Biology subjects

Lu, H.

Publications and source records attributed to Lu, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Peripheral alcohol metabolism dictates ethanol consumption and drinking microstructure in mice

BackgroundEthanol metabolism is intimately linked with the physiological and behavioral aspects of ethanol consumption. Ethanol is mainly oxidized by alcohol dehydrogenase (ADH) to acetaldehyde and further to acetate via aldehyde dehydrogenases (ALDHs). Understanding how ethanol and its metabolites work together to initiate and drive continued ethanol consumption is crucial for identifying interventions for alcohol use disorder (AUD). Therefore, the goal of our study was to determine how ADH1, which is mainly peripherally-expressed and metabolizes >90% of ingested ethanol, modulates ethanol metabolite distribution and downstream behaviors. MethodsEthanol consumption in drinking-in-the-dark (DID) and two-bottle choice (2BC) drinking paradigms, ethanol metabolite concentrations, and lickometry were assessed after ADH1 inhibition and/or in Adh1-knockout (Adh1 KO) mice. ResultsWe found that Adh1 KO mice of both sexes exhibited decreased ethanol consumption and preference compared to wild-type (WT) mice in DID and 2BC. ADH1 inhibitor fomepizole (4-MP) also significantly decreased normal and sweetened ethanol consumption in DID studies. Measurement of ethanol and its metabolites revealed that ethanol was increased at 1h but not 15 min, peripheral acetaldehyde was slightly decreased at both time points, and ethanol-induced increases in acetate were abolished after ethanol administration in Adh1 KO mice compared to controls. Similarly, ethanol accumulation as a function of consumption was 2-fold higher in Adh1 KO or 4-MP treated mice compared to controls. We then used lickometry to determine how this perturbation in ethanol metabolism affects drinking microstructure. Adh1 KO mice consume most of their ethanol in the first 30 min like WT mice but display altered temporal shifts in drinking behaviors and do not form normal bout structures, resulting in lower ethanol consumption. ConclusionsOur study demonstrates that ADH1-mediated ethanol metabolism is a key determinant of ethanol consumption, highlighting a fundamental knowledge gap around how ethanol and its metabolites drive ethanol consumption.

neuroscience↗

bioRxiv2025

WormID-Benchmark: Extracting Whole-Brain Neural Dynamics of C. elegans At the Neuron Resolution

The nematode C. elegans is a premier model organism for studying neural circuit function due to its fully mapped connectome and genetically identifiable neurons. Recent advances in 3D light microscopy and fluorescent protein tagging have enabled whole-brain imaging at single-neuron resolution. However, extracting meaningful neural dynamics from these high-resolution recordings requires addressing three fundamental challenges: (i) accurate detection of individual neurons in fluorescence images, (ii) precise identification of neuron classes based on anatomical and colorimetric cues, and (iii) robust tracking of neurons over time in calcium imaging videos. To systematically evaluate these challenges, we introduce WormID-Bench, a large-scale, multi-laboratory dataset comprising 118 worms from five distinct research groups, along with standardized evaluation metrics for detection, identification, and tracking. Our benchmark reveals that existing computational approaches show substantial room for improvement in sensitivity, specificity, and generalization across diverse experimental conditions. By providing an open and reproducible benchmarking framework1, WormID-Bench aims to accelerate the development of high-throughput and scalable computational tools for whole-brain neural dynamics extraction in C. elegans, setting the stage for broader advancements in functional connectomics.

neuroscience↗

bioRxiv2025

Looking for the optimal pathway to stimulate hippocampus in human participants using transcranial ultrasound stimulation (TUS): a simulation study

At present, very limited methods can directly modulate the neural activities in deep brain structures in human participants. Low-intensity transcranial ultrasound stimulation (TUS), as an emerging and advanced modality of non-invasive brain stimulation (NIBS), has great potential for focally stimulating the subcortical structures that are related to sleep, emotion and the functions of motor of cognition. Due to the focality, the integration of various methods, including magnetic resonance imaging and possible pathways, is important to perform TUS intervention for precise targeting and dosing. Based on structural MRI scans, we constructed a simulation model of low-intensity TUS, with a particular focus on the optimal pathways of targeting hippocampus in human participants. Finally, we outlooked the future perspectives of TUS in clinical applications in neurological and psychiatric fields.

