Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 505 records · Page 28Linked to original sources

bioRxiv2025

Combinatorial Protein Language Model-Guided Engineering of TEV Protease for Enhanced Stability and Production

Industrial enzyme engineering focuses on improvement of enzyme production yield, stability, catalytic activity, and substrate specificity, but often suffers from low efficiency with time-consuming and labor-intensive design and screening processes of massive libraries. Recent advances in AI and machine learning created protein language models trained by numerous datasets and shed new lights to speed up the enzyme engineering processes with high accuracy structural prediction. Here, we developed a highly efficient enzyme engineering strategy combining three protein language models (xTrimoMPNN-Thermo, ESM-IF, and MPNNsol) and use it to generate TEV protease variants with improved expression, stability, and function. The results indicated that a small number of TEV protease designs (<50 designs) were sufficient to develop variants with desired properties, demonstrating its high efficiency. Our strategy could be broadly applied to accelerate designing and engineering various industrial enzymes.

bioengineering↗

bioRxiv2025

Theta-Band Temporal Interference Stimulation of the Dorsal Anterior Cingulate Cortex Enhances Prediction Error Processing in Individuals With Food Addiction

BackgroundPrediction error (PE) signals encode discrepancies between expected and actual outcomes and are linked to medial frontal theta dynamics in the dorsal anterior cingulate cortex (dACC). However, causal evidence that dACC theta mechanisms contribute to PE gain in humans remains limited. Transcranial temporal interference stimulation (tTIS) enables non-invasive modulation of deep cortical targets and provides a strategy to probe dACC theta circuitry. ObjectiveTo determine whether theta-band tTIS targeting the dACC modulates the neural gain of prediction error encoding during reward processing. MethodsThirty-four participants with elevated food addiction-related symptoms were randomized in a single-blind, sham-controlled pre-post design to active theta-band tTIS or sham stimulation. Under satiety, participants completed a food incentive delay task while EEG was recorded before and after stimulation. Feedback-related negativity (FRN) was analyzed at mean and single-trial levels using mixed-effects models with behavioral and Rescorla-Wagner model-derived prediction errors. Stimulus-preceding negativity (SPN) indexed anticipatory processing. ResultsTheta-band tTIS selectively modulated feedback-stage prediction error encoding. It altered the trial-level FRN-prediction error slope, with pre-to-post changes differing between groups for both behavioral ({beta} = 1.74, p = .049) and model-derived prediction errors ({beta} = 1.77, p = .048). At the mean ERP level, FRN became more negative after active stimulation (t16 = 2.75, p = .014), whereas SPN was unaffected. ConclusionTheta-band tTIS targeting the dACC modulates neural sensitivity to prediction errors during reward feedback, providing causal evidence that medial frontal theta dynamics regulate the neural gain of prediction error encoding.

neuroscience↗

bioRxiv2025

Efficient Generation of Humanized Cloned Cattle via Embryonic Stem Cell-Mediated Dual-Round Site-Specific Editing

Transgenic cloning allows genetic modification in cattle, yet its translational potential is constrained by low cloning efficiency and limited gene-editing capacity, due largely to the restricted proliferative ability of somatic donor cells. Pluripotent stem cells (PSCs), with their unlimited self-renewal ability, represent a promising alternative to overcome these bottlenecks. Here, we first established stable bovine epiblast stem cell lines (bEpiSCs) and achieved site-specific integration of the HCSN2-HLF-GFP cassette into the {beta}-casein locus, with high transfection (72.07%) and correct integration efficiency (80.48%). Following Cre LoxP mediated excision of the selectable marker, we obtained marker free HCSN2-HLF bEpiSCs that retained pluripotency markers, tri lineage differentiation potential, and supported target protein expression in immortalized bovine mammary epithelial cells. When used as nuclear donors, these cells produced blastocysts with quality comparable to in vitro fertilization (IVF) embryos. Notably, cloning with HCSN2-HLF bEpiSCs resulted in the birth of twelve calves, with significantly higher birth and survival rates (30.71% and 16.74%, respectively) than those obtained using fibroblasts. Both PCR-based genotyping of the edited loci and microsatellite kinship analysis confirmed that all cloned calves were genetically derived from the HCSN2-HLF bEpiSCs. Collectively, this study establishes an efficient embryonic stem cell based platform for targeted gene editing and rapid production of multigene edited cloned cattle, offering a scalable strategy with strong potential for industrial translation.

