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  1. First molecular genotyping of voltage gated sodium channel alleles in Culex quinquefasciatus populations in Malaysia
    Low VL, Chen CD, Lim PE, Lee HL, Tan TK, Lim YA, et al.
    Pestic Biochem Physiol, 2013 Sep;107(1):127-31.
    PMID: 25149246 DOI: 10.1016/j.pestbp.2013.06.004
    A nationwide investigation was performed to detect the presence of 1014 mutation(s) in voltage gated sodium channel (kdr) gene of Culex quinquefasciatus from 14 residential areas across 13 states and a federal territory in Malaysia. Molecular genotyping of kdr mutation was performed via a modified three tubes allele-specific-polymerase chain reaction (AS-PCR) and direct sequencing of kdr gene. Based on the results of AS-PCR, homozygous susceptible (SS) genotype was found in nine out of 14 populations with 38 individuals from a total sample size of 140. Heterozygous (RS) genotype was most predominant (99 individuals) and distributed across all study sites. Homozygous resistance (RR) genotype was detected in Perak (one individual) and Selangor (two individuals). The resistance kdr allele frequencies ranged from 0.1 to 0.55, with the highest being detected in Cx. quinquefasciatus population from Selangor. This study has documented the first field-evolved instance of 1014F mutation in Malaysian mosquitoes and the findings of this study could be utilized in the implementation of strategic measures in vector control programs in Malaysia.
    Matched MeSH terms: Culex/genetics*; Insect Proteins/genetics*; Voltage-Gated Sodium Channels/genetics*
  2. Fulltext Agrobacterium-mediated transformation of the recalcitrant Vanda Kasem's Delight orchid with higher efficiency
    Gnasekaran P, Antony JJ, Uddain J, Subramaniam S
    ScientificWorldJournal, 2014;2014:583934.
    PMID: 24977213 DOI: 10.1155/2014/583934
    The presented study established Agrobacterium-mediated genetic transformation using protocorm-like bodies (PLBs) for the production of transgenic Vanda Kasem's Delight Tom Boykin (VKD) orchid. Several parameters such as PLB size, immersion period, level of wounding, Agrobacterium density, cocultivation period, and concentration of acetosyringone were tested and quantified using gusA gene expression to optimize the efficiency of Agrobacterium-mediated genetic transformation of VKD's PLBs. Based on the results, 3-4 mm PLBs wounded by scalpel and immersed for 30 minutes in Agrobacterium suspension of 0.8 unit at A 600 nm produced the highest GUS expression. Furthermore, cocultivating infected PLBs for 4 days in the dark on Vacin and Went cocultivation medium containing 200 μM acetosyringone enhanced the GUS expression. PCR analysis of the putative transformants selected in the presence of 250 mg/L cefotaxime and 30 mg/L geneticin proved the presence of wheatwin1, wheatwin2, and nptII genes.
    Matched MeSH terms: DNA, Bacterial/genetics*; Orchidaceae/genetics*; Agrobacterium/genetics*
  3. Fulltext PIK3CA gene amplification and PI3K p110α protein expression in breast carcinoma
    Firoozinia M, Zareian Jahromi M, Moghadamtousi SZ, Nikzad S, Abdul Kadir H
    Int J Med Sci, 2014;11(6):620-5.
