Biology subjects

Wu, Q.

Publications and source records attributed to Wu, Q..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

An activated wheat CCG10-NLR immune receptor forms an octameric resistosome

Nucleotide-binding and leucine-rich repeat (LRR) receptors (NLRs) are widespread intracellular immune sensors across kingdoms. In plants, the G10-type coiled-coil (CCG10)-NLRs form a distinct phylogenetic clade that remains poorly characterized. Here, we identified a gain-of-function (GOF) mutant of Wheat Autoimmunity 3 (WAI3), designated WAI3GOF, which encodes a constitutively activated CCG10-NLR protein due to an amino acid substitution. Cryo-EM structural analysis revealed that activated WAI3 assembles into a distinctive octameric resistosome. Arabidopsis RPS2, another CCG10-NLR, also forms an octamer, indicating a conserved structural property across monocot and dicot plants. The WAI3 resistosome mediates a prolonged and sustained increase in cytosolic calcium influx, facilitated by a unique channel architecture arising from its divergent CC domain configuration. Notably, this domain arrangement may be shared by many plant NLRs that lack the conserved EDVID motif in their CC domains. Our findings uncover a previously uncharacterized resistosome structure and provide insights into plant immune receptor plasticity.

plant biology↗

bioRxiv2025

Aperiodic and Periodic EEG Component Lifespan Trajectories: Monotonic Decrease versus Growth-then-Decline

1.1Unraveling the lifespan trajectories of human brain development is critical for understanding brain health and disease. Recent research demonstrates that electroencephalography signals are composed of periodic and aperiodic components reflecting distinct physiological substrates. This dissociation raises the possibility that they follow different developmental tendencies. Here, we delineate the lifespan trajectories of aperiodic and periodic neural oscillations using a large international cohort (N=1,563, ages 5-95, resting state, eyes closed). We reveal two fundamental developmental patterns: a Monotonic decrease in aperiodic activity and a Growth-and-Decline pattern for periodic activity. Both components have inflections around age 20 and transition to a stable senescent phase around age 40. Spatially, anterior regions mainly exhibit aperiodic activity, while periodic activity concentrate on posterior regions and these patterns remain stable throughout life. Crucially, multimodal analysis shows these trajectories map onto distinct biological substrates. The periodic components Growth and Decline trajectory aligns with GABAergic function and myelination. In contrast, the monotonically decreasing trajectory of aperiodic activity mirrors fundamental biomarkers of biological aging, such as DNA methylation and telomere length. Transforming age to a logarithmic scale simplifies these nonlinear trajectories into a linear decreasing and a piecewise concave linear model for aperiodic and periodic components. This form provides a robust and parsimonious framework for quantifying maturation and identifying neurological deviations. HighlightsO_LIWe delineate distinct lifespan trajectories of aperiodic and periodic neural activity in a large-scale international cohort (N=1,563, ages 5-95). Aperiodic activity undergoes a Monotonic Decrease with age. In contrast, periodic activity follows a Growth-then-Decline trajectory, peaking in early adulthood. C_LIO_LIBoth trajectories feature a critical transition around age 20 and stabilize into a protracted senescent phase from approximately 40 onward. C_LIO_LIThese neural trajectories map onto distinct biological substrates: periodic activity tracks integrative functions (myelination, GABAergic, and aperiodic decline mirrors fundamental aging processes (DNA methylation). C_LIO_LIA stable pattern observed throughout the lifespan is the spatial segregation of neural activity, where aperiodic signals are dominant in anterior regions and periodic signals are concentrated in posterior ones. C_LIO_LILogarithmically transforming age linearized the developmental trajectories, yielding a monotonic decline for the aperiodic component and a concave piecewise for the periodic one. This process establishes robust linear norms for the personalized assessment of brain dysfunction. C_LI

neuroscience↗

bioRxiv2025

OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section

Spatial transcriptomics enables in situ mapping of gene expression, yet no current platform provides single-cell, same-section integration with metabolomics, limiting direct links between transcriptional programsand metabolic phenotypesin native tissue. We present OpenFISH, a rapid, imaging-based spatial transcriptomics method operable on standard microscopes, requiring no proprietary hardware, and fully compatible with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). OpenFISH resolves hundreds of transcripts at subcellular resolution within 24 h and can be performed after MALDI-MSI, preserving metabolite distributions for cell-accurate co-registration on the same section. In mouse brain, integration with MALDI-MSI resolved metabolic heterogeneity at the level of individual cells. OpenFISH also quantified cell type-specific transcriptional activation of transposable elements after systemic lipopolysaccharide (LPS) challenge and detected disrupted spatial organization of D1 striatal neurons in Reeler mutants. Benchmarking showed performance comparable to or exceeding commercial platforms at [~]0.5% of per-sample cost. By enabling same-section, near-single-cell co-mapping of transcripts and metabolites in an accessible workflow, OpenFISH provides a scalable framework for high-content spatial multi-omics across neuroscience, immunology, cancer biology, and beyond.

