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Hossain MU, Ahammad I, Moniruzzaman M, Akter Lubna M, Bhattacharjee A, Mahmud Chowdhury Z, Ahmed I, Hosen MB, Biswas S, Chandra Das K, Keya CA, Salimullah M. Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database. Cancer Rep (Hoboken) 2023; 6:e1906. [PMID: 37867380 PMCID: PMC10728505 DOI: 10.1002/cnr2.1906] [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: 04/29/2023] [Revised: 08/29/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. AIM The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts. METHODS AND RESULTS A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers. CONCLUSION The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.
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Affiliation(s)
| | - Ishtiaque Ahammad
- Bioinformatics DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Md. Moniruzzaman
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | | | | | | | - Istiak Ahmed
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Billal Hosen
- Department of PharmacyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Shourov Biswas
- Department of Clinical OncologyBangabandhu Sheikh Mujib Medical UniversityDhakaBangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and MicrobiologyNorth South UniversityDhakaBangladesh
| | - Md. Salimullah
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
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2
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Hossain MU, Ferdous N, Reza MN, Ahammad I, Tiernan Z, Wang Y, O’Hanlon F, Wu Z, Sarker S, Mohiuddin AKM, Das KC, Keya CA, Salimullah M. Pathogen-driven gene expression patterns lead to a novel approach to the identification of common therapeutic targets. Sci Rep 2022; 12:21070. [PMID: 36473896 PMCID: PMC9726901 DOI: 10.1038/s41598-022-25102-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Developing a common medication strategy for disease control and management could be greatly beneficial. Investigating the differences between diseased and healthy states using differentially expressed genes aids in understanding disease pathophysiology and enables the exploration of protein-drug interactions. This study aimed to find the most common genes in diarrhea-causing bacteria such as Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Escherichia coli, Shigella dysenteriae (CESS) to find new drugs. Thus, differential gene expression datasets of CESS were screened through computational algorithms and programming. Subsequently, hub and common genes were prioritized from the analysis of extensive protein-protein interactions. Binding predictions were performed to identify the common potential therapeutic targets of CESS. We identified a total of 827 dysregulated genes that are highly linked to CESS. Notably, no common gene interaction was found among all CESS bacteria, but we identified 3 common genes in both Salmonella-Escherichia and Escherichia-Campylobacter infections. Later, out of 73 protein complexes, molecular simulations confirmed 5 therapeutic candidates from the CESS. We have developed a new pipeline for identifying therapeutic targets for a common medication strategy against CESS. However, further wet-lab validation is needed to confirm their effectiveness.
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Affiliation(s)
- Mohammad Uzzal Hossain
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK ,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Nadim Ferdous
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Mahjerin Nasrin Reza
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Zachary Tiernan
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK
| | - Yi Wang
- grid.4991.50000 0004 1936 8948Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, OX13QT UK
| | - Fergus O’Hanlon
- grid.4991.50000 0004 1936 8948Mathematical Institute, University of Oxford, Oxford, OX2 6GG UK
| | - Zijia Wu
- grid.4991.50000 0004 1936 8948Department of Chemistry, University of Oxford, Oxford, OX2 6GG UK
| | - Shishir Sarker
- grid.443016.40000 0004 4684 0582Department of Microbiology, Jagannath University, Dhaka, 1100 Bangladesh
| | - A. K. M. Mohiuddin
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, Ministry of Science and Technology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
| | - Chaman Ara Keya
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, Ministry of Science and Technology, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349 Bangladesh
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3
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Chowdhury ZM, Bhattacharjee A, Ahammad I, Hossain MU, Jaber AA, Rahman A, Dev PC, Salimullah M, Keya CA. Exploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae. PLoS One 2022; 17:e0272945. [PMID: 35980906 PMCID: PMC9387852 DOI: 10.1371/journal.pone.0272945] [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: 02/20/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae (S. pneumoniae), the major etiological agent of community-acquired pneumonia (CAP) contributes significantly to the global burden of infectious diseases which is getting resistant day by day. Nearly 30% of the S. pneumoniae genomes encode hypothetical proteins (HPs), and better understandings of these HPs in virulence and pathogenicity plausibly decipher new treatments. Some of the HPs are present across many Streptococcus species, systematic assessment of these unexplored HPs will disclose prospective drug targets. In this study, through a stringent bioinformatics analysis of the core genome and proteome of S. pneumoniae PCS8235, we identified and analyzed 28 HPs that are common in many Streptococcus species and might have a potential role in the virulence or pathogenesis of the bacteria. Functional annotations of the proteins were conducted based on the physicochemical properties, subcellular localization, virulence prediction, protein-protein interactions, and identification of essential genes, to find potentially druggable proteins among 28 HPs. The majority of the HPs are involved in bacterial transcription and translation. Besides, some of them were homologs of enzymes, binding proteins, transporters, and regulators. Protein-protein interactions revealed HP PCS8235_RS05845 made the highest interactions with other HPs and also has TRP structural motif along with virulent and pathogenic properties indicating it has critical cellular functions and might go under unconventional protein secretions. The second highest interacting protein HP PCS8235_RS02595 interacts with the Regulator of chromosomal segregation (RocS) which participates in chromosome segregation and nucleoid protection in S. pneumoniae. In this interacting network, 54% of protein members have virulent properties and 40% contain pathogenic properties. Among them, most of these proteins circulate in the cytoplasmic area and have hydrophilic properties. Finally, molecular docking and dynamics simulation demonstrated that the antimalarial drug Artenimol can act as a drug repurposing candidate against HP PCS8235_RS 04650 of S. pneumoniae. Hence, the present study could aid in drugs against S. pneumoniae.
