Biology subjects

Medina, M.

Publications and source records attributed to Medina, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The impacts of light and location on reproductive timing in the Orbicella species complex

Coral spawning events rely on tight synchronicity of gamete release to increase fertilization success by increasing gamete density in the water. Differences in spawning time can cause temporal reproductive isolation and minimize hybridization with closely related coral species. Sexual reproductive success is important as it generates the genetic diversity necessary for corals to survive large scale environmental stressors such as heat waves and bleaching events. The coordination of coral spawning events within a population maintains species boundaries and increases ecosystem-wide genetic diversity. Here we generate a database of spawning events in conjunction with depth and geographic location of the three species in the Orbicella species complex to assess variability in reproductive timing. The dataset, gathered from published papers, restoration practitioners, scientist throughout the Caribbean, contains almost three decades of data and includes 265 reproductive events. Our findings indicate that some aspects of each spawning season (month and day after the full moon) are influenced by latitude whereas others, such as spawning time in relation to local sunset, may exhibit variation based on geographic location. Combined, our results suggest that the reproductive timeframe of Orbicella spp. is triggered by factors associated with latitudinal gradients, such as the amount of energy from the sun, but the specific time of gamete release may be connected to other environmental factors that occur at a local scale or vary year-to-year.

ecology↗

bioRxiv2026

Functional plasticity of AIF revealed by dimerization and CHCHD4 interaction states

Apoptosis-inducing factor is a mitochondrial flavoprotein that links redox metabolism to mitochondrial homeostasis through its interaction with the disulfide relay protein CHCHD4. Although NADH-dependent AIF dimerization has been proposed as the activated state mediating CHCHD4 engagement, whether it is strictly required for productive AIF-CHCHD4 function remains unclear. Here, combining cellular, biochemical and biophysical approaches, we show that disruption of the AIF dimer interface compromises oxidative phosphorylation, respiratory-chain organization and CHCHD4-dependent mitochondrial homeostasis, yet preserves partial AIF function. Our data reveal that the AIF-CHCHD4 system operates as a conformational dynamic redox module in which distinct AIF oligomeric and redox states sustain CHCHD4 activity with different efficiencies. Mechanistically, dimerization is coupled to NADH-dependent conformational changes that regulate coenzyme binding, charge-transfer complex stabilization and catalytic efficiency. In turn, CHCHD4 binding remodels AIF conformational and redox properties, partially compensating for defects in dimer stabilization or redox coupling. Consistently, a peptide derived from the CHCHD4 N-terminus partially restores redox function in a pathogenic AIF variant defective in dimer stabilization, supporting partner-assisted allosteric regulation as a potential therapeutic strategy.

biochemistry↗

bioRxiv2026

Human claustrum neurons encode uncertainty and prediction errors during aversive learning

Flexible behavior depends on continuous updating of internal models, yet the neural circuits coordinating this process remain poorly understood [1]. The claustrum -- reciprocally connected to nearly the entire neocortex -- is uniquely positioned to influence cortical processing. Here we report single-neuron recordings from the human claustrum during aversive learning [2], with anterior cingulate cortex and amygdala recordings for comparison. Claustrum and anterior cingulate neurons displayed structured, task-related responses. Distinct subpopulations encoded stimulus onset and action-contingent outcomes, with outcome representations diverging between regions. Critically, both regions encoded model-derived latent variables -- uncertainty and prediction error -- but with different temporal profiles: only the anterior cingulate carried uncertainty signals during the intertrial period, while both regions encoded uncertainty and prediction error during the active-avoidance period. The amygdala, by contrast, showed minimal latent-variable modulation. These findings provide evidence that human claustrum neurons track higher-order cognitive variables not directly observable from sensory input, and reveal dissociable roles for the claustrum and anterior cingulate cortex in tracking latent task states.