    PMID: 24782652 DOI: 10.7150/ijms.8251
    A family of PI3Ks is the lipid kinases, which enhance intracellular pools of phosphatidyl inositol 3,4,5-tri-phosphate (PIP3) through phosphorylating its precursor. Amplifications and deletions of genes, as well as somatic missense of the PIK3CA gene have been described in many human cancer varieties, including of the brain, colon, liver, lung and stomach. Immunohistochemistry and Real-time quantitative PCR tests were used to determine the PIK3CA gene amplification (gene copy number) and to detect protein expression, respectively. The results obtained were analysed and the ratio of PIK3CA to β-actin gene copy number was calculated. Positive gene amplification of PIK3CA was appointed as a copy number of ≥4. Also, PI3K p110α protein expression was scored from 0 to 3+ and the scores of 2+ and 3+ were considered as positive for PI3K p110α protein expression. We studied 50 breast carcinoma samples for PI3K p110α protein expression and PIK3CA gene copy numbers. In general, 36 out of 50 (72%) breast carcinoma samples showed a significant increase in PIK3CA gene amplification. 12 out of 50 (24%) showed positive staining, and 38 out of 50 (76%) showed negative staining for PI3K p110α expression. We have identified no significant relationship between PIK3CA amplification, race (p= 0.630) and histological type (p=0. 731) in breast carcinoma, but correlation of PIK3CA amplification and age showed a significant relationship (p=0. 003) between them. No significant relationship has been identified in correlation of PI3K p110α protein expression compared to age (p=0. 284), race (p=0. 546) and histological type (p=0. 285). Amplification of PIK3CA was frequent in breast carcinoma and occurs in stages of breast carcinoma. Our result shows that there is a relationship between gene amplification and age in breast carcinoma. We suggest that PIK3CA is significant in breast tumorigenesis serve as a prevalent mechanism contributes to the oncogenic activation pathway of PIK3CA in breast cancer.
    Matched MeSH terms: Breast Neoplasms/genetics*; Phosphatidylinositol 3-Kinases/genetics; Continental Population Groups/genetics
  4. Fulltext Senescence affects endothelial cells susceptibility to dengue virus infection
    AbuBakar S, Shu MH, Johari J, Wong PF
    Int J Med Sci, 2014;11(6):538-44.
    PMID: 24782642 DOI: 10.7150/ijms.7896
    Alteration in the endothelium leading to increased vascular permeability contributes to plasma leakage seen in dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). An earlier study showed that senescent endothelial cells (ECs) altered the ECs permeability. Here we investigated the susceptibility of senescing human umbilical vein endothelial cells (HUVECs) to dengue virus infection and determined if dengue virus infection induces HUVECs senescence. Our results suggest that DENV type-2 (DENV-2) foci forming unit (FFU) and extracellular virus RNA copy number were reduced by at least 35% and 85% in infection of the intermediate young and early senescent HUVECs, respectively, in comparison to infection of young HUVECs. No to low infectivity was recovered from infection of late senescent HUVECs. DENV infection also increases the percentage of HUVECs expressing senescence-associated (SA)-β-gal, cells arrested at the G2/M phase or 4N DNA content stage and cells with enlarged morphology, indicative of senescing cells. Alteration of HUVECs morphology was recorded using impedance-based real-time cell analysis system following DENV-2 infection. These results suggest that senescing HUVECs do not support DENV infection and DENV infection induces HUVECs senescence. The finding highlights the possible role of induction of senescence in DENV infection of the endothelial cells.
    Matched MeSH terms: Cell Membrane Permeability/genetics; Dengue Virus/genetics; Cell Aging/genetics*
  5. Genomic DNA copy number alterations from precursor oral lesions to oral squamous cell carcinoma
    Salahshourifar I, Vincent-Chong VK, Kallarakkal TG, Zain RB
    Oral Oncol, 2014 May;50(5):404-12.
    PMID: 24613650 DOI: 10.1016/j.oraloncology.2014.02.005
    Oral cancer is a multifactorial disease in which both environmental and genetic factors contribute to the aetiopathogenesis. Oral cancer is the sixth most common cancer worldwide with a higher incidence among Melanesian and South Asian countries. More than 90% of oral cancers are oral squamous cell carcinoma (OSCC). The present study aimed to determine common genomic copy number alterations (CNAs) and their frequency by including 12 studies that have been conducted on OSCCs using array comparative genomic hybridization (aCGH). In addition, we reviewed the literature dealing with CNAs that drive oral precursor lesions to the invasive tumors. Results showed a sequential accumulation of genetic changes from oral precursor lesions to invasive tumors. With the disease progression, accumulation of genetic changes increases in terms of frequency, type and size of the abnormalities, even on different regions of the same chromosome. Gains in 3q (36.5%), 5p (23%), 7p (21%), 8q (47%), 11q (45%), 20q (31%) and losses in 3p (37%), 8p (18%), 9p (10%) and 18q (11%) were the most common observations among those studies. However, losses are less frequent than gains but it appears that they might be the primary clonal events in causing oral cancer.
