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Khan SM, Das T, Chakraborty S, Choudhury AMAR, Karim HF, Mostofa MA, Ahmed HU, Hossain MA, Le Calvez-Kelm F, Hosen MI, Shekhar HU. A transcriptome study of p53-pathway related prognostic gene signature set in bladder cancer. Heliyon 2023; 9:e21058. [PMID: 37876438 PMCID: PMC10590981 DOI: 10.1016/j.heliyon.2023.e21058] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
p53 pathway is important in tumorigenesis. However, no study has been performed to specifically investigate the role of p53 pathway genes in bladder cancer (BLCA). In this study, transcriptomics data of muscle invasive bladder cancer patients (n = 411) from The Cancer Genome Atlas (TCGA) were investigated. Using the hallmark p53 pathway gene set, the Non-Negative Matrix factorization (NMF) analysis identified two subtypes (C1 and C2). Clinical, survival, and immunological analysis were done to validate distinct characteristics of the subtypes. Pathway enrichment analysis showed the subtype C1 with poor prognosis having enrichment in genes of the immunity related pathways, where C2 subtype with better prognosis being enriched in genes of the steroid synthesis and drug metabolism pathways. A signature gene set consisting of MDGA2, GNLY, GGT2, UGT2B4, DLX1, and DSC1 was created followed by a risk model. Their expressions were analyzed in RNA extracted from the blood and matched tumor tissues of BLCA patients (n = 10). DSC1 had significant difference of expression (p = 0.005) between the blood and tumor tissues in our BLCA samples. Contrary to the usual normal bladder tissue to blood ratio, DLX1 expression was lower (p = 0.02734) in tumor tissues than in blood. Being the first research of p53 pathway related signature gene set in bladder cancer, this study potentially has a substantial impact on the development of biomarkers for BLCA.
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Affiliation(s)
- Safayat Mahmud Khan
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tonmoy Das
- Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Sajib Chakraborty
- Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - Howlader Fazlul Karim
- Department. Uro-Oncology, National Institute of Cancer Research Hospital, Bangladesh
| | - Munshi Akid Mostofa
- Department. Uro-Oncology, National Institute of Cancer Research Hospital, Bangladesh
| | - Hasib Uddin Ahmed
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Akmal Hossain
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Florence Le Calvez-Kelm
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), 69372, Lyon, France
| | - Md Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Nabi AHMN, Ebihara A, Shekhar HU. Impacts of SARS-CoV-2 on diabetes mellitus: A pre and post pandemic evaluation. World J Virol 2023; 12:151-171. [PMID: 37396707 PMCID: PMC10311579 DOI: 10.5501/wjv.v12.i3.151] [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] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/24/2023] [Accepted: 04/13/2023] [Indexed: 06/21/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) crippled the whole world and has resulted in large number of morbidity and mortality. The origin of the SARS-CoV-2 is still disputed. The risk of infection with SARS-CoV-2 is dependent on several risk factors as observed in many studies. The severity of the disease depends on many factors including the viral strain, host immunogenetics, environmental factors, host genetics, host nutritional status and presence of comorbidities like hypertension, diabetes, Chronic Obstructive Pulmonary Disease, cardiovascular disease, renal impairment. Diabetes is a metabolic disorder mainly characterized by hyperglycemia. Diabetic individuals are intrinsically prone to infections. SARS-CoV-2 infection in patients with diabetes result in β-cell damage and cytokine storm. Damage to the cells impairs the equilibrium of glucose, leading to hyperglycemia. The ensuing cytokine storm causes insulin resistance, especially in the muscles and liver, which also causes a hyperglycemic state. All of these increase the severity of COVID-19. Genetics also play pivotal role in disease pathogenesis. This review article focuses from the probable sources of coronaviruses and SARS-CoV-2 to its impacts on individuals with diabetes and host genetics in pre- and post-pandemic era.
