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Gonzalez, A.

Publications and source records attributed to Gonzalez, A..

At least 19 recordsLinked to original sources

A bacterial chaperone-usher pathway links interkingdom association to antimicrobial protection of a fungal partner

Antimicrobial compounds (AMCs) influence species-level composition of microbial communities, governing beneficial and pathogenic interactions with plant and mammalian hosts. Phenazine-1-carboxylic acid (PCA) is a bacterially produced, redox-active AMC abundant in the rhizosphere. A recent study discovered the PCA-susceptible fungus Aspergillus calidoustus can grow in PCA-abundant environments by associating with phenazine-tolerant bacteria, including the novel species Paraburkholderia edwinii. P. edwinii's protection response is characterized by adherence to its fungal partner, bacterial aggregation, and sequestration and reduction of PCA, rendering PCA less toxic. Deletion of the bacterial transcriptional repressor HrcA generates a constitutively active protection response and enhanced protection of A. calidoustus. Here, we use the {Delta}hrcA strain to determine whether fungal protection uses bacterial self-protection machinery or dedicated interkingdom mechanisms. We identified a divergent archaic chaperone-usher pathway (CUP) operon encoding a predicted periplasmic chaperone, outer membrane usher, putative major pilin-like subunit, and putative adhesin-like tip protein. While many archaic CUP operons are annotated in diverse bacteria, their functions remain largely unexplored. We show these fungal attachment complex ( fac ) genes promote bacterial-fungal attachment, are required for P. edwinii to sequester and detoxify PCA, and contribute to full fungal protection from PCA stress, despite not being required for P. edwinii's own tolerance of PCA. We further identified the transcription regulator, FacR, that influences expression of the fac system. Understanding the functions of divergent archaic CUP systems may illuminate protective interkingdom partnerships and inform how pathogenic and beneficial microbes gain entry to AMC-replete environments, shaping microbial communities in agricultural and clinical contexts.

microbiology↗

Regulation of polarity during morphological transitions in Aureobasidium pullulans

Many fungi are able to switch between different morphologies by regulating the behavior of the cytoskeleton. In turn, the cytoskeleton is regulated by Rho-family GTPases, whose differing spatiotemporal patterns of activity lead to different modes of growth. The polymorphic fungus Aureobasidium pullulans alternates between multiple growth modes, including multibudding, isotropic, and hyphal growth. Here, we describe hyphal growth and the yeast-to-hyphal transition in this organism, with a focus on cell polarity. Yeast cells switched between cycles of budding and isotropic expansion in a variable manner prior to initiating hyphal extension. Initial hyphal extension proceeded in a stop-and-start manner with frequent pauses, before switching to continuous growth. Hyphal branching occurred from the sides of hyphae, and septation at multiple sites occurred in more mature hyphae. Previous work showed that either of two Rho-family GTPases, Rac1 and Cdc42, were sufficient promote budding. However, while Rac1 was also able to drive hyphal extension without Cdc42, Cdc42 could not promote hyphal growth without Rac1. Our findings provide the basis for an investigation of how polarity components are re-purposed for different fungal growth modalities.

cell biology↗

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.

microbiology↗

A Bayesian Study to Optimally Unveil LDH Kinetic Mechanisms In Vivo

Many life-threatening diseases present characteristic changes in metabolic profiles throughout their progression. For example, an increase in lactic fermentation is characteristic of cancer and is described by the Warburg effect. Yet, only a few methodologies allow for detecting these changes non-invasively and in real-time. Furthermore, the frequent oversight of the systems biochemical mechanisms and the elevated time and resources required for experimentation risk stagnating research. Here, we address both problems thanks to mathematical modelling and Bayesian statistics. Thanks to modelling, we guided understanding of the lactate dehydrogenase system, highlighting the importance of cellular microenvironment effects, membrane transport and enzymatic repression. To deal with increasing model complexity, we introduced and validated a novel Bayesian optimal experimental design approach to maximise the informative content of experiments. Hence, our approach generated fast and efficient lactate dehydrogenase kinetics characterisation, resulting in generalisable and reliable predictions in vitro and in vivo.

