Biology subjects

Mahmud-Un-Nabi, M. A.

Publications and source records attributed to Mahmud-Un-Nabi, M. A..

3 recordsLinked to original sources

bioRxiv2026

Hematological and genetic basis of clinical heterogeneity of HemoglobinE/β-thalassemia

Patients with HbE/{beta}-thalassemia inheriting the same {beta}-globin mutations display varied clinical manifestations, the mechanism of which is only partially known. The study aimed to decipher the heterogenous basis of HbE/{beta}-thalassemia patients in more details by focusing on both hematological and genetic modifiers influencing the disease severity, which included-(i) HbF and HbE levels using Hb electrophoresis, (ii) {beta}-thalassemia mutations, (iii) anti3.7triplication using Gap-PCR, (iv) individual and cumulative effects of HbF-inducing SNPs in 4 major modifier genes, namely HBG2, BCL11A, HBSB1L_MYB intergenic-region, and HBBP1 which were genotyped using DNA sequencing and Real-time PCR-HRM methods. Accordingly, 130 diagnosed Bangladeshi patients with HbE/{beta}-thalassemia were enrolled and categorized as mild, moderate, and severe as per Mahidol scoring system. c.79G>A+IVS1_5G>C was the most predominant (73.8% of total) mutation pair across all the 3 severity groups, indicating secondary modifiers might influence the severity. Our study found both HbF and HbE protective to HbE/{beta}-thalassemia, as both were inversely related to the severity score (HbF: p<0.0001/r=-0.55; HbE: p<0.0001/r=-0.56). Four SNPs-XmnI-G{gamma}, rs2071348 (HBBP1), rs489544 and rs28384513 (HBS1L_MYB) showed significant association with the elevated HbF levels (p=0.005, 0.0001, 0.0001, 0.004 respectively). The multivariate analysis showed that the risk genotypes with single or combination of 2, 3,and 4 SNPs showed gradually increased risk [Odd Ratio (95%CI)= 2.51, 5.47, 19.5, 39.0, respectively] of less severe phenotype, suggesting that these linked SNP variants had a cumulative effect on both HbF level and clinical severity score. However, low HbE level and copresence of anti3.7triplication were found to nullify the ameliorating effect of multiple SNPs.

genetics↗

bioRxiv2025

Culturomics from field-grown crop plants using dilution-to-extinction, two-step library preparation and amplicon sequencing

Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in North Dakota, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant (ASV) detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocols scalability, cost-effectiveness, and robust performance demonstrate its potential for widespread application in agricultural microbiome studies. Impact statementHigh-throughput isolation and characterization of cultivable microbes from plant microbiomes is crucial for advancing microbiome research. However, efficiently recovering a diverse range of bacterial taxa remains a challenge due to high costs and labor-intensive protocols. Our optimized culturomics protocol integrates dilution-to-extinction culturing with a two-step barcoding PCR strategy, enhancing recovery rates and reducing costs while maintaining high accuracy. By employing next-generation sequencing (NGS) and a streamlined bioinformatic pipeline built around the robust DADA2 workflow for amplicon sequencing, the method enables the scalable recovery of hundreds of unique bacterial isolates. This approach makes significant advancements over traditional culturing methods and other high-throughput cultivation protocols, providing an efficient, cost-effective platform for generating microbial collections essential for synthetic communities, comparative genomics, and agricultural microbiome applications. Data summaryAll protocols, sequence data, and analysis codes have been made publicly available in open-access repositories. The authors confirm all supporting data, code, and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2020

Situation of antibiotic resistance in Bangladesh and its association with resistance genes for horizontal transfer

The study investigated the spectrum of antibiotic resistance and the associated genes for aminoglycoside, macrolide and ESBL class of antibiotics using clinical isolates. A total of 430 preserved bacterial strains (Acinetobacter baumannii, n= 20; Pseudomonas aeruginosa, n= 26; Klebsiella pneumoniae, n= 42; E.coli, n= 85; Staphylococcus aureus, n= 84; Salmonella Typhi, n= 82; Enterococcus spp., n= 27; Streptococcus pneumoniae, n= 36 and CNS, n= 28) were examined. The strains were isolated from patients admitted to various tertiary hospitals of Dhaka city between 2015 and 2019 with either acute respiratory infections, wound infections, typhoid fever or diarrhea. The isolates were reconfirmed by appropriate microbiological and biochemical methods. Antimicrobial susceptibility tests were done using Kirby-Bauer disk diffusion approach. PCR amplification using resistance gene-specific primers for aminoglycoside, macrolide and ESBL class of antibiotics was done and the amplified products were confirmed by Sanger sequencing. Of the total isolates, 53% came out as MDR with 96.6% of E. coli and 90% of Staphylococcus aureus. There was a year-wise gradual increase of MDR isolates from 2015-2018 and by 2019 the increase in MDR isolates became almost 2-fold compared to 2015. Among the five ESBL genes investigated, CTXM-1 came out as the most prevalent (63%) followed by NDM-1 (22%) and E. coli isolates were the predominant reservoir of these genes. ErmB (55%) was the most frequently detected macrolide resistance gene, whereas aac(6)-Ib (35.44%) was the most prevalent aminoglycoside resistance gene and these genes were most prevalent in E. coli and P. aeruginosa isolates, respectively. CTXM-1 and ErmB (16.66%) were the most frequent partners of coexistence followed by CTXM-1 and aac(3)-II.

microbiology↗