neuroscience↗

bioRxiv2026

Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

Lysosomal membrane integrity is essential for cellular homeostasis, and its failure drives lysosomal storage disorders (LSD) and neurodegeneration. The dipeptide L-leucyl-L-leucine methyl ester (LLOMe) is widely used to model lysosomal damage, yet its mechanism remains poorly understood. The prevailing view holds that LLOMe polymerizes into membrane-permeabilizing peptide chains within the lysosomal lumen. Using cryo-electron tomography in cultured cells and primary neurons, we visualized the structural basis of LLOMe-induced lysosomal damage. We reveal that LLOMe forms amyloid structures within lysosomes that directly interact with and rupture the limiting membrane through mechanical stress. In vitro reconstitution confirms this amyloid-mediated mechanism. These findings establish a structural paradigm for lysosomal membrane disruption and provide insights into how disease-relevant protein aggregates, implicated in neurodegeneration and LSD, may compromise lysosomal integrity.

cell biology↗

bioRxiv2025

Prohibitin complexes associate with unique membrane microdomains in cells

Prohibitins are multi-subunit protein complexes implicated in a variety of roles in mitochondria, including maintaining cristae architecture, regulating lipid metabolism, and mediating protein quality control. Prohibitins form large, ring-like structures within the mitochondrial inner membrane, and it has been proposed that this unique architecture enables them to organize distinct membrane environments that support their diverse functions. However, the molecular mechanisms driving these structure-function relationships within the native cellular context remain poorly defined. In this work, we combine cellular cryo-electron tomography, subtomogram averaging, and Surface Morphometrics analysis to systematically characterize the structure and local membrane environment of prohibitin complexes in mouse embryonic fibroblast (MEF) cells. We show that prohibitins are enriched in the inner boundary membrane subdomain of the inner mitochondrial membrane. Moreover, we find that a subset of prohibitin complexes exhibits a unique association with a matrix-facing density that resembles an m-AAA protease. Further, we show that prohibitins consistently localize to regions of reduced lipid bilayer thickness across all inner mitochondrial membrane subdomains, suggesting that they locally remodel the membrane to support their function. Together, these findings provide direct structural evidence that prohibitin complexes are associated with unique membrane microdomains in cells and establish a framework for uncovering how the local cellular context enables prohibitin function.

cell biology↗

bioRxiv2025

Tomato pollen tube integrity is critical for pollen function at high temperature and is controlled by RALF signaling.

Reproductive success at high temperature (HT) depends on the ability of pollen to germinate a pollen tube that delivers sperm for double fertilization. We recently found that Solanum lycopersicum (tomato) cultivars capable of setting fruit at HT produce pollen tubes that continue to grow under heat stress. Our present goal is to define the molecular basis of thermotolerant pollen tube growth using quantitative live imaging, transcriptomic and proteomic profiling, and genetic analysis. We found that pollen tube integrity - the ability to maintain an intact tip during germination and elongation - was the pollen performance parameter that distinguished thermotolerant cultivars. We identified the components of the Rapid Alkalinization Factor (RALF) pollen tube integrity signal transduction pathway in tomato and found that RALF peptides repress germination at control temperature and that signaling is antagonized by HT. Loss of a single RALF peptide changes pollen tube cell wall pectin distribution and enhances pollen tube integrity at HT in thermotolerant Heinz, revealing that RALF signaling regulates thermotolerant pollen tube growth and establishing a molecular framework for improving reproductive heat-resilience in crop plants.

plant biology↗

bioRxiv2025

Evaluation of full-length 16S rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes

O_LIThe use of long-read sequencing using portable Oxford Nanopore Technologies (ONT) is becoming increasingly popular in the study of host-associated microbiomes. However, its application has not yet been optimized for characterizing understudied microbiomes, such as those in marine environments. C_LIO_LIWe evaluated the accuracy and consistency of ONT sequencing of full-length 16S rRNA genes for diversity surveys of symbiotic dinoflagellate (family Symbiodiniaceae) microbiomes. C_LIO_LIWhen comparing amplicon sequencing of the full-length bacterial 16S rRNA gene with only its V4 hypervariable gene region using a known microbial community, the former recapitulated the bacterial taxonomic composition more accurately. C_LIO_LIONT sequencing was also highly consistent between sequencing runs and flow cells. C_LIO_LILong-read sequencing technologies enable microbiome surveys using the full-length 16S rRNA gene, achieving higher accuracy and resolution. C_LIO_LIThis work validates ONT long-read sequencing as a powerful tool for marine microbiome studies to catalyze advancements in the fields of ecology and evolution, resource management, and conservation. C_LI

ecology↗

bioRxiv2025

Surface morphometrics reveals local membrane thickness variation in organellar subcompartments

