Biology subjects

Hamon, M.

Publications and source records attributed to Hamon, M..

9 recordsLinked to original sources

bioRxiv2026

Coordinated orienting behavior emerges following unilateral optogenetic activation of Superior Colliculus GABAergic neurons

Orienting coordinates movements of the eyes, whiskers, nose, and other effectors, but how the superior colliculus (SC) recruits these components over time remains unclear. We combined unilateral optogenetic activation of SC GABAergic neurons with high-speed tracking of facial movements and Neuropixels recordings to examine SC-evoked orienting in head-fixed mice. Stimulation recruited movements of the whiskers, nose, eyes, and pupil. Horizontal eye and nose movements were directed contralateral to the stimulated hemisphere, whereas vertical eye movements, pupil dilation, and whisker protraction did not differ significantly between stimulation sides. Nose and whisker movements generally preceded eye movements, followed by slower pupil dilation, revealing a temporally organized response. Recordings from the SC contralateral to the stimulated hemisphere revealed heterogeneous neuronal responses comprising short-latency excitation and delayed excitation or inhibition. Short-latency excitation was similar on trials with and without evoked movements, whereas delayed excitation was greater on trials that evoked eye or nose movements. Neurons modulated during spontaneous nose movements showed corresponding optogenetically evoked responses, linking stimulation-induced activity to endogenous movement-related activity. Thus, activation of SC GABAergic neurons initiates evolving population activity that recruits a coordinated sequence of orienting movements.

neuroscience↗

bioRxiv2026

The ABC-F protein Uup, Rescues Stalled Ribosomal Termination Complexes to Modulate DNA Maintenance

The cytosolic ATP-binding cassette F (ABC-F) family modulates ribosomal activity in eukaryotes and prokaryotes. Although they all bind to the E site of the ribosome, some bacterial ABC-Fs confer resistance to ribosome-targeting antibiotics, while housekeeping members have poorly defined roles. Interestingly, in Escherichia coli, which possesses four ABC-F (EttA, Uup, YbiT and YheS), Uup has been rather implicated in DNA recombination. Using an unbiased approach, we reconcile this apparent discrepancy by showing that Uup's involvement in DNA recombination is indirect and is dictated by Uup-mediated regulation of the last steps of translation that rescues problematic translation of genes involved in DNA maintenance such as ssb and dnaX. Accordingly, the elongated cell phenotype observed in uup deletion background is reverted by expressing a ssb variant that no longer depends on Uup. Unlike its paralog EttA, which helps ribosomes in translating proteins with repeats of negatively charged residues in the N-terminal 30 amino acids, Uup instead facilitates the rescue of stalled translation termination events that, in its absence, are handled by the tmRNA pathway.

microbiology↗

bioRxiv2026

CICADA: A unified framework for NWB-based neurophysiological data analysis

Neurophysiology datasets are becoming increasingly complex, combining behavioral measurements with high-dimensional neuronal activity recordings coming from optical and/or electrophysiological measurements. The Neurodata Without Borders (NWB) standard has emerged in the community as the format of record. While standardized and widely used preprocessing tools generating NWB files have been developed, extensible frameworks for scientific analysis downstream of the NWB ecosystem are still under-represented. We present CICADA, a Python framework dedicated to analysis of neurophysiological data in the standardized NWB format. The toolbox is built as three hierarchically-organized packages: cicada-nwb (NWB access layer), cicada-analysis (plugin-based analysis engine and tool library), and cicada-gui (PyQt5 desktop application at the head of the pipeline). Beyond this architectural separation, CICADA is built around a central design principle: supporting a continuum from turnkey use to full modularity. Researchers can use the complete GUI-driven cicada-gui workflow without writing code, programmatically use existing analysis plugins from cicada-analysis, contribute to new analysis plugins, reuse utilities from cicada-tools, or build entirely custom pipelines on top of the cicada-nwb access layer alone. The same analysis plugin runs identically in interactive GUI and parameter-configured headless modes, enabling reproducible multi-session, multi-animal group analyses. We illustrate the versatility of CICADA with example analyses of behavioral, calcium imaging (two-photon and widefield) and extracellular electrophysiology datasets from rodent laboratories. CICADA is open source, actively maintained, and designed so that any laboratory can contribute at any level of the stack without modifying the core framework.

