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Kang, X.

Publications and source records attributed to Kang, X..

At least 19 recordsLinked to original sources
bioRxiv2026

ReCap enables deep, copy number-scaled cysteine redox proteomics with minimal exogenous oxidation

Cysteine oxidation analyses require the preservation of the redox state present at harvest and quantitative scaling to relate oxidation to protein copy numbers, rather than only providing fractional oxidation data. Here, we present ReCap, a Redox Capture workflow combining Oxi-DIA, an enrichment-free isotope-encoded DIA workflow, with Oxi-Stop, a simple oxygen-exclusion strategy for cryopreserved tissue. In mouse brains, Oxi-DIA quantified 17,809 cysteine sites belonging to 6,085 protein groups in every sample, enabling matched measurements of residue-resolved oxidation and protein abundance. Atmospheric oxygen exposure during 14 days of cryopreservation distorted the measured cysteine redox state. The resultant increase of an estimated 5.3176 x 1011 {micro}g-1 oxidised cysteine molecules was mitigated by Oxi-Stop, which minimised exogenous oxidation during cryopreservation. Copy-number scaling altered the interpretation of cysteine oxidation values. Although cysteine oxidation was detected across 2,371 sites and 1,439 proteins, 20 sites on abundant proteins accounted for 44% of the oxidised signal. ReCap advances redox proteomics from providing a site catalogue into a biologically weighted map of redox information, revealing cysteine oxidation as a sparse, ordered and quantitatively concentrated signal.

biochemistry↗
bioRxiv2026

Generation of Genetically Identical Mammalian Oocytes from Parthenogenetic Double-Haploid Embryonic Stem Cells

Generating genetically identical mammalian oocytes is challenging due to stochastic meiotic recombination. Here, we established parthenogenetic double-haploid embryonic stem cells (PG-DhESCs) possessing complete homozygosity. By employing blastocyst complementation in Prdm14-deficient embryos, we generated chimeric females that produced oocytes derived exclusively from these donor cells. Fertilization of these oocytes yielded viable, fertile, maternally semi-cloned (MSC) mice of both sexes. Although DNA methylation was largely restored during gametogenesis, subtle epigenetic defects correlated with increased body weight in MSC offspring. This study establishes a robust platform combining PG-DhESCs with blastocyst complementation to generate isogenic mammalian oocytes, overcoming traditional limitations in mammalian cloning.

developmental biology↗
bioRxiv2026

Structural basis for saccharide binding by human RNase 2/EDN, a protein combining enzymatic and lectin properties

Human RNase 2 (eosinophil-derived neurotoxin, EDN) is a major eosinophil granule protein of the vertebrate-specific RNase A superfamily and is involved in antiviral response and inflammation. Identifying ligand-binding pockets in EDN is thus relevant to structure-based drug design. In our laboratory we identified by protein crystallography a conserved site at the protein surface binding to carboxylic anion molecules (malonate, tartrate and citrate). Searching for potential biomolecules rich in anion groups and considering previous report of EDN binding to glycosaminoglycans, we explored the protein binding to saccharides. Next, EDN crystals were soaked with mono- and disaccharides, and the 3D structures of ten complexes were solved by X-ray crystallography at atomic resolution. We identified protein binding pockets to glucose, fucose, mannose, sucrose, galactose, trehalose, N-acetyl-D-glucosamine, N-acetylmuramic acid, and the sialic acid N-acetylneuraminic acid. A main site for glucose, fucose, and galactose was located adjacent to the spotted carboxylic anion site. Secondarily, N-acetylneuraminic acid, N-acetylmuramic acid, sucrose, galactose, and mannose shared another protein surface region. Overall, the saccharides clustered into seven defined sites, outlining a conserved recognition pattern, which was further analysed by molecular modelling. Interestingly, within the RNase A family, we find amphibian RNases that were initially isolated as carbohydrate binding proteins and named as leczymes, combining enzymatic and lectin properties. The present data is the first systematic structural characterization of a mammalian sugar-binding RNase within the family. The results highlight unique EDN residues that mediate its sugar specific interactions, of particular interest for a better understanding of the protein physiological role. HighlightsO_LIstructure of RNase 2 in complex with mono and disaccharides at atomic resolution C_LIO_LIidentification of RNase 2 unique sugar binding sites C_LIO_LIcharacterization of a mammalian RNase A family enzyme with lectin properties C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/713198v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1d805f7org.highwire.dtl.DTLVardef@16fcc49org.highwire.dtl.DTLVardef@ccfd92org.highwire.dtl.DTLVardef@1b8f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗
bioRxiv2026

