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  1. Fulltext Genetic clustering and polymorphism of the merozoite surface protein-3 of Plasmodium knowlesi clinical isolates from Peninsular Malaysia
    De Silva JR, Lau YL, Fong MY
    Parasit Vectors, 2017 01 03;10(1):2.
    PMID: 28049516 DOI: 10.1186/s13071-016-1935-1
    BACKGROUND: The simian malaria parasite Plasmodium knowlesi has been reported to cause significant numbers of human infection in South East Asia. Its merozoite surface protein-3 (MSP3) is a protein that belongs to a multi-gene family of proteins first found in Plasmodium falciparum. Several studies have evaluated the potential of P. falciparum MSP3 as a potential vaccine candidate. However, to date no detailed studies have been carried out on P. knowlesi MSP3 gene (pkmsp3). The present study investigates the genetic diversity, and haplotypes groups of pkmsp3 in P. knowlesi clinical samples from Peninsular Malaysia.

    METHODS: Blood samples were collected from P. knowlesi malaria patients within a period of 4 years (2008-2012). The pkmsp3 gene of the isolates was amplified via PCR, and subsequently cloned and sequenced. The full length pkmsp3 sequence was divided into Domain A and Domain B. Natural selection, genetic diversity, and haplotypes of pkmsp3 were analysed using MEGA6 and DnaSP ver. 5.10.00 programmes.

    RESULTS: From 23 samples, 48 pkmsp3 sequences were successfully obtained. At the nucleotide level, 101 synonymous and 238 non-synonymous mutations were observed. Tests of neutrality were not significant for the full length, Domain A or Domain B sequences. However, the dN/dS ratio of Domain B indicates purifying selection for this domain. Analysis of the deduced amino acid sequences revealed 42 different haplotypes. Neighbour Joining phylogenetic tree and haplotype network analyses revealed that the haplotypes clustered into two distinct groups.

    CONCLUSIONS: A moderate level of genetic diversity was observed in the pkmsp3 and only the C-terminal region (Domain B) appeared to be under purifying selection. The separation of the pkmsp3 into two haplotype groups provides further evidence of the existence of two distinct P. knowlesi types or lineages. Future studies should investigate the diversity of pkmsp3 among P. knowlesi isolates in North Borneo, where large numbers of human knowlesi malaria infection still occur.

    Matched MeSH terms: Sequence Analysis, DNA
  2. Fulltext High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia
    Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, et al.
    NPJ Biofilms Microbiomes, 2017;3:34.
    PMID: 29214046 DOI: 10.1038/s41522-017-0040-3
    Colorectal cancer (CRC) remains the third most common cancer worldwide, with a growing incidence among young adults. Multiple studies have presented associations between the gut microbiome and CRC, suggesting a link with cancer risk. Although CRC microbiome studies continue to profile larger patient cohorts with increasingly economical and rapid DNA sequencing platforms, few common associations with CRC have been identified, in part due to limitations in taxonomic resolution and differences in analysis methodologies. Complementing these taxonomic studies is the newly recognized phenomenon that bacterial organization into biofilm structures in the mucus layer of the gut is a consistent feature of right-sided (proximal), but not left-sided (distal) colorectal cancer. In the present study, we performed 16S rRNA gene amplicon sequencing and biofilm quantification in a new cohort of patients from Malaysia, followed by a meta-analysis of eleven additional publicly available data sets on stool and tissue-based CRC microbiota using Resphera Insight, a high-resolution analytical tool for species-level characterization. Results from the Malaysian cohort and the expanded meta-analysis confirm that CRC tissues are enriched for invasive biofilms (particularly on right-sided tumors), a symbiont with capacity for tumorigenesis (Bacteroides fragilis), and oral pathogens including Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus stomatis. Considered in aggregate, species from the Human Oral Microbiome Database are highly enriched in CRC. Although no detected microbial feature was universally present, their substantial overlap and combined prevalence supports a role for the gut microbiota in a significant percentage (>80%) of CRC cases.
    Matched MeSH terms: Sequence Analysis, DNA
  3. Fulltext Hepatitis B Core Antigen in Hepatocytes of Chronic Hepatitis B: Comparison between Indirect Immunofluorescence and Immunoperoxidase Method
    Raihan R, Tabassum S, Al-Mahtab M, Nessa A, Jahan M, Shamim Kabir CM, et al.
    Euroasian J Hepatogastroenterol, 2015 Jan-Jun;5(1):7-10.
    PMID: 29201677 DOI: 10.5005/jp-journals-10018-1120
    Background: Hepatitis B virus (HBV) infection has many faces. Precore and core promoter mutants resemble inactive carrier status. The identification of hepatitis B core antigen (HBcAg) in hepatocytes may have variable clinical significance. The present study was undertaken to detect HBcAg in chronic hepatitis B (CHB) patients and to assess the efficacy of detection system by indirect immunofluorescence (IIF) and indirect immunoperoxidase (IIP).