neuroscience↗

bioRxiv2026

F1F0-ATP-synthase subunit b head-to-head interactions shape intracellular membranes in Escherichia coli

1Intracellular membrane (ICM) compartments in bacteria remain poorly understood. In Escherichia coli, ICMs form upon the overproduction of certain membrane proteins. Here, we investigate at the molecular level how overproduction of subunit b of the F1Fo-ATP synthase complex shapes ICMs. Through a combination of subunit b deletions, electron microscopy, and biochemical analyses, we demonstrate that ICMs network structuration is mediated by the C-terminal domain of subunit b. High-resolution cryo-electron tomography and molecular dynamics simulations reveal that this domain forms tetrameric assemblies, bridging membranes and maintaining a regular 26 nm spacing. Transcriptomic and proteomic analyses further show that the cell responds to ICMs formation by upregulating energy metabolism genes and the ESCRT-III homolog PspA, while downregulating ribosomal and translational machinery. These results uncover a novel mechanism by which the C-terminal domain of subunit b drives the structuring of intracellular membranes. Additionally, they highlight how E. coli adapts to membrane stress by overexpressing membrane-remodeling proteins, a response that shares similarities with intracellular membrane homeostasis mechanisms in photosynthetic bacteria and unicellular algae.

microbiology↗

bioRxiv2026

Hierarchical processing and polarization encoding in the cephalopod visual system

Coleoid cephalopods (octopus, cuttlefish and squid, hereafter cephalopods) have evolved a range of complex visually-guided behaviours, from dexterous hunting to skin-pattern based camouflage and communication1. They have also evolved sensitivity to the polarization of light2, an adaptation thought to help detect camouflaged or semitransparent predators and prey in low visibility underwater environments3-10. How visual information is processed by the cephalopod brain to support their behaviours remains unclear. Here, studying the bigfin reef squid Sepioteuthis lessoniana, we performed calcium imaging and electrophysiological recordings from populations of neurons in the large visual center of the cephalopod brain, the optic lobe (OL). We revealed that the retina-recipient superficial OL contains a diversity of functionally distinct cell types, spatially organized into sub-layers, processing spatio-temporal features of light intensity and possessing polarization angle specificity. More complex features, e.g. direction selectivity, are seen in deeper regions of the OL cortex, which also exhibits spontaneous waves of neural activity in the absence of visual input. Neurons in the downstream OL medulla exhibit visual receptive field sizes and spontaneous activity levels which increase with brain depth, consistent with the hierarchical processing of visual information through the medullas tree-like anatomical organization. Medulla neurons exhibit sensitivity to local decreases in the degree of linear polarization (DoLP), which they integrate additively with light intensity information. Underwater imaging in the squids habitat off the coast of Okinawa, Japan, demonstrate that polarization sensitivity confers a robust short-range boost in object-background contrast over a range of objects and environmental conditions. These findings reveal convergent principles of hierarchical visual processing shared between cephalopods and vertebrates, and highlight how cephalopods utilise their distinct adaptation of polarization sensitivity to solve universal visual challenges underwater.

neuroscience↗

bioRxiv2025

Cell competition overcomes host tissue resistance to unleash tumour growth in a Drosophila brain cancer model

