Biology subjects

Li, G.

Publications and source records attributed to Li, G..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Pentoxifylline, a Non-Antibiotic Drug, Promotes Adaptation of Clinical Isolates of Staphylococcus aureus via Modulating c-di-AMP Signaling

This study investigated how Staphylococcus aureus adapts under pentoxifylline (PTX) therapy through analyzing three phylogenetically related isolates (L1, L2, L3) from a bacteremia patient. Whole genome sequencing revealed L1 contained a 2400-bp insertion disrupting nupC, while L3 harbored mutations in the anti-Shine-Dalgarno sequences of 16S rRNA. Each isolate evolved distinct mechanisms to reduce c-di-AMP levels, accompanied by changes in survival ability and virulence. Molecular analysis demonstrated PTX noncompetitively inhibits GdpP phosphodiesterase, directly modulating cyclic diadenosine monophosphate (c-di-AMP) signaling. Our findings provide novel insights into how non-antibiotic medications shape bacterial adaptation through second messenger modulation, highlighting the complex trade-offs between stress resistance and fitness in clinical settings. ImportanceThis study reveals how pentoxifylline, a non-antibiotic drug, drives Staphylococcus aureus adaptation by modulating c-di-AMP signaling. Our findings highlight the unintended consequences of non-antibiotic medications on bacterial evolution, offering new insights for clinical treatment strategies to mitigate resistance development. HighlightsO_LIPTX noncompetitively inhibits GdpP, modulating bacterial c-di-AMP signaling C_LIO_LIS. aureus evolves distinct mechanisms to reduce c-di-AMP under PTX pressure C_LIO_LINon-antibiotic medications significantly shape bacterial adaptive trajectories C_LI

microbiology↗

bioRxiv2025

Phase separation and coexistence in spatial coordination games between microbes

Dense, microbial communities are shaped by local interactions between cells. Both the nature of interactions, spanning antagonistic to cooperative, and the strength of interactions vary between and across microbial species and strains. These local interactions can influence the emergence and maintenance of microbial diversity. However, it remains challenging to link features of local interactions with spatially mediated coexistence dynamics given the significant variation in the microscopic mechanisms involved in cell-to-cell feedback. Here, we explore how microbial interactions over a broad range of ecological contexts spanning antagonism to cooperation can enable coexistence as spatially explicit domains emerge. To do so, we introduce and analyze a family of stochastic coordination games, where individuals do better when playing (i.e., interacting) with individuals of the same type than when playing with individuals of a different type. Using this game-theoretic framework, we show that the population dynamics for coordination games is governed by a double-well shaped interaction potential. We find that in a spatial setting this double-well potential induces phase separation, facilitating coexistence. Moreover, we show that for microbes engaged in symmetric coordination games, phase separation takes on a universal scaling that follows Model A coarsening, consistent with prior experimental observations for Vibrio cholerae mutual killers. Finally, we derive a PDE equivalent of the spatial stochastic game, confirming both the double-well nature of spatial coordination games and the universality of phase separation. Altogether, this work extends prior findings on the link between microbial interactions and population structure and suggests generic mechanisms embedded in local interactions that can enable coexistence.

microbiology↗

bioRxiv2025

Mycobacterium tuberculosis, Mycobacterium kansasii and Rhodococcus equi induce macrophage necroptosis in the presence of a caspase inhibitor acting on a non-canonical target(s)