Lipid bilayers form the basis of organellar architecture, structure, and compartmentalization in the cell. Decades of biophysical, biochemical, and imaging studies on purified or in vitro reconstituted liposomes have shown that variations in lipid composition influence the physical properties of membranes, such as thickness and curvature. However, similar studies characterizing these membrane properties within the native cellular context have remained technically challenging. Recent advancements in cellular cryo-electron tomography (cryo-ET) imaging enable high-resolution, three-dimensional views of native organellar membrane architecture preserved in near-native conditions. We previously developed a Surface Morphometrics pipeline that generates surface mesh reconstructions to model and quantify cellular membrane ultrastructure from cryo-ET data. Here, we expand this pipeline to measure the distance between the phospholipid head groups (PHG) of the membrane bilayer as a readout of membrane thickness. Using this approach, we demonstrate thickness variations both within and between distinct organellar membranes. We also demonstrate that membrane thickness positively correlates with other features, such as membrane curvedness. Further, we show that subcompartments of the mitochondrial inner membrane exhibit varying membrane thicknesses that are independent of network morphology (i.e., fragmented versus elongated networks). Finally, we demonstrate that large membrane-associated macromolecular complexes exhibit distinct density profiles that correlate with local variations in membrane thickness. Overall, our updated Surface Morphometrics pipeline provides a framework for investigating how changes in membrane composition in various cellular and disease contexts affect organelle ultrastructure and function.

biochemistry↗

bioRxiv2025

Exploring Phage-Staphylococcus aureus Host Dynamics Through Innovative In Vitro Experiment and Pharmacokinetic/pharmacodynamic Modeling

BackgroundPhage therapy is a promising approach against multidrug-resistant Staphylococcus aureus, but its clinical development is limited by gaps in pharmacokinetic/pharmacodynamic (PK/PD) understanding, especially concerning phage self-replication and resistance dynamics. MethodsWe combined in vitro time-kill assays with PK/PD modeling to study three anti-staphylococcal phages (V1SA019, V1SA020, V1SA022) against two S. aureus strains (SH1000 and USA300). A system of differential equations captured the co-dynamics of susceptible, resistant and infected bacteria and free phages. Nonlinear mixed-effect modeling quantified parameter variability. Resistance emergence was monitored through phenotyping and whole-genome sequencing of resistant clones. ResultsPhage-bacteria interactions followed a predator-prey pattern, with early bacterial growth, rapid phage amplification, and subsequent bacterial collapse. However, resistant subpopulations emerged, regrew over time, in a multiplicity of infection (MOI) dependent way. The model accurately described bacterial and phage dynamics and estimated kinetic parameters including adsorption and burst size. Proliferation and inundation thresholds varied by strain and phage. All resistant clones harbored mutations in genes involved in teichoic acid biosynthesis, with associated growth defects. Simulations demonstrated that only phage doses exceeding both susceptible and resistant bacterial inundation thresholds fully suppressed regrowth. ConclusionThis study provides a quantitative framework for understanding phage-S. aureus co-dynamics and resistance emergence. It emphasizes the importance of considering both proliferation and inundation thresholds when designing phage dosing regimens. These findings inform the rational development of phage therapy and support translation toward in vivo and clinical applications.

pharmacology and toxicology↗

bioRxiv2025

Active site tyrosine residues in human NQO1 homodimer are critical for non-synchronous enzyme catalysis at the two active sites.

