Biology subjects

Lee, T.-H.

Publications and source records attributed to Lee, T.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

QuImputer: an LD-informed QUBO/Ising formulation of genotype imputation with quantum-hardware execution

Genotype imputation offers a biological application for optimization methods that may eventually run on larger quantum computers. We developed QuImputer to encode allele-frequency priors and signed linkage disequilibrium (LD) in a reduced Ising/QUBO objective, with only missing genotypes represented as optimization variables. The same objective can be passed to exhaustive classical search, quantum approximate optimization algorithm simulation, or quantum hardware. We evaluated the formulation on 100 rice accessions across 12 chromosomes, estimating LD and allele frequency from the same post-masking observed matrix supplied to Beagle 5.4. Evaluation was restricted to known truth at sites with exact dosage coding and an alternate allele that was not the major allele, with MAF below 0.50, yielding 1.88 billion scored genotypes. Beagle achieved higher rare-ALT sensitivity (2.52% versus 0.54%), F1 (0.047 versus 0.011), Matthews correlation coefficient (0.088 versus 0.044), and pooled hard-call dosage R-squared (0.231 versus 0.014). QuImputer produced fewer false ALT calls, with Type I error of 0.038% versus 0.223%. Analyses of a chromosome-1 subset showed limited local LD support for many masked rare-ALT carriers. In five small IBM Fez validation problems, the selected minimum-energy outputs matched unique all-reference exact optima; the pooled frequency of those optima was 1.21-2.63%. Further IBM Fez executions covered eleven sparse instances with 12-97 variables and a separate 120-variable instance, retaining all measurements. Selected outputs recovered the exact optima in eight instances through 49 variables. Larger instances remained below the all-reference baseline; noiseless comparisons distinguished finite-shot sampling from deviations in hardware output. QuImputer provides an LD-informed formulation and a route to quantum-hardware execution, together with an empirical assessment of the limitations of the evaluated configuration. These results establish a basis for studying richer information models and alternative classical or quantum solvers.

bioinformatics↗

bioRxiv2026

Parent-Child Cortical Similarity Indexes Multiple Dimensions of Sensitivity in the Association Between Family Environment and Adolescent Internalizing Symptoms

Family environment is a robust predictor of adolescent internalizing symptoms, yet its strength varies across adolescents. We tested whether this variation is partly captured by how similar an adolescent's cortical structure is to their parent's and whether different forms of this similarity matter in different cortical systems. In 115 parent-child dyads from two cohorts, structural MRI quantified similarity across 400 cortical parcels in two forms: phenotypic similarity in regional morphometry and architectural similarity in interregional morphometric organization. Parent-child similarity was not directly associated with symptoms, whereas its interactions with family environment were jointly significant (chi-square(4) = 14.92, P = 0.005). Phenotypic similarity in the sensory-limbic system and architectural similarity in the association system each moderated the association between family environment and symptoms (both beta = 0.22). In both cases, the association was strongest among less similar dyads. The phenotypic interaction was distributed across sensory-limbic networks and was not reproduced by similarity to unrelated adults or by the child's cortical atypicality. The architectural interaction was concentrated in the dorsal attention and default mode networks and was distinguishable from unrelated-adult similarity but not from child atypicality. Together, these findings raise the possibility that markers of environmental sensitivity need not reside in the child alone. Parent-child cortical similarity may index a dyadic component of this sensitivity, one not adequately represented by a single similarity score but distributed across forms of similarity and cortical systems.

neuroscience↗

bioRxiv2026

A convergent behavioral-neural profile of parental dysregulation and the link between parent-child brain-state similarity and child negative affect