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Affiliation(s)
- A H M Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Akio Ebihara
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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Akter S, Hossain S, Ali MA, Hosen MI, Shekhar HU. Comprehensive Characterization of the Coding and Non-Coding Single Nucleotide Polymorphisms in the Tumor Protein p63 (TP63) Gene Using In Silico Tools. Biomolecules 2021; 11:1733. [PMID: 34827731 PMCID: PMC8637305 DOI: 10.3390/biom11111733] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/08/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) help to understand the phenotypic variations in humans. Genome-wide association studies (GWAS) have identified SNPs located in the tumor protein 63 (TP63) locus to be associated with the genetic susceptibility of cancers. However, there is a lack of in-depth characterization of the structural and functional impacts of the SNPs located at the TP63 gene. The current study was designed for the comprehensive characterization of the coding and non-coding SNPs in the human TP63 gene for their functional and structural significance. The functional and structural effects of the SNPs were investigated using a wide variety of computational tools and approaches, including molecular dynamics (MD) simulation. The deleterious impact of eight nonsynonymous SNPs (nsSNPs) affecting protein stability, structure, and functions was measured by using 13 bioinformatics tools. These eight nsSNPs are in highly conserved positions in protein and were predicted to decrease protein stability and have a deleterious impact on the TP63 protein function. Molecular docking analysis showed five nsSNPs to reduce the binding affinity of TP63 protein to DNA with significant results for three SNPs (R319H, G349E, and C347F). Further, MD simulations revealed the possible disruption of TP63 and DNA binding, hampering the essential protein function. PolymiRTS study found five non-coding SNPs in miRNA binding sites, and the GTEx portal recognized five eQTLs SNPs in single tissue of the lung, heart (LV), and cerebral hemisphere (brain). Characterized nsSNPs and non-coding SNPs will help researchers to focus on TP63 gene loci and ascertain their association with certain diseases.
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Affiliation(s)
- Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, VA 22030, USA;
| | - Shafaat Hossain
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
| | - Md. Ackas Ali
- Division of Computer Aided Drug-Design, The Red-Green Research Center, 16, Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh;
| | - Md. Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
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Khan SM, Faisal ARM, Nila TA, Binti NN, Hosen MI, Shekhar HU. A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene. PLoS One 2021; 16:e0260054. [PMID: 34793541 PMCID: PMC8601573 DOI: 10.1371/journal.pone.0260054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022] Open
Abstract
PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5' and 3' untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.
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Affiliation(s)
- Safayat Mahmud Khan
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Ar-Rafi Md. Faisal
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Tasnin Akter Nila
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Nabila Nawar Binti
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
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Nawar N, Paul A, Mahmood HN, Faisal MI, Hosen MI, Shekhar HU. Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference. Bioinformation 2021; 17:424-438. [PMID: 34092963 PMCID: PMC8131579 DOI: 10.6026/97320630017424] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Partner and Localizer of BRCA2 or PALB2 is a typical tumor suppressor protein, that responds to DNA double stranded breaks through homologous recombination repair. Heterozygous mutations in PALB2 are known to contribute to the susceptibility of breast and ovarian cancer. However, there is no comprehensive study characterizing the structural and functional impacts of SNPs located in the PALB2 gene. Therefore, it is of interest to document a comprehensive analysis of coding and non-coding SNPs located at the PALB2 loci using in silico tools. The data for 1455 non-synonymous SNPs (nsSNPs) located in the PALB2 loci were retrieved from the dbSNP database. Comprehensive characterization of the SNPs using a combination of in silico tools such as SIFT, PROVEAN, PolyPhen, PANTHER, PhD-SNP, Pmut, MutPred 2.0 and SNAP-2, identified 28 functionally important SNPs. Among these, 16 nsSNPs were further selected for structural analysis using conservation profile and protein stability. The most deleterious nsSNPs were documented within the WD40 domain of PALB2. A general outline of the structural consequences of each variant was developed using the HOPE project data. These 16 mutant structures were further modelled using SWISS Model and three most damaging mutant models (rs78179744, rs180177123 and rs45525135) were identified. The non-coding SNPs in the 3' UTR region of the PALB2 gene were analyzed for altered miRNA target sites. The comprehensive characterization of the coding and non-coding SNPs in the PALB2 locus has provided a list of damaging SNPs with potential disease association. Further validation through genetic association study will reveal their clinical significance.
