Biology subjects

Tahir, M.

Publications and source records attributed to Tahir, M..

9 recordsLinked to original sources

bioRxiv2026

Optimizing the fertilizer N rates at different irrigation levels for optimum yield of wheat and corn at reduced nitrate leaching losses

Optimum irrigation and fertilizer nitrogen (N) rates are important to improve crop yield at reduced environmental risks in the form of NO3-N leaching losses, without any financial loss. The study aimed to investigate the impact of rational irrigation and nitrogen management on wheat and maize crop yield vs. NO3-N leaching losses, with field experiments conducted at the experimental station, University of Agriculture Faisalabad, Pakistan, for two years, with wheat-fallow-corn seasons each year. Suction lysimeter were installed for collection of leachates while soil water balance was computed using the HYDRUS-1D model. We explored the various management strategies, including three irrigation and N levels (sub-optimal, optimal, and supra-optimal, referred to as I1, I2, and I3 for irrigation, and N1, N2, and N3 for nitrogen, respectively) for wheat and maize crops. The three irrigation levels were 325, 400, and 475 mm for wheat, and 375, 525, and 675 mm for maize crops. The three N-levels were 100, 130, and 160 kg ha-1 for wheat, and 220, 270, and 320 kg ha-1 for maize. The results indicated that increasing the irrigation and nitrogen levels significantly improved the growth and yield of both crops during both seasons. The highest grain yield of wheat (4.0 t ha-1) and maize (7.8 t ha-1) was observed with I3N3; however, I2N3 showed statistically no difference in yield, while showing significantly reduced (28.6%) annual NO3-N leaching losses of 23.8 kg ha-1, and the highest financial benefits of 780$. Sub-optimal levels of irrigation and N, though reduced the NO3-N leaching losses, caused significant yield losses, generally unacceptable to the farmers. Irrigation water use efficiency (WUEi) also improved by 12% in wheat and 20% in maize under I2 than that of the I3 level. Besides, considering economic profit, the highest value cost ratio (1.64 and 2.04 in wheat and maize, respectively) was achieved under the I2N3 treatment, as opposed to the other treatments. Based on comprehensive analysis, the I2N3 treatment is recommended for sustainable yield and minimal environmental risk in the wheat-maize cropping system. Moreover, it was observed that the rainy fallow period contributes 14.0-31.5% of the total NO3-N leaching losses. Further investigation is needed to minimize NO3-N leaching losses, especially during the rainy fallow period, by early maize sowing and increasing the efficiency of N fertilizer (such as fertilizer coating) under the flood irrigation system, to achieve the potential goals of sustainable productivity and environmental security.

plant biology↗

bioRxiv2026

Field Modeling Study of Yield Response and Nitrate Leaching with Manure Application and Deficit Irrigation for Maize-Fallow-Wheat Rotation

Efficient nutrient and water management is crucial for enhancing crop productivity, soil health, and mitigating environmental losses in cereal cropping systems of semi-arid regions. A two-year field experiment was conducted to evaluate the effects of dairy manure annual application of 50 Mg ha-1 to maintain recommended fertilizer N, compared to sole urea application with two different irrigation regimes (100% and 75% ETc) on crop yield, water use efficiency, deep percolation, nitrate leaching, and soil quality within a wheat-fallow-maize rotation in Pakistan. Suction lysimeters installed at a depth of 1.2 m were used to collect nitrate-N leachates, while HYDRUS-1D was used to assess daily deep percolation losses. Results indicate that the interaction between manure and irrigation was significant for yield, nitrate-N leaching, and soil health. Manure with deficit irrigation showed wheat and maize yield of 4.36 and 7.80 Mg/ha, irrigation water use efficiency (WUEi) of 1.09 and 1.59 kg/ha/mm, respectively, with no significant increase observed with full irrigation; while a significant decrease was observed in the absence of manure, either with full irrigation or deficit irrigation. Manure with deficit irrigation averaged annual nitrate-N leaching of 17.45 kg/ha, while urea and manure with full irrigation averaged 11.46 and 55.59% increases in nitrate-N leaching losses, respectively, without any yield benefits. Our results indicate that deficit irrigation with manure produces optimum yield with reduced nitrate-N leaching risk and improved soil physical properties.

plant biology↗

bioRxiv2026

SNPstar: A Web Server Linking Allelic Variation to Protein Structure and Function in Arabidopsis thaliana

