sequenced and analysed. Ninety-seven DI domain sequences were obtained. Comparison at the nucleotide level against P. knowlesi strain H as reference sequence showed 21 synonymous and 25 nonsynonymous mutations. Nonetheless, nucleotide sequence analysis revealed low genetic diversity of the DI domain, and it was under purifying (negative) selection. At the amino acid level, 26 different haplotypes were identified and 2 were predominant haplotypes (H1, H2) with high frequencies. Phylogenetic analysis revealed that the 26 haplotypes could be clustered into 2 distinct groups (I and II). Members of the groups were basically derived from haplotypes H1 and H2, respectively.
    Matched MeSH terms: Antigens, Protozoan/genetics*; Membrane Proteins/genetics*; Protozoan Proteins/genetics*; Plasmodium knowlesi/genetics*
  10. 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; Mitochondria/genetics; RNA, Transfer/genetics; Bivalvia/genetics*
  11. Fulltext Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
    Machiela MJ, Zhou W, Karlins E, Sampson JN, Freedman ND, Yang Q, et al.
    Nat Commun, 2016 06 13;7:11843.
    PMID: 27291797 DOI: 10.1038/ncomms11843
    To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
    Matched MeSH terms: Aging/genetics*; DNA Methylation/genetics; Chromosomes, Human, X/genetics*; X Chromosome Inactivation/genetics*
  12. Fulltext Novel Association of WNK4 Gene, Ala589Ser Polymorphism in Essential Hypertension, and Type 2 Diabetes Mellitus in Malaysia
    Ghodsian N, Ismail P, Ahmadloo S, Heidari F, Haghvirdizadeh P, Ataollahi Eshkoor S, et al.
    J Diabetes Res, 2016;2016:8219543.
    PMID: 27314050 DOI: 10.1155/2016/8219543
    With-no-lysine (K) Kinase-4 (WNK4) consisted of unique serine and threonine protein kinases, genetically associated with an autosomal dominant form of hypertension. Argumentative consequences have lately arisen on the association of specific single nucleotide polymorphisms of WNK4 gene and essential hypertension (EHT). The aim of this study was to determine the association of Ala589Ser polymorphism of WNK4 gene with essential hypertensive patients in Malaysia. WNK4 gene polymorphism was specified utilizing mutagenically separated polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method in 320 subjects including 163 cases and 157 controls. Close relation between Ala589Ser polymorphism and elevated systolic and diastolic blood pressure (SBP and DBP) was recognized. Sociodemographic factors including body mass index (BMI), age, the level of fasting blood sugar (FBS), low density lipoprotein (LDL), and triglyceride (TG) in the cases and healthy subjects exhibited strong differences (p < 0.05). The distribution of allele frequency and genotype of WNK4 gene Ala589Ser polymorphism showed significant differences (p < 0.05) between EHT subjects with or without type 2 diabetes mellitus (T2DM) and normotensive subjects, statistically. The WNK4 gene variation influences significantly blood pressure increase. Ala589Ser probably has effects on the enzymic activity leading to enhanced predisposition to the disorder.
    Matched MeSH terms: Diabetes Mellitus, Type 2/genetics*; Hypertension/genetics*; Protein-Serine-Threonine Kinases/genetics*; Asian Continental Ancestry Group/genetics
  13. Fulltext Analysis of selected glutathione S-transferase gene polymorphisms in Malaysian type 2 diabetes mellitus patients with and without cardiovascular disease
    Etemad A, Vasudevan R, Aziz AF, Yusof AK, Khazaei S, Fawzi N, et al.
    Genet. Mol. Res., 2016 Apr 07;15(2).