    Matched MeSH terms: Carcinoma, Squamous Cell/genetics*; Mouth Neoplasms/genetics*; Precancerous Conditions/genetics*
  6. Fulltext High density SNP and SSR-based genetic maps of two independent oil palm hybrids
    Ting NC, Jansen J, Mayes S, Massawe F, Sambanthamurthi R, Ooi LC, et al.
    BMC Genomics, 2014;15:309.
    PMID: 24767304 DOI: 10.1186/1471-2164-15-309
    Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.
    Matched MeSH terms: Microsatellite Repeats/genetics*; Polymorphism, Single Nucleotide/genetics*; Arecaceae/genetics*
  7. Fulltext Analysis of TP53 gene expression and p53 level of human hypopharyngeal FaDu (HTB-43) head and neck cancer cell line after microRNA-181a inhibition
    Cheah YK, Cheng RW, Yeap SK, Khoo CH, See HS
    Genet. Mol. Res., 2014;13(1):1679-83.
    PMID: 24535903 DOI: 10.4238/2014.January.22.4
    The identification of new biomarkers for early detection of highly recurrent head and neck cancer is urgently needed. MicroRNAs (miRNAs) are small and non-coding RNAs that regulate cancer-related gene expression, such as tumor protein 53 (TP53) gene expression. This study was carried out to analyze TP53 gene expression using real-time PCR and to determine changes in intracellular p53 level by flow cytometry after downregulation of miRNA-181a miRNA inhibitor in the FaDu cell line. TP53 gene expression showed a 3-fold increment and the p53 protein level was also increased in the miRNA-181a-treated cells. In conclusion, miRNA-181a binds to the TP53 gene and inhibits its expression, decreasing the synthesis of p53.
    Matched MeSH terms: Head and Neck Neoplasms/genetics*; Tumor Suppressor Protein p53/genetics; MicroRNAs/genetics*
  8. Fulltext Molecular cloning and characterization of novel phytocystatin gene from turmeric, Curcuma longa
    Chan SN, Abu Bakar N, Mahmood M, Ho CL, Shaharuddin NA
    Biomed Res Int, 2014;2014:973790.
    PMID: 25853138 DOI: 10.1155/2014/973790
    Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5'/3' rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis.
    Matched MeSH terms: Plant Proteins/genetics*; Cystatins/genetics*; Curcuma/genetics*
  9. Fulltext Phylodynamic profile of HIV-1 subtype B, CRF01_AE and the recently emerging CRF51_01B among men who have sex with men (MSM) in Singapore
    Ng KT, Ng KY, Khong WX, Chew KK, Singh PK, Yap JK, et al.
    PLoS One, 2013;8(12):e80884.
    PMID: 24312505 DOI: 10.1371/journal.pone.0080884
    HIV-1 subtype B and CRF01_AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatment-naïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01_AE and one within CRF51_01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01_AE. Exponential increase in effective population size for both subtype B and CRF01_AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51_01B lineages were probably generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and CRF51_01B viral strains circulating among MSM in Singapore.
    Matched MeSH terms: HIV-1/genetics*; HIV Infections/genetics*; env Gene Products, Human Immunodeficiency Virus/genetics*
  10. Fulltext A novel Bruton's tyrosine kinase gene (BTK) invariant splice site mutation in a Malaysian family with X-linked agammaglobulinemia
    Chear CT, Gill HK, Ramly NH, Dhaliwal JS, Bujang N, Ripen AM, et al.
    Asian Pac J Allergy Immunol, 2013 Dec;31(4):320-4.
