Biology subjects

WANG, Y.

Publications and source records attributed to WANG, Y..

17 recordsLinked to original sources

bioRxiv2026

Adenosine refines the balance of spermatogonial proliferation and differentiation

The balance between spermatogonial proliferation and differentiation is essential for sustaining male fertility, yet the contribution of cellular metabolism remains poorly understood. Here, we showed that adenosine levels increased significantly during spermatogonial differentiation and promoted the formation of differentiating spermatogonia. Using a conditional knockout mouse model in which Ahcy, a gene encoding an enzyme in adenosine synthesis, is deleted from spermatogonia, we found that disruption of adenosine generation blocked spermatogonial differentiation, resulting in a transient delay in spermatogenesis. We further demonstrated that adenosine exerted its effects partially through ADORA2A- and ADORA2B-mediated signaling. Downregulating these receptor activities by specific inhibitors in spermatogonial culture or by genetic ablation in mice led to increased spermatogonial proliferation. Taken together, our study identified adenosine as a metabolic signal in refining the balance between spermatogonial proliferation and differentiation, linking cellular metabolism to critical developmental timing and stem cell fate decisions.

developmental biology↗

bioRxiv2026

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

The outbreak frequency and geographic distribution of viral pathogens are continuously expanding, making enhanced genomic surveillance an urgent global public health need. Parallel library preparation combining next-generation sequencing (NGS) and third-generation sequencing (TGS) can substantially improve the coverage and resolution of genomic surveillance, representing a key strategy for strengthening surveillance. Here we developed a complete sample-to-result system integrating a programmable active-matrix digital microfluidic (AM-DMF) chip with a bioinformatics analysis pipeline. Compared with conventional manual protocols used in public health laboratories, our system reduces reagent consumption by 72%, shortens library preparation time by 45% and decreases the inter-batch coefficient of variation (CV) by 20%. In 20 RT-qPCR-confirmed clinical samples, the system achieved complete concordance for viral identification and assigned serotypes/genotypes consistent with sequencing-based phylogenetic analysis. This system is field-deployable and enables rapid virus serotyping as well as in-depth genomic surveillance. TeaserA digital microfluidic platform integrating short- and long-read sequencing enables rapid comprehensive viral genome analysis.

bioengineering↗

bioRxiv2026

Interplay between mobile genetic elements drives a fusion-deletion life cycle of plasmids to fuel antimicrobial resistance

Plasmids are key drivers of bacterial adaptation, yet the mechanisms that generate their diversity remain poorly understood. Here, we show that mobile genetic elements (MGEs) orchestrate a fusion-deletion life cycle that repeatedly remodels plasmids during evolution in Staphylococcus aureus. Large-scale genomic analyses reveal that multireplicon plasmids are widespread and strongly enriched in transposases. Using experimental assays, we demonstrate that rare MGE-mediated fusion events, via homologous recombination or transposition, combine distinct plasmids into single multireplicon elements, expanding gene content and transfer potential. Antibiotic pressure selectively enriches these fused plasmids, rescuing bacterial populations under stress, whereas opposing selective forces, including phage predation, favour deletion derivatives that preserve essential functions and phage transmissibility. This cyclical process generates dynamic plasmid repertoires with conserved backbones and diverse accessory modules. We propose that MGE-driven fusion-deletion cycles represent a general principle of plasmid evolution, explaining the rapid emergence and persistence of multidrug-resistant plasmids across bacterial pathogens.

microbiology↗

bioRxiv2025

Kinetic measurements of the fluorescent protein synthesis facilitate determination of the miRNA activity.

Oncogenesis is inevitably associated with microRNA expression deregulation. Thus, development of both miRNA targeting substances or small RNA for ant-cancer therapy have been reported. Specifically, repression of the miR-16-1-3p and miR-16-2-3p activities play pivotal roles in osteosarcoma and many other cancers. The majority of miRNA sensors use protein degradation to measure miRNA activities. Here we report miRNA sensors that use fluorescent protein synthesis rather than degradation to measure miRNA activity. Specifically, miR-16-1-3p and miR-16-2-3p sensors consist of the bidirectional tet-On system driving the expression of the Katusha2S protein that is regulated by the RNA interference and GFP as a reference. These sensors specifically detect mir16-1-3p and mir16-2-3p small RNA mimics in the osteosarcoma cell line after doxycycline induction. Kinetic measurements of the reporter responses to the miRNA mimics revealed that pre-induced sensors reach significant differences from the control faster, within 2h than the sensors that were induced after mimic transfection. Thus, kinetic measurements of the fluorescent protein synthesis during doxycycline induction of the tet-On system are feasible for determination of the small RNA activity.

molecular biology↗

bioRxiv2025

The Small Non-coding RNA miR-16-1-3p Hampers Cancer Stem Cell Self-renewal and Invasiveness, Boosting Chemosensitivity by Adjusting TGF-β1 Signaling via MDM2/p53 Axis in Human Osteosarcoma.