    PMID: 27173202 DOI: 10.4238/gmr.15025845
    Type 2 diabetes mellitus (T2DM) is believed to be associated with excessive production of reactive oxygen species. Glutathione S-transferase (GST) polymorphisms result in decreased or absent enzyme activity and altered oxidative stress, and have been associated with cardiovascular disease (CVD). The present study assessed the effect of GST polymorphisms on the risk of developing T2DM in individuals of Malaysian Malay ethnicity. A total of 287 subjects, consisting of 87 T2DM and 64 CVD/T2DM patients, as well as 136 healthy gender- and age-matched controls were genotyped for selected polymorphisms to evaluate associations with T2DM susceptibility. Genomic DNA was extracted using commercially available kits, and GSTM1, GSTT1, and α-globin sequences were amplified by multiplex polymerase chain reaction. Biochemical parameters were measured with a Hitachi autoanalyzer. The Fisher exact test, the chi-square statistic, and means ± standard deviations were calculated using the SPSS software. Overall, we observed no significant differences regarding genotype and allele frequencies between each group (P = 0.224 and 0.199, respectively). However, in the combined analysis of genotypes and blood measurements, fasting plasma glucose, HbA1c, and triglyceride levels, followed by age, body mass index, waist-hip ratio, systolic blood pressure, and history of T2DM significantly differed according to GST polymorphism (P ˂ 0.05). Genetically induced absence of the GSTT1 enzyme is an independent and powerful predictor of premature vascular morbidity and death in individuals with T2DM, and might be triggered by cigarette smoking's oxidative effects. These polymorphisms could be screened in other ethnicities within Malaysia to determine further possible risk factors.
    Matched MeSH terms: Cardiovascular Diseases/genetics*; Diabetes Mellitus, Type 2/genetics*; Glutathione Transferase/genetics*; alpha-Globins/genetics
  14. Genetic susceptibility to cervical cancer: role of common polymorphisms in apoptosis-related genes
    Tan SC, Ankathil R
    Tumour Biol., 2015 Sep;36(9):6633-44.
    PMID: 26242271 DOI: 10.1007/s13277-015-3868-2
    Cervical cancer is a common malignancy which poses a significant health burden among women, especially those living in the developing countries. Although human papillomavirus (HPV) infection has been unequivocally implicated in the etiopathogenesis of the cancer, it alone is not adequate to contribute to the malignant transformation of cervical cells. Most HPV infections regress spontaneously, and only a small proportion of women have persistent infections which eventually lead to malignancy. This suggests that interplays between HPV infection and other cofactors certainly exist during the process of cervical carcinogenesis, which synergistically contribute to the differential susceptibility of an individual to the malignancy. Undoubtedly, host genetic factors represent a major element involved in such a synergistic interaction, and accumulating evidence suggests that polymorphisms in apoptosis-related genes play an important role in the genetic susceptibility to cervical cancer. This review consolidates the recent literatures on the role of common polymorphisms in apoptosis-related genes in genetic susceptibility to cervical cancer.
    Matched MeSH terms: Uterine Cervical Neoplasms/genetics*; Apoptosis/genetics*; Papillomaviridae/genetics*; Carcinogenesis/genetics
  15. Fulltext Phylogeography of the coastal mosquito Aedes togoi across climatic zones: testing an anthropogenic dispersal hypothesis
    Sota T, Belton P, Tseng M, Yong HS, Mogi M
    PLoS One, 2015;10(6):e0131230.
    PMID: 26107619 DOI: 10.1371/journal.pone.0131230
    The coastal mosquito Aedes togoi occurs more or less continuously from subarctic to subtropic zones along the coasts of the Japanese islands and the East Asian mainland. It occurs also in tropical Southeast Asia and the North American Pacific coast, and the populations there are thought to have been introduced from Japan by ship. To test this hypothesis, the genetic divergence among geographic populations of A. togoi was studied using one mitochondrial and three nuclear gene sequences. We detected 71 mitochondrial haplotypes forming four lineages, with high nucleotide diversity around temperate Japan and declining towards peripheral ranges. The major lineage (L1) comprised 57 haplotypes from temperate and subarctic zones in Japan and Southeast Asia including southern China and Taiwan. Two other lineages were found from subtropical islands (L3) and a subarctic area (L4) of Japan. The Canadian population showed one unique haplotype (L2) diverged from the other lineages. In the combined nuclear gene tree, individuals with mitochondrial L4 haplotypes diverged from those with the other mitochondrial haplotypes L1-L3; although individuals with L1-L3 haplotypes showed shallow divergences in the nuclear gene sequences, individuals from Southeast Asia and Canada each formed a monophyletic group. Overall, the genetic composition of the Southeast Asian populations was closely related to that of temperate Japanese populations, suggesting recent gene flow between these regions. The Canadian population might have originated from anthropogenic introduction from somewhere in Asia, but the possibility that it could have spread across the Beringian land bridge cannot be ruled out.
