Biology subjects

Rieger, D.

Publications and source records attributed to Rieger, D..

10 recordsLinked to original sources

bioRxiv2026

Latent generative search unlocks de novo design of untapped biomolecular interactions at scale

De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, including carbohydrates, provide few of the hydrophobic contacts favoured by current methods and have largely resisted de novo binders. To address this challenge, here we introduce latent generative search for binder design, a novel framework that uses reward-guided search at inference time to steer the Proteina-Complexa generative model. The model codesigns sequence and structure - generating them together in a continuous latent space - and thereby removes the inverse-folding step on which current methods rely. In a screen of more than one million designs by multiplexed phage display, latent generative search produced more validated binders than every other method tested, its codesigned sequences surpassing post hoc redesign. It delivered high-affinity binders across therapeutic receptors, a viral attachment protein and intracellular signalling targets. Our approach also accessed previously untapped biology, generating the first de novo proteins that bind a free carbohydrate, including one that discriminates between blood-group antigens - a polar, flexible target class beyond the reach of current design methods.

bioengineering↗

bioRxiv2026

A generalizable interface-seeded framework for de novo design of functional oligomers

Protein oligomers are ubiquitous in biological systems and essential for function. However, the de novo design of oligomers that controllably assemble in response to exogenous stimuli remains challenging. Here, we present an AI-based generative approach that leverages an interface-seeded strategy for designing responsive homo-oligomers from isolated interaction modules. Experimentally validated designs are highly accurate and explore new-to-nature topologies. We show that designs effectively respond to their chemical triggers with conditional oligomerization or to phosphorylation-driven conformational changes with reversible oligomerization. We further functionalized our responsive assemblies to build ligand-dependent membrane binding systems and phosphorylation-controlled gene regulatory switches. Our framework enables the generalizable design of responsive protein complexes, opening novel possibilities for the engineering of biosynthetic systems with sophisticated regulatory mechanisms.

biochemistry↗

bioRxiv2026

The neuronal clock network in the polar key species Antarctic krill (Euphausia superba)

Organisms are exposed to predictable daily and seasonal environmental oscillations. Biological clocks enable organisms to anticipate these changes and coordinate physiology and behaviour accordingly. While circadian mechanisms are well studied in terrestrial model organisms, little is known about the neuronal organisation of biological clocks in ecologically important species, especially in the marine environment. Antarctic krill (Euphausia superba) is central to the functioning of the Southern Ocean ecosystem and relies on precise timing to cope with the extreme, high-latitude fluctuations in photoperiod, food availability, and sea-ice cover in its habitat. Despite evidence for circadian and seasonal rhythms in krill behaviour and physiology, the neuronal architecture underlying these timing processes has remained unresolved. In this study, we use in situ hybridisation and antibody staining to characterise the circadian clock in the krill brain. Immunostaining with an antibody against crustacean {beta}-Pigment-dispersing hormone ({beta}-PDH) reveals distinct clusters of PDH-positive neurons in the optic lobes and dorsal central brain, along with an extensive PDH-positive fibre network. We further localise transcripts of the core clock genes cryptochrome-2 (cry2) and period (per) in cell clusters in the optic lobes, which also include the PDH-positive neurons. More specifically, PDH-positive neurons are a subgroup of the cry2 and per-positive cells. Together, these findings provide the first description of the neuronal architecture of the circadian clock in Antarctic krill and establish essential groundwork for future studies on biological timing, environmental adaptation, and the resilience of this key species in a rapidly changing Southern Ocean.

neuroscience↗

bioRxiv2025

Computational design and experimental characterization of mini-protein binders targeting Nipah, Langya and Measles virus receptor-binding domains

A lack of reagents represents a major bottleneck in pandemic preparedness and rapid vaccine development. It is therefore important to enable the design of reagents for use in the treatment and diagnosis of emerging viral diseases. Ideally, the design and identification platform is fast, can be performed by testing only a small number of candidates and enables a generally applicable strategy. In this study, we assessed the ability of recently developed computational protein design tools to establish such a workflow for validating paramyxovirus receptor-binding protein de novo binders as such reagents. The family Paramyxoviridae includes various members that cause severe disease and exhibit re-occurring zoonotic spillover events, with documented human infections over the past decades. We successfully designed, identified, and characterized mini-proteins targeting the receptor binding proteins of Nipah virus, Langya virus, and Measles virus while screening as few as 10-16 designs per target. The resulting functional binders have moderate to low nanomolar affinities and display high on-target specificity. We further showed that our most promising Nipah virus receptor-binding protein binder is able to inhibit human receptor binding in vitro and competes for an epitope that overlaps with that of the neutralizing antibody HENV-117. However, despite these promising results, this Nipah binder is only weakly neutralizing, preventing therapeutic applications. Nevertheless, we established a platform, applicable to rapidly generate diagnostically relevant proteins from only a small number of candidates, and developed novel reagents for the Paramyxoviridae family.

bioinformatics↗

bioRxiv2025

RHODOPSIN 7: An ancient non-retinal photoreceptor for contrast vision, darkness detection, and circadian regulation

