Biology subjects

Lee, Y.

Publications and source records attributed to Lee, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Comparative multi-omics profiling of Gossypium hirsutum and Gossypium barbadense fibers at high temporal resolution reveals key differences in polysaccharide composition and associated glycosyltransferases

Among the two allopolyploid cultivated species of cotton, Gossypium barbadense is known for its superior quality fiber compared to G. hirsutum. Length and strength are key determinants of the fiber quality. Although the mature fibers are dried cell walls consisting mainly cellulose, the dynamic remodeling of pectin, xyloglucan, and xylan polysaccharides during fiber growth significantly impact the final fiber quality. Comprehensive knowledge about polysaccharides and their biosynthesis during fiber development of the cultivated species is important for improving fiber quality. In this study, comparative large-scale glycome, transcriptome and proteome profiling were conducted daily on fibers of both cotton species covering critical stages of fiber development spanning primary cell wall synthesis and the transition to secondary wall synthesis. Interspecific comparisons revealed that a delayed accumulation of cellulose content, as well as the occurrence of lower levels and differential compositions of non-fucosylated/fucosylated xyloglucans, homogalacturonans, and highly branched Rhamnogalacturonan-I polysaccharides might be contributing to longer fiber phenotypes of G. barbadense relative to G. hirsutum. Our study also suggests, differential temporal compositions of heteroxylans might contribute to variation in cellulose microfibril arrangement and strength of fiber exists between the two species of cotton. Comparative transcriptomic analysis identified differentially expressed polysaccharide-synthesizing glycosyltransferases that might underlie fiber quality differences between the two species. Transcripts encoding many cell wall localized expansins were more abundant in G. barbadense than in G. hirsutum. Overall, these findings extend our knowledge regarding the molecular factors that contribute to fiber quality and provide insights for targeted cotton fiber improvement. SIGNIFICANCE STATEMENTComparative multi-omics profiling of two major commercial cotton species, Gossypium hirsutum and Gossypium barbadense revealed substantial differences in polysaccharide structures and expressed polysaccharide-synthesizing glycosyltransferases, that potentially contribute to differences in fiber length and strength. The molecular details elucidated in the present study contribute to the goal of improving fiber quality and its commercial value.

plant biology↗

bioRxiv2025

Characterization of Human Anterior Neural Organoids as a Model for Investigating Cohen Syndrome

Neural organoids display three-dimensional (3D) structures that resemble in vivo neural architectures. Previously, we developed a novel two-dimensional (2D) neural induction-based protocol for culturing spinal cord organoids, enabling size control and recapitulating neural tube morphogenesis. In this study, we evaluated the application of this concept to induce the anterior regions of the brain and generate human anterior neural organoids (hANOs). By inducing neuroepithelial (NE) cells in 2D and re-aggregating them led to tube-forming morphogenesis similar to that posterior spinal cord induction. The transcriptome profiles of these hANOs resembled the frontal cortex of 20 weeks post-conception (PCW) human embryos. Using this hANOs protocol, we investigated microcephaly phenotypes associated with Cohen syndrome (CS), caused by biallelic loss-of-function variants in VPS13B gene. Deleting VPS13B in human pluripotent stem cells resulted in Golgi dispersion and growth retardation onset in mutant hANOs, akin to CS patients with postnatal microcephaly. This delay is partly linked to reduced neuronal growth. Additionally, mature CS organoids showed enhanced hyper-excitability associated with an excitatory/inhibitory imbalance. In conclusion, this protocol is suitable for studying microcephaly phenotypes from human genetic mutations due to its simplicity and scalability.

