Biology subjects

Sena, G.

Publications and source records attributed to Sena, G..

7 recordsLinked to original sources

bioRxiv2025

Patterned 3D-printed hydrogel as a novel soilless substrate for plant cultivation

Plant roots need water, micronutrients, and oxygen to maintain cellular metabolism and tissue growth, yet traditional hydroponic systems often lack sufficient oxygen delivery. While 3D printing artificial substrates has been explored to mimic the physical structure of soil, it remains unclear which design parameters are critical for supporting full plant development. Here, we present a synthetic, soilless substrate based on 3D-printed hydrogels incorporating triply periodic minimal surface (TPMS) patterns to create internal air-filled channels. These channels are open to the atmosphere, enabling passive gas exchange throughout the substrate. We tested five TPMS geometries (Lidinoid, Split-P, Schwarz-D, Schwarz-P, and Schoen), each with a near-identical hydrogel volume but with different surface-to-volume ratios. Arabidopsis thaliana seeds germinated directly on the substrates and were monitored for vegetative and reproductive growth over five weeks. Among the designs, the Lidinoid substrate led to the highest number and surface area of leaves, exceeding the aerated hydroponic control in leaf area over most of the time course; it also produced the earliest and most complete flowering, which neither control achieved in the same amount of time. Our results indicate that the surface-to-volume ratio is a key parameter influencing substrate performance; we hypothesise that this reflects its effect on oxygen availability at the root interface, which we did not measure directly. Plants grown on substrates with higher surface areas transitioned to flowering more reliably and rapidly, with flowering efficiency showing a strong positive correlation with surface area. These findings suggest that interconnected air-channel architectures can support full plant development without active aeration, potentially by overcoming the oxygen limitations of traditional hydroponic systems. This work supports the use of additive manufacturing as a powerful tool for engineering soil analogues tailored for indoor agriculture. By combining passive aeration with hydration and nutrient delivery, patterned hydrogels offer a promising, scalable solution for sustainable soilless plant cultivation.

plant biology↗

bioRxiv2023

Intermittent cell division dynamics in regenerating Arabidopsis roots reveals complex long-range interactions

In this work, we present a quantitative comparison of the cell division dynamics between populations of intact and regenerating root tips in the plant model system Arabidopsis thaliana. To achieve the required temporal resolution and to sustain it for the duration of the regeneration process, we adopted a live imaging system based on light-sheet fluorescence microscopy, previously developed in the laboratory. We offer a straightforward quantitative analysis of the temporal and spatial patterns of cell division events showing a statistically significant difference in the frequency of mitotic events and spatial separation of mitotic event clusters between intact and regenerating roots.

plant biology↗

bioRxiv2023

Long-term root electrotropism reveals habituation and hysteresis

Plant roots sense many physical and chemical cues in soil, such as gravity, humidity, light and chemical gradients, and respond by redirecting their growth towards or away from the source of the stimulus. This process is called tropism. While gravitropism is the tendency to follow the gravitational field downwards, electrotropism is the alignment of growth with external electric fields and the induced ionic currents. Although root tropisms are at the core of their ability to explore large volumes of soil in search of water and nutrients, the molecular and physical mechanisms underlying most of them remain poorly understood. We have previously provided a quantitative characterization of root electrotropism in Arabidopsis (Arabidopsis thaliana) primary roots exposed for 5 hours to weak electric fields, showing that auxin asymmetric distribution is not necessary but that cytokinin biosynthesis is. Here, we extend that study showing that long-term electrotropism is characterized by a complex behavior. We describe overshoot and habituation as key traits of long-term root electrotropism in Arabidopsis and provide quantitative data about the role of past exposures in the response to electric fields (hysteresis). On the molecular side, we show that cytokinin, although necessary for root electrotropism, is not asymmetrically distributed during the bending. Overall, the data presented here represent a significant step forward towards the understanding of the molecular mechanisms regulating electrotropism in plants and provide a quantitative platform for future studies on the genetics of this and other tropisms.

plant biology↗

bioRxiv2023

Enhanced germination and electrotactic behaviour of Phytophthora palmivora zoospores in weak electric fields.