systems biology↗

Structured navigation in a goal-directed task reveals flexible spatial coding

Animal survival depends on accurate navigation. The last several decades have revealed that neurons encoding position and orientation can support navigation through the construction of an internal map of space for the external world. However, current experimental approaches for studying this system require tradeoffs between behavioral richness and experimental control; open field tasks often lack structured trials or trajectories and virtual reality paradigms constrain natural movement variables. Here, we introduce a platform that combines freely moving behavior with control over environmental stimuli, trajectories, and reward locations. This platform is compatible with chronic Neuropixels recordings, dynamic optical projection of visual stimuli and real-time pose estimation. Using this platform, we show rats can learn a multistage spatial targeting task and that high density Neuropixels recordings can be performed in conjunction. Recordings in medial entorhinal cortex revealed canonical spatial and head direction tuning, along with population-level activity that tracked distance to task-relevant goals. Together, this platform provides a powerful approach for examining the neural basis of flexible navigation under experimentally controlled yet naturalistic conditions.

neuroscience↗

Food reward in Bottlenose Dolphins (Tursiops truncatus) and Belugas Whales (Delphinapterus leucas) reduces heart rate and increase heart rate variability.

1.BackgroundHeart rate (HR) and HR variability (HRV) reflect the autonomic modulation of cardiac activity and are key indicators of physiological state and stress in vertebrates. However, measuring these parameters in cetaceans has been historically challenging due to the difficulty of recording electrocardiograms (ECGs) underwater. MethodsWe developed an all-in-one ECG suction-cup to record HR during apnea, respiration and food rewards in bottlenose dolphins (Tursiops truncatus, N = 8) and belugas (Delphinapterus leucas, N = 2). Moreover, we obtain comparative measurements of ECG waveform and HR oscillation in one killer whale (Orcinus orca). ResultsSpecies-specific ECG patterns were observed, including biphasic T waves in all three species and bifid P waves unique to belugas. All three species exhibited oscillations in resting HR and pronounced bradycardia during short apnea ([~]1 min), reflecting respiratory-linked autonomic modulation. Moreover, HR oscillations persisted throughout apnea, possibly reflecting a mechanism to cyclically improve body oxygenation during diving. Short-term food deprivation had no significant effects on bottlenose dolphins and belugas HR, while subsequent feeding ad libitum reduced HR (by [~]20% in dolphins, [~]40% in belugas) and increased HRV, suggesting the activation of vagal modulation. ConclusionsThis study establishes baseline HR and HRV parameters during breathing, apnea and food reward in three cetacean species, highlighting autonomic modulation across different behaviors and conditions and validate a non-invasive tool for studying marine mammal physiology.

physiology↗

Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

SARS-CoV-2 primarily infects the respiratory epithelium through entry factors ACE2 and TMPRSS2. However, alternative viral entry receptors and/or modulators of viral entry factors expression may contribute to infection in respiratory as well as non-respiratory tissues, including the kidneys and colon. Using single-cell analyses, we identified novel candidates for spike-mediated viral entry in epithelial cells from diverse fresh human tissues exposed to a labeled spike-pseudotyped virus. Systematic viral tracking revealed tissue-specific membrane receptors that contribute to viral entry, functionally validated in human tissues and partially predicted by molecular modeling. We found ADAM17 and IL1R1, together with canonical molecules, to significantly facilitate viral entry in the lung parenchyma, while entry into the renal cortex was less dependable on canonical factors, but strongly modulated by JAK1/2 engagement. These findings uncover distinct viral entry mechanisms across tissues and suggest novel organ-specific therapeutic targets for patients at risk.

microbiology↗

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

Animal gut microbiomes provide key physiological functions and are critical for host health. They vary dramatically across the animal kingdom, and are shaped by factors including host diet, evolutionary history and environment. However, analyses of gut microbiomes spanning the entire metazoan clade are lacking, limiting our understanding of the fundamental principles governing gut microbiomes. Here we present the Gut Microbiome Tree of Life (GMToL), a curated 16S amplicon dataset of 17,366 samples from 1,553 host species across 26 host classes from 284 studies, enabling analysis of large-scale evolutionary trends. Using ancestral state reconstruction, we provide a critical baseline calculation of major compositional shifts in gut microbiomes throughout animal evolution. We show that the ancestral animal gut was likely dominated by Pseudomonadota. A major shift to Bacteroidota occurred during the evolution of tetrapods, followed by the emergence of Bacillota-dominated guts in mammals and birds. We identify conserved core gut microbes and demonstrate how GMToL can be leveraged to contextualize the evolutionary history of specific microbial taxa. Ultimately, this framework enables the predictive mapping of microbial symbionts across uncharacterized host lineages, and establishes a quantitative baseline for comparative microbiome research at scale.

microbiology↗

Bidirectional network hubs: NT-genes as optimal targets for partial cancer reversal

