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Papa Mze N, Fernand-Laurent C, Daugabel S, Zanzouri O, Juillet SM. Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform. Genes (Basel) 2024; 15:259. [PMID: 38397248 PMCID: PMC10887851 DOI: 10.3390/genes15020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21,955 and 46,856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was quite similar between the two platforms (about USD 1790 for Illumina Miseq and about USD 1833 for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high-quality results with a similar cost.
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Affiliation(s)
- Nasserdine Papa Mze
- Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 177 rue de Versailles, 78150 Le Chesnay, France (O.Z.); (S.M.J.)
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Huang X, Mi J, Denman SE, Basangwangdui, Pingcuozhandui, Zhang Q, Long R, McSweeney CS. Changes in rumen microbial community composition in yak in response to seasonal variations. J Appl Microbiol 2021; 132:1652-1665. [PMID: 34623737 DOI: 10.1111/jam.15322] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022]
Abstract
AIMS Yak is a dominant ruminant, well adapted to grazing on pasture year around in the harsh climate of the 3000-meter-high Qinghai-Tibetan Plateau. The complex microbial community that resides within the yak rumen is responsible for fermentation and contributes to its climatic adaptation. This study aimed to characterize the rumen microbiota responses to wide seasonal variations, especially those necessary for survival in the cold seasons. METHODS AND RESULTS In the present study, we performed 16s rRNA gene sequencing to investigate the seasonal variations in microbiota composition, diversity and associated volatile fatty acids (VFAs) in yak rumen. The results showed that rumen microbiota were dominated by Bacteroides (72.13%-78.54%) and Firmicutes; the relative abundance of Firmicutes was higher in summer (17.44%) than in winter (10.67%; p < 0.05). The distribution of taxa differed among spring, summer and winter rumen communities (PERMANOVA, p = 0.001), whereas other taxa (e.g., Fibrobacter, Verrucomicrobia, Anaerostipes and Paludibacter), which could potentially help overcome harsh climate conditions were observed in higher abundance during the cold spring and winter seasons. The highest total VFA concentration in the yak rumen was obtained in summer (p < 0.05), followed by spring and winter, and both positive and negative correlations between VFAs and specific genera were revealed. CONCLUSIONS Microbiota in yak rumen appear to be highly responsive to seasonal variations. Considering environmental factors, we suggest that seasonal adaptation by microbial communities in rumen enables their hosts to survive seasonal scarcity and cold stress in the spring and winter. SIGNIFICANCE AND IMPACT OF STUDY The present study furthers our understanding of how microbial adaptation to seasonal variations in nutrient availability and climate may function in high plateau ruminants, providing insights into the tripartite relationship between the environment, host and microbiota.
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Affiliation(s)
- Xiaodan Huang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences (TAA AS)), Lhasa, China.,School of Public Health, Lanzhou University, Lanzhou, China
| | - Jiandui Mi
- College of Animal Science, South China Agricultural University, Guangzhou, China.,CSIRO, Agriculture Flagship, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Stuart E Denman
- CSIRO, Agriculture Flagship, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Basangwangdui
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences (TAA AS)), Lhasa, China
| | - Pingcuozhandui
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences (TAA AS)), Lhasa, China
| | - Qiang Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences (TAA AS)), Lhasa, China
| | - Ruijun Long
- School of Life Science, Lanzhou University, Lanzhou, China
| | - Christopher S McSweeney
- CSIRO, Agriculture Flagship, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
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Gaag KJV, Desmyter S, Smit S, Prieto L, Sijen T. Reducing the Number of Mismatches between Hairs and Buccal References When Analysing mtDNA Heteroplasmic Variation by Massively Parallel Sequencing. Genes (Basel) 2020; 11:E1355. [PMID: 33207560 DOI: 10.3390/genes11111355] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/02/2020] [Accepted: 11/11/2020] [Indexed: 11/17/2022] Open
Abstract
In forensics, mitochondrial DNA (mtDNA) analysis is foremost applied to rootless hairs often lacking detectable nuclear DNA. Sanger sequencing is the routine mtDNA method in most forensic laboratories, even though interpretation of mixed samples and heteroplasmic sites can be challenging. Individuals may hold cells with low-level heteroplasmy variants below the detection threshold and other cells where this minor variant is the major one. This difference may be interpreted as a mismatch between reference and evidentiary trace samples, such as buccal specimens and rootless hairs. Such mismatches may be solved by Massively Parallel Sequencing (MPS), allowing more sensitive quantitative analysis for mixed positions than Sanger. The mtDNA control region was analysed in buccal reference samples from 26 individuals and 475 corresponding hairs by MPS and compared to Sanger sequencing data generated on the same samples. With MPS, mixed contributions down to 3% were regarded, leading to a substantial increase in the frequency of heteroplasmy. Our results demonstrate that previously reported mismatches between buccal reference and hair shaft samples by Sanger are detected as low-level heteroplasmy by MPS. A detailed overview of buccal and hair heteroplasmy is provided and implications for MPS-based mtDNA analysis in the context of forensic cases are discussed.