molecular biology↗

bioRxiv2025

An evolutionary leap in plant reproduction: From archegonia and motile sperm to embryo sacs and pollen tubes

The transition of plants from water to land marks a pivotal step in their evolutionary history, with the change in reproductive mode being the most fundamental. This change freed plant reproduction from aquatic dependence, fostering terrestrial lifes prosperity. Key to the shift from archegonial to embryo sac reproduction are pollen tube emergence and female gametophyte changes, though their evolutionary trajectories and mechanisms remain unclear. Ginkgo, a basal gymnosperm, occupies a pivotal position in this transition, retaining motile sperm, simplified archegonia, and primitive pollen tubes, making it an ideal model. To study how the transition between these two reproductive modes occurred, we collected transcriptome data from the reproductive organs of Ginkgo and evolutionarily representative species. Our findings reveal the MYB98-CRP-ECS module- critical for angiosperm pollen tube guidance--in Ginkgos mature archegonia, with pollen tubes containing guidance components. While egg cells are transcriptionally and functionally conserved across land plants, changes in the cell fate of other female gametophyte component cells drove the shift from archegonia to embryo sacs. Pollen tubes may originate from fern male gametophyte internalization and modification. These findings clarify the evolutionary path and molecular basis of this major reproductive transition.

plant biology↗

bioRxiv2025

Epicardial extracellular vesicles modulate gene expression following ischemia-reperfusion injury in heart-on-a-chip

The epicardium is an essential regulator of cardiac development, homeostasis, and injury, yet the composition and impacts of epicardial cell-secreted extracellular vesicles (EVs) remain incompletely understood. Here, we harness an epicardial Biowire platform integrating human stem cell derived epicardial cells with functional myocardium and apply transcriptomics to reveal enriched EV transport in tissues containing epicardial cells. Profiling epicardial-EVs identified key miRNAs and their conservation through stimulated epithelial-to-mesenchymal transition. Supplementation of epicardial-EVs to tissues undergoing ischemia-reperfusion injury influenced gene expression associated with reduction of extracellular matrix remodeling, fibroblast activation, and suppression of cell-ECM interactions. Correlation of EV-miRNAs with mRNA targets highlighted the role of miR-30d-5p, miR-9-5p, miR-16-5p, and the let-7 family in moderating deleterious fibrotic activation and matrix remodelling during myocardial injury in vitro. TeaserCells from the hearts outer surface secrete tiny packages of biomolecules that influence how the heart responds to injury

bioengineering↗

bioRxiv2025

Model of leaf biomass partitioning coefficient in different leaf ranks of rapeseed (Brassica napus L.) main-stem

Leaf growth is a dynamic process, and understanding the number of main-stem leaves and the distribution of leaf biomass at different development stages can provide a theoretical basis for the development of functional-structural rapeseed model. To address the gap in research on the leaf biomass partitioning coefficient model in the crop growth model, we developed the leaf biomass partitioning coefficient model for the main-stem at different leaf ranks in rapeseed. The outdoor experiment with cultivars, Ningyou 18 (V1, conventional), Ningyou 16 (V2, conventional), and Ningza 19 (V3, hybrid), and designed treatment of cultivars x fertilizer x transplanting density in the 2012-2015 growth season. The model was fitted by calculating the ratio of leaf biomass at different leaf ranks on the main-stem to the total leaf biomass on the main-stem, and normalizing the leaf ranks into (0-1] interval. We parameterized the model variables to elucidate how cultivar and environmental conditions influence the leaf biomass partitioning coefficients for different leaf ranks. The descriptive models were validated with independent experimental data, the correlation (r) of simulation and observation values all greater than 0.9 with significant levels at p < 0.001. The absolute values of the average absolute difference (da) are all less than 0.011 g g-1. The ratio of da to the average observation (dap) for the normalized leaf rank, and leaf biomass partitioning coefficient at seedling stage, and budding and bolting stage, and blooming stage, and mature stage are 13.599%, 11.236%, 11.312%, 3.077%, and 8.661%, respectively. The RMSE values are all less than 0.032 g g-1. The models developed in this paper have good performance and reliability for predicting leaf biomass partitioning coefficient of main-stem at different leaf ranks in rapeseed. This study integrates the leaf morphology model of rapeseed with the rapeseed growth model through biomass partitioning, contributing to the development of the functional-structural rapeseed model.