The TGF-{beta} signaling pathway has both tumor-suppressing and metastasis-promoting effects in cancer. However, the molecular determinants governing this switch remain unclear. Here, we explored the miR-16-1-3p/MDM2/p53 axis as a critical conductor of the TGF-{beta}-Smad pathway in osteosarcoma. Although miR-16-1-3p overexpression by itself markedly reduces proliferative and clonogenic potential of U2OS cells, when paired with TGF-{beta} treatment, it significantly increases arrest cells in G1 phase and nearly extinguishing the growth capability of these cells. MiR-16-1-3p overexpression inhibited TGF-induced actin remodeling and EMT featuring, significantly decreasing vimentin levels. TGF-{beta} enhances both 2D and 3D migration, but miR-16-1-3p overexpression, alone or with TGF-{beta}, strongly counteracts its pro-migratory effects. MiR-16-1-3p restored p53 stability by targeting MDM2, redirecting TGF-{beta}-Smad signaling toward p21 activation and proliferation inhibition while attenuating its EMT-promoting capacity. Administration of TGF-{beta} together with miR-16-1-3p dramatically increases the sensitivity of wild-type U2OS cells to cisplatin, exceeding that of TGF-{beta} therapy alone by more than an order of magnitude. Administering TGF-{beta} and miR-16-1-3p together significantly reduces the tumor nodule volume and Ki67 expression, while effectively eradicates metastases in the chicken chorioallantoic membrane (CAM) in vivo model. For the first time, our research demonstrates that miR-16-1-3p shifts TGF-{beta}1 signaling from a facilitator of metastasis to a promoter of anti-growth effects through MDM2 inhibition and p53 stabilization, effectively reducing the self-renewal and invasiveness of cancer stem cells in human osteosarcoma model. This process preserves TGF-{beta}s tumor-suppressive role while limiting its associated cancer risks.

cancer biology↗

bioRxiv2025

RIPK3-dependent sequential recruitment of MLKL and RIPK1 drives PANoptotic cell death and chemokine production

PANoptosis, an immunogenic programmed cell death (PCD) modality, integrates features of pyroptosis, apoptosis, and necroptosis through assembly of the PANoptosome complex. Despite its conceptualization as a distinct PCD form, PANoptosis remains controversial due to insufficient characterization of its morphological hallmarks and molecular regulation. This study aimed to investigate the molecular mechanisms underlying the assembly of PANoptosomes in the PANoptotic pathway. We identified a novel receptor-interacting protein kinase 3 (RIPK3)-initiated PANoptotic pathway that functions without pattern recognition receptors (PRRs) and the ASC (apoptosis-associated speck-like protein containing a CARD) inflammasome. Using multimodal imaging and biochemical approaches, we identify unique morphological signatures distinguishing PANoptotic cells from canonical pyroptotic, apoptotic, or necroptotic counterparts. Mechanistically, RIPK3 forms round homopolymeric scaffolds--distinct from necroptotic amyloid-like fibers--to sequentially recruit MLKL and RIPK1, forming a dynamic RIPK3-MLKL-RIPK1-FADD-caspase-8 complex (RIPK3-PANoptosome). This platform coordinates concurrent activation of pyroptotic, apoptotic, and necroptotic effectors. Cross-regulatory interactions between these pathways establish a homeostatic system where perturbations bias death modality into a certain cell death type, altering the death process and outcomes. Functionally, PANoptotic cells orchestrate chemokine secretion through parallel kinase-dependent (RIPK3-MLKL) and kinase-independent (RIPK1-IKK-NF-{kappa}B) mechanisms, driving macrophage recruitment. Our findings resolve the molecular logic of PANoptosome assembly, redefine PANoptosis as a tunable PCD paradigm, and establish its role in immunomodulation, providing a framework for targeting inflammatory cell death in disease.

cell biology↗

bioRxiv2024

SMARCA4 mutation induces tumor cell-intrinsic defects in enhancer landscape and resistance to immunotherapy

