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Niu, W.

Publications and source records attributed to Niu, W..

At least 19 recordsLinked to original sources

Synaptic microRNA dysregulation orchestrates aberrant glutamatergic transmission in a human neuronal model of 22q11.2 deletion syndrome

22q11.2 Deletion Syndrome (22q11DS), the most prevalent chromosomal microdeletion disorder in humans (incidence ~1 in 4,000 live births), arises from hemizygous deletions of a 1.5-3.0 Mb region on chromosome 22. Notably, 20-30% of individuals with 22q11DS develop schizophrenia (SCZ) by early adulthood, making 22q11DS one of the strongest genetic risk factors for SCZ. However, the mechanisms by which the 22q11.2 deletion perturbs neuronal function and drive psychotic manifestations in 22q11DS remain poorly defined. In this study, we generated human 2D cortical neurons and 3D cortical organoids from induced pluripotent stem cells (iPSCs) derived from clinically well-characterized individuals with 22q11DS. Cellular and electrophysiological analyses revealed that 22q11DS neurons exhibit hyperexcitability, reduced glutamatergic synaptic transmission, and impaired homeostatic synaptic plasticity, which are pathophysiological hallmarks that may be relevant to the clinical, cognitive, and psychophysiological profiles of patients. Transcriptomic profiling of neurons and synaptosomes from 22q11DS cortical organoids uncovered dysregulated immune pathways and synaptic gene networks. Integrative mRNA-microRNA network analysis identified synergistic downregulation of hsa-miR-185-5p and hsa-miR-128-3p at synapses, driving aberrant regulation of immune and synaptic transcripts. Experimental knockdown of these microRNAs in control neurons recapitulated the molecular and functional phenotypes of 22q11DS neurons, thereby establishing a mechanistic link to synaptic dysfunction and impaired plasticity. Collectively, these findings delineate a multimodal mechanistic framework that bridges genetic vulnerability, synaptic pathology, and psychosis penetrance in 22q11DS, positioning dysregulated synaptic microRNAs as nodal regulators of neurodevelopmental networks and potential therapeutic targets.

neuroscience↗

A glial source of noradrenaline shapes synaptic integration and motor adaptation

Noradrenaline is a major neuromodulator that shapes neural circuit dynamics and behavior. Prevailing models attribute noradrenergic supply exclusively to long-range inputs from distant nuclei. Yet noradrenergic input can be weak in regions that nonetheless show marked noradrenergic modulation, suggesting additional sources. This mismatch is salient in the cerebellum, where noradrenaline influences behavior despite sparse innervation. Here, we identify Bergmann glia, radial cerebellar astrocytes, as a source of noradrenaline. Using two-photon imaging and cell-type-specific genetic manipulations, we show that Bergmann glia can synthesize and release noradrenaline through a calcium-dependent mechanism requiring the vesicular monoamine transporter VMAT2. Glia-derived noradrenaline modulates synaptic integration in Purkinje neurons and is required for motor adaptation. Together, these findings identify a glial pathway that complements the canonical long-range view of noradrenaline supply.

neuroscience↗

Visualization of the architecture of flexible chromatin and the binding of chromatin regulators

Chromatin organization plays a central role in regulating genome accessibility and gene expression in eukaryotic cells. However, the inherent flexibility and structural heterogeneity of chromatin pose significant challenges for its structure determination. Here, we use a Nuc-back strategy with cryo-electron tomography (cryo-ET) and subtomogram averaging methods to visualize chromatin at the nucleosome level by averaging nucleosome at moderate-to-high resolution, classifying the fundamental unit of chromatin, i.e., nucleosome, into distinct classes, and linking different nucleosome structures to chromatin architecture. We reveal that nucleosome heterogeneity is a key factor in chromatin flexibility which disrupts interactions between nucleosomes. In addition, this strategy allows for the localization and visualization of chromatin regulators and their structure on chromatin. These results provide a foundation for future research in 3D genome and epigenetic process visualization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/730377v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b003c8org.highwire.dtl.DTLVardef@c86543org.highwire.dtl.DTLVardef@7033f5org.highwire.dtl.DTLVardef@635485_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Sharp and Fast Dynamic Extraction and Tracking of Emitted Cellular Transients