bioinformatics↗

bioRxiv2025

A trade-off mechanism underpins the evolution of a young two-gene sex-determining system in plants

Sexual systems in animals and plants are remarkably diverse, with dioecy having evolved independently in numerous lineages. In plants, dioecy often evolved more recently than in the best-studied animal systems, making plants especially important for understanding how separate sexes evolved independently from functionally hermaphrodite ancestors. Despite long-standing theories of developmental trade-offs in sex allocation, the underlying genetic mechanisms remain elusive. Here, we show that the XY sex determination system in the dioecious plant species Eurycorymbus cavaleriei in Sapindaceae involves two Y-linked mutations that act jointly within the developmental male-female trade-off: YUN{Delta}, a truncated allele that lowers the dosage of the D-class MADS-box gene YUN, and SUNMAO, a novel sRNA locus that silences the X-linked SUN allele. In females, SUN stabilizes the HD-ZIP transcription factor KUN, which is a known sex determinant in another dioecious plant, thereby promoting femaleness by increasing YUN expression; loss of SUN expression, together with the effect of YUN{Delta}, shifts development toward males. Two interlocking regulatory loops in this "SKY" module (SUN-KUN-YUN) fine-tunes YUN dosage. This dioecious system in E. cavaleriei likely evolved by sequential mutations in genes acting in the predicted male-female trade-off system, with their close linkage reflecting a translocation, and later recombination-suppressing inversions.

plant biology↗

bioRxiv2025

Keystone Bacterial Taxa Drive Denitrification and N2O Emission via Adaptive Genomic and Metabolic Strategies in Contrasting Agricultural Soils

Soil denitrification mediated by microbial communities is a major driver of nitrous oxide (N2O) emissions, yet the regulatory roles of keystone taxa remain largely unexplored, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, providing a unique model system for disentangling microbial mechanisms underlying soil-specific denitrification dynamics. Here, we integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the above mentioned two contrasting agricultural soils, BS and FS. Structural equation modeling (SEM) and correlation analyses revealed that keystone taxa are significantly associated with soil denitrification rates and N2O emission patterns. Among these, Ramlibacter ASV104 was identified as a conserved keystone in both soils, exhibiting genomic potential for key denitrification genes (nirK/nirS/norB/nosZ) to mediate N2O turnover. In contrast, Ensifer ASV205 was a FS-specific keystone taxon, exhibiting strain-level niche specialization. Comparative genomics revealed that variations in denitrification gene composition and carbon-nitrogen metabolism enable different Ensifer strains to function either as N2O sources or sinks. This functional divergence was linked to their genomic plasticity and growth strategies under nutrient-rich conditions. Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study improves our understanding of the microbial mechanisms driving N2O emissions and provides a foundation for future strategies targeting microbial taxa to mitigate N2O emissions in agricultural soils. IMPORTANCEThis study provides new insights into the ecological complexity underlying soil N2O emissions by integrating strain-level diversity, genomic attributes, and microbial interaction networks. Key microbial taxa involved in denitrification and N2O emissions were identified in black soil and fluvo-aquic soil. By combining network-based ecological modeling and functional assays, it is revealed that taxa such as Ramlibacter ASV104 and Ensifer ASV205 play significant roles in regulating N2O emissions. Strain-level functional diversity within the keystone taxa of Ensifer ASV205 highlights their varying contributions to nitrogen cycling. Our findings provide a deeper understanding of the microbial mechanisms governing N2O emissions, offering valuable insights for developing microbial-based strategies to mitigate N2O emissions in agricultural soils in the future.

ecology↗

bioRxiv2025

Given the birds, where is the flock? Visual estimation of the location of collections of points

