RESEARCH & GRANTS

Research Grants received

1. Grant ID: SRG-241002

Project: Applying bioinformatics knowledge to investigate genome editing prospects to improve salt tolerance in tomato and generating in planta transformants in farmer popular varieties. 

Principal investigator: Aparna Islam 

Co-Principal Investigator: Tushar Ahmed Shishir

Funding organization: Ministry of Science and Technology, Bangladesh

Fiscal year: 2024 – 2025.

2. Grant ID: RSGI-2024

Project: Bacteriophage-mediated Biofilm Eradication for Enhanced Treatment of Antibiotic-resistant Diarrheal Infections

Principal investigator: Tushar Ahmed Shishir 

Co-Principal Investigator: Iftekhar Bin Naser & Ms. Afia Nowshen

Funding organization: BRAC University

Fiscal year: 2024 – 2025.

3. Grant ID: SU-SEL-24-006

Project: Predictive Design of a Universal ZIKA Vaccine: An In Silico Approach Targeting Conserved and Immunodominant Epitopes.

Principal investigator: Ms. Afia Nowshen 

Co-Principal Investigator: Tushar Ahmed Shishir

Funding organization: Independent University, Bangladesh

Fiscal year: 2024 – 2025.

4. Grant ID: SRG-231002

Project: Analysis of genetic mechanisms associated with salt tolerance in Arabidopsis thaliana and tomato putative antiporter gene; establishment of in planta transformation protocol for farmer popular tomato varieties. 

Principal investigator: Aparna Islam 

Co-Principle investigator: Tushar Ahmed Shishir

Funding organization: Ministry of Science and Technology, Bangladesh

Fiscal year: 2023 – 2024.

Research Projects

Postgraduate Thesis on Bacteriophage Genome Size and Multiplication Rate

September 2018 – October 2019

Supervised by Dr. Iftekhar Bin Naser, Associate Professor at BRAC University, my research explored how genome size influences the multiplication rate of bacteriophages. Key research activities included:

• Investigated bacteriophage propagation time and adsorption rates across bacteriophages with varying genome sizes.

• Conducted comparative studies on large and small genome bacteriophage growth rates under different culturing conditions.

• Performed metagenomic analysis to evaluate the global prevalence of bacteriophages, correlating genome size with distribution trends.

Undergraduate Thesis on Anti-diabetic Combination Therapy Development

January 2017 – October 2017

Supervised by Rubayat Islam Khan, Senior Lecturer at BRAC University, my research aimed to develop a novel anti-diabetic combination therapy involving Linagliptin and Dextromethorphan. Key aspects of the research included:

• Investigated the physical and chemical compatibility of Linagliptin and Dextromethorphan through in-vitro pre-formulation studies.

• Analyzed the dissolution profile and stability of the proposed combination therapy under different conditions.

• Explored formulation strategies to effectively combine Linagliptin and Dextromethorphan for potential use as a novel anti-diabetic therapy.

Research on Bacterial CRISPR Spacer Acquisition Patterns

February 2023 – Present

This research focuses on understanding the mechanisms behind CRISPR spacer acquisition in bacteria. Key activities include:

• Assessing the presence or absence of non-specific spacers within acquired CRISPR arrays.

• Identifying the genomic sources of acquired CRISPR spacers.

• Investigating the prevalence of spacers derived from bacteriophage structural protein-coding genes.

Supervision of Undergraduate Thesis on Plasmid Mispackaging in Bacteriophages

March 2022 – Present

Focused on the mispackaging of plasmids inside bacteriophages and its potential role in horizontal gene transfer. Key aspects of the research include:

• Investigating the occurrence and frequency of plasmid mispackaging within bacteriophages.

• Examining how environmental factors influence the rate of plasmid mispackaging.

• Assessing the implications of plasmid mispackaging on the horizontal transfer of genetic material.

Supervision of Undergraduate Theses on MicroRNA and Targeted Cancer Therapies

January 2022 – Present

Focused on exploring the role of MicroRNAs in colorectal cancer (CRC) and breast cancer (BC) therapies. Key research activities include:

• Analyzing CRC and BC microarray datasets to identify critical molecular pathways involved in cancer progression.

• Investigating the potential of miRNAs to inhibit cancer cell proliferation by targeting specific genes or pathways.

• Identifying novel microRNA candidates with tumor-suppressor effects in CRC and BC.

Co-supervision of Research on Bacterial Diversity and Antibiotic Resistance in Kaptai Lake

January 2022 – Present

This research investigates bacterial diversity and antibiotic resistance in surface water samples from Kaptai Lake, Rangamati. Key activities include:

• Isolating, identifying, and characterizing bacteria from collected water samples.

• Conducting antibiotic susceptibility testing to profile resistance in the isolated strains.

• Performing genome sequencing and analysis to explore microbial composition and genetic diversity.

Supervision of Undergraduate Thesis on Computational Analysis of Human Gut Metagenome Sequences

February 2024 – Present

Focused on analyzing human gut metagenomes to uncover key genetic markers and relationships. Key research activities include:

• Annotating metagenome sequences to identify the prevalence of antimicrobial resistance (AMR) genes.

• Analyzing the abundance of bacteriophage and plasmid sequences within the gut microbiome.

• Exploring correlations between pathogenic genes derived from plasmid and prophage sequences.

Supervision of Graduate Thesis on Self-targeting Spacers (STS) in CRISPR Bacteria

October 2023 – Present

This research delves into the presence and implications of self-targeting spacers (STS) within CRISPR systems of bacteria. Key activities include:

• Analyzing bacterial whole genome sequences to identify CRISPR systems and STS.

• Investigating the relationship between prophage prevalence and STS occurrence.

• Exploring the potential link between STS and increased pathogenicity, particularly in bacteria containing both STS and prophages with high pathogenic gene content.