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Affiliation(s)
| | | | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Abdullah All Jaber
- Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
| | - Anisur Rahman
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
- * E-mail:
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Shaha M, Salimullah M. Intra-genotypic Recombination and Polymorphisms of Hepatitis B Virus Genome Circulating in Bangladesh. Int J Infect Dis 2022. [DOI: 10.1016/j.ijid.2021.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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5
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Sultana S, Khan MN, Hossain MS, Dai J, Rahman MS, Salimullah M. Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis. Front Microbiol 2022; 13:856014. [PMID: 35295300 PMCID: PMC8918984 DOI: 10.3389/fmicb.2022.856014] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/08/2022] [Indexed: 12/03/2022] Open
Abstract
The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.
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Affiliation(s)
- Shirin Sultana
- Aquatic Animal Health Group, Department of Fisheries, University of Dhaka, Dhaka, Bangladesh
- Fisheries Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Md. Nasir Khan
- Fisheries Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Jingcheng Dai
- School of Life Sciences and Technology, Wuhan Polytechnique University, Wuhan, China
| | - Mohammad Shamsur Rahman
- Aquatic Animal Health Group, Department of Fisheries, University of Dhaka, Dhaka, Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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Khatun M, Borphukan B, Alam I, Keya CA, Panditi V, Khan H, Huq S, Reddy MK, Salimullah M. Mitochondria-Targeted SmsHSP24.1 Overexpression Stimulates Early Seedling Vigor and Stress Tolerance by Multi-Pathway Transcriptome-Reprogramming. Front Plant Sci 2021; 12:741898. [PMID: 34887885 PMCID: PMC8649800 DOI: 10.3389/fpls.2021.741898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Among the diverse array of heat shock proteins across the three domains of life, mitochondria-targeted small heat shock proteins (sHSPs) are evolved in the plant lineage. However, they remained mysterious and understudied. In this study, we reported a systematic study of a novel mitochondria-targeted nuclear sHSP from eggplant (Solanum melongena L.; SmsHSP24.1). Differential expression of SmsHSP24.1 indicated its positive role exerted during stress conditions. Escherichia coli-BL21 cell line overexpressing the SmsHSP24.1 showed excellent thermo-tolerance ability, tolerating up to 52°C. Spectrometry and electron microscopy revealed a multimeric structure of the protein which acted as a molecular chaperone at high temperatures. Overexpression of SmsHSP24.1 significantly enhanced resistance against heat, drought, and salt stresses and showed rapid germination in constitutively overexpressed eggplant lines. RNA-seq analysis reveals an apparent upregulation of a set of reactive oxygen species (ROS) scavenging enzymes of the glutathione (GHS) pathway and mitochondrial electron transport chain (ETC). Significant upregulation was also observed in auxin biosynthesis and cell-wall remodeling transcripts in overexpressed lines. qPCR, biochemical and physiological analysis further aligned with the finding of transcriptome analysis and suggested an essential role of SmsHSP24.1 under various stress responses and positive physiological influence on the growth of eggplants. Therefore, this gene has immense potential in engineering stress-resilient crop plants.