    Materials and methods: The study was done in 70 chronic HBV-infected patients. Out of 70 patients, eight (11.4%) were hepatitis B e antigen (HBeAg) positive and 62 (88.57%) were HBeAg negative. Hepatitis B core antigen was detected by indirect immunofluorescence (IIF) and indirect immunoperoxidase (IIP) methods in liver tissue.

    Results: All HBeAg positive patients expressed HBcAg by both IIF and IIP methods. Out of 62 patients with HBeAg-negative CHB, HBcAg was detected by IIF in 55 (88.7%) patients and by IIP in 51 (82.26%) patients. A positive relation among viral load and HBcAg detection was also found. This was more evident in the case of HBeAg negative patients and showed a positive relation with HBV DNA levels.

    Conclusion: Hepatitis B core antigen can be detected using the IIF from formalin fixed paraffin block preparation and also by IIP method. This seems to reflect the magnitudes of HBV replication in CHB.

    How to cite this article: Raihan R, Tabassum S, Al-Mahtab M, Nessa A, Jahan M, Kabir CMS, Kamal M, Aguilar JC. Hepatitis B Core Antigen in Hepatocytes of Chronic Hepatitis B: Comparison between Indirect Immunofluorescence and Immunoperoxidase Method. Euroasian J Hepato-Gastroenterol 2015;5(1):7-10.
    Matched MeSH terms: DNA, Viral
  4. Fulltext Genome sequence of Streptomyces gilvigriseus MUSC 26T isolated from mangrove forest
    Ser HL, Tan WS, Mutalib NA, Yin WF, Chan KG, Goh BH, et al.
    Braz J Microbiol, 2018 02 02;49(2):207-209.
    PMID: 29428207 DOI: 10.1016/j.bjm.2017.04.012
    Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277bp with G+C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.
    Matched MeSH terms: Sequence Analysis, DNA
  5. Fulltext The distribution and characteristics of bacteria in recreational river water of a community resort in Baram, Sarawak, Malaysian Borneo
    Lihan, S., Tian, P.K,, Chiew, T.S., Ching, C.L., Shahbudin, A., Hussain, H., et al.
    International Food Research Journal, 2017;24(5):2238-2245.
    MyJurnal
    Enterobacteriaceae is a large family within the Gram-negative bacteria that primarily inhabits in the gastrointestinal tract of human and animals. The bacteria within this group are readily survived in the environment with some species found living free in the water where energy sources are scarce, making them ideal indicators for faecal contamination of the river water. Some species within the family have been used as indicator for the presence of pathogenic bacteria whilst on the other hand some species have been directly associated with various diseases in human and animals. The main aim of this research study was to determine the distribution and characteristics of the Enterobacteriaceae in water samples collected from river and waterfalls within a community resort. The health risk associated with the bacteria was analysed with regard to their susceptibility to antibiotics. Samples were collected from surface water and water falling down directly from waterfalls of river within the community resort. The samples collected were plated onto Eosine Methylene Blue agar (EMBA) for the isolation of the Enterobacteriaceae. Bacterial colonies growing on the agar were randomly picked, purified, stocked and then identified using API 20E identification kit. DNA fingerprinting using (GTG)5-PCR was utilised to determine their genetic profiles before the isolates were grouped into a dendrogram using RAPDistance software package. The level of antibiotic susceptibility of the bacteria isolates was analysed using disc diffusion technique. This study confirmed the presence of Enterobacter, Klebsiella, Citrobacter, Pantoea and Serratia in the water samples with their single and multiple antibiotic resistance and susceptible characteristics. The dendrogram presented in this study shows genetic similarities and differences among the strains, suggesting while there is a potential for single distribution of a clone, there is also possibility of the distribution of different strains within species in the water environment. Therefore, awareness on the potential risk associated with genetically diverse intermediate and resistant enteric bacteria in the recreational water should be communicated to the public especially communities within the study area.
    Matched MeSH terms: DNA Fingerprinting
  6. Fulltext Genetic and clinical characteristics of Chinese children with Glucokinase-maturity-onset diabetes of the young (GCK-MODY)
    Li X, Ting TH, Sheng H, Liang CL, Shao Y, Jiang M, et al.
    BMC Pediatr, 2018 03 06;18(1):101.
    PMID: 29510678 DOI: 10.1186/s12887-018-1060-8
    BACKGROUND: There is scarcity of information on the clinical features and genetics of glucokinase-maturity-onset diabetes of the young (GCK-MODY) in China. The aim of the study was to investigate the clinical and molecular characteristics of Chinese children with GCK-MODY.