AbstractHuman NQO1 is a flavoenzyme essential for the redox metabolization of many substances and associated with wide-impacting diseases such as cancer and Alzheime[r]s. Recent X-ray crystallographic studies have proposed that a few residues at the active site of NQO1 (including Tyr126 and Tyr128) may control enzyme catalysis and functional negative cooperativity. In this work, we use rapid mixing pre-steady state kinetics and hydrogen-deuterium exchange followed by mass spectrometry (HDX-MS) to evaluate experimentally the role of Tyr126 and Tyr128 in NQO1 functionality by generating mutants to Phe, Ala and Glu. Mutations to Phe caused mild effects, whereas those to Ala significantly decreased hydride transfer efficiency and those to Glu virtually abolished NQO1 activity. Interestingly, structural stability studies by HDX-MS showed significant perturbations particularly affecting the binding site of NADH/NAD+ in the less conservative mutations (particularly to Glu). Mutations of Tyr126 and Tyr128 seem to also modulate the non-synchronous catalysis in the two active sites (negative cooperativity) as well as the selectivity for NADH/NADPH as coenzymes. Our work experimentally demonstrates the critical role of Tyr126 and Tyr128 in the flavin reductive half-reaction of the catalytic cycle of NQO1 in the negative cooperativity, and also suggests that phosphorylation of these two Tyr residues might shut down NQO1 activity reversibly.

biophysics↗

bioRxiv2025

Characterization of Mycobacterium tuberculosis rhodanese-like sulfurtransferase SseA and its newly identified activator Rv3284: A new pathway to exploit as a drug target?

Tuberculosis (TB) remains a critical global health challenge, with Mycobacterium tuberculosis (Mtb) causing 10.8 million cases and 1.25 million deaths in 2023. Key issues include the dormant state of Mtb, resistant to drugs and immune responses, and the emergence of multi-drug-resistant strains. This underscores the need for new therapeutic targets and deeper research into Mtb pathogenesis and immunology. A potential drug target is the enzyme thiosulfate-sulfurtransferase SseA, which plays a role in macrophage infection by Mtb and its resistance to oxidative stress. SseA belongs to the rhodanese-like enzyme family, which catalyzes sulfur transfer reactions essential for Mtb survival. In our research, we identified a new protein (Rv3284), hereinafter referred to as SufEMtb due to its high homology with E. coli SufE, that interacts with SseA and modulates its activity. Sequence analysis and AI molecular modelling revealed detailed insights into their interaction that can contribute to the modulation of SseA activity. This research provides a mechanistic explanation to the need of a partner for SseA activation. Indeed, we propose that SufEMtb enhances SseA enzymatic function by binding to its non-catalytic N-terminal domain and bringing the active sites of the two proteins in close proximity, thus preparing for the activation-enhancing conformational change in a regulatory loop of SseA. This interaction is crucial for the effective enzyme activity and the maintenance of redox homeostasis in Mtb, making the SseA-SufEMtb protein complex a potential target for new TB therapies.

biochemistry↗

bioRxiv2025

Metatranscriptomics sheds light on 'who is doing what' in the coral Porites lutea

Global decline of coral reefs due to climate change necessitates nature-based protection strategies for these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions occurring within the coral holobiont. Using RNAseq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides first transcriptomic evidence of Ostreobiums ability to transfer fixed carbon to other holobiont members and the coral host. Additionally, we highlight critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour distinct microbiomes with wide-ranging functions.

microbiology↗

bioRxiv2024

The Potential of CCA-associated Bacteria to Fight Antimicrobial-Resistant Pathogens: a Genomic Survey

The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from the CCA Hydrolithon boergesenii. After running antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 100 putative Biosynthetic Gene Clusters (BGCs) across the three genomes. Further analysis uncovered BGCs potentially involved in the biosynthesis of novel antimicrobial compounds. Our study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis and highlights the potential of specialized marine environments like CCA biofilms.

genomics↗

bioRxiv2024

A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change

Coral reefs are declining worldwide due to anthropogenic environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata, from Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge and pollution for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical coral holobiont dynamics potentially associated with anthropogenic disturbances.

molecular biology↗

bioRxiv2024

Minimized Sample Consumption for Time-Resolved Serial Crystallography Applied to the Redox Cycle of Human NQO1