bioengineering↗

bioRxiv2025

The atypical antidepressant and cognitive enhancer tianeptine disinhibits hippocampal CA1 pyramidal neurons by reducing GABAergic neurotransmission

Tianeptine is an atypical antidepressant and cognitive enhancer whose actions are thought to be dependent on the activation of opioid receptors, including {micro}-opioid receptors expressed on hippocampal interneurons. Agonists of these receptors can cause a disinhibition of principal neurons by inhibiting GABA release or interneuron firing. However, direct evidence for a similar action of tianeptine has not previously been reported. We therefore studied the effects of tianeptine on in vivo and in vitro measures of inhibitory synaptic transmission. CA1 field excitatory postsynaptic potentials (fEPSPs) and local field potential (LFP) activity were recorded in area CA1 of anaesthetised rats. To obtain a more direct measure of tianeptines actions on GABA release, we also conducted whole-cell patch-clamp recordings of spontaneous and evoked inhibitory postsynaptic potentials (sIPSCs and eIPSCs) in CA1 pyramidal neurons in vitro. Intrahippocampal infusion of tianeptine (15 mM; 1 {micro}l) caused a marked reduction in paired-pulse inhibition (PPI) of the population spike (20-ms inter-stimulus interval) elicited in the CA1 cell-body layer. Separate recordings in the stratum radiatum revealed an enhancement of beta and gamma-frequency LFP activity, an effect of tianeptine that we have reported previously. Infusion of the GABAA receptor antagonist bicuculline caused a similar reduction in PPI but did not induce beta/gamma oscillations. In mouse hippocampal slices, tianeptine (50 {micro}M) reduced both sIPSC frequency and eIPSC amplitude. These results confirm that tianeptine causes a disinhibition of CA1 pyramidal cells, but suggest that a simple blockade of GABAergic transmission is not alone sufficient to explain tianeptines effects on hippocampal network activity.

neuroscience↗

bioRxiv2025

Neocortical temporal patterning by a two-layered regulatory network

In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. The molecular regulation behind this intricate temporal patterning remains elusive. We undertook in-depth single-cell multi-omics analyses, discovering a two-layered regulatory framework at the core of this process. Central to this are global temporal regulators positioned above a temporal network, consisting of series of transcriptional factor (TF) hub groups under sequential state transitions. This temporal network operates not by restricting TF expressions to discrete temporal windows, but through coordinated transcriptional and chromatin-accessibility dynamics that modulate transient TF regulatory activity. Moreover, global temporal regulators specify the duration of each cascading stage and, consequently, the number of progenies generated at each stage. Loss of global temporal regulators protracts RGP lineage progression, whereas their increased activity accelerates it. These findings suggest a two-layer temporal regulatory system controlling RGP lineage progression and neural progeny output duality in mammalian neocortical development.

neuroscience↗

bioRxiv2025

Reciprocal Homoeologous Replacement of MYB Factors Drives the Evolutionary Trade-off between Yield and Fiber Quality in Cotton

