Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Gliomas preferentially develop within the action-mode network

Gliomas tend to arise in specific brain regions and may integrate into functional circuits, suggesting they could be regulated by brain activity. However, it remains unclear whether glioma growth is related to system-level brain networks. Analyzing neuroimaging data from three datasets including 1,310 patients with cerebral gliomas, we identified and replicated a functionally connected glioma network, which overlaps with the action-mode network (AMN), somatomotor network (SMN), and action-related subcortical regions. Resting-state functional connectivity (RSFC) of the AMN successfully predicted the location of glioma occurrence in two independent datasets with complex tumor distributions. Remarkably, no patient had a glioma entirely outside the AMN, and over 89% of patients exhibited gliomas with at least 50% overlap with the network. Moreover, the spatial overlap between glioma location and the AMN demonstrated significant prognostic value in survival analyses, with higher AMN-tumor overlap associated with poorer overall survival. Notably, the acetylcholine transporter, a key player in glioma pathogenesis that drives transcriptional reprogramming, showed an expression pattern overlapping with the AMN. Meta-analytic annotations further linked the glioma network to processes of action initiation, execution, and feedback. These findings indicate that gliomas preferentially arise in circuits involved in action and highlight the central role of the AMN in glioma pathophysiology and growth.

neuroscience↗

bioRxiv2026

Smad7-based biologic targeting epidermis and stroma promotes healing of diabetic wounds in mice and pigs

This study aimed to identify novel mechanisms of diabetic wound healing defects and test a therapeutic intervention using diabetic mouse and pig models. We found Smad7 transgene expression in mouse epidermis promoted wound healing in diabetic mice. To isolate effects of Smad7 on wounds, we created a Smad7-based biologic (Tat-PYC-Smad7) that penetrated cells of the wound. Topical Tat-PYC-Smad7 treatment to diabetic pig and mouse wounds accelerated healing compared to vehicle controls. Tat-PYC-Smad7-treated wounds showed reduced TGF{beta}/NF{kappa}B signaling, faster re-epithelialization and better extracellular matrix remodeling. Tat-PYC-Smad7 also attenuated neutrophil NETosis, potentially acting through reductions in MPO enzymatic activity and MPO nuclear entry, consequently reducing chromatin decondensation and the release of NET components. Our study revealed that Tat-PYC-Smad7 promoted diabetic wound healing by targeting keratinocytes and neutrophils, providing insight into mechanisms of diabetic wound healing defects targetable by Smad7-based therapy.

immunology↗

bioRxiv2025

Evolution tunes functional sub-state interconversion to boost enzyme function

Enzymes do not operate as static structures, but continuously fluctuate between different conformations. Enzymes therefore dynamically sample conformations with varying catalytic activity. However, it remains largely unexplored whether evolution can exploit the conformational dynamics between sub-states to improve activity. Here, we dissect the evolutionary trajectory of the {beta}-lactamase OXA-48 toward improved ceftazidime hydrolysis. Evolution relieved conformational bottlenecks by promoting alternate functional sub-states, gradually shifting the rate-limiting step from substrate binding to sub-state interconversion, and finally to the chemical step. Reorganization of the conformational landscape enhanced OXA-48s ability to hydrolyze ceftazidime and introduced a trade-off in its native activity against meropenem. This trade-off stemmed from catalytic incompatibility between the native and the evolved sub-state populations. Our findings highlight the transitions between functional sub-states as a mechanism of natural selection, shaping functional divergence and offering new strategies for enzyme and antibiotic engineering.

molecular biology↗

bioRxiv2025

Pan-cancer tumor classification by a holistic tumor microenvironment atlas

The tumor microenvironment (TME) heterogeneity presents a major bottleneck to effective cancer immunotherapies. We address this by establishing a pan-cancer tumor classification system based on the holistic TME cellular components. First, using single-cell transcriptomes from 1,271 patients across 26 cancer types, we compile a TME cellular atlas, leading to the identification of recurrent cell states and multicellular modules across cancer types. Among these, we highlight a type I interferon (IFN-I)-related multicellular module, including IFIT1+ tumor-associated macrophages, as a critical contributor to immune-activation TMEs. From a holistic perspective, pan-cancer TMEs exhibit trichotomous patterns predominantly driven by T, myeloid, and stromal compartments. Leveraging fine-grained TME cellular composition, we further stratify all tumors into 10 stable groups. These groups display varying responses to immune checkpoint blockade (ICB), and each rationally selected therapeutic strategy specifically perturbs the corresponding expression signature. Our pan-cancer tumor classification scheme reveals the underlying patterns of TME heterogeneity and provides a framework for stratifying patients, guiding treatment selection, and developing novel therapeutic options.