neuroscience↗

bioRxiv2025

Neutrophils respond with pathogen-specific defenses during bacterial pneumonia

Neutrophils have historically been envisioned as a homogenous population of short-lived innate immune cells that migrate to sites of infection, kill pathogens, and die. Recent work, including studies in pneumonia models, has shown that neutrophil transcriptomes reflect the environment from which they were isolated. We used high-parameter spectral flow cytometry to compare and contrast a wide array of surface proteins on neutrophils from different tissues, infections, host age, pathogen virulence, and across multiple time-points of pneumonia. Circulating and airspace neutrophils consistently differed, and surface protein phenotypes unique to each infection setting were identified, revealing tissue-specific and microbe-specific neutrophil plasticity. Phenotypic differences in circulating neutrophils from mice infected with different pathogens (E. coli, S. pneumoniae, S. aureus, and P. aeruginosa) identified, even in the absence of bacteremia. Neutrophil activation state was diminished with less virulent pathogens and host age. In the airspace, VISTA, CD200R, and PD-L1 were selectively high on BAL neutrophils (BALN) during S. pneumoniae infection, and we identified pro-degranulation-like (CD88High VISTAHigh PD-L1+ CD101-) neutrophils in S. pneumoniae and pro-phagocytosis-like (CD101+ CD18Low PD-L1-) neutrophils in E. coli infections. Stimulation of VISTA with its ligand VISG-3 enhanced the neutrophil respiratory burst, degranulation, and killing of S. pneumoniae but not E. coli. We conclude that neutrophil cell surface protein expression depends on anatomic location and infection type, resulting in pathogen-specific neutrophil-mediated immune defense in discreet areas of the pneumonic lung. Graphical AbstractIn brief, Pihl et al. have found that neutrophil cell surface phenotype varies drastically based on tissue, time post-infection, and infection. BALN from early infections have higher activation and maturation statuses, while blood neutrophils are more migration primed, and late infections have more immune-suppressive and altered pathogen killing statuses. Neutrophil phenotype is skewed towards pro-phagocytosis associated marker expression on BALN from E. coli-infected mice while S. pneumoniae results in a pro-degranulation phenotype. In vitro BMN stimulation of VISTA with VSIG-3 results in degranulation, respiratory burst, and pathogen specific killing of S. pneumoniae but not E. coli. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/649365v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@4e4829org.highwire.dtl.DTLVardef@1638108org.highwire.dtl.DTLVardef@1ac413dorg.highwire.dtl.DTLVardef@1ef36b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

SpatialAgent: An Autonomous AI Agent for Spatial Biology

Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we present SpatialAgent, an autonomous AI agent for spatial biology research. SpatialAgent couples large language models with a Plan-Act-Conclude architecture, dynamic tool and skill retrieval, multimodal interpretation, and verification modules that audit generated claims. It supports the full discovery loop, from gene-panel design and multimodal annotation to trajectory inference, cell-cell communication analysis, imputation, and hypothesis generation. Across human and mouse brain, heart, tonsil, colon, and prostate datasets, SpatialAgent outperformed established computational baselines and matched or surpassed expert scientists in key tasks. In open-ended case studies, it recovered known tissue organization and generated spatially grounded hypotheses. In a prospective mouse prostate cancer Xenium study, it designed a compact 100-gene add-on panel that profiled 4.2 million cells across 21 samples, improved cell-type and malignant-state prediction, and captured spatially structured tumor and microenvironment programs. SpatialAgent establishes a framework for autonomous and collaborative discovery in spatial biology.

bioinformatics↗

bioRxiv2025

Automated, high-throughput in-situ hybridization of Lytechinus pictus embryos

Despite the reach of in situ hybridization (ISH) in developmental biology, it has rarely been used at scale. The major limitation has been the throughput of the assay, which typically relies upon labor intensive manual steps. The goal of this study was to develop a fully automated hybridization chain reaction (HCR) pipeline capable of large-scale gene expression pattern profiling, with dramatically reduced cost and effort, in the sea urchin Lytechinus pictus. Our resulting pipeline, which we term high throughput (HT)-HCR, can process 192 gene probe sets on whole-mount embryos within 32 hours. The unique qualities of the sea urchin embryo enabled us to automate the entire HCR assay in a 96-well plate format, and utilize highly miniaturized reaction volumes, a general purpose robotic liquid handler, and automated confocal microscopy. From this approach we produced high quality localization data for 101 target genes across three developmental stages of L. pictus. The results reveal the localization of previously undescribed physiological genes, as well as canonical developmental transcription factors. HT-HCR represents a log order increase in the rate at which spatial transcriptomic data can be resolved in the sea urchin. This study paves the way for localization of understudied genes and for sophisticated perturbation analysis. Summary StatementWe developed an automated high-throughput HCR pipeline to rapidly map expression of 101 genes in sea urchin embryos, enabling large-scale discovery of novel developmental gene expression patterns.

developmental biology↗

bioRxiv2025

Loss of the Integrator and Nuclear Exosome Targeting complexes disrupts oogenesis and causes the emergenceof atypical transcripts in Drosophila