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Affiliation(s)
- Muslima Khatun
- Plant Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Bhabesh Borphukan
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Iftekhar Alam
- Plant Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Varakumar Panditi
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Haseena Khan
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Saaimatul Huq
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Malireddy K. Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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7
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Ahammad I, Hossain MU, Rahman A, Chowdhury ZM, Bhattacharjee A, Das KC, Keya CA, Salimullah M. Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. PLoS One 2021; 16:e0258019. [PMID: 34587212 PMCID: PMC8480844 DOI: 10.1371/journal.pone.0258019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022] Open
Abstract
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Anisur Rahman
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | | | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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8
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Rahman M, Islam MA, Das KC, Salimullah M, Mollah MZI, Khan RA. Effect of gamma radiation on microbial load, physico-chemical and sensory characteristics of common spices for storage. J Food Sci Technol 2021; 58:3579-3588. [PMID: 34366475 PMCID: PMC8292502 DOI: 10.1007/s13197-021-05087-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022]
Abstract
The effect of gamma radiation on the decontamination of microbial population, physico-chemical, radiation sensitivity and sensory characteristics of common spices for storage were evaluated. Spices were irradiated with gamma doses of 0 (as control), 2, 4, 6, 8 and 10 kGy, packed in the glass vials and stored at room temperature (22 ± 2°C) in the laboratory. In this research, Bacillus, Salmonella and Listeria species were identified in un-irradiated spice samples. Results also indicated that gamma radiation reduced the total microbial population compared to control and optimum gamma radiation doses (6 kGy for red chili and turmeric; 4 kGy for cumin, coriander, garlic and black pepper; 2 kGy for ginger powder samples) were identified for decontamination of the organisms in the studied spices. It was concluded that no significant differences before and after gamma radiation were observed in physico-chemical, nutritional and sensory properties but significantly changed in microbial load in spices samples.
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Affiliation(s)
- Mahfuzur Rahman
- Department of Nuclear Science & Engineering, Military Institute of Science and Technology, Dhaka, 1216 Bangladesh
| | - M. A. Islam
- Institute of Nuclear Science & Technology, Atomic Energy Research Establishment, Savar, Dhaka, 1349 Bangladesh
| | - Keshob C. Das
- National Institute of Biotechnology, Savar, Dhaka, 1349 Bangladesh
| | - Md. Salimullah
- National Institute of Biotechnology, Savar, Dhaka, 1349 Bangladesh
| | - M. Z. I. Mollah
- Institute of Radiation and Polymer Technology, Atomic Energy Research Establishment, Savar, Dhaka, 1349 Bangladesh
| | - Ruhul A. Khan
- Institute of Radiation and Polymer Technology, Atomic Energy Research Establishment, Savar, Dhaka, 1349 Bangladesh
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Jahan M, Bhattacharjee A, Rahmat R, Islam SMR, Akhter T, Ahammad I, Hossain MU, Munshi SU, Salimullah M. Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh. Microbiol Resour Announc 2021; 10:e0049621. [PMID: 34292071 PMCID: PMC8297457 DOI: 10.1128/mra.00496-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/15/2021] [Indexed: 11/30/2022] Open
Abstract
Mutations, deletions, and the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may pose a serious health threat. Here, we report the genome sequences of SARS-CoV-2 viruses that were collected from SARS-CoV-2-infected patients during the end phase of the first wave of the COVID-19 pandemic in Dhaka, Bangladesh.
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Affiliation(s)
- Munira Jahan
- Department of Virology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Raad Rahmat
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Mohakhali, Dhaka, Bangladesh
| | - S. M. Rashedul Islam
- Department of Virology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Tahmina Akhter
- Department of Virology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Saif Ullah Munshi
- Department of Virology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - M. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
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10
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Hossain MU, Ahammad I, Bhattacharjee A, Chowdhury ZM, Hossain Emon MT, Chandra Das K, Keya CA, Salimullah M. Whole genome sequencing for revealing the point mutations of SARS-CoV-2 genome in Bangladeshi isolates and their structural effects on viral proteins. RSC Adv 2021; 11:38868-38879. [PMID: 35493250 PMCID: PMC9044322 DOI: 10.1039/d1ra05327b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/11/2021] [Accepted: 10/30/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 mutational impact analysis.
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Affiliation(s)
- Mohammad Uzzal Hossain
- Department of Pharmacology, University of Oxford, Oxford OX1 3PT, UK
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Md. Tabassum Hossain Emon
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
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11
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Moniruzzaman M, Ahmed I, Huq S, All Mahmud MS, Begum S, Mahzabin Amin U, Rahman MH, Sarker PK, Hossain MU, Das KC, Salimullah M. Association of polymorphism in heat shock protein 70 genes with type 2 diabetes in Bangladeshi population. Mol Genet Genomic Med 2020; 8:e1073. [PMID: 31816668 PMCID: PMC7005638 DOI: 10.1002/mgg3.1073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/18/2019] [Revised: 09/12/2019] [Accepted: 11/14/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a chronic disorder of which stress is a major contributor. Under stressful condition, body synthesizes a family of molecular chaperone called Heat-shock proteins (HSPs). Current study assessed the frequency and association of HSP70-hom + 2,437 T/C polymorphism with T2DM risk among Bangladeshis. METHODS This polymorphism was selected through bioinformatics analyses and identified by PCR-RFLP method. RESULTS Bioinformatics analysis identified this SNP as missense mutation which could destabilize the final HSP product. Heterozygous mutant (CT) genotype was significantly associated with T2DM incidence among the studied populations (p = .015). Further analysis revealed a strong association with female patients (p = .002), while the male group showed no association (p = .958). Moreover, the C allele was significantly associated among all diabetic patients (p = .016) and particularly in the female patient group (p = .001). However, under stressful condition, males with CT genotype were at high risk for T2DM incidence whereas, females with CT genotype showed no significant association. CONCLUSIONS HSP70-hom + 2,437 T/C polymorphism was found to be significantly associated with T2DM incidence in the Bangladeshi population in both stress-dependent and independent manners.