Genetically encoded fluorescent sensors have expanded our ability to image cellular activity and transmitter release. Yet, sparse and low-salience events remain difficult to resolve against complex and fluctuating fluorescence backgrounds. Here we introduce DETECT, Dynamic Extraction and Tracking of Emitted Cellular Transients, which combines adaptive background suppression, probabilistic classification and multi-object tracking to extract fluorescence events while preserving their identity. Across synthetic datasets, DETECT improved detection and segmentation accuracy and reduced computational cost relative to established event-based methods. We validated DETECT across confocal, two-photon and miniscope imaging, ex vivo and in vivo, using calcium indicators and monoamine sensors. Beyond its technical performance, DETECT extends event-based analysis to low-salience fluorescence signals while resolving events spanning broad ranges of amplitude, morphology and dynamics. By resolving spontaneous dopamine and noradrenaline signals as distinct, trackable release events, DETECT reveals the spatiotemporal organization of neuromodulatory activity and provides a broadly applicable approach to quantitative fluorescence analysis.

neuroscience↗

Convergent effects of neurodevelopmental disorder-associated variants at mitochondria

Investigations into the molecular pathogenesis of clinically defined neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD) and schizophrenia (SCZ) have produced evidence implicating dysfunctional mitochondrial metabolism. However, the functional connection between risk variants and mitochondrial proteins largely remains unclear. We tested the hypothesis that proteins encoded by NDD-associated copy number variants (CNVs) and SCZ risk genes are enriched within the mitochondrial interactome. We found that NDD- and SCZ-associated genes exhibit mitochondrial association comparable to their overlap with synaptic proteins, with interaction networks converging most strongly on mitochondrial translation. Two high-risk CNVs, the 3q29 deletion (3q29Del) and the 22q11.2 deletion (22q11Del), confer similar risks for ASD and SCZ and have independently been linked to mitochondrial phenotypes. To test whether these CNVs produce convergent effects on mitochondrial proteins in developing human neural tissue, we generated an isogenic series of 3q29Del and 22q11Del induced-pluripotent stem cells (iPSCs) and differentiated them into forebrain cortical organoids. Quantitative proteomic analysis showed high similarity in the profiles of dysregulated proteins in 3q29Del and 22q11Del compared to isogenic controls. Enrichment analysis of proteins altered in both variants revealed significant convergence on the mitochondrial ribosome and translation machinery. Furthermore, manipulation of mitochondrial translation elicited similar proteomic and functional responses in organoids and neural progenitor cells across both CNVs. These findings indicate that NDD-associated genes have rich interactions with mitochondrial proteins and that two of the strongest risk factors for NDDs may similarly disrupt neural mitochondrial metabolism through impaired mitochondrial translation.

neuroscience↗

Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains. We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a [~]8% increase to the available genomic data for P. putida. Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes such as PcaI and PcaJ revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

bioengineering↗

Cryopreservation of Human Cortical Organoids Using Vitrification.

Cryopreservation at ultra-low temperatures is a valuable tool for preserving cells and tissues used in research. However, few protocols exist for the preservation of brain organoid models. Current methods for preserving human cortical organoids (hCOs) rely on conventional slow cooling approaches with organoids suspended in a medium containing a cocktail of cryoprotectants. In contrast, we have optimized a vitrification technique previously used to cryopreserve human embryos and oocytes for application to hCOs. We have successfully cryopreserved hCOs that were generated by two different protocols. The vitrified organoids demonstrate a growth rate, cytoarchitecture, cell type composition and electrical activity comparable to non-vitrified controls. Our hCO cryopreservation method provides a useful alternative approach for bio-banking and cross-institutional collaboration using cortical organoids as their model system. Highlights- Human pluripotent stem cell (hPSC) derived hCOs can be cryopreserved using vitrification. - Vitrified hCOs develop similarly to non-vitrified controls. - Vitrified hCOs can be stored long-term and shipped to other institutions. MotivationMany methods of cryopreservation have been developed for the maintenance of cell lines, organoid models and tissues. Most organoid models have been successfully preserved using conventional slow-cooling methods; however, human cortical organoids have been difficult to preserve. Our findings demonstrate that the vitrification of cortical organoids preserves their structure, cell type diversity and function upon rewarming and continued culture.

neuroscience↗

Temporal Configuration as a New Feature of Sound: Psychological and Neurophysiological Evidence, Cross-species Consistency and Underlying Neuronal Mechanisms

