Biology subjects

Pop, S.

Publications and source records attributed to Pop, S..

13 recordsLinked to original sources

bioRxiv2026

Natural statistics of host odours predict species-specific olfactory behaviours in Drosophilids

Animals rely on olfaction to locate food, mates, and suitable habitats, yet natural odour environments contain thousands of volatile molecules, creating a high-dimensional sensory problem for both nervous systems and the researchers who study them 1-5. For example, a banana emits around 100 individual volatiles4,6. It remains unclear which components of complex odour blends animals have evolved to use as behavioural cues. Here, combining fieldwork, chemical and behavioural analyses, we show across multiple Drosophila species that behaviourally relevant cues can be predicted directly from the statistical structure of natural odour environments. Animals preferentially respond to components that are most distinctive within their natural host odour blends, and therefore most ecologically informative. These cues can be either major or minor blend components. Our results indicate that host-guided olfactory behaviours have evolved to exploit the statistical structure of natural odour environments by selectively targeting the most informative features of odour blends.

neuroscience↗

bioRxiv2025

ISLET-1 knockdown causes abnormal peripheral axonal growth of mesencephalic trigeminal neurones in the chick embryo

The trigeminal is one of the best characterized sensory systems in amniotes. It comprises two populations of first-order sensory neurons: the trigeminal ganglion (TG) which are peripheral to the central nervous system and the mesencephalic trigeminal nucleus (MTN), the only sensory neurons that lie within the central nervous system in amniotes. Islet-1, a LIM homeodomain transcription factor, which plays essential roles during embryogenesis, contributes to axon pathfinding of sensory neurons in the TG. However, if Islet-1 plays a similar role for the MTN neurons is unknown. To answer whether Islet-1 is as important for axon guidance in these centrally - located sensory neurons as it is for the peripherally-located TG neurons, we investigated the effect of reduced Islet-1 expression on axonal pathfinding in the chick MTN. We employed in ovo electroporation to transfect short interfering RNA for Islet-1 (si-Islet-1) into the dorsal midbrain. Our findings showed that, within the central nervous system, Islet-1 knockdown did not affect axonal growth direction of MTN neurons. However, outside the central nervous system a reduction of Islet-1 led to disorganized axonal growth. We observed an abnormal organisation in the maxillary division of the trigeminal nerve when Islet-1 was reduced in MTN neurons.

developmental biology↗

bioRxiv2025

Pattern-triggered immunity in blue and white seed cultivars of Papaver somniferum

Papaver somniferum (poppy) is a traditional component of Central and Eastern European cuisine and an important oilseed crop in the region. The crucial thread for poppy stable yield is pathogen infection. Thus, we need to understand poppy defence mechanisms in detail. The first robust layer of plant immunity, which plays a crucial role in combat against pathogens, is pattern-triggered immunity (PTI). Here, we provide the first insights into PTI in poppy. We selected four poppy varieties used in the food industry. We investigated poppy response to various peptide elicitors acting as microbe-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs). Flg22 induced the most robust reactive oxygen species (ROS) burst among all tested peptides. Flg22 also triggered putative mitogen-activated protein kinase (MAPK) phosphorylation and seedling growth inhibition in all tested cultivars. We identified PsWRKY22 and PsPR2 as candidate marker genes suitable for monitoring poppy PTI responses. The tested poppy cultivars have low levels of salicylic acid. Callose accumulation was triggered by wounding but not by flg22. For studying PTI in poppy, wounding is a challenge that needs to be considered as it can obscure potential PTI responses. Our findings highlight conserved aspects of poppy immunity and challenges in studying poppy PTI. The established pipeline facilitates improving our understanding of poppy immunity and has the potential for widespread application in poppy breeding and improving selection for broad-spectrum disease resistance provided by enhanced PTI. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/639761v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1680d52org.highwire.dtl.DTLVardef@42895eorg.highwire.dtl.DTLVardef@488ffeorg.highwire.dtl.DTLVardef@1e5a95d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract The establishment of the methods for studying pattern-triggered immunity (PTI) in Papaver somniferum L. (poppy) was inspired by the knowledge of the model plant Arabidopsis thaliana. The study showed a similarity between Arabidopsis and poppy in response to flg22 but also pointed out the obstacles for PTI analysis in poppy and the differences compared to the model plant. Created with BioRender.com. C_FIG

plant biology↗

bioRxiv2022

Microinjection in C. elegans by direct penetration of elastomeric membranes

The nematode worm C. elegans is widely used in basic and translational research. The creation of transgenic strains by injecting DNA constructs into the worms gonad is an essential step in many C. elegans research projects. This paper describes the fabrication and use of a minimalist microfluidic chip for performing microinjections. The worm is immobilized in a tight-fitting microchannel one sidewall of which is a thin elastomeric membrane which the injection pipette penetrates to reach the worm. The pipette is neither broken nor clogged by passing through the membrane, and the membrane reseals when the pipette is withdrawn. Rates of survival and transgenesis are similar to those in the conventional method. Novice users found injections using the device easier to learn than the conventional method. The principle of direct penetration of elastomeric membranes is readily adaptable to microinjections in a wide range of organisms including cells, embryos, and other small animal models. It could therefore lead to a new generation of microinjection systems for basic, translational, and industrial applications.

bioengineering↗

bioRxiv2021

A Gene Replacement Humanization Platform for Rapid Functional Testing of Clinical Variants in Epilepsy-associated STXBP1.