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Affiliation(s)
- Noshin Nawar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Anik Paul
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Hamida Nooreen Mahmood
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Ismail Faisal
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
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Rahman T, Faisal ARM, Khanam T, Shekhar HU. Recurrent Indoor Environmental Pollution and Its Impact on Health and Oxidative Stress of the Textile Workers in Bangladesh. Environ Health Insights 2020; 14:1178630220938393. [PMID: 32843838 PMCID: PMC7418231 DOI: 10.1177/1178630220938393] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Perennial indoor environmental pollution in the textile industrial area is a potential health hazard for workers engaged in this line of work, resulting in mental aberration to severe health risks. This study was designed to investigate the indoor environmental quality of textile industries and correlate its effect on the occupational health and well-being of the textile workers by measuring plasma oxidative stress status in textile workers and healthy control subjects. Environmental samples were collected from 15 textile industries located in Dhaka division, and 30 volunteer textile workers and 30 volunteer office workers (control) aged 18 to 57 years participated in the study. The concentration of plasma ascorbic acid (P-ASC), plasma malondialdehyde (P-MDA), and plasma conjugated diene (P-CD) was measured in both groups. The noise level (78.0 ± 0.68 dB) and the formaldehyde level (141.80 ± 4.47 µg/m3) were found to be significantly higher in the indoor environmental area compared with those in the control area (70.17 ± 0.25 dB and 108.0 ± 0.76 µg/m3, respectively). Furthermore, the daily average concentration of suspended particulate matters (PMs), that is, PM2.5 (322.2 ± 13.46 µg/m3) and PM10 (411.0 ± 17.57 µg/m3), was also found to be significantly higher in the indoor environmental air compared with that in the control area (78.59 ± 1.66 and 174.0 ± 2.33 µg/m3, respectively). The levels of P-MDA (0.37 ± 0.03 nmol/L) and P-CD (14.74 ± 0.61 nmol/L) were significantly increased, whereas the level of P-ASC level (0.46 ± 0.04 mg/dL) was markedly decreased in the textile workers compared with the healthy control subjects (0.18 ± 0.01 nmol/L of P-MDA, 10.04 ± 0.44 nmol/L of P-CD, and 1.29 ± 0.06 mg/dL of P-ASC). The textile plants were found to have significantly elevated levels of indoor environmental pollutants compared with those in the control area, and the textile workers were significantly exposed to oxidative stresses compared with the control subjects. The use of noise pads and high-efficiency air filters is perhaps highly instrumental to put an end to this prevailing situation. Moreover, to overcome the oxidative stresses among workers, supplementation of antioxidant vitamins (ie, ascorbic acid and/or vitamin E) may be beneficial. In addition, to prevent serious health-related issues, proper precautions should be taken to protect the occupational health of the textile workers.
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Affiliation(s)
- Tania Rahman
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Ar-Rafi Md. Faisal
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Tahura Khanam
- Qtex Solutions Limited, 1st ISO 17020:2012 Accredited Environmental inspection body in Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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Noor FA, Sultana N, Bhuyan GS, Islam MT, Hossain M, Sarker SK, Islam K, Khan WA, Rahman M, Qadri SK, Shekhar HU, Qadri F, Qadri SS, Mannoor K. Nationwide carrier detection and molecular characterization of β-thalassemia and hemoglobin E variants in Bangladeshi population. Orphanet J Rare Dis 2020; 15:15. [PMID: 31941534 PMCID: PMC6961315 DOI: 10.1186/s13023-020-1294-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 08/20/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Background ß-thalassemia is one of the most common inherited blood disorders in the world and a major deterrent to the public health of Bangladesh. The management of thalassemia patients requires lifelong frequent blood transfusion and the available treatment options are unsatisfactory. A national policy on thalassemia prevention is mandatory in Bangladesh. However, precise and up-to-date information on the frequency of ß-thalassemia carriers are missing due to lack of accurate diagnostic approaches, limited access to information and absence of national screening program. This study aims to determine the nationwide carrier frequency of hemoglobin E (HbE) and β- thalassemia and mutation spectrum among the carriers using molecular, hematological and biochemical methods. Methods The study enrolled