The long-standing phenotypic trade-off between Upland cotton (Gossypium hirsutum, high yield) and Sea Island cotton (G. barbadense, high quality) represents a major bottleneck in cotton breeding and industrialization. Despite rapid advances in genomics, the genomic structural variations driving the divergence of these two domestication strategies, and their subsequent impact on downstream transcriptional networks, remain unclear. This study integrates multi-tissue transcriptomic atlases spanning the full growth period with pan-genomic analyses of both Upland and Sea Island cotton, proposing a "Reciprocal Selective Retention (RSR)" strategy adopted by the two species during evolution. Transcriptomic analysis revealed that while the transcriptional chassis of the two species is highly conserved, a drastic "phase inversion" occurs during fiber development. Sea Island cotton appears to trade off for quality by specifically activating a "delayed elongation" module (at 20 DPA), whereas Upland cotton initiates a "precocious filling" program to pursue yield. Further Weighted Gene Co-expression Network Analysis (WGCNA), combined with genomic Presence/Absence Variation (PAV) analysis, identified a set of key transcription factors exhibiting a "3-vs-3" reciprocal loss pattern. Upland cotton specifically retained CRF10, WIND1, and MYB93, constructing a genetic foundation of "robust root system and strong regeneration" to support high yield. Conversely, Sea Island cotton specifically retained MYB111 and ERF105/017 to maintain long-staple characteristics and environmental buffering. Whole-genome structural variation and microsynteny analyses confirmed that these differences stem from asymmetric physical deletions (e.g., a 5 kb deletion in MYB111) or fragment sequence collapse (e.g., a 15.9 kb sequence divergence in MYB93) on homologous chromosomes. The RSR model proposed in this study not only offers a novel insight into the genetic roots of the negative correlation between yield and quality but also provides clear genomic targets for precision improvement using gene-editing technologies such as CRISPR.

genomics↗

bioRxiv2025

Aging-induced hepatocyte CD44 drives IL6/STAT3 signaling and associates with impaired neighboring T cell function.

Liver cancer incidences increase dramatically beyond 55 years of age, suggesting that age-associated changes contribute critically to tumor initiation. However, the mechanisms linking liver aging and cancer initiation are not well defined. This study investigates the role of CD44, a marker of liver tumor-initiating cells (TIC), in age-associated liver pathophysiology. Aged livers showed accumulation of CD44-expressing hepatocytes exhibiting enrichment of immune modulatory genes and activation of the immunosuppressive IL6/JAK/STAT3 pathway. Indeed, in adoptive transfer assays, antigen-exposed CD8+ T cells mounted a lower IFN-{gamma} response in aged livers than in young livers, indicating an immunosuppressive aged milieu. Concordantly, spatial analyses showed that the proximal neighbourhoods of Cd44-expressing hepatocytes are enriched in T cells exhibiting reduced cytokine and chemokine gene expression. Finally, hepatocyte-specific knock out of Cd44 mitigated the IL6/JAK/STAT3 gene signature in aged livers. Overall, these findings suggest that CD44 expression in aged hepatocytes promotes activation of the immunosuppressive IL6/JAK/STAT3 pathway and this is associated with impaired T cell effector function.

cell biology↗

bioRxiv2025

HypoxamicroRNA-210 protects against hepatic steatosis by inhibiting CIDEC expression

Background and AimsMetabolic dysfunction-associated steatotic liver disease (MASLD) is a major global health burden. Although hypoxia is known to contribute to MASLD pathogenesis, the role of hypoxia signaling remains poorly defined. We investigated whether HypoxamicroRNA-210 (miR-210), a key hypoxia-inducible microRNA, regulates hepatic lipid metabolism and MASLD development. MethodsSerum miR-210 levels were quantified in MASLD patients and matched controls. Human hepatic spheroids and HepG2 cells were exposed to fatty acids to assess miR-210 induction and lipid accumulation. miR-210 knockout mice were fed a Western diet to evaluate hepatic steatosis and transcriptomic changes using RNA sequencing. RNA pull-down and 3UTR-driven luciferase reporter assays were employed to identify miR-210 targets. Functional effects of miR-210 mimic were examined in knockout mice, db/db mice, and in vitro human hepatic spheroid models. ResultsSerum miR-210 levels were significantly reduced in MASLD patients compared with matched controls. Consistently, human hepatic spheroids did not appropriately increase miR-210 expression in response to fatty acid-induced intracellular hypoxia. This blunted miR-210 response contributed to hepatic lipid accumulation, as loss of miR-210 in a mouse model of MASLD led to increased hepatic lipid deposition and activation of lipid metabolic pathways. We identified CIDEC as a direct miR-210 target mediating its inhibitory effects on hepatic lipid accumulation, and restoring miR-210 expression suppressed CIDEC and reduced hepatic lipid content in knockout mice on a Western diet. Moreover, miR-210 attenuated lipid accumulation in both in vitro human hepatic spheroids and in vivo db/db mice models of MASLD. ConclusionsmiR-210 protects against hepatic steatosis by inhibiting CIDEC expression, suggesting miR-210-CIDEC axis as a promising therapeutic target for reducing hepatic lipid accumulation and preventing MASLD progression. Impact and ImplicationsThis study addresses a critical gap in understanding how hypoxia signaling shapes MASLD and uncovers a novel pathogenic mechanism of hepatic steatosis arising from fatty acids-induced dysregulation of miR-210. Impaired hypoxia responses, via blunted miR-210 induction, contribute to hepatic lipid accumulation through upregulation of CIDEC, a newly identified target of miR-210. These findings establish miR-210 as a novel regulator of hepatic lipid homeostasis and underscore its therapeutic potential. Interventions aimed at restoring miR-210 function in the liver may offer a promising strategy to ameliorate hepatic steatosis and prevent MASLD progression.