EnzySeek: Efficient Exploration of Enzyme Reaction Pathways Using AI Agents

With the rapid development of Large Language Models (LLMs) and Agent technologies, AI can assist in solving a variety of real-world problems across multiple domains, such as autonomous driving, drug discovery, and materials design. In this work, we present EnzySeek, an enzyme catalysis AI agent designed to assist researchers in enzyme catalysis simulations. First, we constructed a domain-specific knowledge base by curating thousands of papers related to enzyme catalysis. Second, we customized Model Context Protocol (MCP) interfaces for each step of the enzyme catalysis simulation workflow, enabling these functions to be invoked by LLMs. Finally, we configured an agent capable of simultaneously referencing past empirical studies on enzyme catalysis, autonomously executing tool calls, and analyzing as well as presenting the results. EnzySeeks capabilities cover multiple aspects, including protein structure prediction, molecular docking, system preparation and parameterization, molecular dynamics (MD) simulations, and QM/MM calculations. The conclusions drawn by EnzySeek are primarily based on the results of QM/MM calculations. We employed the semi-empirical quantum mechanical method GFN2-xTB to calculate the QM region of the system. Benchmark results indicate that the GFN2-xTB method can achieve high efficiency while maintaining accuracy. The EnzySeek agent is designed to continuously learn from newly published literature and past computational tasks. During its operation, every AI decision is manually verified and scored by human experts. This human-in-the-loop validation provides the AI with sufficient case-based support, ultimately contributing to the full automation of enzyme catalysis computations. All data generated during the simulations are compiled into a dataset, which is used to establish evaluation criteria specific to enzyme catalysis computational results.

biochemistry↗
bioRxiv2026

Carbon dioxide sequestration into biomineral armor by ants

Over geologic time, Earths climate has been shaped by the capture and conversion of atmospheric carbon dioxide (CO2) into stable carbonate minerals, including dolomite [CaMg(CO3)2]. Accelerating natural carbon mineralization offers significant potential for mitigating anthropogenic climate change. Using stable carbon isotope tracking, nano-scale secondary ion mass spectroscopy, and 13C SSNMR, we show that, paralleling global biosphere-level processes, Sericomyrmex amabilis fungus-farming ants rapidly convert CO2 in their nest chambers into a biomineral layer covering their exoskeletons. We further reveal that biogenic carbon mineralization by these ants produces partially ordered dolomite. This rapid sequestration of CO2 into defensive armor in ants provides a fascinating natural example of mediation of potentially toxic accumulation of atmospheric CO2 that could inform human efforts to mitigate climate change.

ecology↗
bioRxiv2026

Autistic Children Show Reduced Activity in Left Superior Temporal Cortex in Response to Social-emotional Meaning in Language

Autistic children often differ from non-autistic peers in social interaction, emotional processing, and language communication. While the neural differences between autistic and non-autistic children in processing paralinguistic social-emotional cues, such as emotional prosody, are well-documented, much less is known about how the brain processes the social-emotional meaning carried by the language content itself. In non-autistic adults, the left superior temporal sulcus (STS) and adjacent gyrus show a social-emotional bias, responding more strongly to social-emotional content than to content describing inanimate objects. We investigated whether this bias is present in children and whether it is altered in autistic children. We recruited 78 right-handed children who underwent functional magnetic resonance imaging (fMRI) scanning while listening to sentences describing either people in emotional situations (social-emotional sentences) or non-human objects, events, or concepts (object sentences). After excluding those with excessive head motion, we analyzed data from 58 of them (37 autistic and 21 non-autistic; mean age 10 years). Across the sample as a whole, the left STS responded more strongly to social-emotional sentences than to object sentences, indicating that this social-emotional bias is already present in childhood. Importantly, this bias was reduced in autistic children compared to non-autistic controls, whereas no group difference was observed in general auditory or lexico-syntactic processing. This reduced activity in the left STS in response to social-emotional semantics may contribute to autistic children's social communication challenges.

