Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes.

Silencing of ATP Synthase β Impairs Egg Development in the Leafhopper Scaphoideus titanus, Vector of the Phytoplasma Associated with Grapevine Flavescence Dorée

Scaphoideus titanus (Hemiptera: Cicadellidae) is the natural vector of Flavescence dorée phytoplasma, a quarantine pest of grapevine with severe impact on European viticulture. RNA interference (RNAi) machinery components are present in S. titanus transcriptome and injection of ATP synthase β dsRNAs into adults caused gene silencing, starting three days post injection (dpi) up to 20 dpi, leading to decrease cognate protein. Silencing of this gene in the closely related leafhopper Euscelidiusvariegatus previously showed female sterility and lack of mature eggs in ovaries. Here, alteration of developing egg morphology in S. titanus ovaries as well as overexpression of hexamerin transcript (amino acid storage protein) and cathepsin L protein (lysosome proteinase) were observed in dsATP-injected females. To evaluate RNAi-specificity, E.variegatus was used as dsRNA-receiving model-species. Different doses of two sets of dsRNA-constructs targeting distinct portions of ATP synthase β gene of both species induced silencing, lack of egg development, and female sterility in E. variegatus, indicating that off-target effects must be evaluated case by case. The effectiveness of RNAi in S. titanus provides a powerful tool for functional genomics of this non-model species and paves the way toward RNAi-based strategies to limit vector population, despite several technical and regulatory constraints that still need to be overcome to allow open field application.

Technological Approach to Mind Everywhere (TAME): an experimentally- grounded framework for understanding diverse bodies and minds

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME - Technological Approach to Mind Everywhere - a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can scale during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.

Phenotyping single-cell motility in microfluidic confinement

At all scales, the movement patterns of organisms serve as dynamic read-outs of their behaviour and physiology. We devised a novel droplet microfluidics assay to encapsulate single algal microswimmers inside closed arenas, and comprehensively studied their roaming behaviour subject to a large number of environmental stimuli. We compared two model species, Chlamydomonas reinhardtii (freshwater alga, 2 cilia), and Pyramimonas octopus (marine alga, 8 cilia), and detailed their highly-stereotyped behaviours and the emergence of a trio of macroscopic swimming states (smooth-forward, quiescent, tumbling or excitable backward). Harnessing ultralong timeseries statistics, we reconstructed the species-dependent reaction network that underlies the choice of locomotor behaviour in these aneural organisms, and discovered the presence of macroscopic non-equilibrium probability fluxes in these active systems. We also revealed for the first time how microswimmer motility changes instantaneously when a chemical is added to their microhabitat, by inducing deterministic fusion between paired droplets - one containing a trapped cell, and the other, a pharmacological agent that perturbs cellular excitability. By coupling single-cell entrapment with unprecedented tracking resolution, speed and duration, our approach offers unique and potent opportunities for diagnostics, drug-screening, and for querying the genetic basis of micro-organismal behaviour.

JaponicusDB: Rapid deployment of a model organism database for an emerging model species

The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

Characterization Of Interspecific Gene Flows at The Genome-wide Level in a Natural Ecosystem The Massane Forest Reveals New Insights Into Horizontal Transfer In plants.

Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in plants, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that only LTRs-retrotransposons and predominantly those from the Copia superfamily were transferred between these wild species. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.

Toward a Computational Neuroethology of Vocal Communication: From Bioacoustics to Neurophysiology, Emerging Tools and Future Directions

Recently developed methods in computational neuroethology have enabled increasingly detailed and comprehensive quantification of animal movements and behavioral kinematics. Vocal communication behavior is well poised for application of similar large-scale quantification methods in the service of physiological and ethological studies. This review describes emerging techniques that can be applied to acoustic and vocal communication signals with the goal of enabling study beyond a small number of model species. We review a range of modern computational methods for bioacoustics, signal processing, and brain-behavior mapping. Along with a discussion of recent advances and techniques, we include challenges and broader goals in establishing a framework for the computational neuroethology of vocal communication.

No support for a meiosis suppressor in Daphnia pulex: Comparison of linkage maps reveals normal recombination in males of obligate parthenogenetic lineages.

It is often assumed that obligate parthenogenesis (OP) evolves by a disruption of meiosis and recombination. One emblematic example that appears to support this view is the crustacean Daphnia pulex. Here, by constructing high-density linkage maps, we estimate genome-wide recombination rates in males that are occasionally produced by OP lineages, as well as in males and females of cyclical parthenogenetic (CP) lineages. The results show no significant differences in recombination rates and patterns between CP and OP males nor between CP males and CP females. The observation that recombination is not suppressed in OP males invalidates the hypothesis of a general meiosis suppressor responsible for OP. Rather, our findings suggest that in D. pulex, as in other species where OP evolves from CP ancestors, the CP to OP transition evolves through a re-use of the parthenogenesis pathways already present in CP and through their extension to the entire life cycle, at least in females. In addition to the implications for the evolution of OP, the genetic maps produced by this study constitute an important genomic resource for the model species Daphnia.

From Bioinspired to Bioinformed: Benefits of Greater Engagement From Biologists

Bioinspiration and biomimetics is a rapidly growing field where insights from biology are used to solve current design challenges. Nature provides an abundance of inspiration to draw upon, yet biological information is under-exploited due to a concerning lack of engagement from biologists. To assess the extent of this problem, we surveyed the current state of the field using the Web of Science database and found that only 41% of publications on bioinspired or biomimetic research included an author affiliated with a biology-related department or organisation. In addition, most publications focus exclusively on a limited range of popular model species. Considering these findings, we highlight key reasons why greater engagement from biologists will enable new and significant insights from natural selection and the diversity of life. Likewise, biologists are missing unique opportunities to study biological phenomena from the perspective of other disciplines, particularly engineering. We discuss the importance of striving toward a bioinformed approach, as current limitations in the field can only be overcome with a greater understanding of the ecological and evolutionary contexts behind each bioinspired/biomimetic solution.