BackgroundThe complexity of gene regulatory networks, involving thousands of genes, poses a fundamental challenge to understanding cancer phenotype reversal. However, recent evidence suggests that the effective dimensionality of normal and tumor transcriptional manifolds is low, and that small panels of genes can discriminate perfectly between normal and tumor samples. MethodsWe build upon two previously developed concepts: (i) highly accurate normal and tumor gene markers (namely, N-and T-markers), defined as genes with exclusive expression intervals in normal and tumor samples, respectively; and (ii) gene deregulation networks (GDNs), represented as directed acyclic graphs encoding causal relationships between gene deregulation events. A subset of genes appearing in both marker classes (NT-markers) act as bridging nodes between the N-and T-GDNs. Starting from these elements, we introduce a quantitative dynamical model based on node frequency and connectivity to assess how gene intervention effects propagate through the GDN and thereby predict their overall impact on the tumor tissue. ResultsAccording to the model, interventions on pure T-markers (T-markers that are not NT-markers) produce effects largely confined to the T-GDN, with a minimal perturbation of the N-network. Interventions on pure N-markers (N-markers that are not NT-markers) generate a perturbation of both networks, but with limited effect. In contrast, interventions on NT-markers with high activation frequency in both tumors and normal state (e.g., AGER in lung adenocarcinoma: 98% in tumor samples, 75% in normal samples) can induce bidirectional phenotype shifts. For an effective combination of targets, coverage across tumor samples must be maximized. At the same time, in the T-GDN the number of nodes unreached by the reverse cascade following the intervention must be minimized, as these regions may act as escape routes for the tumor. Escape probability further depends on the tumor stage and the tumors activation rate of new T-genes. When targeting NT genes, high frequency in normal samples should also be prioritized. ConclusionsHigh-frequency NT-genes, due to dual network connectivity and tissue relevance, represent optimal targets for achieving at least partial phenotype reversal. This framework provides a quantitative guide for prioritizing gene therapy targets and designing combination strategies that balance coverage, escape minimization, and normal tissue relevance.

systems biology↗

Galectin-8 regulates primary cilium in hypothalamic neurons through anL-type calcium channel/Aurora kinaseA/HDAC6 pathway impacting body energy balance

OBJETIVEFood intake, energy expenditure, and metabolic homeostasis depend on hypothalamic neurons responses to peripheral signals, such as leptin, involving the primary cilium (PC). The PC is crucial for signal transduction and is dynamically regulated by assembly/disassembly or reabsorption of its microtubules-based axoneme. Absence or reduction in the length of PC is associated with obesity and type-2 diabetes (T2D). In other cellular systems, PC reabsorption is primarily regulated by calcium-mediated activation of the Aurora kinase A (AurkA)/histone deacetylase C6 (HDAC6) axis, which promotes axonemal disassembly. Here, we explore the role of Galectin-8 (Gal-8), a glycan-binding protein, in regulating PC structure and signaling related to metabolic parameters in hypothalamic neurons. METHODSGal-8 effects were assessed in hypothalamic Clu-177 cells by analyzing the PC presence and length by immunofluorescence, PC dynamics, and intracellular calcium changes by in vivo cell imaging, activation of FAK, Src, AurkA, HDAC6 and STAT3 by immunoblot, and Gal-8 interactions with {beta}1-integrins by pull-down assays. Gal-8-KO mice were used to evaluate PC length in hypothalamic neurons, metabolic phenotype, and responses to Gal-8 intranasal administration. RESULTSIn Clu-177 cells, Gal-8 induced PC reabsorption and reduced responsiveness to leptin signaling towards STAT3 activation. PC reabsorption involves glycan-mediated Gal-8 interactions with a5b1 and a3b1 integrins, activation of FAK and Src leading to calcium influx through L-type calcium channels (LTCC), and subsequent AurkA/HDAC6 axis activation. Gal-8-KO mice showed longer PC in hypothalamic neurons, higher STAT3 activation, decreased body weight and food intake, improved glucose tolerance, higher locomotor activity, and a glycolytic respiratory exchange rate (RER). Daily intranasal Gal-8 administration for 4 days restored hypothalamic PC length and STAT3 signaling, as well as RER in Gal-8-KO mice to the level of WT mice. CONCLUSIONSEndogenous Gal-8 is required to maintain PC structure and leptin signaling in hypothalamic neurons, impacting body weight, energy balance, and glucose homeostasis. The mechanism involves calcium influx via LTCC downstream of b1-integrin/FAK/Src signaling and subsequent AurkA/HDAC6 axis activation. Both Gal-8 and the AurkA/HDAC6 axis may offer new therapeutic opportunities for treating metabolic diseases characterized by ciliogenesis impairment, including obesity and type-2 diabetes.