Many visual tasks resemble statistical judgments, estimating the center of a cloud of identical items for example. In statistical form, the observer sees a sample drawn from an invisible probability density function (PDF) : the observer attempts to estimate the location of the PDF. He receives larger rewards for lower variance. Optimal minimum variance estimators are different for different distributions. We evaluated performance for three location families (Gaussian, Laplacian, and Uniform). How does human perceptual organization stack up against optimal perceptual estimation? We found that observers adopted distinct estimators for distinct distribution families, each approximately minimizing variance for its family. To explain observers ability to adapt to different distributional families, we propose that observers adopt a single estimator based on clusters in the sample. This Visual Cluster Model accounted for performance across distributions, suggesting that perceptual grouping first aggregates parts into clusters and only then into a whole. Significance statementImagine a flock of birds. We can predict where additional birds might appear by estimating the probability density function (PDF) of the birds. We compared performance in estimating the location of PDFs drawn from Gaussian, Laplacian or Uniform location families, rewarding lower variance. The optimal estimators for the three families are different. Observers approximately minimized variance for each condition and used different estimators for different families. How could they do so? We propose that observers use a single estimator based on sample clusters: perceptual grouping first aggregates parts into clusters and only then into a whole.

neuroscience↗

bioRxiv2025

A Novel 'Three-in-one' Mucosal Vaccine Elicits Broad Protection against Three Distinct Clusters of ACE2-using Sarbecoviruseses

With the persistent risk of coronavirus epidemics, the development of universal vaccines is urgently needed and challenging to achieve. In this study, we aimed to design a multivalent immunogen to provide broad protection against diverse ACE2-using sarbecoviruses, which pose a significant threat to global health. Our analysis revealed that the receptor-binding domains (RBDs) of ACE2-using sarbecoviruses segregate into three antigenically distinct clusters, including one cluster that encompasses viruses related to SARS-CoV-2. Based on these findings, we engineered a three-in-one immunogen, designated as 3Rs-NC, which incorporates representative RBDs from all three clusters. 3Rs-NC preserved the natural epitope configuration of each monomeric RBD component, and efficiently elicited high levels of neutralizing antibodies against representative viruses and closely related sarbecoviruses. When administered intranasally with flagellin-based mucosal adjuvant KFD, 3Rs-NC induced robust and durable RBD-specific serum IgG and mucosal IgA responses in mice. Furthermore, KFD-adjuvanted 3Rs-NC conferred sustained protection in both the upper and lower respiratory tracts against SARS-CoV-2 Omicron BA.1 and SARS-like coronavirus WIV1. Additionally, 3Rs-NC immunization protected mice from lethal challenge of SARS-like coronavirus rRsSHC014S, with more efficient protection observed in female mice than male mice. This needle-free three-in-one vaccine represents a promising candidate for a universal mucosal vaccine against ACE2-using sarbecoviruses and could serve as a foundational component of three-in-one vaccine series to form a comprehensive coronavirus vaccine package. HighlightO_LInovel three-in-one immunogen 3Rs-NC induced a high level of neutralizing antibodies against three distinct ACE2-using Sabecovirus clusters. C_LIO_LIadministration of 3Rs-NC plus KFD adjuvant (3Rs-NC+KFDi.n) generated potent and long-lasting RBD-specific serum IgG and mucosal IgA. C_LIO_LI3Rs-NC+KFDi.n provided long-term protection in both upper- and lower-respiratory tracts in mice. C_LIO_LI3Rs-NC+KFDi.n could serve as a foundational component for next-generation coronavirus vaccine strategies. C_LI

immunology↗

bioRxiv2025

Microbiome-Dependent Functional Responses to Structurally Distinct Oligosaccharides Revealed by Metaproteomics

Dietary oligosaccharides are prebiotics that fuel gut microbes, but individual microbiomes may respond differently depending on oligosaccharide structures as well as microbiome composition and function. The extent to which specific gut microbial communities exhibit personalized functional responses to distinct oligosaccharides remains underexplored. We applied a standardized ex vivo microbiome culture, called RapidAIM, coupled with metaproteomics to examine how six structurally diverse oligosaccharides affect the gut microbiota functional response. Our study shows that while human gut microbiomes share some commonalities in utilizing oligosaccharides (e.g. prioritizing dietary fibers over mucin), the fine-scale metabolic and taxonomic responses are highly individualized. Such findings underscore the importance of considering personal microbiome profiles when predicting the outcome of prebiotic interventions. In a broader context, our metaproteomic approach provides a framework for identifying optimal prebiotic choices tailored to individual microbiomes. Ultimately, understanding these personalized responses could inform precision nutrition strategies.

microbiology↗

bioRxiv2025

Small RNA ASpks2 Promote Mycobacterium tuberculosis Survival in Macrophages via Targeting Polyketide Synthase 2