    PMID: 24383975 DOI: 10.12932/AP0304.31.4.2013
    X-linked agammaglobulinemia (XLA) is a rare genetic disorder caused by mutations in the Bruton's tyrosine kinase (BTK) gene. These mutations cause defects in early B cell development. A patient with no circulating B cells and low serum immunoglobulin isotypes was studied as were his mother and sister. Monocyte BTK protein expression was evaluated by flow cytometry. The mutation was determined using PCR and followed by sequencing. Flow cytometry showed the patient lacked BTK protein expression in his monocytes while the mother and sister had 62% and 40% of the monocytes showing BTK protein expressions respectively. The patient had a novel base substitution in the first nucleotide of intron 9 in the BTK gene, and the mutation was IVS9+1G
    Matched MeSH terms: Agammaglobulinemia/genetics*; Protein-Tyrosine Kinases/genetics*; Genetic Diseases, X-Linked/genetics*
  11. Identification of immunogenic proteins of Candida parapsilosis by serological proteome analysis
    Lee PY, Gam LH, Yong VC, Rosli R, Ng KP, Chong PP
    J Appl Microbiol, 2014 Apr;116(4):999-1009.
    PMID: 24299471 DOI: 10.1111/jam.12408
    Systemic candidiasis is the leading fungal bloodstream infection, and its incidence has been on the rise. Recently, Candida parapsilosis has emerged as an increasingly prevalent fungal pathogen, but little is known about its antigenic profile. Hence, the current work was performed to discover immunogenic proteins of C. parapsilosis using serological proteome analysis.
    Matched MeSH terms: Antigens, Fungal/genetics; Candida/genetics; Proteome/genetics
  12. The influence of antibiotic resistance gene carriage on biofilm formation by two Escherichia coli strains associated with urinary tract infections
    Teh AH, Wang Y, Dykes GA
    Can J Microbiol, 2014 Feb;60(2):105-11.
    PMID: 24498987 DOI: 10.1139/cjm-2013-0633
    Urinary tract infections (UTI) caused by uropathogenic Escherichia coli are one of the most common forms of human disease. In this study, the effect of the presence of newly acquired antibiotic resistance genes on biofilm formation of UTI-associated E. coli strains was examined. Two clinical UTI-associated E. coli strains (SMC18 and SMC20) carrying different combinations of virulence genes were transformed with pGEM-T, pGEM-T::KmΔAmp, or pGEM-T::Km to construct ampicillin-resistant (Km(S)Amp(R)), kanamycin-resistant (Km(R)Amp(S)), or ampicillin- and kanamycin-resistant (Km(R)Amp(R)) strains. Transformed and wild-type strains were characterized for biofilm formation, bacterial surface hydrophobicity, auto-aggregation, morphology, and attachment to abiotic surfaces. Transformation with a plasmid carrying an ampicillin resistance gene alone decreased (p < 0.05) biofilm formation by SMC18 (8 virulence marker genes) but increased (p < 0.05) biofilm formation by SMC20 (5 virulence marker genes). On the other hand, transformation with a plasmid carrying a kanamycin resistance gene alone or both ampicillin and kanamycin resistance genes resulted in a decrease (p < 0.05) in biofilm formation by SMC18 but did not affect (p > 0.05) the biofilm formation by SMC20. Our results suggest that transformation of UTI-associated E. coli with plasmids carrying different antibiotic resistance gene(s) had a significant impact on biofilm formation and that these effects were both strain dependent and varied between different antibiotics.
    Matched MeSH terms: Drug Resistance, Microbial/genetics*; Escherichia coli/genetics; Plasmids/genetics
  13. Analysis of differentially expressed proteins in late-stationary growth phase of Mycobacterium tuberculosis H37Rv
    Ang KC, Ibrahim P, Gam LH
    Biotechnol Appl Biochem, 2014 Mar-Apr;61(2):153-64.