Soil-dwelling microorganisms use a variety of chemical and physical signals to navigate their environment. Plant roots produce endogenous electric fields which result in characteristic current profiles. Such electrical signatures are hypothesised to be used by pathogens and symbionts to track and colonise plant roots. The oomycete pathogen Phytophthora palmivora generates motile zoospores which swim towards the positive pole when exposed to an external electric field in vitro. Here, we provide a quantitative characterization of their electrotactic behaviour in 3D. We found that a weak electric field (0.7 - 1.0 V/cm) is sufficient to induce an accumulation of zoospore at the positive pole, without affecting their encystment rate. We also show that the same external electric field increases the zoospore germination rate and orients the germ tubes growth. We conclude that several early stages of the P. palmivora infection cycle are affected by external electric fields. Taken together, our results are compatible with the hypothesis that pathogens use plant endogenous electric fields for host targeting.

biophysics↗

bioRxiv2020

Root electrotropism in Arabidopsis does not depend on auxin distribution, requires cytokinin biosynthesis and follows a power-law response curve

An efficient foraging strategy for plant roots relies on the ability to sense multiple physical and chemical cues in soil and to reorient growth accordingly (tropism). Root tropisms range from sensing gravity (gravitropism), light (phototropism), water (hydrotropism), touch (thigmotropism) and more. Electrotropism, also known as galvanotropism, is the phenomenon of aligning growth with external electric fields and currents. Although observed in a few species since the end of the 19th century, the molecular and physical mechanism of root electrotropism remains elusive, limiting the comparison to more defined sensing pathways in plants. Here we provide a first quantitative and molecular characterisation of root electrotropism in the model system Arabidopsis thaliana, showing that it does not depend on an asymmetric distribution of the plant hormone auxin, but that instead it requires the biosynthesis of a second hormone, cytokinin. We also show that the dose-response kinetics of the early steps of root electrotropism follows a power law analogous to the one observed in some physiological reactions in animals. A future full molecular and quantitative characterisation of root electrotropism would represent a step forward towards a better understanding of signal integration in plants, and an independent outgroup for comparative analysis of electroreception in animals and fungi.

plant biology↗

bioRxiv2018

Tracking transient fluorescent events in structured point clouds

BackgroundParticle-tracking in 3D is an indispensable computational tool to extract critical information on dynamical processes from raw time-lapse imaging. This is particularly true with in vivo time-lapse fluorescence imaging in cell and developmental biology, where complex dynamics are observed at high temporal resolution. Common tracking algorithms used with time-lapse data in fluorescence microscopy typically assume a continuous signal where background, recognisable keypoints and independently moving objects of interest are permanently visible. Under these conditions, simple registration and identity management algorithms can track the objects of interest over time. In contrast, here we consider the case of transient signals and objects whose movements are constrained within a tissue, where standard algorithms fail to provide robust tracking. ResultsTo optimize 3D tracking in these conditions, we propose the merging of registration and tracking tasks into a fuzzy registration algorithm to solve the identity management problem. We describe the design and application of such an algorithm, illustrated in the domain of plant biology, and make it available as an open-source software implementation. The algorithm is tested on mitotic events in 4D data-sets obtained with light-sheet fluorescence microscopy on growing Arabidopsis thaliana roots expressing CYCB::GFP. We validate the method by comparing the algorithm performance against both surrogate data and manual tracking. ConclusionThis method fills a gap in existing tracking techniques, following mitotic events in challenging data-sets using transient fluorescent markers in unregistered images.

bioinformatics↗

bioRxiv2018

Linear stability analysis of morphodynamics during tissue regeneration in plants

One of the key characteristics of multicellular organisms is the ability to establish and maintain shapes, or morphologies, under a variety of physical and chemical perturbations. A quantitative description of the underlying morphological dynamics is a critical step to fully understand the self-organising properties of multicellular systems. Although many powerful mathematical tools have been developed to analyse stochastic dynamics, rarely these are applied to experimental developmental biology.\n\nHere, we take root tip regeneration in the plant model system Arabidopsis thaliana as an example of robust morphogenesis in living tissue, and present a novel approach to quantify and model the relaxation of the system to its unperturbed morphology. By generating and analysing time-lapse series of regenerating root tips captured with confocal microscopy, we are able to extract and model the dynamics of key morphological traits at cellular resolution. We present a linear stability analysis of its Markovian dynamics, with the stationary state representing the intact root in the space of morphological traits. We find that the resulting eigenvalues can be classified into two groups, suggesting the co-existence of two distinct temporal scales during the process of regeneration.\n\nWe discuss the possible biological implications of our specific results, and suggest future experiments to further probe the self-organising properties of living tissue.

systems biology↗