Biology subjects

Raible, F.

Publications and source records attributed to Raible, F..

9 recordsLinked to original sources

bioRxiv2024

A c-opsin functions in a ciliary-marginal zone-like stem cell region of an invertebrate camera-type eye

Camera-type eyes in vertebrates and invertebrates are striking examples of parallel evolution of a complex structure. Comparisons between such structures can help to deduce their organizational principles. We analyzed the camera-type adult eyes of the bristleworm Platynereis dumerilii. Employing single-cell RNA sequencing, we identified neurogenic cells in the worms adult brains. Among those are distinct neural stem cells in its adult eye, adjacent to the glass body/lens, that produce cells in radial lines, reminiscent of stem cells in the vertebrate eye ciliary marginal zone. A subset of these proliferating cells expresses the photoreceptor gene c-opsin1. c-opsin1 knock-out reduces eye cell proliferation and influences differentiation. During reproductive maturation, proliferation in eye and brain sharply declines, while cells upregulate molecular characteristics of mammalian adult neural stem cell quiescence. Our data reveal new insights into nervous system functional development and evolution.

developmental biology↗

bioRxiv2024

Molecular profile, source and lineage restriction of stem cells in an annelid regeneration model

Regeneration of missing body parts can be observed in diverse animal phyla, but it remains unclear to which extent these capacities rely on shared or divergent principles. Research into this question requires detailed knowledge about the involved molecular and cellular principles in suitable reference models. By combining single-cell RNA sequencing and mosaic transgenesis in the marine annelid Platynereis dumerilii, we map cellular profiles and lineage restrictions during posterior regeneration. Our data reveal cell-type specific injury responses, re-expression of positional identity factors, and the re-emergence of stem cell signatures in multiple cell populations. Epidermis and mesodermal coelomic tissue produce distinct putative posterior stem cells (PSCs) in the emerging blastema. A novel mosaic transgenesis strategy reveals both developmental compartments and lineage restrictions during regenerative growth. Our work supports the notion that posterior regeneration involves dedifferentiation, and reveals molecular and mechanistic parallels between annelid and vertebrate regeneration.

developmental biology↗

bioRxiv2024

Elongation capacity of polyunsaturated fatty acids in the annelid Platynereis dumerilii

In animals, elongation of very long-chain fatty acid (Elovl) proteins play pivotal functions in the biosynthesis of fatty acids, including the physiologically essential long-chain polyunsaturated fatty acids (LC-PUFA). Polychaetes have important roles in marine ecosystems, contributing not only to nutrient recycling but also exhibiting a distinctive capacity for biosynthesising LC-PUFA, as emphasised in previous research. In order to expand our current understanding of the LC-PUFA biosynthesis in polychaetes, the present study conducted a thorough molecular and functional characterisation of Elovl occurring in the model organism Platynereis dumerilii. In this study, we identify six Elovl proteins in the genome of P. dumerilii. The sequence and phylogenetic analyses established that four Elovl, identified as Elovl2/5, Elovl4 (two genes) and Elovl1/7, have putative functions in the LC-PUFA biosynthesis. Functional characterisation in yeast confirmed the roles of these elongases in the LC-PUFA biosynthetic pathways, demonstrating that P. dumerilii possesses a varied and functionally diverse complement of Elovl enzymes that, along the enzymatic specificities of previously characterised desaturases, enable P. dumerilii to perform all the reactions required for the biosynthesis of the LC-PUFA. Importantly, we uncovered that one of the two Elovl4-encoding genes from P. dumerilii is remarkably long in comparison with any other animals Elovl, which contains a C terminal KH domain unique among Elovl enzymes. The distinctive expression pattern of this protein in photoreceptors strongly suggests a central role in vision.

biochemistry↗

bioRxiv2022

A fast and versatile method for simultaneous HCR, immunohistochemistry and EdU labeling (SHInE)

Access to newer, fast and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is increased need for in situ visualization of gene expression or encoded proteins to validate, localize or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here we introduce a versatile protocol that combines in situ hybridization chain reaction (HCR), immunohistochemistry (IHC) and proliferative cell labeling using 5-ethynyl-2-deoxyuridine (EdU), and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression and protein localization in bristleworm heads and trunks.

developmental biology↗

bioRxiv2022

Molecular characteristics of diel rhythmic diversity reveal disconnection between different levels of organismal rhythmicity

The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for the rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were reproducibly maintained for several weeks independent of basic culture conditions, such as population density or feeding. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wildtype worms showed that 24h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. Phenotype-specific cycling of distinct matrix metalloproteinase transcripts, encoding extracellular enzymes that modulate synaptic circuit function and neuropeptide signaling, like pigment dispersing factor (PDF), prompted us to functionally investigate Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts on overall activity levels, but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, variations of this exist as a reproducible continuum. We hypothesize that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous marine environments and potentially also to the effects of climate change, which is however endangered with shrinking population sizes and hence diversity.

animal behavior and cognition↗

bioRxiv2021

A Cryptochrome adopts distinct moon- and sunlight states and functions as moonlight interpreter in monthly oscillator entrainment