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Affiliation(s)
- Md. Moniruzzaman
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Irfan Ahmed
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Saaimatul Huq
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | | | - Sonya Begum
- Department of Biotechnology and Genetic engineeringMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - U.S. Mahzabin Amin
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Md. Hadisur Rahman
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Palash Kumar Sarker
- Microbial Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | | | - Keshob Chandra Das
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
| | - Md. Salimullah
- Molecular Biotechnology DivisionNational Institute of BiotechnologyDhakaBangladesh
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Alim M, Hossain M, Nusrat J, Rubaya, Salimullah M, Shu-Hong Z, Alam J. Genetic effects of leptin receptor (LEPR) polymorphism on litter size in a Black Bengal goat population. ANIM BIOL 2019. [DOI: 10.1163/15707563-00001079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The leptin receptor (LEPR) is involved in central signaling for both energy homeostasis and reproduction. The present study investigates the association of the LEPR gene with the prolificacy of Black Bengal goat. Two single nucleotide polymorphisms (SNPs) in intron 3 and one SNP in exon 4 in the LEPR gene were identified by pooled DNA sequencing. The identified SNPs were genotyped by the direct sequencing method from 84 Black Bengal does. A synonymous mutation (Lysine > Lysine) was found as a polymorphism in exon 4. The effects of the different genotypes on litter size traits were estimated using linear models. Our results show that goats with heterozygous genotype AG at the loci g.104911A>G and g.105151A>G showed the highest prolificacy performance when compared with the other, homozygous genotypes. Dominance and additive effects were observed at the considered loci. No significant allele substitution effects were found for any locus. Our results indicate preliminarily that LEPR may have some association with prolificacy and could be a candidate gene to improve the prolificacy in goat.
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Affiliation(s)
- M.A. Alim
- 1Animal Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - M.M.K. Hossain
- 1Animal Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - J. Nusrat
- 1Animal Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Rubaya
- 1Animal Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - M. Salimullah
- 2Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Z. Shu-Hong
- 3College of Animal Science and Technology, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jahangir Alam
- 1Animal Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
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Hossain MU, Omar TM, Alam I, Das KC, Mohiuddin AKM, Keya CA, Salimullah M. Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset. PLoS One 2018; 13:e0198170. [PMID: 29883471 PMCID: PMC5993290 DOI: 10.1371/journal.pone.0198170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 05/10/2017] [Accepted: 05/15/2018] [Indexed: 11/19/2022] Open
Abstract
The bacterial species Campylobacter jejuni RM1221 (CjR) is the primary cause of campylobacteriosis which poses a global threat for human health. Over the years the efficacy of antibiotic treatment is becoming more fruitless due to the development of multiple drug resistant strains. Therefore, identification of new drug targets is a valuable tool for the development of new treatments for affected patients and can be obtained by targeting essential protein(s) of CjR. We conducted this in silico study in order to identify therapeutic targets by subtractive CjR proteome analysis. The most important proteins of the CjR proteome, which includes chokepoint enzymes, plasmid, virulence and antibiotic resistant proteins were annotated and subjected to subtractive analyses to filter out the CjR essential proteins from duplicate or human homologous proteins. Through the subtractive and characterization analysis we have identified 38 eligible therapeutic targets including 1 potential vaccine target. Also, 12 potential targets were found in interactive network, 5 targets to be dealt with FDA approved drugs and one pathway as potential pathway based drug target. In addition, a comprehensive database 'CampyNIBase' has also been developed. Besides the results of this study, the database is enriched with other information such as 3D models of the identified targets, experimental structures and Expressed Sequence Tag (EST) sequences. This study, including the database might be exploited for future research and the identification of effective therapeutics against campylobacteriosis. URL: (http://nib.portal.gov.bd/site/page/4516e965-8935-4129-8c3f-df95e754c562#Banner).