    METHODS: Eleven children with asymptomatic hyperglycemia and clinically suspected GCK-MODY were identified from the database of children with diabetes in the biggest children's hospital in South China. Clinical data were obtained from medical records. Blood was collected from the patients and their parents for glucokinase (GCK) gene analysis. Parents without diabetes were tested for fasting glucose and HbA1c. Clinical information and blood for GCK gene analysis were obtained from grandparents with diabetes. GCK gene mutational analysis was performed by polymerase chain reaction and direct sequencing. Patients without a GCK gene mutation were screened by targeted next-generation sequencing (NGS) technology for other MODY genes.

    RESULTS: Nine children tested positive for GCK gene mutations while two were negative. The nine GCK-MODY patients were from unrelated families, aged 1 month to 9 years and 1 month at first detection of hyperglycaemia. Fasting glucose was elevated (6.1-8.5 mmol/L), HbA1c 5.2-6.7% (33.3-49.7 mmol/mol), both remained stable on follow-up over 9 months to 5 years. Five detected mutations had been previously reported: p.Val182Met, c.679 + 1G > A, p.Gly295Ser, p.Arg191Gln and p.Met41Thr. Four mutations were novel: c.483 + 2 T > A, p.Ser151del, p.Met57GlyfsX29 and p.Val374_Ala377del. No mutations were identified in the other two patients, who were also tested by NGS.