Macrophages are the predominant cell type infected by Mycobacterium tuberculosis (Mtb) in tuberculosis (TB). Death of Mtb-infected macrophages promotes tissue pathology and releases Mtb to infect other cells, suggesting that inhibiting the death of Mtb-infected macrophages could be an adjunctive treatment of TB. Prospects for such an intervention depend on identifying the molecular pathways leading to cell death. We previously reported that the death of Mtb-infected mouse macrophages in vitro depends on type I interferon (IFN) and that the ensuing upregulation of cis-aconitate decarboxylase (ACOD1; IRG1) contributes to cell death by exacerbating Mtb-induced lysosomal membrane permeabilization. Here we report that death of Mtb-infected primary mouse macrophages in vitro became necroptotic and die faster in the presence of benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (z-VAD) acting on a target other than caspase-8. Macrophages infected with Mycobacterium kansasii and Rhodococcus equi likewise underwent z-VAD-dependent necroptosis. In C57BL/6 mice, which are relatively TB-resistant, we saw no impact of MLKL deficiency on bacterial burden or pulmonary pathology. In contrast, in Sp140-/- mice on the C57BL/6 background, which express high levels of type I IFN after Mtb infection and develop necrotic pulmonary lesions, MLKL-deficiency reduced bacterial burden and pathology after high-dose infection. This report illustrates that off-target action(s) of a caspase-8 inhibitor can switch the cell death pathway to necroptosis in macrophages infected with various Gram-positive pathogens. In turn, this opens the possibility that pathophysiologic circumstances may lead to inhibition of the same target(s) that z-VAD inhibited in our studies. That may be what allows MLKL to exacerbate tuberculosis in mice that are prone to formation of necrotic lesions. Author SummaryTuberculosis (TB), caused by the bacillus Mycobacterium tuberculosis (Mtb), led to about 1.3 million deaths in 2023. The rapid emergence of drug resistance and slow pace of new drug development prompt attention to adjunctive host-directed therapies, an approach that relies on a thorough and detailed understanding of host-Mtb interactions. Mtb infection of macrophages can kill them, promoting tissue pathology and releasing of Mtb to infect other cells. Here we find that a pan-caspase inhibitor z-VAD hastened the death of Mtb-infected macrophages and converted the mode of cell death to RIPK1-RIPK3-MLKL-dependent necroptosis. However, the functional target(s) of z-VAD-FMK and the activation mechanism of RIPK3 differ from the canonical pathways. The pan-caspase inhibitor also promoted rapid, necroptotic death of macrophages infected with Mycobacterium kansasii and Rhodococcus equi. We further found that MLKL-deficiency in Sp140-/- mice on the C57BL/6 background resulted in less weight loss, lower Mtb burdens and mitigation of lung pathology after high-dose Mtb infection. Our findings suggest that necroptosis can contribute to TB pathogenesis in some circumstances. Further identification of the death pathway-switching mechanism could deepen our understanding of host-Mtb interactions and aid in the design of adjunctive host-directed therapies.

microbiology↗

bioRxiv2025

KICDB: A Causality-Oriented Multi-Omics Database for Kinase Inhibitor-Induced Cardiotoxicity

BackgroundKinase inhibitors (KIs) are mainstays of targeted cancer therapy, but their clinical utility is frequently limited by cardiotoxicity. A systematic resource to explore the underlying causal mechanisms is urgently needed. MethodsWe present the KICDB (Kinase Inhibitor Cardiotoxicity Database), a comprehensive and interactive web server. KICDB is built upon a framework integrating large-scale transcriptomics meta-analysis with causal inference. ResultsThis database centralizes the findings from a comprehensive meta-analysis of 26 kinase inhibitors (KIs) across 7 studies (n=5291) identified 8,907 significant gene expression changes in human cardiomyocytes. To establish causality, we performed a two-pronged Mendelian randomization (MR) analysis testing hundreds of downstream genes and a panel of 43 key kinase proteins against 46 cardiovascular outcomes. This large-scale analysis revealed 26 significant causal associations, implicating novel molecular mediators in KI-induced cardiotoxicity. ConclusionsKICDB serves as a valuable and accessible platform for the cardio-oncology community. By integrating transcriptomic signatures with causal inference data, the database empowers researchers to formulate mechanistic hypotheses, accelerate biomarker validation, and guide the design of future cardioprotective strategies. URL: https://zhang-lab-database.shinyapps.io/KICDB/ Key PointsO_LIWe developed KICDB, a comprehensive and publicly accessible web server, to systematically investigate the causal mechanisms of KI-induced cardiotoxicity. C_LIO_LIKICDB integrates a large-scale meta-analysis of transcriptomic data from 26 KIs with a robust Mendelian randomization (MR) framework to move beyond correlation and infer causality. C_LIO_LIThe analysis identified 8,907 significant gene expression changes and 26 significant causal associations between KI-associated genes and 46 cardiovascular outcomes. C_LI

bioinformatics↗

bioRxiv2025

Hypobaric hypoxia drives citrate cycle reprogramming to suppress tumor progression

