Biology subjects

Hassan, T.

Publications and source records attributed to Hassan, T..

5 recordsLinked to original sources

bioRxiv2026

GreenSloth: a curated database and executable platform for mechanistic photosynthesis models

Mechanistic models of photosynthesis have expanded substantially over the past decades, covering processes from light reactions to carbon fixation. However, these models remain fragmented across the literature, inconsistently implemented, and difficult to reproduce or reuse, limiting their adoption beyond the research group that developed them. Here, we present GreenSloth, a freely accessible web-based database of 22 published mechanistic photosynthesis models, reimplemented as standardized, executable Python objects within MxlPy, an open-source framework for mechanistic biological modeling. Although the database is primarily designed for dynamic mechanistic models formulated as ordinary differential equations, the current implementation also includes the fields most widely cited steady-state mechanistic model and its variants. GreenSloth provides a structured environment for model discovery, comparison, and reuse, addressing reproducibility challenges in the field and enabling integration into emerging hybrid modeling approaches. It is also interactive: each model runs directly in the browser, with no installation, environment setup, or programming required. The resource is openly accessible and designed for long-term community maintenance, hoping to position itself as foundational infrastructure for the photosynthesis modeling community. Database URLhttps://greensloth.rwth-aachen.de/

systems biology↗

bioRxiv2026

Disentangling the sucrose metabolism of the corn smut Ustilago maydis reveals unexpected complexity

The race for carbohydrates shapes organismic interactions. In plant pathogenic fungi, sucrose is a key nutrient as it constitutes the major transport sugar in plants. Here, we investigate sucrose acquisition in the corn smut fungus Ustilago maydis, a biotrophic pathogen that transitions from yeast-like to hyphal growth for infection. We establish that the fungus encodes a secreted acidic invertase, Suc2, with a dimeric canonical glycoside hydrolase 32 architecture. Comparative biochemical analyses across fungal homologs indicate that this dimeric architecture represents the predominant state, whereas higher-order oligomers, as initially described for Saccharomyces cerevisiae Suc2, are restricted to a subset of lineages. Unexpectedly, elimination of Suc2 did not impair yeast-like growth on sucrose. Similarly, deletion of genes for sucrose transporter Srt1 and cytosolic hydrolase Suc1, typically associated with intracellular sucrose metabolism, did not abolish growth. Instead, sucrose utilization during yeast-like growth depended on a repurposed non-canonical module comprising maltose transporter Agt1 and intracellular (iso)maltases. In contrast, pathogenic development strongly relied on the canonical intracellular sucrose utilization pathway mediated by Srt1 and Agt1. Infection was strongly diminished in strains unable to metabolise sucrose, confirming its central nutritional role for the fungus. Together, our work defines the complete sucrose utilization repertoire of U. maydis and uncovers a lifestyle-dependent metabolic switch between alternative sucrose acquisition strategies. Flexible carbon acquisition might represent a widespread adaptive strategy in basidiomycete pathogenic fungi.

microbiology↗

bioRxiv2026

Cooperation, privatization and cheating in microbial exoenzyme synthesis: theoretical analysis in view of biotechnological applications

This study presents a mathematical framework for investigating the dynamics of coexistence and competition among heterotrophic microbes across different time scales. Focusing on metabolic interactions, we examine how three strategies: public metabolizing, private metabolizing, and cheating, shape population behaviour. The framework integrates generalized Lotka-Volterra dynamics with evolutionary game theory to capture the effects of resource exchange, particularly glucose made available by public metabolizers and sucrose as a shared substrate driving population growth. Game-theoretic payoffs encode ecological costs and benefits, enabling analysis of frequency-dependent interactions among strategies. To capture evolutionary realism, we implement laboratory-inspired simulations in which strategies can switch between generations, mimicking mutation or phenotypic plasticity in microbial populations. These eco-evolutionary dynamics reveal conditions under which all three strategies coexist at interior equilibria and show how variation in growth advantages and, illustratively, phenotype-switching perturbations produce evolutionary shifts. Numerical analysis identifies ecological thresholds and fitness asymmetries that determine system robustness, long-term coexistence, and the persistence of a synthetic, cross-kingdom system linked by nutrient exchange. Together, these insights provide general principles for microbial coexistence and offer design guidelines for ecosystem engineering, biotechnological applications, and the construction of stable synthetic communities under ecological and evolutionary constraints.

ecology↗

bioRxiv2026

Context-dependent siderophore exploitability shapes microbial community structure

1)Siderophores are classically viewed as shared iron-scavenging public goods, yet their ecological roles in multispecies communities remain poorly defined. Here, we establish a synthetic microbial community to dissect how different siderophores, their uptake compatibility and spatial structure shape iron competition. Using Corynebacterium glutamicum as a model, we show that this siderophore non-producer accesses diverse xenosiderophores, including enterobactin secreted by Escherichia coli. However, exploitation was constrained and co-cultures converged to stable compositions. Dose-response experiments combined with mathematical modelling indicated that the producer retains more effective access to enterobactin than the exploiter. Presence of Pseudomonas putida altered this interaction, as it exploited enterobactin while producing pyoverdine, a siderophore inaccessible to the other community members that restricted their iron access. Across different cultivation scales, community dynamics was strongly influenced by spatial organization and initial composition. These findings identify siderophores as context-dependent iron-allocation agents that can promote microbial coexistence or exclusion.

microbiology↗

bioRxiv2025

Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds

Lactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains, isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the genera Pediococcus and Lactiplantibacillus.

genomics↗