molecular biology↗

bioRxiv2025

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms

RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in iPSC-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that ASD risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between splicing and polyadenylation. Finally, our atlas enables variant reinterpretation in ASD, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.

bioinformatics↗

bioRxiv2025

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

bioRxiv2025

TUPAD: A Tn5-Mediated, Pre-amplification/Adapter-Dimer-Free Platform for Ultra-Uniform, One-Step PGT Profiling with High Stability and Broad Compatibility

High-throughput sequencing stands as a cornerstone of clinical molecular diagnostics, particularly in preimplantation genetic testing (PGT)--a key application where the selection of chromosomally normal embryos is critical to enhancing in vitro fertilization (IVF) success rates. A fundamental challenge inherent to PGT, however, lies in the ultra-low gDNA input (typically <100 pg) from embryo biopsies. To mitigate this limitation, traditional workflows rely on whole genome amplification (WGA) technologies, such as MDA, PicoPlex, and MALBAC. Yet these WGA-based protocols inherently entail pre-amplification of gDNA prior to standard library construction---a step that introduces significant coverage bias and compromised uniformity. These are intrinsic flaws irreparable by downstream library preparation or bioinformatics analysis, ultimately leading to clinical uncertainty in the interpretation of copy number variations (CNVs). In this study, we developed TUPAD (Tn5-Mediated, Uniform Pre-amplification-free and Adapter-Dimer-Free Library preparation), a transformative technology that bypasses the limitations of traditional WGA. By engineering a novel adapter-dimer-free transposon system, TUPAD enables high-efficiency library construction from as little as 1 picogram (pg) of gDNA. This breakthrough allows for a pre-amplification-free workflow, effectively eliminating the primary source of amplification bias. Compared to existing WGA standards, these advantages are fully retained in embryo biopsy and positive sample testing, TUPAD consistently generates highly uniform library data, significantly enhancing the detection limit and accuracy of CNVs and other genomic variants. Beyond these performance advantages, TUPAD also cuts wet-lab processing time by 50%. Practical validation confirms TUPAD results are stable, reliable, with proven practical utility in PGT testing.

molecular biology↗

bioRxiv2025

IGHV3-53 antibody abundance drives divergent SARS-CoV-2 immune imprinting

The mechanisms driving divergent SARS-CoV-2 immune imprinting in populations with distinct SARS-CoV-2 exposure histories remain unclear. However, conventional wild-type mouse models fail to recapitulate severe imprinting, even after potent ancestral-strain mRNA immunization, hindering imprinting-related mechanistic investigation and vaccine evaluation. Here, we surprisingly found that V(D)J-humanized mice could faithfully recapitulate human severe imprinting phenotypes. Comprehensive antibody repertoire analysis and deep mutational scanning-based epitope mapping of 583 monoclonal antibodies from these models revealed that the pre-existing IGHV3-53/66 antibody abundance determine imprinting severity through antibody-mediated masking of Omicron-specific epitopes. Both passive IGHV3-53/66 antibody transfer and IGHV3-53 knock-in were sufficient to induce severe imprinting in wild-type mice. Together, these findings demonstrate that the V(D)J germline repertoire--even a single germline-encoded antibody response--can profoundly shape humoral imprinting severity. Accordingly, we established an IGHV3-53 knock-in mouse model that accurately recapitulates the human antibody landscape, providing a valuable tool for guiding future COVID-19 vaccine updates.