a total of 1877 individuals (60.1% male and 39.9% female) aged between 18 and 35 years. Total sample size and its division-wise breakdown were calculated in proportion to national and division-wise population. Venous blood was collected and subjected to CBC analysis and Hb-electrophoresis for each participant. Serum ferritin was measured to detect coexistence of iron deficiency anemia with thalassemia carrier. DNA-based High Resolution Melting (HRM) curve analysis was performed for confirmation of carrier status by mutation detection. Results Of 11.89% (95% CI, 10.43–13.35) carriers of β-globin gene mutations, 8.68% (95% CI, 7.41–9.95) had HbE trait (ETT) and 2.24% (95% CI, 1.57–2.91) had beta-thalassemia trait (BTT). Among eight divisions, Rangpur had the highest carrier frequency of 27.1% (ETT-25%, BTT-2.1%), whereas Khulna had the lowest frequency of 4.2% (ETT-4.2% only). Moreover, α- thalassemia, HbD trait, HbE disease, hereditary persistence of HbF were detected in 0.11, 0.16, 0.43 and 0.16% participants, respectively. HRM could identify two individuals with reported pathogenic mutations in both alleles who were erroneously interpreted as carriers by hematological indices. Finally, a total of nine different mutations including a novel mutation (c.151A > G) were detected in the β-globin gene. Conclusions Since carrier frequency for both HbE and β-thalassemia is alarmingly high in Bangladesh, a nationwide awareness and prevention program should be made mandatory to halt the current deteriorating situations. Mutation-based confirmation is highly recommended for the inconclusive cases with conventional carrier screening methods to avoid any faulty detection of thalassemia carriers.
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Affiliation(s)
- Farjana Akther Noor
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh.,Department of Biochemistry and Molecular Biology, University of Dhaka, Shahbagh, Dhaka, 1000, Bangladesh
| | - Nusrat Sultana
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh.,Department of Virology, Dhaka Medical College Hospital, Shahbagh, Dhaka, 1000, Bangladesh
| | - Golam Sarower Bhuyan
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Tarikul Islam
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohabbat Hossain
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Suprovath Kumar Sarker
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Khaleda Islam
- Directorate General of Health Services, MoHFW, Government of Bangladesh, Mohakhali, Dhaka, 1212, Bangladesh
| | - Waqar Ahmed Khan
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Sher-e-Bangla Nagar, Dhaka, 1207, Bangladesh
| | - Mujahida Rahman
- Department of Hematology, Bangabandhu Sheikh Mujib Medical University, Shahbagh, Dhaka, 1000, Bangladesh
| | - Syeda Kashfi Qadri
- Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, Singapore
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Shahbagh, Dhaka, 1000, Bangladesh
| | - Firdausi Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh.,Department of Enteric and Respiratory Infectious Diseases, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, 1212, Bangladesh
| | - Syed Saleheen Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Kaiissar Mannoor
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh.
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Abstract
Lead exposure can damage cells directly by effecting DNA or indirectly by modifying proteins and enzymes. In Bangladesh, many working children are exposed to a very high level of lead during their early life due to their involvement with lead-oriented professions. This imposes a severe threat to the growth and development of the children. Therefore to study the effect of lead, we enrolled 60 age-matched male children, from an area of old Dhaka city, where battery-recycling shops are located, depending on their blood lead concentration. If the children had a plasma lead concentration above the WHO recommended threshold level of 10 µg/dl, we grouped them as test subjects and others as control subjects to determine the effect of lead on different biochemical parameters of the body. Compared to the controls, acculumlation of the lipid peroxidation product, malondialdehyde, increased significantly in test subjects ( p < 0.01). Lead exposure also increased the protein carbonyl content ( p < 0.05) and significantly decreased the plasma glutathione levels of test subjects compared to the controls ( p < 0.05). While comparing the lead-exposed group against controls, it was found that the percentage of damaged DNA, as measured using the Comet assay, significantly increased in tail ( p < 0.01) and decreased in head regions. All of these results suggest that high-plasma lead content may induce an oxidative stress to the study population, which may lead to DNA damage.