neuroscience↗
bioRxiv2025

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Withdrawal StatementThe authors have withdrawn this preprint because the co-authors were not in agreement about posting the work in its current form. The authors request that this work not be cited. Please contact the corresponding author (Dr. Xunlei Kang, kangxu@health.missouri.edu) with questions.

cancer biology↗
bioRxiv2025

Environmental Heterogeneity Altered the Growth Fitness of Antibiotic-Resistant Mutants and the Resistance Prevalence in Escherichia coli populations

Antibiotic resistance is one of the most critical issues in public health. As antibiotic-resistant bacteria emerge under certain selection pressure, their further proliferation can facilitate the prevalence and maintenance of the antibiotic resistance. Here, we investigated which environmental factors could affect the growth fitness of antibiotic-resistant Escherichia coli strains using growth competition assays. We found that when antibiotic resistance selection pressure was removed, lower temperature and nutrient limitations, especially iron (Fe) deficiency, fostered a better fitness to resistant mutants when co-cultivated with the wild type, whereas changes in pH or salinity (Na or K) did not. Moreover, the growth advantage of resistant mutants under the selection pressure was reversed by suboptimal conditions like acidic/basic pH, high K salinity, and Fe limitation. These identified key environmental factors influencing the growth fitness of antibiotic-resistant mutants provide important insights into the prediction and mitigation of antibiotic resistance in heterogeneous environments.

microbiology↗
bioRxiv2025

Selective abundance of the stemness-promoting cluster miR-290-295 within the adult substantia nigra dopamine neurons is neuroprotective via preservation of protein synthesis

Locomotor, reward and other critical functions of the body are regulated by the ventral midbrain, with the central role played by dopamine (DA) neurons. The function of these cells from the early development to maturity is critically dependent on the orchestrated expression of coding and non-coding genes. For example, in the stem cells the miR-290-295 cluster constitutes the majority of expressed microRNAs and is critical for stemness in rodents. During development towards various terminally differentiated lineages, such as neurons, the cells typically switch off transcription of these stem cell-specific microRNAs. Here we report that within the adult Substantia Nigra pars compacta (SNpc), the miR-290-295 cluster is exclusively expressed in DA neurons (SNDA), preventing the locomotor deficits and maintaining an adequate expression of proteins involved in DA biogenesis, such as tyrosine hydroxylase (TH), dopa decarboxylase (DDC) and DA transporter (DAT). Importantly, a global knock-out of the miR-290-295 cluster leads to decreased numbers of SNDA neurons in adult mice. Using in vitro and in vivo DA cell-specific loss-of-function models, we demonstrated that miR-292a-3p, the most abundant microRNA in this cluster, directly targets PTEN, a phosphatase antagonizing the neuroprotective phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)-AKT-mechanistic target of rapamycin kinase (mTOR) pathways regulating translation initiation. Accordingly, when labelled with the click chemistry-compatible methionine analogue L-azidohomoalanine, miR-290-295 cluster-deficient SNDA neurons revealed a drastic impairment of protein synthesis, which is critical for DA biogenesis. Our surprising findings demonstrate for the first time a selective expression of stem cell-specific and stemness-promoting microRNAs in a distinct population of mature neurons to maintain their physiological functions in the adulthood, suggesting that similar epigenetic disinhibition mechanisms may be also critical for other terminally differentiated cells across species.

neuroscience↗
bioRxiv2025

Wnt11 Positively Regulates Neonatal Cardiomyocyte Maturation at the Interphase of Life via Frizzled 4 Receptor

