Biology subjects

Basharat, Z.

Publications and source records attributed to Basharat, Z..

5 recordsLinked to original sources

bioRxiv2023

Degradation of sulphonated mono and di-azo dye as the sole carbon source in Serratia marcescens: Insights from combined wet and dry lab analysis

The high production volume of azo dyes for manufacturing and treating various consumer products leads to deleterious environmental consequences. Bacterial agents present in the environment can degrade these dyes. We, hereby, report the isolation, decolourization and degradation of a mono (Methyl orange) and di-azoic (Congo red) compound of this class of dyes by a versatile bacterium Serratia marcescens. Our isolate showed the capability of sulphonated azo dye utilization/degradation i.e. Methyl orange and Congo red usage, with no inhibitory effects on its growth in minimal medium. The calorimetric analysis showed 80.83% decolourization of Methyl orange and 92.7% decolourization of Congo red after 7 days of incubation in a shaking incubator at pH: 7 and temperature: 37 {degrees}C. An azoreductase enzyme of [~]25 KDa was detected after SDS-PAGE analysis. Quantitative and qualitative testing of the degradation phenomenon was followed by in silico analysis. Structural modeling followed by molecular docking in Molecular Operating Environment revealed numerous residues involved in binding and assisting degradation. Changes in the apo, holo, and dye-bound enzyme energy profiles were also observed. This is the first study reporting the capability of Serratia marcescens to use azo dyes/sulphonated azo dyes as the sole carbon source and the detailed computational analysis of the degradation phenomenon. We hope that these findings will be of use to environmental scientists, aid in better dye-degrading mutant creation to help craft future remediation strategies for sulphonated azo dyes.

microbiology↗

bioRxiv2023

Nanopore sequencing of antibiotic-resistant Klebsiella pneumoniae JRCGR1 isolate from Pakistan and country scale pan-genomics

Klebsiella pneumoniae is a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulent K. pneumoniae from Pakistan.

genomics↗

bioRxiv2022

Nanopore sequencing of human associated methicillin-resistant Staphylococcus aureus RWP1 genome for inferring antibiotic resistant gene, plasmid and prophage information

Methicillin-resistant Staphylococcus aureus (MRSA) is a gram-positive bacterium and responsible for several infections in the human. Here, Oxford nanopore mediated whole genome sequencing is reported for human host associated strain. The genome size obtained was of ~3 MB, while GC content was 32.9%. Approximately 3600 CDSs, 62 tRNAs and 16 rRNAs were identified. Phage segments were present, with two complete intact phages. Type I and type IV restriction elements were also detected, along with five plasmids. Several antibiotic resistance genes were also mined, with a key mutation in the fluoroquinolone resistant gyrA, phosphonic acid resistant murA transferase and fusidic acid resistant fusA genes. Sequence type was determined as 4803. Comparative analysis with MRSA isolates from Pakistan (n=20) revealed an open pan-genome, with 1,934 CDSs forming core genome.

genomics↗

bioRxiv2018

Theoretical Insights from Binding of Neigleria fowleri Cell Division Proteins with Amoebicidal Quassinoids

The ameboflagellate Neigleria fowleri, also known as brain eating amoeba is responsible for fatal primary amoebic meningoencephalitis (PAM) infection in humans. Cell division proteins (CDPs) in N. fowleri have been uncharacterized until now, despite their importance in the initiation of cell division and proliferation of the pathogen. Here, we report characterization and structural assembly of eight such proteins associated with division and docking them with anti-amoebic quassinoid compounds. Quassinoids have been implicated as inhibitors of cell proliferation of amoeboid species as well as tumor cells. Here, they were screened computationally to find interaction mechanism as well as binding energies with CDPs of N. fowleri. The identified inhibitors could play a role in prevention of cell division and hence, stop N. fowleri growth and proliferation during infection. This study supports CDPs as a target for anti-amoebic intervention and identifies quassinoid phytochemical compounds as suitable for optimization into a new therapy against N. fowleri.

bioinformatics↗

bioRxiv2018

Drug target identification and virtual screening in pursuit of phytochemical intervention of Mycobacterium chelonae

Mycobacterium chelonae is a rapidly growing mycobacterium present in the environment. It is associated with skin and soft tissue infections including abscess, cellulitis and osteomyelitis. Other infections by this bacterium are post-operative/transplant-associated, catheter, prostheses and even concomitant to haemodialytic procedures. In this study, we employ a subtractive genomics approach to predict the potential therapeutic candidates, intended for experimental research against this bacterium. A computational workflow was devised and executed to procure core proteome targets essential to the pathogen but with no similarity to the human host. Initially, essential Mycobacterium chelonae proteins were predicted through homology searching of core proteome content from 19 different bacteria. Druggable proteins were then identified and N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) was chosen as a case study from identified therapeutic targets, based on its important bifunctional role. Structure modeling was followed by virtual screening of phytochemicals (N > 10,000) against it. 4,4-[(1E)-5-hydroxy-4-(methoxymethyl)-1-pentene-1,5-diyl]diphenol, apigenin-7-O-beta-gluconopyranoside and methyl rosmarinate were screened as compounds having best potential for binding GlmU. Phytotherapy helps curb the menace of antibiotic resistance so treatment of Mycobacterium chelonae infection through this method is recommended.

bioinformatics↗