Biology subjects

Babin, M.

Publications and source records attributed to Babin, M..

6 recordsLinked to original sources

bioRxiv2026

Silicon exaptation discovers antimicrobial peptides

Advances in machine learning (ML) have enabled the de novo design of synthetic proteins and peptides tailored for specific structural or functional properties. As ML becomes a central tool in forward design, we suggest that its value extends beyond optimizing known objectives. It can also lead to what we term here in this work as silicon exaptation, revealing unexpected functional properties that were never part of the original design goals. This reflects a principle common in biology, that repurposes traits where features evolved for one role can later enable unforeseen functions. In this context, these accidental findings are not constrained by preconceptions but arise from latent function emergence and the algorithm's gradual drift, a new process that can co-evolves with human curiosity, intuition, and interpretive reasoning, which can be used to recognize unexpected patterns and transform them into new discoveries. In this study, we discovered a set of peptides through silicon exaptation, in which the ML pipeline was originally optimized for structural characteristics unrelated to any antimicrobial functionalities. The peptides were originally designed to adopt defined secondary structures in response to environmental stimuli, with no antimicrobial properties intended or included in the training objectives. We systematically evaluated the antimicrobial potential of these peptides using broth microdilution assays and membrane integrity tests, identifying several candidates with potent and selective antibacterial activity without detectable cytotoxicity toward mammalian cells.

molecular biology↗

bioRxiv2026

Paradoxical energetics in the polar diatom Fragilariopsis cylindrus exposed to extreme low light

In the Arctic Ocean, diatoms initiate blooms under sea ice at extreme low-light levels, yet the limits and mechanisms behind this capability remain unknown. We investigated the steady-state physiological and molecular responses of the polar diatom Fragilariopsis cylindrus across a light gradient (0.1 to 30 {micro}mol photons m-2 s-1), representative of under-ice winter to early spring conditions, and reveals distinct strategies to cope with low light at both ends of this range. While cells optimize photon capture efficiency between 3 and 15 {micro}mol photons m-2 s-1 relative to 30 {micro}mol photons m-2 s-1, this strategy collapses below 1 {micro}mol photons m-2 s-1. In this dim-light regime, cells activate non-photochemical quenching and a sustained xanthophyll cycle, which indicates a paradoxical requirement for energy dissipation despite extreme photon scarcity. While cell division arrests at 0.18 {micro}mol photons m-2 s-1, photosynthetic electron transport seems to remain possible down to 0.1 {micro}mol photons m-2 s-1, which suggests an uncoupling between photosynthesis and biomass accumulation. Crucially, this low-light regime occurs without the consumption of reserves and represents a physiological state distinct from metabolic hypometabolism in prolonged darkness. We propose that this dim-light physiological state arises when residual light absorption exceeds the energetic requirements for cellular maintenance in the absence of division. The result is a regulated imbalance dissipated through heat and carbon excretion. This mechanism allows polar diatoms to maintain a primed photosynthetic metabolism to facilitate rapid growth recovery upon the return of light after the winter solstice.

plant biology↗

bioRxiv2025

Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control

Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for survival and therefore represent excellent models to understand the diversity of gene regulatory mechanisms, yet chromatin-based mechanisms have never been explored in these organisms. In this study, we combined genome-wide profiling of histone and DNA modifications with transcriptomic analyses of the marine polar diatom Fragilariopsis cylindrus upon entry and exit of a 3-month-long polar night. We show that, in agreement with its established role in transcription facilitation, histone H2B monobiquitination (H2Bub) is modulated at active genes upon prolonged darkness to light re-exposure. In contrast, histone H3 lysine 27 trimethylation (H3K27me3) and DNA cytosine methylation (CG methylation), two modifications typically associated with the silencing of genes or transposable elements (TEs), remained stable throughout the transitions, reinforcing their role in transcriptional repression, particularly at TEs but also at a few genes. We further demonstrate that H3K27me3 and DNA methylation are physically associated at TEs, probably reflecting a dual locking system enabling F.cylindrus cells to cope with the invasive nature of these genetic elements under extreme environmental conditions. These findings enhance our understanding of genome and epigenome regulation in diatoms in response to environmental variability and open new avenues for exploring the role played by chromatin-level regulation in the unique evolutionary history of polar unicellular eukaryotes.

genomics↗

bioRxiv2023

Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

Diatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain Arctic and Antarctic ecosystems. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their resilience to the long polar night. Here, we report an integrative approach revealing that in prolonged darkness, diatom cells enter a state of quiescence associated with reduced metabolic and transcriptional activity during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate, and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis. Cell division resumed rates similar to those before darkness. Our study demonstrates the remarkable robustness of polar diatoms to prolonged darkness at low temperatures. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/524047v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1da578corg.highwire.dtl.DTLVardef@1a9ac5borg.highwire.dtl.DTLVardef@729265org.highwire.dtl.DTLVardef@1e94c18_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserTo survive the long winter, polar diatoms slow down metabolism and express genes to assure survival following return to light.

ecology↗

bioRxiv2022

Global observation of plankton communities from space

Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a. The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

ecology↗

bioRxiv2020

Environmental vulnerability of the global ocean plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network - the community interactome - and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar), and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change, and forecasted most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for ocean monitoring of climate change.

ecology↗