Congenital heart defects (CHDs) affect 1% of live births and remain the leading cause of infant morbidity and early mortality. While most studies focus on the genetic basis of CHDs, relatively little is known about the interplay between intrinsic signaling and external environmental factors in the progression of CHDs after birth during the perinatal circulatory transition window when environmental stress factors are prevalent. We recently explored such interplay through a newly identified gene-environment regulatory circuit involving Wnt11 signaling and systemic hypoxia. Specifically, we demonstrated that activation of the Wnt11/Rb1 axis is critical for normal chamber-specific development after birth. This regulatory switch is disrupted by systemic hypoxia more robustly in the right ventricle (RV) than the left ventricle (LV), leading to enhanced neonatal cardiomyocyte cell cycle activity in an RV-specific manner, resulting in delayed maturation and attenuation of ventricular patterning in response to systemic hypoxia stress in the neonatal heart. Furthermore, we found that the Wnt11/Rb1 axis is also inactivated in infantile hearts with cyanotic CHDs, such as tetralogy of Fallot (TOF), potentially contributing to hypoxia-associated RV abnormalities in this context. However, the molecular players of this signaling cascade in neonatal cardiomyocyte remain largely unknown. Herein, we report that Frizzled 4 (Fzd4) acts as a specific upstream receptor for Wnt11 in neonatal cardiomyocytes. Specifically, Fzd4 exhibited an expression pattern like Wnt11 in neonatal heart perinatal circulatory transition under normal and hypoxemic environments. Furthermore, Fzd4 loss in neonatal cardiomyocytes stimulated cardiomyocyte cell cycle activity and disrupted the Wnt11-Rb1 signaling axis mirroring the impact of the Wnt11-deficient cardiomyocyte phenotype. Finally, co-immunoprecipitation analysis confirmed the Wnt11-Fzd4 binding in isolated neonatal cardiomyocytes and intact hearts. These results demonstrate that Fzd4 is a specific and required upstream receptor for the Wnt11-Rb1 signaling activity in the neonatal heart and provides mechanistic insights into the essential role of Wnt11 as a key positive regulator of neonatal cardiomyocyte transition from proliferative to mature phenotype at the interphase of life.

cell biology↗
bioRxiv2025

g.nome, A Transparent Bioinformatics Pipeline that Enables Differential Expression and Alternative Splicing Analysis by Non-Computational Biologists

Reproducibility and accessibility are cardinal principles in the rapidly evolving field of bioinformatics. As the collection of biological data grows, proper use of pipelines to analyze datasets can become a bottleneck restricting efficient analysis. Biologists who collect data and test hypotheses may not have strong computational backgrounds and may not be able to fully understand the underlying strengths and weaknesses of computational approaches or fully exploit their data. Some data may be misunderstood and, perhaps more importantly, critical findings may remain unobserved. High throughput RNA sequencing (RNAseq) has advanced our understanding of transcriptomics across diverse applications. Here we introduce g.nome, a bioinformatics platform that integrates contemporary tools necessary for independent analysis. A user-friendly graphical interface simplifies running jobs and allows simplified analysis of different datasets by non-bioinformaticians. g.nome was used to analyze the consequences of localizing the critical RNAi factor argonaute (AGO) to nuclei of colorectal cancer cell line HCT116. Analysis using the pipeline facilitated the straightforward identification of splicing changes and the prioritization of these splicing changes for validation and further experimental analysis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/652286v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@f0fa7org.highwire.dtl.DTLVardef@ccac5borg.highwire.dtl.DTLVardef@147c331org.highwire.dtl.DTLVardef@5fe66c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗
bioRxiv2025

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The first organ to develop in utero, the human heart undergoes significant changes during development and must sustain its function over a lifetime. To better characterize molecular changes in human cardiac cell-types across sex, aging, developmental and disease, we analyzed single nucleus RNA sequencing (snRNA-seq) datasets from 299 donors, identifying many more differentially expressed genes (DEGs) across developmental and disease states than by sex and age. In cardiomyocytes and most non-cardiomyocyte cell types, developmental and disease DEGs showed significant overlap. Cardiac development and disease were associated with convergent changes in non-cardiomyocyte intercellular communication, including TGF{beta} signaling, but differences in cell-type proportions. By integrating snRNA-seq with 106 snATAC-seq datasets, we reveal potential transcriptional factors driving fetal reactivation in disease. Finally, using spatial transcriptomics data, we identify that fetal reactivation is highly localized in niches. This work offers the largest multimodal, cell-type resolved interrogation of the human heart, providing insights into convergence in development and disease.

