Displaying publications 301 - 320 of 584 in total

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  1. Resistance gene cloning from a wild crop relative by sequence capture and association genetics
    Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, et al.
    Nat Biotechnol, 2019 02;37(2):139-143.
    PMID: 30718880 DOI: 10.1038/s41587-018-0007-9
    Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.
    Matched MeSH terms: Phenotype
  2. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.)
    Li BJ, Zhu ZX, Gu XH, Lin HR, Xia JH
    Mar Biotechnol (NY), 2019 Jun;21(3):384-395.
    PMID: 30863905 DOI: 10.1007/s10126-019-09888-9
    Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p 
    Matched MeSH terms: Phenotype
  3. Fulltext Absence of 1061C deletion in A2 blood subgroup validated through gene sequencing in the Malaysian population
    Anbukarsu, Aruna, Mohd Nazif Samat @ Darawi and Mohd Nazil Salleh
    Life Sciences, Medicine and Biomedicine, 2019;3(1):1-6.
    MyJurnal
    ABO blood grouping is an important antigenic blood typing tools in blood transfusion and organ transplants. Mismatching of blood during transfusion would lead to undesired transfusion reactions. Due to rare occurrence of rare blood group such as A2 subtype, regular blood grouping technique would have missed the identification of blood group. Objectives: In this study, the identification of A2 subgroup using routine serological technique was validated via DNA sequencing technique. Materials and Methods: A total of 656 students participated in this study consist of Malay (87.0 %), Chinese (0.4 %), Indian (11.4 %) and others ethnic group (0.9%) respectively. Monoclonal antisera A, B, AB, D, A1 lectin and H lectin were used to identify the antigen on red blood cells. DNA sequence analysis was applied to examine single nucleotide polymorphisms (SNPs) at position 467 (substitution of C>T) and 1061 (deletion of C) on coding region of ABO gene. Results: Our findings showed of 656 blood samples, 256 (39.0%) were blood group O, 190 (29.0%) were blood group B, 179 (27.3%) were blood group A and 31(4.7%) were blood group AB. The frequency of A1 subgroup is 177 (99.0%) and A2 subgroup is 2 (1.0%). From 179 A blood group, only 2 samples showed negative reaction towards anti-A1 lectin. DNA sequence analysis revealed the SNPs at nucleotide 1061 position in sample 2, however this mutation was absence in sample 1, suggesting presence of another mutation that may result in the A2 phenotype. Conclusion: The current study reported the absence of 1061C deletion in A2 blood group sample among Malaysian population.
    Matched MeSH terms: Phenotype
  4. Metabolic utilization of human osteoblast cell line hFOB 1.19 under normoxic and hypoxic conditions: A phenotypic microarray analysis
    Cui YC, Qiu YS, Wu Q, Bu G, Peli A, Teh SW, et al.
    Exp Biol Med (Maywood), 2021 May;246(10):1177-1183.
    PMID: 33535809 DOI: 10.1177/1535370220985468
    Osteoblasts play an important role in bone regeneration and repair. The hypoxia condition in bone occurs when bone undergoes fracture, and this will trigger a series of biochemical and mechanical changes to enable bone repair. Hence, it is interesting to observe the metabolites and metabolism changes when osteoblasts are exposed to hypoxic condition. This study has looked into the response of human osteoblast hFOB 1.19 under normoxic and hypoxic conditions by observing the cell growth and utilization of metabolites via Phenotype MicroArrays™ under these two different oxygen concentrations. The cell growth of hFOB 1.19 under hypoxic condition showed better growth compared to hFOB 1.19 under normal condition. In this study, osteoblast used glycolysis as the main pathway to produce energy as hFOB 1.19 in both hypoxic and normoxic conditions showed cell growth in well containing dextrin, glycogen, maltotriose, D-maltose, D-glucose-6-phospate, D-glucose, D-mannose, D-Turanose, D-fructose-6-phosphate, D-galactose, uridine, adenosine, inosine and α-keto-glutaric acid. In hypoxia, the cells have utilized additional metabolites such as α-D-glucose-1-phosphate and D-fructose, indicating possible activation of glycogen synthesis and glycogenolysis to metabolize α-D-glucose-1-phosphate. Meanwhile, during normoxia, D-L-α-glycerol phosphate was used, and this implies that the osteoblast may use glycerol-3-phosphate shuttle and oxidative phosphorylation to metabolize glycerol-3-phosphate.
