Projects

Project Outcome: I analyzed bulk RNA-seq data. I also learned dissection, cryosection, using fluorescent and confocal microscopes, histopathology, immunostaining, and in situ hybridization. 

Using cutting edge technologies we tried to observe the regional mutational alteration of SARS-CoV-2 in the southern region of Bangladesh. In this study, I performed total 58 whole genome sequences of SARS-CoV-2 strains isolated patients from Noakhali, a South-Eastern district in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in S, six in N, two in M, one in E protein and the S protein variation, Y204F, identified in two of our sequenced strains, has not been reported from any other countries in the GISAID database (https://doi.org/10.21203/rs.3.rs-437228/v1).  Later as a part of this project, I led a team for in-silico based research and we successfully completed two long projects. We explored deleterious mutations from SARS-CoV-2 variants for prophylactic vaccine development (https://doi.org/10.3389/fphar.2023.1090717) and also interestingly identified common deleterious mutation from death patients sequences (https://doi.org/10.1038/s41598-023-45517-1).

Founding Sources: We gratefully acknowledge the Board of Trustees of North South University for funding this project.

Determining and monitoring contagious infectious diseases like SARS-CoV-2 in developing countries is indeed challenging due to a complex interplay of resource limitations, inadequate infrastructure, and socio-economic factors. These difficulties hinder effective surveillance, hotspot identification, trend monitoring, and future predictions.  In this project, I proposed and developed a surveillance tool for infectious disease. Leveraging whole genome sequencing, RT-qPCR, and molecular techniques, we were the first to successfully detect SARS-CoV-2 genetic materials from wastewater in Bangladesh (10.1016/j.scitotenv.2021.145724). To observe the correlation of SARS-CoV-2 viral load in the wastewater with the clinical sample, I collected 30 days of wastewater from positive patients’ houses and observed 7450 to 23,000 gene copies/1000 mL where 47 % (57/120) positive samples from wastewater and 35 % (128/360) from clinical samples (10.1016/j.scitotenv.2022.159350). In addition, I extended this project on a large scale for major 14 districts from onsite sanitation ( https://doi.org/10.1016/j.envpol.2022.119679) and collaborated with over 200 experts in the Microbiology from around the world. The results from this project directly helped the government to predict hotspots, identify risky areas, and maintain lockdowns.

Founding Sources: This research was funded and supported by Water Aid Bangladesh, North South University, Dhaka, COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University (NSTU), Noakhali, Bangladesh, the International Training Network of Bangladesh University of Engineering and Technology (ITN-BUET) - Centre for Water Supply and Waste Management, and KTH Royal Institute of Technology, Sweden. 

To date, in Bangladesh, several studies have been conducted among the women of PROM and none of the studies has investigated the vaginal and urinary tract pathogens, which are allegedly known as major preventable risk factors for PROM. Hence, this study conducted to fill the knowledge gap by identifying the risk factors to be categorized as personal, behavioral, social, and pathophysiological as well as infections by common pathogens. The research team believes that this study will contribute to national knowledge for the prediction and prevention of PROM, thereby decreasing preventable maternal and neonatal mortality and morbidity. 

Founding Sources: This reseach is funded by Integrated Health Science Research and Development Fund (Government of Bangladesh).

Different genetic polymorphisms linked with Cervical cancer, the association between the HOTAIR rs7958904 variant and cervical cancer is being reported for the first time in Bangladeshi women. In this study, I performed molecular work from extraction of RNA to data analysis including TaqMan based RT-qPCR. We identified the correlation between HOTAIR rs7958904 polymorphism and cervical cancer risk from preidentified 200 cervical cancer patients and for control 148 healthy women. The genotype distribution of cases showed GG (22%), CG (52%), CC (26%), where controls GG (35.8%), CG (50.7%), CC (13.5%), and the Hardy–Weinberg equilibrium identified no deviation in genotype distribution. In addition, in-silico study for HOTAIR gene expression was also performed using different databases including GEPIA, UALCAN, and GTEx (10.1007/s43032-024-01679-5). In addition to finding out the solution, I also tried to find out an in-silico drug where we have found a potential candidate from the medicinal plant Andrographis paniculata against the E6 protein of high-risk HPV-16 subtype and published in Scientific Reports (https://doi.org/10.1038/s41598-024-65112-2).  I also worked on a research project to screen cervical cancer in high and low-risk groups for Human Papillomavirus using RT-PCR as a project coordinator. Other conventional test procedures also applied for the identification of cervical cancer, including visual inspection with acetic acid (VIA), Pap smear (Pap test), and Colposcopy, in this project to find out the most feasible diagnostic way in the peripheral area of Bangladesh.

Founding Sources: Research Cell, Noakhali Science and Technology University and National Science and Technology Fellowship 2019, Ministry of Science and Technology, Bangladesh, have partially funded this research work.

