Biology subjects

Wahab, A.

Publications and source records attributed to Wahab, A..

6 recordsLinked to original sources

bioRxiv2025

Proteomic characterization of major fish allergy responsive protein parvalbumins in Hilsa (Tenualosa ilisha): A commercially important fish in Southeast Asia

The protein parvalbumin (PRV)-beta (PRVB) is the primary cause of food allergies to bony fish. Although PRVB is a well-characterized protein in many bony fishes, little is known about the Hilsa, an anadromous fish with great economic importance and predominantly found in Southeast Asia. In this study, we characterized the Hilsa PRV utilizing various proteomic approaches in response to two major riverine habitats and developmental stages. Unique peptide sets corresponding to three PRV isoforms were identified in Hilsa muscle tissues. Label-free quantitative proteomic analysis coupled with ELISA revealed higher levels of PRVB in young fish compared to adults, irrespective of their riverine habitats. A comparative quantitative analysis of PRVB further demonstrated that Hilsa had less PRVB than other commonly consumed freshwater fish species. Multiple reaction monitoring (MRM)-based targeted proteomic approach showed the potential of PRV as a marker protein for allergen quantitation and authenticating the presence of Hilsa in a complex freshwater fish mixture. Our findings collectively offer fundamental knowledge on Hilsa PRVs for further investigation on the food safety and quality evaluation of Hilsa fish.

biochemistry↗

bioRxiv2022

Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches

Protein is the building block for all organisms. Protein structure prediction is always a complicated task in the field of proteomics. DNA and protein databases can find the primary sequence of the peptide chain and even similar sequences in different proteins. Mainly, there are two methodologies based on the presence or absence of a template for Protein structure prediction. Template-based structure prediction (threading and homology modeling) and Template-free structure prediction (ab initio). Numerous web-based servers that either use templates or do not can help us forecast the structure of proteins. In this current study, ORF7a, a transmembrane protein of the SARS-coronavirus, is predicted using Phyre2, IntFOLD, and Robetta. The protein sequence is straightforwardly entered into the sequence bar on all three web servers. Their findings provided information on the domain, the region with the disorder, the global and local quality score, the predicted structure, and the estimated error plot. Our study presents the structural details of the SARS-CoV protein ORF7a. This immunomodulatory component binds to immune cells and induces severe inflammatory reactions.

microbiology↗

bioRxiv2021

Sex Identification in Cattle, based on Amelogenin Gene

Sex identification is considered an important step in the field of forensic sciences, wildlife and livestock breeding management. In the current experiment we used Amelogenin gene as a biological marker for polymerase chain reaction test to identify the sex of cattle from blood remnants, collected at slaughter house. Due to the conserved region of the gene on both sex chromosomes (X and Y) a single primers pair was employed to amplify the gene in a single polymerase chain reaction. In case of band patterns, a 178 base pair fragment for AMELY and a 241 base pair fragment for AMELX genes were produced. The primers competence and exactness was initially checked on known gender cattle samples and then applied to unknown cattle samples for the validation of the experiment. PCR amplicons of unknown gender showed only one band (241-bp) for female DNA and two bands (241-bp, 178-bp) for male DNA, on the platform of agarose gel upon electrophoresis. Our findings showed that the PCR protocol based on AMELX/Y gene is a reliable technique for the identification of cattle sex.

zoology↗

bioRxiv2020

Genetic models suggest single and multiple origins of dihydrofolate reductase mutations in Plasmodium vivax