    CONCLUSIONS: GCK gene mutations are detected in Chinese children and their family members with typical clinical features of GCK-MODY. Four novel mutations are detected.
    Matched MeSH terms: DNA Mutational Analysis
  7. GENIPAC: A Genomic Information Portal for Head and Neck Cancer Cell Systems
    Lee BKB, Gan CP, Chang JK, Tan JL, Fadlullah MZ, Abdul Rahman ZA, et al.
    J Dent Res, 2018 07;97(8):909-916.
    PMID: 29512401 DOI: 10.1177/0022034518759038
    Head and neck cancer (HNC)-derived cell lines represent fundamental models for studying the biological mechanisms underlying cancer development and precision therapies. However, mining the genomic information of HNC cells from available databases requires knowledge on bioinformatics and computational skill sets. Here, we developed a user-friendly web resource for exploring, visualizing, and analyzing genomics information of commonly used HNC cell lines. We populated the current version of GENIPAC with 44 HNC cell lines from 3 studies: ORL Series, OPC-22, and H Series. Specifically, the mRNA expressions for all the 3 studies were derived with RNA-seq. The copy number alterations analysis of ORL Series was performed on the Genome Wide Human Cytoscan HD array, while copy number alterations for OPC-22 were derived from whole exome sequencing. Mutations from ORL Series and H Series were derived from RNA-seq information, while OPC-22 was based on whole exome sequencing. All genomic information was preprocessed with customized scripts and underwent data validation and correction through data set validator tools provided by cBioPortal. The clinical and genomic information of 44 HNC cell lines are easily assessable in GENIPAC. The functional utility of GENIPAC was demonstrated with some of the genomic alterations that are commonly reported in HNC, such as TP53, EGFR, CCND1, and PIK3CA. We showed that these genomic alterations as reported in The Cancer Genome Atlas database were recapitulated in the HNC cell lines in GENIPAC. Importantly, genomic alterations within pathways could be simultaneously visualized. We developed GENIPAC to create access to genomic information on HNC cell lines. This cancer omics initiative will help the research community to accelerate better understanding of HNC and the development of new precision therapeutic options for HNC treatment. GENIPAC is freely available at http://genipac.cancerresearch.my/ .
    Matched MeSH terms: DNA Copy Number Variations
  8. Characterization and pathogenicity of Fusarium species associated with leaf spot of mango (Mangifera indica L.)
    Omar NH, Mohd M, Mohamed Nor NMI, Zakaria L
    Microb Pathog, 2018 Jan;114:362-368.
    PMID: 29233777 DOI: 10.1016/j.micpath.2017.12.026
    Leaf spot diseases are mainly caused by fungi including Fusarium. In the present study several species of Fusarium were isolated from the leaf spot lesion of mango (Mangifera indica L.) Based on morphological characteristics, TEF-1α sequences and phylogenetic analysis, five species were identified as F. proliferatum, F. semitectum, F. mangiferae, F. solani and F. chlamydosporum. Pathogenicity test indicated that representative isolates of F. proliferatum, F. semitectum and F. chlamydosporum were pathogenic on mango leaves causing leaf spot with low to moderate virulence. Nevertheless, abundance of spots on the leaf can disrupt photosynthesis which in turn reduced growth, and lead to susceptibility to infection by opportunistic pathogens due to weakening of the plant. Fusarium solani and F. mangiferae were non-pathogenic and it is possible that both species are saprophyte which associated with nutrient availability on the surface of the leaf through decaying leave tissues. The occurrence of Fusarium spp. on the leaf spot lesion and the effect from the disease needs to be considered when developing disease management method of mango cultivation as numerous spot on the leaves could effect the photosynthesis process and finally giving low yield and less quality of mango.
    Matched MeSH terms: DNA, Fungal
