Biology subjects

Faruk, M. O.

Publications and source records attributed to Faruk, M. O..

4 recordsLinked to original sources

bioRxiv2024

Genomic characterization and functional insights of multidrug-resistant Klebsiella pneumoniae strain BCSIR-JUMIID

Klebsiella pneumoniae is a prominent opportunistic pathogen associated with multidrug resistance (MDR) and high morbidity and mortality rates in healthcare settings. The emergence of strains resistant to last-resort antibiotics, such as colistin and carbapenems, poses significant therapeutic challenges. This study presents the complete genome analysis of the MDR strain K. pneumoniae BCSIR-JUMIID to elucidate its genetic architecture, resistance mechanisms, and virulence factors. The genome of K. pneumoniae BCSIR-JUMIID, isolated from a pharmaceutical wastewater in Dhaka, Bangladesh, was sequenced using next-generation sequencing technologies. Bioinformatics tools were employed for genome assembly, annotation, and functional analysis. Phylogenetic relationships were established through whole-genome comparisons. Antibiotic resistance genes, virulence factors, and mobile genetic elements were identified using the Comprehensive Antibiotic Resistance Database (CARD), ResFinder-4.5.0, Virulence Factors Database (VFDB), and various phage identification tools. The genome of K. pneumoniae BCSIR-JUMIID consists of 5,769,218 bp with a G+C content of 56.79%, assembled into 343 contigs. A total of 6,062 coding sequences (CDS), including 1,087 hypothetical proteins, 49 tRNA genes, and 4 rRNA genes, were identified. Key loci involved in capsular polysaccharide and O-antigen biosynthesis (KL150, KL107-D1, O3b) were detected. A diverse array of antibiotic resistance genes was uncovered, including those conferring resistance to beta-lactams, quinolones, and colistin. Phage analysis revealed the presence of multiple dsDNA bacteriophages, and CRISPR-Cas systems indicated robust phage defense mechanisms. The genomic analysis of K. pneumoniae BCSIR-JUMIID provides a detailed understanding of its resistance and virulence mechanisms, highlighting its potential for horizontal gene transfer and rapid adaptation. These findings underscore the necessity for continued surveillance and novel therapeutic strategies to combat MDR K. pneumoniae infections effectively.

microbiology↗

bioRxiv2024

PANOMIQ: A Unified Approach to Whole-Genome, Exome, and Microbiome Data Analysis

The integration of whole-genome sequencing (WGS), whole-exome sequencing (WES), and microbiome analysis has become essential for advancing our understanding of complex biological systems. However, the fragmented nature of current analytical tools often complicates the process, leading to inefficiencies and potential data loss. To address this challenge, we present PANOMIQ, a comprehensive software solution that unifies the analysis of WGS, WES, and microbiome data into a single, streamlined pipeline. PANOMIQ is designed to facilitate the entire analysis process from raw data to interpretable results. It is the fastest algorithm that can achieve results much more quickly compared to traditional pipeline approaches of WGS and WES analysis. It incorporates advanced algorithms for high-accuracy variant calling in both WGS and WES, along with robust tools for characterizing microbial communities. The softwares modular architecture allows for seamless integration of these diverse data types, enabling researchers to uncover complex interactions between host genomics and microbiomes. In this study, we demonstrate the capabilities of PANOMIQ by applying it to a series of datasets encompassing a wide range of applications, including disease association studies and environmental microbiome profiling. Our results highlight PANOMIQs ability to deliver comprehensive insights, significantly reducing the time and computational resources required for multi-omic analysis. By providing a unified platform for WGS, WES, and microbiome analysis, PANOMIQ offers a powerful tool for researchers aiming to explore the full spectrum of genomic and microbial diversity. This software not only simplifies the analytical workflow but also enhances the depth of biological interpretation, paving the way for more integrated and holistic studies in genomics and microbiology.

bioinformatics↗

bioRxiv2023

NMDAR Phosphoproteome Controls Synaptic Growth and Learning

In the mammalian brain, NMDA receptors (NMDARs) activation triggers a calcium-dependent signal transduction cascade resulting in postsynaptic remodeling and behavioral learning. However, the phosphoprotein signal flow through this transduction network is poorly understood. Here, we show that NMDAR-dependent phosphorylation drives the assembly of protein signaling complexes that regulate synaptic morphology and behavior. We performed large-scale phosphoproteomic analyses of protein kinase target proteins in successive layers of the signaling network in mouse striatal/accumbal slices. NMDARs activation resulted in the phosphorylation of 194 proteins, including Rho GTPase regulators. CaMKII-mediated phosphorylation of ARHGEF2 increased its RhoGEF activity, thereby activating the RhoA-Rho-kinase pathway. Subsequent phosphoproteomics of Rho-kinase revealed 221 protein targets, including SHANK3. Experimental validation revealed a pathway from NMDAR-dependent calcium influx through CaMKII, ARHGEF2, Rho-kinase, and SHANK3 to coordinate assembly of an actin-tethered postsynaptic complex of SHANK3/NMDAR/PSD95/DLGAP3 for spine growth and aversive learning. These findings show that NMDARs initiate metabolic phosphorylation for learning.

neuroscience↗

bioRxiv2023

Bacterial risk evaluation of widely consumed fast foods by the younger population in Bangladesh and its potential health effects

Food-borne illness is a significant public health concern in Bangladesh, especially among the younger generation. They often consume spicy street foods, such as Fusca, Hog plum bedfellow, and Chotpoti. These foods can be contaminated with harmful bacteria, which can cause various diseases, including diarrhea, cholera, and dysentery. This study investigated the microbiological quality of three commonly consumed street foods in Bangladesh. We collected samples of Fusca, Hog plum bedfellow, and Chotpoti from different vendors in Dhaka and analyzed them in a laboratory. We found that all three of the food samples were contaminated with a variety of bacteria, including Bacillus spp., Haemophilus spp., Salmonella spp., Klebsiella spp., Staphylococcus spp., and Streptococcus spp. Some of these bacteria, such as Haemophilus spp., were resistant to the antibiotic ciprofloxacin. Our findings suggest that there is a high risk of food-borne illness associated with the consumption of street foods in Bangladesh. We urge vendors and consumers to take steps to improve food safety, such as proper food handling and cooking and clean water and utensils.

microbiology↗