Biology subjects

Hussain, S.

Publications and source records attributed to Hussain, S..

5 recordsLinked to original sources

bioRxiv2018

Mutation of influenza A virus PA-X decreases pathogenicity in chicken embryos and can increase the yield of reassortant candidate vaccine viruses

The PA-X protein of influenza A virus has roles in host cell shut-off and viral pathogenesis. While most strains are predicted to encode PA-X, strain-dependent variations in activity have been noted. We found that PA-X protein from A/PR/8/34 (PR8) strain had significantly lower repressive activity against cellular gene expression compared with PA-Xs from the avian strains A/turkey/England/50-92/91 (H5N1) (T/E) and A/chicken/Rostock/34 (H7N1). Loss of normal PA-X expression, either by mutation of the frameshift site or by truncating the X-ORF, had little effect on the infectious virus titre of PR8 or PR8 7:1 reassortants with T/E segment 3 grown in embryonated hens eggs. However, in both virus backgrounds, mutation of PA-X led to decreased embryo mortality and lower overall pathology; effects that were more pronounced in the PR8 strain than the T/E reassortant, despite the low shut-off activity of the PR8 PA-X. Purified PA-X mutant virus particles displayed an increased ratio of HA to NP and M1 compared to their WT counterparts, suggesting altered virion composition. When the PA-X gene was mutated in the background of poorly growing PR8 6:2 vaccine reassortant analogues containing the HA and NA segments from H1N1 2009 pandemic viruses or an avian H7N3 strain, HA yield increased up to 2-fold. This suggests that the PR8 PA-X protein may harbour a function unrelated to host cell shut-off and that disruption of the PA-X gene has the potential to improve the HA yield of vaccine viruses.\n\nIMPORTANCEInfluenza A virus is a widespread pathogen that affects both man and a variety of animal species, causing regular epidemics and sporadic pandemics with major public health and economic consequences. A better understanding of virus biology is therefore important. The primary control measure is vaccination, which for humans, mostly relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of interest. However, not all reassortants replicate well enough to supply sufficient virus antigen for demand. The significance of our research lies in identifying that mutation of the PA-X gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the pathogenicity of the virus in embryonated eggs.

microbiology↗

bioRxiv2018

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

Most methods for statistical analysis of RNA-seq data take a matrix of abundance estimates for some type of genomic features as their input, and consequently the quality of any obtained results are directly dependent on the quality of these abundances. Here, we present the junction coverage compatibility (JCC) score, which provides a way to evaluate the reliability of transcript-level abundance estimates as well as the accuracy of transcript annotation catalogs. It works by comparing the observed number of reads spanning each annotated splice junction in a genomic region to the predicted number of junction-spanning reads, inferred from the estimated transcript abundances and the genomic coordinates of the corresponding annotated transcripts. We show that while most genes show good agreement between the observed and predicted junction coverages, there is a small set of genes that do not. Genes with poor agreement are found regardless of the method used to estimate transcript abundances, and the corresponding transcript abundances should be treated with care in any downstream analyses.

bioinformatics↗

bioRxiv2018

Functional Role of Annexins in Zebrafish Caudal Fin Regeneration: A Gene Knockdown Approach in Regenerating Tissue.

Regeneration is an adaptive phenomenon with wide biological implications spread heterogeneously in almost all the organism including human beings. The ability of regeneration varies from species to species for its impediment. Epimorphic regeneration of zebrafish caudal fin tissue is most widely studied regeneration mechanism for its discrete and rapid regenerative capability. Several genes/proteins were found to be associated with zebrafish caudal fin tissue regeneration. Here, we have evaluated the functional role of Annexin 2a and 2b genes in adult zebrafish caudal fin tissue undergoing regeneration using a novel CRSISPR-Cas9 gene knock down approach. Knock down of both the genes individually elicited in decelerated regeneration and down regulation of target genes and its partner genes/proteins such as ANXA1a, ANXA5b and ANXA13. This study validates a novel gene targeting approach and the possible role of annexin in regeneration mechanism.

developmental biology↗

bioRxiv2018

SCRUTINIZATION OF SOIL SEED BANK FROM ARID TO MESIC HABITATS OF DERA GHAZI KHAN

The research was conducted to investigate the persistent soil seed bank composition and its relation to the above-ground vegetation of upland area (piedmont) to low land area (alluvial) landscape from arid to mesic region of Dera Ghazi Khan. A transact of 40 kilometers was laid down from arid to mesic habitat. At each 2 km a quadrate of 1 m-2 sizes was thrown in the field to collect a soil sample of 2kg from soil cores ranging 0-15 cm deep for the analysis of soil seed bank. Twenty different sites were sampled by throwing 6 quadrates at each site making a total of 120 samples. Three thousand seeds were obtained of 50 different species from all the collected samples. Soil seed bank density m-2 was higher in the alluvial plains of Dera Ghazi Khan. Most of the perennial species, which were xerophytic in nature such as Aerua persica, Calotropis procera, Fagonia indica, Leptadaenia pyrotechnica, Peganum hermala, Rhazya stricta and Suaeda fructicosa were found in the piedmont (arid) soil habitat and the soil seed bank relatively less than the species found in the alluvial (Mesic) soil habitat, which were mostly of annual life span such as Chenopodium murale, Euphorbia prostrata, Medicago denticulata, Fumaria indica, and Withania somnifera. From this study it is concluded that the similarity found between soil seed bank and above ground vegetation of both historic types of habitats piedmont (arid) and alluvial (mesic) of Dera Ghazi Khan

ecology↗

bioRxiv2017

MreB Filaments Create Rod Shape By Aligning Along Principal Membrane Curvature.

MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion and increased glycan crosslinking. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape.

microbiology↗