High altitude residents present lower tumor incidence and mortality than plain residents, suggesting that hypobaric hypoxia displays protective effect against tumor development. The results of our studies showed that hypobaric hypoxia exposure significantly suppressed tumor progression in subcutaneous bearing and lung metastasis tumor models. With single-cell transcriptome analysis, we identified HIF-1 pathway was significantly downregulated in tumor tissues with high altitude hypoxia, leading to decreased glycolysis and angiogenesis and improved antitumor immune response. Mechanistically, systemic hypoxia rewired citric acid cycle, with enhanced CS and IDH2 expression and reduced OGDH and SUCLG2 expression, to induce -ketoglutarate accumulation and succinate decline in tumor microenvironment, further mediating HIF-1 pathway inhibition. Moreover, hypobaric hypoxia treatment significantly improved the antitumor effects of adjuvant therapies (including chemotherapy, anti-angiogenic therapy and immunotherapy). Our findings reveal the role and mechanism of hypobaric hypoxia for tumor regression and yield new insights into tumor therapy.

cancer biology↗

bioRxiv2025

DAXX governs the silencing of LINE1 during spermatogenesis in mice

The suppression of transposable elements in germline is critical for safeguarding fertility. Here we identify that the DAXX, a potent transcription repressor and an H3.3 chaperone, is indispensable for transposable elements silencing during spermatogenesis. Male mice with conditional knockout of Daxx in germ cells mediated by Ddx4-cre display delayed meiotic progression, deformed and reduced production of sperms, and an age-dependent decline in fertility. The ablation of DAXX results in activation of evolutionarily young LINE1 and ERVs subfamilies. Mechanistically, DAXX interacts with DMAP1 to maintain DNA methylation of LINE1 in meiotic cells. In summary, this study identifies DAXX as a previously unknown regulator of spermatogenesis and demonstrates that it functions as an epigenetic regulator to maintain the silencing the young LINE1 by DNA methylation.

developmental biology↗

bioRxiv2025

Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology

Previous investigations of whole thalamus and thalamic nuclei volumes in post-trauma psychopathology have been sparse, limited in scope, and yielded inconsistent results. To address this, volumetric estimates of whole thalamus and thalamic nuclei were obtained from structural brain MRI scans from 2,058 participants across 20 worldwide sites in the ENIGMA PTSD working group. Thalamic volumes were compared between trauma-exposed participants with posttraumatic stress disorder (PTSD) (n=238), major depressive disorder (MDD) (n=184), comorbid PTSD+MDD (n=618), and trauma-exposed control participants (n=1,018). PTSD and MDD symptom severity, PTSD symptom clusters, and childhood trauma were similarly examined for associations with thalamic volume. Participants with PTSD only compared to controls had smaller thalamic nuclei volumes in sensorimotor nuclei, including the parafascicular (Pf), ventral anterior magnocellular (VAmc), medial pulvinar (PuM), and anterior pulvinar (PuA) nuclei of the thalamus. MDD only and comorbid PTSD+MDD participants exhibited smaller mediodorsal thalamus volumes compared to controls. Overall PTSD and MDD symptom severity negatively correlated with the volume of the mediodorsal thalamus. A significant interaction between PTSD and MDD severity was found, such that MDD severity was positively associated with thalamic volume only among individuals with high PTSD severity. Avoidance and hyperarousal symptoms of PTSD were positively associated with thalamic volume, while re- experiencing and negative mood/cognition symptoms were negatively associated with thalamic volume. Childhood physical and emotional abuse were positively and negatively associated with thalamic volume, respectively. Whole thalamus volume and volumes of the sensorimotor and limbic thalamus may play an important role in the development of PTSD and MDD in the aftermath of trauma exposure. The interaction between PTSD and MDD symptoms and contrasting effects across PTSD symptom clusters and types of childhood adversity suggests multiple neurobiological mechanisms are involved in shaping thalamic volume post-trauma.

neuroscience↗

bioRxiv2025

Structural insights into Measles virus RNA synthesis: C protein-mediated regulation of replication-transcription switch and allosteric inhibition by ERDRP-0519

Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent RNA polymerase (RdRP) complex for transcription and replication. In measles virus (MeV), the nonstructural protein C has long been implicated in regulating RNA synthesis, yet its precise role remains unclear. Here, we show that the MeV C protein directly associates with the RdRP complex. Using cryo-electron microscopy, we determined atomic-resolution structures of the MeV polymerase with and without C, revealing that C binding stabilizes the accessory domains of L and locks the complex into a replication-competent elongation state. Biochemical data further show that C promotes N protein recruitment, enhancing polymerase processivity through facilitating encapsidation during replication. Additionally, we also resolved high-resolution structures of MeV and Nipah virus (NiV) polymerases bound to ERDRP-0519, an orally available morbillivirus inhibitor. Unexpectedly, the compound occupies a previously unrecognized allosteric pocket within the RdRp domain, rather than the predicted PRNTase domain, overlapping conserved resistance sites. This binding induces conformational changes in palm subdomain, blocking RNA template and nucleotide engagement, thereby halting RNA synthesis. These findings uncover distinct regulatory and inhibitory mechanisms in paramyxovirus polymerases and provide a structural framework for the rational design of broad-spectrum antivirals targeting MeV, NiV, and potentially other clinically relevant nsNSVs.

microbiology↗

bioRxiv2025

The neurotrophin DNT-2 regulates cell survival and connectivity via the Toll-2 receptor during visual system development of Drosophila

During development, neurons are produced in excess and those that receive trophic support are maintained, whereas excess neurons are eliminated, enabling the establishment of appropriate neural circuits. In vertebrates, neurotrophin ligands promote cell survival during periods of naturally occurring cell death, by signalling through p75 and Trk receptors. In the Drosophila optic lobe, a wave of apoptosis occurs during neural circuit development; however, whether this also involves neurotrophism remains unresolved. Drosophila neurotrophins (DNTs) are encoded by spatzle (spz) paralogue genes and bind Toll receptors instead. Here, we focused on DNT-3 (previously known as spz-3) and DNT-2 (also known as spz-5) to ask whether they underlie neurotrophism in visual system development. We show that DNT-3 (spz-3) and DNT-2 (spz-5) are both expressed in the retina and in medulla neurons, and multiple Tolls are expressed across lamina and medulla neurons. Over-expression of DNT-3 (spz-3) and DNT-2 (spz-5) could rescue natural occurring cell death, whereas their loss of function caused cell death, showing that DNT-3 and DNT-2 can, and are required to, promote cell survival during optic lobe development. Importantly, DNT-2 is expressed in Mi1 neurons and Toll-2 in connecting L1 neurons. We show that DNT-2 functions in concert with Toll-2, as Toll-2 RNAi knock-down prevented the rescue of apoptosis by DNT-2 over-expression and all Toll-2+ neurons were lost in DNT-2 mutants. Furthermore, alterations in DNT-2 or Toll-2 expression levels impaired connectivity of L1 neurons at the M1 medulla layer and altered dendritic morphology of L1 neurons. These data suggest that L1 neurons could take up DNT-2 secreted from medulla neurons during the establishment of connectivity patterns. As DNT-3 (spz-3) and DNT-2 (spz-5) are expressed in the medulla and they could influence both lamina and medulla neurons, this suggests that their function maintaining cell survival could enable the stabilisation or alignment of connected neurons across medulla columns.

developmental biology↗

bioRxiv2025

Germline de novo mutation rate of the highly heterozygous amphioxus genome

Germline de novo mutations (DNMs) are the ultimate source of heritable variation, yet their patterns in highly heterozygous genomes remain poorly understood. Amphioxus, an early-branching chordate with exceptionally high genomic heterozygosity (3.2[~]4.2% in sequenced species), offers a unique model to explore mutational dynamics in such contexts. It is unclear whether high heterozygosity in amphioxus is due to a large effective population size, an increased mutation rate, or both. Here, we perform deep short-read whole genome sequencing of a two-generation pedigree of the amphioxus Branchiostoma floridae comprising two parents and 104 offspring, and develop a framework based on allele-aware parental assemblies as the reference to accurately identify DNMs. We detect 205 high-confidence DNMs, yielding a genome-wide mutation rate of 5.10 x 10-9 per base per generation, which is comparable to that of vertebrates. Combining this estimate with observed nucleotide diversity, we obtain an effective population size of [~]1.9 million, indicating that the elevated heterozygosity mainly results from a large effective population size. We observe a maternal-origin bias when considering all DNMs but a paternal-origin bias for early-occurring ones. Amphioxus harbors a much smaller fraction of CpG>TpG DNMs relative to vertebrates, attributable to its low methylation levels. We also investigate putative post-zygotic mutations in the offspring, revealing an unexpected paternal-origin bias. These suggest some distinct mutational mechanisms in amphioxus. Our study not only provides the first DNM measurement for amphioxus but also offers a generalizable strategy for studying DNMs in highly heterozygous genomes, facilitating mutation rate studies across chordates and other lineages.