cell biology↗

Hippocampal patterns and associative memory: Distinct intracranial EEG temporal encoding patterns support memory

Episodic memory depends on neural representations encoded in the hippocampus. Experimental and computational evidence suggests that the hippocampus encodes pattern-separated representations that support later recall of episodic event elements. While extant data in humans predominantly focus on assaying the relationship between the similarity of spatial neural patterns at encoding and later memory performance, similarity of neural patterns in the temporal domain may also reveal encoding computations predictive of future memory. To examine how the similarity among temporal patterns of hippocampal activity during encoding relates to later episodic retrieval (associative cued recall and recognition memory), hippocampal activity was recorded from human participants (n=7) with implanted intracranial electrodes while they encoded arbitrary (A-B) paired-associates. Subsequent memory analyses first revealed that hippocampal high-frequency broadband power (HFB; 70-180Hz) was linked to a graded increase in memory strength; HFB power was greater during the encoding of pairs later correctly recalled relative to events later recognized and was lowest for events later forgotten. Second, and critically, subsequent memory analyses further revealed that more distinctive temporal patterns in the hippocampus during encoding -- indexed by the similarity of the HFB timeseries elicited by a given event to that elicited by other events -- were associated with superior subsequent memory performance. Finally, exploratory analyses revealed stimulus category effects on hippocampal HFB power during encoding and retrieval cuing. These results indicate that the temporal distinctiveness of hippocampal traces during encoding is important for subsequent retrieval of episodic event elements, consistent with theories that posit that pattern separation facilitates future remembering.

neuroscience↗

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

Microbially modified bile acids shape host physiology by regulating nutrient absorption, glucose homeostasis, circadian rhythms and thermoregulation. Here we identify a previously unrecognized drug-activating function of microbial bile acid conjugation. By systematically mining human LC-MS/MS datasets across public repositories and linking uncharacterized bile acid spectra to health-associated metadata, we discovered conjugates of the >75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-{gamma} in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4 T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance.

biochemistry↗

Enabling Megascale Microbiome Analysis with DartUniFrac

We introduce a new algorithm, DartUniFrac, and a near-optimal implementation with GPU acceleration, up to three orders of magnitude faster than the state of the art and scaling to millions of samples (pairwise) and billions of taxa. DartUniFrac connects UniFrac with weighted Jaccard similarity and exploits sketching algorithms for fast computation. We benchmark DartUniFrac against exact UniFrac implementations, demonstrating that DartUniFrac is statistically indistinguishable from them on real-world microbiome and metagenomic datasets.

bioinformatics↗

Weak dispersal and landscape size inevitably promote local biodiversity in heterogeneous metacommunities of competing species

We provide a general theoretical explanation for a longstanding result in spatial ecology: weak dispersal among habitat patches promotes local biodiversity. Using analytical approximations of spatial Lotka-Volterra competition models, we show that species persistence in heterogeneous landscapes can be expressed as a function of regional abundance and local invasion growth rates. We further demonstrate that local multispecies coexistence is governed by the feasibility domain, linking spatial coexistence to a structural property of nonspatial competitive systems. Together, these results explain why weak dispersal increases local species richness and why this effect strengthens with landscape size. We test these predictions using numerical simulations and find that the theory breaks down only when both dispersal and competitive interactions are very strong, in which case dispersal has a unimodal effect on coexistence. In contrast, landscape size retains a positive effect on coexistence whenever an effect is detectable. We then apply the theory to long-term data from a natural Daphnia metacommunity. We detect strong preemptive competition among species and find no detectable effect of dispersal rate on local coexistence, whereas species co-occurrence increases with local landscape size, as predicted by theory. Together, our results identify how dispersal, interaction strength, and landscape size jointly regulate biodiversity in competitive systems.