genomics↗
bioRxiv2025

Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants

Light is essential for photosynthesis; however, excess light can increase the accumulation of photoinhibitory reactive oxygen species that reduce photosynthetic efficiency. Plants have evolved photoprotective non-photochemical quenching (NPQ) pathways to dissipate excess light energy. In tobacco and soybean (C3 plants), overexpression of three NPQ genes, violaxanthin de-epoxidase (VDE), Photosystem II Subunit S (PsbS), and zeaxanthin epoxidase (ZEP), hereafter VPZ, resulted in faster NPQ induction and relaxation kinetics, and increased crop yields in field conditions. NPQ is well-studied in C3 plants; however, NPQ and the translatability of the VPZ approach in C4 plants is poorly understood. The green foxtail Setaria viridis is an excellent model to study photosynthesis and photoprotection in C4 plants. To understand the regulation of NPQ and photosynthesis in C4 plants, we performed transient overexpression in Setaria protoplasts and generated (and employed) stable transgenic Setaria plants overexpressing one of the three Arabidopsis NPQ genes or all three NPQ genes (AtVPZ lines). Overexpressing (OE) AtVDE and AtZEP in Setaria produced similar results as in C3 plants, with increased or reduced zeaxanthin (thus NPQ), respectively. However, overexpressing AtPsbS appeared to be challenging in Setaria, with largely reduced NPQ in protoplasts and under-represented homozygous AtPsbS-OE lines, potentially due to competitive and tight heterodimerization of AtPsbS and SvPsbS proteins. Furthermore, Setaria AtVPZ lines had increased zeaxanthin, faster NPQ induction, higher NPQ level, but slower NPQ relaxation. Despite this, AtVPZ lines had improved growth as compared to wildtype under several conditions, especially high temperatures, which is not related to the faster relaxation of NPQ but may be attributable to increased zeaxanthin and NPQ in C4 plants. Our results identified shared and unique characteristics of the NPQ pathway in C4 model Setaria as compared to C3 plants and provide insights to improve C4 crop yields under fluctuating environmental conditions.

plant biology↗
bioRxiv2024

Overexpression of Xanthophyll Cycle Genes Leads to Faster NPQ Acclimation in the C4 Monocot Setaria viridis

Slow relaxation and induction of Non-Photochemical Quenching (NPQ) limits plant productivity under fluctuating light in C3 plants but it is unknown if this trait extends to C4 plants. Three genes have been implicated in determining NPQ induction and relaxation rates under intermittent leaf shading; VDE and ZEP interconvert the xanthophyll pigments violaxanthin and zeaxanthin, and PsbS regulates the overall level of NPQ. Here we report the overexpression of the Arabidopsis thaliana VDE, ZEP, and PsbS in the NADP-Malic Enzyme C4 monocot Setaria viridis. We demonstrate these transgenic plants have faster NPQ induction and relaxation under fluctuating light but observe no impact on Photosystem II photochemistry yield. Under illumination, faster NPQ induction resulted in higher transient NPQ levels and a lower overall chlorophyll fluorescence yield. Together this introduces the potential for lower productivity due to over-quenching of chlorophyll during light fluctuation. Although we observed faster NPQ acclimation rates in our transgenic lines, hyperspectral imaging and pigment analysis suggest that there is little photosynthetic advantage to increasing NPQ acclimation over wildtype due to naturally fast C4 acclimation rates. These results indicate that further work is necessary in evaluating the role of NPQ acclimation in C4 growth dynamics towards the goal of improving crop productivity.

plant biology↗
bioRxiv2024

NAD+ - and EVA1-C-dependent reversal of neurological deficits is mediated by differential alternative RNA splicing in tauopathic animal models

