Prediction and experimental evidence of the optimisation of the angular branching process in the thallus growth of Podospora anserina

Based upon apical growth and hyphal branching, the two main processes that drive the growth pattern of a fungal network, we propose here a two-dimensions simulation based on a binary-tree modelling allowing us to extract the main characteristics of a generic thallus growth. In particular, we showed that, in a homogeneous environment, the fungal growth can be optimized for exploration and exploitation of its surroundings with a specific angular distribution of apical branching. Two complementary methods of extracting angle values have been used to confront the result of the simulation with experimental data obtained from the thallus growth of the saprophytic filamentous fungus Podospora anserina. Finally, we propose here a validated model that, while being computationally low-cost, is powerful enough to test quickly multiple conditions and constraints. It will allow in future works to deepen the characterization of the growth dynamic of fungal network, in addition to laboratory experiments, that could be sometimes expensive, tedious or of limited scope.Comment: Submitted to Scientific Repor

Multiscale characterization of the growth dynamics of a fungal network : study of the filamentous fungus Podospora anserina

La forme végétative des champignons filamenteux est constituée par un réseau branchant d'hyphes en croissance, le mycélium. Cette structure dynamique permet le développement optimal de l'organisme jusqu'à la reproduction, en lui conférant une capacité d'exploration et d'exploitation efficace de son environnement. Dans cette étude, la dynamique de croissance en deux dimensions du champignon filamenteux Podospora anserina a été caractérisée par une approche multi-échelle. À partir d'un dispositif de microscopie en champ clair développé au laboratoire, nous obtenons une collection d'images du mycélium, régulièrement réparties sur les 20 premières heures de croissance à partir de la germination d'une ascospore. Les images couvrent l'intégralité de la surface du mycélium (jusqu'à 1 cm), tout en conservant une résolution permettant de distinguer individuellement les hyphes (5 µm). L'analyse du réseau mycélien dans sa globalité s'appuie sur l'extraction de grandeurs dynamiques caractéristiques du développement et de la complexité du réseau : longueur du mycélium, nombre d'apex et de noeuds (connexions entre les hyphes), ou encore surfaces délimitées par les hyphes. Ainsi, les profils de croissance de mycéliums résultant de conditions de croissance variées (contraintes nutritives, lumineuses ou de température) ont été précisément quantifiés. D'autre part, une analyse à l'échelle de l'hyphe (environ 5 µm) a permis de caractériser les vitesses de croissance des apex, la répartition des branchements le long de l'hyphe, et les interactions entre deux branches proches au sein du mycélium. Une distinction claire entre hyphes latérales et apicales a pu ainsi être établie. De plus, en nous appuyant sur une simulation du réseau mycélien de P. anserina sous la forme d'un arbre binaire, et calibrée à partir des données expérimentales, nous montrons comment le mycélium optimise extension et densification. Tout, d'abord la distribution observée des angles de branchement apicaux correspond à la maximisation de l'extension radiale et orthoradiale du thalle, tout en minimisant les chevauchements. Dans un deuxième temps, nous montrons que les hyphes latérales maximisent l'exploitation du substrat par croissance radiale de la densité en retard de phase avec le front d'exploration. Enfin, des structures intracellulaires ont été observées par une approche de microscopie en fluorescence. En particulier, la dynamique des noyaux, du Spitzenkörper, et la répartition des septa chez P. anserina ont été analysées.The vegetative form of filamentous fungi is constituted by a branching network of growing hyphae, the mycelium. This dynamical structure allows for the optimal development of the organism until reproduction, giving it a capacity to explore and exploit its environment efficiently. In this study, the two-dimensional growth dynamics of the filamentous fungus Podospora anserina was characterized using a multiscale approach. From a bright field microscopy device developed in the laboratory, we obtain a collection of images of the mycelium, evenly distributed over the first 20 hours of growth from the germination of an ascospore. The images cover the entire surface of the mycelium (up to 1 cm), while keeping a resolution allowing us to distinguish individual hyphae (5 µm). The analysis of the mycelial network as a whole was based on the extraction of dynamical quantities which are characteristic of the development and the complexity of the network: length of the mycelium, number of apexes and nodes (connections between hyphae), or surfaces delimited by hyphae. The growth profiles of mycelia resulting from various growth conditions (nutrient, light or temperature constraints) were precisely quantified. On the other hand, an analysis at the hypha scale (about 5 µm) enabled us to characterize the growth rates of the apexes, the distribution of branches along the hypha, and the interactions between two close branches within the mycelium. A clear distinction between lateral and apical hyphae could be established. Furthermore, based on a simulation of the mycelial network of P. anserina in the form of a binary tree, and calibrated from experimental data, we showed how the mycelium optimizes extension and densification. First, the observed distribution of apical branching angles corresponds to the maximization of radial and orthoradial extension of the thallus, while minimizing overlaps. Second, we showed that lateral hyphae maximize substrate exploitation by radial density growth lagging behind the exploration front. Finally, intracellular structures were observed by a fluorescence microscopy approach. In particular, the dynamics of the nuclei, the Spitzenkörper, and the distribution of septa in P. anserina were analyzed