Cancer genomic studies have identified frequent alterations in components of the SWI/SNF (SWItch/Sucrose Non- Fermenting) chromatin remodeling complex including SMARCA4 and ARID1A. Importantly, clinical reports indicate that SMARCA4-mutant lung cancers respond poorly to immunotherapy and have dismal prognosis. However, the mechanistic basis of immunotherapy resistance is unknown. Here, we corroborated the clinical findings by using immune-humanized, syngeneic, and genetically engineered mouse models of lung cancer harboring SMARCA4 deficiency. Specifically, we show that SMARCA4 loss caused decreased response to anti-PD1 immunotherapy associated with significantly reduced infiltration of dendritic cells (DCs) and CD4+ T cells into the tumor microenvironment (TME). Mechanistically, we show that SMARCA4 loss in tumor cells led to profound downregulation of STING, IL1{beta} and other components of the innate immune system as well as inflammatory cytokines that are required for efficient recruitment and activity of immune cells. We establish that this deregulation of gene expression is caused by cancer cell-intrinsic reprogramming of the enhancer landscape with marked loss of chromatin accessibility at enhancers of genes involved in innate immune response such as STING, IL1{beta}, type I IFN and inflammatory cytokines. Interestingly, we observed that transcription factor NF-{kappa}B binding motif was highly enriched in enhancers that lose accessibility upon SMARCA4 deficiency. Finally, we confirmed that SMARCA4 and NF-{kappa}B co-occupy the same genomic loci on enhancers associated with STING and IL1{beta}, indicating a functional interplay between SMARCA4 and NF-{kappa}B. Taken together, our findings provide the mechanistic basis for the poor response of SMARCA4-mutant tumors to anti-PD1 immunotherapy and establish a functional link between SMARCA4 and NF-{kappa}B on innate immune and inflammatory gene expression regulation.

immunology↗

bioRxiv2023

The exotic thymidine modification 5-hydroxymethyluridine in dinoflagellate Amphidinium carterae

Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) is present at unusually high levels and its function remains an enigma in dinoflagellates chromosomal DNA. Here, we demonstrate that 5hmU exhibits content variations in different dinoflagellates and is generated at the poly-nucleotide level through hydroxylation of thymidine. Importantly, we identified the enzyme, which is a putative dinoflagellate TET/JBP homologue, catalyzing 5hmU production using either in vivo or in vitro biochemical assay. Based on the near-chromosomal level genome assembly of dinoflagellate Amphidinium carterae, we depicted a comprehensive 5hmU landscape and found that most 5hmU peaks share a conserved TG-rich motif, and are significantly enriched in repeat elements, which mark partially overlapping regions with 5-methylcytosine (5mC) sites. Moreover, inhibition of 5hmU via dioxygenase inhibitor leads to transcriptional activation of 5hmU-marked transposable elements (TEs), implying that 5hmU appears to serve as epigenetic marks for silencing retrotransposon. Together, our results revealed the biogenesis, genome-wide landscape and molecular function of dinoflagellate 5hmU, providing mechanic insight into the function of this enigmatic DNA mark.

molecular biology↗

bioRxiv2023

The highly abundant mRNA m1A modification: a new layer of gene regulation in dinoflagellates

The N1-methyladenosine (m1A) is a positively charged RNA modification known to disrupt base pairing and influence RNA stability. Despite its limited presence in the mRNA of various organism models, including yeast, mouse, and human, the exact processes of m1A biosynthesis, distribution, regulation, and function remain controversial. Dinoflagellates are a major group of single-celled eukaryotic phytoplankton having peculiar crystalline chromosomes. Their genes are arranged in unidirectional gene clusters along the chromosomes and only have minimal transcriptional regulation, implying the involvement of other critical regulatory mechanisms in gene expression. Here, we found that m1A rather than m6A is the most prevalent mRNA modification in dinoflagellates and asymmetrically distributed along mature transcripts. Utilizing the dinoflagellate species Amphidinium carterae as a study model, we identified 13481 m1A peaks characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 10794 genes, many of which are involved in carbon and nitrogen metabolism. With enrichment around stop codon region and 3 UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion (N-depletion) treatment led to significant global decrease of mRNA m1A amount, causing dramatic variation in translation rates with minimal changes in transcription. Additionally, our analysis uncovered distinctive methylation patterns of m1A modification that appears to post-transcriptionally modulate gene expression through regulating translation efficiency. Thus, our findings provide the first comprehensive m1A map of dinoflagellate mRNA, shedding light on its crucial role as a post-transcriptional regulatory layer to compensate the degeneration of transcriptional regulation in dinoflagellate. This study also sets the stage for further investigation into the biogenesis and functional significance of mRNA m1A in eukaryotes.