Aberrant alternative splicing (ASEs) is an aging hallmark to Alzheimers Disease (AD). Although NAD+ and related metabolites can slow down AD, NAD+ on ASEs in AD remain unclear. Mouse transcriptomic data revealed NR-induced ASEs, focusing on the Eva1-C locus. AI-based algorithms predicted EVA1-C protein structures and protein-protein interactions. AD postmortem brain samples and tauopathy models including transgenic mice and worm was used for validation. NAD+ abundance/metabolic status modulates ASEs and the expression of EVA1-C isoforms, which in turn regulate the interaction with BAG-1 and HSP70 proteins. Importantly, EVA1-C is dramatically reduced in 20 Braak 5/6 AD patients compared to cognitive normal humans in different brain regions. NAD+ metabolism modulates abundance of specific mRNA isoforms, and that ASEs influence disease progression in model tauopathies and potentially AD. These results could facilitate future development of NAD+-based splice-switching therapeutics for AD. TeaserUnveiling the Link Between NAD+ Metabolism and Alzheimers Disease: Discovering the Role of Alternative RNA Splicing in Disease Progression and Potential Therapeutic Targets

neuroscience↗
bioRxiv2024

Avian-restrict Salmonella transition to endemicity is accompanied by localized resistome adaptation

Bacterial regional demonstration after global dissemination is an essential pathway for selecting distinct finesses. However, the evolution of the resistome during the transition to endemicity remains unaddressed. Using the most comprehensive whole-genome sequencing dataset of Salmonella enterica serovar Gallinarum (S. Gallinarum) collected from 15 countries, including 45 newly recovered samples from two related local regions, we established the relationship among avian-specific pathogen genetic profiles and localization patterns. Initially, we revealed the international transmission and evolutionary history of S. Gallinarum to recent endemicity through phylogenetic analysis conducted using a spatiotemporal Bayesian framework. Our findings indicate that the independent acquisition of the resistome via the mobilome, primarily through plasmids and transposons shapes a unique antimicrobial resistance profile among different lineages. Notably, the mobilome-resistome combination among distinct lineages exhibits a geographical-specific manner, further supporting a localized endemic mobilome-driven process. Collectively, this study elucidates resistome adaptation in the endemic transition of an avian-specific pathogen, likely driven by the localized farming style, and provides valuable insights for targeted interventions.

microbiology↗
bioRxiv2024

Characterization of Multicellular Niches Supporting Hematopoietic Stem Cells Within Distinct Zones

Previous studies of hematopoietic stem cells (HSCs) primarily focused on single cell-based niche models, yielding fruitful but conflicting findings1-5. Here we report our investigation on the fetal liver (FL) as the primary fetal hematopoietic site using spatial transcriptomics. Our study reveals two distinct niches: the portal-vessel (PV) niche and the sinusoidal niche. The PV niche, composing N-cadherin (N-cad)HiPdgfr+ mesenchymal stromal cells (MSCs), endothelial cells (ECs), and N-cadLoAlbumin+ hepatoblasts, maintains quiescent and multipotential FL-HSCs. Conversely, the sinusoidal niche, comprising ECs, hepatoblasts and hepatocytes, as well as potential macrophages and megakaryocytes, supports proliferative FL-HSCs biased towards myeloid lineages. Unlike prior reports on the role of Cxcl12, with its depletion from vessel-associated stromal cells leading to 80% of HSCs reduction in the adult bone marrow (BM)6,7, depletion of Cxcl12 via Cdh2CreERT (encoding N-cad) induces altered localization of HSCs from the PV to the sinusoidal niches, resulting in an increase of HSC number but with myeloid-bias. Similarly, we discovered that adult BM encompasses two niches within different zones, each composed of multi-cellular components: trabecular bone area (TBA, or metaphysis) supporting deep-quiescent HSCs, and central marrow (CM, or diaphysis) fostering heterogenous proliferative HSCs. This study transforms our understanding of niches by shifting from single cell-based to multicellular components within distinct zones, illuminating the intricate regulation of HSCs tailored to their different cycling states.

developmental biology↗