Biology subjects

Hussain, S.

Publications and source records attributed to Hussain, S..

66 records · Page 4Linked to original sources

bioRxiv2019

Individual and concurrent effects of drought and chilling stresses on morpho-physiological characteristics and oxidative metabolism of maize cultivars

Maize belongs to tropical environment and is extremely sensitive to drought and chilling stress, particularly at early developmental stages. The present study investigated the individual and combine effects of drought (15% PEG-Solution) and chilling stress (15{degrees}C/12{degrees}C) on the morpho-physiological growth, osmolyte accumulation, production and regulations of reactive oxygen species (ROS) and the activities of antioxidants in two maize hybrids i.e., XD889 and XD319 and two inbred cultivars i.e., Yu13 and Yu37. Individual and combined drought and chilling stresses stimulated the production of O2{square}, H2O2, OH{square} and enhanced malondialdehyde (MDA) contents which led to reduced photosynthetic pigments and morphological growth. Drought, chilling and drought + chilling stress conditions induced the compatible osmolytes, ROS detoxifying proteins and antioxidants to counterbalanced the oxidative damage. It was found that the concurrent occurrence of drought + chilling stress was more lethal for maize seedling growth than the drought and chilling individual stresses. However, the performance of hybrid maize cultivars (XD889 and XD319) was better than the inbred maize cultivars (Yu13 and Yu37). For improving tolerance to individual and concurrent drought and chilling stress in maize, future research focus should be on developing genetically engineer plants that have the ability to generate specific response against sub-optimal temperature and water deficit conditions.

plant biology↗

bioRxiv2019

TLR5 participates in the TLR4 receptor complex and biases towards MyD88-dependent signaling in environmental lung injury

Lung disease causes significant morbidity and mortality, and is exacerbated by environmental injury, e.g. through lipopolysaccharide (LPS) or ozone (O3). Toll-like receptors (TLRs) orchestrate immune responses to injury by recognizing pathogen- or danger-associated molecular patterns. TLR4, the prototypic receptor for LPS, also mediates inflammation after O3, triggered by endogenous hyaluronan. Regulation of TLR4 signaling is incompletely understood. TLR5, the flagellin receptor, is expressed in alveolar macrophages, and regulates immune responses to environmental injury. Using in vivo animal models of TLR4-mediated inflammations (LPS, O3, hyaluronan), we show that TLR5 impacts the in vivo response to LPS, hyaluronan and O3. We demonstrate that immune cells of human carriers of a dominant negative TLR5 allele have decreased inflammatory response to O3 exposure ex vivo and LPS exposure in vitro. Using primary murine macrophages, we find that TLR5 physically associates with TLR4 and biases TLR4 signaling towards the MyD88 pathway. Our results suggest an updated paradigm for TLR4/TLR5 signaling.

immunology↗

bioRxiv2019

Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling

Transcriptional control has been earnestly pursued for the regulation of cellular proliferation associated with cancer progression. The foundational paradigm of targeting transcription factors has yielded exquisite specificity, but many factors cannot yet be targeted. In contrast, targeting epigenetic factors to control chromatin structure and consequential gene expression generally yields more global effects on transcription. Our working paradigm targets neither specific transcription factors nor global epigenetic factors but ATP-dependent chromatin remodeling factors that regulate expression of a limited set of genes. Active DNA-dependent ATPase A Domain inhibitor (ADAADi) synthesized by aminoglycoside phosphotransferases is the first-in-class inhibitor of ATP-dependent chromatin remodeling proteins that targets the ATPase domain of these proteins. Mammalian cells are sensitive to ADAADi but cell lines are variable in their individual responses to the inhibitor. The ADAADi product can be generated from a variety of aminoglycoside substrates with cells showing differential responses to ADAADi depending on the starting aminoglycoside. RNA seq analysis demonstrated that targeting the chromatin remodeling by treatment with a sub-lethal concentration of ADAADi yields alterations to the transcriptional network of the cell. Predominantly, the tumor-promoting genes were repressed while pro-apoptotic and tumor suppressors genes were upregulated on treatment with ADAADi, leading to apoptotic-type cell death. Treatment with ADAADi reversed the EMT process as well as inhibited migration of cells and their colony forming ability. In conjunction with the previous report that treatment with ADAADi regresses tumors in mouse model, this chromatin remodeling inhibitor shows promising anti-tumor properties by targeting the main hallmarks of cancer.

molecular biology↗

bioRxiv2019

Integration of a FT expression cassette into CRISPR/Cas9 construct enables fast generation and easy identification of transgene-free mutants in Arabidopsis

