Displaying publications 221 - 240 of 8105 in total

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  1. Fulltext Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers
    Ting NC, Jansen J, Nagappan J, Ishak Z, Chin CW, Tan SG, et al.
    PLoS One, 2013;8(1):e53076.
    PMID: 23382832 DOI: 10.1371/journal.pone.0053076
    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.
    Matched MeSH terms: Polymorphism, Restriction Fragment Length/genetics; Seeds/genetics*; Microsatellite Repeats/genetics*; Arecaceae/genetics; Quantitative Trait Loci/genetics*; Plant Development/genetics*
  2. Next generation sequencing yields the complete mitochondrial genome of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae)
    Loh KH, Shao KT, Chen HM, Chen CH, Chong VC, Loo PL, et al.
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4230-4231.
    PMID: 26000942
    In this study, the complete mitogenome sequence of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,576 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Zebra moray is 30.2% for A, 26.8% for C, 17.2% for G, and 25.8% for T and show 80% identities to Kidako moray, Gymnothorax kidako. The complete mitogenome of the Zebra moray provides an essential and important DNA molecular data for further phylogeography and evolutionary analysis for moray eel phylogeny.
    Matched MeSH terms: Base Composition/genetics; Eels/genetics*; RNA, Transfer/genetics; Equidae/genetics*; Genes, rRNA/genetics; Genome, Mitochondrial/genetics*
  3. Autophagy and senescence: A new insight in selected human diseases
    Rajendran P, Alzahrani AM, Hanieh HN, Kumar SA, Ben Ammar R, Rengarajan T, et al.
    J Cell Physiol, 2019 12;234(12):21485-21492.
    PMID: 31144309 DOI: 10.1002/jcp.28895
    Senescence and autophagy play important roles in homeostasis. Cellular senescence and autophagy commonly cause several degenerative processes, including oxidative stress, DNA damage, telomere shortening, and oncogenic stress; hence, both events are known to be interrelated. Autophagy is well known for its disruptive effect on human diseases, and it is currently proposed to have a direct effect on triggering senescence and quiescence. However, it is yet to be proven whether autophagy has a positive or negative impact on senescence. It is known that elevated levels of autophagy induce cell death, whereas inadequate autophagy can trigger cellular senescence. Both have important roles in human diseases such as aging, renal degeneration, neurodegenerative disorders, and cancer. Therefore, this review aims to highlight the relevance of senescence and autophagy in selected human ailments through a summary of recent findings on the connection and effects of autophagy and senescence in these diseases.
    Matched MeSH terms: Aging/genetics; Autophagy/genetics; Homeostasis/genetics; Telomere/genetics; Cell Aging/genetics; Telomere Shortening/genetics
  4. Fulltext Prevalence of BRCA1 and BRCA2 pathogenic variants in a large, unselected breast cancer cohort
    Li J, Wen WX, Eklund M, Kvist A, Eriksson M, Christensen HN, et al.
    Int J Cancer, 2019 03 01;144(5):1195-1204.
    PMID: 30175445 DOI: 10.1002/ijc.31841
    Breast cancer patients with BRCA1/2-driven tumors may benefit from targeted therapy. It is not clear whether current BRCA screening guidelines are effective at identifying these patients. The purpose of our study was to evaluate the prevalence of inherited BRCA1/2 pathogenic variants in a large, clinically representative breast cancer cohort and to estimate the proportion of BRCA1/2 carriers not detected by selectively screening individuals with the highest probability of being carriers according to current clinical guidelines. The study included 5,122 unselected Swedish breast cancer patients diagnosed from 2001 to 2008. Target sequence enrichment (48.48 Fluidigm Access Arrays) and sequencing were performed (Illumina Hi-Seq 2,500 instrument, v4 chemistry). Differences in patient and tumor characteristics of BRCA1/2 carriers who were already identified as part of clinical BRCA1/2 testing routines and additional BRCA1/2 carriers found by sequencing the entire study population were compared using logistic regression models. Ninety-two of 5,099 patients with valid variant calls were identified as BRCA1/2 carriers by screening all study participants (1.8%). Only 416 study participants (8.2%) were screened as part of clinical practice, but this identified 35 out of 92 carriers (38.0%). Clinically identified carriers were younger, less likely postmenopausal and more likely to be associated with familiar ovarian cancer compared to the additional carriers identified by screening all patients. More BRCA2 (34/42, 81.0%) than BRCA1 carriers (23/50, 46%) were missed by clinical screening. In conclusion, BRCA1/2 mutation prevalence in unselected breast cancer patients was 1.8%. Six in ten BRCA carriers were not detected by selective clinical screening of individuals.