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Affiliation(s)
- Mohammad Arif
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Mm Towhidul Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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Islam MT, Sarkar SK, Sultana N, Begum MN, Bhuyan GS, Talukder S, Muraduzzaman AKM, Alauddin M, Islam MS, Biswas PP, Biswas A, Qadri SK, Shirin T, Banu B, Sadya S, Hussain M, Sarwardi G, Khan WA, Mannan MA, Shekhar HU, Chowdhury EK, Sajib AA, Akhteruzzaman S, Qadri SS, Qadri F, Mannoor K. High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh. BMC Genet 2018; 19:1. [PMID: 29295702 PMCID: PMC5751541 DOI: 10.1186/s12863-017-0594-3] [Citation(s) in RCA: 17] [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: 09/19/2017] [Accepted: 12/22/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh. RESULTS Our HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result. CONCLUSIONS Targeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and electrophortic indices in order to avoid false positive and false negative results.
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Affiliation(s)
- Md Tarikul Islam
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Suprovath Kumar Sarkar
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Nusrat Sultana
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Mst Noorjahan Begum
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Golam Sarower Bhuyan
- Infectious Diseases Laboratory, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Shezote Talukder
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - A K M Muraduzzaman
- Department of Virology, Institute of Epidemiology, Disease Control and Research, Mohakhali, Dhaka, Bangladesh
| | - Md Alauddin
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Mohammad Sazzadul Islam
- Infectious Diseases Laboratory, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Pritha Promita Biswas
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Aparna Biswas
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Syeda Kashfi Qadri
- Department of Paediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, Singapore
| | - Tahmina Shirin
- Department of Virology, Institute of Epidemiology, Disease Control and Research, Mohakhali, Dhaka, Bangladesh
| | - Bilquis Banu
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Salma Sadya
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Manzoor Hussain
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Golam Sarwardi
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Waqar Ahmed Khan
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammad Abdul Mannan
- Department of Neonatology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Syed Saleheen Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Firdausi Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.,Department of Enteric and Respiratory Infectious Diseases, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kaiissar Mannoor
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.
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Faisal ARM, Imtiaz SH, Zerin T, Rahman T, Shekhar HU. Computer aided epitope design as a peptide vaccine component against Lassa virus. Bioinformation 2017; 13:417-429. [PMID: 29379262 PMCID: PMC5767920 DOI: 10.6026/97320630013417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 11/26/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022] Open
Abstract
Lassa virus (LASV) is an arena virus causing hemorrhagic fever and it is endemic in several regions of West Africa. The disease-causing
virus records high mortality rate in endemic regions due to lack of appropriate treatment and prevention strategies. Therefore, it is of
interest to design and develop viable vaccine components against the virus. We used the Lassa virus envelope glyco-proteins as a
vaccine target to identify linear peptides as potential epitopes with immunogenic properties by computer aided epitope prediction
tools. We report a T-cell epitope 'LLGTFTWTL' and a B-cell epitope 'AELKCFGNTAVAKCNE' with predicted potential
immunogenicity for further in vivo and in vitro consideration.
