Identification and characterization of copy number variations (CNVs) in dengue patients and its impact with vascular leakage / Zuraihan Zakaria

Dengue fever is a mosquito-borne tropical disease caused by dengue virus. When infected by any of the four serotypes of dengue viruses, individuals may be asymptomatic or develop a dengue fever. The latter group can progress into severe form of dengue and the etiology of this is still uncertain. This study aims to elucidate copy number variations (CNVs) of the host genes as the factor causing dengue pathogenesis. Blood samples were collected from hospitalized dengue patients and proceeded to DNA extraction. DNA samples (136) were used for genotyping with Human Genome GeneChip 6.0. CNVs were called using Genotyping Console (GTC) 4.1 and Nexus Copy Number 7.0. Results from both algorithms were merged and stringent CNVs were filtered with three public databases; DGV, HapMap3 and SGVP in search for rare casespecific CNVs. Case-specific underlying genes were used in functional analysis with DAVID and IPA to explicate the dengue related biological processes. Significant genes of interest from both softwares were validated using qPCR. Hundred and thirty-six DNA samples from hospitalized dengue patients in four different hospitals were genotyped. A total number of 50,864 (24,806 gains and 26,059 loss) and 34,257 (31,725 gains and 2,534 loss) CNV events were discovered by GTC and Nexus, respectively. After merging, only 3,052 (2,132 gain and 920 loss) stringent CNVs were left. After filtering with public known databases, of the 385 novel rare CNVs, 257 were specific for cases, and 128 were specific for controls, respectively (p = 0.388). Six hundred and eighty genes were found underlying the CNVs specific for cases and were eventually loaded into functional analysis softwares. GO terms from unbiased DAVID analysis such as defense response (p<0.001; Benjamini corrected p = 0.034), inflammatory response (p<0.001; Benjamini corrected p = 0.04) and response to cytokine stimulus (p<0.001; Benjamini corrected p = 0.038). From the biased IPA analysis, the candidate genes were clustered into enrichment with antigen presentation pathway as the most significant (p <0.001), followed by IL-12 signaling and production in macrophages (p <0.001), and interferon signaling (p <0.001). Genes from both significant GO terms and pathways; namely BCKDHB, CTSB, MR1, TAP2, TNFRS1B and CXCR4 were considered for validation using qPCR. The 9 out of 10 similarities between SNP 6.0 genotyping and qPCR supported the reliability of this assay. In conclusion, the rare CNVs may be involved in dengue pathogenesis. The rare CNV, which has been reported in other diseases (neuropsychiatric diseases, congenital heart disease and dilated cardiomyopathy), is reported for the first time in infectious diseases

Identification and characterization of copy number variations (CNVs) in dengue patients and its impact with vascular leakage / Zuraihan Zakaria

Dengue fever is a mosquito-borne tropical disease caused by dengue virus. When infected by any of the four serotypes of dengue viruses, individuals may be asymptomatic or develop a dengue fever. The latter group can progress into severe form of dengue and the etiology of this is still uncertain. This study aims to elucidate copy number variations (CNVs) of the host genes as the factor causing dengue pathogenesis. Blood samples were collected from hospitalized dengue patients and proceeded to DNA extraction. DNA samples (136) were used for genotyping with Human Genome GeneChip 6.0. CNVs were called using Genotyping Console (GTC) 4.1 and Nexus Copy Number 7.0. Results from both algorithms were merged and stringent CNVs were filtered with three public databases; DGV, HapMap3 and SGVP in search for rare case- specific CNVs. Casespecific underlying genes were used in functional analysis with DAVID and IPA to explicate the dengue related biological processes. Significant genes of interest from both softwares were validated using qPCR. Hundred and thirty-six DNA samples from hospitalized dengue patients in four different hospitals were genotyped. A total number of 50,864 (24,806 gains and 26,059 loss) and 34,257 (31,725 gains and 2,534 loss) CNV events were discovered by GTC and Nexus, respectively. After merging, only 3,052 (2,132 gain and 920 loss) stringent CNVs were left