Primary tumours of the central nervous system are extremely aggressive and often incurable. While tumours are known to interact with their microenvironment, how the interplay between tumour cells and the host tissue controls tumour progression remains elusive. We addressed this question in a Drosophila model of cancer stem cell-driven tumour which originates during development and grows extensively within a network of cortex glia cells (CG) through adulthood. We found that tumour growth induces progressive remodeling of the CG network and leads to CG apoptosis through cancer stem cell-driven competition, a process which in turn unleashes tumour growth. Notably, preventing CG death reduces tumour growth, revealing a resistance capacity within the CG. Transcriptional profiling of CG cells at different stages revealed a biphasic response, featuring an early specific signature followed by a later collapse of essential cellular functions and pathways, including the conserved JNK pathway. JNK signalling in CG normally plays a neuroprotective role and initially hinders tumour progression, providing resistance. However, its subsequent downregulation eventually brings the collapse of the host tissue, ultimately curbing tumour growth. This study uncovers a dynamic and complex interplay between host tissue resistance and tumour-driven competition, which shapes tumour progression.

cell biology↗

bioRxiv2023

An oxadiazole-based compound potentiates anti- tuberculosis treatment by increasing host resistance via zinc poisoning

Anti-tuberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high content imaging, we identified novel 1,2,4-oxadiazole-based compounds, that allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, M. tuberculosis became even more sensitive to anti-tuberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.

microbiology↗

bioRxiv2023

New RoxS sRNA targets identified in B. subtilis by pulsed SILAC

Non-coding RNAs (sRNA) play a key role in controlling gene expression in bacteria, typically by base-pairing with ribosome binding sites to block translation. The modification of ribosome traffic along the mRNA generally affects its stability. However, a few cases have been described in bacteria where sRNAs can affect translation without a major impact on mRNA stability. To identify new sRNA targets in B. subtilis potentially belonging to this class of mRNAs, we used pulsed-SILAC (stable isotope labeling by amino acids in cell culture) to label newly synthesized proteins after short expression of the RoxS sRNA, the best characterized sRNA in this bacterium. RoxS sRNA was previously shown to interfere with the expression of genes involved in central metabolism, permitting control of the NAD+/NADH ratio in B. subtilis. In this study, we confirmed most of the known targets of RoxS, showing the efficiency of the method. We further expanded the number of mRNA targets encoding enzymes of the TCA cycle and identified new targets primarily regulated at the translational level. One of these is YcsA, a tartrate dehydrogenase that uses NAD+ as co-factor, in excellent agreement with the proposed role of RoxS in Firmicutes. ImportanceNon-coding RNA (sRNA) play an important role in bacterial adaptation and virulence. The identification of the most complete set of targets for these regulatory RNAs is key to fully identify the perimeter of its function(s). Most sRNAs modify both the translation (directly) and mRNA stability (indirectly) of their targets. However, sRNAs can also influence the translation efficiency of the target primarily, with little or no impact on mRNA stability. The characterization of these targets is challenging. We describe here the application of the pulsed SILAC method to identify these targets and obtain the most complete list of targets for a defined sRNA.

microbiology↗

bioRxiv2021

The Polo kinase Cdc5 is regulated at multiple levels in the adaptation response to telomere dysfunction

Telomere dysfunction activates the DNA damage checkpoint to induce a cell cycle arrest. After an extended period of time, however, cells can bypass the arrest and undergo cell division despite the persistence of the initial damage, a process called adaptation to DNA damage. The Polo kinase Cdc5 in Saccharomyces cerevisiae is essential for adaptation and for many other cell-cycle processes. How the regulation of Cdc5 in response to telomere dysfunction relates to adaptation is not clear. Here, we report that Cdc5 protein level decreases after telomere dysfunction in a Mec1-, Rad53- and Ndd1-dependent manner. This regulation of Cdc5 is important to maintain long-term cell cycle arrest but not for the initial checkpoint arrest. We find that both Cdc5 and the adaptation-deficient mutant protein Cdc5-ad are heavily phosphorylated and several phosphorylation sites modulate adaptation efficiency. The PP2A phosphatases are involved in Cdc5-ad phosphorylation status and contribute to adaptation mechanisms. We finally propose that Cdc5 orchestrates multiple cell cycle pathways to promote adaptation.

genetics↗