  9. First molecular detection of porcine bocavirus in Malaysia
    Mohan Jacob D, Lee CY, Arshad SS, Selvarajah GT, Bande F, Ong BL, et al.
    Trop Anim Health Prod, 2018 Apr;50(4):733-739.
    PMID: 29243138 DOI: 10.1007/s11250-017-1489-z
    Several strains of porcine bocaviruses have been reported worldwide since their first detection in Sweden in 2009. Subsequently, the virus has been reported to be associated with gastrointestinal and respiratory signs in weaner and grower pigs. Although Malaysia is host to a self-sufficient swine livestock industry, there is no study that describes porcine bocavirus in the country. This report is the first to describe porcine bocavirus (PBoV) in Malaysian swine herds. PBoV was identified in various tissues from sick and runt pigs using the conventional PCR method with primers targeting conserved regions encoding for the nonstructural protein (NS1) gene. Out of 103 samples tested from 17 pigs, 32 samples from 15 pigs were positive for porcine bocavirus. In addition, a higher detection rate was identified from mesenteric lymph nodes (52.9%), followed by tonsil (37.0%), and lungs (33.3%). Pairwise comparison and phylogenetic analyses based on a 658-bp fragment of NS1 gene revealed that the Malaysian PBoV strains are highly similar to PBoV3 isolated in Minnesota, USA. The presence of porcine bocavirus in Malaysia and their phylogenetic bond was marked for the first time by this study. Further studies will establish the molecular epidemiology of PBoV in Malaysia and clarify pathogenicity of the local isolates.
    Matched MeSH terms: DNA Primers
  10. Fulltext Human TGF-β1 deficiency causes severe inflammatory bowel disease and encephalopathy
    Kotlarz D, Marquardt B, Barøy T, Lee WS, Konnikova L, Hollizeck S, et al.
    Nat Genet, 2018 Mar;50(3):344-348.
    PMID: 29483653 DOI: 10.1038/s41588-018-0063-6
    Transforming growth factor (TGF)-β1 (encoded by TGFB1) is the prototypic member of the TGF-β family of 33 proteins that orchestrate embryogenesis, development and tissue homeostasis1,2. Following its discovery 3 , enormous interest and numerous controversies have emerged about the role of TGF-β in coordinating the balance of pro- and anti-oncogenic properties4,5, pro- and anti-inflammatory effects 6 , or pro- and anti-fibrinogenic characteristics 7 . Here we describe three individuals from two pedigrees with biallelic loss-of-function mutations in the TGFB1 gene who presented with severe infantile inflammatory bowel disease (IBD) and central nervous system (CNS) disease associated with epilepsy, brain atrophy and posterior leukoencephalopathy. The proteins encoded by the mutated TGFB1 alleles were characterized by impaired secretion, function or stability of the TGF-β1-LAP complex, which is suggestive of perturbed bioavailability of TGF-β1. Our study shows that TGF-β1 has a critical and nonredundant role in the development and homeostasis of intestinal immunity and the CNS in humans.
    Matched MeSH terms: DNA Mutational Analysis
  11. Prevalence and sociodemographic correlates of cervicovaginal human papillomavirus (HPV) carriage in a cross-sectional, multiethnic, community-based female Asian population
    Khoo SP, Bhoo-Pathy N, Yap SH, Anwar Shafii MK, Hairizan Nasir N, Belinson J, et al.
    Sex Transm Infect, 2018 06;94(4):277-283.
    PMID: 29180538 DOI: 10.1136/sextrans-2017-053320
    OBJECTIVES: Cervical cancer is a largely preventable disease, and the strategic implementation of a cervical cancer prevention programme is partly dependent on the impact of human papillomavirus (HPV) infection interpreted within the context of the country's sociodemographic attributes. The objective of this study is to determine the prevalence of cervicovaginal HPV infection among a healthy, community-based, multiethnic Malaysian population. The HPV prevalence was subsequently correlated to the individual's sociodemographics and sexual/reproductive history. Of significance, the observed prevalence captured was in a birth cohort not included in the national school-based HPV vaccination programme.