cancer biology↗

bioRxiv2025

Biophysically Grounded Deep Learning Improves Protein-Protein ΔΔG Prediction

Accurate {Delta}{Delta}G prediction requires integrating machine learning with biophysical insight. Existing approaches typically prioritize one while neglecting the other. We introduce an encoder-agnostic framework that injects interpretable biophysical priors into residue-level deep learning representations via cross-embedding attention. ProtBFF consistently improves performance under homology-based-clustering evaluation and enables general-purpose encoders to surpass state-of-the-art specialized models or larger models. Our results show that integrating simple, mechanistic priors into pretrained representations yields more trust-worthy predictors, offering a practical solution for broader protein engineering applications. Codegithub.com/Jfeldman34/ProtBFF

bioinformatics↗

bioRxiv2025

Flu Virus Infection in Juvenile Mice Leads to Lifelong Multi-Organ Damage and Parkinsonian Pathological Changes in Aging

The widespread prevalence of Long COVID underscores the potential for viral infections to exert prolonged effects on hosts long after initial recovery. Despite this recognition, the long-term and even lifelong consequences of viral infections remain poorly understood. In this study, we infected juvenile mice with influenza viruses and systematically examined the lifelong effects (from 4 to 450 days post-infection) of these infections. Pathological analysis revealed persistent lifelong damage in multiple organs, including chronic lung inflammation and fibrosis, along with significant cardiac and renal pathology. Viral infection led to substantial neuronal loss in key brain regions of mice (hippocampal CA1, CA3, and striatum) during middle and old age. Strikingly, we identified two hallmark pathological features of Parkinsons disease - dopaminergic neuron degeneration and Lewy body-like -synuclein inclusions - in middle and aged infected mice. Transcriptomic profiling demonstrated sustained upregulation of inflammation-related genes in both lung and blood tissues, correlating with observed pathological changes. Lung-derived secreted proteins, encoded by differentially expressed genes, may mediate cross-organ communication affecting cardiac, renal, and neurological function. Brain transcriptome analysis at three months post-infection revealed downregulation of neurodevelopmental genes, potentially contributing to subsequent neuronal loss and Parkinsonian pathology. These findings collectively suggest that pulmonary influenza infection can induce systemic multi-organ effects through both secretory pathways and chronic inflammatory responses. The study offers crucial insights for developing more effective strategies to prevent and manage infectious diseases and their long-term sequelae.

microbiology↗

bioRxiv2025

Ser129 Phosphorylation Paradox: Non-phosphorylated α-Synuclein Drives Parkinson' s Disease-like Pathogenesis in Vivo

Accumulation of phosphorylated -synuclein at serine 129 is a hallmark of Parkinsons disease (PD), but its pathogenic role remains controversial. We conducted longitudinal studies using non-phosphorylatable S129A and phosphomimetic S129D -synuclein global knock-in mice. Unexpectedly, the S129A mice--rather than S129D mice--developed reproducible olfactory, motor, and cognitive deficits, dopaminergic dysfunction and neurodegeneration, -synuclein insolubility, and Lewy-like inclusions by 3 to 9 months, with progressive worsening up to 12 months of age. Spatial transcriptomics and electron microscopy revealed mitochondrial, synaptic, and protein ubiquitination abnormalities in the substantia nigra of S129A -synuclein mice. Viral vector-mediated nigral overexpression of S129D--synuclein or systemic administration of an anti--synuclein-aggregation drug partially alleviated the early neurological phenotypes of S129A mice. These results implicate non-phosphorylatable -synuclein as a direct pathogenic driver for PD.

neuroscience↗

bioRxiv2025

Naturally occurring mutations in replication proteins of a small RNA virus that alter the number, sizes, and relative abundances of subgenomic RNAs