    Matched MeSH terms: Phenotype
  5. Fulltext Clinical Phenotype of LRRK2 R1441C in 2 Chinese Sisters
    Lim SY, Lim JL, Ahmad-Annuar A, Lohmann K, Tan AH, Lim KB, et al.
    Neurodegener Dis, 2020;20(1):39-45.
    PMID: 32580205 DOI: 10.1159/000508131
    Pathogenic and risk variants in the LRRK2 gene are among the main genetic contributors to Parkinson's disease (PD) worldwide, and LRRK2-targeted therapies for patients with PARK-LRRK2are now entering clinical trials. However, in contrast to the LRRK2 G2019S mutation commonly found in Caucasians, North-African Arabs, and Ashkenazi Jews, relatively little is known about other causative LRRK2 mutations, and data on genotype-phenotype correlations are largely lacking. This report is from an ongoing multicentre study in which next-generation sequencing-based PD gene panel testing has so far been conducted on 499 PD patients of various ethnicities from Malaysia. We describe 2 sisters of Chinese ancestry with PD who carry the R1441C mutation in LRRK2 (which in Asians has been reported in only 2 Chinese patients previously), and highlight interesting clinical observations made over a decade of close follow-up. We further explored the feasibility of using a brief, expert-administered rating scale (the Clinical Impression of Severity Index; CISI-PD) to capture data on global disease severity in a large (n = 820) unselected cohort of PD patients, including severely disabled individuals typically excluded from research studies. All patients in this study were managed and evaluated by the same PD neurologist, and these data were used to make broad comparisons between the monogenic PD cases versus the overall "real world" PD cohort. This report contributes to the scarce literature on R1441C PARK-LRRK2, offering insights into natural history and epidemiological aspects, and provides support for the application of a simple and reliable clinical tool that can improve the inclusion of under-represented patient groups in PD research.
    Matched MeSH terms: Phenotype
  6. An overview of the phenotypic and genotypic characteristics of multidrug-resistant Mycobacterium tuberculosis isolates from four Asian countries
    Ang CF, Ong CS, Rukmana A, Pham Thi KL, Yap SF, Ngeow YF, et al.
    J Med Microbiol, 2008 Aug;57(Pt 8):1039-1040.
    PMID: 18628510 DOI: 10.1099/jmm.0.47850-0
    Matched MeSH terms: Phenotype
  7. Fulltext Hyaluronatelyase production by Streptococcus pneumoniae isolated from patients and carriers
    Yusof HA, Desa M NM, Masri SN, Malina O, Jamal F
    Trop Biomed, 2015 Sep;32(3):413-8.
    PMID: 26695201 MyJurnal
    Hyaluronatelyase produced by various microorganisms are capable of degrading hyaluronic acid in connective tissues and initiating the spread of infection by opening an access for the pathogen into host tissues. The present study attempts to determine the distribution of hyaluronatelyase-producing Streptococcus pneumoniae among invasive, non invasive and carriage isolates, and correlate it with the clinical sources, year of isolation, colonial morphology and their serotypes. A total of 100 isolates from various clinical samples were selected and screened for hyaluronatelyase production and presence of the encoding SpnHyl gene. All isolates possessed SpnHyl gene. Ninety-six isolates including 34 carriage isolates were positive for production of hyaluronatelyase. Four hyaluronatelyase-negative isolates were from blood (2 isolates) and sputum (2 isolates). No significant association was detected among hyaluronatelyase production and bacterial characteristics except for colonial morphology (p = 0.040). High percentages of hyaluronatelyase production in these isolates suggest their possible role as human pathogens.
    Matched MeSH terms: Phenotype
  8. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery
    Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, et al.
    Microbiol Res, 2021 May;246:126674.
    PMID: 33549960 DOI: 10.1016/j.micres.2020.126674
    Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
    Matched MeSH terms: Phenotype
  9. Fulltext Germline variants are associated with increased primary melanoma tumor thickness at diagnosis
    Mangantig E, MacGregor S, Iles MM, Scolyer RA, Cust AE, Hayward NK, et al.