ecology↗

Komagataella phaffii encodes two functional Pho4 transcription factors

The transcription factor Pho4 is crucial for the response to phosphate starvation in many fungi, and it has been linked to tolerance to alkalinization of the medium and to pathogenicity. It is widely accepted that it is encoded by a single gene. However, the industrially relevant yeast Komagataella phaffii might contain two Pho4-encoding genes (PAS_chr1-1_0265 and PAS_chr2-1_0177, designated here PHO4(A) and PHO4(B), respectively), which have never been functionally characterized. The phenotypic analysis of single and double mutants suggests that Pho4(B) plays a major role in the adaptation to Pi scarcity. While single mutants exhibited limited and non-overlapping phenotypic defects, the pho4(A) pho4(B) strain was sensitive to multiple types of stress, including phosphate starvation and alkaline pH. Transcriptomic analysis confirms that Pho4(B) is crucial for the transcriptional response to phosphate starvation, including induction of typical gene markers (PHO5, PHO89, VTC1, etc.). However, by using a GFP reporter we found that PHO4(A) also participates in the induction of PHO89 under high pH stress. Expression of both PHO4(A) and PHO4(B) in S. cerevisiae complemented the pho4 mutation under phosphate limitation by restoring growth, expression of the Pho84 transporter and secreted phosphatase activity. These results indicate that both transcription factors display partially overlapping functions, responding differently to diverse stimuli, and that together they constitute a key component in the adaptation to a variety of stresses. Therefore, K. phaffii is an exceptional example among fungi that encodes two Pho4 functional transcription factors.

molecular biology↗

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one the most lethal cancer types. While infections with hepatitis B or hepatitis C viruses remain the primary risk factors for HCC development worldwide, metabolic disease-associated steatohepatitis has become the fastest growing etiology of HCC, particularly in the West. Our study characterizes, for the first time, the remodeling of the translation landscape in steatohepatitis-associated HCC using ribosome profiling and mass spectrometry techniques. In striking contrast with the transcriptional alterations, which do not show strong dependence on associated co-morbidity, translational alterations are broader in the steatohepatitis compared to the viral background. These alterations affect hundreds of genes, whose products are often involved in subcellular protein localization. By quantifying the relationship between the ribosome occupancy of upstream or downstream open reading frames (uORFs or dORFs) and coding regions (CDSs), we provide evidence of uORFs attenuating the translation efficiency of CDSs in HCC. We also identify numerous novel translated regions, including from RNAs currently annotated as non-coding, some yielding peptides that can be reproducibly identified in mass spectrometry datasets. Our study thus provides novel molecular data on HCC with a focus on the steatohepatitis etiology, reveals unexpectedly extensive translational control in this co-morbidity, and gives multiple hints and candidate targets for follow-up experiments.

systems biology↗

A searchable metadata network graph for microbiome metabolomics

Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available datasets with 144,424 mass spectrometry files from humans, animals, and microbial culture systems. MicrobiomeMASST integrates monocultures, synthetic communities, and host-associated samples across multiple body sites and plants. MS/MS spectra can be queried to trace occurrence across hosts, experimental conditions, and interventions, enabling cross-study integration. We demonstrate this framework by contextualizing microbial-conjugated bile acids and interrogating microbiome-mediated drug metabolism. Screening gut bacteria revealed deprolylation of the angiotensin-converting enzyme (ACE) inhibitor prodrug enalapril. Using microbiomeMASST, we traced this metabolite across human cohorts, microbial isolates, environmental samples, and in Gorilla gorilla. Structural modeling and enzymatic assays showed that microbial deprolylation abolishes ACE inhibition, thereby inactivating its therapeutic effect. Together, microbiomeMASST links MS/MS spectra to biological context, converting isolated observations into an interpretable microbiome map for cross-study analysis.

biochemistry↗

NK Cells Engineered with a Chimeric Antigen Receptor Delay HIV Rebound and Reshape HIV Reservoir Composition

Durable HIV remission will require strategies that eliminate or permanently silence the latent reservoir that persists despite antiretroviral therapy (ART). Natural killer (NK) cells possess inherent antiviral activity, but unmodified NK cells have limited ability to recognize or clear latently infected cells during ART suppression. We engineered allogeneic human primary NK cells expressing a truncated CD4-based chimeric antigen receptor (D1D2-CAR) that targets the conserved CD4 binding site on HIV Env without permitting viral entry, and evaluated their activities in humanized mice infected with barcoded CCR5-tropic HIV. D1D2-CAR NK cells selectively killed HIV-infected primary CD4 T cells in vitro and significantly delayed viral rebound following ART interruption in humanized mice compared to GFP-NK or no NK control groups. Barcoded HIV tracking showed that CAR-NK treatment reduced the number, diversity, and inter-organ overlap of rebounding viral RNA and proviral DNA lineages, yielding rebound driven by a restricted set of dominant clones. Integration site and chromatin analysis further demonstrated selective depletion of proviruses positioned in genes, enhancers, promoters, and open chromatin. These findings show that CAR-NK cells can target rare reactivation events during ART suppression and reshape the reservoir toward a less rebound-competent, epigenetically repressive state.

immunology↗