    Matched MeSH terms: Breast Neoplasms/genetics*; Mutation/genetics*; Ovarian Neoplasms/genetics; BRCA1 Protein/genetics*; Genetic Predisposition to Disease/genetics*; BRCA2 Protein/genetics*
  5. Fulltext The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella
    Kushwaha SK, Bhavesh NLS, Abdella B, Lahiri C, Marathe SA
    Sci Rep, 2020 12 03;10(1):21156.
    PMID: 33273523 DOI: 10.1038/s41598-020-77890-6
    Salmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition and/or exchange of various virulence factors influences the evolutionary framework. To gain insights into evolution of Salmonella in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains differed in their CRISPR1-leader and cas operon features assorting into two main clades, CRISPR1-STY/cas-STY and CRISPR1-STM/cas-STM, comprising majorly typhoidal and non-typhoidal Salmonella serovars respectively. Serovars of these two clades displayed better relatedness, concerning CRISPR1-leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region could be through a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system. As opposed to broad-host-range, the host-specific serovars harbor fewer spacers. Mapping of protospacer sources suggested a partial correlation of spacer content with habitat diversity of the serovars. Some serovars like serovar Enteritidis and Typhimurium that inhabit similar environment/infect similar hosts hardly shared their protospacer sources.
    Matched MeSH terms: Operon/genetics; Salmonella/genetics*; Conserved Sequence/genetics; Interspersed Repetitive Sequences/genetics; DNA, Intergenic/genetics; CRISPR-Cas Systems/genetics*
  6. In vitro evidence consistent with an interaction between wild-type and mutant SOD1 protein associated with canine degenerative myelopathy
    Qi Y, Montague P, Loney C, Campbell C, Shafie INF, Anderson TJ, et al.
    Eur J Neurosci, 2019 12;50(12):3896-3905.
    PMID: 31336405 DOI: 10.1111/ejn.14526
    Canine degenerative myelopathy (DM) is a progressive neurological disorder that may be considered to be a large animal model for specific forms of the fatal human disease, familial amyotrophic lateral sclerosis (fALS). DM is associated with a c118G>A mutation of the superoxide dismutase 1 (Sod1) gene, and a significant proportion of cases are inherited in an autosomal recessive manner in contrast to the largely, but not exclusively, dominant mode of inheritance in fALS. The consensus view is that these Sod1/SOD1 mutations result in a toxic gain of function but the mechanisms remain unclear. Here we used an in vitro neuroblastoma cell line transfection system to monitor wild-type and mutant forms of SOD1 fusion proteins containing either a Cherry or an enhanced green fluorescent protein (EGFP) tag. These fusion proteins retained SOD1 enzymatic activity on a native gel assay system. We demonstrate that SOD1 aggregate density is significantly higher in DM transfectants compared to wild-type. In addition, we show by co-immunoprecipitation and confocal microscopy, evidence for a potential interaction between wild-type and mutant forms of SOD1 in co-transfected cells. While in vitro studies have shown SOD1 heterodimer formation in fALS models, this is the first report for DM SOD1. Therefore, despite for the majority of cases there is a difference in the mode of inheritance between fALS and DM, a similar interaction between wild-type and mutant SOD1 forms can occur. Clarifying the role of SOD1 in DM may also be of benefit to understanding the role of SOD1 in fALS.
    Matched MeSH terms: Amyotrophic Lateral Sclerosis/genetics*; Mutation/genetics*; Spinal Cord Diseases/genetics; Superoxide Dismutase/genetics*; Green Fluorescent Proteins/genetics; Superoxide Dismutase-1/genetics*
  7. Phylogenetic analysis of different breeds of domestic chickens in selected area of Peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers
    Yap FC, Yan YJ, Loon KT, Zhen JL, Kamau NW, Kumaran JV
    Anim Biotechnol, 2010 Oct;21(4):226-40.
    PMID: 20967642 DOI: 10.1080/10495398.2010.506334
    The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.
    Matched MeSH terms: Chickens/genetics*; DNA/genetics; DNA, Mitochondrial/genetics; Genetic Markers/genetics; Genetics, Population; Cytochromes b/genetics*
  8. Fulltext Molecular evidence of the hybrid origin of Cryptocoryne ×purpurea Ridl. nothovar. purpurea (Araceae)
    Rosazlina R, Jacobsen N, Ørgaard M, Othman AS
    PLoS One, 2021;16(1):e0239499.
    PMID: 33476321 DOI: 10.1371/journal.pone.0239499
    Natural hybridization has been considered a source of taxonomic complexity in Cryptocoryne. A combined study of DNA sequencing data from the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the trnK-matK region of chloroplast DNA was used to identify the parents of Cryptocoryne putative hybrids from Peninsular Malaysia. Based on the intermediate morphology and sympatric distribution area, the plants were tentatively identified as the hybrid Cryptocoryne ×purpurea nothovar. purpurea. The plants were pollen sterile and had long been considered as hybrids, supposedly between two related and co-existing species, C. cordata var. cordata and C. griffithii. The status of C. ×purpurea nothovar. purpurea was independently confirmed by the presence of an additive ITS sequence pattern from these two parental species in hybrid individuals. An analysis of the chloroplast trnK-matK sequences showed that the hybridization is bidirectional with the putative hybrids sharing identical sequences from C. cordata var. cordata and C. griffithii, indicating that both putative parental species had been the maternal parent in different accessions.
    Matched MeSH terms: Chimera/genetics; DNA, Ribosomal/genetics; Hybridization, Genetic/genetics; DNA, Chloroplast/genetics*; DNA, Ribosomal Spacer/genetics; Araceae/genetics*
  9. Draft genome sequence of Parvularcula flava strain NH6-79 T, revealing its role as a cellulolytic enzymes producer
    Abdul Karim MH, Lam MQ, Chen SJ, Yahya A, Shahir S, Shamsir MS, et al.
    Arch Microbiol, 2020 Nov;202(9):2591-2597.
    PMID: 32607725 DOI: 10.1007/s00203-020-01967-z
    To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content of 59.87%. From a total of 3,465 genes predicted, 96 of them are annotated as glycoside hydrolases (GHs). Within these GHs, 20 encoded genes are related to cellulosic biomass degradation, including 12 endoglucanases (5 GH10, 4 GH5, and 3 GH51), 2 exoglucanases (GH9) and 6 β-glucosidases (GH3). In addition, highest relative enzyme activities (endoglucanase, exoglucanase, and β-glucosidase) were observed at 27th hour when the strain was cultured in the carboxymethyl cellulose/Avicel®-containing medium for 45 h. The combination of genome analysis with experimental studies indicated the ability of strain NH6-79 T to produce extracellular endoglucanase, exoglucanase, and β-glucosidase. These findings suggest the potential of Parvularcula flava strain NH6-79 T in cellulose-containing biomass degradation and that the strain could be used in cellulosic biorefining process.
    Matched MeSH terms: Bacterial Proteins/genetics; beta-Glucosidase/genetics; Cellulase/genetics; Glycoside Hydrolases/genetics*; Genome, Bacterial/genetics*; Alphaproteobacteria/genetics*
  10. New insights on brain-derived neurotrophic factor epigenetics: from depression to memory extinction
    Poon CH, Heng BC, Lim LW
    Ann N Y Acad Sci, 2021 01;1484(1):9-31.
    PMID: 32808327 DOI: 10.1111/nyas.14458
    Advances in characterizing molecular profiles provide valuable insights and opportunities for deciphering the neuropathology of depression. Although abnormal brain-derived neurotrophic factor (BDNF) expression in depression has gained much support from preclinical and clinical research, how it mediates behavioral alterations in the depressed state remains largely obscure. Environmental factors contribute significantly to the onset of depression and produce robust epigenetic changes. Epigenetic regulation of BDNF, as one of the most characterized gene loci in epigenetics, has recently emerged as a target in research on memory and psychiatric disorders. Specifically, epigenetic alterations of BDNF exons are heavily involved in mediating memory functions and antidepressant effects. In this review, we discuss key research on stress-induced depression from both preclinical and clinical studies, which revealed that differential epigenetic regulation of specific BDNF exons is associated with depression pathophysiology. Considering that BDNF has a central role in depression, we argue that memory extinction, an adaptive response to fear exposure, is dependent on BDNF modulation and holds promise as a prospective target for alleviating or treating depression and anxiety disorders.
    Matched MeSH terms: Anxiety Disorders/genetics; Depression/genetics*; Memory Disorders/genetics*; Promoter Regions, Genetic/genetics; Brain-Derived Neurotrophic Factor/genetics*; Epigenesis, Genetic/genetics*
  11. Fulltext Effect of different cloning strategies in pET-28a on solubility and functionality of a staphylococcal phage endolysin
    Tham HY, Song AA, Yusoff K, Tan GH
    Biotechniques, 2020 09;69(3):161-170.
    PMID: 32787565 DOI: 10.2144/btn-2020-0034
    Endolysins have been studied intensively as an alternative to antibiotics. In this study, endolysin derived from a phage which infects methicillin-resistant Staphylococcus aureus (MRSA) was cloned and expressed in Escherichia coli pET28a. Initially, the endolysin was cloned using BamHI/XhoI, resulting in expression of a recombinant endolysin which was expressed in inclusion bodies. While solubilization was successful, the protein remained nonfunctional. Recloning the endolysin using NcoI/XhoI resulted in expression of soluble and functional proteins at 18°C. The endolysin was able to form halo zones on MRSA plates and showed a reduction in turbidity of MRSA growth. Therefore, cloning strategies should be chosen carefully even in an established expression system as they could greatly affect the functionality of the expressed protein.
    Matched MeSH terms: Bacteriophages/genetics*; Escherichia coli/genetics; Gene Expression Regulation/genetics; Endopeptidases/genetics*; Recombinant Proteins/genetics*; Methicillin-Resistant Staphylococcus aureus/genetics*
  12. Fulltext Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken
    Nematbakhsh S, Pei Pei C, Selamat J, Nordin N, Idris LH, Abdull Razis AF
    Genes (Basel), 2021 03 13;12(3).
    PMID: 33805667 DOI: 10.3390/genes12030414
    In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer's health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality.
    Matched MeSH terms: Chickens/genetics*; Gene Expression Regulation/genetics*; Lipogenesis/genetics*; Adipogenesis/genetics*; Lipid Metabolism/genetics*; Gene Regulatory Networks/genetics*
  13. Structural analysis of a missense mutation (Val414Phe) in the catalytic core domain of the factor XIII(A) subunit
    Aslam S, Yee VC, Narayanan S, Duraisamy G, Standen GR
    Br J Haematol, 1997 Aug;98(2):346-52.
    PMID: 9266932
    Molecular analysis has been performed on a Malaysian patient with a severe bleeding disorder due to factor XIII(A) subunit deficiency. Total mRNA was isolated from the patient's leucocytes and four overlapping segments corresponding to the entire coding region of the A subunit cDNA were amplified by RT-PCR. The cDNA segments amplified efficiently and were of expected size. Direct sequencing of the complete reading frame revealed a single homozygous base change (nt 1327G-T) in exon 10 corresponding to a missense mutation, Val414Phe, in the catalytic core domain of the A subunit monomer. The mutation eliminates a BsaJ1 restriction site and family screening showed that both parents were heterozygous for the defect. The base substitution was absent in 55 normal individuals. Val414 is a highly conserved residue in the calcium-dependent transglutaminase enzyme family. Computer modelling based on 3D crystallographic data predicts that the bulky aromatic side chain of the substituted phenylalanine residue distorts protein folding and destabilizes the molecule. In addition, conformation changes in the adjacent catalytic and calcium binding regions of the A subunit are likely to impair the enzymatic activity of any protein synthesized.
    Matched MeSH terms: DNA/genetics; Exons/genetics; Factor XIII/genetics*; Factor XIII Deficiency/genetics*; Mutation/genetics*; RNA/genetics
  14. Multiple alpha-globin genes in crab-eating macaques (Macaca fascicularis)
    Takenaka A, Ueda S, Terao K, Takenaka O
    Mol Biol Evol, 1991 May;8(3):320-6.
    PMID: 2072861
    Alpha-globin genes in crab-eating macaques were found to be triplicated at high frequencies according to restriction-enzyme comparisons. The frequencies of triplicated alpha-globin genes in macaques originally from Malaysia and Indonesia were 0.432 and 0.275, respectively, while no triplication was found in individuals from either the Philippines or northern and central Thailand. Quadruplicated alpha-globin genes were also observed, at frequencies of 0.045 (Malaysia), 0.075 (Indonesia), and 0.021 (the Philippines). A single locus was detected in only one of 40 chromosomes from Indonesia (frequency 0.025).
    Matched MeSH terms: Animals, Wild/genetics; DNA/genetics; Globins/genetics*; Macaca fascicularis/genetics*; Malaria/genetics; Monkey Diseases/genetics
  15. Fulltext Exome Sequencing Identifies Potentially Druggable Mutations in Nasopharyngeal Carcinoma
    Chow YP, Tan LP, Chai SJ, Abdul Aziz N, Choo SW, Lim PV, et al.
    Sci Rep, 2017 03 03;7:42980.
    PMID: 28256603 DOI: 10.1038/srep42980
    In this study, we first performed whole exome sequencing of DNA from 10 untreated and clinically annotated fresh frozen nasopharyngeal carcinoma (NPC) biopsies and matched bloods to identify somatically mutated genes that may be amenable to targeted therapeutic strategies. We identified a total of 323 mutations which were either non-synonymous (n = 238) or synonymous (n = 85). Furthermore, our analysis revealed genes in key cancer pathways (DNA repair, cell cycle regulation, apoptosis, immune response, lipid signaling) were mutated, of which those in the lipid-signaling pathway were the most enriched. We next extended our analysis on a prioritized sub-set of 37 mutated genes plus top 5 mutated cancer genes listed in COSMIC using a custom designed HaloPlex target enrichment panel with an additional 88 NPC samples. Our analysis identified 160 additional non-synonymous mutations in 37/42 genes in 66/88 samples. Of these, 99/160 mutations within potentially druggable pathways were further selected for validation. Sanger sequencing revealed that 77/99 variants were true positives, giving an accuracy of 78%. Taken together, our study indicated that ~72% (n = 71/98) of NPC samples harbored mutations in one of the four cancer pathways (EGFR-PI3K-Akt-mTOR, NOTCH, NF-κB, DNA repair) which may be potentially useful as predictive biomarkers of response to matched targeted therapies.
    Matched MeSH terms: Carcinoma/genetics; DNA Repair/genetics; Nasopharyngeal Neoplasms/genetics; Biomarkers, Tumor/genetics; Signal Transduction/genetics; Exome/genetics*
  16. Hidrotic ectodermal dysplasia: study of a large Chinese pedigree
    Rajagopalan K, Tay CH
    Arch Dermatol, 1977 Apr;113(4):481-5.
    PMID: 139851
    Hidrotic ectodermaldysplasia was found, to our knowledge, for the first time in a Chinese family in Malaysia, and it affected 15 members in five generations. The disease, which is transmitted as a non-sex-linked autosomal dominant trait, presumably originated from southern China. All 15 members had the typical nail, hair, and skin lesions, and we observed three different types of nail defects. Scalp alopeica was more extensive in the female members while keratoderma of the palms and soles was more notable in the male members. The nail and skin lesions also became severer with age. Except for the infectious eczematoid dermatitis present in the propositus, none had other skin or systemic disorders. All were relatively healthy and had normal life expectancies;
    Matched MeSH terms: Alopecia/genetics; Ectodermal Dysplasia/genetics*; Foot Dermatoses/genetics; Hand Dermatoses/genetics; Keratoderma, Palmoplantar/genetics; Nails, Malformed/genetics
  17. An analysis of genetic association in opioid dependence susceptibility
    Nagaya D, Zahari Z, Saleem M, Yahaya BH, Tan SC, Yusoff NM
    J Clin Pharm Ther, 2018 Feb;43(1):80-86.
    PMID: 28656735 DOI: 10.1111/jcpt.12585
    WHAT IS KNOWN: Drug addiction is a novelty-seeking personality trait that is associated with the candidate genes OPRD1 (opioid delta receptors), OPRK1 (opioid kappa receptors) and PDYN (prodynorphin). However, associations between single nucleotide polymorphisms (SNPs) rs1042114 (80G>T) of the OPRD1 gene, rs702764 (843 A>G) of the OPRK1 gene, and rs910080 (3' UTR _743T>C), rs1997794 (5' UTR -381A>G) and rs1022563 (3' UTR) of the PDYN gene and novelty seeking remain controversial as reported results have not been reproducible.