neuroscience↗

bioRxiv2025

DNA topological regulation by topoisomerase IIbeta-DNA-PK interaction is important for controlled hypoxia-inducible gene expression

Hypoxic stress responses are essential for cellular and organismal survival and drive gene regulation across diverse biological pathways, including cell cycle progression and energy metabolism. Here, we show that topoisomerase II{beta} (TOP2B) regulates DNA topology and transcription of hypoxia-inducible genes (HIGs) in a DNA-dependent protein kinase (DNA-PK)-dependent manner. Integrated cellular, biochemical, and genomic analyses reveal an antagonistic yet correlated relationship between TOP2B and DNA-PK activities. Under normoxic conditions, TOP2B associates with HIGs and represses transcription by suppressing DNA negative supercoiling formation and accessibility. Under hypoxic exposure, TOP2B dissociates from HIGs, while DNA-PK and HIF1 are recruited to activate HIGs. Notably, DNA-PK is required for the repressive function of TOP2B, as DNA-PK knockout abrogates TOP2B release and activity, resulting in elevated expression of a number of HIGs. Mechanistically, DNA-PK phosphorylates TOP2B at T1403, stimulating its catalytic activity to restrain DNA unwinding and accessibility, thereby suppressing HIG transcription. Collectively, these findings identify a novel role for TOP2B and DNA-PK-mediated regulation of TOP2B as key transcriptional regulators of HIG expression. We propose that phosphorylation-dependent modulation of TOP2B activity is coordinated with transcriptional states and determines DNA topology to regulate Pol II transcription.

molecular biology↗

bioRxiv2025

Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump

Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth. Here we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5 and 3 selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.

bioinformatics↗

bioRxiv2024

A regulator controls both DNA damage response and anti-phage defense networks in Moraxellaceae

DNA damage chemicals, including many antibiotics, often induce prophage induction and phage outbreaks in microbial communities, a major threat to bacterial survival. Moraxellaceae contains clinically highly relevant strains with outstanding antibiotic and radio resistance, yet their cellular-level regulation in DNA damage response and anti-phage defense is largely unknown. Here, we identified a WYL family protein that had replaced the ubiquitous SOS system in evolution and directly regulated a transcriptional network of both DNA repair genes and anti-phage defense genes under DNA damage stress. This study depicts a mechanism that how bacteria maintain immunity to phages without compromising on antibiotic resistance, and sheds light on controlling the resistance of Moraxellaceae strains in clinical practice.

microbiology↗

bioRxiv2024

In vivo engineered quadrivalent CAR-macrophages break tumor barrier,remodel TME and overcome tumor heterogeneity through antigen spreading

CAR-macrophages have shown promising prospect in treating solid tumors. Ex vivo engineered CAR-macrophages face the challenge of low transfection efficiency, long preparation cycle, and limited cell number. Here, we designed two novel CAR molecules, GPC3-CAR-Super IL-2 and FAP-CAR-{bigtriangleup}TGF{beta}RII from the perspective of targeting tumor cells and improving tumor microenvironment, and generated quadrivalent CAR-macrophages in vivo for treating solid tumors by the LNP-mRNA system. We found that in vivo engineered quadrivalent CAR-macrophages can strongly activate tumor immunity and achieve complete tumor regression without significant side effects. Mechanically, in vivo engineered quadrivalent CAR-macrophages broke down physical barriers around the tumor constructed by CAFs and significantly promoted infiltration and expansion of CD8+ T cells. Moreover, the transiently formed CAR-macrophages in vivo are sufficient to form long-lasting T cell memory which can effectively prevent tumor recurrence. Most importantly, in vivo engineered CAR-macrophages also stimulated T cell memory against antigen-negative tumor cells through antigen spreading, which might effectively prevent the immune escape of heterogeneous tumor cells. Overall, we developed a platform of in vivo CAR-macrophages with dual roles as a tumor-killing effector cell and a recurrence-preventing vaccine.

