Instituto de Biología Funcional y Genómica

Microbial contamination in food processing remains a persistent and complex challenge. Understanding the sources, contributing factors, and control measures is essential for effective mitigation. In this study we employed a combination of metagenomic sequencing, targeted culturomics, and whole-genome sequencing of key isolates to gain a comprehensive view of bacterial dynamics and functional capabilities throughout a working shift in a beef slaughter and cutting facility. This allowed us to identify which bacteria are i) most prevalent in the clean facility before the start of the work, ii) able to establish themselves over time, and iii) detectable in the final product. We further generated a functional profile of the microbial community within the facility, with a particular focus on antimicrobial resistance and biofilm formation genes, and the presence of specific pathogens and spoilage organisms. Both culture-based and sequencing data showed that Psychrobacter and Pseudomonas strains present in the final product were also detected on the membrane skinner, a machine used to remove all the excess tissues from meat, and in the drains even after cleaning. We found a high number of genes involved in biofilm formation in Psychrobacter immobilis, a characteristic that may explain their biofilm capacity and the survival of this species during the cleaning process and persistence throughout the facility. Taken together, our findings suggest potential sources of contamination and highlight the advantages of integrating culture-dependent methods with high-throughput sequencing technologies to enhance microbial monitoring and control strategies in food production environments.

Chromosome dynamics, recombination, and nucleolar organization intersect during meiotic prophase I, yet how the recombination context influences nucleolar architecture remains unclear. We analyzed the nucleolar pool of Cdc14 in Saccharomyces cerevisiae under matched prophase I gating and a uniform, frame-based operational definition of transient two-focus episodes. In a prophase-arrest reference, Cdc14–mCherry formed a predominant single nucleolar focus with occasional, reversible two-focus episodes that Nop56–GFP placed within the nucleolar compartment (nucleolar splitting). Splitting rose sharply when interhomolog recombination was compromised and remained elevated when Spo11 catalytic activity was abolished, indicating that increased DSB formation is not required and pointing instead to the homolog engagement state as a key variable. Population checkpoint readouts did not map onto the phenotype: Hop1 phosphorylation differed strongly across genotypes, yet splitting remained high in recombination-defective and DSB-free contexts and low in the reference. Timing analyses showed that events concentrated early and declined in the reference, whereas recombination-defective and DSB-free backgrounds retained activity into later windows across thresholds. We propose that nucleolar splitting reflects a rheological response of the nucleolus to chromosome-scale forces that vary with homolog engagement, consistent with contributions from DSB-independent chromosome dynamics such as telomere clustering, telomere-led rapid prophase movements, and centromere coupling/pairing. Together, these data support the nucleolus as a mesoscale, mechanically sensitive readout of meiotic chromosome dynamics.

Defects in chromosome synapsis and meiotic recombination activate a checkpoint that, in budding yeast, delays exit from meiotic prophase I by inhibiting the Ndt80-dependent expression of regulators including the cyclin CLB1 and the polo-like kinase (PLK) CDC5. Additionally, Swe1-mediated inhibitory phosphorylation of cyclin-dependent kinase 1 (Cdk1/Cdc28) reinforces this arrest. Once the checkpoint is released, Cdk1 activation is essential for meiosis I entry and requires removal of inhibitory phosphorylation on tyrosine 19, governed by the opposing activities of the Swe1 kinase and the Mih1 phosphatase. Here, we dissect how this network is rewired at the prophase I to meiosis I transition. We show that Swe1 is essential for checkpoint maintenance, but not for its initial activation. We also demonstrate that Cdc5 promotes Cdk1 activation through a dual mechanism: by inducing Swe1 degradation and facilitating Mih1 nuclear translocation. Unlike in mitosis, Cdc5-dependent Swe1 degradation in meiosis does not require CDK-mediated priming and can occur when both proteins are artificially colocalized, indicating a distinct regulatory mode. Our findings uncover a novel function for Cdc5 in promoting meiotic cell cycle progression beyond its known roles in recombination and synaptonemal complex disassembly, highlighting how conserved cell cycle regulators are adapted to meiosis.