genomics↗

bioRxiv2025

NuMA promotes constitutive heterochromatin compaction by stabilizing linker histone H1 on chromatin

Heterochromatin has been widely recognized to exert pivotal functions of silencing specific genes and maintenance of genome stability. However, the mechanisms underlying heterochromatin formation and maintenance remain to be fully elucidated. Here, we discovered that the critical mitotic regulator NuMA, as a nucleoskeleton protein, is required for constitutive heterochromatin organization at the level of nucleosomes in the interphase. Depletion of NuMA results in shortened nucleosome repeat length (NRL), dispersed nucleosome clutches and increased chromatin accessibility in heterochromatin regions. Afterwards, epigenetic maintenance and transcription repression in constitutive heterochromatin are disrupted upon NuMA-depletion, particularly the up-regulated transcription level of the non-coding long terminal repeat (LTR) elements, indicating the crucial roles of NuMA in cell differentiation and senescence. We revealed that such functions of NuMA rely on its interaction with linker histone H1, which stabilizes H1s binding to chromatin and facilitates nucleosome stacking. We provided direct structural evidence of NuMAs stabilization effect at the highest spatial resolution of nucleosomes through in situ cryo-ET. Notably, we found that NuMA oligomerizes into quasi-meshwork in nucleoplasm and highly co-localizes with H1 on the chromatin, providing the organization basis for NuMA as a nucleoskeleton protein in chromatin architecture regulation. Collectively, our findings illuminate the concerted effect of nucleoskeleton protein and linker histone on chromatin compaction at the level of nucleosomes, which unveil a new layer of mechanisms by which nucleoskeleton regulates heterochromatin formation and maintenance.

biophysics↗

bioRxiv2025

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

Peptide nucleic acid (PNA), a synthetic nucleic acid analog, exhibits substantial potential in biotechnology and therapeutic applications due to its high binding affinity and nuclease/protease resistance. Chemically modified PNAs capable of forming stable triplex structures with double-stranded RNAs (dsRNAs) under near-physiological conditions further expand their utility by enabling sequence-specific precise targeting and probing of functional RNA structural motifs. However, the presence of inverted Watson-Crick pairs (C-G and U-A) may significantly weaken the triplex formation of the dsRNA-binding PNAs (dbPNAs). Our previous work demonstrated that dbPNA P3 (composed of L, T, and Q monomers for the recognition of G-C, A-U, and C-G base pairs, respectively) can stimulate ribosomal frameshifting by binding to rHP2, a model RNA hairpin structure in an mRNA, albeit with suboptimal efficiency, due to its significantly weakened Q*C-G triple formation. We hypothesize that incorporating s2U adjacent to Q may offer unique stacking and hydrogen bonding interactions facilitating the development of isoenergetic dbPNA-based probes binding toward dsRNAs with varied sequences. In this study, we investigate how incorporating s2U adjacent to Q residues in P3 influences its binding to rHP2. Bio-layer interferometry (BLI) and non-denaturing polyacrylamide gel electrophoresis (PAGE) analyses demonstrate that substituting T with s2U at the N-terminal position adjacent to Q (P3-2QT) enhances binding affinity by [~]10-fold compared to unmodified P3, whereas C-terminal substitution (P3-TQ2) yields only a 2-fold improvement. Consistent with these findings, a cell-free dual-luciferase reporter assay reveals that P3-2QT significantly increases ribosomal frameshifting efficiency compared to P3 and P3-TQ2. Molecular dynamics simulations further indicate that P3-2QT maintains enhanced PNA-PNA stacking stability, particularly between s2U3 and Q4, suggesting a structural basis for its superior activity. Intriguingly, analogous s2U substitution in the P5 oligomer with the Q replaced by L does not confer a comparable enhancement in binding to the target RNA (rHP1) and frameshifting stimulation, highlighting the context-dependent nature of this modification. To assess the broader applicability of the s2U-Q motif, we examined its effect in dbPNAs targeting the RNA panhandle structure of influenza virus A and precursor microRNA-21, respectively. Both PAGE and BLI data confirm that s2U incorporation improves binding affinity, reinforcing the generality of this strategy. These findings underscore the potential of sequence-dependent uracil thiolation in optimizing triplex-forming dsRNA-binding PNAs, warranting further exploration of modified nucleobase designs to enhance their binding and functional properties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/662161v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15d86aborg.highwire.dtl.DTLVardef@1347369org.highwire.dtl.DTLVardef@852040org.highwire.dtl.DTLVardef@84b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThiolation of uracil upstream of Q base in PNA markedly enhances triplex binding affinity and enables isoenergetic and orthogonal targeting/activation. C_LIO_LIN-terminal s2U modification adjacent to Q residues increases PNA-dsRNA binding by [~]10-fold and significantly boosts ribosomal frameshifting efficiency. C_LIO_LIBiophysical assays and molecular dynamics simulations reveal that thiolation improves PNA stacking stability and slows dissociation, thereby enhancing functional activity toward structured RNA targets. C_LIO_LIThe general applicability of s2U modification is demonstrated with influenza A virus RNA panhandle structure and precursor micoRNA-21 targets, underscoring its broad potential for optimizing PNA-based therapeutics and biotechnological tools. C_LI