bioengineering↗

bioRxiv2024

Functional MRI reveals regional changes of brain activity after five days of focal high-density theta burst stimulation (hdTBS) of the rat brain

BackgroundThe therapeutic effects of transcranial magnetic stimulation (TMS) likely stem from neuroplasticity induced by repeated sessions over time. While animal models offer insights into TMS-induced plasticity, a rodent model that faithfully replicates prolonged TMS conditions in humans is still lacking. Objective/HypothesisDevelop a rat model that mimics the spatial and temporal patterns of TMS in humans. MethodsExperiments were conducted on two cohorts of healthy adult rats (N=33). In cohort 1, rats underwent surgical implantation of microelectrodes for motor evoked potential (MEP) recording. With a rodent-specific coil and the high-density theta burst stimulation (hdTBS) paradigm, under awake condition, rats received daily TMS at 100% motor threshold for five days (days 1-5) to the hindlimb motor cortex. Cortical excitability was measured by input-output (I-O) curves on Day 0 (pre-hdTBS baseline) and Day 6 (post-hdTBS). The second cohort received identical TMS and underwent fMRI to map cerebral blood volume (CBV) on Days 0 and 6. ResultsDaily hdTBS session for 5 days significantly up-shifted I-O curves only in the TMS group (N=9), not in the sham group (N=7), indicating enhanced cortical excitability. fMRI data showed that, compared to sham group (N=9), rats receiving hdTBS (N=8) had increased basal CBV in several brain regions proximal and distal to the stimulation site, suggesting enhanced basal metabolism. Conclusion(s)Daily hdTBS session for 5 days focally delivered to the motor cortex of naive rats significantly altered basal brain activity in a network of brain regions, opening a novel platform for further investigating TMS-induced plasticity.

neuroscience↗

bioRxiv2024

Genetic-Dependent Brain Signatures of Resilience: Interactions among Childhood Abuse, Genetic Risks and Brain Function

Resilience to emotional disorders is critical for adolescent mental health, especially following childhood abuse. Yet, brain signatures of resilience remain undetermined due to the differential susceptibility of the brains emotion processing system to environmental stresses. Analyzing brains responses to angry faces in a longitudinally large-scale adolescent cohort (IMAGEN), we identified two functional networks related to the orbitofrontal and occipital regions as candidate brain signatures of resilience. In girls, but not boys, higher activation in the orbitofrontal-related network was associated with fewer emotional symptoms following childhood abuse, but only when the polygenic burden for depression was high. This finding defined a genetic-dependent brain (GDB) signature of resilience. Notably, this GDB signature predicted subsequent emotional disorders in late adolescence, extending into early adulthood and generalizable to another independent prospective cohort (ABCD). Our findings underscore the genetic modulation of resilience-brain connections, laying the foundation for enhancing adolescent mental health through resilience promotion.

neuroscience↗

bioRxiv2024

Synaptonemal complex protects double-Holliday junctions during meiosis

Chromosomal linkages formed through crossover recombination are essential for accurate segregation of homologous chromosomes during meiosis1. The DNA events of recombination are linked to structural components of meiotic chromosomes2. Imperatively, the biased resolution of double-Holliday junction intermediates (dHJs) into crossovers3,4 occurs within the synaptonemal complex (SC), the meiosis-specific structure that mediates end-to-end synapsis of homologs during the pachytene stage5,6. However, the SCs roles in crossover-specific dHJ resolution remains unclear. Here, we show that key SC components function through dependent and interdependent relationships to protect dHJs from aberrant "dissolution" into noncrossover products. Conditional ablation experiments reveal that cohesin, the core of SC lateral elements, is required to maintain both synapsis and dHJ-associated crossover recombination complexes (CRCs) during pachytene. The SC central region transverse-filament protein is also required to maintain CRCs. Reciprocally, stability of the SC central region requires the continuous presence of CRCs, thereby coupling synapsis and desynapsis to dHJ formation and resolution. However, dHJ protection and maintenance of CRCs can occur without end-to-end homolog synapsis mediated by the central element of the SC central region. We conclude that local ensembles of SC components are sufficient to enable crossover-specific dHJ resolution and thereby ensure the linkage and segregation of homologous chromosomes.