Supervision of Undergraduate Thesis on Comparative Proteomic Analysis of Arabidopsis thaliana and Solanum lycopersicum

November 2023 – Present

This research focuses on understanding the proteomic and genomic differences between Arabidopsis thaliana and Solanum lycopersicum (tomato). Key activities include:

• Conducting extensive genomics and proteomic analyses of both plant species.

• Examining the structural effects of mutations in Solanum antiporter proteins related to salt susceptibility.

• Developing gene-editing strategies to improve tomato salt tolerance based on the identified mutations.

Computational Investigation of Hypothetical Proteins in Bacteriophages and Bacteria

October 2022 – Present

This research focuses on understanding the functional roles of hypothetical proteins in bacteriophages and bacteria. Key activities include:

• Conducting genome analysis to identify hypothetical proteins in bacteriophages and bacterial genomes.

• Predicting the functional characteristics of these hypothetical proteins using computational methods.

• Exploring their potential roles in bacteriophage-host interactions and bacterial physiology.

Supervision of Undergraduate Thesis on Computational Analysis of Antimicrobial Resistance (AMR) Emergence

August 2021 – Present

This research investigates the evolution of AMR over time and its geographic patterns. Key activities include:

• Performing a global analysis of AMR gene evolution over the past twenty years.

• Conducting comparative analyses of AMR genes between developed and developing countries.

• Applying statistical methods to explore the spatial and temporal dynamics of AMR gene distribution.

Investigation of Medicinal Plants Through In-vitro and In-silico Phytochemical Screening

July 2021 – October 2022

This research focused on the phytochemical analysis and efficacy testing of medicinal plants. Key activities include:

• Conducted surveys and in-vitro analyses of Molineria capitulata to evaluate its effectiveness against chickenpox.

• Performed phytochemical analysis of Molineria capitulata using GC-MS techniques.

• Applied docking and molecular dynamics (MD) simulations to explore interactions between phytochemical compounds and chickenpox surface proteins.

Analysis of Risks in Phage Therapy Using Bacteriophages

February 2021 – Present

Focused on evaluating potential risks associated with phage therapy. Key activities include:

• Identifying antibiotic-resistance and toxin genes within bacteriophage genomes.

• Conducting comparative analyses to assess the distribution of these harmful genes across various bacteriophage species.

• Investigating correlations between these genes in bacteriophages and their bacterial hosts.

Investigation of Analgesic and Antioxidant Properties of Allophylus villosus and Mycetia sinensis 

July 2020 – October 2023

This research evaluated the pain-relieving and antioxidant effects of Allophylus villosus and Mycetia sinensis. Key activities include:

• Conducted FTIR and GC-MS analyses to identify and characterize phytochemicals.

• Conducted in vivo analgesic experiments on Swiss albino mice using extracts from both plants.

• Performed in-silico analyses to assess inhibitory activities on COX-2 and 15-LOX-2 enzymes.

• Utilized phytochemical screening techniques including DPPH, ARA, FRAP, and H2O2 scavenging assays.

• Executed molecular docking, ADMET studies, DFT, and MDS to evaluate the efficacy of phytocompounds in drug-like activities.

Computational Analysis of SARS-CoV-2 Sequences

April 2020 – May 2022

Conducted in-depth analyses of SARS-CoV-2 sequences to understand various aspects of the virus. Key activities include:

• Investigating the source, diversity, evolution, and transmission of SARS-CoV-2 in Bangladesh.

• Analyzing mutations and their impact on protein properties such as solvent accessibility, secondary structure, disorder properties, and proteome stability.

• Examining the effects of mutations on the spike protein of the Omicron variant of SARS-CoV-2.

Comprehensive Computational Analysis of Bacteriophages

January 2019 – November 2020

Conducted in-depth computational studies on bacteriophages with a focus on their role in bacterial genomes. Key activities include:

• Isolating and analyzing bacteriophages from wastewater, including four Escherichia coli and one Vibrio cholerae phages.

• Investigating the correlation between CRISPR spacers and prophage numbers in bacterial genomes, focusing on their role in the adaptive immune system.

• Examining the impact of prophages on bacterial pathogenicity and their contribution to antibiotic resistance.

Study on Toxicogenic Vibrio cholerae O1 and Autoinducer-2 Overproducing Variants

July 2018 – May 2020

This research explored the relationship between Vibrio cholerae O1 and non-O1 non-O139 variants in the context of autoinducer-2 production. Key findings include:

• Identified and characterized a non-cholera Vibrio variant (non-O1, non-O139) that overproduces autoinducer-2, with a notable correlation to the prevalence of pathogenic Vibrio cholerae O1.

• Discovered mutations in the cqsS gene, which encodes the receptor for autoinducer-2, in these variants. Interestingly, their culture supernatants enhanced the resuscitation of CVEC in water.

• Established that this non-cholera Vibrio variant may play a significant role in resuscitating latent pathogenic strains, potentially contributing to seasonal cholera outbreaks.

Collaborative Research Projects

February 2018 – Present

Engaged in various research projects with collaborators from different universities of Bangladesh and abroad. Some of the research are:

• Characterization, plasmid profiling, and determination of antibiotic resistance pattern of bacteria isolated from different parts of Dhaka city.

• An isolation and characterization process established a phage library of 52 phages.

• Phage-antibiotic combination therapy for combating antibiotic-resistant Vibrio cholerae.

• Determining the lytic capabilities of bacteriophages based on bacterial concentration.

• Quorum sensing effect of Escherichia coli on environmental bacteriophages.

• Impact of cell-free DNA (exDNA) and sunlight on bacterial propagation.

• Transfer of chromosomal genes across species boundaries triggered by bacteriophage infection.