Caractérisation multi-échelle de la dynamique de croissance d'un réseau fongique : étude du champignon filamenteux Podospora anserina

The vegetative form of filamentous fungi is constituted by a branching network of growing hyphae, the mycelium. This dynamical structure allows for the optimal development of the organism until reproduction, giving it a capacity to explore and exploit its environment efficiently. In this study, the two-dimensional growth dynamics of the filamentous fungus Podospora anserina was characterized using a multiscale approach. From a bright field microscopy device developed in the laboratory, we obtain a collection of images of the mycelium, evenly distributed over the first 20 hours of growth from the germination of an ascospore. The images cover the entire surface of the mycelium (up to 1 cm), while keeping a resolution allowing us to distinguish individual hyphae (5 µm). The analysis of the mycelial network as a whole was based on the extraction of dynamical quantities which are characteristic of the development and the complexity of the network: length of the mycelium, number of apexes and nodes (connections between hyphae), or surfaces delimited by hyphae. The growth profiles of mycelia resulting from various growth conditions (nutrient, light or temperature constraints) were precisely quantified. On the other hand, an analysis at the hypha scale (about 5 µm) enabled us to characterize the growth rates of the apexes, the distribution of branches along the hypha, and the interactions between two close branches within the mycelium. A clear distinction between lateral and apical hyphae could be established. Furthermore, based on a simulation of the mycelial network of P. anserina in the form of a binary tree, and calibrated from experimental data, we showed how the mycelium optimizes extension and densification. First, the observed distribution of apical branching angles corresponds to the maximization of radial and orthoradial extension of the thallus, while minimizing overlaps. Second, we showed that lateral hyphae maximize substrate exploitation by radial density growth lagging behind the exploration front. Finally, intracellular structures were observed by a fluorescence microscopy approach. In particular, the dynamics of the nuclei, the Spitzenkörper, and the distribution of septa in P. anserina were analyzed.La forme végétative des champignons filamenteux est constituée par un réseau branchant d'hyphes en croissance, le mycélium. Cette structure dynamique permet le développement optimal de l'organisme jusqu'à la reproduction, en lui conférant une capacité d'exploration et d'exploitation efficace de son environnement. Dans cette étude, la dynamique de croissance en deux dimensions du champignon filamenteux Podospora anserina a été caractérisée par une approche multi-échelle. À partir d'un dispositif de microscopie en champ clair développé au laboratoire, nous obtenons une collection d'images du mycélium, régulièrement réparties sur les 20 premières heures de croissance à partir de la germination d'une ascospore. Les images couvrent l'intégralité de la surface du mycélium (jusqu'à 1 cm), tout en conservant une résolution permettant de distinguer individuellement les hyphes (5 µm). L'analyse du réseau mycélien dans sa globalité s'appuie sur l'extraction de grandeurs dynamiques caractéristiques du développement et de la complexité du réseau : longueur du mycélium, nombre d'apex et de noeuds (connexions entre les hyphes), ou encore surfaces délimitées par les hyphes. Ainsi, les profils de croissance de mycéliums résultant de conditions de croissance variées (contraintes nutritives, lumineuses ou de température) ont été précisément quantifiés. D'autre part, une analyse à l'échelle de l'hyphe (environ 5 µm) a permis de caractériser les vitesses de croissance des apex, la répartition des branchements le long de l'hyphe, et les interactions entre deux branches proches au sein du mycélium. Une distinction claire entre hyphes latérales et apicales a pu ainsi être établie. De plus, en nous appuyant sur une simulation du réseau mycélien de P. anserina sous la forme d'un arbre binaire, et calibrée à partir des données expérimentales, nous montrons comment le mycélium optimise extension et densification. Tout, d'abord la distribution observée des angles de branchement apicaux correspond à la maximisation de l'extension radiale et orthoradiale du thalle, tout en minimisant les chevauchements. Dans un deuxième temps, nous montrons que les hyphes latérales maximisent l'exploitation du substrat par croissance radiale de la densité en retard de phase avec le front d'exploration. Enfin, des structures intracellulaires ont été observées par une approche de microscopie en fluorescence. En particulier, la dynamique des noyaux, du Spitzenkörper, et la répartition des septa chez P. anserina ont été analysées