Sample consumption for serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) remains a major limitation preventing broader use of this powerful technology in macromolecular crystallography. This drawback is exacerbated in the case of time-resolved (TR)-SFX experiments, where the amount of sample required per reaction time point is multiplied by the number of time points investigated. Thus, in order to reduce the limitation of sample consumption, here we demonstrate the implementation of segmented droplet generation in conjunction with a mix-and-inject approach for TR studies on NAD(P)H:quinone oxidoreductase 1 (NQO1). We present the design and application of mix-and-inject segmented droplet injectors for the Single Particles, Clusters, and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument at the European XFEL (EuXFEL) with a synchronized droplet injection approach that allows liquid phase protein crystal injection. We carried out TR-crystallography experiments with this approach for a 305 ms and a 1190 ms time point in the reaction of NQO1 with its coenzyme NADH. With this successful TR-SFX approach, up to 97% of the sample has been conserved compared to continuous crystal suspension injection with a gas dynamic virtual nozzle. Furthermore, the obtained structural information for the reaction of NQO1 with NADH is an important part of the future elucidation of the reaction mechanism of this crucial therapeutic enzyme.

biochemistry↗

bioRxiv2023

Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations

The human NQO1 (hNQO1) is a FAD-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics, and it is over-expressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. The use of room temperature serial crystallography with microcrystals has been key to study this mechanism. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Altogether, these results pave the way for future time-resolved studies, both at XFELs and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.

biochemistry↗

bioRxiv2023

Anatomically-specific coupling between innate immune gene repertoire and microbiome structure during coral evolution.

Tropical reef-building corals exist in intimate symbiosis with diverse microbes and viruses. Coral microbiomes are generally much less diverse than their environment, but across studied corals, the biodiversity of these microbiomes varies greatly. It has previously been hypothesized that differences in coral innate immunity in general, and the copy number of TIR-domain containing innate immune genes in particular, may drive interspecific differences in microbiome structure. Despite many existing studies of coral microbiomes, this hypothesis has previously been difficult to test due to a lack of consistently collected cross-species data on coral microbiomes. In this manuscript, we reannotate TIR-domain containing genes across diverse coral genomes, and use phylogenetic comparative methods to compare these innate immune gene copy numbers against 16S rRNA marker gene data on coral mucus, tissue, and skeleton microbiomes from the Global Coral Microbiome Project (GCMP). The copy number of Toll-like receptor (TLRs) and Interleukin-1 receptor (IL-1Rs) gene families, as well as the total genomic count of their constituent domains (LRR and TIR domains; and Ig and TIR domains, respectively), explained most interspecific differences in microbiome richness and beta-diversity among corals with sequenced genomes. We find that these correlations are also anatomically specific, with an especially strong correlation between IL-1R gene copy numbers and microbiome richness in the corals endolithic skeleton. Together, these results suggest innate immunity may play a key role in sculpting microbiome structure in corals.

immunology↗

bioRxiv2023

Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution

Evolutionary tradeoffs between life-history strategies are central to animal evolution. However, because microbes can influence aspects of host physiology, behavior, and resistance to stress or disease, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a highly biodiverse and data-rich host system to test this idea, made more relevant by increases in coral disease outbreaks as a result of anthropogenic changes to climate and reef ecosystems. Identifying factors that determine coral disease susceptibility has therefore become a focus for reef conservation efforts. Using a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425 million years of coral evolution by combining a cross-species coral microbiome survey (the "Global Coral Microbiome Project") with long-term disease prevalence data at multiple sites. Interpreting these data in their phylogenetic context, we show that microbial dominance and composition predict disease susceptibility. We trace this dominance-disease association to a single putatively beneficial bacterial symbiont, Endozoicomonas, whose relative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera. Conversely, Endozoicomonas abundances in coral tissue strongly correlated with high growth rates. These results demonstrate that the evolution of microbial symbiosis in corals correlates with both disease prevalence and growth rate. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbiosis influences animal life-history tradeoffs, and in efforts to use microbes to increase coral growth or disease resistance in-situ. Significance StatementThe evolution of tropical corals, like that of many organisms, involves tradeoffs in life-history strategy. We sought to test whether microbes influence coral life-history traits. Comparative data from a census of modern coral microbes, combined with long term disease surveys in three regions, provide evidence for a correlation between microbiome structure, growth rate, and disease susceptibility during coral evolution. These trends were driven primarily by changes in the relative abundance of Endozoicomonas in coral tissue microbiomes, suggesting the novel hypothesis that Endozoicomonas may allow corals to grow more quickly at the cost of greater vulnerability to disease. Thus, symbiosis with microbes may be an important aspect of animal life-history strategy.

microbiology↗