Parent-child neural similarity is often interpreted as a marker of attunement, but its developmental significance may not be uniformly positive across family environments. We tested whether the parent's own emotional and regulatory profile, measured both behaviorally and neurally, moderates the developmental significance of parent-child neural similarity. Applying a hidden Markov model (HMM-MAR; K = 6 states) to whole-brain fMRI timeseries from 32 parent-youth dyads who separately watched the same emotional film, we derived per-dyad measures of brain-state similarity. Parent-child dyads showed greater brain-state similarity than parent-shuffle null pairs (d = -0.55, p = .004), indicating dyad-specific alignment beyond responses shared across viewers of the same film. Parent self-reported internalizing showed only a weak direct relation to child negative affect (r = .31, p = .085). However, the association between neural similarity and child negative affect depended on parent internalizing (b = 5.62, p = .018; R^2): stronger parent-child similarity predicted higher child negative affect when parents reported higher, but not lower, internalizing. A parallel interaction emerged when parent internalizing was replaced by a neural index of the parent's own state dynamics (parent neural-state unpredictability, Htrans; b = 5.95, p = .004), indicating that the effect reflects the parent's broader regulatory profile rather than a single measurement modality. Both interactions were clearest in the primary model and only partially robust across model orders and parcellations. These findings suggest that dyadic neural similarity should be interpreted in context: resembling a parent with a dysregulated profile may confer risk rather than protection.

neuroscience↗

bioRxiv2026

Hypoxia drives asymmetric envelope remodelling to promote membrane adaptation and antibiotic tolerance in mycobacteria

Mycobacterium tuberculosis persists within the host by adapting to stressful microenvironments, with hypoxia representing a key clinically relevant challenge. However, how hypoxia alters mycobacterial membrane organization and function remains poorly understood. Using Mycobacterium smegmatis as a model, we combined membrane biophysics, layer-resolved lipidomics, and membrane-drug interaction analyses to characterize envelope adaptation under oxygen limitation. Hypoxia induced asymmetric remodelling of the cell envelope, with the inner membrane becoming more ordered and less hydrated, while the outer membrane exhibited increased fluidity and hydration. Lipidomic analyses revealed corresponding membrane-specific changes, including enrichment of saturated, tightly packed lipids in the inner membrane and unsaturated, inverted-conical lipids in the outer membrane. Functionally, hypoxic cells showed reduced envelope permeability and decreased susceptibility to rifampicin, while membrane partitioning studies suggested reduced rifampicin association with hypoxia-adapted inner membranes. We identify asymmetric envelope remodeling as a previously unrecognized principle of bacterial adaptation to environmental stress. Rather than responding as a uniform structure, the mycobacterial envelope undergoes coordinated but divergent remodeling in its constituent membrane layers during hypoxia. This spatially resolved response couples inner membrane rigidification with outer membrane fluidization, generating a functionally specialized envelope architecture that simultaneously preserves membrane integrity, modulates permeability, and reduces antibiotic association. These findings suggest that membrane asymmetry is not merely a structural feature of complex bacterial envelopes but an actively regulated adaptive strategy that links environmental sensing to stress resilience and antimicrobial tolerance

biophysics↗

bioRxiv2026

Family Conflict and Parent-Child Similarity in Affective Valuation

How children come to evaluate social-affective cues is shaped within the family, yet the neural expression of this process and its dependence on family relationships remain unclear. We tested whether parent-child similarity in the neural coding of affective judgment varies with family environment, and whether it relates to youth affective distress. Twenty-five parent-child dyads (youth, mean age 11.8; parents mean age 42 years) judged faces morphed along an angry-to-happy continuum as positive or negative during fMRI. For each participant, we defined an evaluative choice axis distinguishing faces judged positive from negative, independent of expression intensity. Using searchlight-based parent-child cross-decoding, we tested whether one dyad members evaluative coding predicted the other members judgments, indexing shared evaluative coding rather than shared sensitivity to expression intensity. Inference focused a priori on medial prefrontal cortex. There was no reliable average parent-child neural similarity across the sample. Instead, higher family conflict was associated with lower parent-child neural similarity in ventromedial prefrontal cortex (vmPFC). Demonstrating specificity to negative relational strain, this effect was not observed for complementary dimensions of family cohesion or identity. Moreover, the effect was specific to true dyads rather than random pairings and to vmPFC rather than a face-selective network or other medial prefrontal regions. Lower vmPFC similarity showed a preliminary association with higher youth affective distress. These findings indicate that affective valuation, rather than sensory encoding, may be a representational level at which perceived family conflict is reflected in parent-child neural similarity.

neuroscience↗

bioRxiv2026

Positive Interpretation of Emotional Ambiguity Across Development: LC-dlPFC Circuitry

Emotionally ambiguous facial expressions provide a tractable model for studying how uncertain affective information is resolved into categorical judgments. Here we tested whether developmental differences in this process are reflected in locus coeruleus (LC) circuitry and how these neural effects relate to behavioral and decision-process indices of interpretive bias. Participants from late childhood through middle-aged adulthood completed an angry-to-happy facial morph task during fMRI. Behavioral responses were analyzed using signal detection theory, and drift-diffusion modeling, and fMRI data were analyzed using LC-seeded generalized psychophysiological interaction and trial-level neural models. Positive bias increased systematically across development. Drift-diffusion analyses showed that this shift was captured specifically by drift intercept, a stimulus-independent evaluative component of evidence accumulation, rather than by perceptual sensitivity, starting point, or response caution. At the neural level, the association between LC-dlPFC coupling and positive bias was strongest in middle-aged adults. Trial-level analyses further indicated that dlPFC carried the clearer moment-to-moment evaluative signal, whereas LC contributed through slower temporal properties, indexed by the Hurst exponent, that shaped bias-related cortical coupling. Importantly, higher LC structural integrity (contrast-to-noise ratio) was associated with lower LC temporal persistence and, in turn, more negative LC-dlPFC coupling. Together, these findings suggest that age-related differences in positive interpretation are not simply differences in perceptual sensitivity or response tendency, but reflect age-graded variation in evaluative evidence accumulation supported by LC-dlPFC circuitry. This work extends recent evidence implicating LC-prefrontal connectivity in ambiguity processing and identifies evaluative drift bias as an age-graded circuit-level signature of emotional ambiguity resolution. Significance StatementHow the brain resolves emotionally ambiguous faces across development is poorly understood. Using psychometric, drift-diffusion, and fMRI analyses in youth, emerging adults, and middle-aged adults, we show that age-related increases in positive interpretation are explained by drift intercept, a stimulus-independent evaluative component of evidence accumulation, rather than by perceptual sensitivity or starting-point bias. LC-dlPFC coupling tracked this same bias dimension. Trial-level analyses suggested that dlPFC carried the clearer moment-to-moment evaluative signal, whereas LC contributed through slower temporal properties of bias-related coupling. These findings identify evaluative drift bias as a measurable circuit-linked mechanism of emotional ambiguity resolution.

neuroscience↗

bioRxiv2026

Distinct Neural Systems Supporting Afferent and Efferent Autonomic Activity

Numerous studies have reported brain correlates of autonomic activity. However, ambiguity exists regarding whether those correlates reflect receiving or sending out autonomic signals. Additionally, little is known about how emotion and aging interact with brain-autonomic coordination. Based on time-varying heart rate variability (HRV) and blood oxygenation level dependent (BOLD) data (N = 104 younger; N = 51 older adults), we found insular and cingulate activity was negatively correlated with HRV during emotion regulation. We further examined the afferent and efferent nature of HRV-BOLD correlations during rest (N = 102 younger; N = 51 older adults). Functionally afferent regions where decreases in HRV were associated with subsequently increased BOLD activity included the posterior insula, postcentral gyrus and frontal pole. Functionally efferent regions where increased activity was associated with subsequently increased HRV included the anterior insula and cingulate. Information appeared to flow in one direction as the afferent regions activity Granger-predicted the efferent regions activity. Together, our findings suggest a feedback loop where decreased HRV increases the afferent regions activity, which activates the efferent regions, leading to increased HRV. Aging seems to affect this system; the efferent and afferent regions scarcely overlapped for younger adults, but did overlap for older adults.

neuroscience↗

bioRxiv2026

Iron-dependent reprogramming of damage-associated peptide receptor signaling coordinates immunity and phosphate stress adaptation

Plant adaptation to inorganic phosphate (Pi) limitation entails extensive developmental and metabolic reprogramming, collectively termed the phosphate starvation response (PSR). How plants balance nutrient acquisition with immune competence remains unresolved. Here, we show that PSR selectively remodels pattern-recognition receptor (PRR) signaling in Arabidopsis thaliana. Membrane proteomics reveals increased abundance of the Pep receptor PEPR1 under Pi deficiency, whereas most receptor kinases, including the microbial PRRs FLS2 and CERK1, are reduced. Immunoblotting further shows increased PEPR2 abundance. Consistently, Pep-triggered responses are strongly potentiated under Pi depletion, while flagellin- and chitin-induced responses are not, indicating selective PEPR sensitization rather than global immune suppression. This sensitization requires the PSR-associated ferroxidases LPR1/LPR2, NADPH oxidases RBOHD/RBOHF, and transcription factor WRKY33, linking iron-dependent redox remodeling to immune amplification. Beyond inducible defense, PEPRs promote basal PSR transcriptional reprogramming and growth under Pi limitation. Loss of PEPR1/PEPR2 compromises bacterial resistance and alters root-associated microbiota assembly under nutrient deficiency. Together, Pi depletion selectively sensitizes specific PRR pathways. PEPRs exhibit context-dependent dual functionality, promoting either immunity or nutrient stress adaptation, potentially in response to distinct PROPEP-derived ligands, thereby supporting nutrient acquisition without compromising immune vigilance. These findings provide a framework for how nutritional status selectively remodels PRR signaling to coordinate immunity with nutrient stress adaptation.

plant biology↗

bioRxiv2025

De Novo Computational Design of VHH Nanobodies Against LGR5

VHH discovery traditionally relies on animal immunization or large-scale library screening, methods that are slow, costly, and often ineffective for challenging targets such as GPCRs. We present a fully de novo computational pipeline for epitope-directed VHH design, integrating generative backbone modeling, deep learning-based sequence optimization, and iterative experimental feedback. Using LGR5 as a model, we progressed from in silico design to functional binders without structural templates. Across three design-test-learn cycles, millions of candidates were reduced to epitope-specific binders with nanomolar affinity and high thermal stability (melting temperature [Tm] > 65 {degrees}C). Cryogenic electron microscopy (cryo-EM) confirmed atomic-level agreement (RMSD {approx} 2.2 [A]). This structure-validated approach accelerates timelines, reduces cost, and is broadly applicable to GPCRs and other membrane proteins, enabling "on-demand" therapeutic antibody generation.

bioengineering↗

bioRxiv2025

Automated Locus Coeruleus segmentation and age-related signal changes across Neuromelanin-sensitive MRI and T1/T2-weighted images

The locus coeruleus (LC) plays a key role in stress response, attention, and cognitive function, with its integrity closely linked to neuromelanin accumulation. Neuromelanin-sensitive MRI (NM-MRI) has enabled in vivo imaging of the LC, but automated segmentation remains challenging due to its small size, low contrast, and anatomical variability. This study aimed to evaluate the accuracy of automatic LC segmentation using multi-atlas nonlinear warping applied to high-resolution T1/T2-weighted images and to compare LC intensity characteristics across NM-MRI, T1w, and T2w images. Additionally, we examined developmental changes in LC signal from childhood through adulthood. We analyzed MRI data from 134 participants (ages 8[~]64) with NM-MRI, T1w, and T2w scans, alongside 652 participants (ages 6[~]22) from the Human Connectome Project in Development (HCP-D). LC intensity measures were compared across imaging modalities and analyzed for age-related trends. Automatic LC segmentation achieved high spatial overlap with manual tracings (up to 95% after one voxel 2D-dilation). Statistically estimated high (or low)-intensity values (mean {+/-} 2{sigma}) from automated LC masks provided a more stable and noise-resilient alternative to local peak intensity measures. Age-related LC signal changes are most clearly observed in NM-MRI and T2w imaging, with significant developmental shifts emerging during adolescence. These findings support the conventional T2w imaging as an indirect marker of neuromelanin accumulation and highlight the possibility of age-specific analyses in LC imaging studies.

neuroscience↗

bioRxiv2025

From Family Relationship to Regulation: Parent-Child Amygdala Activation Similarity is Linked to Prefrontal Recruitment and Youth Emotional Adaptation

Extensive research highlights the importance of parent-child similarity at psychological, behavioral, and physiological levels in fostering childrens adaptation. While emerging studies have begun to explore neural similarity, little is known about the factors that influence parent- child neural similarity during adolescence or how such similarity may support youth emotional adaptation when coping with heightened uncertainty. The current study investigated the relations among family relationship quality, parent-youth neural similarity, and youth emotional adaptation using task-based fMRI. With 50 participants (25 parent-youth dyads; parent: Mage = 43.88{+/-}7.42 years, 72% female; youths: Mage = 11.16{+/-}2.85 years, 44% female), we found that higher parent-youth neural similarity in the amygdala activation patterns during emotionally uncertain situations was associated with better youths emotional adaptation, as indicated by lower levels of anxiety and depression and higher resilience. This neural similarity mediated the beneficial effects of positive family relationships on youths emotional adaptation. Additionally, amygdala activation similarity was associated with amygdala to dorsolateral prefrontal cortex (dlPFC) connectivity during uncertainty in youth, revealed by generalized psychophysiological interaction (gPPI) analyses. This amygdala-dlPFC connectivity, in turn, was linked to better emotional adaptation in youth. Importantly, these findings were specific to uncertainty-related bottom-up processing, rather than effortful top-down regulation processing or responses to certain aversive stimuli. These findings offer new insight into how relational and neural factors jointly shape youth emotional adaptation, and suggest that parent-child neural similarity in the amygdala may serve as a mechanism for supporting implicit emotion regulation, helping youth cope with uncertain situations. Significance StatementDuring adolescence, youth begin to expand their social worlds beyond the family, yet family relationships continue to shape how they navigate emotionally complex environments. How do these relationships influence youth brain function and emotional well-being? Using task-based fMRI, we found that greater parent-child neural similarity in the amygdala during emotionally uncertain situations is associated with youths lower anxiety and depression and greater resilience. This amygdala neural similarity was also linked to prefrontal engagement in youth during early arousal stage, supporting adaptive implicit regulation under uncertainty. These findings suggest that neural alignment between parents and youths may serve as a key mechanism by which positive family relationships promote emotional adaptation, highlighting the enduring role of family context in adolescent brain development.

neuroscience↗

bioRxiv2025

Multi-omics integration uncovers host-microbiota crosstalk underlying sexual differentiation in the shortfin eel Anguilla bicolor pacifica

The global decline in anguillid eel populations has intensified interest in understanding their biology for conservation and aquaculture. While host-gut microbiota interactions are well-characterized in homeotherms, these relationships remain poorly understood in poikilotherms during sexual differentiation. We examined gut microbiota dynamics across developmental stages in the shortfin eel Anguilla bicolor pacifica, which exhibits early sexual differentiation and a relatively short life cycle. Glass eels were cultivated in controlled freshwater conditions for three years, with sampling at key stages: glass eel, elver, sex-undetermined eel, and sex-determined eel. Full-length 16S rRNA gene sequencing revealed significant compositional shifts during development, with higher bacterial richness in adults versus younger eels. Early stages were dominated by Pseudomonadota, while sex-determined adults showed increased Deinococcota abundance. Network analysis identified Deinococcus, Sphingomonas, and Variovorax as key genera in sex-determined eels, with positive correlations between anti-Mullerian hormone gene expression and these taxa. We isolated 66 gut bacterial strains capable of metabolizing sex hormones under microaerobic conditions. These isolates, representing 22 genera across four phyla, demonstrated diverse metabolic capabilities from partial oxidation to complete steroid mineralization. Multiple strains achieved complete estradiol degradation as single isolates--a rare metabolic capability of environmental microorganisms. Comparative genomic analysis revealed widespread steroid-metabolizing genes, with Deinococcus species showing previously unreported hormone degradation capabilities. Our multi-omics analysis demonstrates that gut microbiota composition and function are intimately linked to eel sexual development, suggesting bidirectional host-microbe interactions influencing reproductive physiology. These findings advance understanding of host-microbiota interactions in aquatic vertebrates and provide implications for eel aquaculture and conservation.

microbiology↗

bioRxiv2025

Mechanosensitive Endothelial METTL7A Regulates Internal m7G mRNA Methylation and Protects Against Atherosclerosis

BACKGROUNDInternal N7-methylguanosine (m7G) is a recently identified chemical modification of mammalian mRNA and a component of the epitranscriptome. While the epitranscriptome plays a key role in regulating RNA metabolism and cellular function, the specific contribution of internal m7G to cardiovascular health and disease remains unknown. Atherosclerosis preferentially develops at sites where disturbed blood flow activates endothelial cells, but whether internal m7G and its regulatory machinery influence endothelial mechanotransduction and atherogenesis is unclear. METHODSWe integrated epitranscriptomic profiling, human tissue analysis, genetically modified mouse models, and targeted nanomedicine approaches to investigate the role of Methyltransferase-like protein 7A (METTL7A), a putative internal m7G methyltransferase, in regulating the flow-sensitive endothelial transcriptome and atherosclerosis. Vascular endothelial cells were subjected to well-defined athero-protective and athero-prone flow waveforms in vitro and in vivo. METTL7A function was assessed using RNA sequencing (RNA-seq), liquid chromatography-tandem mass spectrometry (LC-MS/MS), crosslinking immunoprecipitation sequencing (CLIP-seq), RNA stability assays, and a CRISPR-Cas-inspired RNA targeting system (CIRTS). METTL7A expression in human coronary arteries with and without atherosclerosis was evaluated by RNA-seq and immunostaining. In vivo atherosclerosis studies were conducted in both global and endothelial-specific Mettl7a1 knockout mice. Endothelial METTL7A expression was restored using cationic polymer-based nanoparticles delivering CDH5 promoter-driven METTL7A plasmids or VCAM1-targeted lipid nanoparticles delivering N1-methylpseudouridine (m{superscript 1}{Psi})-modified METTL7A mRNA. RESULTSAthero-protective unidirectional flow significantly induced METTL7A expression, which promoted internal m7G methylation of endothelial transcripts, while other major epitranscriptomic marks and cap-associated m7G were not affected by METTL7A. METTL7A preferentially binds to AG-enriched motifs in protein-coding mRNAs and plays a key role in regulating KLF4 and NFKBIA transcripts, enhancing their internal m7G and stability and supporting vascular homeostasis. In contrast, endothelial METTL7A expression was significantly reduced by disturbed blood flow and in human atherosclerotic lesions. Global or endothelial-specific loss of METTL7A exacerbated disturbed flow-induced atherosclerosis in mice, independent of serum lipid levels. Restoration of endothelial METTL7A, via nanoparticle-mediated plasmid or m1{Psi} mRNA delivery, markedly reduced lesion formation in Mettl7a1-/- and ApoE-/- mice. CONCLUSIONSThese findings establish METTL7A as a previously unrecognized mechanosensitive methyltransferase that maintains endothelial homeostasis by stabilizing key anti-inflammatory transcripts, KLF4 and NFKBIA, through internal m7G methylation. Loss of METTL7A disrupts endothelial function and accelerates atherogenesis in response to disturbed flow. Therapeutic restoration of endothelial METTL7A, via targeted nanoparticle-mediated gene or m1{Psi} mRNA delivery, significantly lessens atherosclerosis. Collectively, these results uncover a novel epitranscriptomic mechanism governing vascular health and position METTL7A as a promising target for precision nanomedicine in atherosclerotic cardiovascular disease.

molecular biology↗

bioRxiv2025

Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of chromatin arrays

Chromatin condensation is dynamically regulated throughout the cell cycle and plays key roles in modulating gene accessibility at the highest physical level in a cell. The DNA-histone dynamics in short- and long-range inter-nucleosomal interactions are central to the regulation mechanisms of chromatin condensation which remain under active investigation. We employed 12-mer nucleosome arrays to investigate the roles of histone chaperone Nap1, and histone H3 and H4 N-terminal tails and their acetylation in regulating the formation and the properties of phase-separated chromatin condensates. These arrays form liquid-like condensate droplets under a physiological salt condition of 150 mM NaCl. According to our results from bright-field microscopy, fluorescence recovery after photobleaching, optical super-resolution imaging, and microrheology with optical tweezers, histone H4 tail lysine residues are the main drivers of liquid-liquid phase separation of chromatin arrays. We also found that the condensed liquid-like droplets contain both a mobile fraction and a relatively immobile structural scaffold and that histone chaperone Nap1 and histone H3 tail acetylation facilitate DNA-histone dynamics within the structural scaffold to lower the overall viscosity of the droplets. These results suggest that histone chaperone and histone H3/H4 tails play critical roles in regulating chromatin condensation and gene accessibility in condensed chromatin.

biophysics↗

bioRxiv2024

Aromatase-independent estrogenesis: Wood-Ljungdahl pathway likely contributed to the emergence of estrogens in the biosphere

Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O2-dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut of the great blue-spotted mudskipper (Boleophthalmus pectinirostris). This strain exhibits unprecedented testosterone fermentation pathways, transforming testosterone into estrogens and androstanediol under anaerobic conditions. Physiological experiments revealed that strain TUW77 grows exclusively on testosterone, utilizing the androgenic C-19 methyl group as both the carbon source and electron donor. The genomic analysis identified three copies of a polycistronic gene cluster, abeABC (anaerobic bacterial estrogenesis), encoding components of a classic cobalamin-dependent methyltransferase system. These genes, highly expressed under testosterone-fed conditions, show up to 57% protein identity to the characterized EmtAB from denitrifying Denitratisoma spp., known for methylating estrogen into androgen (the reverse reaction). Tiered transcriptomic and proteomic analyses suggest that the removed C-19 methyl group is completely oxidized to CO2 via the oxidative Wood-Ljungdahl pathway, while the reducing equivalents (NADH) fully reduce remaining testosterone to androstanediol. Consistently, the addition of anthraquinone-2,6-disulfonate, an extracellular electron acceptor, to testosterone-fed TUW77 cultures enabled complete testosterone conversion into estrogen without androstanediol accumulation (anaerobic testosterone oxidation). This discovery of aromatase-independent estrogenesis in anaerobic bacteria suggests that the ancient Wood-Ljungdahl pathway may have contributed to the emergence of estrogens in the early biosphere. SignificanceUsing a testosterone-grown anaerobic bacterium as a model organism, we characterized this unusual anaerobic estrogenesis at the molecular level. Our findings challenge the long-held belief that estrogen production is exclusive to aromatase-containing vertebrates, expanding our understanding of steroid hormone biosynthesis across domains of life. The involvement of ancient strictly anaerobic Peptococcaceae members and the Wood-Ljungdahl pathway suggests that bacterial estrogenesis may predate O2-dependent estrogenesis in vertebrates. Furthermore, the identification of estrogen-producing bacteria in animal guts opens new avenues for potential microbiome-based hypoestrogenism therapies to supplement estrogen in menopausal or ovariectomized females, offering an innovative alternative to current hormone replacement strategies.

microbiology↗

bioRxiv2024

Inversed association of locus coeruleus MRI integrity with structural volume and its impact on individual's inattentiveness

The locus coeruleus (LC) is a nucleus within the brainstem associated with physiological arousal and altered structure and function in the context of neurodegenerative disorders. Pathologies related to difficulties with attention have previously been associated with abnormalities in neurotransmitter production and sensitivity, suggesting the possibility of abnormality in neurotransmitter producing neural regions. One such region is the LC, associated with norepinephrine production. To examine the possibility that LC alteration is associated with inattentive symptom reporting, a set of analyses have been performed with 141 individuals age-ranged from 8 to 54. We found that the structural integrity value of the LC, especially on the right hemisphere, showed a significant negative association with the level of individuals inattentiveness score. Furthermore, LC volume size was significantly positively associated with inattention, and this finding was also lateralized to the right LC. Interestingly, an inverse association was found between structural integrity and volume size. These findings support the relationship between LC and attention-related behavior through both neuromelanin-sensitive and structural imaging, with important implications for the association between regional structure and function.

neuroscience↗

bioRxiv2024

Native Korean wild mice (Mus musculus): molecular phylogeny and morphometrics

Taxonomic status of house mice in the Korean Peninsula remains poorly understood. Here, we analyze genetic and morphological characteristics of mice from Korea and evaluate their phylogenetic relationships to the well-known primary subspecies. Using a comprehensive set of publicly available genetic data (mtDNA cytb gene), Korean mice including our specimens from islands, mountains, and agricultural fields were identified to Mus mus musculus. External morphology, such as tail ratios of our specimens, resembled previously assigned subspecies (e.g., M. m. molossinus, M. m. utsuryonis, and M. m. yamashinai), suggesting a single subspecific group within M. m. musculus. Korean mice displayed a distinctive landmark configuration around the snout, with a relatively short and slender premaxillary tooth-patch width (PMXW) and a larger maxillary tooth-row length (MXTL) compared to laboratory strains derived from M. m. domesticus. Our investigation provides insights into the phylogenetic relationships and taxonomic status of Korean mice relative to the primary lineages of M. musculus subspecies. Understanding the evolutionary history of Korean M. m. musculus sheds new light on how their spatiotemporal dynamics led to diversification, with the Korean Peninsula serving as an ecological bridge between East Eurasia and neighboring regions.

zoology↗

bioRxiv2024

Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development

HighlightsO_LIWe identified Clostridium innocuum as a key player in gut progesterone metabolism. C_LIO_LIProgesterone is converted into epipregnanolone with negligible progestogenic activity. C_LIO_LIWe identified the enzyme and mechanisms of microbial epipregnanolone production. C_LIO_LIC. innocuum caused decreased serum progesterone and follicular arrest in female mice. C_LIO_LIC. innocuum is a causal factor of progesterone resistance in women taking progesterone. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/585140v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14cceaborg.highwire.dtl.DTLVardef@1946432org.highwire.dtl.DTLVardef@13e46d2org.highwire.dtl.DTLVardef@19b9a25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChen et al. identified Clostridium innocuum as a major species involved in gut progesterone metabolism, with epipregnanolone as the main product, and elucidated the molecular mechanisms. C. innocuum inactivates gut progesterone in female mice, leading to decreased circulating progesterone levels. C. innocuum is also a causal factor of follicular arrest. Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5{beta}-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum-administered female C57BL/6 mice (aged 7 weeks) exhibited decreased serum progesterone levels ([~]35%). Clostridium-specific antibiotics (metronidazole) restored low serum progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone.

microbiology↗