Neural expression of the transcription factor THAP1 during development in rat

Loss of function mutations in THAP1 has been associated with primary generalized and focal dystonia in children and adults. THAP1 encodes a transcription factor (THAP1) that harbors an atypical zinc finger domain and plays a critical role in G1-S cell cycle control. Current thinking suggests that dystonia may be a neurodevelopmental circuit disorder. Hence, THAP1 may participate in the development of the nervous system. Herein, we report the neurodevelopmental expression patterns of Thap1 transcript and THAP1 protein from the early postnatal period through adulthood in the rat brain, spinal cord and dorsal root ganglia (DRG). We detected Thap1 transcript and THAP1-immunoreactivity (IR) in the cerebral cortex, cerebellum, striatum, substantia nigra, thalamus, spinal cord and DRG. Thap1 transcript expression was higher in the brain than in spinal cord and DRG at P1 and P7 and declined to similar levels at P14 and later time points in all regions except the cerebellum, where it remained high through adulthood. In the brain, THAP1 expression was highest in early development, particularly in the cerebellum at P7. In addition to Purkinje cells in the cerebellum, THAP1-IR was also localized to pyramidal neurons in the cerebral cortex, relay neurons in the thalamus, medium spiny and cholinergic neurons in the striatum, dopaminergic neurons in the substantia nigra, and pyramidal and interneurons in the hippocampus. In the cerebellar cortex, THAP1-IR was prominently distributed in the perikarya and proximal dendrites of Purkinje cells at early time-points. In contrast, it was more diffusely distributed throughout the dendritic arbor of adult Purkinje cells producing a moderate diffuse staining pattern in the molecular layer. At all time points, nuclear IR was weaker than cytoplasmic IR. The prominent cytoplasmic and developmentally regulated expression of THAP1 suggests that THAP1 may function as part of a cell surface-nucleus signaling cascade involved in terminal neural differentiation. © 2012 IBRO

Prediction and experimental evidence of different growth phases of the Podospora anserina hyphal network

Abstract Under ideal conditions, the growth of the mycelial network of a filamentous fungus is monotonous, showing an ever increasing complexity with time. The components of the network growth are very simple and based on two mechanisms: the elongation of each hypha, and their multiplication by successive branching. These two mechanisms are sufficient to produce a complex network, and could be localized only at the tips of hyphae. However, branching can be of two types, apical or lateral, depending on its location on the hyphae, therefore imposing the redistribution of the necessary material in the whole mycelium. From an evolutionary point of view, maintaining different branching processes, with additional energy needs for structure and metabolism, is intriguing. We propose in this work to discuss the advantages of each branching type using a new observable for the network growth, allowing us to compare growth configurations. For this purpose, we build on experimental observations of the Podospora anserina mycelium growth, enabling us to feed and constrain a lattice-free modeling of this network based on a binary tree. First, we report the set of statistics related to the branches of P. anserina that we have implemented into the model. Then, we build the density observable, allowing us to discuss the succession of growth phases. We predict that density over time is not monotonic, but shows a decay growth phase, clearly separated from an other one by a stationary phase. The time of appearance of this stable region appears to be driven solely by the growth rate. Finally, we show that density is an appropriate observable to differentiate growth stress

Efficient Conversion of Epoxides into Carbonates with CO2 and a Single Organocatalyst: Laboratory and Kilogram-Scale Experiments

International audienceCheap and readily-available 2-aminopyridine and related compounds can be used as organocatalysts for the conversion of epoxides into cyclic carbonates. This reaction gives high conversions under solvent-free conditions, and is amenable to a kilogram-scale under mild conditions

Characterization of spatio-temporal dynamics of the constrained network of the filamentous fungus Podospora anserina using a geomatics-based approach.