Mycobacterium tuberculosis is the causative pathogen of human tuberculosis and a leading cause of death worldwide attributed to a single infectious agent. While small non-coding RNAs (sRNAs) have emerged as key regulators of bacterial pathogenicity, their specific roles and mechanisms in M. tuberculosis remain poorly understood. Here, we employed label-free quantitative proteomics, parallel reaction monitoring, and sRNA-seq analyses to identify proteomic differences between the virulent H37Rv and attenuated H37Ra strains. Bioinformatic analysis revealed significant enrichment of differentially expressed proteins involved in lipid metabolism and fatty acid biosynthesis, key pathways linked to M. tuberculosis virulence. We identified a novel sRNA, ASpks2, which was significantly downregulated in H37Rv. Functional validation demonstrated that ASpks2 directly targets the polyketide synthase 2 (pks2), modulating its expression to enhance M. tuberculosis survival in human macrophages THP-1 cells. By correlating the omics data with functional studies, this study identified a novel sRNA and its regulatory network in M. tuberculosis, which provides novel insight into the molecular pathogenesis of M. tuberculosis and may serve as a basis for the development of targeted therapies.

microbiology↗

bioRxiv2025

Structural Basis for Cas9-Directed Spacer Acquisition in Type II-A CRISPR-Cas Systems

CRISPR-Cas systems confer prokaryotic adaptive immunity by integrating foreign DNA (prespacers) into host arrays. Type II-A systems employ Cas9 for protospacer adjacent motif (PAM) recognition and coordinate with Csn2 and the Cas1-Cas2 integrase during spacer acquisition, yet their structural basis remains unresolved. Here, we report cryo-EM structures of the Enterococcus faecalis Cas9-Csn2-Cas1-Cas2 supercomplex in apo and DNA-bound states. The apo-state structure (Cas92-Csn28-Cas18-Cas24) adopts a resting conformation, with Cas9 locked in a nuclease-inactive state and Cas1-Cas2 sterically blocked from prespacer loading. Upon DNA engagement, Cas9 undergoes a conformational transition, forming a prespacer catching complex that threads the DNA through Csn2s central channel. This architecture enables Cas9 to interrogate the PAM sequence while sliding along the DNA, with Cas9 and Csn2 jointly define a 30-bp DNA segment which matches the prespacer length. Subsequent dissociation of Cas9 triggers a structural reconfiguration of the Csn2-Cas1-Cas2 assembly. The PAM-proximal DNA becomes accessible, and Cas1-Cas2 relocates to bind to the exposed DNA, enabling further prespacer processing and directional integration. These findings reveal how Cas9 collaborates with Csn2 and Cas1-Cas2 to couple PAM recognition with prespacer selection, resolving the dynamic structural transitions that ensure fidelity during type II-A CRISPR adaptation.

molecular biology↗

bioRxiv2025

AID-mediated protein knockdown reveals the requirement of NANOS2 in prenatal gonocytes for establishing functional spermatogonial stem cells

The RNA-binding protein NANOS2 plays a crucial role in male gonocyte development and the maintenance of spermatogonial stem cells. In the absence of the Nanos2 gene (Nanos2-KO), germ cells fail to enter G0 arrest and initiate the male differentiation program (including DNA methylation and the piRNA pathway), ultimately undergoing apoptosis before birth. Nanos2 transcription begins at embryonic day 12.5 (E12.5) and terminates at E15.5. However, as the NANOS2 protein continues to be stably expressed beyond E15.5, it is important to elucidate the function of NANOS2 during this post-E15.5 period in germ cell fate determination. To address the functional significance of sustained NANOS2 protein expression, we employed an auxin-inducible degron (AID2) system to achieve rapid degradation of NANOS2 after E15.5. Within 24 hours of 5-Ph-IAA administration, NANOS2 protein was efficiently depleted. As a result, germ cells resumed the cell cycle, exhibited aberrant gene expression patterns similar to Nanos2- KO gonocytes, and underwent apoptosis if NANOS2 depletion occurred at E15.5 or E16.5. Although some surviving cells initiated spermatogenesis and expressed PLZF and GFRA1 after birth, further spermatogenesis was not observed. These findings reveal that sustained NANOS2 protein expression during the embryonic stage is essential for establishing functional spermatogonial stem cells, highlighting a previously unrecognized regulatory mechanism in male germ cell development.

developmental biology↗

bioRxiv2025

ZNF638 represses the transcription of HBV closed circular DNA involving HUSH complex-mediated histone modifications of epigenetic silencing