cell biology↗

bioRxiv2024

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation

Rice (Oryza sativa) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous O. longistaminata genome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 343-Mb telomere-to-telomere (T2T) genome assembly for this species, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between the O. longistaminata and O. sativa. A total of 2,466 segmentally duplicated genes were identified and enriched in cellular amino acid metabolic processes. We detected a slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of O. longistaminata provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.

genomics↗

bioRxiv2024

ADAR1 orchestrates the ZBP1-mediated PANoptosis and heart transplant rejection

BackgroundPANoptosis is an integrated form of cell death that combines features of pyroptosis, apoptosis, and necroptosis and is regulated by a complex network of signaling proteins. The roles of ADAR1 (adenosine deaminase acting on RNA 1) and RIPK1 (receptor-interacting serine/threonine-protein kinase 1) in orchestrating the ZBP1 (Z-DNA binding protein 1)-RIPK3 complex to mediate PANoptosis is not fully understood, particularly in the context of heart transplantation. ObjectiveThis study investigated how ADAR1 and RIPK1 coordinate the activation of the ZBP1-RIPK3 complex to mediate PANoptosis and its implications in mouse heart transplantation. MethodsUsing both in vitro and in vivo models, we analyzed the interactions between ADAR1, RIPK1, ZBP1, and RIPK3. We employed western blotting, and siRNA to elucidate the dynamics of these interactions. Additionally, we assessed the impact of ZBP1 on mouse heart transplantation outcomes. ResultsOur studies revealed that ADAR1 regulates the activation of the ZBP1-RIPK3 complex for PANoptosis. The interaction of ADAR1 with ZBP1 protected against Z-DNA-induced cell death by limiting activations of ZBP1 and RIPK3. In mouse heart transplantation study, we found that ZBP1 and its ligand Z-DNA/Z-RNA were significantly increased in the graft post-transplantation. Furthermore, ZBP1 deficiency in the heart graft inhibited cardiac PANoptosis, attenuated acute graft injury, and induced long-term graft survival. ConclusionThis study elucidates the role of ADAR1 in ZBP1-mediated PANoptosis. Inhibition of ZBP1 can prevent heart graft injury and rejection. Understanding these mechanisms provides valuable insights into the regulation of cell death and may inform the development of novel therapeutic strategies to improve transplant outcomes.

molecular biology↗

bioRxiv2024

Developmental control of E-cadherin junctions by mechanical contractility in Drosophila embryos

Adherens junctions are very plastic structures that change their composition and structure depending on the state of the epithelial tissue, involving mechanical stress and tissue dynamics. In Drosophila embryos, adherens junctions mature only during gastrulation following their formation a few minutes before during cellularization. Although the developmental maturation is obvious during gastrulation, the factors and conditions controlling it have remained unclear. Here, we assay the levels, distribution pattern, and mobility of E-cadherin during Drosophila gastrulation. Indicating a maturation, we find an increase in total levels at junctions and a drop in the mobile fraction of E-cadherin molecules. Both developmental changes depend on Myo-II contractility. Consistent with stereotypic Myo-II regulation, we find that interference with Rho signaling leads to corresponding changes in E-cadherin levels and mobility, at least in part. Besides Rho signaling, Src42A contributes to junction maturation, as tested by both loss-function and gain-of-function situations. Together, we demonstrate developmental maturation of adherens junctions and identify Rho signaling and Src42A as upstream regulatory pathways.