immunology↗

bioRxiv2025

Theta and beta account for the two-impacted components of social influence on risk decision-making

Social influence in risky decision-making means changing risky behavior after observing others choices. Although attributes prioritization can alter subjective value of a particular option while choice bias can affect the tendency toward it, previous studies have not simultaneously examined these two components. Here, participants made risky or safety choices, observed a model whose risk preference either matched (control) or opposed (inconsistent) their own, then repeated the task. Behavioral and EEG data were collected, and drift-diffusion model (DDM) was used to decompose different components. After observing an opposing preference, risk-seeking participants chose safety options more often, and risk-aversion participants chose risky options more often, indicating social influence. Model comparison favored an attribute-wise DDM. Social influence altered two distinct components in risky decisions: the weight of amount in value computation (more negative after observing the opposing model) and the starting point (shifting toward the options chosen more often). Multivariate pattern analysis linked these components to distinct neural signatures: theta activity ({approx}500 ms after option onset) tracked the amount weighting, whereas pre-option beta activity tracked the starting point. Together, the results show that social influence reshapes risky decisions by reweighting amount and shifting choice bias, each supported by dissociable electrophysiological dynamics.

animal behavior and cognition↗

bioRxiv2025

Selective labeling supports 5-thiooxazole post-translational modification in bufferins

Multinuclear nonheme iron-dependent oxidases (MNIOs) constitute one of the largest families of enzymes involved in natural product biosynthesis. Distinct MNIO subfamilies utilize molecular oxygen to catalyze a wide variety of complex peptide rearrangements, including {beta}-carbon excision and heterocyclization. Highly homologous MNIOs have been proposed to install either oxazolone-thioamides or 5-thiooxazoles as cysteine post-translational modifications in the closely related bufferin and EGKCG families of peptide chalkophores. These alternative structures prompted discussion of the subtle mechanistic features of MNIO enzymes that might determine reaction outcome. Here, we combine uniform 15N labeling with cysteine-specific carbonyl 13C labeling to unambiguously assign 5-thiooxazoles as the cysteine modifications in bufferins. Together with the recent identification of 5-thiooxazoles in three members of the sister EGKCG family and the re-assignment of the cysteine modification in oxazolin, these findings confirm that closely related MNIOs catalyze identical post-translational modifications.

biochemistry↗

bioRxiv2025

Distributed fMRI patterns coupled to low-frequency cardiorespiratory dynamics provide markers of aging

How aging affects brain-body connections can be investigated through changes in the coupling between functional magnetic resonance imaging (fMRI) signals and bodily autonomic processes across the adult lifespan. Recent studies using univariate approaches have identified age-related changes in the association between fMRI signals from multiple individual brain regions and low-frequency respiratory and cardiac activity. Here, we investigate if whole-brain spatial fMRI patterns associated with low-frequency physiological processes (heart rate and respiratory volume fluctuations) present generalizable changes with age. Data from human participants of both sexes are included in the analysis. We find that chronological age can be predicted statistically beyond chance from patterns of low-frequency fMRI-physiology coupling, even after accounting for individual differences in physiological signal characteristics and brain anatomy. Notably, brain areas implicated in central autonomic regulation, including nodes within salience and ventral attention networks (e.g., insula and middle cingulate cortex), are amongst the strongest contributors to age prediction. Further, we observe that after removing physiological effects from fMRI data, the residual blood oxygen level-dependent (BOLD) signal variability is still a reliable indicator of age. Together, these findings underscore the close integration between brain and body physiology, and highlight this interaction as a potential biomarker of the aging process. Significance StatementThe association between brain activity and respiratory or cardiac activity is often dismissed as "noise" in functional magnetic resonance imaging (fMRI) studies. However, emerging evidence suggests that coupling between fMRI and peripheral physiological signals can provide valuable insight into the brain-body connection. In this study, we show that whole brain patterns of coupling between fMRI signals and low-frequency respiratory and cardiac processes can reliably predict age across the adult lifespan. Brain regions involved in autonomic regulation, such as insula and cingulate cortex, were among the most informative predictors of age. These findings suggest that fMRI-physiology coupling may capture aging-related changes in brain vascular health and autonomic function and may have broader relevance for tracking disease-related disruptions in brain-body interaction.