1Animals rely on light not only for vision but also to adapt behavior to their environment through non-image-forming pathways. In Drosophila, most rhodopsins mediate retinal image formation, but RHODOPSIN 7 (RH7) is widely expressed in the brain and optic lobe, acting as a non-canonical light sensor reminiscent of mammalian melanopsin. We combined expression mapping, behavioral assays, and phylogenetic comparisons to investigate its function. RH7 detects temporal changes in luminance, guiding rapid behavioral responses, and regulating daily activity patterns. Flies lacking RH7 are less active during the dark phase, while strains with constitutively active RH7 show increased activity. Phylogenetic analyses suggest that RH7 is an ancient rhodopsin present across panarthropods, representing an intermediate between G protein-coupled receptors and specialized rhodopsins, highlighting a key step in the evolution of non-visual light perception. These findings show that RH7 functions as a melanopsin-like sensor, shaping behavior, and illuminating the origins of light detection.

neuroscience↗

bioRxiv2023

Synaptic and peptidergic connectomes of the Drosophila circadian clock

The circadian clock and its output pathways play a pivotal role in optimizing daily processes. To obtain novel insights into how diverse rhythmic physiology and behaviors are orchestrated, we have generated the first comprehensive connectivity map of an animal circadian clock using the Drosophila FlyWire brain connectome. Intriguingly, we identified additional dorsal clock neurons, thus showing that the Drosophila circadian network contains [~]240 instead of 150 neurons. We also revealed extensive contralateral synaptic connectivity within the network and discovered novel indirect light input pathways to the clock neurons. Interestingly, we observed sparse monosynaptic connectivity between clock neurons and down-stream higher-order brain centers and neurosecretory cells known to regulate behavior and physiology. Therefore, we integrated single-cell transcriptomics and receptor mapping to decipher putative paracrine peptidergic signaling by clock neurons. Our analyses identified additional novel neuropeptides expressed in clock neurons and suggest that peptidergic signaling significantly enriches interconnectivity within the clock network.

neuroscience↗

bioRxiv2023

PDF neuropeptide signals independently of Bruchpilot-labelled active zones in daily remodelled terminals of Drosophila clock neurons

The small ventrolateral neurons (sLNvs) are key components of the central clock in the Drosophila brain. They signal via the neuropeptide Pigment-dispersing factor (PDF) to align the molecular clockwork of different central clock neurons and to modulate downstream circuits. The dorsal terminals of the sLNvs undergo daily morphological changes that have been shown to affect presynaptic sites organised by the active zone protein Bruchpilot (BRP), a homolog of mammalian ELKS proteins. Although the circadian plasticity of the sLNv terminals is well established, whether and how it is related to the rhythmic release of PDF remains ill-defined. Here, we combined expansion microscopy with labelling of active zones by endogenously tagged BRP to examine the spatial correlation between PDF-containing dense-core vesicles and BRP-labelled active zones. We found that the number of BRP-labelled punctae in the sLNv terminals remained stable while their density changed during circadian plasticity. The relative distance between BRP- and PDF-labelled punctae was increased in the morning, around the reported time of PDF release. Spontaneous dense-core vesicle release profiles of the sLNvs in a publicly available ssTEM dataset (FAFB) consistently lacked spatial correlation to BRP-organised active zones. RNAi-mediated downregulation of brp and other active zone proteins expressed by the sLNvs did not affect PDF-dependent locomotor rhythmicity. In contrast, down-regulation of genes of the canonical vesicle release machinery, the dense-core vesicle-related protein CADPS, as well as PDF impaired locomotor rhythmicity. Taken together, our study suggests that PDF release from the sLNvs is independent of BRP-organised active zones which seem not to be circadianly destroyed and re-established.

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↗

bioRxiv2019

Natural Zeitgebers cannot compensate for the loss of a functional circadian clock in timing of a vital behaviour in Drosophila

The adaptive significance of adjusting behavioural activities to the right time of the day is intuitive. Laboratory studies have implicated an important role of circadian clocks in behavioural timing and rhythmicity. Yet, recent studies on clock-mutant animals questioned this importance under more naturalistic settings, as various clock mutants showed nearly normal diel activity rhythms under semi-natural Zeitgeber conditions. We here report evidence that proper timing of eclosion, a vital behaviour of the fruit fly Drosophila melanogaster, requires a functional molecular clock even under quasi-natural conditions. In contrast to wildtype flies, period01 mutants with a defective molecular clock eclose mostly arrhythmically in a temperate environment even in the presence of a full complement of abiotic Zeitgebers. Moreover, period01 mutants eclose during a much larger portion of the day, and peak eclosion time becomes more susceptible to variable day-to-day changes of light and temperature. Under the same conditions, flies with impaired peptidergic inter-clock signalling (pdf01 and han5304 mutants) stayed largely rhythmic with normal gate sizes. Our results suggest that the presence of natural Zeitgebers can mitigate a loss of peptide-mediated phasing between central clock neuron groups, but cannot substitute for the lack of a functional molecular clock under natural temperate conditions.

animal behavior and cognition↗

bioRxiv2018

The Drosophila microbiome has a limited influence on sleep, activity, and courtship behaviors

In animals, commensal microbes modulate various physiological functions, including behavior. While microbiota exposure is required for normal behavior in mammals, it is not known how widely this dependency is present in other animal species. We proposed the hypothesis that the microbiome has a major influence on the behavior of the vinegar fly (Drosophila melanogaster), a major invertebrate model organism. Several assays were used to test the contribution of the microbiome on some well-characterized behaviors: defensive behavior, sleep, locomotion, and courtship in microbe-bearing, control flies and two generations of germ-free animals. None of the behaviors were largely influenced by the absence of a microbiome, and the small or moderate effects were not generalizable between replicates and/or generations. These results refute the hypothesis, indicating that the Drosophila microbiome does not have a major influence over several behaviors fundamental to the animals survival and reproduction. The impact of commensal microbes on animal behaviour may not be broadly conserved.

neuroscience↗