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Affiliation(s)
- Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Taimur Md. Omar
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Iftekhar Alam
- Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - A. K. M. Mohiuddin
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North south University, Bashundhara, Dhaka, Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
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Barman NC, Zohora FT, Das KC, Mowla MG, Banu NA, Salimullah M, Hashem A. Production, partial optimization and characterization of keratinase enzyme by Arthrobacter sp. NFH5 isolated from soil samples. AMB Express 2017; 7:181. [PMID: 28936604 PMCID: PMC5608654 DOI: 10.1186/s13568-017-0462-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 01/21/2017] [Accepted: 08/01/2017] [Indexed: 01/11/2023] Open
Abstract
The study was conducted to select the best promising keratinolytic bacterial strain. A good keratinase positive bacterium isolated from the soil samples of Hazaribagh tannery industrial zone, Dhaka was identified as Arthrobacter genus depending on the conventional techniques and confirmed as Arthrobacter sp. by sequencing 16S rRNA gene. The medium components and culture conditions were optimized to enhance keratinase production through shake flask culture. Keratin and feather powder (10 g/l or 1%) were good substrates for the highest keratinase production along with yeast extract (0.2 g/l or 0.02%) as an organic nitrogen source and potassium nitrate (1 g or 0.1%) as an inorganic nitrogen source. Maximum yield of keratinase was found after 24 h of incubation at 37 °C with an initial pH of 7.0 and inoculums volume 5% under 150 rpm when keratin, yeast extract and potassium nitrate were used as nutrient sources. Keratinase production was more than 5.0-fold increased when all optimized parameters were applied simultaneously. The optimum reaction temperature and pH were determined to be 40 °C and 8.0 respectively for crude keratinase activity. Therefore, Arthrobacter sp. NFH5 might be used for large scale production of keratinase for industrial purposes in less time.
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Kinoshita Y, Tayama T, Kitamura K, Salimullah M, Uchida H, Suzuki M, Husimi Y, Nishigaki K. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer. BMC Biotechnol 2010; 10:71. [PMID: 20923572 PMCID: PMC2959086 DOI: 10.1186/1472-6750-10-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 03/01/2010] [Accepted: 10/06/2010] [Indexed: 11/15/2022] Open
Abstract
Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
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Affiliation(s)
- Yasunori Kinoshita
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
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Zaid RB, Nargis M, Neelotpol S, Sayeed MA, Banu A, Shurovi S, Hassan KN, Salimullah M, Ali L, Azad Khan AK. Importance of Acetylator Phenotype in the Identity of Asian Populations. Hum Biol 2007; 79:363-8. [DOI: 10.1353/hub.2007.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Salimullah M, Mori M, Nishigaki K. High-throughput three-dimensional gel electrophoresis for versatile utilities: a stacked slice-gel system for separation and reactions (4SR). Genomics Proteomics Bioinformatics 2006; 4:26-33. [PMID: 16689699 PMCID: PMC5054028 DOI: 10.1016/s1672-0229(06)60013-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A novel high-throughput system, called the stacked slice-gel system for separation and reactions (4SR), was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional (m × n) sample loading system. For this purpose, high-throughput multi-micro vessels (MMVs) containing variable numbers of wells (100 wells in this paper) have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.
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Affiliation(s)
- Md. Salimullah
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
| | - Masaki Mori
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
- Rational Evolutionary Design of Advanced Biomolecules (REDS) Group, Saitama Small Enterprise Promotion Corporation, SKIP City, Kawaguchi 333-0844, Japan
- Corresponding author.
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Salimullah M, Rizwan AM, Nambu M, Nitta H, Shukla PK. Dust-lower-hybrid drift instabilities with dust charge fluctuations in an inhomogeneous dusty magnetoplasma. Phys Rev E 2004; 70:026404. [PMID: 15447598 DOI: 10.1103/physreve.70.026404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Indexed: 11/07/2022]
Abstract
Effects of a uniform magnetic field, the plasma inhomogeneity, and dust charge fluctuations on low-frequency dust-lower-hybrid drift waves have been investigated. Charging currents of electrons and ions to a spherical dust grain in a nonuniform magnetized dusty plasma have been calculated to study the charge fluctuation induced damping or growth of low-frequency drift waves. It is found that for strongly magnetized electrons and ions, the charge fluctuation damping is reduced significantly from that of an unmagnetized plasma. For sufficiently hot electrons, the drift wave exhibits instability in the absence of dust charge fluctuation damping.
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Affiliation(s)
- M Salimullah
- Department of Physics, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh.
