Genomics and Molecular Epidemiology Lab

Department of Biotechnology and Genetic Engineering Noakhali Science and technology University



An in-silico approach to design potential siRNAs against the ORF57 of Kaposi’s sarcoma-associated herpesvirus

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

COVID-19 in Bangladesh: An Exploratory Data Analysis and Prediction of Neurological Syndrome Using Machine Learning Algorithms Based on Comorbidity

COVID-19 is caused by the SARS-CoV-2 virus, which has infected millions of people worldwide and claimed many lives. This highly contagious virus can infect people of all ages, but the symptoms and fatality are higher in elderly and comorbid patients. Many COVID-19 survivors have experienced a number of clinical consequences following their recovery. In order to have better knowledge about the long-COVID effects, we focused on the immediate and post-COVID-19 consequences in healthy and comorbid individuals and developed a statistical model based on comorbidity in Bangladesh. The dataset was gathered through a phone conversation with patients who had been infected with COVID-19 and had recovered. The results demonstrated that out of 705 patients, 66.3% were comorbid individuals prior to COVID-19 infection. Exploratory data analysis showed that the clinical complications are higher in the comorbid patients following COVID-19 recovery. Comorbidity-based analysis of long-COVID neurological consequences was investigated and risk of mental confusion was predicted using a variety of machine learning algorithms. On the basis of the accuracy evaluation metrics, decision trees provide the most accurate prediction. The findings of the study revealed that individuals with comorbidity have a greater likelihood of experiencing mental confusion after COVID-19 recovery. Furthermore, this study is likely to assist individuals dealing with immediate and post-COVID-19 complications and its management.

In-silico analysis unravels the structural and functional consequences of non-synonymous SNPs in the human IL-10 gene

Background Interleukin-10 (IL-10) is an anti-inflammatory cytokine that affects different immune cells. It is also associated with the stimulation of the T and B cells for the production of antibodies. Several genetic polymorphisms in the IL-10 gene have been reported to cause or aggravate certain diseases like inflammatory bowel disease, rheumatoid arthritis, systemic sclerosis, asthma, etc. However, the disease susceptibility and abnormal function of the mutated IL-10 variants remain obscure. Results In this study, we used seven bioinformatics tools (SIFT, PROVEAN, PMut, PANTHER, PolyPhen-2, PHD-SNP, and SNPs&GO) to predict the disease susceptible non-synonymous SNPs (nsSNPs) of IL-10. Nine nsSNPs of IL-10 were predicted to be potentially deleterious: R42G, R45Q, F48L, E72G, M95T, A98D, R125S, Y155C, and I168T. Except two, all of the putative deleterious mutations are found in the highly conserved region of IL-10 protein structure, thus affecting the protein's stability. The 3-D structure of mutant proteins was modeled by project HOPE, and the protein–protein interactions were assessed with STRING. The predicted nsSNPs: R42Q, R45Q, F48L, E72G, and I168T are situated in the binding site region of the IL-10R1 receptor. Disruption of binding affinity with its receptor leads to deregulation of the JAK-STAT pathway and results in enhanced inflammation that imbalance in cellular signaling. Finally, Kaplan–Meier Plotter analysis displayed that deregulation of IL-10 expression affects gastric and ovarian cancer patients' survival rate. Thus, IL-10 could be useful as a potential prognostic marker gene for some cancers. Conclusion This study has determined the deleterious nsSNPs of IL-10 that might contribute to the malfunction of IL-10 protein and ultimately lead to the IL-10 associated diseases.

New Research Test

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