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Zhao H, Jiang X, Chu W. Shifts in the gut microbiota of mice in response to dexamethasone administration. Int Microbiol 2020; 23:565-573. [PMID: 32356148 DOI: 10.1007/s10123-020-00129-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/14/2020] [Accepted: 04/13/2020] [Indexed: 01/06/2023]
Abstract
Glucocorticoids (GCs) are an important anti-inflammatory drug, used widely, regardless of its side effects. GCs can affect intestinal flora directly or indirectly, though few studies have focused on the changes of gut microbiota composition. In this study, ICR mice were randomly divided into three groups, gavage administration with saline, and different doses of dexamethasone (DEX): 0.1 mg/kg and 1 mg/kg. Five days later, the microbial diversity of the colon contents was analyzed. A significant loss in weight was observed in the DEX1.0 group as compared with the control group (P = 0.011). The gut microbiota richness (ACE, P = 0.01; Chao, P = 0.013) and diversity (Shannon, P = 0.035; Simpson, P = 0.032) were decreased in DEX group. The proportions of genus Butyricicoccus, Oscillibacter, Anaerotruncus, Ruminiclostridium, Ruminococcaceae, and Lachnospiraceae were the most abundant and predominant followed by Lactobacillus, Pseudomonas, and Enterorhabdus. Dex administration led to changes in the liver/body ratio and spleen/body ratio. The results obtained from our study indicate that DEX can decrease the level of WBC and change the structure of the gut microbiota composition; moreover, the results of this study provide new insight into alleviating the clinical side effects of GC therapy.
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Affiliation(s)
- Haichao Zhao
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Xueyuan Jiang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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Liu K, Zhang Y, Li Q, Li H, Long D, Yan S, Huang W, Long R, Huang X. Ethnic Differences Shape the Alpha but Not Beta Diversity of Gut Microbiota from School Children in the Absence of Environmental Differences. Microorganisms 2020; 8:microorganisms8020254. [PMID: 32075068 PMCID: PMC7074779 DOI: 10.3390/microorganisms8020254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/30/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Although the human gut microbiome is shaped by factors such as diet, environment, and genetic background, most studies investigating the relationship between ethnicity and microbiota have compared groups living in separate geographical locations. To isolate the effects of ethnicity on microbial diversity by minimizing environmental differences, we selected 143 school children from Han, Tibetan, and Hui populations from the same town on the Qinghai–Tibetan Plateau for fecal microbiome 16S rDNA sequencing. We characterized the diversity, identified signature taxa, and performed correlation analysis between diet and community composition. Firmicutes (47.61%) and Bacteroidetes (38.05%) were dominant phyla among the three ethnic groups; seven genera showed significant differences in relative abundance. Tibetan populations had a higher relative abundance of Oscillibacter and Barnesiella, compared with Han and Hui populations. Alpha diversity analyses (observed species, ACE, and Shannon indices) showed that the Tibetan population had the highest diversity compared to the Hui and Han groups, whereas beta diversity analysis revealed no significant differences between groups. The consumption of grains, milk, eggs, and fruits were positively correlated with specific taxa. Under similar environments and diet, ethnic background significantly contributed to differences in alpha diversity but not beta diversity of gut microbiota.
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Affiliation(s)
- Ke Liu
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
| | - Yongling Zhang
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
| | - Qinglin Li
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
| | - Huan Li
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
| | - Danfeng Long
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
| | - Shijuan Yan
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
- Agro-biological Gene Research Center, Guangzhou Academy of Agricultural Sciences, Tianhe Distinct, Guangzhou 510640, China;
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangzhou Academy of Agricultural Sciences, Tianhe Distinct, Guangzhou 510640, China;
| | - Ruijun Long
- School of Life Science, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China
- Correspondence: (R.L.); (X.H.); Tel.: +86-13993108160 (X.H.)