Many positive-strand (+) RNA viruses produce subgenomic RNAs (sgRNAs) in infected cells. sgRNAs are synthesized by virus-encoded replication proteins (RPs), but whether RPs regulate the number and sizes of sgRNAs remains largely unknown. We report multiple naturally occurring mutations within the RPs of turnip crinkle virus (TCV) that alter the number, sizes, and relative abundances of TCV sgRNAs. TCV is a (+) RNA virus that normally produces two sgRNAs: the 1,724-nucleotide (nt) sgRNA1 expressing movement proteins, and the 1,449-nt sgRNA2 expressing capsid protein. A single amino acid change, A113V, within a region shared by TCV RPs p28 and p88, diminished sgRNA1 levels and delayed viral systemic spread. Interestingly, three second-site RP mutations emerged in infected plants that, alone or in combination with A113V, resulted in over-production of sgRNA1 or accumulation of two alternative sgRNAs of 1,876 and 1,601 nt, and rescued A113V defects. The alternative sgRNAs originated from nearly identical recombination events, their size difference reflecting varying 5 extensions. Structural modeling of the TCV replication complex showed a conical ring architecture containing p28, p88, and a partially double-stranded RNA. While A113 may interact with TCV genomic RNA or host factors to promote (-) sgRNA1 synthesis, the second-site mutations likely influenced binding and entry of RNA template into the p88 active site. They may stall RNA synthesis at specific hotspots and stimulate template switching, thereby generating alternative (-) sgRNAs. Our findings reveal previously unrecognized constraints on viral RPs that ensure production of sgRNAs with precise sizes and abundances. Author summaryMany (+)-strand viruses, such as SARS-CoV-1 and -2, Chikungunya virus, and tomato mosaic virus, synthesize subgenomic RNAs (sgRNAs) during cellular infections. Targeting sgRNA production could prove to be an effective antiviral strategy, as sgRNAs are needed to express diverse proteins critical for viral survival and transmission. Although sgRNA production requires virus-encoded replication proteins (RPs), whether RPs also dictate the number, sizes, and relative abundances of viral sgRNAs remain to be thoroughly investigated. We identified and characterized four naturally occurring mutations in RPs of the plant-infecting turnip crinkle virus that specifically perturbed one of the sgRNAs. Our findings uncover novel constraints on viral RPs that safeguard sgRNA integrity, and avail them as potential targets for controlling pathogenic viruses.

plant biology↗

bioRxiv2025

The glutamine transporter Slc38a1 is widely expressed in the embryonic neurogenic niches and impacts neuronal volume, survival, and morphology

The amino acid glutamine, and its derivatives glutamate and GABA, are pivotal for neurogenesis. However, how glutamine is mechanistically supplied to the cells in the neurogenic niches and its broader impact on neurodevelopment, remain poorly characterized. The Solute carrier family 38 member 1 (Slc38a1) exhibits high affinity for glutamine and accumulates glutamine in select cells. We investigated whether Slc38a1 is essential for neurogenesis and whether it has an impact on brain structure and function. Slc38a1 mRNA transcript and protein are widely expressed in the embryonic brain, including in the dorsal pallium and sub-pallium. At embryonic day 15.5, Slc38a1 localizes in neuronal stem cells in the ventricular zone in the forebrain, while it localizes in mature neurons in the sub-ventricular zone of the hindbrain. In the adult brain, Slc38a1 is not detected in neuronal stem cells in the sub-granular zone, however, it is highly enriched in mature local parvalbumin+ and somatostatin+ interneurons and ependyma. Analyses of single-cell RNA sequencing data further reveal that both the number of Slc38a1-expressing cells and the average transcript level of Slc38a1 are significantly higher in embryo brain cells compared to adults. In the embryo, Slc38a1 transcripts are particularly enriched in immature neuronal lineages and embryonic oligodendrocyte precursor populations, whereas in the adult, expression is more prominent in neural progenitor cells and radial glia. Disruption of Slc38a1 in mice impacts body weight, brain size and glutamatergic neuronal volume, while dendritic arborization is diminished and cellular life span is shortened. Altogether, Slc38a1 is essential for normal neurodevelopment, indirectly regulates adult neurogenesis in the sub-granular zone and influence neuronal morphology and cell viability.

neuroscience↗

bioRxiv2025

Mitochondrial control of fuel switching via carnitine biosynthesis

Environmental adaptation often involves a shift in energy utilization toward mitochondrial fatty acid oxidation, which requires carnitine. Besides dietary sources of animal origin, carnitine biosynthesis from trimethyllysine (TML) is essential, particularly for those who consume plant-based diets; however, its molecular regulation and physiological role remain elusive. Here, we identify SLC25A45 as a mitochondrial TML carrier that controls carnitine biosynthesis and fuel switching. SLC25A45 deficiency decreased the carnitine pool and impaired mitochondrial fatty acid oxidation, shifting reliance to carbohydrate metabolism. Slc25a45-deficient mice were cold-intolerant and resistant to lipid mobilization by GLP1 receptor agonist (GLP-1RA), rendering them resistant to adipose tissue loss. Our study suggests that mitochondria serve as a regulatory checkpoint in fuel switching, with implications for metabolic adaptation and the efficacy of GLP-1RA-based anti-obesity therapy.