    METHODS: This was a cross-sectional study where 1293 healthy women aged between 18 and 60 years were recruited via convenience sampling from five community-based clinics in Selangor, Malaysia. Cervicovaginal self-samples were obtained and DNA was extracted for HPV detection and genotyping. A comprehensive questionnaire was administered to determine the sociodemographics and behavioural patterns of participants.

    RESULTS: The median age at enrolment was 37 years old (IQR: 30-47). In total, 86/1190 (7.2%) of the samples collected were positive for HPV infection, with the highest HPV prevalence (11.9%) detected in the subgroup of 18-24 years old. The top three most prevalent HPV genotypes were HPV 16, 52 and 58. The independent risk factors associated with higher rates of HPV infection included Indian ethnicity, widowed status and women with partners who are away from home for long periods and/or has another sexual partner.

    CONCLUSIONS: The overall prevalence of HPV infection in this Malaysian multiethnic population was 7.2%, with 6.5% being high-risk genotypes. The top three most common high-risk HPV types were HPV 16, 52 and 58. This information is important for the planning of primary (HPV vaccination) and secondary (screening) cervical cancer prevention programmes in Malaysia.

    Matched MeSH terms: DNA
  12. Fulltext A combined human case of Dirofilaria ursi infection in dorsal subcutaneous tissue and Anisakis simplex sensu stricto (s.s.) infection in ventral subcutaneous tissue
    Yamada M, Shishito N, Nozawa Y, Uni S, Nishioka K, Nakaya T
    Trop Med Health, 2017;45:26.
    PMID: 29118653 DOI: 10.1186/s41182-017-0067-4
    Background: Dirofilaria ursi is a filarial nematode that parasitizes the subcutaneous tissues of the American black bear (Ursus americanus) and Japanese black bear (Ursus thiabetanus japonicus). D. ursi that has parasitized black bears has the potential to subsequently infect humans. In addition, extra-gastrointestinal anisakiasis is less common in Japan.

    Case presentation: We report a case of ventral subcutaneous anisakiasis and dorsal subcutaneous dirofilariasis that was acquired in Fukushima, in the northern part of Japan. The patient was an 83-year-old Japanese female, and subcutaneous parasitic granulomas were present on her left abdomen (near the navel) and left scapula. A pathological examination of the surgically dissected tissue sections from each region demonstrated eosinophilic granulomas containing different species of parasites. To enable the morphological and molecular identification of these parasites, DNA was extracted from paraffin-embedded sections using DEXPAT reagent, and the cytochrome oxidase 2 (COX2), internal transcribed spacer 1 (ITS1), 5.8S and ITS2 regions of the Anisakis larvae, and the 5S rRNA region of the male Dirofilaria were sequenced. The PCR products were examined and compared with DNA databases. Molecular analysis of the COX2 and 5S rRNA sequences of each worm revealed that the nematode found in the ventral region belonged to Anisakis simplex sensu stricto (s.s.) and the male Dirofilaria found in the dorsal region was classified as D. ursi.