biochemistry↗

bioRxiv2025

PathoEye: a deep learning framework for the whole-slide image analysis of skin tissue

ObjectiveTo provide an interpretable computational framework for the examination of whole-slide images (WSI) in skin biopsies, PathoEye focuses on the dermis-epidermis junctional (DEJ) areas, also known as the basement membrane zone (BMZ), to enrich the pathological features of various skin diseases. MethodsWe presented PathoEye for WSI analysis in dermatology, which integrates epidermis-guided sampling, deep learning and radiomics. It enables unsupervised semantic segmentation of the BMZ and extracts distinct features associated with various skin conditions. ResultsPathoEye performs comparably with existing methods in binary classification tasks, while outperforming them in multi-classification tasks involving different skin conditions. It enables the investigation of histopathological aberrations in aged skin compared with young skin. Additionally, it highlighted the texture changes in the BMZ of young skin compared with aged skin. Further experimental analyses revealed that senescence cells were enriched in the BMZ, and the turnover of basement membrane (BM) components, including COL17A1, COL4A2, and ITGA6, was increased in aged skin. ConclusionPathoEye is a comprehensive tool for characterizing the unique features of different skin conditions associated with BMZ, thereby ensuring its potential applications in skin disease diagnosis and treatment planning.

bioinformatics↗

bioRxiv2025

Geno-pheno characterization of crop rhizospheres: An integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture

1In this study, we examined phenotypic and compositional patterns in rhizosphere microbial communities across conventionally and organically managed farms to assess impacts on soil microbiomes. We employed newly developed single-cell Raman microspectroscopy (SCRS)-based community phenotypic profiling analysis with microbiome 16S rRNA gene amplicon sequencing to compare the soil microbial communities of alfalfa, carrot, corn, lettuce, potato, soybean, squash, tomato, triticale, wheat, oat, and pea grown under either conventional or organic agriculture across farms in New York State (USA). Distinct microbiome clustering patterns indicated that organic and conventional production methods imposed strong selective pressures, shaping microbial assemblages within each group more distinctly than site or plant species variations. Using SCRS-based microbial phenotyping, we identified distinct microbial adaptations in agricultural soils, with organic systems favoring lipid-accumulating phenotypes for energy storage and stress resilience in low-input environments, while higher nutrient availability in conventional systems promoted carbon-rich phenotypes, enhancing rapid carbon assimilation and biomass production. Through network analysis of ecological hub species, we identified Pseudomonas, a plant growth-promoting rhizobacteria (PGPR), along with several nitrogen-fixing prokaryotes as core members within conventional agricultural systems. In contrast, organically managed soils featured PGPR taxa from the Bacilli class and contained microorganisms carrying antibiotic resistance genes, potentially indicating the presence of antibiotic resistance genes within organic agricultural environments. Overall, we found that the novel inclusion of microbial phenotyping methods, such as SCRS, can describe unique linkages between microbiome structure and their physiology that are distinctive between conventional and organic agricultural systems. 2 ImportanceOur study successfully integrated single-cell Raman microspectroscopy and amplicon sequencing, two established techniques for analyzing microbial communities and their functions, enabling a link between genotype and phenotype to better characterize ecosystem dynamics. While few studies have explored microbial phenotypes alongside community composition to infer agricultural management differences, our research offered key insights into functional relevance of microbial communities to agricultural practices, demonstrating how management strategies influenced microbial adaptation. These findings advance microbial ecology research, demonstrating how agricultural management strategies influence microbiome structure and function, reinforcing the importance of phenotypic profiling in sustainable agriculture.