Nuclear RNA homeostasis depends on the balance of transcription, RNA processing, degradation, and transport between the nucleus and cytoplasm. RNA degradation directed by the Integrator, nuclear exosome targeting (NEXT), and nuclear exosome complexes controls the accumulation of aberrant nuclear RNA. Here, we report that Drosophila oogenesis requires the Integrator, NEXT, and nuclear exosome complexes. Depletion of Integrator, NEXT, or nuclear exosome components in Drosophila female germ cells causes infertility and accumulation of 3' extended snRNAs, promoter upstream transcripts (PROMPTs), and cryptic transcripts. Our data highlight the essential role of nuclear RNA degradation and processing in Drosophila oogenesis and provide a catalog of RNAs whose nuclear levels are regulated by these three complexes. We propose that Integrator, NEXT, and the nuclear exosome support oogenesis by ensuring that inappropriate transcription does not overwhelm the limited supply of proteins that bind, process, and traffic RNA.

molecular biology↗

bioRxiv2025

An innovative approach in identifying a network of priority wetland sites in the East Asian-Australasian Flyway for a new sustainable management investment programme

The East Asian-Australasian Flyway (EAAF) is widely recognised to be the most threatened of the eight flyways in the world, with wetlands rapidly lost due to land cover change, unsustainable use, and the wider impacts of climate change. The recently established Regional Flyway Initiative aims to bring a network of priority wetlands in the EAAF under improved protection, management, and restoration in 10 Asian countries, while mobilising resources for sustainable agriculture, aquaculture, ecotourism, and other livelihoods for local communities. A major step in the development of this initiative is the identification of priority wetland sites through the application of international criteria, based on modern waterbird count data collated from wetland sites across Asia. Through existing analyses and stakeholder consultations, we short-listed 400 internationally important wetlands as candidate sites for further assessment. Count data of EAAF waterbird species was then assessed against international criteria aligned with the Convention on Wetlands (Ramsar Convention), the EAAF Partnerships Flyway Site Network and Important Bird Areas and Biodiversity for each site to iteratively identify a subset of priority sites, drawing on newly available species population thresholds. Each site was scored and ranked using a metric (Prioritisation Criterion1) calculated from the proportions of every occurring EAAF species against published population thresholds. We identified a total of 147 wetland sites of high conservation priority across the 10 countries, thereby representing the full suite of wetland landscapes and habitats in Asia, both freshwater and coastal, all critical sites for the conservation of migratory waterbirds in the flyway. At least 34 threatened species, including significant proportions of their global populations are represented in this network of 147 sites. To ensure that conservation opportunities are maximised for species and ecosystem services, there is a need to ensure that selected sites and landscapes are reconciled with the conservation and development priorities of each country, and to evaluate priority sites for their ecosystem services.

ecology↗

bioRxiv2025

Cross-family interactions of vascular endothelial growth factors and platelet-derived growth factors on the endothelial cell surface: A computational model

Angiogenesis, the formation of new vessels from existing vessels, is mediated by vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF). Despite discoveries supporting the cross-family interactions between VEGF and PDGF families, sharing the binding partners between them makes it challenging to identify growth factors that predominantly affect angiogenesis. Systems biology offers promises to untangle this complexity. Thus, in this study, we developed a mass-action kinetics-based computational model for cross-family interactions between VEGFs (VEGF-A, VEGF-B, and PlGF) and PDGFs (PDGF-AA, PDGF-AB, and PDGF-BB) with their receptors (VEGFR1, VEGFR2, NRP1, PDGFR, and PDGFR{beta}). The model, parametrized with our literature mining and surface resonance plasmon assays, was validated by comparing the concentration of VEGFR1 complexes with a previously constructed angiogenesis model. The model predictions include five outcomes: 1) the percentage of free or bound ligands and 2) receptors, 3) the concentration of free ligands, 4) the percentage of ligands occupying each receptor, and 5) the concentration of ligands that is bound to each receptor. We found that at equimolar ligand concentrations (1 nM), PlGF and VEGF-A were the main binding partners of VEGFR1 and VEGFR2, respectively. Varying the density of receptors resulted in the following five outcomes: 1) Increasing VEGFR1 density depletes the free PlGF concentration, 2) increasing VEGFR2 density decreases PDGF:PDGFR complexes, 3) increased NRP1 density generates a biphasic concentration of the free PlGF, 4) increased PDGFR density increases PDGFs:PDGFR binding, and 5) increasing PDGFR{beta} density increases VEGF-A:PDGFR{beta}. Our model offers a reproducible, fundamental framework for exploring cross-family interactions that can be extended to the tissue level or intracellular molecular level. Also, our model may help develop therapeutic strategies in pathological angiogenesis by identifying the dominant complex in the cell signaling. Author summaryNew blood vessel formation from existing ones is essential for growth, healing, and reproduction. However, when this process is disrupted--either too much or too little--it can contribute to diseases such as cancer and peripheral arterial disease. Two key families of proteins, vascular endothelial growth factors (VEGFs) and platelet-derived growth factors (PDGFs), regulate this process. Traditionally, scientists believed that VEGFs only bind to VEGF receptors and PDGFs to PDGF receptors. However, recent findings show that these proteins can interact with each others receptors, making it more challenging to understand and control blood vessel formation. To clarify these complex interactions, we combined computer modeling with biological data to map out which proteins bind to which receptors and to what extent. Our findings show that when VEGFs and PDGFs are present in equal amounts, VEGFs are the primary binding partners for VEGF receptors. We also explored how changes in receptor levels affect these interactions in disease-like conditions. This work provides a foundational computational model for studying cross-family interactions, which can be expanded to investigate tissue-level effects and processes inside cells. Ultimately, our model may help develop better treatments for diseases linked to abnormal blood vessel growth by identifying key protein-receptor interactions.