biochemistry↗

bioRxiv2025

Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35

Mitochondria provide a variety of metabolites, in addition to ATP, to meet cell-specific needs. One such metabolite is phosphoenolpyruvate (PEP), which contains a higher-energy phosphate bond than ATP and has diverse biological functions. However, how mitochondria-generated PEP is delivered to the cytosol and fulfills cell-specific requirements remains elusive. Here, we show that SLC25A35 regulates mitochondrial PEP efflux and glyceroneogenesis in lipogenic cells that utilize the pyruvate-to-PEP bypass. Reconstitution and structural studies demonstrated PEP transport by SLC25A35 in a pH gradient-dependent manner. Loss of SLC25A35 in adipocytes impaired the conversion of mitochondrial PEP into glycerol-3-phosphate, thereby reducing glycerolipid synthesis. Significantly, hepatic inhibition of SLC25A35 in obese mice alleviated steatosis and improved systemic glucose homeostasis. Together, these results suggest that mitochondria facilitate glycerolipid synthesis by providing PEP via SLC25A35, offering lipogenic mitochondria as a target to limit glycerolipid synthesis, a pivotal step in the pathogenesis of hepatic steatosis and Type 2 diabetes.

cell biology↗

bioRxiv2025

Monitor individual health and improve breeding success in Crested ibis (Nipponia nippon)

Biodiversity loss has become a pressing issue, requiring effective conservation measures. Drawing lessons from successful examples is essential. The Crested ibis (Nipponia nippon), once critically endangered but now recovering through intensive conservation programs, provides an informative model for evaluating and improving conservation practices. Using 17 years of monitoring data from a captive population spanning eight generations, we applied quantitative genetic tools (Animal Model) to characterize individual growth and improve breeding success of this endangered species. We found that body weight from Day 0 to Day 42 exhibited significant heritability (h2 = 0.195, 95% HPD 0.139 [~] 0.250). As for growth curve parameters, growth time-scale parameter a (h2 = 0.33, 95% HPD: 0.14 [~] 0.55) and growth-rate coefficient b (h2 = 0.22, 95% HPD: 0.10 [~] 0.34) were also significantly heritable, while the heritability of potential maximum weight M was relatively low (h2 = 0.023, 95% HPD: 0.00 [~] 0.16). We further estimated the breeding values of these phenotypical traits to inform future breeding and selections. Intergenerational analyses showed the estimated breeding values for body weight exhibited a tendency to increase, accompanied by a slower growth rate, though trends did not differ significantly from expectations under genetic drift. Comparison of parental and offspring growth trajectories revealed that healthy offspring closely follow parental growth trajectories, whereas unhealthy individuals display reduced growth. Given the multiple breeding times of this long-lived species, this approach enables effective monitoring of individual growth and health, allowing timely veterinary interventions so to enhance conservation efficiency.

zoology↗

bioRxiv2025

Evaluate and simulate the reproduction and survival of a reintroduced population in an endangered bird species Crested ibis (Nipponia nippon)

