Biology subjects

Hasan, M. M.

Publications and source records attributed to Hasan, M. M..

23 records · Page 2Linked to original sources

bioRxiv2020

Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes

Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. Nearly 0.4 million mutations were identified so far in [~]60,000 SARS-CoV-2 genomic sequences. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Phylogenetic analyses indicates that in Bangladesh, SARS-CoV-2 viruses might arrived through infected travelers from European countries, and the GR clade was found as predominant in this region. We found 2602 mutations including 1602 missense mutations, 612 synonymous mutations, 36 insertions and deletions with 352 other mutations types. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (95.6%) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M and N of genomes, having nucleotide shift at G614 (n=459), were significantly higher (p[≤]0.001) than those having mutation at D614 (n=215). Previously reported frequent mutations such as P4715L, D614G, R203K, G204R and I300F were also prevalent in Bangladeshi isolates. Additionally, 87 unique amino acid changes were revealed and were categorized as originating from different cities of Bangladesh. The analyses would increase our understanding of variations in virus genomes circulating in Bangladesh and elsewhere and help develop novel therapeutic targets against SARS-CoV-2.

genomics↗

bioRxiv2020

Colistin Susceptibility Pattern In Gram Negative Bacilli Isolated From Patients Of Dhaka Medical College Hospital With Distribution Of Antibiotic Resistance Genes Among Them.

Colistin is one of the last resort of antibiotics used specifically in the treatment of multidrug resistant gram negative bacilli. Though an older class of antibiotic with no use in last four decades, resurgence of colistin use is also causing emergence of colistin resistant gram negative bacilli.The aim of this cross sectional study was to investigate the colistin susceptibility and resistant pattern along with colistin resistant genes in gram negative bacilli among different samples in Dhaka medical college hospital. Total 300 samples (wound swab, urine, endotracheal aspirate, blood and sputum) were collected from 2015 to 2016. 204 gram negative bacilli were isolated and tested for resistance to colistin by disc diffusion method. Then, the prevalence of colistin resistant genes (pmrA, pmrB, pmrC, mgrB, phoP, phoQ, lpxA, lpxC, lpxD, mcr-1) was detected by polymerase chain reaction method (PCR). Among 204 gram negative bacilli, 22 (10.78%) colistin resistance was identified. PCR analysis revealed that 50% of these isolates contained pmrA gene, followed by phoP gene (27.27%). The prevalence of pmrB, phoQ, mgrB, lpxC and lpxD were 22.72%, 13.63%, 13.63%, 13.63%, 13.63%, and 13.63% respectively among the isolates. Colistin resistance is widespread among gram negative bacilli isolated from human infections. Colistin resistance (10.78%) found in the study is quite alarming. A restricted and rational use of the colistin is the need of hour.

microbiology↗

bioRxiv2020

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach

The newly identified SARS-CoV-2 has now been reported from around 183 countries with more than a million confirmed human cases including more than 68000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins have gotten substantial attention recently. Spike glycoprotein is widely considered as a possible target to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment tools. In this study, 483 unique variations have been identified among the genomes including 25 non-synonymous mutations and one deletion in the spike protein of SARS-CoV-2. Among the 26 variations detected, 12 variations were located at the N-terminal domain and 6 variations at the receptor-binding domain (RBD) which might alter the interaction with receptor molecules. In addition, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on our findings, potential inhibitors can be designed and tested targeting these proposed sites of variation.

bioinformatics↗

bioRxiv2018

Deciphering the molecular pathways of apoptosis using leaf extract of Basella alba against Ehrlichs Ascites Carcinoma (EAC) cell line in Swiss albino mice model

A series of programmed cell death that plays a vital role in the exclusion of abnormal cells without any ruin into the surrounding neighboring cells is called Apoptosis. Generally, it occurs in multi-cellular organisms through an orderly and autonomously processes that is controlled by proper function of various genes. In the current studies, cell apoptosis in EAC cells treated with different fractions (BLP-01, BLP-02 and BLP-03) of leaf extract of B. alba was detected by conducting several bio-assays such as cell growth inhibition, fluorescence and optical microscopy, DNA fragmentation and PCR amplification etc. The results of these experiments indicate that the plant extracts are able to inhibit cell growth significantly where mor- phological features of apoptosis were appeared under both fluorescence and optical microscope. The PCR amplification results showed that the leaf extracts of B. alba were able to cause EAC cell apoptosis in both the extrinsic and intrinsic pathway. An excellent figure of fragmented DNA was found in DNA fragmentation assay when the gel was observed under UV light which confirms the cell apoptosis. The current findings suggest that the samples of this experiment occupy fascinating competence to conduct cell apoptosis and become an ideal resource for cancer research as well as drugs development for cancer treatment.

molecular biology↗

bioRxiv2018

Phylogeny and distinct properties of major intrinsic proteins in the genomes of six Phytophthora species suggest their novel functions in Phytophthora

ABSTRACTMajor intrinsic proteins (MIPs), commonly known as aquaporins, facilitate the membrane diffusion of water and some other non- polar solutes. MIPs might be involved in host-pathogen interactions. Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. These Phytophthora species are devastating plant pathogens and members of oomycetes, a distinct lineage of fungus-like eukaryotic microbes. Phylogenetic analysis showed that the Phytophthora MIPs (PMIPs) formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger’s positions in PMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PMIPs were also divergent from those in plants. We further deciphered group-specific consensus sequences/motifs in different loops and transmembrane helices of PMIPs, which were distinct from those in plants, animals, and microbes. The data collectively supported the notion that PMIPs might have novel functions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