systems biology↗

bioRxiv2025

The astrocyte Fabp7 gene regulates diurnal seizure threshold and activity-dependent gene expression in mice

Epileptic seizures are often influenced by time-of-day and changes in vigilance state, yet the molecular and cellular mechanisms underpinning these associations remain poorly understood. Astrocytes, a pivotal type of glial cell, play a critical role in modulating neuronal excitability and circadian rhythms, and they express Fatty Acid Binding Protein 7 (Fabp7), a molecule vital for sleep regulation, lipid signaling, and gene transcription. This study investigates the role of Fabp7 in determining time-of-day dependent seizure susceptibility. We assessed electroshock seizure thresholds in male C57/BL6N wild-type (WT) and Fabp7 knockout (KO) mice. Results demonstrated that, compared to WT mice, Fabp7 KO mice displayed significantly elevated general and maximal electroshock seizure thresholds (GEST and MEST) during the dark phase, but not during the light phase. To explore the impact of Fabp7 on activity-dependent gene expression during seizures, we conducted RNA sequencing (RNA-seq) on cortical and hippocampal tissues from WT and Fabp7 KO mice following MEST and SHAM procedures during the dark period. While immediate early genes (IEGs) showed considerable differential expression between WT-MEST and WT-SHAM, this expression was absent in Fabp7 KO-MEST compared to Fabp7 KO-SHAM. Gene ontology analyses revealed significant overlaps between the WT-MEST:WT-SHAM and Fabp7 KO-SHAM:WT-SHAM comparisons, indicating that the basal mRNA expression profiles in Fabp7 KO brains resemble those of WT brains in a post-ictal state. Collectively, these findings suggest that Fabp7 is a key regulator of time-of-day dependent neural excitability and that astrocyte-mediated signaling pathways involving Fabp7 interact with neuronal activity to influence gene expression in response to seizures. Significance StatementChanges in sleep/wake state and/or circadian time-of-day are thought to influence neural excitability, which may confer seizure susceptibility. Here we describe a role for astrocytic Fabp7 in regulating nocturnal seizure threshold and gene expression associated with differences in seizure susceptibility, introducing an astrocyte factor that may represent a novel antiepileptic target for drug development.

neuroscience↗

bioRxiv2025

Cholesterol taste avoidance in Drosophila melanogaster

The question as to whether animals taste cholesterol taste is not resolved. This study investigates whether the fruit fly, Drosophila melanogaster, is capable of detecting cholesterol through their gustatory system. We found that flies are indifferent to low levels of cholesterol and avoid higher levels. The avoidance is mediated by gustatory receptor neurons (GRNs), demonstrating that flies can taste cholesterol. The cholesterol responsive GRNs comprise a subset that also respond to bitter substances. Cholesterol detection depends on five ionotropic receptor (IR) family members, and disrupting any of these genes impairs the flies ability to avoid cholesterol. Ectopic expressions of these IRs in GRNs reveals two classes of cholesterol receptors, each with three shared IRs and one unique subunit. Additionally, expressing cholesterol receptors in sugar-responsive GRNs confers attraction to cholesterol. This study reveals that flies can taste cholesterol, and that the detection depends on IRs in GRNs.

neuroscience↗

bioRxiv2025

Proteomics-based models of gene expression and cellular control of cotton fiber development

The shapes and material properties of cotton seed coat trichoblasts are the basis of a multibillion-dollar natural fiber industry. As such, these highly specialized cells are low-hanging fruit for intentional trait engineering. However, broad successes will require more mechanistic knowledge about their systems-level cellular controls. This time-series study integrates daily measurements of purified fiber transcriptomes and proteomes with multiscale fiber phenotyping datasets that span the same developmental interval. Abundance profiles of the subcellular proteomes are the foundation of the analyses. This resource article provides direct information concerning which homoeologs operate and informative depictions of how compartmentalized cellular systems change during developmental transitions. Prediction accuracy was partially validated by analysis of the protein expression group 11, which contained multiple known secondary cell wall cellulose synthases and dozens of unknown proteins and an averaged profile that was strongly correlated with a sharp state transition in cellulose microfibril alignment and increased cellulose content. The dataset as a whole can serve as a hypothesis-generating machine to guide future experiments that relate to cell shape and growth rate control, reversible tissue formation, and cell wall remodeling. Integration of mRNA and protein abundance revealed widespread evidence for post-transcriptional control. In addition, there were hundreds of transcriptionally controlled genes with differing timepoints of transition. This latter gene set can be used to more reliably analyze transcriptional control networks and to generate collections of gene expression drivers for cotton fiber research. The protein and transcript data are organized into user-friendly tables and a web interface that can be searched using any plant ortholog of interest based on developmental time, abundance, annotations, or phenotypic association.

plant biology↗

bioRxiv2025

Genome diversity and phylogeny of the section Alatae of genus Lemna (Lemnaceae), comprising the presumed species Lemna aequinoctialis, Le. perpusilla and Le. aoukikusa

O_LIThe Section Alatae of genus Lemna of the monocotyledonous aquatic duckweed family (Lemnaceae) consists of rather diverse accessions with unknown phylogeny and unclear taxonomic assignment. In contrast to other duckweeds, some Alatae accessions, in addition to mainly vegetative propagation, produce readily flowers and viable seeds. We analyzed the genomic diversity and phylogenetic relationship of 52 Alatae accessions. C_LIO_LIFor this purpose, we applied multiple molecular and cytogenetic approaches, including plastid and nuclear sequence polymorphisms, chromosome counting, genome size determination and genomic in situ hybridization in combination with geographic distribution. C_LIO_LIWe uncovered ploidy variation, recurrent hybridization, and backcrosses between diploid species and their hybrids. The latter successfully spread over three continents. C_LIO_LIThe results elucidate the evolution of Alatae accessions (summarized in Fig. 7) and explain the difficult taxonomic assignment of distinct accessions. Our study might be an example for analogous studies to resolve the hitherto unclear relationships among accessions of the duckweed genera Wolffiella and Wolffia. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/632899v1_fig7.gif" ALT="Figure 7"> View larger version (23K): org.highwire.dtl.DTLVardef@d05f08org.highwire.dtl.DTLVardef@f33c5org.highwire.dtl.DTLVardef@ff7adorg.highwire.dtl.DTLVardef@4da6e4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 7C_FLOATNO Hypothetical scenario of evolution within Lemna Section Alatae. In bold are accessions from America. The classically defined diploid species Le. aequinoctialis and Le. perpusilla sensu stricto were confirmed by the applied molecular methods. The previously named Le. aoukikusa accessions were uncovered as tetraploid interspecific hybrids between Le. aequinoctialis and Le. perpusilla. In addition, further tri- and tetraploid hybrids as well as tri- and tetraploid "Backcross hybrids" were detected from the USA and China, respectively. C_FIG

evolutionary biology↗

bioRxiv2025

Real-time fMRI neurofeedback modulates auditory cortex activity and connectivity in schizophrenia patients with auditory hallucinations: A controlled study

Background and HypothesisWe have reported previously a reduction in superior temporal gyrus (STG) activation and in auditory verbal hallucinations (AHs) after real-time fMRI neurofeedback (NFB) in schizophrenia patients with AHs. Study DesignWith this randomized, participant-blinded, sham-controlled trial, we expanded our previous results. Specifically, we examined neurofeedback effects from the STG, an area associated with auditory hallucinations. The effects were compared to Sham-NFB from the motor cortex, a region unrelated to hallucinations. Twenty-three adults with schizophrenia or schizoaffective disorder and frequent medication-resistant hallucinations performed mindfulness meditation to ignore pre-recorded strangers voices while receiving neurofeedback either from the STG (n=10, Real-NFB) or motor cortex (n=13 Sham-NFB). Individuals randomized to Sham-NFB received Real-NFB in a subsequent visit, providing a within-subject Real-after-Sham-NFB comparison. Study ResultsBoth groups showed reduced AHs after NFB, with no group differences. Compared to the Sham-NFB group, the Real-NFB group showed more reduced activation in secondary auditory cortex (AC) and more reduced connectivity between AC and cognitive control regions including dorsolateral prefrontal cortex (DLPFC) and anterior cingulate. The connectivity reduction was also observed in the Real-after-Sham-NFB condition. Secondary AC-DLPFC connectivity reduction correlated with hallucination reduction in the Real-NFB group. Replicating prior results, both groups showed reduced primary auditory cortex activation, suggesting mindfulness meditation may regulate bottom-up processes involved in hallucinations. ConclusionsOur findings emphasize delivering NFB from brain regions involved in medication-resistant AHs. They provide insights into auditory cortex and cognitive control network interactions, highlighting complex processing dynamics and top-down modulation of sensory information.

neuroscience↗

bioRxiv2025

Distinct modes of dopamine modulation on striatopallidal synaptic transmission

Dopamine (DA) affects voluntary movement by modulating basal ganglia function. In the classical model, DA depletion leads to overactivity of the indirect pathway and excessively inhibits the thalamus, resulting in hypokinesia. The contribution of DA on striatopallidal synapses, an initial hub in the indirect pathway connecting the striatum to the external globus pallidus (GPe), remains poorly understood because of the sparse DA innervation. Here, we combine optogenetic projection targeting, whole cell patch clamp recordings in acute brain slices from mice, and computational modeling to overcome this limitation. We show that DA activates D2R receptors (D2Rs) and D4 receptors (D4Rs) differentially in distinct GPe subregions. In a pinwheel-like fashion, dorsolateral and ventromedial GPe expresses high levels of D2Rs, which exert presynaptic inhibition, while in dorsomedial and ventrolateral GPe D4Rs cause postsynaptic inhibition. DA depletion by 6-OHDA (6-hydroxydopamine) reverses the region- specific effect of DA, shifting it in the opposite direction and contributing to hypokinesia. These findings reveal the mechanism by which the different modality information conveyed spatially through the indirect pathway is differentially modulated by DA at striatopallidal synapses.

neuroscience↗

bioRxiv2025

Real-time fMRI neurofeedback reduces default mode network and auditory cortex functional connectivity in schizophrenia

Background and HypothesisAuditory verbal hallucinations (AHs) are a cardinal symptom of schizophrenia that can cause distress but are not always responsive to antipsychotic medications. There is a critical need to develop novel interventions that target neural mechanisms underlying AHs. We developed a real-time fMRI neurofeedback (NFB) paradigm for AHs that aims at modulating default mode network (DMN) functional connectivity. Study DesignPatients with schizophrenia or schizoaffective disorders who were experiencing AHs (N = 25) attempted to decrease brain activation while listening to sentences recorded in another persons voice and increase brain activation while listening to sentences recorded in their own voice. Participants randomly assigned to the real group (n = 12) received neurofeedback based on signals from their auditory cortex in the superior temporal gyrus (STG) and those assigned to the sham group (n = 13) received neurofeedback based on motor cortex signals. Study ResultsAnalyzing resting state fMRI data collected pre- and post-NFB, we found that: (1) at baseline, stronger within-DMN connectivity between the medial prefrontal cortex (MPFC) and posterior cingulate cortex was associated with higher AHs severity; (2) after NFB, participants in the real group, compared to those in the sham group, showed greater reduction in functional connectivity between the MPFC and auditory cortices in the STG and middle temporal gyrus (MTG). Notably, the reduction in MPFC-STG/MTG connectivity was found in all participants in the real group. ConclusionsThese findings suggest that NFB can effectively and non-invasively modulate functional connectivity in regions associated with AHs in psychosis.