PurposeFunctional evidence is a pillar of variant interpretation according to ACMG guidelines. Functional evidence can be obtained in a variety of models and assay systems, including patient-derived tissues and iPSCs, in vitro cellular assays, and in vivo assays. Here we evaluate the reliability and practicality of variant interpretation in the small animal model, C. elegans, through a series of experiments evaluating the function of syntaxin binding protein, STXBP1, a well-known causative gene for Early infantile epileptic encephalopathy 1 (EIEE1). MethodsUsing CRISPR, we replaced the coding sequence for unc-18 with the coding sequence for the human ortholog STXBP1. Next, we used CRISPR to introduce precise point mutations in the human STXBP1 coding sequence, reflecting three clinical categories (benign, pathogenic, and variants of uncertain significance (VUS)). We quantified 26 features of the resulting worms movement to train Random Forest (RF) and Support Vector Machines (SVM) machine learning classifiers on known pathogenic and benign variants. We characterized the classifiers, and then used the behavioral data from the VUS-expressing animals to predict the categorization of the VUS. ResultsWhereas knock-out worms without unc-18 are severely impaired in motor function, worms expressing STXBP1 in its place have restored motor function. We produced worms with STXBP1 variants previously classified by ACMG criteria, including 25 benign variants, 32 pathogenic, and 24 variants of uncertain significance (VUS). Using either SVM or RF classifiers, we were able to obtain a sensitivity of 0.84-0.97 on known benign and pathogenic strains. By comparing multiple ML classification methods, we were able to classify 9 of the VUS as functionally abnormal, suggesting that these VUS are likely to be pathogenic. ConclusionsWe demonstrate that automated analysis of a small animal system is an effective, scalable, and fast way to understand functional consequences of variants in STXBP1, one of the most common causes of genetic epilepsies and neurodevelopmental disorders.

genetics↗

bioRxiv2021

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

Neurons draw on alternative splicing for their increased transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. We found that in Drosophila, this splicing program is restricted to neurons by the post-transcriptional processing of the enhancer of microexons (eMIC) domain in Srrm234 by Elav and Fne. eMIC deficiency or misexpression leads to widespread neurological alterations largely emerging from impaired neuronal activity, as revealed by a combination of neuronal imaging experiments and cell-type-specific rescues. These defects are associated with the genome-wide skipping of short neural exons, which are strongly enriched in ion channels. Remarkably, we found no overlap of eMIC-regulated exons between flies and mice, illustrating how ancient post-transcriptional programs can evolve independently in different phyla to impact distinct cellular modules while maintaining cell-type specificity.

molecular biology↗

bioRxiv2021

Proapoptotic RHG genes and mitochondria play a key non-apoptotic role in remodelling the Drosophila sensory system

Caspases are best known for their role in programmed cell death but have also been found to be important in several non-apoptotic phenomena such as cell fate specification, cell migration and terminal differentiation. The dynamics of such sub-lethal caspase events and the molecular mechanisms regulating them are still largely unknown. As more tools for visualizing and manipulating caspase activation in vivo become available, greater insights into this biology are being made. Using a new and sensitive in vivo effector caspase probe, called SR4VH, we demonstrate that effector caspases are activated in pruning sensory neurons earlier than previously thought and that the level of caspase activation in these neurons is consistently lower than in neurons undergoing cell death. We reveal that Grim and Reaper, two of the four pro-apoptotic RHG proteins, are required for sensory neuron pruning and that disrupting the dynamics of the mitochondrial network prevents effector caspase activation in both pruning and dying sensory neurons. Overall, our findings demonstrate that a sublethal deployment of the apoptotic machinery is critical for remodelling dendrites and also reveal a direct link between mitochondria and sensory neuron cell death in vivo.

developmental biology↗

bioRxiv2020

Actin-based protrusions lead microtubules during stereotyped axon initiation in spinal neurons in vivo

In vitro, developing neurons progress through well-defined stages to form an axon and multiple dendrites. In vivo, neurons are derived from progenitors within a polarised neuroepithelium and it is not clear how axon initiation observed in vitro relates to what occurs in a complex, three-dimensional in vivo environment. Here we show that the position of axon initiation in embryonic zebrafish spinal neurons is extremely consistent across neuronal sub-types. We investigated what mechanisms may regulate axon positioning in vivo and found that microtubule organising centres are located distant from the site of axon initiation in contrast to that observed in vitro, and that microtubule plus-ends are not enriched in the axon during axon initiation. F-actin accumulation precedes axon formation and nascent axons form but are not stabilised in the absence of microtubules. Laminin depletion removes a spatial cue for axon initiation but axon initiation remains robust.

developmental biology↗

bioRxiv2020

LED Zappelin': An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging.

Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on the in vivo tetrachromatic zebrafish retina and for optogenetic circuit mapping in Drosophila. https://github.com/BadenLab/LED-Zappelin

neuroscience↗

bioRxiv2019

Patterned cell death sculpts functional and adaptive neural networks in flies

Changes to the structure and function of neural networks are thought to underlie the evolutionary adaptation of animal behaviours. Among the many developmental phenomena that generate change programmed cell death appears to play a key role. We show that cell death occurs continuously throughout insect neurogenesis and happens soon after neurons are born. Focusing on two dipterans which have lost flight during evolution we reveal that reductions in populations of flight interneurons are likely caused by increased cell death during development. Mimicking an evolutionary role for increasing cell numbers, we artificially block programmed cell death in the medial neuroblast lineage in Drosophila melanogaster, which results in the production of undead neurons with complex arborisations and distinct neurotransmitter identities. Activation of these undead neurons and recordings of neural activity in behaving animals demonstrate that they are functional. Our findings suggest that the evolutionary modulation of death-based patterning could generate novel network configurations.

neuroscience↗

bioRxiv2018

Label free 3D analysis of organelles in living cells by refractive index shows pre-mitotic organelle spinning in mammalian stem cells

Holo-tomographic microscopy (HTM) is a label-free non-phototoxic microscopy method reporting the fine changes of a cells refractive indexes (RI) in 3D. By combining HTM with epifluorescence, we demonstrate that cellular organelles such as Lipid droplets and mitochondria show a specific RI signature that distinguishes them with high resolution and contrast. We further show that HTM allows to follow in unprecedented ways the dynamics of mitochondria, lipid droplets as well as that of endocytic structures in live cells over long period of time, which led us to observe to our knowledge for the first time a global organelle spinning occurring before mitosis.

cell biology↗

bioRxiv2017

Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity

Building arborisations of the right size and shape is fundamental for neural network function. Live imaging studies in vertebrate brains strongly suggest that nascent synapses are critical for branch growth during the development of axonal and dendritic arborisations. The molecular mechanisms underlying such synaptotropic events are largely unknown.\n\nHere we present a novel system in Drosophila for studying the development of complex axonal arborisations live, in vivo during metamorphosis. In these growing axonal arborisations we see a relationship between the punctate localisations of presynaptic components and branch dynamics that is very similar to synaptotropic growth described in fish and frogs. These presynaptic components however do not appear to represent functional presynaptic release sites and are not paired with clusters of neurotransmitter receptors. Pharmacological and genetic knockdowns of evoked and spontaneous neurotransmission do not impact the outgrowth of these neurons. Instead, we find that axonal branch growth is regulated by the dynamic focal localisations of synaptic adhesion proteins Neurexin and Neuroligin. These adhesion complexes provide selective stability for filopodia by a stick and grow-based mechanism wholly independent of synaptic activity.

neuroscience↗

bioRxiv2017

Local Signal Processing In Mouse Horizontal Cell Dendrites

The mouse retina contains a single type of horizontal cell, a GABAergic interneuron that samples from all cone photoreceptors within reach and modulates their glutamatergic output via parallel feedback mechanisms. Because horizontal cells form an electrically-coupled network, they have been implicated in global signal processing, such as large scale contrast enhancement. Recently, it has been proposed that horizontal cells can also act locally at the level of individual cone photoreceptors. To test this possibility physiologically, we used two-photon microscopy to record light stimulus-evoked Ca2+ signals in cone axon terminals and horizontal cell dendrites as well as glutamate release in the outer plexiform layer. By selectively stimulating the two mouse cone opsins with green and UV light, we assessed whether signals from individual cones remain \"isolated\" within horizontal cell dendritic tips, or whether they spread across the dendritic arbour. Consistent with the mouse s opsin expression gradient, we found that the Ca2+ signals recorded from dendrites of dorsal horizontal cells were dominated by M- and those of ventral horizontal cells by S-opsin activation. The signals measured in neighbouring horizontal cell dendritic tips varied markedly in their chromatic preference, arguing against global processing. Rather, our experimental data and results from biophysically realistic modelling support the idea that horizontal cells can process cone input locally, extending the \"classical\" view of horizontal cells function. Pharmacologically removing horizontal cells from the circuitry reduced the sensitivity of the cone signal to low frequencies, suggesting that local horizontal cell feedback shapes the temporal properties of cone output.\n\nHighlightsO_LILight-evoked Ca2+ signals in horizontal cell dendrites reflect opsin gradient\nC_LIO_LIChromatic preferences in neighbouring dendritic tips vary markedly\nC_LIO_LIMouse horizontal cells process cone photoreceptor input locally\nC_LIO_LILocal horizontal cell feedback shapes the temporal properties of cone output\nC_LI\n\neTOC BlurbChapot et al. show that local light responses in mouse horizontal cell dendrites inherit properties, including chromatic preference, from the presynaptic cone photoreceptor, suggesting that their dendrites can provide \"private\" feedback to cones, for instance, to shape the temporal filtering properties of the cone synapse.

neuroscience↗