ecology↗

bioRxiv2025

Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis

The increasing scale and complexity of neuroimaging datasets aggregated from multiple study sites present substantial analytic challenges, as existing statistical analysis tools struggle to handle missing voxel-data, suffer from limited computational speed and inefficient memory allocation, and are restricted in the types of statistical designs they are able to model. We introduce Image-Based Meta- & Mega-Analysis (IBMMA), a novel software package implemented in R and Python that provides a unified framework for analyzing diverse neuroimaging features, efficiently handles large-scale datasets through parallel processing, offers flexible statistical modeling options, and properly manages missing voxel-data commonly encountered in multi-site studies. IBMMA produced stronger effect sizes and revealed findings in brain regions that traditional software overlooked due to missing voxel-data resulting in gaps in brain coverage. IBMMA has the potential to accelerate discoveries in neuroscience and enhance the clinical utility of neuroimaging findings.

neuroscience↗

bioRxiv2025

Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm differentiation

The development of multicellular organisms requires precise coordination between cell division and differentiation. Cell division generates the necessary number of cells, while differentiation creates distinct cell identities, forming tissues and organs. The transcription factors SOX2 and PAX6 specify neuroepithelial cells, the earliest neural progenitor cells (NPCs) during brain development. How lineage specification is coordinated with the cell cycle is not fully understood. Here, we show that PAX6 expression occurs during a narrow time window--between 48 and 72 hours--after neural induction of human embryonic stem cells (ESCs). Flow cytometry analyses and time-lapse imaging further show that PAX6 expression starts during the G2 phase of the cell cycle. We identify a novel 500-bp PAX6 promoter that drives its G2-specific expression. PAX6 expression is independent of known regulators of cell-cycle-dependent transcription, suggesting the existence of a novel mechanism. S-phase block by hydroxyurea prevents PAX6 expression and differentiation into NPC. Thus, NPC fate specification is coupled to cell cycle progression and occurs after the completion of DNA replication. This post-replicative lineage commitment ensures the creation of two daughter cells of identical cell fate following cell division.

cell biology↗

bioRxiv2025

Cold-induced suppression of myogenesis in skeletal muscle stem cells contributes to delayed muscle regeneration during hibernation

Mammalian hibernators experience profound cold stress and prolonged physical inactivity during torpor periods; however, it is unclear how skeletal muscle stem cells (satellite cells; SCs) respond to these challenges. In this study, we demonstrate that SCs from a mammalian hibernator, Syrian hamster exhibit remarkable resistance to cold-induced cell death, which is associated with intrinsically higher expression of the antioxidant enzyme GPX4, which likely contributes to the suppression of ferroptosis. RNA-seq analysis revealed widespread downregulation of myogenesis-related genes following cold exposure, which suggests suppression of the myogenic program. Consistently, SCs exposed to cold stress exhibited reduced activation and differentiation capacities upon subsequent rewarming, with an increased number of quiescent Pax7-positive/MyoD-negative cells. Muscle regeneration was markedly delayed during hibernation, accompanied by decreased SC activation and macrophage infiltration, suggesting that cold-induced suppression of SC function underlies limited regenerative capacity in hibernating hamsters. Our results provide insight into the unique physiology of mammalian hibernators: SC viability is preserved, whereas regenerative activity is selectively suppressed during hibernation.

physiology↗

bioRxiv2025

A hierarchy of time constants and reliable signal propagation in the marmoset cortex

A hierarchy of timescales in the cerebral cortex is functionally desirable for rapid information processing in sensory areas and slow time integration in association areas. Here, through an analysis of electrocorticography (ECoG) data, we identified a timescale hierarchy in the neocortex of marmoset, a primate species commonly used in neuroscience. Constrained by the anatomical and electrophysiological data, we developed a multi-regional model of the marmoset neocortex that captures the observed timescale hierarchy phenomenon. Furthermore, we used the model to investigate how the neocortex reconciles information integration on distinct timescales in local areas with reliable signal propagation globally across regions. We found that a near-criticality state is optimal for both localized signal integration within areas and reliable signal propagation across areas in the multi-regional neocortex. Our model also mechanically explains recent experimental observations that the structural and functional connectivities are less correlated in association areas than in sensory areas.

neuroscience↗