The CRISPR/Cas9 genome editing technique has been widely used to generate transgene-free mutants in different plant species. Several different methods including fluorescence marker-assisted visual screen of transgene-free mutants and programmed self-elimination of CRISPR/Cas9 construct have been use to increase the efficiency of genome edited transgene-free mutants isolation, but the overall time length required to obtain transgene-free mutants has remained unchanged in these methods. We report here a method for fast generation and easy identification of transgene-free mutants in Arabidopsis. By generating and using a single FT expression cassette-containing CRISPR/Cas9 construct, we targeted two sites of the AITR1 gene. We obtained many early bolting plants in T1 generation, and found that about two thirds of these plants have detectable mutations. We then analyzed T2 generations of two representative lines of genome edited early bolting T1 plants, and identified plants without early bolting phenotype, i.e., transgene-free plants, for both lines. Further more, homologues aitr1 mutants were successful obtained for both lines from these transgene-free plants. Taken together, these results suggest that the method described here enables fast generation, and at the mean time, easy identification of transgene-free mutants in plants.

plant biology↗

bioRxiv2019

Tomato spotted wilt virus manipulates the reproduction of its insect vector, western flower thrips (Frankliniella occidentalis), to facilitate transmission

BACKGROUNDTomato spotted wilt virus (TSWV), one of the most devastating viruses of ornamental plants and vegetable crops worldwide, is transmitted by the western flower thrips, Frankliniella occidentalis (Pergande), in a persistent-propagative manner. How TSWV manipulates the reproduction of its vector to enhance transmission and whether infection with TSWV changes the mating behaviour of this thrips vector are not fully understood.\n\nRESULTSIn this study, we found that TSWV-exposed thrips, in general, had a significantly longer developmental time than did non-exposed individuals. Such an increase was predominantly seen in adults, a stage associated with dispersal and virus transmission. TSWV-exposed F. occidentalis produced substantially more progeny than did non-exposed thrips. Interestingly, most of the increase in progeny came from an increase in males, a sex with a greater dispersal and virus transmission capability. Specifically, the sex ratio of progeny shifted from female biased (2-7:1) to evenly split or male biased. Regarding mating behaviour, compared to virus-free controls, TSWV-exposed F. occidentalis had significantly longer copulation duration, were more active in males, and remated less often in females.\n\nCONCLUSIONThese combined results suggest that TSWV alters the reproductive behaviour of its insect vector, F. occidentalis, to promote virus transmission. Consequently, a monitoring program capable of earlier detection of the virus and a reduced economic threshold for vector (thrips) control should be in consideration for the long-term, sustainable management of TSWV.

ecology↗

bioRxiv2019

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

A platform for highly parallel direct sequencing of native RNA strands was recently described by Oxford Nanopore Technologies (ONT); in order to assess overall performance in transcript-level investigations, the technology was applied for sequencing sets of synthetic transcripts as well as a yeast transcriptome. However, despite initial efforts it remains crucial to further investigate characteristics of ONT native RNA sequencing when applied to much more complex transcriptomes. Here we thus undertook extensive native RNA sequencing of polyA+ RNA from two human cell lines, and thereby analysed ~5.2 million aligned native RNA reads which consisted of a total of ~4.6 billion bases. To enable informative comparisons, we also performed relevant ONT direct cDNA- and Illumina-sequencing. We find that while native RNA sequencing does enable some of the anticipated advantages, key unexpected aspects hamper its performance, most notably the quite frequent inability to obtain full-length transcripts from single reads, as well as difficulties to unambiguously infer their true transcript of origin. While characterising issues that need to be addressed when investigating more complex transcriptomes, our study highlights that with some defined improvements, native RNA sequencing could be an important addition to the mammalian transcriptomics toolbox.

bioinformatics↗

bioRxiv2019

Segment 2 from influenza A(H1N1)pdm09 viruses confers temperature sensitive HA yield on candidate vaccine virus growth in eggs that is complemented by PB2 701D

Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with a high-yielding egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 H1N1 pandemic (pdm09) high-growth reassortants (HGRs) selected by this process contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6:2 or 5:3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5:3 viruses replicated better in MDCK-SIAT1 cells than the 6:2 viruses, but the 6:2 CVVs gave higher HA antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as HA yields from eggs for the 5:3 viruses improved substantially when viruses were grown at 35{degrees}C compared with 37.5{degrees}C, whereas 6:2 virus yield did not. Authentic 5:3 pdm09 HGRs, X-179A and X-181, were not markedly temperature-sensitive however, despite their PB1 sequences being identical to that of Cal7, suggestive of compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified single changes in PB2 and NP, 5 in NS1, and 1 in NS2. PB2 N701D but not NP T130A affected the temperature dependency of viral transcription. Furthermore, introducing the PB2 701D change into a 5:3 CVV mimic improved and drastically reduced the temperature sensitivity of HA yield. We conclude that RG PR8 backbones used for vaccine manufacture in eggs should contain PB2 701D to maximise virus yield.

microbiology↗

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↗