Understanding how natural genetic variants affect protein structure and function is central to plant biology. The 1001 Genomes Project has catalogued millions of single nucleotide polymorphisms (SNPs) across more than a thousand Arabidopsis thaliana accessions, offering an unprecedented opportunity to relate sequence variation to three-dimensional protein structure and population context. Yet, realizing it requires tools that integrate these scales in one accessible framework. Here we present SNPstar, a web server that links allelic variation in A. thaliana to AlphaFold3-predicted structures through a gene-centric, interactive interface. SNPstar annotates each variant with descriptive features, thermodynamic stability estimates, protein domain context, and genome-wide association results, and computes haplotypes and proteotypes that group accessions by shared DNA or protein sequence. Researchers can characterize variants, visualize their structural context, map their geographic distribution, and prioritize accessions for experimental validation without local computational infrastructure. We demonstrate SNPstar with two case studies. The first recapitulates known loss-of-function variation in the cadmium transporter HMA3, validating that SNPstar prioritizes functionally consequential alleles. The second uses SNPstar-defined proteotypes to identify an N-terminal SNP combination in ARGONAUTE 2 that distinguishes accessions differing in in vitro siRNA-directed target cleavage, linking protein-coding variation to a measurable molecular phenotype. SNPstar thus helps translate natural variation into mechanistic insight.

plant biology↗

bioRxiv2025

3D Biomimetic Liver Cancer Model: Diethylnitrosamine-Induced Proteomic Dysregulations in Stromal-Epithelial Milieu

Hydrogel-based three-dimensional (3D) co-culture systems are emerging as biomimetic platforms that more accurately recapitulate tissue architecture and microenvironmental interactions compared to conventional two-dimensional (2D) cultures. This study introduces an engineered 3D liver-like model to investigate compartment-specific responses to the potent hepatocarcinogen Diethylnitrosamine (DEN), with a focus on early events in carcinogenesis and tumor-stroma interactions. AML12 and 3T3 cell lines were treated with DEN or vehicle either in 2D culture or in 3D hydrogels in four experimental groups: (1) DEN-treated AML12 with vehicle-treated 3T3, (2) DEN-treated 3T3 with vehicle-treated AML12, (3) both cell types DEN-treated, and (4) both vehicle-treated. The cultured recombinants were subjected to proteomic profiling via mass spectrometry, followed by bioinformatics analysis and the results were validated through immunocytochemical staining (ICC). Gene ontology analysis revealed that cytoskeletal, RNA metabolism, and scaffold/adaptor proteins were among the most significantly enriched in 3D versus 2D models. Structural proteins emerged exclusively in mixed 3D co-cultures, reinforcing the organotypic nature of the system. Enriched pathways in 3D included intermediate filament organization, actin dynamics, and focal adhesion--pathways closely associated with liver carcinogenesis. Protein-protein interaction analysis demonstrated maximal network complexity in 3D cultures where both compartments were DEN-exposed. Survival analysis further identified poor-prognosis biomarkers (KRT20, KRT15, KRT14) uniquely enriched in this condition. ICC staining supported the proteomic findings. This organoid-like 3D co-culture model provides a physiologically relevant platform for investigating early-stage liver carcinogenesis and highlights the critical role of stromal-epithelial interactions. Its ability to replicate organ-level complexity and generate clinically relevant proteomic signatures supports its utility in translational cancer research and future drug discovery applications.

cancer biology↗

bioRxiv2025

Differential Proteomic Analysis of DEN-Induced Hepatocellular Carcinoma in Male and Female Balb/c Mice Reveals Novel Gender Specific Markers

BackgroundHepatocellular carcinoma (HCC) is one of the leading causes of hepatic malignancy with a higher prevalence in males compared to females, however, the distinct underlying mechanisms contributing to this disparity remain poorly understood. MethodsIn this study, we aimed to investigate comparative proteome profiling of a diethylnitrosamine (DEN) induced HCC model in male and female Balb/c mice. We extracted proteins from liver tissue of DEN treated male and female mice and their corresponding controls and subjected them to mass spectrometry and subsequent bioinformatics analyses. ResultsWe identified 170 and 233 differentially expressed proteins (DEPs) in female and male mice, respectively. We identified chemical carcinogenesis and cortical cytoskeleton as the shared pathways between the two groups. In addition, we identified distinct signaling pathways in DEN-treated male and female mice. Female mice showed enrichment in oxidative phosphorylation, fatty acid biosynthesis, metabolism and degradation and cytochrome P450 clusters. In contrast, in male mice, these pathways were enriched in cholesterol metabolism, coagulation and mRNA processing. Further, we identified top ten genes ranked by highest maximal clique centrality, by protein-protein interaction analysis of differentially expressed proteins (DEPs) in both sexes. Of these hub genes, female mice showed upregulation of NDUFA8 and ATP5H and were associated with poor patient survival. On the other hand, In DEN-treated male mice upregulation of FGG, FGA, HPX and SERPINC1 were associated with poor survival. ConclusionIn conclusion, our research provides gender-specific proteomic signatures in DEN-induced HCC. The identification of proteins associated cholesterol metabolism and coagulation in males, and mitochondrial complex I proteins in females as prognostic markers suggests novel therapeutic targets that may inform gender-tailored treatment strategies for HCC. Simple SummaryHepatocellular carcinoma (HCC) is a common and deadly liver cancer that affects men more than women. To understand the biological reasons behind this difference, we developed a liver cancer model in male and female mice using a chemical called diethylnitrosamine (DEN). We then studied the proteins involved in tumor development using advanced techniques like mass spectrometry and bioinformatics. We found that different sets of proteins and biological pathways were active in males and females. In males, ribosomal and RNA-binding proteins were linked to worse survival, while in females, mitochondrial proteins were more important. These findings suggest that men and women may need different strategies for diagnosing and treating HCC, and they offer new gender-specific targets for future therapies.