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Hasanat MA, Rumi MAK, Alam MN, Ahmed S, Hasan KN, Khan AYMH, Salimullah M, Mahtab H, Khan AKA. Urinary iodine status and thyroid dysfunction: a Bangladesh perspective. Bangladesh Med Res Counc Bull 2004; 30:16-24. [PMID: 15376465] [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] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Iodine deficiency is endemic in Bangladesh. Compulsory iodization of table salt was introduced since 1993 to prevent and improve thyroid disorders in the country. Urinary iodine status, thyroid function and antithyroid antibodies were studied in 397 newly diagnosed thyroid patients and 94 age-sex matched controls. Among thyroid patients, 96 were hyperthyroid, 185 euthyroid and 116 hypothyroid. Mean and median urinary iodine were higher (p=0.075) in thyroid patients (26.13+/-0.91 and 23.03) than controls (22.65+/-1.47 and 18.59); in hyperthyroid and euthyroid than hypothyroid (p=0.020); in multinodular (28.08+/-2.80 and 26.94) and diffuse (27.35+/-1.19 and 26.71) goitre than uninodular (23.91+/-2.37 and 19.14) and nongoitrous (NG, 21.5+/-2.05 and 18.27) (p=0.098) patients but no sex difference (p=0.466). Antimicrosomal (26.7%) and antithyroglobulin (34%) antibodies were more frequently positive among thyroid patients than controls (6.4% and 12.8% respectively) (p=0.00002 and p=0.00005 respectively). Antibody positivity was higher in diffuse (82/228) and multinodular (20/47) goitre than nongoitrous (20/56) and uninodular (13/66) goitre (p=0.046) as well as in hypothyroid (55.2%) and hyperthyroid (36.5%) than euthyroid (19.5%) patients (P<0.001). Urinary iodine correlated neither with antimicrosomal (thyroid patients: p=0.597 and control: p=0.112) nor with antithyroglobulin (thyroid patients: p=0.388 and control: p=0.195) antibody. Thyroid autoimmunity and dysfunction seems common; and interaction of salt iodization with iodine status and thyroid disorders may be important in Bangladesh.
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Affiliation(s)
- M A Hasanat
- Deptt of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka
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20
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Salimullah M, Sandberg I, Shukla PK. Dust charge fluctuations in a magnetized dusty plasma. Phys Rev E Stat Nonlin Soft Matter Phys 2003; 68:027403. [PMID: 14525157 DOI: 10.1103/physreve.68.027403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2002] [Revised: 05/16/2003] [Indexed: 05/24/2023]
Abstract
Charging currents of electrons and ions to a spherical dust grain in a uniform magnetized dusty plasma have been examined. It is found that the external magnetic field reduces the charging currents, thereby decreasing the dust charge fluctuation damping of a low-frequency electrostatic wave in a dusty plasma.
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Affiliation(s)
- M Salimullah
- Institut für Theoretische Physik IV, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany.
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21
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Parvez MAK, Hasan KN, Rumi MAK, Ahmed S, Salimullah M, Tahera Y, Gomes DJ, Huq F, Hassan MS. PCR can help early diagnosis of pulmonary tuberculosis. Southeast Asian J Trop Med Public Health 2003; 34:147-53. [PMID: 12971527] [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] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
One hundred and fifty-one patients, clinically suspected for pulmonary tuberculosis (age: 31 +/- 13 years, male/female: 112/39), were investigated to evaluate the diagnostic potential of polymerase chain reaction (PCR) based detection of the Mycobacterium tuberculosis complex in sputum. The diagnostic efficacy of PCR was compared with culture of Mycobacterium tuberculosis on egg-based Lowenstein-Jensen modified medium. PCR detected 71.5% (108/151), whereas culture detected 66.2% (100/151) of the clinically suspected patients. There was a significant association between the results of PCR and culture (chi2 = 59.524, p < 0.001). However, 23.2% (35/151) samples were found negative in both culture and PCR. Considering culture as the gold standard, the sensitivity of the PCR was 92%. and its specificity 70%. This lower apparent specificity may be due to the higher sensitivity of PCR.
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Affiliation(s)
- M A K Parvez
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), Dhaka, Bangladesh
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Aziz MM, Hasan KN, Hasanat MA, Siddiqui MA, Salimullah M, Chowdhury AK, Ahmed M, Alam MN, Hassan MS. Predominance of the DEN-3 genotype during the recent dengue outbreak in Bangladesh. Southeast Asian J Trop Med Public Health 2002; 33:42-8. [PMID: 12118459] [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] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
A recent outbreak of dengue in Bangladesh was marked by many fatal complications. As clinical virulence varies among the genotypes of dengue virus, a study was conducted to investigate the molecular genotypes of dengue in Bangladesh. Reverse transcription polymerase chain reaction was used to determine viral genotypes using oligonucleotide generic primers that produce a 511 bp product. The resulting product was typed by nested PCR with strain-specific primers, yielding 482 (DEN-1), 119 (DEN-2), 290 (DEN-3) and 392 (DEN-4), visualized on UV transilluminator after electrophoresis on 2% agarose gel stained with ethidium bromide. Of 45 clinically diagnosed dengue patients (mean age 28 years; male/female 30/15), 19 (42.2%) had detectable viral RNA in their blood. However, during the first 5 days of fever in 30 patients, the frequency was 60% (18/30), implying that the sooner serum is drawn after the fever, the greater the chances of detecting viral RNA. DEN-3 was detected in all except 2 patients who were infected with DEN-2. DEN-2 (two cases) and DEN-4 (one case) were present as co-infections with DEN-3. All of the patients presented with fever, anorexia and vomiting; many had headache and general body ache; a few had a rash. About a quarter had suffered episodes of bleeding, while ascites, pleural effusion and CNS symptoms were found in a few patients Patients positive for viral RNA were also positive for anti-dengue IgM (p=0.007) in subsequent sampling. The study suggests the predominance of DEN-3 infection with occasional co-infection with other types, during the recent outbreak of dengue in Bangladesh.