In their natural environment, fungi are subjected to a wide variety of environmental stresses which they must cope with by constantly adapting the architecture of their growing network. In this work, our objective was to finely characterize the thallus development of the filamentous fungus Podospora anserina subjected to different constraints that are simple to implement in vitro and that can be considered as relevant environmental stresses, such as a nutrient-poor environment or non-optimal temperatures. At the Petri dish scale, the observations showed that the fungal thallus is differentially affected (thallus diameter, mycelium aspect) according to the stresses but these observations remain qualitative. At the hyphal scale, we showed that the extraction of the usual quantities (i.e. apex, node, length) does not allow to distinguish the different thallus under stress, these quantities being globally affected by the application of a stress in comparison with a thallus having grown under optimal conditions. Thanks to an original geomatics-based approach based on the use of automatized Geographic Information System (GIS) tools, we were able to produce maps and metrics characterizing the growth dynamics of the networks and then to highlight some very different dynamics of network densification according to the applied stresses. The fungal thallus is then considered as a map and we are no longer interested in the quantity of material (hyphae) produced but in the empty spaces between the hyphae, the intra-thallus surfaces. This study contributes to a better understanding of how filamentous fungi adapt the growth and densification of their network to potentially adverse environmental changes

Assessing the impact of population decline on mating system in the overexploited Mediterranean red coral

11 pages, 2 figures, 4 tables, supporting information https://doi.org/10.1002/aqc.3327.-- This is the pre-peer reviewed version of the following article: Jean‐Baptiste Ledoux, Silvia Frias‐Vidal, Ignasi Montero‐Serra,Agostinho Antunes, Clara Casado Bueno, Sergi Civit, Paula Lopez‐Sendino, Cristina Linares, Joaquim Garrabou, Assessing the impact of population decline on mating system in the overexploited Mediterranean red coral Aquatic Conservation - Marine and Freshwater Ecosystems 30(6): 1149-1159 (2020), which has been published in final form at https://doi.org/10.1002/aqc.3327. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsUnderstanding the interactions among demographic parameters, mating system and population dynamics is key to predict the response of populations to global change. The Mediterranean red coral is a precious octocoral suffering from population decline due to overfishing and warming-driven mass mortality events. While the demographic consequences of these two pressures are well characterized, little is known regarding their impact on population dynamics and evolution of red coral populations. The main objective of this study was to fill this gap focusing more particularly on mating pattern and genetic drift. Combining sibship and progeny arrays analyses, a genetic characterization of the red coral mating system was conducted. In addition, a synchronic approach was developed comparing mating patterns in two populations with contrasting demographic patterns: a pristine-like population and a declining population. The results show that polyandry is likely to be the norm in red coral. The similar patterns of genetic diversity between adults and larvae combined with the lack of differential reproductive success among putative fathers did not support significant sweepstakes effects during larval production. While instantaneous biparental inbreeding was detected, no long-term inbreeding was observed even in the declining population. Mating patterns and effective population sizes in the two populations were not statistically different. Nevertheless, a trend towards a slightly higher inbreeding and a lower number of breeders was observed in the declining population. Accordingly, we hypothesized that an increase in male gamete dispersal may buffer the increase of genetic drift expected in the declining population. This feedback between demographic decline and reproductive pattern may potentially take part in the long-term persistence of red coral populations. However, the negative trend reported in the declining population unambiguously supports the need to maintain high densities of reproductive colonies to the functioning of red coral populationsThis research was supported by national funds through FCT‐Foundation for Science and Technology within the scope of UIDB/04423/2020 and UIDP/04423/2020., the Spanish MINECO (CGL2012‐32194), the TOTAL Foundation PERFECT project, the MIMOSA project funded by the foundation Prince Albert II de Monaco, and the European Union's Horizon 2020 research and innovation programme under grant agreement N° 689518 (MERCES). [...] J.B.L. was supported by a postdoctoral grant (SFRH/BPD/74400/2010) from Fundação para a Ciência e a Tecnologia (FCT), C.L. by a Ramon y Cajal (RyC‐2011‐08135), IMS by a FPI grant (BES‐2013‐066150) and S.C. by research project SGR 622 (GRBIO) from the Departament d’ Economia i Coneixement de la Generalitat de Catalunya and (PGC2018‐095931‐B‐I00) MINECO (Spain). Genotyping was performed at the Genome Transcriptome Facility of Bordeaux (grants from the Conseil Régional d'Aquitaine n°20030304002FA and 20040305003FA, from the European Union FEDER n°2003227 and from Investissements d'Avenir ANR‐10‐EQPX‐16‐01)With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI