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Xia, X.

Publications and source records attributed to Xia, X..

At least 19 recordsLinked to original sources

Oxidative Stress and Tissue Remodeling in a Rat Abdominal Seroma Model

Seroma is a common complication following abdominoplasty and other procedures involving extensive soft tissue dissection. Although animal seroma models have been reported, the stromal pathology underlying post-abdominoplasty seroma, particularly the role of oxidative stress, remains poorly characterized. Here, we developed a rat abdominal seroma model by surgically separating the subcutaneous tissue from the underlying muscle fascia and investigated the temporal evolution of the associated stromal response. Seroma developed in 9 of 20 operated rats, corresponding to a formation rate of 45.0%. Longitudinal ultrasound demonstrated that fluid accumulation peaked around postoperative day (POD) 7 and largely resolved by POD30. Despite macroscopic fluid resolution, substantial stromal remodeling persisted. Compared with normal abdominal tissue, seroma-associated tissues at POD14 and POD35 exhibited increased collagen deposition, macrophage accumulation, oxidative injury, and vascular remodeling. Additionally, at POD35, macrophage accumulation and 4-hydroxynonenal staining were greater than at POD14, whereas collagen deposition and vascular density remained elevated with no significant differences between postoperative time points. To our knowledge, this study presents the first rat model specifically designed to reproduce post-abdominoplasty seroma and the first temporal characterization of oxidative stress within seroma-associated tissue. These findings reveal that seroma fluid resolution does not coincide with stromal recovery and identify persistent oxidative stress, inflammation, fibrosis, and vascular remodeling as important features of seroma pathology.

bioengineering↗

Spatial transcriptomics reveals selective vulnerability of cardiac neural crest-derived glial cells in human myocardial infarction

Cardiac neural crest-derived glial cells (CNGs) are recently identified glial cells that support cardiac autonomic innervation and maintain sympathetic-parasympathetic balance. Their fate in myocardial infarction (MI) is unknown. Here, we analyzed 16 human cardiac spatial transcriptomes spanning normal myocardium (n=4), infarct zone (n=5), border zone (inner, n=1; outer, n=3), and remote zone (n=3). CNGs (S100B+/GFAP+, CD68- spots) were selectively lost along a spatial gradient from healthy tissue to the infarct core (Spearman rho = -0.92, p = 4.5 x 10-7). Tissue-area-corrected analysis confirmed that CNG loss (26% retained in infarct zone vs. normal; p = 0.016) vastly exceeded overall tissue loss, indicating selective vulnerability rather than bulk tissue destruction. Mechanistically, oxidative phosphorylation (OXPHOS) activity in CNG-positive spots correlated positively with CNG survival (partial rho = 0.65, p = 0.009 after controlling for spot composition), consistent with a high metabolic demand underlying their ischemic sensitivity. Pyroptosis - but not ferroptosis or apoptosis - signatures correlated with CNG loss (partial rho = -0.67, p = 0.006). These findings identify CNGs as selectively vulnerable cellular components of the cardiac autonomic system in MI and nominate metabolic failure and pyroptosis as candidate mechanisms, providing a spatially resolved foundation for future mechanistic and interventional studies.

bioinformatics↗

Marmosets adaptively accumulate dynamic sequential evidence to make decisions

The bounded accumulation model is a dominant theoretical framework to characterize evidence accumulation during decision-making. Using a dynamic sequential tone accumulation (DSTA) task in marmosets, we found that the contribution of late tones to decisions was greater for weaker than for stronger evidence strength-an effect we term evidence-strength-dependent temporal weighting (ETW). Rigorous exclusionary analyses and drift-diffusion modeling further revealed that the bounded accumulation mechanism alone fails to account for this effect, and the online modulation of attentional engagement was identified as the necessary mechanism in addition to the bounded accumulation. Our work thus establishes that attentional engagement is adaptively modulated by evidence strength during complex decision-making.

neuroscience↗

Salicylic acid mediates graft incompatibility by repressing auxin-dependent vascular reconnection in tomato

Graft incompatibility limits the combination of scions and rootstocks, yet the signals that block vascular reconnection remain poorly understood. Using incompatible tomato-pepper (Solanum lycopersicum-Capsicum annuum) grafts, we found that salicylic acid (SA) overaccumulates at the graft junction, predominantly in the rootstock, while incompatible scions exhibit enhanced pattern-triggered immunity. SA-deficient nahG-expressing tomato failed to rescue incompatibility and instead showed severely impaired self-graft healing, indicating that successful tissue reunion requires an optimal, rather than minimal, SA response. Defense-associated genes remained activated in failed grafts regardless of SA accumulation, placing SA downstream of incompatibility determination. Exogenous SA application phenocopied incompatibility, blocking xylem reconnection, inducing cell death, and suppressing auxin signaling. Incompatible grafts similarly displayed reduced auxin accumulation and response at the graft junction. Exogenous auxin partially rescued xylem reconnection in incompatible grafts but failed to activate cambial regulator genes or fully restore compatibility. We propose that graft compatibility depends on SA-auxin homeostasis, where moderate SA supports wound-associated defense and regeneration, whereas excessive SA suppresses the auxin-dependent program required for xylem differentiation. These findings identify SA as a dose-dependent regulator of graft healing in tomato and link excessive immune activation to failed vascular regeneration.

plant biology↗

Adult Clock Neuron Somatic Neuropeptide Release and Cytonemes Regulate Sleep

Drosophila s-LNv clock neurons promote nighttime sleep by releasing the neuropeptide sNPF to activate sNPF receptors (sNPF-Rs) on l-LNv clock neurons. Behavior is controlled by synaptic transmission, but s-LNv and l-LNv neurons are not connected directly by chemical synapses. To investigate the basis of sNPF/sNPF-R communication between LNv neurons, the spread of sNPF was imaged in the adult brain. We report the daily midmorning burst of sNPF released from s-LNv terminals does not reach l-LNv neurons or s-LNv somata. Instead, sNPF released by the s-LNv soma late at night in response to sleep-promoting IP3 signaling reaches l-LNv somata, but not their terminals. In addition to communication by neuropeptide diffusion, analysis of fly connectomes revealed that adult s-LNv and l-LNv neurons form non-synaptic direct contacts mediated by cytonemes. Remarkably, genetically perturbing LNv neuron cytonemes alters sleep latency, but not nighttime sleep, the target of somatic sNPF release, or circadian behavior, which depends on PDF neuropeptide released by LNv terminals. Therefore, three distinct aspects of adult rhythmic behavior are produced by terminals, the soma and cytonemes, with the latter possibly acting via contacts that are not currently annotated in the connectome.

neuroscience↗

The FKBP42, TWISTED DWARF1, prioritizes auxin over brassinosteroidtransport by peptidyl-prolyl cis-trans isomerization of ABCB1

The ATP-binding cassette (ABC) transporter ABCB1 transports both auxins and the brassinosteroid brassinolide (BL). ABCB1-mediated auxin (IAA) transport depends on interaction with the FKBP42 protein TWISTED DWARF1 (TWD1), yet the mechanism underlying substrate selectivity remains unclear. Here, we confirm dual IAA and BL transport by ABCB1 and show that the two substrates compete for ABCB1-mediated transport. We demonstrate that a conserved proline residue (P1008) is required for IAA, but not BL, transport. Furthermore, we identify TWD1 as a calmodulin-activated peptidyl-prolyl cis-trans isomerase (PPIase) that selectively enhances IAA, but not BL, transport through isomerization of the E1007-P1008 peptide bond. Loss of TWD1 PPIase activity abolishes ABCB1-mediated IAA export without affecting BL transport, revealing a regulatory mechanism that prioritizes auxin over brassinosteroid transport. Cryo-EM, molecular docking, and molecular dynamics simulations of wild-type ABCB1 and the ABCB1P1008G variant suggest that the P1008 loop mediates long-range communication between the nucleotide-binding domain surface and the substrate-binding pocket, thereby providing a structural mechanism by which TWD1 modulates substrate specificity. In summary, our findings establish the structural basis of ABCB1 substrate selectivity and uncover a post-translational mechanism that selectively regulates auxin transport while preserving brassinosteroid transport. One Sentence SummaryTWD1 prioritizes ABCB1-mediated auxin over brassinosteroid transport

biochemistry↗

Pyruvate-driven hydrogen production promotes polyphenol bioconversion by gut bacteria

Gut microbial biotransformation of poorly absorbable polyphenols into bioactive, bioavailable metabolites is increasingly recognized as a key mechanism underlying their health benefits of polyphenols. Microbial ellagic acid (EA)-to-urolithin conversion represents a typical example, but the environmental factors that facilitate such metabolism remain underexplored. We discovered that urolithin production by a gut commensal bacterium, Gordonibacter urolithinfaciens (G. uro), is metabolically repressed by arginine. To overcome such limitations, we developed PhenolBoost Medium (PBM) that induces a metabolic shift by suppressing the arginine deiminase pathway while activating pyruvate metabolism and hydrogen production in G. uro, thereby driving urolithin dehydroxylation. Transcriptomic profiling and 13C-isotopic tracing analysis revealed that pyruvate metabolism in PBM upregulates hydrogenase expression, facilitating the dehydroxylation of EA. PBM also promoted the complete conversion of EA to urolithin A in G. uro-Enterocloster bolteae co-culture, and other polyphenol biotransformations. In addition, co-culturing G. uro with hydrogen-producing Bacteroides species significantly increased urolithin production. Furthermore, an arginine-limited, pyruvate-enriched dietary regimen proved effective in vivo, resulting in significantly higher urolithin production and bioavailability in a mouse model. Our findings reveal the critical role of hydrogen in facilitating polyphenol dehydroxylation, and offer a viable nutritional strategy for boosting microbial production of beneficial metabolites from polyphenols.

microbiology↗

Exploring L-tyrosine and L-DOPA biosynthesis in faba bean (Vicia faba L.)

Background and AimsL-DOPA is an important pharmaceutical that accumulates to high levels in the legume faba bean (Vicia faba). L-DOPA is likely derived from L-tyrosine but the responsible enzyme (L-tyrosine oxidase) remains unknown. Availability of L-tyrosine may be a key factor controlling L-DOPA accumulation. In legumes, L-tyrosine is supplied via either a plastidial TyrA enzyme (ADH) or a deregulated cytosolic homolog (PDH). This study aimed at identifying L-tyrosine oxidase and TyrA genes from faba bean. MethodsWe used gene-to-metabolite correlations and homology-based searches to select fifteen L-tyrosine oxidase candidates, which were tested in yeast and in the model plant Nicotiana benthamiana. We also used isotopically labeled L-tyrosine to measure biosynthetic activity in different faba bean tissues and to test an alternative biosynthetic hypothesis. Three faba bean TyrA genes were inferred by homology and assayed in N. benthamiana by co-expression with a known L-tyrosine oxidase, CYP76AD6. Key ResultsNone of the L-tyrosine oxidase candidates produced L-DOPA upon heterologous expression. Feeding experiments showed a lack of correlation between L-DOPA accumulation and biosynthetic capacity. Feeding studies also disproved an alternative route to L-DOPA by oxidation of 4-hydroxyphenylpyruvate. Of the TyrA genes, two were able to increase L-tyrosine levels in N. benthamiana 2-3-fold (VfADH and VfPDH), and one of them was able to boost the levels of L-DOPA derivatives up to 6-fold (VfADH). ConclusionsThe faba bean L-tyrosine oxidase remains unidentified, with a possible transport of L-DOPA across tissues likely having confounded our correlation-based selection strategies. In N. benthamiana, both VfADH and VfPDH can increase the levels of L-tyrosine, while VfADH can further boost the levels of L-DOPA derivatives. Our work delivers a strategy to boost the provision of L-tyrosine in N. benthamiana and provides valuable insights in the search for the elusive L-tyrosine oxidase from faba bean.

plant biology↗

Type 2 diabetes amplifies environmental Pb toxicity and intergenerational risk

Type 2 diabetes (T2D) and environmental lead (Pb) exposure intersect as prevalent global health challenges. Prior studies report elevated blood Pb in T2D, but the underlying mechanism and directionality remain unresolved. Here we show that T2D fundamentally alters Pb toxicokinetics, converting otherwise modest exposure into progressive organ injury and heritable risk. In a human cohort, elevated blood Pb in T2D specifically associated with impaired renal function rather than glycaemic control or adiposity. In db/db mice, diabetes increased oral Pb absorption through delayed gastrointestinal transit and epithelial barrier dysfunction, leading to enhanced systemic retention. With sustained exposure, renal Pb accumulation induced tubular stress that reduced effective clearance, creating a feed-forward loop in which diabetes promotes Pb retention and retained Pb accelerates kidney injury. Chronic Pb exposure exacerbated diabetic kidney injury without inducing hyperglycaemia, and short-course chelation attenuated renal stress markers. Beyond somatic toxicity, combined paternal T2D and Pb exposure programmed renal and neurobehavioral phenotypes across generations via sperm RNA. These findings redefine Pb from a passive environmental exposure to a context-dependent driver of disease, identify T2D as a vulnerability state that reshapes toxicant handling, and establish a mechanistic link between metabolic disease, environmental exposure and intergenerational risk. This work highlights the need for vulnerability-informed clinical management and environmental regulation in populations burdened by T2D.

genetics↗

In Vivo Surface Reconstruction of Three Signal-defined Intracortical Layers Using 5T 3D FLAIR MR Imaging

BackgroundIn vivo whole-cortex quantification of intracortical signal-defined layering on the routinely acquired structural MRI remains limited. PurposeTo develop and validate an automated framework to reconstruct three intracortical signal-defined layers from 5T three-dimensional (3D) T2-weighted fluid-attenuated inversion recovery (FLAIR) and to characterize whole-cortex morphometrics and regional organization across a prespecified cortical organizational framework. Materials and MethodsIn this retrospective study, 5T 3D FLAIR images were acquired between February and July 2024. Brain Multi-Layer Surface Reconstruction (BrainMLSR) reconstructed three intracortical signal-defined layers, and derived intracortical layer thickness and surface area measures and ratios. Performance was evaluated against manual annotations and assessed for test-retest repeatability (n=13) and cross-site feasibility (n=2). Paired two-tailed t-tests and linear mixed-effects models were used. A proof-of-concept analysis compared Heschls gyrus ratios between 19 patients with temporal lobe epilepsy (TLE) and 19 age-matched healthy controls (HC). ResultsA total of 270 healthy participants (mean age, 54.4{+/-}14.5 years; 146 men) were included. Agreement with manual hypointense-layer annotations was high (Dice, 0.960{+/-}0.003), and was similar in the cross-site dataset (Dice, 0.954{+/-}0.009). In the test-retest dataset, average symmetric surface distance was less than 0.1 mm. Across prespecified systems, thickness and surface area ratios varied by region; within an auditory-perisylvian hierarchy, banksSTS showed a localized turning point with an increased hyperintense layer thickness ratio and decreased hypointense layer thickness ratio, accompanied by inflections in surface area ratios (P < .001). In bilateral Heschls gyrus, hypointense (left: 0.619{+/-}0.262 vs 0.881{+/-}0.102; right: 0.607{+/-}0.310 vs 0.907{+/-}0.141 mm) and isointense (left: 0.406{+/-}0.225 vs 0.678{+/-}0.128; right: 0.478{+/-}0.232 vs 0.808{+/-}0.176 mm) layer thicknesses were lower in TLE than in HC (all P<.001). ConclusionBrainMLSR enabled accurate and repeatable in vivo reconstruction of three intracortical signal-defined layers from a single 5T 3D T2-weighted FLAIR acquisition and provided whole-cortex boundary-based morphometry with interpretable regional organization. Key ResultsO_LIIn this retrospective study of 270 participants, Brain Multi-Layer Surface Reconstruction (BrainMLSR) showed high agreement with hypointense-layer annotations (Dice, 0.960{+/-}0.003). C_LIO_LIWithin an auditory-perisylvian hierarchy, the hyperintense-layer thickness ratio peaked (0.620{+/-}0.003) and the hypointense-layer ratio was the lowest (0.156{+/-}0.002) in the bank of the superior temporal sulcus (P < .001). C_LIO_LIIn a proof-of-concept analysis, patients with temporal lobe epilepsy (vs healthy controls) had higher hyperintense-layer thicknesses ratio in the left hemisphere (0.523{+/-}0.085 vs 0.417{+/-}0.036, P<.001). C_LI SummaryAn automated multiple-layer surface reconstruction framework (BrainMLSR), applied to 5T 3D T2-weighted FLAIR images, produced reproducible whole-cortex, signal-defined laminar morphometry and demonstrated coherent patterns across prespecified cortical organizational framework.

neuroscience↗

A Multi-Organ Single-Cell Atlas Maps Allergen and Organ-Specific Cellular Dynamics in the Progression from Food Allergy to Anaphylactic Shock

The transition from food allergic sensitization to life-threatening anaphylactic shock (AS) with complex multi-organ cellular interactions has been poorly understood. We herein conducted a multi-organ single-cell sequencing of heart, lung, and intestinal tissues from mouse models of food allergy, sensitized to bovine serum albumin (BSA) or ovalbumin (OVA), across both sensitization (Phase I) and anaphylactic shock (Phase II). We found that organ-specific pathologies included cardiac vascular dysfunction with pericyte loss and cardiomyocyte adaptation, distinct lung responses (Th2/B-cell predominance with BSA vs. neutrophilia with OVA), and profound intestinal remodeling featuring Paneth cell expansion. We also identified conserved inflammatory pathways (e.g., NOD-like receptor, NF-{kappa}B, JAK-STAT signaling) and unique organ specific signatures. Notably, phase-dependent reprogramming showed NLRP3 inflammasome activation and suppressed anti-inflammatory responses during AS. Cell-cell communication networks shifted from stromal-immune crosstalk in Phase I to dominant myeloid-vascular/neuroimmune interactions in Phase II. We further linked early extracellular matrix remodeling to late-stage neuromodulatory responses in Schwann and smooth muscle cells. This multi-organ atlas elucidates the coordinated, organ-selective immune cascade driving FA to AS progression, providing a foundational resource for developing targeted therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/703914v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@19ffd9forg.highwire.dtl.DTLVardef@c3fda3org.highwire.dtl.DTLVardef@141174corg.highwire.dtl.DTLVardef@60ac5b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Fully computational design of PAM-relaxed Staphylococcus aureus Cas9 with expanded targeting capability

CRISPR-Cas9 nucleases have transformed genome engineering, yet their application is often constrained by protospacer-adjacent motif (PAM) requirements. Staphylococcus aureus Cas9 (SaCas9) is particularly attractive for in vivo applications due to its compact size; however, its NNGRRT PAM limits targetable genomic sites. Here, we report KRH, a SaCas9 variant designed entirely from the wild-type enzyme through a fully computational point-mutation design workflow, UniDesign, without additional experimental optimization. As expected, KRH efficiently recognizes an expanded NNNRRT PAM and exhibits substantially enhanced editing efficiency at non-canonical PAM sites, with improvements of up to 116-fold over the wild type. KRH achieves genome- and base-editing efficiencies comparable to, or exceeding, those of the well-known evolution-derived KKH variant. Computational modeling by UniDesign provides a mechanistic explanation for the PAM relaxation observed in both KRH and KKH, with structural and energetic analyses revealing that KRH relaxes PAM specificity by fine-tuning the balance between sequence-specific interactions with PAM bases and nonspecific contacts with the DNA backbone. Beyond its practical utility, KRH demonstrates that computational design can identify a minimal set of mutations sufficient to remodel the PAM interface while preserving high nuclease activity. This approach recapitulates--and in some cases surpasses--the performance of evolution-derived variants, offering a scalable strategy for high-throughput Cas9 engineering. Overall, these results establish KRH as a blueprint for rationally engineered, PAM-relaxed nucleases and underscores the power of computational design to accelerate next-generation genome editing.

bioengineering↗

Cross-species etiologically informed stratification enables T cell receptor-based diagnosis of Parkinson's Disease

BackgroundDeveloping peripheral blood-based diagnostic models for idiopathic Parkinsons disease (iPD), particularly those leveraging the T-cell receptor (TCR) repertoire, has long been considered infeasible because patient-derived TCRs appear to lack convergent sequence motifs. We reasoned that this apparent absence of shared TCR features likely reflects both insufficient sample sizes and unaccounted immune heterogeneity within the iPD population. MethodsWe reconstructed TCR repertoires from the two largest iPD cohorts currently available, anchoring them with three mechanistically distinct mouse models to stratify patients into model-anchored informed subtypes. Within these data-driven subtypes, we trained subtype-specific, multimodal multi-instance classifiers. ResultsWe demonstrated that iPD patients can be successfully stratified into model-anchored informed subtypes. Furthermore, the trained subtype-specific, multimodal multi-instance classifiers achieved an Area Under Curve (AUC) exceeding 0.8 for both subtypes. ConclusionsOur findings underscore the critical role of disease stratification in enabling TCR repertoire-based modeling in neurodegenerative diseases.

neuroscience↗

PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy

Distinguishing among neuronal cell types is crucial for deciphering complex neural networks and brain functions. However, the current repertoire of cell-labeling tools compatible with light microscopy (LM) and/or electron microscopy (EM) is limited compared to the vast number of cell types in the brain. Here, we introduce PKU (polymer king-size unit) tags, genetically encoded "shape tags" that leverage the polymerization of self-assembling proteins, spectrally distinct fluorescent proteins and, optionally, a nuclear targeting sequence to generate a series of multi-shaped (spherical or filamentous), multi-colored (blue, green, red, near-infrared) and multi-localized (cytosolic or nuclear) tags. By co-expressing multiple PKU tags within the same cell, a combinatorial strategy further expands the repertoire, which can theoretically yield hundreds of unique labeling patterns. Expressing PKU tags in vivo provides multi-cell-type labeling and neuronal circuit tracing, without altering the animals behavior or transcriptomic profiles. Moreover, when fused to the peroxidase APEX2, PKU tags maintain their shape-specific features, providing shape "barcoding" using EM. Thus, PKU tags represent a versatile and efficient toolkit for studying connectomics using both LM and EM.

neuroscience↗

β2 and β3a regulatory subunits can coassemble in the same BK channels

Ca2+- and voltage-activated BK-type K+ channels are influenced profoundly by associated regulatory subunits, including {beta} subunits (Kcnmb1-4; {beta}1-{beta}4). Although overlap in expression of different BK {beta} subunits occurs in native tissues, whether they can coassemble in the same channel complex is not known. We coexpress {beta}2- and {beta}3a subunits together with BK and, through a combination of macroscopic and single channel recordings, along with quantitative pull-down of tagged subunits, test whether coassembly can occur. We evaluate two models: 1) random mixing in which {beta}2 and {beta}3a subunits co-assemble in the same channels, and 2) segregated in which {beta}2 and {beta}3a are found in separate complexes. Our results support the view that, for {beta}2 and {beta}3a, BK currents arise from the random, independent assembly of both subunits in the same channels. Single channel recordings directly confirm coassembly of {beta}2 and {beta}3a subunits in the same channels. Quantitative biochemical analysis of coexpression of tagged BK subunits also reveals that ternary complexes form.

biophysics↗

Functional recovery by transplantation of human iPSC-derived A2B5 positive neural progenitor cell after spinal cord injury in mice