The role of Interleukin-10 in Helicobacter pylori infection

Background & Aims: Helicobacter pylori (H. pylori) chronic infection is the major cause of peptic ulceration and gastric cancer. Strains with the cag pathogenicity island (cagPaI) are more strongly associated with disease. In earlier studies, higher levels of interleukin-10 (IL-10) were found in human gastric biopsies with the highest H. pylori colonisation density grading. In the current study, experiments were performed to determine if this effect could be replicated in vitro using human gastric epithelial cell lines. Although IL-10 is abundant in the gastric mucosa, the nature of its interaction with the epithelium is unknown. IL-10 receptor (IL-10R) expression on gastric epithelial cells was therefore investigated. Materials & Methods: H. pylori was co-cultured with the human gastric epithelial cell lines AGS, MKN28 and MKN45 in the presence or absence of recombinant human IL-10 (rIL-10). Bacterial densities were assessed by viable count assays. Immunofluorescence microscopy, flow cytometry, RT-PCR and western blotting were used to investigate the presence of IL-10R (IL-10Rα and IL-10Rβ subunits) on gastric epithelial cell lines. An IL-10 Fluorokine Kit (R&D Systems) was also used to quantify IL-10 binding onto gastric epithelial cells. Results: Addition of rIL-10 significantly increased the density of H. pylori cagPaI positive strains indirectly through effects on gastric epithelial cells. No such differences were observed with cagPaI negative strains. AGS cells expressed both IL 10Rα and IL-10Rβ constitutively but IL-10Rβ expression was increased with infection. Conversely, the binding of IL-10 was decreased when AGS cells were infected with H. pylori. Conclusion: This study highlighted a novel finding of constitutive IL-10R expression in AGS cells. Interestingly, H. pylori infection of AGS cells downregulated the binding of IL-10 to its receptor. The higher level expression of IL-10Rβ following infection was in opposition to this. Possibly IL-10Rβ could be sequestered into other cytokine receptor complexes and therefore is not participate in IL-10 binding. These studies have shown that IL-10 has a more complex role in the interaction between H. pylori and its host. The IL-10 response now also appears to influence the density of H. pylori in the stomach, via cagPaI-dependent effects on epithelial cells. More work must be carried out to investigate the mechanisms behind this effect

The role of Interleukin-10 in Helicobacter pylori infection

Background & Aims: Helicobacter pylori (H. pylori) chronic infection is the major cause of peptic ulceration and gastric cancer. Strains with the cag pathogenicity island (cagPaI) are more strongly associated with disease. In earlier studies, higher levels of interleukin-10 (IL-10) were found in human gastric biopsies with the highest H. pylori colonisation density grading. In the current study, experiments were performed to determine if this effect could be replicated in vitro using human gastric epithelial cell lines. Although IL-10 is abundant in the gastric mucosa, the nature of its interaction with the epithelium is unknown. IL-10 receptor (IL-10R) expression on gastric epithelial cells was therefore investigated. Materials & Methods: H. pylori was co-cultured with the human gastric epithelial cell lines AGS, MKN28 and MKN45 in the presence or absence of recombinant human IL-10 (rIL-10). Bacterial densities were assessed by viable count assays. Immunofluorescence microscopy, flow cytometry, RT-PCR and western blotting were used to investigate the presence of IL-10R (IL-10Rα and IL-10Rβ subunits) on gastric epithelial cell lines. An IL-10 Fluorokine Kit (R&D Systems) was also used to quantify IL-10 binding onto gastric epithelial cells. Results: Addition of rIL-10 significantly increased the density of H. pylori cagPaI positive strains indirectly through effects on gastric epithelial cells. No such differences were observed with cagPaI negative strains. AGS cells expressed both IL 10Rα and IL-10Rβ constitutively but IL-10Rβ expression was increased with infection. Conversely, the binding of IL-10 was decreased when AGS cells were infected with H. pylori. Conclusion: This study highlighted a novel finding of constitutive IL-10R expression in AGS cells. Interestingly, H. pylori infection of AGS cells downregulated the binding of IL-10 to its receptor. The higher level expression of IL-10Rβ following infection was in opposition to this. Possibly IL-10Rβ could be sequestered into other cytokine receptor complexes and therefore is not participate in IL-10 binding. These studies have shown that IL-10 has a more complex role in the interaction between H. pylori and its host. The IL-10 response now also appears to influence the density of H. pylori in the stomach, via cagPaI-dependent effects on epithelial cells. More work must be carried out to investigate the mechanisms behind this effect

Program literasi Bahasa Melayu murid tahun tiga Sekolah Kebangsaan Tiong, Kota Bharu Kelantan / Helmey Zainee Binti Mohd Zain and Zuraihan binti Zakaria

Literasi bahasa ditakrifkan sebagai kemampuan minimum untuk membaca dan menulis dalam sesuatu bahasa. Pertubuhan Pendidikan Sains dan Kebudayaan Bangsa-bangsa Bersatu mendefinisikan seseorang yang mempunyai keupayaan literasi ialah seseorang yang dapat membaca dan menulis sesuatu pernyataan yang pendek dan mudah dalam kehidupan hariannya. Satu program literasi bahasa Melayu telah dilaksanakan di Sekolah Kebangsaan Tiong Kota Bharu Kelantan oleh tujuh orang tenaga pengajar dari Pusat Pengajian Bahasa Literasi dan Terjemahan, Universiti Sains Malaysia Kampus Kesihatan. Seramai 15 orang murid tahun tiga yang menghadapi masalah dalam penguasaan pembacaan dan penulisan dalam bahasa Melayu telah dipilih bagi menyertai program ini. Program ini telah dijalankan selama dua tahun iaitu pada tahun 2011 dan tahun 2012. Fokus utama kajian adalah untuk menganalisis keberkesanan program ini. Oleh itu dapatan kajian dapat memberi petunjuk tentang keberkesanan program literasi bahasa Melayu yang telah dijalankan terhadap 15 orang murid tahun tiga Sekolah Rendah Kebangsaan Tiong, Kota Bharu