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Affiliation(s)
- Ar-Rafi Md Faisal
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Syed Hassan Imtiaz
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Tasnim Zerin
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Tania Rahman
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Karim MF, Ismail M, Hasan AKMM, Shekhar HU. Hematological and biochemical status of Beta-thalassemia major patients in Bangladesh: A comparative analysis. Int J Hematol Oncol Stem Cell Res 2016; 10:7-12. [PMID: 27047645 PMCID: PMC4818791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Thalassemia is one of the most common hereditary disorders and Beta-thalassemia major is its severe form. The present study is concerned with the analysis of liver function, thyroid function and estimation of critical serum ions as well as hematological characteristics in beta-thalassemia patients and controls. SUBJECTS AND METHODS The study included 54 patients with beta-thalassemia major and 54 healthy individuals matched by sex and age. The activity of Alanine transaminase (ALT), Alkaline phosphatase (ALP) and Aspartate transaminase (AST) were assessed in order to evaluate the liver function. Serum content of iron (Fe), calcium (Ca), magnesium (Mg), sodium (Na) and potassium (K) were also estimated. Tri iodothyronine (T3), Thyroxin (T4) and Thyroid-stimulating hormone (TSH) levels were assessed in order to evaluate the thyroid function. Hemoglobin (Hb), ferritin, hematocrit (HCT), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration(MCHC), total iron binding capacity (TIBC) and creatinine level were also measured. RESULTS Significantly, higher ALT (P< 0.001), AST (P< 0.05), ALP (P< 0.001) activities and lower creatinine (P< 0.001) level in beta-thalassemia patients were found in comparison to healthy individuals. Lower serum level of calcium (P< 0.05), magnesium (P< 0.05) and higher level of iron (P> 0.05), sodium (P> 0.05) and potassium (P > 0.05) have been found in patients in comparison to healthy individuals. Hematological parameters like Hb (P< 0.001), ferritin (P< 0.05), HCT (P< 0.001), MCV (P< 0.05) and MCH (P< 0.05) have been significantly reduced in patients except MCHC (P> 0.05). No significant difference was observed in thyroid function between patients and control group. CONCLUSIONS Our study demonstrates that beta-thalassemia patients and controls have difference in liver function, thyroid function, serum contents of ions and hematological characteristics.
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Islam JMM, Ismail M, Islam MR, Hossain MF, Shekhar HU. Boosting the Food Functionality (In Vivo and In Vitro) of Spirulina by Gamma Radiation: An Inspiring Approach. International Journal of Food Engineering 2015. [DOI: 10.1515/ijfe-2014-0342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Foods (natural or processed) containing known biologically active compounds, which supplies clinically established and well-documented health benefits, are termed as functional food. Study objectives were to boost food functionality of spirulina, to optimize the required radiation dose, and to test functionality of spirulina both in vitro and in vivo. For this purpose fat binding capacity, sugar binding capacity, hydration property, antioxidative property, total polyphenol content were assessed at different radiation doses. A total of 30 rats were divided into three groups to carry out in vivo experiments to validate the outcomes of in vitro experiments. Targeted physico-chemical properties of spirulina were increased at their maximum level at 15 kGy radiation dose. In vivo experiments validated the outcomes of in vitro experiments. Though gamma radiation improves food functionality of spirulina at various radiation doses, but the optimum dose is recommended as 15 kGy.
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Hossain MF, Ismail M, Tanu AR, Shekhar HU. Respiratory Burst Enzymes, Pro-Oxidants and Antioxidants Status in Bangladeshi Population with β-Thalassemia Major. N Am J Med Sci 2015; 7:253-8. [PMID: 26199921 PMCID: PMC4488991 DOI: 10.4103/1947-2714.159329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Oxidative stress is intimately associated with many diseases, including β-thalassemia. AIM The study was to estimate the status of respiratory burst enzymes, pro-oxidants, and antioxidants in β-thalassemia major patients in Bangladesh and to compare with apparently healthy individuals. MATERIALS AND METHODS A total of 49 subjects were recruited which included 25 patients (age range 5 to 40 years) with β-thalassemia major and 24 controls (age and sex matched). Superoxide dismutase (SOD) and catalase (CAT) represented respiratory burst enzymes; malondialdehyde (MDA), lipid hydroperoxide (LHP), and xanthine oxidase (XO) were measured as pro-oxidants; and glutathione S transferase (GST), vitamin C (Vit.C), and glutathione (GSH) were the measured antioxidants. RESULTS The activity of SOD was significantly (P < 0.001) increased by about 79% and the activity of CAT was significantly (P < 0.001) decreased by more than 34% in the blood of β-thalassemia major patients compared to the control group. The content of pro-oxidants such as MDA, LHP, and XO was significantly (P < 0.001) higher in patients by about 228%, 241.3% and 148.1% respectively compared to control group. The level of GSH and Vit.C were significantly (P = 0.000) decreased in patients by about 59% and 81% versus the healthy group, respectively; and GST activity was significantly (P < 0.001) declined by 44.25% in patients group. CONCLUSION β-thalassemia major patients demonstrate raised oxidative stress compared to healthy subjects.