developmental biology↗

bioRxiv2024

Non-Invasive Quality Control of Organoid Cultures Using Mesofluidic CSTR Bioreactors and High-Content Imaging

Human brain organoids produce anatomically relevant cellular structures and recapitulate key aspects of in vivo brain function, which holds great potential to model neurological diseases and screen therapeutics. However, the long growth time of 3D systems complicates the culturing of brain organoids and results in heterogeneity across samples hampering their applications. We developed an integrated platform to enable robust and long-term culturing of 3D brain organoids. We designed a mesofluidic bioreactor device based on a reaction-diffusion scaling theory, which achieves robust media exchange for sufficient nutrient delivery in long-term culture. We integrated this device with longitudinal tracking and machine learning-based classification tools to enable non-invasive quality control of live organoids. This integrated platform allows for sample pre-selection for downstream molecular analysis. Transcriptome analyses of organoids revealed that our mesofluidic bioreactor promoted organoid development while reducing cell death. Our platform thus offers a generalizable tool to establish reproducible culture standards for 3D cellular systems for a variety of applications beyond brain organoids.

bioengineering↗

bioRxiv2024

BMAP: a comprehensive and reproducible biomedical data analysis platform

In the realm of biomedical research, efficient data analysis and processing are crucial due to the escalating volume and complexity of data generated by research teams. Managing these vast arrays of localized data presents significant challenges, necessitating precise, efficient, and reproducible analysis methodologies to ensure the integrity and reliability of scientific outcomes. Traditional management of analysis codes, computing environments, and the inherent difficulties in result traceability due to team dynamics often lead to inefficiencies and potential risks in maintaining academic integrity. Furthermore, while online storage platforms such as Dryad, GitHub, and Docker facilitate data, code, and environment management, they do not inherently guarantee the reproducibility of results, with issues like data incompleteness, forgotten parameters, or software discrepancies posing additional challenges. To address these critical gaps, we developed a BioMedical data Analysis Platform (BMAP) to offer online and localized categorized management of research assets. BMAP enhances workflow efficiency by transforming complex pipelines into user-friendly web applications, promoting consistency and standardization across team analyses. Its comprehensive web analysis module and seamless integration with data and computing resources support automated result reproducibility and visualization. According to the assessment, 1,692 omics-related figures from 101 recent articles, across 45 visualization types, were tested with BMAP, which could cover 37.8% of the types and 64.3% of the figures. BMAP also enables the sharing and enhancement of research methods through its cloud platform, allowing researchers to utilize the previously developed and validated tools, thereby reducing redundant effort and minimizing analytical discrepancies due to methodological differences.

bioinformatics↗

bioRxiv2024

GlyTrait Brings Insights into Functional Glycosylation

Glycomics research often grapples with the interpretability and biological relevance of glycomics data. Using glycosylation derived traits are promising methods for more in-depth biological insights, yet no such bioinformatic tool exists for such task. Here, we developed GlyTrait, a Python-based framework designed to enhance glycomics analysis through the innovative calculation and interpretation of derived traits from N-glycome data. GlyTrait automates the derivation of biologically significant traits, shifting focus from mere glycan abundances to functional glycan properties such as branching and fucosylation. GlyTrait extends the well-established nomenclatures and definitions of derived traits in the N-glycomics community, allowing for fast exploration and analysis of N-glycome data effortlessly. Furthermore, with the well-designed formula grammar, custom derived traits could be materialized without any knowledge of coding. Besides, a two-step post-filtering process reduces information redundancy, maintaining only the most informative traits. Finally, subsequent statistical and interpretable machine learning analysis provide robust insights into the glycosylation patterns associated with disease states. This comprehensive approach not only improves the statistical power and sensitivity compared to traditional methods, but also enhances the interpretability of glycomics data. GlyTraits efficacy is demonstrated through the re-analysis of published glycoengineered CHO cell lines and visceral leishmaniasis patient data, alongside a newly conducted pilot study for hepatocellular carcinoma (HCC) N-glycan biomarker discovery. We are confident in GlyTraits potential to become an indispensable tool for the glycomics community. Significance StatementGlycomics data is often challenging to interpret and analyze for biological relevance. GlyTrait, a Python-based tool, addresses this by automatically calculating biologically significant traits from N-glycome data, focusing on functional properties like glycan branching and fucosylation rather than mere abundance. This tool enhances data interpretability, reduces redundancy through post-filtering, and employs statistical methods to uncover glycosylation patterns linked to diseases. Demonstrated on various published datasets, as well as a newly conducted pilot study with 165 samples for hepatocellular carcinoma N-glycan biomarker discovery, GlyTrait proves to be a powerful tool. It improves the understanding of glycosylation changes in conditions like cancer, thereby benefiting the glycomics community.

