Biology subjects

Duffy, C. D. P.

Publications and source records attributed to Duffy, C. D. P..

4 recordsLinked to original sources

bioRxiv2025

Evaluating Transcriptomic Integration for Cyanobacterial Constraint-based Metabolic Modelling

1Metabolic modelling has wide-ranging applications, including for the production of high-value compounds, understanding complex disease and analysing community interactions. Integrating transcriptomic data with genome-scale metabolic models is crucial for deepening our understanding of complex biological systems, as it enables the development of models tailored to specific conditions, such as particular tissues, environments, or experimental setups. Relatively little attention has been given to the assessment of such integration methods in predicting intracellular fluxes. While a few validation studies offer some insights, their scope remains limited, particularly for organisms like cyanobacteria, for which little metabolic flux data are available. Cyanobacteria hold significant biotechnological potential due to their ability to synthesize a wide range of high-value compounds with minimal resource inputs [21]. The impact of specific methodological decisions on integration, however, has scarcely been assessed beyond human models, with no thorough exploration of parameter choices in valve-based integration methods. By implementing a novel analysis pipeline, we evaluated these methodological decisions using the genome-scale model for Synechocystis sp. PCC 6803 (iSynCJ816 [17]) with existing transcriptomic data in biomass-optimised scenarios. Our analyses indicate that selecting an appropriate integration method may not always be straightforward and depends on the initial model configuration - a factor which is often overlooked during integration. By evaluating sets of methods, we identified a trade-off between the buffering of light into the system and maintenance of flux near system boundaries. We suggest that the use of the lazy-step mapping function with importance-based scaling results in the best predictions, particularly when these can be validated with experimental data. When using one-size-fits-all scaling with the lazy-step mapping function, it appears preferable to use light buffering to avoid inappropriate bound changes near the photosystems, a factor which importance-based scaling may help to compensate for. In cases where no experimental data can be used for validation, the novel thresholding approach could be adopted as this showed some improvements upon the standard Lazy method.

systems biology↗

bioRxiv2024

Predicting photosynthetic structures using thermodynamics and machine learning

Oxygenic photosynthesis is responsible for nearly all biomass production on Earth, and may have been a prerequisite for establishing a complex biosphere rich in multicellular life. Life on Earth has evolved to perform photosynthesis in a wide range of light environments, but with a common basic architecture of a light-harvesting antenna system coupled to a photochemical reaction centre. Using a generalized thermodynamic model of light-harvesting, coupled with an evolutionary algorithm, we predict the type of light-harvesting structures that might evolve in light of different intensities and spectral profiles. We reproduce qualitatively the pigment composition, linear absorption profile and structural topology of the antenna systems of multiple types of oxygenic photoautotrophs, suggesting that the same physical principles underlie the development of distinct antenna structures in various light environments. Finally we apply our model to representative light environments that would exist on Earth-like exoplanets, predicting that both oxygenic and anoxygenic photosynthesis could evolve around low mass stars, though the latter would seem to work better around the coolest M-dwarfs. We see this as an interesting first step toward a general evolutionary model of basic biological processes and proof that it is meaningful to hypothesize on the nature of biology beyond Earth.

biophysics↗

bioRxiv2021

Trivial Excitation Energy Transfer to Carotenoids is an Unlikely Mechanism for Non-Photochemical Quenching in LHCII

Higher plants defend themselves from bursts of intense light via the mechanism of Non-Photochemical Quenching (NPQ). It involves the Photosystem II (PSII) antenna protein (LHCII) adopting a conformation that favours excitation quenching. In recent years several structural models have suggested that quenching proceeds via energy transfer to the optically forbidden and short-lived S1 states of a carotenoid. It was proposed that this pathway was controlled by subtle changes in the relative orientation of a small number of pigments. However, quantum chemical calculations of S1 properties are not trivial and therefore its energy, oscillator strength and lifetime are treated as rather loose parameters. Moreover, the models were based either on a single LHCII crystal structure or Molecular Dynamics (MD trajectories) about a single minimum. Here we try and address these limitations by parameterizing the vibronic structure and relaxation dynamics of lutein in terms of observable quantities, namely linear absorption (LA) transient absorption (TA) and two-photon excitation (TPE) spectra. We also analyze a number of minima taken from an exhaustive meta-dynamical search of the LHCII potential energy surface. We show that trivial, Coulomb-mediated energy transfer to S1 is an unlikely quenching mechanism. Pigment movements are insufficient to switch the system between quenched and unquenched states. Modulation of S1 energy level as a quenching switch is similarly unlikely. Moreover, the quenching predicted by previous models is likely an artefact of quantum chemical over-estimation of S1 oscillator strength and the real mechanism likely involves non-trivial inter-molecular states.

biophysics↗

bioRxiv2020

Regulation of light harvesting in multimeric and monomeric photosystem II supercomplexes

An intriguing architecture called semi-crystalline photosystem II (PSII) array has been observed in the thylakoid membranes in vascular plants. It is an array of PSII-light harvesting complex II (LHCII) supercomplexes only appears in the low-light, whose functional role has not been clarified. We identified PSII-LHCII supercomplexes in their monomeric and multimeric forms in the low-light acclimated spinach leaves and prepared them using sucrose density gradient-ultracentrifugation in the presence of amphipol A8-35. When the leaves were acclimated to high-light, however, only monomeric forms were present. Single particle electron microscopy identified that the multimeric PSII-LHCII supercomplexes were composed of two ( megacomplex) or three ( arraycomplex) units of PSII-LHCII supercomplexes, which aligned like a fraction of the semi-crystalline array. Further characterization using fluorescence analysis revealed that multimeric forms have a higher light-harvesting capability, but a lower thermal dissipation capability than the monomeric form, suggesting such a configurational conversion of PSII-LHCII supercomplexes possibly serves as a structural basis for the plants acclimation to environmental light.

plant biology↗