    Conclusion: The present case showed a combined human case of D. ursi and A. simplex s.s. infections in subcutaneous tissues. The results of this study will contribute to the identification of unknown parasites in histological sections.
    Matched MeSH terms: DNA
  13. Fulltext The Effect of Oxidative Stress Towards The Expression of Thiamine Biosynthesis Genes (THIC and THI1/THI4) in Oil Palm (Elaeis guineensis)
    Idris ZHC, Abidin AAZ, Subki A, Yusof ZNB
    Trop Life Sci Res, 2018 Mar;29(1):71-85.
    PMID: 29644016 MyJurnal DOI: 10.21315/tlsr2018.29.1.5
    Thiamine is known to be an important compound in human diet and it is a cofactor required for vital metabolic processes such as acetyl-CoA biosynthesis, amino acid biosynthesis, Krebs and Calvin cycle. Besides that, thiamine has been shown to be involved in plant protection against stress. In this study, the level of expression of THIC and THI1/THI4, the genes for the first two enzymes in the thiamine biosynthesis pathway were observed when oil palm (Elaeis guineensis) was subjected to oxidative stress. Primers were designed based on the consensus sequence of thiamine biosynthesis genes obtained from Arabidopsis thaliana, Zea mays, Oryza sativa, and Alnus glutinosa. Oxidative stress were induced with various concentrations of paraquat and samplings were done at various time points post-stress induction. The expression of THIC and THI1/THI4 genes were observed via RT-PCR and qPCR analysis. The expression of THIC was increased 2-fold, while THI1/THI4 gene transcript was increased 4-fold upon induction of oxidative stress. These findings showed that oil palm responded to oxidative stress by over-expressing the genes involved in thiamine biosynthesis. These findings support the suggestion that thiamine may play an important role in plant protection against stress.
    Matched MeSH terms: DNA Primers
  14. Re-Expression of Bone Marrow Proteoglycan-2 by 5-Azacytidine is associated with STAT3 Inactivation and Sensitivity Response to Imatinib in Resistant CML Cells
    Al-Jamal HAN, Johan MF, Mat Jusoh SA, Ismail I, Wan Taib WR
    Asian Pac J Cancer Prev, 2018 Jun 25;19(6):1585-1590.
    PMID: 29936783
    Background: Epigenetic silencing of tumor suppressor genes (TSG) is involved in development and
    progression of cancers. Re-expression of TSG is inversely proportionate with STAT3 signaling pathways.
    Demethylation of DNA by 5-Azacytidine (5-Aza) results in re-expression of silenced TSG. Forced expression of
    PRG2 by 5-Aza induced apoptosis in cancer cells. Imatinib is a tyrosine kinase inhibitor that potently inhibits BCR/
    ABL tyrosine kinase resulting in hematological remission in CML patients. However, majority of CML patients treated
    with imatinib would develop resistance under prolonged therapy. Methods: CML cells resistant to imatinib were
    treated with 5-Aza and cytotoxicity of imatinib and apoptosis were determined by MTS and annexin-V, respectively.
    Gene expression analysis was detected by real time-PCR, STATs activity examined using Western blot and methylation
    status of PRG2 was determined by pyrosequencing analysis. Result: Expression of PRG2 was significantly higher in
    K562-R+5-Aza cells compared to K562 and K562-R (p=0.001). Methylation of PRG2 gene was significantly decreased
    in K562-R+5-Aza cells compared to other cells (p=0.021). STAT3 was inactivated in K562-R+5-Aza cells which showed
    higher sensitivity to imatinib. Conclusion: PRG2 gene is a TSG and its overexpression might induce sensitivity to
    imatinib. However, further studies are required to evaluate the negative regulations of PRG2 on STAT3 signaling.
    Matched MeSH terms: DNA
  15. Fulltext Citrus bent leaf viroid
    Khoo, Ying Wei, Iftikhar, Yasir, Kong, Lih Ling, Ganesan Vadamalai
    The Pertanika Journal of Scholarly Research Reviews, 2017;3(3):31-40.
    MyJurnal
    Citrus bent leaf viroid (CBLVd) from genus Apscaviroid, is one of the widely distributed viroids among the seven citrus viroids. It is comprised of three variants: Citrus viroid-Ia (CVd-Ia) (327 - 329 nucleotides), Citrus viroid-Ib (CVd-Ib) (315 - 319 nucleotides) and Citrus viroid-I-low sequence similarity (CVd-I-LSS) (325 - 330 nucleotides). Virulence of CBLVd totally expressed on citrus plants. Etrog citron (Citrus medica (L.)) coinfected with CBLVd, Citrus exocortis viroid (CEVd), Citrus viroid-III (CVd-III) and Citrus viroid-V (CVd-V) showed epinasty, leaf rolling, and stunting. CBLVd has been reported to reduce the canopy proportion and fruit production of citrus trees inserted on trifoliate orange rootstock. Moreover, citrus tree infected with singly CBLVd or in combinations with CEVd, Hop stunt viroid (CVd-II) and CVd-III induced dwarfing have been associated with poor development of the root system. Reverse-transcriptase polymerase chain reaction (RT-PCR) amplification and multiplex reverse-transcriptase polymerase chain reaction (MRT-PCR) amplification have been widely used to detect citrus viroids including CBLVd. As citrus viroids are emerging threats in citrus groves, therefore, this review covers the evolution, geographical distribution and epidemiology, economic impact and symptomatology, host range and transmission, detection, and management will be helpful in formulating the integrated management strategies for CBLVd.