bioinformatics↗

bioRxiv2024

The Mammalian KU70 C-terminus SAP Domain Is Required to Repair Exogenous DNA Damage

The mammalian non-homologous end joining (NHEJ) is required for V(D)J recombination as well as coping with exogenously induced DNA double strand breaks (DSBs). Initiated by the binding of KU70/KU80 (KU) dimer to DNA ends and the subsequent recruitment of the DNA- dependent protein kinase catalytic subunit (DNA-PKcs), NHEJ plays a key role in DNA repair. While there has been significant structural understandings of how KU70 participates in NHEJ, the specific function of its highly conserved C-terminal SAP domain remains elusive. In this study, we developed a novel mouse model by deleting the SAP domain but preserving the KU70 nuclear localization and its dimerization ability with KU80. We found that the KU70 SAP deletion did not affect the V(D)J recombination or animal development but significantly impaired the animals and cells in repairing exogenously induced DSBs. We further showed an inability of KU70-{Delta}SAP cells to retain the DNA Ligase IV (LIG4) and other NHEJ co-factors on chromatin, and a spreading pattern of DSB marker {gamma}H2AX in KU70-{Delta}SAP cells after DNA damage. Our findings suggest that a specific inhibition of the SAP function may offer an opportunity to modulate cell sensitivity to therapeutic DSB-inducing agents without interfering with the developmental function of KU70. KeyPointsO_LIGeneration of a novel transgenic mouse line lacking the C-terminal conserved KU70-SAP domain C_LIO_LIKU70-SAP defends against exogenous DSBs, but unessential for development and V(D)J recombination C_LIO_LIKU70-SAP aids in recruiting and retaining NHEJ components, such as LIG4, to DSB sites C_LI

cancer biology↗

bioRxiv2024

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

The famous model organism - Saccharomyces cerevisiae is widely present in a variety of natural and human-associated habitats. Despite extensive studies of this organism, the metabolic mechanisms driving its adaptation to varying niches remain elusive. We here gathered genomic resources from 1,807 S. cerevisiae strains and assembled them into a high-quality pan-genome, facilitating the comprehensive characterization of genetic diversity across isolates. Utilizing the pan-genome, 1,807 strain-specific genome-scale metabolic models (ssGEMs) were generated, which performed well in quantitative predictions of cellular phenotypes, thus helping to examine the metabolic disparities among all S. cerevisiae strains. Integrative analyses of fluxomic and transcriptomics with ssGEMs showcased the ubiquitous transcriptional regulation in certain metabolic sub-pathways (i.e., amino acid synthesis) at a population level. Additionally, the gene/reaction loss analysis through the ssGEMs refined by transcriptomics showed that S. cerevisiae strains from various ecological niches had undergone reductive evolution at both the genomic and metabolic network levels when compared to wild isolates. Finally, the compiled analyses of the pan-genome, transcriptome, and metabolic fluxome revealed remarkable metabolic differences among S. cerevisiae strains originating from distinct oxygen-limited niches, including human gut and cheese environments, and identified convergent metabolic evolution, such as downregulation of oxidative phosphorylation pathways. Together, these results illustrate how yeast adapts to distinct niches modulated by genomic and metabolic reprogramming, and provide computational resources for translating yeast genotype to fitness in future studies.

systems biology↗