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, No. 222 TianshuiNanlu, Lanzhou 730000, China; (K.L.); (Y.Z.); (Q.L.); (H.L.); (D.L.); (S.Y.)
- Correspondence: (R.L.); (X.H.); Tel.: +86-13993108160 (X.H.)
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Khongnomnan K, Poomipak W, Praianantathavorn K, Saengchoowong S, Pisitkun T, Poovorawan Y, Payungporn S. Human MicroRNAs Expression Profiles in Influenza B Virus-Infected Cells based on Illumina MiSeq Platform. Microrna 2018; 7:204-214. [PMID: 29766833 DOI: 10.2174/2211536607666180515111048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/12/2018] [Accepted: 05/08/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Influenza B virus causes influenza-like illness in humans. MicroRNAs (miRNAs) are small non-coding RNAs regulating gene expression through mRNA degradation or translational repression. MiRNAs have evolved to regulate many cellular processes including the viral infection response. OBJECTIVE This study aims to investigate the miRNA profiles of human cells infected with influenza B virus. METHODS A549 cells were infected with influenza B viruses (MOI = 0.5). MiRNAs were extracted at 24 and 48 hours post-infection. MiRNAs were used to construct four DNA libraries: influenza Binfected and an uninfected control for both time points. Then high-throughput sequencing was performed using the Miseq platform (Illumina). Sequencing data were analyzed by Miseq reporter software. The miRNAs were categorized and counted based on the frequency of reads. All filtered contigs were aligned with data from miRbase. The relative expression of each miRNA between uninfected and influenza B-infected cells was calculated. RESULTS There were 13 down-regulated miRNAs and 21 up-regulated miRNAs observed in influenza B infected cells at 24 hours post infection. At 48 hours post infection, 14 miRNAs were downregulated, whereas 8 miRNAs were up-regulated. CONCLUSION This study suggested that miRNAs may play important roles in host gene regulation in response to viral infection.
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Affiliation(s)
- Kritsada Khongnomnan
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Witthaya Poomipak
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Suthat Saengchoowong
- Joint Chulalongkorn University-University of Liverpool PhD Programme, Graduate Division, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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van der Gaag KJ, de Leeuw RH, Laros JFJ, den Dunnen JT, de Knijff P. Short hypervariable microhaplotypes: A novel set of very short high discriminating power loci without stutter artefacts. Forensic Sci Int Genet 2018; 35:169-175. [PMID: 29852469 DOI: 10.1016/j.fsigen.2018.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/03/2018] [Accepted: 05/16/2018] [Indexed: 12/12/2022]
Abstract
Since two decades, short tandem repeats (STRs) are the preferred markers for human identification, routinely analysed by fragment length analysis. Here we present a novel set of short hypervariable autosomal microhaplotypes (MH) that have four or more SNPs in a span of less than 70 nucleotides (nt). These MHs display a discriminating power approaching that of STRs and provide a powerful alternative for the analysis;1;is of forensic samples that are problematic when the STR fragment size range exceeds the integrity range of severely degraded DNA or when multiple donors contribute to an evidentiary stain and STR stutter artefacts complicate profile interpretation. MH typing was developed using the power of massively parallel sequencing (MPS) enabling new powerful, fast and efficient SNP-based approaches. MH candidates were obtained from queries in data of the 1000 Genomes, and Genome of the Netherlands (GoNL) projects. Wet-lab analysis of 276 globally dispersed samples and 97 samples of nine large CEPH families assisted locus selection and corroboration of informative value. We infer that MHs represent an alternative marker type with good discriminating power per locus (allowing the use of a limited number of loci), small amplicon sizes and absence of stutter artefacts that can be especially helpful when unbalanced mixed samples are submitted for human identification.
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Affiliation(s)
- Kristiaan J van der Gaag
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands; Division of Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497GB, The Hague, The Netherlands.
| | - Rick H de Leeuw
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands.
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands.
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands.
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands.
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Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, Yin WF, Chan KG. Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI. PeerJ 2015; 3:e1225. [PMID: 26336650 PMCID: PMC4556143 DOI: 10.7717/peerj.1225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023] Open
Abstract
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.
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Affiliation(s)
- Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kah-Yan How
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Siew-Kim Lee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Delicia Yong
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia
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