Biology subjects

Waqas, M.

Publications and source records attributed to Waqas, M..

6 recordsLinked to original sources

bioRxiv2026

Discovering genetic loci associated with rate of vegetative index gain using UAV-based phenomics in spring wheat

In wheat, the pre-heading stage determines spikelet formation, floret fertility, and canopy development, making it a critical window for early stress detection and yield potential. The genetic basis of pre-heading canopy development in wheat has remained constrained by the conventional phenotyping due to the low temporal resolution. Here, we quantified the rate of vegetation index gain (RVIs) during tillering to heading stages using UAV-mounted multispectral sensor in 196 spring wheat cultivars representing 112 years of breeding history. RVIs were calculated using six vegetation indices for consecutive two growing seasons, and genome wide association study (GWAS) was performed on RVIs, grain yield (GY) and thousand grain weight (TGW) using a wheat 37K SNP array. RVIs showed significant positive correlations with grain yield (r=0.28-0.43; p<0.001) and consistently increased in the modern cultivars compared to old cultivars. This indicated that resource remobilization during pre-heading canopy development significantly contributed to GY during modern wheat breeding. GWAS identified 67 loci, including 12 Group-I loci associated only with RVIs, and 18 Group-II loci associated with both RVIs and yield traits. Two stable loci on chr1B and chr5D consistently increased GY and RVIs across environments, and the tag SNPs were converted to selectable KASP markers. The allelic distribution on global wheat collection of [~]3000 accessions showcased that favorable alleles on both loci were dominant in cultivars compared to landraces. Similarly, favorable alleles showed more frequency in winter type than spring type. Across breeding eras both alleles showed increasing trend with chr5D reaching near fixation and chr1B remaining partially enriched in modern cultivars. Our work on capturing pre-heading canopy development, discovery of two stable loci underpinning yield and RVIs, and development of KASP markers provided a strong foundation to HTP assisted genetic dissection of GY and facilitated the understanding of canopy dynamics and yield formation.

plant biology↗

bioRxiv2024

Different hydrological conditions after permafrost thaw result in distinct microbial community compositions

Permafrost degradation leads to the formation of contrasting hydrological conditions such as water-saturated anoxic and dry oxic soils, which significantly influence the bacterial community structure and abundance. To investigate the bacterial abundance and diversity under these hydrological conditions, we collected soil samples from different horizons of both dry and wet degraded permafrost soils and non-degraded intact permafrost soil for comparison. The bacterial alpha diversity, measured by the Observed and Chao1 indices, was significantly greater in wet degraded permafrost soil (wet site) and intact permafrost soil (intact site) than in dry degraded permafrost soils (dry site). Notably, the wet and intact sites exhibited similar levels of alpha diversity as well as shared greater number of zOTUs. The relative proportion of most bacterial taxa was significantly differed among the sites. At the class level, dry site was dominated mainly by K-strategic bacteria like aliphatic degraders (Thermoleophilia), acidophilic and cellulolytic (Acidobacteriae), while wet site was dominated by mainly r-strategic bacteria from class Gammaproteobacteria and anoxygenic aerobic phototrophs (Gemmatimonadetes). According to Spearman correlation analysis, the relative proportion of bacterial taxa in dry and wet sites showed significant correlation with soil physicochemical parameters, whereas fewer correlations were found in intact site. The relative proportion of Pseudomonadota classes and Acidobacteriota were positively correlated with SOC, N, and C:N ratio, but were negatively correlated with pH in both dry and wet sites. In contrast, anaerobic methylotrophs (Methylomirabilota), anoxygenic photoheterotrops (Chloroflexota), Gemmatimonadota and filamentous Actinobacteriota were negatively correlated with SOC, N, and C:N. Additionally, strong correlations were observed between bacterial taxa and extracellular enzyme activities, where Alphaproteobacteria, Gammaproteobacteria, and Acidobacteriota showed positive correlations with both hydrolytic and oxidative enzymes in dry and wet sites, except for PerOx in wet site where they showed negative correlation. Conversely, Gemmatimonadota and Actinobacteriota displayed negative correlations with enzymes in dry and wet site, except for the PerOx in wet site, where they showed positive correlation.

ecology↗

bioRxiv2024

Stick together: Isolation and characterization of exopolysaccharide producing bacteria from degraded permafrost soils