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Affiliation(s)
- M M Aziz
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders BIRDEM, Dhaka
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Nambu M, Salimullah M, Bingham R. Effect of a magnetic field on the wake potential in a dusty plasma with streaming ions. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 63:056403. [PMID: 11415015 DOI: 10.1103/physreve.63.056403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2000] [Indexed: 05/23/2023]
Abstract
The wake potential of a test dust particulate due to an ion cyclotron wave in a dusty plasma with streaming ions is calculated. The role of the external magnetic field on the periodic attractive forces is clarified. The amplitude of wake potential is reduced because the overshielding by streaming ions is inhibited in the presence of the external magnetic field.
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Affiliation(s)
- M Nambu
- Tokyo Metropolitan Institute of Technology, Asahigaoka, Hino, Tokyo 191-0065, Japan
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Sayeed MA, Hassan MS, Hasan KN, Parvez MA, Khan AY, Salimullah M, Khanam PA, Mahtab H, Khan AK. Genetic background of diabetic and nondiabetic sibs in young Bangladeshis. Bangladesh Med Res Counc Bull 2000; 26:69-74. [PMID: 11766001] [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] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The prevalence of diabetes mellitus in the young is higher in Bangladesh like other Asian developing nations. Albeit, undernutrition has been shown to be associated with diabetes in the young, not all such individuals are diabetic. Diabetes Mellitus is a multigenic disease. In IDDM, DR3/4 heterozygotes were shown to have a greatly increased risk of developing the disease, suggesting the concept of genetic factor(s) being involved in the development of diabetes. Therefore, this study was undertaken to determine the distribution of HLA class II alleles (DRB) and to identify the HLA associated risk for developing diabetes mellitus in the young Bangladeshis. A total of fifty individuals were investigated. Half of them (n=25) were diabetic patients, registered in BIRDEM and half the participants were their non-diabetic sibs. A genomic DNA PCR and Enzyme Linked Probe Hybridization Assay (ELPHA, Bio-test, Germany) was used to determine HLA class II alleles (DRB1, DRB 3, 4, 5) by in vitro amplification of DRB gene. Among all the sero-equivalent antigens found in the study subjects, the prevalence of DR15 (DR2) was overrepresented, both in the diabetic subjects and in their non-diabetic sibs. Moreover, compared with the non-diabetic group the diabetic patients showed higher frequency of DR15 alleles (39 and 25%) though the difference was not significant (chisq. 1.7, p>0.05). Next to DR15, DR4 was the most prevalent HLA-DRB gene found in the study population. Interestingly, the frequency of DR4 was higher in the diabetic than in the non-diabetic group (20 vs. 14%). The study showed that the DR15 and DR4 were the most prevalent in the study population. Moreover, DR7 though not very significant, was higher in non-diabetic compared to their diabetic sibs. Comparison between the diabetic and non-diabetic sibs could have been interesting and significant but we could not confirm our findings, possibly, due to small sample size. A study in a larger paired sample of unrelated population is also needed to substantiate our findings, and also to prove the susceptibility or resistant haplotype in the young diabetic subjects.