The moons monthly cycle synchronizes reproduction in countless marine organisms. The mass-spawning bristle worm Platynereis dumerilii uses an endogenous monthly oscillator to phase reproduction to specific days. Classical work showed that this oscillator is set by full moon. But how do organisms recognize such a specific moon phase? We uncover that the light receptor L-Cryptochrome (L-Cry) is able to discriminate between different moonlight durations, as well as between sun- and moonlight. Consistent with L-Crys function as light valence interpreter, its genetic loss leads to a faster re-entrainment under artificially strong nocturnal light. This suggests that L-Cry blocks "wrong" light from impacting on the monthly oscillator. A biochemical characterization of purified L-Cry protein, exposed to naturalistic sun- or moonlight, reveals the formation of distinct sun- and moonlight states characterized by different photoreduction- and recovery kinetics of L-Crys co-factor Flavin Adenine Dinucleotide. In vivo, L-Crys sun-versus moonlight states correlate with distinct sub-cellular localizations, indicating different signalling. In contrast, r-Opsin1, the most abundant ocular opsin, is not required for monthly oscillator entrainment. Our work reveals a new concept for correct moonlight interpretation involving a "valence interpreter" that provides entraining photoreceptor(s) with light source and moon phase information. These findings advance our mechanistic understanding of a fundamental biological phenomenon: moon-controlled monthly timing. Such level of understanding is also an essential prerequisite to tackle anthropogenic threats on marine ecology.

neuroscience↗

bioRxiv2021

Two light sensors decode moonlight versus sunlight to adjust a plastic circadian/circalunidian clock to moon phase

Many species synchronize their physiology and behavior to specific hours. It is commonly assumed that sunlight acts as the main entrainment signal for ~24h clocks. However, the moon provides similarly regular time information, and increasingly studies report correlations between diel behavior and lunidian cycles. Yet, mechanistic insight into the possible influences of the moon on ~24hr timers is scarce. We studied Platynereis dumerilii and uncover that the moon, besides its role in monthly timing, also schedules the exact hour of nocturnal swarming onset to the nights darkest times. Moonlight adjusts a plastic clock, exhibiting <24h (moonlit) or >24h (no moon) periodicity. Abundance, light sensitivity, and genetic requirement indicate Platynereis r-Opsin1 as receptor to determine moonrise, while the cryptochrome L-Cry is required to discriminate between moon- and sunlight valence. Comparative experiments in Drosophila suggest that Cryptochromes requirement for light valence interpretation is conserved. Its exact biochemical properties differ, however, between species with dissimilar timing ecology. Our work advances the molecular understanding of lunar impact on fundamental rhythmic processes, including those of marine mass spawners endangered by anthropogenic change.

neuroscience↗

bioRxiv2021

Analyses of cephalic and non-cephalic sensory cell types provide insight into joint photo- and mechanoreceptor evolution

Rhabdomeric Opsins (r-Opsins) are light-sensors in cephalic eye photoreceptors, but also function in additional sensory organs. This has prompted questions on the evolutionary relationship of these cell types, and if ancient r-Opsins cells were non-photosensory. Our profiling of cephalic and non-cephalic r-opsin1-expressing cells of the marine bristleworm Platynereis dumerilii reveals shared and distinct features. Non-cephalic cells possess a full set of phototransduction components, but also a mechanosensory signature. We determine that Pdu-r-Opsin1 is a Gq-coupled blue-light receptor. Profiling of cells from r-opsin1 mutants versus wild-types, and a comparison under different light conditions reveals that in the non-cephalic cells, light - mediated by r-Opsin1 - adjusts the expression level of a calcium transporter relevant for auditory mechanosensation in vertebrates. We establish a deep learning-based quantitative behavioral analysis for animal trunk movements, and identify a light-and r-Opsin-1-dependent fine-tuning of the worms undulatory movements in headless trunks, which are known to require mechanosensory feedback. Our results suggest an evolutionary concept in which r-Opsins act as ancient, light-dependent modulators of mechanosensation, and suggest that light-independent mechanosensory roles of r-Opsins likely evolved secondarily.

developmental biology↗

bioRxiv2019

A scalable culturing system for the marine annelid Platynereis dumerilii.

Platynereis dumerilii is a marine segmented worm (annelid) with externally fertilized embryos and it can be cultured for the full life cycle in the laboratory. The accessibility of embryos and larvae combined with the breadth of the established molecular and functional techniques has made P. dumerilii an attractive model for studying development, cell lineages, cell type evolution, reproduction, regeneration, the nervous system, and behavior. Traditionally, these worms have been kept in rooms dedicated for their culture. This allows for the regulation of temperature and light cycles, which is critical to synchronizing sexual maturation. However, regulating the conditions of a whole room present limitations, especially if experiments require being able to change culturing conditions. Here we present scalable and flexible culture methods that provide ability to control the environmental conditions, and have a multi-purpose culture space. We provide a closed setup shelving design with proper light conditions necessary for P. dumerilii to mature. We also implemented a standardized method of feeding P. dumerilii cultures with powdered spirulina which relieves the ambiguity associated with using frozen spinach, and helps standardize nutrition conditions across experiments and across different labs. By using these methods, we were able to raise mature P. dumerilii, capable of spawning and producing viable embryos for experimentation and replenishing culture populations. These methods will allow for the further accessibility of P. dumerilii as a model system, and they can be adapted for other aquatic organisms.

developmental biology↗