Bacterial exopolysaccharides (EPSs) are the high-molecular-weight polymers secreted into their surrounding that play a crucial role in bacterial survival, environmental adaptation, biofilms formation, and interaction with surrounding matrices. EPSs may also contribute to soil structure development by enhancing soil aggregate stability, promoting soil cohesion, and interacting with soil particles through their diverse functional group constituents and conditioning film characteristics. This study aimed to isolate and characterize potential EPSs-producing bacteria from the active layer of two different hydrological landscape of degraded permafrost soils, and from undisturbed intact permafrost soil. A total of 54 bacterial isolates were obtained, representing three phyla: Firmicutes, Actinomycetota, and Pseudomonadota. EPSs production was assessed by determining the polysaccharide content measured as glucose equivalent, and 26 isolates were identified as potential EPSs producers. Among the isolates, Curtobacterium oceanosedimentum, Frigoribacterium faeni, Streptomyces strains, Neobacillus bataviensis and Mesobacillus subterraneus exhibited the highest polysaccharide yield. The carbohydrate content of the extracted EPSs varied in both composition and quantity across the different isolates. Uronic acids such as glucuronic acid was found in the EPSs produced by the isolates closely related to Curtobacterium oceanosedimentum and Neobacillus bataviensis, while the amino hexoses were identified in EPSs extracted from various isolates, including those affiliated with Bacillus, Streptomyces, Luteimonas, and Phyllobacterium. The potential EPSs producing bacteria were also found inhabiting in the different horizons of both degraded permafrost soil and undisturbed intact permafrost soil, by determining their relative proportion within the total bacterial community based on 16S rRNA gene sequences similarities.

microbiology↗

bioRxiv2024

The methane-cycling microbiome in intact and degraded permafrost soils of the pan-Arctic

The methane-cycling microbiomes in Arctic permafrost-affected soils play crucial roles in the production and consumption of this important greenhouse gas. However, little is known about the distributions of Arctic methanogens and methanotrophs across the regional scale and along the vertical soil profile, as well as their responses to the widespread permafrost thaw. Using a unique sample set from nine different locations across the pan-Arctic, we identified methanogen and methanotroph phylotypes in 729 datasets of 16S rRNA gene amplicons. In 621 samples of intact permafrost soils across the pan-Arctic, only 22 methanogen and 26 methanotroph phylotypes were identified. Relative abundances of both functional groups varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations, with the hydrogenotrophic Methanobacterium lacus dominating. Remarkably, the permafrost soil methane filter was almost exclusively comprised of a few phylotypes closely related to the obligate methanotrophic species Methylobacter tundripaludum. In degraded permafrost sites in Alaska, M. tundripaludum also dominated the methanotroph microbiome in the wet site. However, in dry, water-drained former permafrost site, Methylocapsa phylotypes, closely related with the atmospheric methane oxidizing bacteria, were exclusively found and dominant, indicating a massive restructuring of the methanotroph guild that consequently resulted in functional changes from a soil methane filter to an atmospheric methane sink. This study provides first insights into the identity and intricate spatial distribution of methanotrophs and methanogens in permafrost soils at a pan-Arctic scale and their responses to different water status after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic CH4 dynamics in a warming climate and that under future dry conditions more atmospheric CH4 uptake in Arctic upland soils might happen.

microbiology↗

bioRxiv2021

Designing Novel and Potent Inhibitors for Multi Drug-Resistant Tuberculosis: A Computational Approach

Tuberculosis is a major global health problem and is still among the top 10 causes of death. The increasing rate of drug resistance to infectious agents has provoked an urgent need to discover novel anti-tuberculosis agents with novel modes of action. In this study, small molecule inhibitors of the proteins encoded by the drug resistant genes, i.e., katG, gyrA, pncA and rpoB of Mycobacterium tuberculosis (M. tuberculosis), were identified using computational methods. In the ligand base pharmacophore, an already reported four ligands for the four proteins encoded by the resistant genes of M. tuberculosis were selected for the generation of pharmacophores. The validated pharmacophores model of all the four proteins, generated on the basis of ligand base, were selected for further screening of ZINC drug like database. As screening results 486 structurally diverse hits for katG, 542 for PncA, 112 for rpoB and 365 for gyrA were mapped and filtered via Lipinskis rule of five. Finally, on the basis of docking score and binding interactions, ten small molecules were selected for each protein as novel inhibitors. These selected novel inhibitors have significant interaction with the active site of the protein and a strong possibility to act as an additional starting opinion in the development of new and potential inhibitors. The result indicates that novel inhibitors could be a promising lead compound and be effective in treating sensitive as well as multi drug resistant tuberculosis.

bioinformatics↗

bioRxiv2020

Alzheimer's disease risk gene BIN1 induces Tau-dependent network hyperexcitability

Genome-wide association studies identified the BIN1 locus as a leading modulator of genetic risk in Alzheimers disease (AD). One limitation in understanding BIN1s contribution to AD is its unknown function in the brain. AD-associated BIN1 variants are generally noncoding and likely change expression. Here, we determined the effects of increasing expression of the major neuronal isoform of human BIN1 in cultured hippocampal neurons. Higher BIN1 induced network hyperexcitability on multielectrode arrays, increased frequency of synaptic transmission, and elevated calcium transients, indicating that increasing BIN1 drives greater neuronal activity. In exploring the mechanism of these effects on neuronal physiology, we found that BIN1 interacted with L-type voltage-gated calcium channels (LVGCCs) and that BIN1-LVGCCs interactions were modulated by Tau in vitro and in vivo. Finally, Tau reduction prevented BIN1-induced network hyperexcitability. These data shed light on BIN1s neuronal function and suggest that it may contribute to Tau-dependent hyperexcitability in AD.

neuroscience↗