    Matched MeSH terms: Aedes/genetics*; DNA, Mitochondrial/genetics; Genetics, Population*
  16. Fulltext Expression and Characterization of Geobacillus stearothermophilus SR74 Recombinant α-Amylase in Pichia pastoris
    Gandhi S, Salleh AB, Rahman RN, Chor Leow T, Oslan SN
    Biomed Res Int, 2015;2015:529059.
    PMID: 26090417 DOI: 10.1155/2015/529059
    Geobacillus stearothermophilus SR74 is a locally isolated thermophilic bacteria producing thermostable and thermoactive α-amylase. Increased production and commercialization of thermostable α-amylase strongly warrant the need of a suitable expression system. In this study, the gene encoding the thermostable α-amylase in G. stearothermophilus SR74 was amplified, sequenced, and subcloned into P. pastoris GS115 strain under the control of a methanol inducible promoter, alcohol oxidase (AOX). Methanol induced recombinant expression and secretion of the protein resulted in high levels of extracellular amylase production. YPTM medium supplemented with methanol (1% v/v) was the best medium and once optimized, the maximum recombinant α-amylase SR74 achieved in shake flask was 28.6 U mL(-1) at 120 h after induction. The recombinant 59 kDa α-amylase SR74 was purified 1.9-fold using affinity chromatography with a product yield of 52.6% and a specific activity of 151.8 U mg(-1). The optimum pH of α-amylase SR74 was 7.0 and the enzyme was stable between pH 6.0-8.0. The purified enzyme was thermostable and thermoactive, exhibiting maximum activity at 65°C with a half-life (t₁/₂) of 88 min at 60°C. In conclusion, thermostable α-amylase SR74 from G. stearothermophilus SR74 would be beneficial for industrial applications, especially in liquefying saccrification.
    Matched MeSH terms: alpha-Amylases/genetics*; Geobacillus stearothermophilus/genetics; Pichia/genetics; Recombinant Proteins/genetics*
  17. Mitochondrial genomes of the jungle crow Corvus macrorhynchos (Passeriformes: Corvidae) from shed feathers and a phylogenetic analysis of genus Corvus using mitochondrial protein-coding genes
    Krzeminska U, Wilson R, Rahman S, Song BK, Seneviratne S, Gan HM, et al.
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2668-70.
    PMID: 26075478 DOI: 10.3109/19401736.2015.1043540
    The complete mitochondrial genomes of two jungle crows (Corvus macrorhynchos) were sequenced. DNA was extracted from tissue samples obtained from shed feathers collected in the field in Sri Lanka and sequenced using the Illumina MiSeq Personal Sequencer. Jungle crow mitogenomes have a structural organization typical of the genus Corvus and are 16,927 bp and 17,066 bp in length, both comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes, and a non-coding control region. In addition, we complement already available house crow (Corvus spelendens) mitogenome resources by sequencing an individual from Singapore. A phylogenetic tree constructed from Corvidae family mitogenome sequences available on GenBank is presented. We confirm the monophyly of the genus Corvus and propose to use complete mitogenome resources for further intra- and interspecies genetic studies.
    Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Transfer/genetics; Passeriformes/genetics*; Genome, Mitochondrial/genetics*
  18. Draft genome sequence of Vitellibacter vladivostokensis KMM 3516(T): a protease-producing bacterium
    Thevarajoo S, Selvaratnam C, Chan KG, Goh KM, Chong CS
    Mar Genomics, 2015 Oct;23:49-50.
    PMID: 25957696 DOI: 10.1016/j.margen.2015.04.009
    Type strain Vitellibacter vladivostokensis KMM 3516(T) (=NBRC 16718(T)) belongs to the phylum Cytophaga-Flavobacterium-Bacteroides. To date, no genomes of the Vitellibacter spp. have been reported, and their metabolic pathways are unknown. This study reports the draft genome sequence of V. vladivostokensis. Moreover, mining of genes associated with proteolytic enzymes was performed to provide insights for further enzyme characterization.