    Matched MeSH terms: DNA-Directed RNA Polymerases
  16. Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis)
    Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, et al.
    J Hered, 2018 06 27;109(5):553-565.
    PMID: 29684146 DOI: 10.1093/jhered/esy019
    The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.
    Matched MeSH terms: DNA, Mitochondrial
  17. Fulltext Improved de novo genomic assembly for the domestic donkey
    Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, et al.
    Sci Adv, 2018 04;4(4):eaaq0392.
    PMID: 29740610 DOI: 10.1126/sciadv.aaq0392
    Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.
    Matched MeSH terms: DNA, Mitochondrial
  18. First Report of Achlya oblongata Infection in Freshwater-Reared Asian Seabass Lates calcarifer
    Lau LM, Hatai K, Fukano H, Kurata O
    J Aquat Anim Health, 2018 12;30(4):239-244.
    PMID: 29710400 DOI: 10.1002/aah.10018
    In September 2014, a freshwater oomycete was first isolated from Asian Seabass Lates calcarifer fry that were reared in freshwater at a fish hatchery in Sabah, Malaysia. A fungal strain was isolated from infected fry by using glucose yeast extract (GY) agar. From morphological identification, the strain belonged to the genus Achlya based on the mode of zoospore release. Molecular phylogenetic analysis of the internal transcribed spacer region sequences from the strain showed high similarity (99-100%) to Achlya oblongata. The isolate was able to grow on GY agar incubated at 15-35°C, in GY broth adjusted to pH 3.0-11.0, and in up to 1.0% NaCl. This is the first report of Achlya infection in freshwater-reared Asian Seabass in Malaysia.
    Matched MeSH terms: Sequence Analysis, DNA
  19. Fulltext Risk of Escherichia coli O157:H7 infection linked to the consumption of beef
    Premarathne J.M.K.J.K., New, C.Y., Ubong, A, Nakaguchi, Y., Nishibuchi, M., Son, R.
    Food Research, 2017;1(3):67-76.
    MyJurnal
    Escherichia coli O157:H7 is a major food-borne pathogen that has resulted in numerous
    outbreaks around the world. Widespread distribution of the organism in various ecological
    niches impedes the control measures. This study aimed to detect and quantify E. coli O157:H7
    in beef sold in wet markets and hypermarkets in Malaysia and to determine the risk of E. coli
    O157:H7 infection linked to consumption of beef. The rfbO157 and flicH7 primers targeted on
    somatic antigen (O157) and flagellar antigen (H7) respectively of E. coli O157:H7 was used for
    the MPN-PCR method. A total of 99 beef samples were collected from local wet markets and
    hypermarkets. The highest E. coli O157:H7 contamination rate was observed in beef samples
    collected from wet markets (89.50%), whereas the contamination rate in hyper market A and B
    were compratively low (35.35 and 20% respectively). However, the microbial load was highest
    in the beef samples from hypermarket A (1100 MPN/g) while E. coli O157:H7 bacterial load
    in beef samples from hypermarket B and wet market ranged from 3 to 93 MPN/g and 3 to 240
    MPN/g, respectively. Using the Quantitative Microbial Risk Assessment (QMRA) approach
    the risk was estimated incorporating the findings of the prevalence study and predictions
    based on home storage, cooking and consumption patterns. Three different exposure pathways
    were investigated to estimate the risk associated with contaminated beef and Monte Carlo
    simulation was used to determine the level of uncertainty. The developed model predicated that
    consumption of contaminated beef can be accountable for 1.83E+06 E. coli O157:H7 cases per
    year in Malaysia. The reliability of the model, data gaps and further research needs, is discussed.
    Through continuous improvement Quantitative Microbial Risk Assessment provides valuable
    insight into controlling and prevention strategies.
    Matched MeSH terms: DNA Primers
  20. Morphological and Molecular Evidence for Multiple Taxa in Simulium parahiyangum (Diptera: Simuliidae), a Geographic Generalist Black Fly in Southeast Asia
    Takaoka H, Low VL, Srisuka W, Ya'cob Z, Saeung A
    J Med Entomol, 2018 Oct 25;55(6):1453-1463.
    PMID: 30060220 DOI: 10.1093/jme/tjy109
    Seven populations of Simulium parahiyangum Takaoka & Sigit (Diptera: Simuliidae), a geographically widespread nominal species of black fly in Southeast Asia, were morphologically and molecularly studied. Three morphoforms based on male and pupal morphological features, and two primary lineages based on the COI gene sequence analysis were recognized. Morphoform 1 (lineage 1) from Sarawak, Malaysia, is identified as S. parahiyangum sensu stricto and morphoform 2 (lineage 2) from Thailand and Vietnam, and morphoform 3 (lineage 1) from Peninsular Malaysia are each regarded as distinct species, although morphoform 3 is partially homosequential for the COI gene with morphoform 1. Morphoforms 2 and 3 are described as Simulium ngaoense sp. nov. and Simulium sazalyi sp. nov., respectively. Overall, S. parahiyangum is not a single geographic generalist but a composite of multiple species.
    Matched MeSH terms: DNA Barcoding, Taxonomic
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