    PMID: 23826872 DOI: 10.1002/bab.1137
    Mycobacterium tuberculosis is a causative agent of tuberculosis (TB). The ability of M. tuberculosis to be quiescent in the cell has caused the emergence of latent infection. A comprehensive proteomic analysis of M. tuberculosis H37Rv over three growth phases, namely mid-log (14-day culture), early stationary (28-day culture), and late stationary (50-day culture), was performed in order to study the change in proteome from the mid-log phase to late-stationary phase. Combination methods of two-dimensional electrophoresis (2-DE) and tandem mass spectrometry were used to generate proteome maps of M. tuberculosis at different growth phases. Ten proteins were detected differentially expressed in the late-stationary phase compared with the other two phases. These proteins were SucD, TrpD, and Rv2161c, which belong to metabolic pathway proteins; FadE5, AccD5, DesA1, and Rv1139c are proteins involved in cell wall or lipid biosynthesis, whereas TB21.7 and Rv3224 are conserved hypothetical proteins with unknown function. A surface antigen protein, DesA1, was not detectable in the late-stationary phase, although present in both log and early-stationary phases. The changes in the expression levels of these proteins were in line with the growth environment changes of the bacteria from mid-log phase to late-stationary phase. The information gathered may be valuable in the intervention against latent TB infection.
    Matched MeSH terms: Bacterial Proteins/genetics; Mycobacterium tuberculosis/genetics*; Proteome/genetics
  14. Fulltext Specialized Hydrocarbonoclastic Bacteria Prevailing in Seawater around a Port in the Strait of Malacca
    Teramoto M, Queck SY, Ohnishi K
    PLoS One, 2013;8(6):e66594.
    PMID: 23824553 DOI: 10.1371/journal.pone.0066594
    Major degraders of petroleum hydrocarbons in tropical seas have been indicated only by laboratory culturing and never through observing the bacterial community structure in actual environments. To demonstrate the major degraders of petroleum hydrocarbons spilt in actual tropical seas, indigenous bacterial community in seawater at Sentosa (close to a port) and East Coast Park (far from a port) in Singapore was analyzed. Bacterial species was more diverse at Sentosa than at the Park, and the composition was different: γ-Proteobacteria (57.3%) dominated at Sentosa, while they did not at the Park. Specialized hydrocarbonoclastic bacteria (SHCB), which use limited carbon sources with a preference for petroleum hydrocarbons, were found as abundant species at Sentosa, indicating petroleum contamination. On the other hand, SHCB were not the abundant species at the Park. The abundant species of SHCB at Sentosa were Oleibacter marinus and Alcanivorax species (strain 2A75 type), which have previously been indicated by laboratory culturing as important petroleum-aliphatic-hydrocarbon degraders in tropical seas. Together with the fact that SHCB have been identified as major degraders of petroleum hydrocarbons in marine environments, these results demonstrate that the O. marinus and Alcanivorax species (strain 2A75 type) would be major degraders of petroleum aliphatic hydrocarbons spilt in actual tropical seas.
    Matched MeSH terms: Bacteria/genetics; RNA, Bacterial/genetics; RNA, Ribosomal, 16S/genetics
  15. Intracellular production of IFN-alpha 2b in Lactococcus lactis
    Bayat O, Baradaran A, Ariff A, Mohamad R, Rahim RA
    Biotechnol Lett, 2014 Mar;36(3):581-5.
    PMID: 24185903 DOI: 10.1007/s10529-013-1390-4
    Human interferon alpha (IFN-α) was expressed in two strains of Lactococcus lactis by aid of two promoters (P32 and Pnis) giving rise to two recombinant strains: MG:IFN and NZ:IFN, respectively. The expression of IFN was confirmed by ELISA and western blotting. Highest production was achieved using glucose for growth of both recombinant strains with nisin, used for induction of the recombinant strain with Pnis promoter, at 30 ng/ml. The optimum time for MG:IFN was 9 h and for NZ:IFN was 4.5 h. The highest productions by MG:IFN and NZ:IFN were 1.9 and 2.4 μg IFN/l, respectively. Both of the expressed IFNs showed bioactivities of 1.9 × 10(6) IU/mg that were acceptable for further clinical studies.