O_LIReintroduction programs are critical for restoring endangered species. However, scientific assessments and management recommendations based on comprehensive vital rates across the entire life cycle remain limited for such programs. The Crested ibis (Nipponia nippon), once nearly extinct, has been the focus of intensive conservation efforts, including reintroduction into its historical range. Here, we systematically evaluate the success of a Crested ibis reintroduction population by integrating long-term field monitoring with population dynamic modeling. C_LIO_LIWe conducted a systematic, multi-year (2023-2025) demographic study of a reintroduced Crested ibis population in Dongzhai National Nature Reserve, China. From 2013 to 2023, a total of 133 captive Crested ibises were released in seven batches within the nature reserve. By 2025, the wild population had exceeded 500. Based on the combination of field monitoring (n = 176 pairs) and GPS telemetry (n = 74 GPS tags, the longest monitoring time lasting 4 years), we quantified reproductive output and mortality rates across six life stages: nest building, incubation, offspring provisioning, fledgling (< 1 year), sub-adult (1-2 years), and adult (> 2 years). C_LIO_LIThe results show that the average clutch size of this population is 3.24 {+/-} 0.08, and each pair of parent birds can rear 1.31 {+/-} 0.12 nestlings to fledging each year. We found that high mortality during the incubation (32.5%, n = 425 eggs), offspring provisioning (34.1%, n = 287 chicks), and fledgling stages (38.6%, n = 63 birds). Key causes included unfertilized eggs, predation, starvation, and human disturbance. On the other hand, the mortalities in the nest building (9.1%, n = 176 pairs), sub-adult (9.8%, n = 28 birds) and adult stage (21.3%, n = 15 birds) were relatively low. Stage-structured matrix model shows a positive population growth of this reintroduced population (growth rate {lambda} = 1.053), with the population expected to increase 13-fold over 50 years (6,858 individuals). Sensitivity analysis indicates that adult survival had the strongest influence on population growth. Correspondingly, we predict that by 2075, its distribution range will expand 13-fold in tandem with population growth, exceeding 51,000 km{superscript 2} and covering several surrounding cities. C_LIO_LIOur comprehensive monitoring, evaluation, and simulation across the full life-cycle confirm that the reintroduced population is successfully established and self-sustaining. This finding addresses a critical research gap: the lack of a scientific and systematic framework for assessing population reintroductions in endangered species. Furthermore, we identified key conservation practices to enhance population growth and stability, including predator control, supplemental feeding, the rescue of weak chicks, and reducing human disturbance through public engagement. To ensure long-term viability, we also recommend implementing genetic management to avoid inbreeding. The resulting framework provides a practical model for improving reintroduction success and promoting species recovery in other endangered species. C_LI

ecology↗

bioRxiv2025

Melody: Decoding the Sequence Determinants of Locus-Specific DNA Methylation Across Human Tissues

DNA methylation is a fundamental epigenetic modification that plays crucial roles in transcriptional regulation, cellular differentiation, and genome stability. However, how locus-specific DNA methylation is determined by intrinsic DNA sequence remains poorly understood. Here, we introduce Melody, a deep learning framework that predicts DNA methylation from 10-kb genomic sequences, enabling the integration of both local and long-range sequence signals. Across 39 human tissues, Melody accurately predicts methylation profiles and consistently outperforms existing state-of- the-art methods in whole-chromosome, hypomethylated-region, and cell-type-specific benchmarks. Melody also generalizes to methylation quantitative trait locus (meQTL) effect prediction and identifies regulatory sequence motifs associated with methylation variability. To extend prediction beyond profiled tissues, we further develop Melody-G, which incorporates single-cell RNA-seq foundation model embeddings to infer methylation states in previously unseen cell types directly from transcriptomic data. Together, Melody provides a unified framework for linking genomic sequence and cellular state to DNA methylation and offers new insights into the regulatory logic governing the human methylome.

bioinformatics↗

bioRxiv2025

Ferroptosis governs lymphatic vessel growth and regression

Whether, when, and how lymphatic vessels undergo cell death remains poorly understood. Here we identify ferroptosis as a physiological, cell-intrinsic regulator of the lymphatic endothelial cell survival during development and following injury, in stark contrast to the resilient organotypic blood endothelial cells. The lymphatic susceptibility to ferroptosis stems from tampered cystine/ hydropersulfide metabolism, alongside reduced glutathione availability triggered by an SH3RF3 E3 ligase mediated GPX4 degradation, and enhanced integration of polyunsaturated fatty acid enriched membrane phospholipids. Inducing ferroptosis genetically or pharmacologically elevated lymphatic lipid peroxidation, halted embryonic lymphangiogenesis and prevented post-injury lymphatic overgrowth while simultaneously shaped immune responses. Conversely, ferroptosis inhibition through saturated fatty acid supplementation led to pathological lymphatic hyperplasia. Targeting lymphatic ferroptotic mechanisms holds promise against pathological lymphatic growth in response to injury.