Natural sounds are defined not only by their spectral content but also by their fine temporal structure. Here we show that millisecond-scale temporal configuration--defined by the ordering of inter-click intervals (ICIs) within a click train--behaves as a distinct auditory feature, conserved across species and emerging hierarchically along the auditory pathway. Human listeners reliably discriminated click trains that shared the same average ICI but differed in temporal configuration, and these differences elicited robust mismatch negativity (MMN) responses in an oddball paradigm, indicating automatic cortical deviance detection. Awake rats showed analogous MMN-like ECoG responses to configuration changes, demonstrating cross-species generality. Neuropixels recordings along the inferior colliculus-medial geniculate body-primary auditory cortex (IC-MGB-A1) axis revealed minimal configuration sensitivity in IC, intermediate sensitivity in MGB, and strong stimulus-specific adaptation to temporal configuration in A1. Reversible cooling of auditory cortex reduced configuration sensitivity in MGB, implicating corticothalamic feedback in shaping thalamic representations. Layer-resolved analyses further showed that supragranular A1 neurons carry stronger configuration-specific adaptation than infragranular neurons. These findings identify temporal configuration as a feature-like dimension of sound and delineate a hierarchical, feedback-dependent IC-MGB-A1 circuit architecture for encoding fine temporal structure in the mammalian brain.

neuroscience↗

A signal of temporal integration in the human auditory brain: psychological insights, EEG evidence, and clinical application

Temporal integration, the process by which the auditory system combines sound information over a curtain period to form a coherent auditory object, is essential for coherent auditory perception, yet its neural mechanisms remain underexplored. We use a "transitional click train" paradigm, which concatenates two click trains with slightly differing inter-click intervals (ICIs), to investigate temporal integration in the human cortex. Using a 64-channel electroencephalogram (EEG), we recorded responses from 42 healthy participants exposed to regular and irregular transitional click trains and conducted change detection tasks. Regular transitional click trains elicited significant change responses in the human cortex, indicative of temporal integration, whereas irregular trains did not. These neural responses were modulated by ICI length, ICI contrast, and regularity. Behavioral data mirrored EEG findings, showing enhanced detection for regular conditions compared to irregular conditions and pure tones. Furthermore, variations in change responses were associated with decision-making processes. Temporal continuity was critical, as introducing gaps between click trains diminished both behavioral and neural responses. In clinical assessments, 22 coma patients exhibited diminished or absent change responses, effectively distinguishing them from healthy individuals. Our findings identify distinct neural markers of temporal integration and highlight the potential of transitional click trains for clinical diagnostics.

neuroscience↗

The Glutamatergic Projection from the Substantia Nigra Pars Reticulata to the Dorsal Raphe Nucleus Facilitates Social Hierarchy in Mice

Social hierarchy constitutes a fundamental organizational characteristic among various social species, significantly influencing individual survival, health, and reproductive success within these societies. Neurons in the substantia nigra pars reticulata (SNr) exhibit extensive connectivity with the dorsal raphe nucleus (DRN), a critical structure implicated in social interaction, reward processing, and the establishment of social rank. However, the specific neuronal types within the SNr, as well as the associated neural circuits that regulate social dominance, remain inadequately characterized. This study aims to elucidate the crucial role of SNr glutamatergic neurons in the establishment and maintenance of social hierarchy in mice. Employing fiber photometry, we observed that the activation of SNr glutamatergic neurons increased during the initiation of effortful behaviors in the tube test. Further investigations revealed that optogenetic activation or chemogenetic inhibition of the glutamatergic neural circuit connecting the SNr to the DRN induced upward or downward shifts in social ranks, respectively. Additionally, our findings indicate that the activation of SNr glutamatergic terminals in the DRN reduces anxiety levels in mice. Collectively, these results underscore the critical role of the glutamatergic pathway from the SNr to the DRN in regulating social hierarchy. This work enhances our understanding of the functions of SNr glutamatergic neurons in both physiological contexts and neurological disorders.