neuroscience↗

bioRxiv2025

Post-weaning social isolation impairs the orbitofrontal cortical circuit subserving contagious pain and prosocial behaviors

Empathic behaviors are sensitive to environmental factors like post-weaning social isolation (SI), yet the mechanisms by which SI affects empathy remain unclear. Here, we show that mice subjected to SI exhibit marked impairments in contagious pain and prosocial behaviors, including allo-grooming and allo-licking toward cagemates experiencing inflammatory pain. Mechanistically, we identify the glutamatergic projection from the ventromedial thalamic nucleus (VM) to the orbitofrontal cortex (OFC) as critical for these empathy-like responses. SI induces hypoexcitability of OFC glutamatergic neurons and attenuates excitatory synaptic transmission within the VM[->]OFC pathway. Remarkably, chemogenetic activation of OFC neurons or the VM[->]OFC projection restores empathic behaviors in SI mice. Furthermore, we uncover a molecular basis for SI-induced OFC hypoexcitability: the downregulation of Grik3, encoding a kainate-type glutamate receptor subunit. These findings reveal a previously uncharacterized thalamocortical mechanism through which early-life social deprivation disrupts empathic behaviors, offering insights into the underpinnings of social-affective dysfunction.

neuroscience↗

bioRxiv2025

Torsins Organize CLCC1 Assembly to Safeguard ER Bilayer and Lipid Homeostasis

The TMEM41B scramblase and its regulatory partner CLCC1 initiate lipid flux by equilibrating newly-synthesized phospholipids across the endoplasmic reticulum (ER) bilayer, a fundamental process required for diverse events ranging from membrane biogenesis to bulk lipid supply. Loss of CLCC1/TMEM41B causes ER bilayer imbalance, inducing giant ER-enclosed lipid droplets (geLDs) and driving rapid progression into severe MASH. Here we identify CLCC1 as the long-missing client of the lumenal Torsin ATPases, which selectively engage oligomerized CLCC1 at sites of ER bilayer imbalance. Hepatic TorsinA inactivation triggers geLD formation amid disrupted lipoprotein biogenesis and severe MASH, closely phenocopying CLCC1/TMEM41B deficiency. Mechanistically, Torsins act as foldases that drive CLCC1 oligomerization for its recruitment to imbalanced bilayers. Remarkably, ectopic CLCC1 expression reverses cellular and systemic lipid disorders arising from hepatic TorsinA deficiency. Hence, Torsin ATPases emerge as fundamental regulators that organizes CLCC1 and the downstream TMEM41B scramblase to govern lipid partitioning and membrane homeostasis.

cell biology↗

bioRxiv2025

Attention to Psuedo-Tone Melodies Enhances Cortical but Not Brainstem Responses in Humans

Auditory selective attention, the ability to focus on specific sounds while ignoring competitors, enables communication in complex soundscapes. Though attention clearly modulates cortical responses to sound, whether and where this modulation occurs in subcortical structures remains disputed. Here, we use electroencephalography to record cortical and subcortical (auditory brainstem responses, ABRs) activity during a selective attention task. Human participants attend to a 3-note melody in one pitch range presented to one ear while ignoring a competing, interleaved melody in a different pitch range played to the other ear (Laffere et al., 2020, 2021). The melodies consist of pitch-evoking pseudo-tones formed by convolving a periodic impulse train with a brief tone pip. These stimuli allow us to measure both ABRs (elicited by each individual tone pip within a pseudo-note) and cortical responses (elicited by the onsets of pseudo-notes) simultaneously. We observed robust ABRs, but no evidence of modulation by attention. Conversely, cortical responses, measured by event related potentials (ERPs), demonstrated attentional modulation of the P1-N1 peak. We conclude that attentional modulation within the brainstem is not measurable in the well-defined peaks of the ABR, which themselves reflect processing up to the input stage to the inferior colliculus.

neuroscience↗