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Affiliation(s)
- M A Sayeed
- Research Division, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), Dhaka
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Abstract
To study autoimmunity among thyroid diseases, 397 thyroid patients (age 30 (13) years; M/F 75/322) from two referral centres in Bangladesh and 94 healthy controls (age 30 (13) years; M/F 24/70) were studied for antimicrosomal and antithyroglobulin antibodies. Thyroid patients were clinically grouped as suspected autoimmune thyroid disease (AITD), non-autoimmune, or indeterminate groups (where no decision could be reached). Antimicrosomal antibody was strongly positive in 19.4% and weakly positive in 7.3% of patients but only 4.3% and 2.1% respectively in the controls (chi(2) = 17.852; p = 0.000) whereas strong and weak positivity were 27.2% and 6. 8% in patients compared with 8.5% and 4.3% respectively in the controls (chi(2) = 16.916; p = 0.000) for antithyroglobulin antibody. Antibodies were positive in 63.0% with Hashimoto's thyroiditis, 36.4% with Graves' disease, and 44.7% with atrophic thyroiditis among the autoimmune group. In the non-autoimmune group antibodies were positive in 100% with multinodular hypothyroidism, 46.7% with subacute thyroiditis, 40.0% with suspected iodine deficiency goitre, 31.3% with toxic multinodular goitre, 30.8% with non-toxic solitary nodules, and 19.4% with simple diffuse goitre. None was positive for antimicrosomal antibody without being positive for antithyroglobulin antibody. The two antibodies strongly correlated in both patients (r = 0.977, p = 0.000) and controls (r = 0.986, p = 0.000). About 9% (36/397) of patients were mismatched with the final diagnosis on antibody measurement; most of them had Hashimoto's thyroiditis (33/36). Prevalence of AITD among thyroid patients was 48.36%. Specificity of antimicrosomal and antithyroglobulin antibodies were 93% and 87%. It was concluded that AITD is not uncommon in Bangladesh; antimicrosomal antibody is a useful marker for AITD and unless antibodies are checked, an appreciable number of patients with AITDs will remain undetected.
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Affiliation(s)
- M A Hasanat
- Endocrine Clinic, Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh.
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Salimullah M, Tahera Y, Siddiqui MA, Salam MA, Rumi MA, Huq F, Hassan MS. Prevalence of human immunodeficiency virus infection among tuberculosis cases in some clinics in Dhaka, Bangladesh. Trans R Soc Trop Med Hyg 2000; 94:276. [PMID: 10974997 DOI: 10.1016/s0035-9203(00)90319-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- M Salimullah
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), Dhaka, Bangladesh
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Ferdous T, Amin MR, Salimullah M. Modulational instability of beat waves in a transversely magnetized plasma: Ion effects. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1996; 53:5218-5227. [PMID: 9964855 DOI: 10.1103/physreve.53.5218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Amin MR, Ferdous T, Salimullah M. Decay instability of an electron plasma wave in a dusty plasma. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1996; 53:2740-2746. [PMID: 9964563 DOI: 10.1103/physreve.53.2740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ferdous T, Salahuddin M, Amin MR, Salimullah M. Stimulated Brillouin scattering of laser radiation in a compensated magnetoactive semiconductor. Phys Rev B Condens Matter 1995; 52:9044-9049. [PMID: 9979894 DOI: 10.1103/physrevb.52.9044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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30
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Salimullah M, Ferdousi T, Majid F. Stimulated Brillouin scattering of electromagnetic waves in magnetized semiconductor plasmas. Phys Rev B Condens Matter 1994; 50:14104-14111. [PMID: 9975627 DOI: 10.1103/physrevb.50.14104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Mamun AA, Salimullah M. Parametric excitation of Alfvén and helicon waves in a magnetoactive compensated semiconductor by microwave radiation. Phys Rev B Condens Matter 1991; 44:8685-8693. [PMID: 9998824 DOI: 10.1103/physrevb.44.8685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Salimullah M, Hassan MH. Relativistic stimulated Brillouin and Raman scattering in a laser-produced plasma. Phys Rev A 1990; 41:6963-6967. [PMID: 9903113 DOI: 10.1103/physreva.41.6963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Salimullah M, Alam MN. Harmonic generation of Alfvén and helicon waves in semiconductors. Phys Rev B Condens Matter 1989; 39:3771-3775. [PMID: 9948699 DOI: 10.1103/physrevb.39.3771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Banerjee AK, Alam MN, Salimullah M. Stimulated Brillouin scattering of Alfvén waves in compensated semiconductors. Phys Rev B Condens Matter 1988; 37:1180-1185. [PMID: 9944624 DOI: 10.1103/physrevb.37.1180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Salimullah M, Hossain MA, Alam MN, Salahuddin M. Filamentation instability of an Alfvén wave in a compensated semiconductor. Phys Rev B Condens Matter 1987; 35:2303-2307. [PMID: 9941680 DOI: 10.1103/physrevb.35.2303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Salimullah M. Decay instability of beat waves in a plasma. Phys Rev A Gen Phys 1986; 33:3537-3539. [PMID: 9897076 DOI: 10.1103/physreva.33.3537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Salimullah M, Liu YG, Haines MG. Filamentation instability of beat waves in a hot magnetized plasma. Phys Rev A Gen Phys 1985; 32:1852-1857. [PMID: 9896274 DOI: 10.1103/physreva.32.1852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Salimullah M, Liu YG. Filamentation instability of the electron plasma wave at the difference frequency of two laser beams in a plasma. Phys Rev A Gen Phys 1985; 31:4005-4007. [PMID: 9895996 DOI: 10.1103/physreva.31.4005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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