Biology subjects

Martinez-Perez, C.

Publications and source records attributed to Martinez-Perez, C..

8 recordsLinked to original sources

bioRxiv2026

Deciphering the association of spatial landscapes of DCIS with recurrence as invasive breast cancer

Stromal cell composition has been proposed as a potential biomarker in ductal carcinoma in situ (DCIS) for assessing the risk of subsequent recurrence or progression to invasive breast cancer (IBC). However, the characteristics of the tumor microenvironment within DCIS associated with these outcomes remain poorly understood. Here, we perform spatial transcriptomic analyses of 49 primary DCIS specimens from patients with no recurrence, DCIS recurrence, or recurrence as IBC. Cell mapping reveals spatially organized stromal cell gradients within DCIS, with enrichment of TREM2+ macrophages and myofibroblastic cancer-associated fibroblasts (myCAFs) in tumor-proximal niches. Notably, the abundance of TREM2+ macrophages near tumor nests is associated with subsequent recurrence as IBC. Moreover, ligand-receptor pair analysis identifies GRN--SORT1, SPP1--CD44, and LGALS9--CD44 interactions as spatially plausible signaling interactions between TREM2+ macrophages and epithelial cells. Finally, these findings are validated at the protein level by multiplex immunostaining of serial sections. This study characterizes the spatial landscape of the DCIS tumor microenvironment associated with subsequent recurrence, providing a basis for developing biomarkers of disease progression and identifying potential therapeutic targets.

cancer biology↗

bioRxiv2026

Heritable diel energy reserves enhance diatom growth

Diatoms are important drivers of marine primary production and biogeochemistry1-4. Compared to other phytoplankton groups, diatoms divide more asynchronously (i.e., divisions occur in a manner that is less aligned with the diel cycle) under non-limiting conditions, resulting in divisions occurring during both day and night5-16. However, the mechanisms and rates of asynchronous division have remained elusive. Here, using microfluidics-based time-resolved cell tracking, we measure the growth dynamics of individual cells of the diatom Thalassiosira pseudonana and show that cells growing mostly during the dark phase achieve rapid generation times (8 hours), dividing as fast as cells growing fully in light. We found that this remarkable ability of rapid growth in the dark is a consequence of the light history of both the cell and its parent cell, as light history controls the amount of photosynthetic energy the cell has stored in the form of the polysaccharide chrysolaminarin when entering the night. Furthermore, a mathematical model of this mechanism yields an up to 14% increase in the daily asynchronous population growth rate compared to growth without diel energy reserves when nutrients are non-limiting. This results in an up to 17-fold predicted increase in cell abundance over a typical 10-day diatom bloom, the maximal growth advantage of heritable chrysolaminarin during exponential phases of growth. By directly demonstrating and quantifying the benefit of chrysolaminarin under different diel conditions, this work provides a mechanistic understanding of how heritable diel energy reserves contribute to the rapid growth of diatom populations in the ocean. Beyond the specific discovery of the role of heritable energy reserves, we anticipate that our experimental approach can be broadly utilized in phytoplankton research by providing a blueprint to study phytoplankton physiology and ecology at the single-cell level, revealing novel mechanisms normally obscured in bulk growth assays.

microbiology↗

bioRxiv2025

Breaching the diatom frustule: Alteromonas macleodii triggers protoplast emergence and programmed necrotic-like cell death in the oceanic diatom Thalassiosira rotula

Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. While the role of bacteria in recycling organic matter is well established, their potential to actively induce algal death remains poorly understood. Here we examined the interaction between the bloom-forming diatom Thalassiosira rotula and a known member of its microbiome, Alteromonas macleodii. Microscopy revealed that A. macleodii breached the diatoms silica frustule, inducing >95% of diatom cells to emerge from their shells within 72 hours, exposing protoplasts to lysis and exploitation. This algicidal interaction is species-specific and contact-dependent. Dual transcriptomics revealed programmed necrotic-like cell death underpins T. rotulas terminal morphological change, alongside bacterial upregulation of motility, chemotaxis, and coordinated metabolism to exploit the diatom host. These findings indicate the presence of a programmed necrosis-like pathway in diatoms, akin to that known in mammals. They also reveal a novel algicidal strategy, recasting A. macleodii as a specialized antagonist capable of influencing bloom termination and removing the ballast provided by diatom frustules, thereby reshaping carbon cycling in the ocean.

microbiology↗

bioRxiv2025

GUARDIANS OF THE CELL: COCCOSPHERE PREVENTS OPPORTUNISTIC BACTERIA ATTACK IN HEAVY CALCIFYING COCCOLITHOPHORE

Coccolithophores are responsible for 40-60% of marine calcium carbonate production. This occurs through the biomineralization of extracellular calcium carbonate plates that encase the cell in a structure called the coccosphere. Despite its central role in ocean biogeochemistry, the function of coccolithophore calcification remains unresolved. One hypothesis is that the coccosphere acts as a physical shield, deterring predators and microbes. While its protective role has been investigated against grazers and viruses, its function in bacterial defense remains untested. Here, we investigate the interaction between heavily calcified Coccolithus braarudii and the bacterial pathogen Phaeobacter inhibens, known for its lethal Jekyll and Hyde relationship with the bloom-forming Gephyrocapsa huxleyi. We find that in C. braarudii, no P. inhibens pathogenicity is observed--unless the algae are decalcified. Upon decalcification, the relationship with P. inhibens becomes pathogenic, leading to algal cell death. Mortality of decalcified cells is specific to interactions with P. inhibens and is attachment-mediated: no toxicity is observed when cells are exposed to P. inhibens supernatant or to growth-inhibiting concentrations of indole-3-acetic acid-- identified in the P. inhibens-G. huxleyi system. Attachment requirement is further supported by scanning electron microscopy, which reveals extensive bacterial colonization on decalcified but not on calcified C. braarudii with P. inhibens. These findings provide the first experimental evidence that the coccosphere acts as a physical barrier against bacterial attack, underscoring its defensive role in coccolithophores.