Hepatitis B virus (HBV) infection poses a critical threat to public health burden worldwide. As the major template of viral transcription, the covalently closed circular DNAs (cccDNAs) of HBV was known to form microchromosomes and interact with various host proteins. In the present study, ZNF638 was found to significantly reduce the transcription of HBV into pgRNAs, and subsequently reduce cccDNA formation and viral propagation. We discovered that ZNF638 was able to bind the preS and S gene regions of HBV, repressing the transcription of cccDNA upon increased modification of H3K9me3 mediated by SETDB1. This epigenetic silencing of cccDNA transcription was further demonstrated to involve the activity of HUSH, a multi-protein complex to mediate epigenetic modifications of histone into suppressed nucleosomes. In in vivo models, we evaluated the effects of ZNF638 deficiency on HBV-targeting siRNA therapy. A significant reduction of the efficacy was observed in animals with reduced ZNF638 expression. In summary, we report that ZNF638 is a potent host factor to repress the transcription of HBV DNAs and to attenuate HBV infection. The role of ZNF638 on HBV repression involves its binding to cccDNA at specific regions for recruiting HUSH complex to write H3K9me3 histone marks for epigenetic silencing. ZNF638 serves as a critical host factor to associate HBV infection and disease progression. Additionally, ZNF638 serves as a potential indicator to predict the outcome of HBV-targeting siRNA therapy.

biochemistry↗

bioRxiv2025

EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/649266v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@14dd0b1org.highwire.dtl.DTLVardef@1c04a79org.highwire.dtl.DTLVardef@159894dorg.highwire.dtl.DTLVardef@1454a01_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG HighlightsO_LIEasyMultiProfiler provides unified integration of microbial multi-omics data C_LIO_LIEasyMultiProfiler enables natural language-style analytical workflows C_LIO_LIEasyMultiProfiler solves key challenges in standardization and reproducibility C_LIO_LIEasyMultiProfiler extracts meaningful biological insights efficiently C_LI Host-microbiome interactions are crucial in maintaining physiological homeostasis and influencing disease progression. While traditional microbiome research, focused on microbial diversity and abundance, provided essential frameworks, the integration of multi-omics approaches established a far more comprehensive, systems-level understanding of microbiome functionality. However, significant methodological challenges in multi-omics data integration remain, including inconsistent sample coverage, heterogeneous data formats, and complex downstream analytical workflows. These challenges impact the reproducibility and reliability of results and underscore the critical requirement for developing standardized, systematic workflows. Thus, we developed the EasyMultiProfiler (EMP) workflow, a streamlined and efficient analytical framework for multi-omics data analysis. EMP provides a comprehensive infrastructure based on the SummarizedExperiment and MultiAssayExperiment classes, creating a unified framework for storing and analyzing omics data. The frameworks architecture comprises five interconnected functional modules: data extraction, preparation, support, analysis, and visualization. These modules are smoothly integrated into natural language-style analytical workflows, offering users an efficient and standardized solution for multi-omics analysis. EMP addresses critical challenges in multi-omics data analysis, including data integration, workflow standardization, and result reproducibility. The platforms modular architecture and intuitive interface provide researchers and clinicians with a robust, flexible workflow to systematically extract biologically relevant insights from complex multi-omics datasets.

bioinformatics↗

bioRxiv2025

Prevention of Transgene Silencing During Human PluripotentStem Cell Differentiation

While high and stable transgene expression can be achieved in undifferentiated pluripotent stem cells, conventional transgene expression systems are often silenced upon differentiation. Silencing occurs with both randomly integrated transgenes, introduced via transposase or lentiviral methods, and with transgenes targeted to specific genomic sites, including at commonly used safe harbor loci. The challenge to robustly express experimental transgenes in differentiated pluripotent stem cells is a major bottleneck in the field for applications such as CRISPR screening. Here, we conducted a comparative analysis to systematically evaluate the impact of various promoters, transcriptional regulatory elements, insulators, and genomic integration sites on transgene silencing during neuronal differentiation. Our findings reveal that specific combinations of promoters and transcriptional stability elements are able to prevent transgene silencing during differentiation, whereas chromatin insulators had less impact on silencing and three novel safe harbor integration sites performed similarly to the CLYBL locus. Guided by these insights we developed the PiggyBac vector TK4, which showed complete resistance to transgene silencing across various neuronal and microglial differentiation protocols from six different pluripotent stem cell lines, as independently confirmed by seven different laboratories. This construct will be highly useful for assays requiring stable transgene expression during differentiation, and holds the potential for broad applications in various research fields.

neuroscience↗

bioRxiv2025

A reference genome assembly of the alpine forage grass Elymus nutans

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans, representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred [~]3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies.

plant biology↗