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Affiliation(s)
- Md. Faruk Hossain
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Arifur Rahman Tanu
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Tanu AR, Ashraf MA, Hossain MF, Ismail M, Shekhar HU. Identification and validation of T-cell epitopes in outer membrane protein (OMP) of Salmonella typhi. Bioinformation 2014; 10:480-6. [PMID: 25258481 PMCID: PMC4166765 DOI: 10.6026/97320630010480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/04/2014] [Indexed: 11/23/2022] Open
Abstract
This study aims to design epitope-based peptides for the utility of vaccine development by targeting outer membrane protein F
(Omp F), because two available licensed vaccines, live oral Ty21a and injectable polysaccharide, are 50% to 80% protective with a
higher rate of side effects. Conventional vaccines take longer time for development and have less differentiation power between
vaccinated and infected cells. On the other hand, Peptide-based vaccines present few advantages over other vaccines, such as
stability of peptide, ease to manufacture, better storage, avoidance of infectious agents during manufacture, and different
molecules can be linked with peptides to enhance their immunogenicity. Omp F is highly conserved and facilitates attachment and
fusion of Salmonella typhi with host cells. Using various databases and tools, immune parameters of conserved sequences from Omp
F of different isolates of Salmonella typhi were tested to predict probable epitopes. Binding analysis of the peptides with MHC
molecules, epitopes conservancy, population coverage, and linear B cell epitope prediction were analyzed. Among all those
predicted peptides, ESYTDMAPY epitope interacted with six MHC alleles and it shows highest amount of interaction compared to
others. The cumulative population coverage for these epitopes as vaccine candidates was approximately 70%. Structural analysis
suggested that epitope ESYTDMAPY fitted well into the epitope-binding groove of HLA-C*12:03, as this HLA molecule was
common which interact with each and every predicted epitopes. So, this potential epitope may be linked with other molecules to
enhance its immunogenicity and used for vaccine development.
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Affiliation(s)
- Arifur Rahman Tanu
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Mohammad Arif Ashraf
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Faruk Hossain
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Ismail
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Shekhar HU. Comment on: oxidative stress and antioxidant status in beta-thalassemia heterozygotes. Rev Bras Hematol Hemoter 2014; 35:385-6. [PMID: 24478601 PMCID: PMC3905817 DOI: 10.5581/1516-8484.20130125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/05/2013] [Indexed: 11/27/2022] Open
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Uddin MM, Akteruzzaman S, Rahman T, Hasan AKMM, Shekhar HU. Pattern of β-Thalassemia and Other Haemoglobinopathies: A Cross-Sectional Study in Bangladesh. ISRN Hematol 2012; 2012:659191. [PMID: 22778980 PMCID: PMC3384890 DOI: 10.5402/2012/659191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/24/2012] [Indexed: 11/23/2022]
Abstract
Thalassemia and other structural haemoglobinopathies are the major erythrocyte formation disorder prevalent in certain parts of the world including Bangladesh. We investigated 600 cases of anaemic patients referred from various parts of the country for diagnosis and counselling during 3 months (April to June 2011) of time. The most common form of haemoglobin (Hb) formation disorder observed in 600 subjects studied was β-thalassemia minor (21.3%). Two other conditions, such as E-β-Thalassemia and HbE trait, were also fairly common (13.5 and 12.1%, resp.) in the total subjects studied. Other forms of haemoglobin formation disorders observed were HbE disease (9.2%), Hb D/S trait (0.7%), β-thalassemia major (0.5%), and δ-β-thalassemia (0.5%). The majority of the haemoglobinopathies belonged to neonatal to childhood period (0-15 years), followed by reproductive age group (16-45 years). Few old-age (46+ years) cases were also detected in course of clinical complications.