    Hum Mol Genet, 2021 01 06;29(21):3578-3587.
    PMID: 33410475 DOI: 10.1093/hmg/ddaa222
    Germline genetic variants have been identified, which predispose individuals and families to develop melanoma. Tumor thickness is the strongest predictor of outcome for clinically localized primary melanoma patients. We sought to determine whether there is a heritable genetic contribution to variation in tumor thickness. If confirmed, this will justify the search for specific genetic variants influencing tumor thickness. To address this, we estimated the proportion of variation in tumor thickness attributable to genome-wide genetic variation (variant-based heritability) using unrelated patients with measured primary cutaneous melanoma thickness. As a secondary analysis, we conducted a genome-wide association study (GWAS) of tumor thickness. The analyses utilized 10 604 individuals with primary cutaneous melanoma drawn from nine GWAS datasets from eight cohorts recruited from the general population, primary care and melanoma treatment centers. Following quality control and filtering to unrelated individuals with study phenotypes, 8125 patients were used in the primary analysis to test whether tumor thickness is heritable. An expanded set of 8505 individuals (47.6% female) were analyzed for the secondary GWAS meta-analysis. Analyses were adjusted for participant age, sex, cohort and ancestry. We found that 26.6% (SE 11.9%, P = 0.0128) of variation in tumor thickness is attributable to genome-wide genetic variation. While requiring replication, a chromosome 11 locus was associated (P 
    Matched MeSH terms: Phenotype
  10. Fulltext Ageing Effects, Generation Means, and Path Coefficient Analyses on High Kernel Elongation in Mahsuri Mutan and Basmati 370 Rice Populations
    Ab Halim AAB, Rafii MY, Osman MB, Oladosu Y, Chukwu SC
    Biomed Res Int, 2021;2021:8350136.
    PMID: 34095311 DOI: 10.1155/2021/8350136
    High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.
    Matched MeSH terms: Phenotype
  11. Interference Potential of Tannins and Chlorophylls in Zebrafish Phenotypic-Based Assays
    Samat N, Ng MF, Ruslan NF, Okuda KS, Tan PJ, Patel V
    Assay Drug Dev Technol, 2018 10;16(7):408-419.
    PMID: 29985634 DOI: 10.1089/adt.2017.833
    Natural products are prolific producers of diverse chemical scaffolds, which have yielded several clinically useful drugs. However, the complex features of natural products present challenges for identifying bioactive molecules using high-throughput screens. For most assays, measured endpoints are either colorimetric or luminescence based. Thus, the presence of the major metabolites, tannins, and chlorophylls, in natural products could potentially interfere with these measurements to give either false-positive or false-negative hits. In this context, zebrafish phenotypic assays provide an alternative approach to bioprospect naturally occurring bioactive compounds. Whether tannins and/or chlorophylls interfere in zebrafish phenotypic assays, is unclear. In this study, we evaluated the interference potential of tannins and chlorophylls against efficacy of known small-molecule inhibitors that are known to cause phenotypic abnormalities in developing zebrafish embryos. First, we fractionated tannin-enriched fraction (TEF) and chlorophyll-enriched fraction (CEF) from Camellia sinensis and cotreated them with PD0325901 [mitogen-activated protein kinase-kinase (MEK) inhibitor] and sunitinib malate (SM; anti-[lymph]angiogenic drug). While TEF and CEF did not interfere with phenotypic or molecular endpoints of PD0325901, TEF at 100 μg/mL partially masked the antiangiogenic effect of SM. On the other hand, CEF (100 μg/mL) was toxic when treated up to 6 dpf. Furthermore, CEF at 100 μg/mL potentially enhanced the activity of γ-secretase inhibitors, resulting in toxicity of treated embryos. Our study provides evidence that the presence of tannin and/or chlorophyll in natural products do interfere with zebrafish phenotype assays used for identifying potential hits. However, this may be target/assay dependent and thus requiring additional optimization steps to assess interference potential of tannins and chlorophylls before performing any screening assay.