    Matched MeSH terms: Recombinant Proteins/genetics; Lactococcus lactis/genetics; Interferon-alpha/genetics
  16. Fulltext Genetic assemblage of Sarcocystis spp. in Malaysian snakes
    Lau YL, Chang PY, Subramaniam V, Ng YH, Mahmud R, Ahmad AF, et al.
    Parasit Vectors, 2013 Sep 09;6(1):257.
    PMID: 24010903 DOI: 10.1186/1756-3305-6-257
    BACKGROUND: Sarcocystis species are protozoan parasites with a wide host range including snakes. Although there were several reports of Sarcocytis species in snakes, their distribution and prevalence are still not fully explored.

    METHODS: In this study, fecal specimens of several snake species in Malaysia were examined for the presence of Sarcocystis by PCR of 18S rDNA sequence. Microscopy examination of the fecal specimens for sporocysts was not carried as it was difficult to determine the species of the infecting Sarcocystis.

    RESULTS: Of the 28 snake fecal specimens, 7 were positive by PCR. BLASTn and phylogenetic analyses of the amplified 18S rDNA sequences revealed the snakes were infected with either S. nesbitti, S. singaporensis, S. zuoi or undefined Sarcocystis species.

    CONCLUSION: This study is the first to report Sarcocystis infection in a cobra, and S. nesbitti in a reticulated python.

    Matched MeSH terms: RNA, Ribosomal, 18S/genetics; Sarcocystis/genetics*; DNA, Protozoan/genetics
  17. Deep parallel sequencing reveals conserved and novel miRNAs in gill and hepatopancreas of giant freshwater prawn
    Tan TT, Chen M, Harikrishna JA, Khairuddin N, Mohd Shamsudin MI, Zhang G, et al.
    Fish Shellfish Immunol, 2013 Oct;35(4):1061-9.
    PMID: 23816854 DOI: 10.1016/j.fsi.2013.06.017
    MicroRNAs (miRNAs) are ~20-22 nucleotides, non protein-coding RNA regulatory genes that post-transcriptionally regulate many protein-coding genes, influencing critical biological and metabolic processes. While the number of known microRNA is increasing, there is currently no published data for miRNA from giant freshwater prawns, Macrobrachium rosenbergii (M. rosenbergii), a commercially cultured and economically important food species. In this study, we identified novel miRNAs in the gill and hepatopancreas of M. rosenbergii. Through a deep parallel sequencing analysis and an in silico data analysis approach, 327 miRNA families were identified from small RNA libraries with reference to both the de novo transcriptome of M. rosenbergii obtained from RNA-Seq and to miRBase (Release 18.0, November 2012). Based on the identified mature miRNA and recovered precursor sequences that form appropriate hairpin structures, three conserved miRNA (miR125, miR750, miR993) and 27 novel miRNA candidates encoding messenger-like non-coding RNA were identified. miR-125, miR-750, G-m0002/H-m0009, G-m0005, G-m0008/H-m0016, G-m0011/H-m0027 and G-m0015 were selected for experimental validation with stem-loop quantitative RT-PCR and were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.835178 for miRNA in gill, r = 0.724131 for miRNA in hepatopancreas). Using a combinatorial approach of pathway enrichment analysis and inverse expression relationship of miRNA and mRNA, four co-expressed novel miRNA candidates (G-m0005, G-m0008/H-m0016, G-m0011/H-m0027, and G-m0015) were found to be associated with energy metabolism. In addition, the expression of the three novel miRNA candidates (G-m0005, G-m0008/H-m0016, and G-m0011/H-m0027) were also found to be significantly reduced at 9 and 24 h post infection in M. rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus, suggesting a functional role of these miRNAs in crustacean immune defense.