Human induced pluripotent stem cells (hiPSCs) hold great potential for patient-specific therapies. Transplantation of hiPSC-derived neural progenitor cells (NPCs) is a promising reparative strategy for spinal cord injury (SCI), but clinical translation requires efficient differentiation into desired neural lineages and purification before transplantation. Here, differentiated hiPSCs--reprogrammed from human skin fibroblasts using Sendai virus-mediated expression of OCT4, SOX2, KLF4, and C-MYC--into neural rosettes expressing SOX1 and PAX6, followed by neuronal precursors ({beta}-tubulin III/NESTIN) and glial precursors (GFAP/NESTIN). Both neuronal and glial precursors expressed the A2B5 surface antigen. A2B5+ NPCs, purified by fluorescence-activated cell sorting (FACS), proliferated in vitro with mitogens and differentiated into mature neurons and astrocytes under lineage-specific conditions. NOD-SCID mice received a T9 contusion injury followed by transplantation of A2B5+ NPCs, human fibroblasts, or control medium at 8 days post-injury. At two months, grafted NPCs showed robust survival, progressive neuronal maturation ({beta}-tubulin III [->] doublecortin [->] NeuN), and astrocytic differentiation (GFAP), particularly in spared white matter. Transplantation significantly increased spared white matter volume and improved hindlimb locomotor recovery, with no teratoma formation observed. These results demonstrate that hiPSC-derived, FACS-purified A2B5+ NPCs can survive, differentiate into neurons and astrocytes, and enhance functional recovery after SCI. This approach offers a safe and effective candidate cell source for treating SCI and potentially other neurological disorders.

neuroscience↗

Modeling structural variations sequencing information to address missing heritability and enhance risk prediction

Missing heritability remains a significant challenge in genome-wide studies focused on single nucleotide polymorphisms (SNPs) when analyzing the genetic basis of complex traits. Structural variations (SVs), which span broader genomic regions and often exert larger functional impacts than SNPs, hold promise for capturing this heritability. Although graph-based pangenomes have advanced SV detection and association analysis, traditional SNP-centric frameworks typically overlook detailed SV sequence information, treating overlapping SVs as independent variants and leading to reduced statistical power. To overcome this limitation, we developed SVrefiner, an algorithm that aligns overlapping SVs and partitions them into non-overlapping refined SVs (rSVs) based on sequence congruence. By generating precise genotype matrices, SVrefiner enables more accurate association studies. When applied to human, tomato, and pig genomes, SVrefiner delineated 48,712 rSVs from 77,696 human SVs, 6,607 rSVs from 51,561 tomato SVs, and 5,237 rSVs from 142,784 pig SVs. Incorporating rSVs alongside SNPs, indels, and unrefined SVs enhanced heritability estimates by up to 24.47%. Further, refined analysis revealed that gene expression traits are often influenced by specific SV subregions rather than entire SVs. Notably, integration of rSVs in human datasets increased total eQTLs by 71.56%, with cis- and trans-eQTLs rising by 21.3% and 94.4%, respectively. Mean risk prediction accuracy across over 16,000 traits improved by as much as 16.8%. These findings deepen the understanding of complex trait heritability and demonstrate the utility of rSVs for genetic improvement and disease risk assessment.

genetics↗

Efficient spatial gene expression profiling using split-probe ligation and rolling circle amplification

Spatial transcriptomics has transformed our understanding of gene regulation by enabling high-resolution mapping of RNA molecules within their native cellular and tissue environments. This is typically accomplished by capturing or imaging RNA in situ, thereby preserving spatial context. Here, we introduce an in situ RNA imaging method based on split-probe ligation and rolling circle amplification (RCA) for profiling spatial gene expression. In this approach, split-probes hybridize to adjacent regions of a target RNA fragment and are then enzymatically ligated to form circular DNA templates, which are subsequently amplified via RCA to boost signal. We demonstrate that this method enables robust in situ RNA detection and genotyping in both tissue sections and whole-mount tissue samples. By coupling this technique with in situ sequencing, we mapped the spatial expression patterns of 82 genes in the kidneys of healthy and diabetic male and female mice. This analysis revealed distinct localization of Aqp4 in proximal tubules and principal cells of the collecting ducts, and uncovered sex-specific transcriptomic alterations in diabetic kidneys with spatial resolution. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/668044v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@c8efaborg.highwire.dtl.DTLVardef@1eef010org.highwire.dtl.DTLVardef@1d2bbd7org.highwire.dtl.DTLVardef@2a482b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