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Affiliation(s)
- M Mesbah Uddin
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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Ferdaus MZ, Hasan AKMM, Shekhar HU. Analysis of serum lipid profiles, metal ions and thyroid hormones levels abnormalities in beta-thalassaemic children of Bangladesh. J PAK MED ASSOC 2010; 60:360-364. [PMID: 20527607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
OBJECTIVE To assess the serum lipid profile of cardiovascular disease free male and female children with beta-thalassaemia. Levels of zinc, copper and magnesium in the serum were also determined along with the Thyroid profile. METHODS From January to December 2007, we enrolled 121 consecutive patients with beta-thalassaemia that visited The Thalassaemia Center at Dhaka Shishu (Children) Hospital, Bangladesh every month for routine examinations. Fasting blood lipid levels were measured in all participants. Zinc, Copper and Magnesium levels in serums were determined. Thyroid function was also assessed by evaluating T3, T4 and TSH levels. RESULTS Of the 121 patients, 65 were males (10.14 +/- 3.91 years) and 56 were females (9.08 +/- 4.32 years). Data analysis revealed that 2.0% males and 4.35% females had high total serum cholesterol, and 28.57% males and 21.74% females had high triglyceride levels. In addition, mean HDL-cholesterol levels were 21.14 +/- 5.82 mg/dl in males and 21.17 +/- 6.02 mg/dl in females; total-cholesterol to HDL-cholesterol ratios were 5.47 +/- 1.66 and 5.96 +/- 2.81 in males and females respectively. About 60% patients showed low serum level of Zn and Cu. Hypothyroidism was detected in 30% patients and 23% patients had abnormal experimental values of all the study parameters. CONCLUSIONS The majority of the patients had blood lipid levels (by the exception of HDL-cholesterol) within the normal range, and consequently the prevalence of lipid abnormalities was much lower as compared to the general population of the same age. Interestingly, the total-cholesterol to HDL-cholesterol ratio was high in our patients, and may underline the importance of this index for the prognosis of future cardiac events in these patients. The serum Zn and Cu levels were low in most of the patients which may cause some metabolic abnormalities in future. Most of the patients also showed hypothyroidism indicating the presence of endocrine complications.
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Ichimura T, Kubota H, Goma T, Mizushima N, Ohsumi Y, Iwago M, Kakiuchi K, Shekhar HU, Shinkawa T, Taoka M, Ito T, Isobe T. Transcriptomic and Proteomic Analysis of a 14-3-3 Gene-Deficient Yeast. Biochemistry 2004; 43:6149-58. [PMID: 15147199 DOI: 10.1021/bi035421i] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BMH1 and BMH2 encode Saccharomyces cerevisiae 14-3-3 homologues whose exact functions have remained unclear. The present work compares the transcriptomic and proteomic profiles of the wild type and a BMH1/2-deficient S. cerevisiae mutant (bmhDelta) using DNA microarrays and two-dimensional polyacrylamide gel electrophoresis. It is reported here that, although the global patterns of gene and protein expression are very similar between the two types of yeast cells, a subset of genes and proteins (a total of 220 genes) is significantly induced or reduced in the absence of Bmh1/2p. These genes include approximately 60 elements that could be linked to the reported phenotypes of the bmhDelta mutant (e.g., accumulation of glycogen and hypersensitivity to environmental stress) and/or could be the potential downstream targets of interacting partners of Bmh1/2p such as Msn2p and Rtg3p. Importantly, >30% of the identified genes (71 genes) were found to be associated with carbon (C) and nitrogen (N) metabolism and transport, thereby suggesting that Bmh1/2p may play a major role in the regulation of C/N-responsive cellular processes. This study presents the first comprehensive overview of the genes and proteins that are affected by the depletion of Bmh1/2p and extends the scope of knowledge of the regulatory roles of Bmh1/2p in S. cerevisiae.
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Affiliation(s)
- Tohru Ichimura
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan.
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Abstract
Two triterpenoids, phragmalin triacetate (1) and lupeol (2) were isolated from an ethyl acetate extract of the stem bark of Crataeva nurvala (Capparidaceae) by repeated chromatography over silica gel. The structures of these compounds were determined by spectroscopic analyses (UV, IR, 1H NMR, 13C NMR and EIMS). This is the first report of the systematic phytochemical investigation and the presence of these compounds 1 and 2 from this plant. Key words: Crataeva, Capparidaceae, Phragmalin triacetate and Lupeol. Â DOI = 10.3329/dujps.v7i1.1221 Dhaka Univ. J. Pharm. Sci. 7(1): 71-74, 2008 (June)
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