Glycolysis is primarily involved in ATP production but also modulates oxidative stress. Chronic alcohol consumption is correlated with an increased incidence of multiple diseases, including cancer and neurodegenerative diseases (NDDs), though the underlying mechanisms remain unclear. Guided by a literature review and bioinformatics analysis, we evaluated the expression of 22 genes encoding various isoforms of seven glycolytic enzymes (GEs) in the peripheral blood of patients with alcohol use disorder (AUD), individuals with acute alcohol consumption (AAC), and their respective control groups using qPCR. In parallel, we evaluated the expression of selected genes coding for GEs linked to NDDs, as well as astrocytic markers in primary mouse astrocyte cultures exposed to ethanol. Thirteen GE-related genes, including non-canonical isoforms, were significantly dysregulated in AUD patients; notably, eight of these genes showed similar alterations in individuals with AAC. Several enzymes encoded by these genes are known to be regulated by oxidative stress. Ethanol-exposed astrocytes also showed altered expression of glycolytic genes associated with NDDs and astrocyte function. These findings indicate that glycolytic dysregulation is driven by ethanol intake, regardless of exposure duration or organic damage, highlighting a link between ethanol-driven redox imbalance and glycolytic remodeling, which could contribute to organ damage.

Originally known for its function in the cell cycle, the anaphase-promoting complex/cyclosome (APC/C) also plays a crucial role in regulating differentiation and maintaining cell identity. However, the mechanisms by which APC/C mediates developmental processes are not fully understood. In this study, we show that APC/C and its activator FZR-1 regulate the chromatin regulators MES-4 and MES-3. These proteins are part of histone methylation complexes essential for maintaining germline stem cell (GSC) identity in the germ line of Caenorhabditis elegans. APC/CFZR-1 facilitates the degradation of MES-4 and MES-3 when GSCs transition toward differentiating into oocytes. The activity of APC/CFZR-1 is restricted by the Notch signaling pathway provided by the distal tip cell, which is responsible for maintaining the stemness of the GSC pool. This negative regulation enables the accumulation of MES-3 and MES-4 in GSCs, offering an additional component by which niche activity modulates the C. elegans germ line.

Obesity poses a global health challenge, demanding a deeper understanding of adipose tissue (AT) and its mitochondria. This study describes the role of the mitochondrial protein Methylation-controlled J protein (MCJ/DnaJC15) in orchestrating brown adipose tissue (BAT) thermogenesis. Here we show how MCJ expression decreases during obesity, as evident in human and mouse adipose tissue samples. MCJKO mice, even without UCP1, a fundamental thermogenic protein, exhibit elevated BAT thermogenesis. Electron microscopy unveils changes in mitochondrial morphology resembling BAT activation. Proteomic analysis confirms these findings and suggests involvement of the eIF2α mediated stress response. The pivotal role of eIF2α is scrutinized by in vivo CRISPR deletion of eIF2α in MCJKO mice, abrogating thermogenesis. These findings uncover the importance of MCJ as a regulator of BAT thermogenesis, presenting it as a promising target for obesity therapy.

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3-→NO2-→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2- and N2O in a NO3--filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3-→NO2- module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3-→NO2- module. Results also capture observations that NO3- is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.

Abstract Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N 2 O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain only subsets (“modules”) of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the observed prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when growth is limited by organic matter (OM), explaining the viability of populations respiring nitrite and N 2 O in a nitrate-filled ocean. Results predict denitrifier community succession along environmental gradients: shorter versus longer modules are favored when OM versus N limits growth, respectively, suggesting a niche for the NO 3 − ⟶NO 2 − module in free-living communities and for the complete pathway in organic particles, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO 3 − ⟶NO 2 − module. Results also capture observations that nitrate is the dominant source of N 2 O. These results advance the mechanistic understanding of the relationship between microbial ecology and N loss, which is essential for accurately predicting the ocean’s future.

SUMMARYThe cytoskeletal protein actin is crucial for cell shape and integrity throughout eukaryotes. Actin filaments perform essential biological functions, including muscle contraction, cell division and tissue morphogenesis. These diverse activities are achieved through the ability of actin filaments to be arranged into precise architectures. Much progress has been made in defining the proteome of the actin cytoskeleton, but a detailed appreciation of the dynamic organizational state of the actin filaments themselves has been hindered by available tools. Fluorescence polarization microscopy is uniquely placed for measuring actin filament organization by exploiting the sensitivity of polarized light excitation to the orientation of fluorophores attached to actin filaments. By engineering fusions of five widely used actin localization reporters to fluorescent proteins with constrained mobility, we have succeeded in developing genetically-encoded, green- and red-fluorescent-protein-based reporters for non-invasive, quantitative measurements of actin filament organization in living cells and tissues by fluorescence polarization microscopy.