cancer biology↗

bioRxiv2025

Isolation and characterization of synaptic structures from human neural organoids

Human neural organoids (NOs) provide a powerful platform for investigating synaptic development and dysfunction during early neurodevelopment. However, methodologies for isolating functional synaptic structures from these models remain limited. Here, we present a differential centrifugation protocol enabling the enrichment of growth cone particles (GCPs) and immature synaptosomes from air-liquid interface cerebral organoids (ALI-COs) at distinct developmental stages (day 90 and 150). Notably, the method avoids density gradients, requires minimal starting material while maintaining reproducibility across human and murine tissues. Quantitative proteomic profiling revealed significant enrichment of growth cone markers (e.g. GAP43) and classical synaptosomal proteins (e.g. PCLO, BSN, SYN1). Transmission electron microscopy (TEM) confirmed the presence of membrane-enclosed GCPs with fibrous content and mitochondria in day 90 isolates, and immature synaptosomes containing synaptic vesicles on day 150. Functional viability of both types of synaptic structures was demonstrated through KCl-induced depolarization, which triggered phosphorylation changes in growth cone proteins (GAP43, MARCKS, MARCKSL1), cytoskeletal regulators (DCLK1, SHTN1, MARK4, MAP1B) and protein kinases (CAMK2G, PRKCE) in day 90 GCPs, as well as classical synaptic vesicle cycle proteins (SYN1, DNM1, RPH3A) at day 150. Overall, this study establishes a centrifugation-based protocol for isolating growth cones and immature synapses from human organoids, capturing key stages of synaptic development and enabling scalable, patient-compatible models to study synaptic function and dysfunction in neurodevelopmental and neurodegenerative disorders.

neuroscience↗

bioRxiv2023

Palmitoylation of gasdermin D directs its membrane translocation and pore formation in pyroptosis

Gasdermin D (GSDMD)-mediated macrophage pyroptosis plays a critical role in inflammation and host defense. Plasma membrane perforation elicited by caspase-cleaved GSDMD N-terminal domain (GSDMD-NT) triggers membrane rupture and subsequent pyroptotic cell death, resulting in release of pro-inflammatory IL-1{beta} and IL-18. However, the biological processes leading to its membrane translocation and pore formation are not fully understood. Here, using a proteomics approach, we identified fatty acid synthase (FASN) as a GSDMD-binding partner and demonstrated that post-translational palmitoylation of GSDMD at Cys191/Cys192 (human/mouse) led to membrane translocation of GSDMD-NT but not full-length GSDMD. GSDMD lipidation, mediated by palmitoyl acyltransferases ZDHHC5/9 and facilitated by LPS-induced reactive oxygen species (ROS), was essential for GSDMD pore-forming activity and pyroptosis. Inhibition of GSDMD palmitoylation with palmitate analog 2-bromopalmitate or a cell permeable GSDMD-specific competing peptide suppressed pyroptosis and IL-1{beta} release in macrophages, mitigated organ damage, and extended the survival of septic mice. Collectively, we establish GSDMD-NT palmitoylation as a key regulatory mechanism controlling GSDMD membrane localization and activation, providing a novel target for modulating immune activity in infectious and inflammatory diseases. One Sentence SummaryLPS-induced palmitoylation at Cys191/Cys192 is required for GSDMD membrane translocation and its pore-forming activity in macrophages.

immunology↗

bioRxiv2020

Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies

Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrated robust, sensitive, and reproducible data generation across eleven sites in nine countries on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality.

molecular biology↗

bioRxiv2020

Increasing proteome coverage using cysteine-specific DIA Mass spectrometry - Cys-DIA

We report a Data Independent Analysis (DIA) mass spectrometric method for quantitative proteomics based on cysteine-containing peptides derived by tryptic digestion from biological samples (termed Cys-DIA). This technology significantly increases the coverage of the identifiable and quantifiable proteome in DIA/SWATH analyses by >35% compared to the conventional DIA/SWATH methods. The strategy was applied here to illustrate the quantitative difference in the proteome between isogenic human cancer cell lines with different metastatic capabilities.

biochemistry↗