cell biology↗

bioRxiv2025

Inferring virtual cell environments using multi-agent reinforcement learning

1Single cells interact continuously to form a cell environment that drives key biological processes. Cells and cell environments are highly dynamic across time and space, fundamentally governed by molecular mechanisms, such as gene expression. Recent sequencing techniques measure single-cell-level gene expression under specific conditions, either temporally or spatially. Using these datasets, emerging works, such as virtual cells, can learn biologically useful representations of individual cells. However, these representations are typically static and overlook the underlying cell environment and its dynamics. To address this, we developed CellTRIP, a multi-agent reinforcement learning method that infers a virtual cell environment to simulate the cell dynamics and interactions underlying given single-cell data. Specifically, cells are modeled as individual agents with dynamic interactions, which can be learned through self-attention mechanisms via reinforcement learning. CellTRIP also applies novel truncated reward boot-strapping and adaptive input rescaling to stabilize training. We can in-silico manipulate any combination of cells and genes in our learned virtual cell environment, predict spatial and/or temporal cell changes, and prioritize corresponding genes at the single-cell level. We applied and benchmarked CellTRIP on various simulated and real gene expression datasets, including recapitulating cellular dynamic processes simulated by gene regulatory networks and stochastic models, imputing spatial organization of mouse cortical cells, predicting developmental gene expression changes after drug treatment in cancer cells, and spatiotemporal reconstruction of Drosophila embryonic development, demonstrating its outperformance and broad applicability. Interactive manipulation of those virtual cell environments, including in-silico perturbation, can prioritize spatial and developmental genes for single-cell-level changes, enabling the generation of new insights into cell dynamics over time and space. CellTRIP is open source as a general tool and available at github.com/daifengwanglab/CellTRIP.

bioinformatics↗

bioRxiv2025

Optimization of fermentation conditions for Metarhizium robertsii and its effect on rice growth

Metarhizium robertsii is an important entomopathogenic fungus and plant endophyte, possessing dual functionality as both an insecticide and a plant growth promoter, which has led to its widespread application in agriculture. However, the effects and underlying mechanisms of M. robertsii (MAA)in promoting rice growth remain poorly understood. This study confirmed the growth-promoting effects of MAA and its fermentation supernatant on rice. Based on single-factor and response surface methodology experiments, the fermentation conditions of MAA were subsequently optimized using rice root length as a key indicator, and the potential mechanisms behind this growth promotion were preliminarily investigated. The results demonstrated that both MAA and its fermentation supernatant exerted significant growth-promoting effects on rice. Sucrose and peptone were identified as the optimal carbon and nitrogen sources, respectively. The most pronounced effect was observed when the fermentation supernatant, produced under the conditions of pH 6.0, 0.2% {beta}-Ala, and 100 mol/L Al2(SO4)3, was applied, resulting in a 21.7% increase in rice root length compared to the control group. Furthermore, significant enhancements in chlorophyll content and denser root hairs were recorded in rice treated with the MAA fermentation supernatant, with the chlorophyll content increasing by 28.17% compared to the control. These findings provide a theoretical basis for the development and application of green and efficient bio-inoculants. IMPORTANCEMetarhizium robertsii is an endogenous plant fungus that can be effective for efficient insect control, but the plant-promoting effect of this fungus and its related studies are less reported. The colonization ability and growth promotion effect of Metarhizium robertsii on different crops vary. In this study, a sterile hydroponic system for rice was established. The research found that Metarhizium robertsii can colonize the root system of rice, significantly promoting rice growth, and its growtion-promoting effect is affected by the differences in its fermentation products. After the optimization of the response surface of the fermentation conditions of Metarhizium robertsii, its growth-promoting ability increased by 21.7%. Developing microbial biofertilizers/biopesticides as a basis for reducing chemical inputs in rice cultivation.

microbiology↗

bioRxiv2025

Candling analysis of egg development in an endangered bird species Crested ibis (Nipponia nippon)

Identifying key factors influencing the survival of animals, particularly rare and endangered species is crucial to biodiversity conservation. In birds, hatching failure is pronounced in endangered species. Accurate assessment of egg development and the ability to distinguish non-viable eggs are essential prerequisites for identifying the causes of hatching failure and applying appropriate conservation practices. The Crested ibis (Nipponia nippon), a flagship endangered species, has a long history of captive breeding, which has contributed to population recovery. However, little is known about the specific process and characteristics of its egg development. In this study, we provided the first comprehensive description of normal egg development in the Crested ibis, including both the changes observed in unfertilized eggs during incubation and embryonic development via candling (n = 106 eggs, with 1,423 candling images), a commonly used non-invasive method for assessing egg fertility and embryonic status, and offered a practical reference for assessing fertilization status and embryo viability. In addition, we estimated the timing of embryo mortality and found that most deaths occurred during mid-incubation (Day 7[~]15) (n = 12, 60.0%) and shortly before hatching (Day 23[~]29) (n = 7, 35.0%), highlighting these critical periods that require particular attention. This species-specific documentation of egg development provides a valuable reference for accurately assessing embryonic progress, evaluating environmental effects on survival, and guiding adaptive management, benefiting both captive breeding programs and field conservation efforts.

zoology↗