microbiology↗

bioRxiv2025

Precise 3D Tracking of Highly Non-planar Eukaryotic Flagellar Beating Patterns using Digital Holographic Microscopy

Precise tracking of the rapid and complex three-dimensional movement of eukaryotic flagella is important for understanding their roles in cellular motility, sensory functions, and resource acquisition. Yet, achieving accurate 3D kinematic reconstruction of flagellar beating patterns, particularly highly non-planar ones, remains challenging. Here we present holoV3C, a method based on Digital Holographic Microscopy (DHM) that allows precise, label-free 3D tracking of highly non-planar eukaryotic flagella with high temporal resolution. This algorithm leverages phase anomaly detection to provide a combination of high temporal and axial resolution, with 0.25 m for beating mouse sperm flagella and down to 53 nm for polystyrene particles, across large sampling volumes in a computationally efficient manner. Algorithmic validation is performed by tracking mouse sperm flagella over time, capturing approximately 600 points along a single flagellum to achieve high axial resolution. Furthermore, we apply holoV3C to reconstruct the highly non-planar beating dynamics of the 200-nm-diameter flagellum of the protist Reclinomonas americana with a temporal resolution of 200 frames per second. By enabling 3D tracking of non-planar eukaryotic flagella, holoV3C can yield important insights to advance our understanding of flagellar dynamics, opening new avenues in the study of microorganism motility and its ecological roles.

biophysics↗

bioRxiv2025

Risk-reward trade-off in motility endurance generates dichotomy in search strategies among copiotrophic marine bacteria

Coptiotrophic marine bacteria contribute significantly to carbon storage in the ocean by remineralizing organic carbon present in nutrient-rich hotspots amidst oligotrophic waters. Motility is both highly beneficial and costly in such environments, presenting copiotrophs with a risk-reward trade-off in search behavior. Here we studied the motility endurance of 26 marine isolates using video microscopy and cell tracking over two days of carbon starvation. We found that this cost-benefit trade-off results in a distinct dichotomy among marine bacteria: risk-averse copiotrophs ceased motility within hours ( limostatic), whereas risk-prone copiotrophs converted 10% of their biomass per day into energy to retain motility for the two days of observation ( limokinetic). We identified a genomic component of this dichotomy, sufficiently robust to predict the response of additional species with 83% accuracy and the prevalence of both strategies in the ocean. This dichotomy can facilitate the incorporation of the bacterial contribution in ocean carbon cycle models.

microbiology↗

bioRxiv2025

Bacteria induce an amoeboid phase in coccolithophores that persists after bloom collapse

Coccolithophores, who contribute approximately 1-10% of phytoplankton biomass, are crucial players in the oceans biogeochemical cycles. Significant contributions come from bloom-forming species including Gephyrocapsa huxleyi (formerly Emiliania huxleyi), which has served as a model system for investigating algal-bacterial and agal-viral interactions as well as algal fitness responses to environmental changes. Coccolithophores follow a biphasic lifecycle, existing as motile haploid and non-motile diploid phases. Here we characterize a third, amoeboid phase, using a combination of light, electron and phase amplitude modulation (PAM) microscopy. Using time-resolved imaging we captured the rapid morphological transition from a spherical haploid to an elongated motile amoeboid cell. Cell tracking revealed slower and more directional swimming compared to haploid cells. Amoeboid metamorphosis was triggered by exposure to bacteria, including strains isolated from G. huxleyi blooms and known G. huxleyi pathogens, but not by a range of classical phytoplankton stressors, including viral infection and oxidative stress. Further, the sub-population of haploids which switched to the amoeboid phase persisted past the rapid crash of the haploid population. This amoeboid phase was only observed in the primary bloom-forming coccolithophore species G. huxleyi and Geopharycapsa oceanica in stationary phase when exposed to high bacterial concentrations, typical of late-stage algal bloom events. Photophysiology of amoeboid cells was confirmed to be unaltered via PAM microscopy, indicating these cells are metabolically active. These findings highlight a previously uncharacterized morphotype in this important phytoplankton species and suggest that the amoeboid phase could be a bacteria-resistant morphotype following algal bloom collapse.

microbiology↗

bioRxiv2022

Conservation of energetic pathways for electroautotrophy in the uncultivated candidate order Tenderiales

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics we identified conserved orthologous genes within the Tenderiales and nearest neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga". The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane bound energy transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggests the Tenderiales have an distribution unlimited ecological role coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. ImportanceElectromicrobiology enables enrichment and identification of chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation. The recently described order Tenderiales contains the uncultivated electroautotroph "Candidatus Tenderia electrophaga". The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome assembled genomes. This conservation extends to near neighbors of the Tenderiales, but not to other well-studied chemolithotrophs including iron and sulfur oxidizers. Our findings suggest that extracellular electron uptake may be pervasive among the Tenderiales and the geographic location from which metagenome assembled genomes were recovered offers clues to their natural ecological niche.

microbiology↗