neuroscience↗

Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex

Tuberous Sclerosis Complex (TSC), an autosomal dominant condition, is caused by heterozygous mutations in either the TSC1 or TSC2 genes, manifesting in systemic growth of benign tumors. In addition to brain lesions, neurologic sequelae represent the greatest morbidity in TSC patients. Investigations utilizing TSC1/2-knockout animal or human stem cell models suggest that TSC deficiency-causing hyper-activation of mTOR signaling might precipitate anomalous neurodevelopmental processes. However, how the pathogenic variants of TSC1/2 genes affect the longitudinal trajectory of human brain development remains largely unexplored. Here, we employed 3-dimensional cortical organoids derived from induced pluripotent stem cells (iPSCs) from TSC patients harboring TSC2 variants, alongside organoids from age- and sex-matched healthy individuals as controls. Through comprehensively longitudinal molecular and cellular analyses of TSC organoids, we found that TSC2 pathogenic variants dysregulate neurogenesis, synaptogenesis, and gliogenesis, particularly for reactive astrogliosis. The altered developmental trajectory of TSC organoids significantly resembles the molecular signatures of neuropsychiatric disorders, including autism spectrum disorders, epilepsy, and intellectual disability. Intriguingly, single cell transcriptomic analyses on TSC organoids revealed that TSC2 pathogenic variants disrupt the neuron/reactive astrocyte crosstalk within the NLGN-NRXN signaling network. Furthermore, cellular and electrophysiological assessments of TSC cortical organoids, along with proteomic analyses of synaptosomes, demonstrated that the TSC2 variants precipitate perturbations in synaptic transmission, neuronal network activity, mitochondrial translational integrity, and neurofilament formation. Notably, similar perturbations were observed in surgically resected cortical specimens from TSC patients. Collectively, our study illustrates that disease-associated TSC2 variants disrupt the neurodevelopmental trajectories through perturbations of gene regulatory networks during early cortical development, leading to mitochondrial dysfunction, aberrant neurofilament formation, impaired synaptic formation and neuronal network activity.

neuroscience↗

Non-Invasive Quality Control of Organoid Cultures Using Mesofluidic CSTR Bioreactors and High-Content Imaging

Human brain organoids produce anatomically relevant cellular structures and recapitulate key aspects of in vivo brain function, which holds great potential to model neurological diseases and screen therapeutics. However, the long growth time of 3D systems complicates the culturing of brain organoids and results in heterogeneity across samples hampering their applications. We developed an integrated platform to enable robust and long-term culturing of 3D brain organoids. We designed a mesofluidic bioreactor device based on a reaction-diffusion scaling theory, which achieves robust media exchange for sufficient nutrient delivery in long-term culture. We integrated this device with longitudinal tracking and machine learning-based classification tools to enable non-invasive quality control of live organoids. This integrated platform allows for sample pre-selection for downstream molecular analysis. Transcriptome analyses of organoids revealed that our mesofluidic bioreactor promoted organoid development while reducing cell death. Our platform thus offers a generalizable tool to establish reproducible culture standards for 3D cellular systems for a variety of applications beyond brain organoids.

bioengineering↗

Epidemiological evaluation and identification of the insect vector of soybean stay-green associated virus

In recent years, the emergence of soybean stay-green syndrome (SGS), also referred to as "zhengqing", in the Huang-Huai-Hai region of China has resulted in significant yield losses, with some areas experiencing a complete reduction in seed yield. SGS is a phenomenon characterized by the delayed senescence of soybean, resulting in stay-green leaves, flat pods, and stunted seed development at harvest. Our group was the first to identify a distinct geminivirus, named soybean stay-green associated geminivirus (SoSGV), as the causative agent of SGS by fulfilling Kochs postulate. To further understand the epidemiology of SoSGV, in this study, we collected 368 stay-green samples from 17 regions in 8 provinces including the Huang-Huai-Hai region and surrounding areas of China. The results showed that 228 samples tested positive for SoSGV (61.96%), and 96.93% of these positive samples showed severe pod deflation. Our epidemiological assessment reveals SGS caused by the SoSGV is prevalent in the fields, and it is undergoing geographical expansion and genetic differentiation. Additionally, we determined the other natural hosts grown in the Huang-Huai-Hai region of China. By capturing insects in the field and conducting laboratory vector transmission tests, we confirmed that the common brown leafhopper (Orosius orientalis) is the transmitting vector of SoSGV. With a better understanding of the epidemiology of SoSGV and its transmission, we can develop more effective strategies for managing and mitigating its impact on soybean yields.

