Diez-Hermano, S. | bioRxiv Science

bioRxiv2023

Diversity of RNA viruses in declining Mediterranean forests

Global change alters forestry habitats and facilitates the entry of new pathogens that dont share a co-evolution history with the forest, leading them into a spiral of decline. As a result, relationships between forests organisms get disbalanced. Under this scenario, RNA viruses are of particular interest, as they participate in many of such relationships thanks to their ability to infect a wide range of hosts, even from different kingdoms of life. For this reason, the study of RNA viruses is essential to understand how viral flow across different hosts might occur, and to prevent possible outbreaks of diseases in the future. In this work the RNA virus diversity found in trees, arthropods and fungi from declining Mediterranean forests is described. To this extent, three habitats (Quercus ilex, Castanea sativa and Pinus radiata) were sampled and RNAseq was performed on tree tissues, arthropods and fungi. 146 viral sequences were detected by searching for matches to conserved motifs of the RNA-dependent RNA polymerase (RdRP) using Palmscan. Up to 15 viral families were identified, with Botourmiaviridae (28.7%) and Partitiviridae (9.6%) being the most abundant. In terms of genome type, ssRNA(+) viruses were the most represented (83.5%), followed by dsRNA (15%) and two ssRNA(-) representatives. Viruses belonging to families with cross-kingdom capabilities such as Hypoviridae (1), Mitoviridae (6) and Narnaviridae (5) were also found. Distribution of viruses across ecosystems was: Q.ilex (57.5%), P.radiata (26.7%) and C.sativa (15.8%). Interestingly, two RdRP sequences had no matches in available viral databases. This work constitutes a starting point to gain insight into virus evolution and diversity occurring in forests affected by decline, as well as searching for novel viruses that might be participating in unknown infectious pathways.

microbiology↗

bioRxiv2021

Benchmarking of tools for axon length measurement in individually-labeled projection neurons

Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools - design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length - in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. Additionally, the computational results were compared with estimated and direct measurements of individual axon lengths performed on actual brain tissue sections, to analyze the practical difficulties and biases arising in real cases. The evaluated reliability of each axon length estimation method is then balanced with the required human effort, experience and know-how, and economic affordability. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research. AUTHOR SUMMARYCharacterization of single neurons is a crucial step to understand how neural circuitry operates. Visualization of individual neurons is feasible thanks to labelling techniques that allows precise measurements at cellular resolution. This milestone gave access to powerful estimators of the functional impact of a neuron, such as axon length. Although techniques relying on direct 3D reconstruction of individual axons are the gold standard, handiness and accessibility are still an issue. Indirect estimations of axon length have been proposed as agile and effective alternatives, each offering different solutions to the accuracy-cost tradeoff. In this work we report a computational benchmarking between three experimental tools used for axon length estimation on brain tissue sections. Performance of each tool was simulated and tested for 951 3D-reconstructed axons, by comparing estimated axon lengths against direct measurements. Assessment of suitability to different research and funding circumstances is also provided, taking into consideration factors such as training expertise, economic cost and required equipment, alongside methodological results. These findings could be an important reference for research on neuronal wiring, as well as for broader studies involving neuroanatomical and neural circuit modelling.

neuroscience↗