    Matched MeSH terms: Phenotype
  12. Fulltext Mutations in KIF27, GNAS and IFT140 genes in a patient with VACTERL association: a case report
    Siti Aishah Sulaiman, Nor Azian Abdul Murad, Chow, Yock Ping, Zam Zureena Mohd Rani, Salwati Shuib, Dayang Anita A. Aziz, et al.
    Asia-Pacific Journal of Molecular Medicine, 2018;8(2):1-10.
    MyJurnal
    VACTERL association is a rare genetic disorder involving at least three of the following congenital
    malformations: vertebral defects (V), anal atresia (A), cardiac defects (C), trachea-oesophageal fistula with
    or without oesophageal atresia (TE), renal anomalies (R) and limb abnormalities (L). Until now, the
    aetiology of VACTERL association is unknown, particularly at the molecular level. Here, we performed
    whole exome sequencing (WES) of an infant with VACTERL association. The patient was delivered
    prematurely at 30 weeks and had 4/6 of the VACTERL malformations. Trio-WES analysis was performed
    using Torrent Suite and ANNOVAR. Polymorphisms with an allele frequency of >0.01 were excluded, and
    the remaining variants were filtered based on de novo mutations, autosomal recessive, X-linked and di-genic
    inheritance traits. In this patient, no homozygous, compound heterozygous or X-linked mutations was
    associated with VACTERL. However, we identified two heterozygous mutations; KIF27
    (ENST00000297814: c.3004A> C:p.N1002H) and GNAS (ENST00000371098: c.205C>A:p.H69N) genes that
    were inherited from her father and mother respectively. A de novo, IFT140 gene mutation
    (ENST00000426508: c.683C>G:p.S228C) was also identified in this patient. The VACTERL phenotype in
    this patient may due to heterozygous mutations affecting KIF27 and GNAS genes, inherited via autosomal
    recessive trait. In addition, the IFT140 gene mutation may also be involved. These genes are known to be
    directly or non-directly involved in the sonic hedgehog signalling that is known to be implicated in
    VACTERL. This is the first report of these genetic mutations in association with VACTERL.
    Matched MeSH terms: Phenotype
  13. Rapid detection of α-thalassaemia variants using droplet digital PCR
    Lee TY, Lai MI, Ramachandran V, Tan JA, Teh LK, Othman R, et al.
    Int J Lab Hematol, 2016 Aug;38(4):435-43.
    PMID: 27349818 DOI: 10.1111/ijlh.12520
    INTRODUCTION: Alpha thalassaemia is a highly prevalent disease globally and is a well-known public health problem in Malaysia. The deletional forms of the mutation are the most common forms found in alpha thalassaemia. The three most common deletional alpha thalassaemia found in this region include --(SEA) deletion, -α(3.7) rightward and -α(4.2) leftward deletions. The prevalence rate of triplication alpha cases such as ααα(anti3.7) and ααα(anti4.2) is not known in Malaysia although it plays a role in exacerbating the clinical phenotypes in beta thalassaemia carriers. Recently, there have been more reported cases of rare alpha thalassaemia mutations due to the advancement of molecular techniques involved in thalassaemia detections. Therefore, it is essential to develop a new method which allows the detection of different alpha thalassaemia mutations including the rare ones simultaneously and accurately.

    METHODS: The purpose of this study was to design an assay for the detection of triplications, common and rare deletional alpha thalassaemia using droplet digital PCR (ddPCR).

    RESULTS: This is a quantitative detection method to measure the changes of copy number which can detect deletions, duplications and triplications of the alpha globin gene simultaneously.

    CONCLUSION: In conclusion, ddPCR is an alternative method for rapid detection of alpha thalassaemia variants in Malaysia.

    Matched MeSH terms: Phenotype
  14. Fulltext Association between polymorphisms of insulin and insulin receptor gene with childhood obesity in malay population
    Christinal Teh Pey Wen, Nurul Adibah Nizam, Abdul Rahman Jamal, Wan Zurinah Wan Ngah, Chong, Pei Nee, Poh, Bee Koon
    Jurnal Sains Kesihatan Malaysia, 2016;14(1):5-9.
    MyJurnal
    Childhood obesity is a global epidemic, which leads to the increasing number of studies on genetic locations associated with obesity-related traits. Polymorphisms of insulin (INS) gene have been shown to be associated with obesity-related phenotypes in Europeans; while insulin receptor (INSR) gene has been associated with energy regulation. Therefore, this study was conducted to investigate the association between the INS (rs689) and INSR (rs3745551) gene polymorphisms with childhood obesity risk in a Malay childhood population. Normal weight (538) and overweight or obese (557) children aged 6-12 years old were genotyped using semi-automated Sequenom iPLEX® Gold. Body mass index (BMI) was calculated from measured body weight and height. The rs689 (T/T: 0.006, A/T: 0.159 and A/A: 0.835) and rs3745551 (G/G: 0.054, A/G: 0.378 and A/A: 0.568) genotype distributions were consistent with Hardy Weinberg equilibrium. The T-minor allele frequency for rs689 was 8.6% and G-minor allele frequency for rs3745551 was 24.3%. Minor allele of INS gene polymorphisms significantly increased risk of obesity among Malay children (sex- and age-adjusted
    OR=1.580; 95%CI: 1.134-2.201). However, INSR gene polymorphisms were not significantly associated with childhood obesity. In conclusion, the polymorphisms of INS gene, rather than INSR gene, were associated with childhood obesity in the Malay population.
    Matched MeSH terms: Phenotype
  15. Fulltext Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus)
    da Silva LG, Kawanishi K, Henschel P, Kittle A, Sanei A, Reebin A, et al.
    PLoS One, 2017;12(4):e0170378.
    PMID: 28379961 DOI: 10.1371/journal.pone.0170378
    The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species' range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger's rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.
    Matched MeSH terms: Phenotype
  16. Fulltext Genome analysis of streptococcus gordonii sk12
    Khairuldin AM, Ibrahim IK, Wakiyuddin SB, Z, Wenning, AO, Lesley, SJ, Nicholas, et al.
    Ann Dent, 2014;21(2):17-26.
    MyJurnal
    The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causative agent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemia in immune-supressed patients. In this study, we analysed the genome of a representative strain, Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understanding of the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput Illumina HiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12 was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomic features. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with a genome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmed that SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, we predicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicity in infective endocarditis. We also discovered an intact prophage which might be recently integrated into the SK12 genome. Examination of genes present in genomic islands revealed that this oral strain
    might has potential to acquire new phenotypes/traits including strong defence system, bacitracin
    resistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improves our understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate how this species is able to transition between living as an oral commensal and potentially causing the lifethreatening condition infective endocarditis.
    Matched MeSH terms: Phenotype
  17. Fulltext Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice
    Cui Y, Song BK, Li LF, Li YL, Huang Z, Caicedo AL, et al.
    G3 (Bethesda), 2016 Dec 07;6(12):4105-4114.
    PMID: 27729434 DOI: 10.1534/g3.116.035881
    Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.
    Matched MeSH terms: Phenotype
  18. The skin barrier function gene SPINK5 is associated with challenge-proven IgE-mediated food allergy in infants
    Ashley SE, Tan HT, Vuillermin P, Dharmage SC, Tang MLK, Koplin J, et al.
    Allergy, 2017 Sep;72(9):1356-1364.
    PMID: 28213955 DOI: 10.1111/all.13143
    BACKGROUND: A defective skin barrier is hypothesized to be an important route of sensitization to dietary antigens and may lead to food allergy in some children. Missense mutations in the serine peptidase inhibitor Kazal type 5 (SPINK5) skin barrier gene have previously been associated with allergic conditions.

    OBJECTIVE: To determine whether genetic variants in and around SPINK5 are associated with IgE-mediated food allergy.

    METHOD: We genotyped 71 "tag" single nucleotide polymorphisms (tag-SNPs) within a region spanning ~263 kb including SPINK5 (~61 kb) in n=722 (n=367 food-allergic, n=199 food-sensitized-tolerant and n=156 non-food-allergic controls) 12-month-old infants (discovery sample) phenotyped for food allergy with the gold standard oral food challenge. Transepidermal water loss (TEWL) measures were collected at 12 months from a subset (n=150) of these individuals. SNPs were tested for association with food allergy using the Cochran-Mantel-Haenszel test adjusting for ancestry strata. Association analyses were replicated in an independent sample group derived from four paediatric cohorts, total n=533 (n=203 food-allergic, n=330 non-food-allergic), mean age 2.5 years, with food allergy defined by either clinical history of reactivity, 95% positive predictive value (PPV) or challenge, corrected for ancestry by principal components.

    RESULTS: SPINK5 variant rs9325071 (A⟶G) was associated with challenge-proven food allergy in the discovery sample (P=.001, OR=2.95, CI=1.49-5.83). This association was further supported by replication (P=.007, OR=1.58, CI=1.13-2.20) and by meta-analysis (P=.0004, OR=1.65). Variant rs9325071 is associated with decreased SPINK5 gene expression in the skin in publicly available genotype-tissue expression data, and we generated preliminary evidence for association of this SNP with elevated TEWL also.

    CONCLUSIONS: We report, for the first time, association between SPINK5 variant rs9325071 and challenge-proven IgE-mediated food allergy.

    Matched MeSH terms: Phenotype
  19. Fulltext Identification of Predictive DNA Methylation Biomarkers for Chemotherapy Response in Colorectal Cancer
    Baharudin R, Ab Mutalib NS, Othman SN, Sagap I, Rose IM, Mohd Mokhtar N, et al.
    Front Pharmacol, 2017;8:47.
    PMID: 28243201 DOI: 10.3389/fphar.2017.00047
    Resistance to 5-Fluorouracil (5-FU) is a major obstacle to the successful treatment of colorectal cancer (CRC) and posed an increased risk of recurrence. DNA methylation has been suggested as one of the underlying mechanisms for recurrent disease and its contribution to the development of drug resistance remains to be clarified. This study aimed to determine the methylation phenotype in CRC for identification of predictive markers for chemotherapy response. We performed DNA methylation profiling on 43 non-recurrent and five recurrent CRC patients using the Illumina Infinium HumanMethylation450 Beadchip assay. In addition, CRC cells with different genetic backgrounds, response to 5-FU and global methylation levels (HT29 and SW48) were treated with 5-FU and DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-azadC). The singular and combined effects of these two drug classes on cell viability and global methylation profiles were investigated. Our genome-wide methylation study on the clinical specimens showed that recurrent CRCs exhibited higher methylation levels compared to non-recurrent CRCs. We identified 4787 significantly differentially methylated genes (P < 0.05); 3112 genes were hyper- while 1675 genes were hypomethylated in the recurrent group compared to the non-recurrent. Fifty eight and 47 of the significantly hypermethylated and hypomethylated genes have an absolute recurrent/non-recurrent methylation difference of ≥20%. Most of the hypermethylated genes were involved in the MAPK signaling pathway which is a key regulator for apoptosis while the hypomethylated genes were involved in the PI3K-AKT signaling pathway and proliferation process. We also demonstrate that 5-azadC treatment enhanced response to 5-FU which resulted in significant growth inhibition compared to 5-FU alone in hypermethylated cell lines SW48. In conclusion, we found the evidence of five potentially biologically important genes in recurrent CRCs that could possibly serve as a new potential therapeutic targets for patients with chemoresistance. We postulate that aberrant methylation of CCNEI, CCNDBP1, PON3, DDX43, and CHL1 in CRC might be associated with the recurrence of CRC and 5-azadC-mediated restoration of 5-FU sensitivity is mediated at least in part by MAPK signaling pathway.
    Matched MeSH terms: Phenotype
  20. Haptoglobin, transferrin and serum albumin variants in the Dayaks of Sarawak
    Ganesan J, Eng LI, Poon OB
    Humangenetik, 1975 Oct 07;29(4):281-3.
    PMID: 1176143
    The Land Dayaks and the Sea Kayaks of Sarawak were surveyed for haptoglobin, transferrin and serum albumin variants. The Hp1 gene frequency was 0.385 in 283 Land Dayaks as well as in 205 Sea Kayaks. The TfDChi gene frequency in 283 Land Dayaks was 0.030 and in 188 Sea Kayaks it was 0.040. Serum albumin Medan was found in one of the 188 Sea Kayaks.
    Matched MeSH terms: Phenotype
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