Pyrimethamine was first introduced for the treatment of malaria in Asia and Africa during the early 1980s, replacing chloroquine, and has become the first line of drugs in many countries. In recent years, development of pyrimethamine resistance in Plasmodium vivax has become a barrier to effective malaria control strategies. Here, we describe the use of meta-barcoded deep amplicon sequencing technology to assess the evolutionary origin of pyrimethamine resistance by analysing the flanking region of dihydrofolate reductase (dhfr) locus. The genetic modelling suggests that 58R and 173L single mutants and 58R/117N double mutants are present on a single lineage; suggesting a single origin of these mutations. The triple mutants (57L/58R/117N, 58R/61M/117N and 58R/117N/173L) share the lineage of 58R/117N, suggesting a common origin. In contrast, the 117N mutant is present on two separate lineages suggesting that there are multiple origins of this mutation. We characterised the allele frequency of the P. vivax dhfr locus. Our results support the view that the single mutation of 117N and double mutations of 58R/117N arise commonly, whereas the single mutation of 173L and triple mutations of 57L/58R/117N, 58R/61M/117N and 58R/117N/173L are less common. Our work will help to inform mitigation strategies for pyrimethamine resistance in P. vivax.

genetics↗

bioRxiv2019

Novel metabarcoded DNA sequencing tool for the detection of Plasmodium species in malaria positive patients

Various PCR based methods have been described for the diagnosis of malaria, but most depend on the use of Plasmodium species-specific probes and primers; hence only the tested species are identified and there is limited available data on the true circulating species diversity. Sensitive diagnostic tools and platforms for their use are needed to detect Plasmodium species in both clinical cases and asymptomatic infections that contribute to disease transmission. We have been recently developed for the first time a novel high throughput haemoprotobiome metabarcoded DNA sequencing method and applied it for the quantification of haemoprotozoan parasites (Theleria and Babesia) of livestock. Here, we describe a novel, high throughput method using an Illumina MiSeq platform to demonstrate the proportions of Plasmodium species in metabarcoded DNA samples derived from human malaria patients. Plasmodium falciparum and Plasmodium vivax positive control gDNA was used to prepare mock DNA pools of parasites to evaluate the detection threshold of the assay for each of the two species and to assess the accuracy of proportional quantification. We then applied the assay to malaria-positive human samples to show the species composition of Plasmodium communities in the Punjab province of Pakistan and in the Afghanistan-Pakistan tribal areas. The diagnostic performance of the deep amplicon sequencing method was compared to an immunochromatographic assay that is widely used in the region. Metabarcoded DNA sequencing showed better diagnostic performance, greatly increasing the estimated prevalence of Plasmodium infection. The next-generation sequencing method using metabarcoded DNA has potential applications in the diagnosis, surveillance, treatment, and control of Plasmodium infections, as well as to study the parasite biology.

genetics↗

bioRxiv2018

Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2)

The AbsA1-AbsA2 two component signalling system of Streptomyces coelicolor has long been known to exert a powerful negative influence on the production of the antibiotics actinorhodin, undecylprodiginine and the Calcium-Dependent Antibiotic (CDA). Here we report the analysis of a{Delta} absA2 deletion strain, which exhibits the classic precocious antibiotic hyper-production phenotype, and its complementation by an N-terminal triple-FLAG-tagged version of AbsA2. The complemented and non-complemented{Delta} absA2 mutant strains were used in large-scale microarray-based time-course experiments to investigate the effect of deleting absA2 on gene expression and to identify the in vivo AbsA2 DNA-binding target sites using ChIP-on chip. We show that in addition to binding to the promoter regions of redZ and actII-orfIV AbsA2 binds to several previously unidentified sites within the cda biosynthetic gene cluster within and/or upstream of SCO3215 - SCO3216, SCO3217, SCO3229 - SCO3230, and SCO3226, and we relate the pattern of AbsA2 binding to the results of the transcriptomic study and antibiotic phenotypic assays. Interestingly, dual biphasic ChIP peaks were observed with AbsA2 binding across the regulatory genes actII-orfIV and redZ and the absA2 gene itself, while more conventional single promoter-proximal peaks were seen at the CDA biosynthetic genes suggesting a different mechanism of regulation of the former loci. Taken together the results shed light on the complex mechanism of regulation of antibiotic biosynthesis in Streptomyces coelicolor and the important role of AbsA2 in controlling the expression of three antibiotic biosynthetic gene clusters.

genomics↗