microbiology↗

Self-organizing Single-Rosette Brain Organoids from Human Pluripotent Stem Cells

The field of brain organoid research is complicated by morphological variability with multiple neural rosette structures per organoid. We have developed a new human brain organoid technique that generates self-organizing, single-rosette spheroids (SOSRS) with reproducible size, cortical-like lamination, and cell diversity. Rather than patterning a 3-dimensional embryoid body, we initiate brain organoid formation from a 2-dimensional monolayer of human pluripotent stem cells (hPSCs) that is patterned with small molecules into neuroepithelium and differentiated to cells of the developing dorsal cerebral cortex. This approach recapitulates the 2D to 3D transition from neural plate to neural tube that occurs during neurodevelopment. The vast majority of monolayer fragments form spheres with a single central lumen and consistent growth rates. Over time, the SOSRS develop appropriately ordered lamination consistent with six cortical layers by immunocytochemistry and single cell RNA-sequencing. The reproducibility of this method has allowed us to demonstrate robust structural phenotypes arising from chemical teratogen exposure or when modeling a genetic neurodevelopmental epileptic disorder. This platform should advance studies of human cortical development, brain disorder mechanisms, and precision therapies. SUMMARY STATEMENTSimple procedure for generating reproducible single rosette cortical brain organoids used to identify robust structural phenotypes with neuroteratogen exposure and in a genetic neurodevelopmental disease model.

neuroscience↗

Machine-learning from Pseudomonas putida transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1,993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

systems biology↗

Genetic Encoding of A Nonhydrolyzable Phosphotyrosine Analog in Mammalian Cells

Protein tyrosine phosphorylation plays a critical role in signal transduction and the regulation of many cellular processes. It is of great significance to understand the underlying regulatory mechanism of particular tyrosine phosphorylation events. Here we report the genetic incorporation of a phosphotyrosine (pTyr) analog, p-carboxymethyl-L-phenylalanine (CMF), into proteins in mammalian cells. This nonhydrolyzable pTyr analog can facilitate biological studies by removing complications caused by the dynamic interconversion between the phosphorylated and non-phosphorylated isoforms of a protein. The developed methodology was demonstrated by using the human signal transducer and activator of transcription-1 (STAT1) as a model protein for homogeneous and defined incorporation of CMF. This tool will greatly enhance ones capability to study protein tyrosine phosphorylation-associated biomolecular and cellular events, and enhance biomedical research that target protein tyrosine phosphorylation, which will have a broad impact to both fundamental studies and practical applications.

bioengineering↗

Mouse oocytes develop in cysts with the help of nurse cells

Mammalian oocytes develop initially in cysts containing many more germ cells than the primordial oocytes they generate. We identified abundant nurse cells with reduced unique molecular identifiers (UMI)/cell from ovaries aged E14.5 to P1. Low UMI nurse cells are found in cysts and express the same major meiotic genes as pro-oocytes of the same stage, suggesting they are oocyte sisters that are signaled to transfer cytoplasm at different times and only subsequently diverge. Oocyte vs nurse cell selection occurs in cysts with a robust microtubule cytoskeleton, that closely interact with somatic cells and that develop a dense actin cytoskeleton around nurse cell nuclei that are held back from cytoplasmic transfer. Mouse and Drosophila nurse cells undergo programmed cell death by acidification from adjacent somatic pre-granulosa cells that express V-ATPases and cathepsin proteins. Disrupting acidification in cultured mouse ovaries blocked nurse cell turnover. About 200 genes are induced in mouse dictyate oocytes as previously reported, including Tuba1c and Tubb2b, genes that we find contribute to Balbiani body formation. Thus, mouse oocytes are specified within germline cysts and develop with the assistance of nurse cells using highly conserved mechanisms.

developmental biology↗

Differentiating Drosophila female germ cells initiate Polycomb silencing by altering PRC2 sampling

Polycomb silencing represses gene expression and provides a molecular memory of chromatin state that is essential for animal development. We show that Drosophila female germline stem cells (GSCs) provide a powerful system for studying Polycomb silencing and how it is established. GSCs resemble pluripotent mammalian embryonic cells in lacking silenced chromatin, but most GSC daughters, like typical somatic cells, induce Polycomb silencing as they differentiate into nurse cells. Developmentally controlled changes in the levels of two Polycomb repressive complex 2 (PRC2)-interacting proteins, Pcl and Scm, initiate differentiation. In germline stem cells, abundant Pcl inhibits silencing by slowing PRC2 and diverting it from PRE sequences. During differentiation, core PRC2 represses inactive loci while Scm and residual Pcl cooperate to enrich PRC2 and silence traditional Polycomb domains. We propose that PRC2-interacting proteins regulate the transition from a variable to stable transcription state during differentiation by altering the rate that PRC2 samples regulatory sequences.

developmental biology↗