    Matched MeSH terms: RNA, Messenger/genetics; Palaemonidae/genetics*; MicroRNAs/genetics*
  18. Fulltext HLA DR/DQ type in a Malay population in Kelantan, Malaysia
    Azira NM, Zeehaida M, Nurul Khaiza Y
    Malays J Pathol, 2013 Jun;35(1):65-9.
    PMID: 23817396 MyJurnal
    The human leucocyte antigen (HLA) has been documented to be involved in various disease susceptibilities or in resistance against certain diseases. An important element in susceptibility and resistance to disease is ethnic genetic constitution. Cognizant of this, the present study aimed at studying the prevalence of particular HLA class II in a normal healthy Malay population which may serve as a guide for further genetic and immunological studies related to the Malay Malaysian population. The study involved 40 normal healthy Malay persons in Kelantan. HLA typing was conducted on venous blood samples through a polymerase chain reaction-sequence specific primer method (low resolution Olerup SSP© HLA Typing Kits). The study found HLA DR12 and HLA DQ8 to be the most frequent HLA class II type. HLA DQ5 was significantly associated with female subjects.
    Matched MeSH terms: HLA-DQ Antigens/genetics*; HLA-DR Antigens/genetics*; Asian Continental Ancestry Group/genetics
  19. Fulltext SNP array technology: an array of hope in breast cancer research
    Ho CC, Mun KS, Naidu R
    Malays J Pathol, 2013 Jun;35(1):33-43.
    PMID: 23817393 MyJurnal
    Breast cancer is the most common malignancy in women worldwide. The incidence of breast cancer in Malaysia is lower compared to international statistics, with peak occurrence in the age group between 50 to 59 years of age and mortality rates of 18.6%. Despite current diagnostic and prognostic methods, the outcome for individual subjects remain poor. This is in part due to breast cancers' wide genetic heterogeneity. Various platforms for genetics studies are now employed to determine the identity of these genetic abnormalities, including microarray methods like high density single-nucleotide-polymorphism (SNP) oligonucleotide arrays which combine the power of chromosomal comparative genomic hybridization (cCGH) and loss of heterozygosity (LOH) in the offering of higher-resolution mappings. These platforms and their applications in highlighting the genomic alteration frameworks manifested in breast carcinoma will be discussed.
    Matched MeSH terms: Breast Neoplasms/genetics*; Loss of Heterozygosity/genetics; Polymorphism, Single Nucleotide/genetics*
  20. Do folate, vitamins B₆ and B₁₂ play a role in the pathogenesis of migraine? The role of pharmacoepigenomics
    Shaik MM, Tan HL, Kamal MA, Gan SH
    CNS Neurol Disord Drug Targets, 2014;13(5):828-35.
    PMID: 24040787
    Migraine is a neurovascular disease that has classically been attributed to multifactorial aetiologies, with genetic components and environmental interactions considered the main influence. Genes such as flavoenzyme 5, 10- methylenetetrahydrofolate reductase (MTHFR), especially the C677T variant, have been associated with elevated plasma homocysteine levels. This elevation in homocysteine results in an array of metabolic disorders and increased risk of complex diseases, including migraine. Catalysation of homocysteine requires the presence of vitamins B6, B12 and folate. Deficiencies in these cofactor vitamins result in hypomethylation, which triggers migraine. Because migraine predominantly affects females, it is hypothesised that fluctuating oestrogen levels, which are governed by oestrogen receptor 1 polymorphisms, are important. Another important factor is homocysteine, the production of which is dependent upon MTHFR and B vitamins. Gene expression is modulated through epigenetic mechanisms, which involve methionine. Additionally, folate plays a major role in DNA synthesis. We propose that vitamin B intake, coupled with MTHFR and oestrogen receptor 1 polymorphisms, causes differential DNA methylation and gene expression that may contribute to the occurrence of migraine.
    Matched MeSH terms: Migraine Disorders/genetics*; Mutation/genetics; Pharmacogenetics*; Methylenetetrahydrofolate Reductase (NADPH2)/genetics
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