    OBJECTIVE: The goal of this study was to determine the frequencies of SNPs rs1042114, rs702764, rs1997794, rs1022563 and rs910080 in the Malaysian population and to study their association with opioid dependence in Malaysian Malays.

    METHODS: A total of 459 Malay male with opioid dependence and 543 healthy male (controls) subjects were included in this study. SNPs were genotyped using the TaqMan SNP genotyping assay. Statistical analysis was performed using Golden Helix SVS software suite to identify the distribution of allele and genotype frequencies, and SNP-SNP interactions were also analysed in this study.

    RESULTS AND DISCUSSION: SNP rs1042114 in the OPRD1 gene is strongly associated with opiate addiction (P=.0001). In individuals homozygous for this risk allele, the likelihood of opiate addiction is increased by a factor 1.62 (95% confidence interval (CI) 1.412-1.875). Polymorphic alleles at SNP rs702764 of OPRK1 were not associated with opioid dependence. A significant association between opioid dependence and SNP rs910080 of PDYN (P=.0217) was detected, but there was no association for SNPs rs199774 and rs1022563. A significant interaction was also identified between homozygous wild-type genotype TT of rs702764 with the risk genotypes TG/GG of rs1042114 (odds ratio (OR)=2.111 (95% CI 1.227-3.631), P=.0069) and with the risk genotypes GA/AA of rs910080 (OR=1.415 (95% CI 1.04-1.912), P=.0239).

    WHAT IS NEW AND CONCLUSION: The results indicate that SNPs rs1042114 and rs910080 contribute to vulnerability to opioid dependence in the Malaysian Malay population. These results will help us to understand the effect of the SNPs and the SNP-SNP interaction on opioid dependence and may assist in efforts to screen vulnerable individuals and match them with individually tailored prevention and treatment strategies.

    Matched MeSH terms: Gene Frequency/genetics; Opioid-Related Disorders/genetics*; Receptors, Opioid, delta/genetics*; Receptors, Opioid, kappa/genetics*; Genetic Predisposition to Disease/genetics*; Polymorphism, Single Nucleotide/genetics*
  18. Fulltext Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm
    Wong YC, Teh HF, Mebus K, Ooi TEK, Kwong QB, Koo KL, et al.
    BMC Genomics, 2017 06 21;18(1):470.
    PMID: 28637447 DOI: 10.1186/s12864-017-3855-7
    BACKGROUND: The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations.

    RESULTS: A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms.

    CONCLUSIONS: Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to production of high-yielding oil palms and have implications for breeding to maximize oil production.

    Matched MeSH terms: Citric Acid Cycle/genetics; Fruit/genetics*; Glycolysis/genetics; Transcription Factors/genetics; Arecaceae/genetics*; Lipid Metabolism/genetics
  19. Distribution of adeB and NDM-1 genes in multidrug resistant Acinetobacter baumannii isolated from infected wound of patients admitted in a tertiary care hospital in Bangladesh
    Hasan MJ, Shamsuzzaman SM
    Malays J Pathol, 2017 Dec;39(3):277-283.
    PMID: 29279590
    BACKGROUND: The adeB gene in Acinetobacter baumannii regulates the bacterial internal drug efflux pump that plays a significant role in drug resistance. The aim of our study was to determine the occurrence of adeB gene in multidrug resistant and New Delhi metallo-beta-lactamase-1 (NDM- 1) gene in imipenem resistant Acinetobacter baumannii isolated from wound swab samples in a tertiary care hospital of Bangladesh.

    METHODS: A total of 345 wound swab samples were tested for bacterial pathogens. Acinetobacter baumannii was identified by culture and biochemical tests. Antimicrobial susceptibility pattern was determined by the disc diffusion method according to CLSI standards. Extended spectrum beta-lactamases were screened using the double disc synergy technique. Gene encoding AdeB efflux pump and NDM-1 were detected by Polymerase Chain Reaction (PCR).

    RESULTS: A total 22 (6.37%) Acinetobacter baumannii were identified from 345 wound swab samples and 20 (91%) of them were multidrug resistant. High resistance rates to some antibiotics were seen namely, cefotaxime (95%), amoxyclavulanic acid (90%) and ceftriaxone (82%). All the identified Acinetobacter baumannii were sensitive to colistin and 82% to imipenem. Two (9%) ESBL producing Acinetobacter baumannii strains were detected. adeB gene was detected in 16 (80%) out of 20 multidrug resistant Acinetobacter baumannii. 4 (18%) of 22 Acinetobacter baumannii were imipenem resistant. NDM-1 gene was detected in 2 (50%) of the imipenem resistant strains of Acinetobacter baumannii.

    CONCLUSION: The results of this study provide insight into the role of adeB gene as a potential regulator of drug resistance in Acinetobacter baumanni in Bangladesh. NDM-1 gene also contributes in developing such resistance for Acinetobacter baumannii.

    Matched MeSH terms: Acinetobacter Infections/genetics*; Bacterial Proteins/genetics*; beta-Lactamases/genetics*; Wound Infection/genetics*; Drug Resistance, Multiple/genetics*; Membrane Transport Proteins/genetics*
  20. 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*; Genetics, Population*; Genetic Variation/genetics*; Locus Control Region/genetics; Genome, Mitochondrial/genetics*
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