My hands-on research training in the isolation and identification of bacteria during undergraduate laboratory coursework at Noakhali Science and Technology University (NSTU), Bangladesh inspired me to explore more on bacterial and viral pathogenesis, host multiplication, and searching therapeutic intervention. I actively participated various reseach projects and contribute significantly. In one of of such project, we detect the multidru resistant pathogenic Bacillus spp. from Noakhali in Bangladesh, and our study will shed light on the adverse effects of feed-borne Bacillus spp. emerging from animal feed to the food chain. I performed bacteriological, antibiogram, and molecular part for a project detecting the presence of multidrug resistant pathogenic foodborne Bacillus spp. from 180 distinct poultry feeds, milk, eggs, and human stool (https://doi.org/10.3389/fmicb.2021.783103). We found 50% nheABC, 80% entFM, and 71% cytK pathogenic gene including various MDR Bacillus spp. notably 100% β-lactamase resistant (https://doi.org/10.1186/s12866-024-03199-3). Our findings will be used to assess the risk and apply food safety measures to ensure food security. I completed another collaborative study where we used whole genome sequencing to analyze two multidrug resistant E. coli strains isolated from mammary tissue (G2M6U) and fecal sample (G6M1F) of experimentally induced mastitis mice (https://doi.org/10.1016/j.heliyon.2024.e26723). In addition, I contributed to perform molecular reseach to detect the virulence genes of APEC (avian pathogenic Escherichia coli) isolated from poultry in Noakhali. (https://doi.org/10.3329/brc.v7i1.54253).

Funding Sources: The study for food borne pathogen was funded by the Science and Technology Partnership Program, Ministry of Science and Technology of China [grant No. KY202204001]. This study was supported in part by the Ministry of Science and Technology (MoST), China [grant No.2022YFC2304000]. The work for multidrug-resistant Escherichia coli isolated from mammary tissue and gut of mastitis induced micewas supported by the research grants received from the Research Management Wing (RMW), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Bangladesh (Grant No.: 18, FY 2023–2025). 

 Aspirin is known as a potent anti-inflammatory drug, but its role in adipogenesis, adipocyte-specific inflammation, and metabolic syndrome is not well characterized.  Thus, in this project, we aimed to determine the effect of low-dose aspirin on obesity, obesity-induced inflammation, and metabolic syndrome. Further, we extendede this project to investigate how AA supplementation affects obesity, adipocyte morphology, inflammation, and AA cascade signaling.  I analyzed mRNA expression levels to clarify the effect of aspirin and arachidonic acid on obesity. This research finding indicated the reduction of adipocyte inflammation in obese group mice compared to the untreated effect of aspirin (10.1016/j.prostaglandins.2022.106664) and arachidonic acid on obesity for obese group (10.1016/j.bbrc.2022.03.089).

Salinity poses a significant challenge for growing agricultural products, like rice, in the coastal regions. It is crucial to enhance production because of limited arable land and the high growth rate of the population. This study targeted to identify HPGPR from legume root nodules and assessed their effects on rice plants experiencing salt stress in coastal regions of Bangladesh. In the coastal area to enhance rice growth, I identified three halotolerant plant growth-promoting rhizobacteria through morpho-biochemical and molecular (16S rRNA gene sequence) (10.1016/j.scitotenv.2023.163774). Recently, I completed another project where I analyzed three bacterial whole genome sequences, molecular docking, and different characterization as a potential candidate for bioethanol (https://doi.org/10.1016/j.scitotenv.2023.166704). The objective of this study is to characterize three bacterial strains isolated from the milieux of cow rumen and forest soil and explore their capabilities of breaking down lignocellulose – an essential process in bioethanol production. Using biochemical and genomic analyses these strains were identified as Bacillus sp. HSTU-bmb18, Bacillus sp. HSTU-bmb19, and Citrobacter sp. HSTU-bmb20. Genomic analysis of the strains unveiled validated model hemicellulases, multicopper oxidases, and pectate lyases.

Dengue cases are increasing day by day in Bangladesh with significant deaths. Without lab facilities, I tried to run some of the secondary data based and in-silico projects. In one of the collaborative team work I explored the association between meteorological factors and recent outbreak data is the first study where we are aware of the use of maximum time series models in Bangladesh (10.3390/ijerph20065152). In another project where I guided young researcher to find out computational based phytochemicals from Vernonia cinerea as potential inhibitors of nonstructural protein 1 (NSP1) in dengue virus serotype-2 (https://doi.org/10.3389/fphar.2024.1465827).

The lack of antiviral drugs, vaccines, and escalating drug resistance for  infections diseases such as SARS-CoV-2, Dengue, Human Papilloma Virus, and others need to develope new targets. Leveraging high-throughput sequencing technologies, and using secondary data my team focuses on identification of novel drug targets. Employing bacterial or viral whole genome sequencing, and RNA-Seq data from server, we delve into the transcriptome and trying to discovery of new solutions against specific infections.