neuroscience↗

bioRxiv2024

Integrative analysis of angiogenic signaling in obesity: capillary features and VEGF binding kinetics

Obesity is a global health crisis, with its prevalence particularly severe in the United States, where over 42% of adults are classified as obese. Obesity is driven by complex molecular and tissue-level mechanisms that remain poorly understood. Among these, angiogenesis--primarily mediated by vascular endothelial growth factor (VEGF-A)--is critical for adipose tissue expansion but presents unique challenges for therapeutic targeting due to its intricate regulation. Systems biology approaches have advanced our understanding of VEGF-A signaling in vascular diseases, but their application to obesity is limited by scattered and sometimes contradictory data. To address this gap, we performed a comprehensive analysis of the existing literature to synthesize key findings, standardize data, and provide a holistic perspective on the adipose vascular microenvironment. The data mining revealed five key findings: (1) obesity increases adipocyte size by 78%; (2) vessel density in adipose tissue decreases by 51% in obese mice, with vessels being 47-58% smaller and 4-9 times denser in comparison with tumor vessels; (3) capillary basement membrane thickness remains similar regardless of obesity; (4) VEGF-A shows the strongest binding affinity for VEGFR1, with four times stronger affinity for VEGFR2 than for NRP1; and (5) binding affinities measured by radioligand binding assay and surface plasmon resonance (SPR) are significantly different. These consolidated findings provide essential parameters for systems biology modeling, new insights into obesity-induced changes in adipose tissue, and a foundation for developing angiogenesis-targeting therapies for obesity.

bioengineering↗

bioRxiv2024

Conformational dynamics of a histidine molecular switch in a cation/proton antiporter

Multisubunit Mrp type sodium proton (Na+/H+) antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea under challenging conditions. Several subunits of the membrane protein complex are closely related to the membrane bound subunits of mitochondrial respiratory complex I, a key enzyme in aerobic energy metabolism. The molecular mechanism of ion translocation by complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, we combine the power of site-directed mutagenesis and large-scale atomistic molecular dynamics simulations to elucidate the molecular basis of proton-conducting function of the MrpA subunit of the antiporter. We show that point mutations directly affect the transport activity by perturbing the conformational dynamics of a key histidine residue that acts as a molecular switch. Importantly, we find that charge and protonation state variations drive hydrogen bonding rearrangements and hydration changes, which result in coupled sidechain and backbone level conformational changes of the histidine and neighboring residues. We propose the histidine switch as a unique functional element central to proton transport function in Mrp antiporters and respiratory complex I. Significance statementEnergy conversion in biology is catalyzed by several membrane-bound enzyme complexes that drive transmembrane charge translocation. A key question is how these charges are moved against a membrane gradient in an efficient manner, i.e., what kind of gating and fail-safe mechanisms are employed by the proteins to ensure charge transfer directionality. By studying cation/proton Mrp antiporter, which shares homology with the mitochondrial complex I, we describe a conserved histidine residue acting as a molecular switch crucial for gating transfer of protons. Our work emphasizes the functional significance of conserved and conformationally mobile motifs in proteins. The results will benefit the mechanistic understanding of naturally existing proteins and design of artificial enzymes.

biophysics↗

bioRxiv2024

A core set of neural states underlying memory reactivation of naturalistic events in the posterior medial cortex

In the posterior midline default mode network, spatial activity patterns similar to those during the initial experience are reactivated during the successful recall of past events. Prior studies have shown that these event-specific activity patterns are consistent across individuals recalling a shared experience, suggesting that common functional responses underlying episodic recall do exist. However, the spatial organization of function during episodic encoding and subsequent recall, especially in the absence of external stimuli, remains poorly understood. To address this, we leverage fMRI data collected during the encoding and recall of naturalistic movies to identify a core set of neural states in the posterior medial cortex. These states are stimulus-locked, reactivated during recall, and have a shared spatial organization across brains (i.e., individuals). We show that a surprisingly small number of these states (16 states across hemispheres) is sufficient to achieve the same levels of reactivation in the posterior medial cortex as when using the standard methods of the field. Additionally, these states are linked to actions and social-affective features of events in the movies. Our findings elucidate the properties of a common, spatially organized code within the posterior default mode network which appears during natural recollection of memories.

neuroscience↗