    Matched MeSH terms: Bacterial Proteins/genetics; Peptide Hydrolases/genetics; Genome, Bacterial/genetics*; Bacteroidetes/genetics*
  19. Fulltext Detection of mitochondrial COII DNA sequences in ant guts as a method for assessing termite predation by ants
    Fayle TM, Scholtz O, Dumbrell AJ, Russell S, Segar ST, Eggleton P
    PLoS One, 2015;10(4):e0122533.
    PMID: 25853549 DOI: 10.1371/journal.pone.0122533
    Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest. We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2 % of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1 % of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63 % (5/7; Camponotus sp. 1) to 0 % (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consumption across ant taxa, and no evidence for species-specific ant-termite predation. In all three ant species with identifiable termite DNA in multiple individuals, multiple termite species were represented. Furthermore, the two termite species that were detected on multiple occasions in ant guts were in both cases found in multiple ant species, suggesting that ant-termite food webs are not strongly compartmentalised. However, two ant species were found to consume only Anoplotermes-group termites, indicating possible predatory specialisation at a higher taxonomic level. Using a laboratory feeding test, we were able to detect termite COII sequences in ant guts up to 2 h after feeding, indicating that our method only detects recent feeding events. Our data provide tentative support for the hypothesis that unspecialised termite predation by ants is widespread and highlight the use of molecular approaches for future studies of ant-termite food webs.
    Matched MeSH terms: Ants/genetics; Electron Transport Complex IV/genetics*; DNA, Mitochondrial/genetics; Isoptera/genetics
  20. Downregulation of CRNN gene and genomic instability at 1q21.3 in oral squamous cell carcinoma
    Salahshourifar I, Vincent-Chong VK, Chang HY, Ser HL, Ramanathan A, Kallarakkal TG, et al.
    Clin Oral Investig, 2015 Dec;19(9):2273-83.
    PMID: 25846277 DOI: 10.1007/s00784-015-1467-7
    OBJECTIVES: This study includes the direct sequencing of cornulin (CRNN) gene to elucidate the possible mechanism of CRNN downregulation and explore the genetic imbalances at 1q21.3 across oral squamous cell carcinoma (OSCC) samples.

    MATERIALS AND METHODS: In mutation screening of CRNN gene, gDNA from OSCC tissues were extracted, amplified, and followed by direct sequencing. OSCC samples were also subjected to fragment analysis on CRNN gene to investigate its microsatellite instability (MSI) and loss of heterozygosity (LOH). Immunohistochemistry was performed to validate CRNN downregulation in OSCC samples.

    RESULTS: No pathogenic mutation was found in CRNN gene, while high frequency of allelic imbalances was found at 1q21.3 region. MSI was found more frequent (25.3 %) than LOH (9.3 %). Approximately 22.6 % of cases had high MSI which reflects higher probability of inactivation of DNA mismatch repair genes. MSI showed significant association with no betel quid chewing (p = 0.003) and tongue subsite (p = 0.026). LOH was associated with ethnicity (p = 0.008) and advanced staging (p = 0.039). The LOH at 1q21.3 was identified to be as an independent prognostic marker in OSCC (HRR = 7.15 (95 % CI, 1.41-36.25), p = 0.018). Downregulation of CRNN was found among MSI-positive OSCCs and was associated with poor prognosis (p = 0.044).

    CONCLUSION: This study showed a significant correlation between LOH/MSI at 1q21.3 with clinical outcomes and that downregulation of CRNN gene could be considered as a prognostic marker of OSCC.

    CLINICAL RELEVANCE: Insights of the downregulation mode of CRNN gene lays the basis of drug development on this gene as well as revealing its prognostic value.

    Matched MeSH terms: Carcinoma, Squamous Cell/genetics*; Membrane Proteins/genetics*; Mouth Neoplasms/genetics*; Neoplasm Proteins/genetics*
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