molecular biology↗

bioRxiv2023

AI becomes a masterbrain scientist

Recent rapid and unexpected advancements in Artificial Intelligence (AI) have dramatically shocked the world. Large language models, such as ChatGPT and GPT-4, have demonstrated remarkable potential in aggregating and organizing knowledge while providing insights and solutions to specific questions. In this study, we further explore the possibility of GPT-4 taking on a central role in a complete closed-loop biological research, functioning as a masterbrain scientist responsible for generating hypotheses, designing experiments, analyzing results, and drawing conclusions. Our findings suggest that AI has the potential to evolve into a genuine scientist, and could lead an unprecedented revolution in the area of science.

bioinformatics↗

bioRxiv2023

Determining Best Practice for the Spatial Poisson Process in Species Distribution Modelling

Poisson processes have become a prominent tool in species distribution modelling when analysing citizen science data based on presence records. This study examines four distinct statistical approaches, each of which utilises a different approximation to fit a Poisson point process. These include two Poisson regressions with either uniform weights or the more elaborate Berman-Turner device, as well as two logistic regressions, namely the infinitely weighted logistic regression method and Baddeleys logistic regression developed in the context of spatial Gibbs processes. This last method has not been considered in depth in the context of Poisson point processes in the previous literature. A comprehensive comparison has been conducted on the performance of these four approaches using both simulated and actual presence data sets. When the number of dummy points is sufficiently large, all approaches converge, with the Berman-Turner device demonstrating the most consistent performance. A Poisson process model was developed to accurately predict the distribution of Arctotheca calendula, an invasive weed in Australia that does not appear to have been the subject of any species niche modelling analysis in the existing literature. Our findings are valuable for ecologists and other non-statistical experts who wish to implement the best practices for predicting species distribution using Poisson point processes.

ecology↗

bioRxiv2022

A machine learning method for estimating the probability of presence using presence-background data

Estimating the prevalence or the absolute probability of presence of a species from presence-background data has become a controversial topic in species distribution modelling. In this paper we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with unfounded model assumptions would render fragile estimation/prediction of the desired probabilities. Rather we propose the local knowledge condition, which relaxes the pre-determined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the CLK method utilising the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling.

ecology↗

bioRxiv2022

Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench

Hailed as "The Fourth Pole", the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla : Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.

microbiology↗

bioRxiv2022

Dynamic characteristics and Functional Analysis Provide new insights into the role of GauERF105 in resistance against Verticillium wilt in Cotton

Verticillium wilt is the most devastating disease of cotton and it results in huge yield losses every year in the fields. The underlying mechanisms of VW in cotton are not well explored yet. In the current approach we used the transcriptome data from G. australe in response to Verticillium wilt attack to mine the ERF TFs and prove their potential role in resistance against VW attack in cotton. We identified 23 ERFs in total, and on the basis of expression at different time points i.e., 24h, 48h and 72h post inoculation and selected GauERF105 for further validation. We performed VIGS in cotton and over expression in Arabidopsis respectively. Moreover, DAB and trypan staining also suggests that the impact of disease was more in the wildtype as compared to transgene lines. On the basis of our results, we confirmed that GauERF105 is the key candidate and playing a key role for defending cotton against VW attack. Current finding might be helpful for generating resistance germplasm in cotton and it will be beneficial to recover the yield losses in field.

pathology↗

bioRxiv2021

2-kupl: mapping-free variant detection from DNA-seq data of matched samples

The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats. Herein, we introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves a higher precision than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease.

bioinformatics↗

bioRxiv2020

Augmenting Vascular Disease Diagnosis by Vasculature-awareUnsupervised Learning

Vascular diseases are among the leading causes of death and threaten human health worldwide. Imaging examination of vascular pathology with reduced invasiveness is challenging due to the intrinsic vasculature complexity and the non-uniform scattering from bio-tissues. Here, we report VasNet, a vasculature-aware unsupervised learning algorithm that augments pathovascular recognition from small sets of unlabeled fluorescence and digital subtraction angiography (DSA) images. The VasNet adopts the multi-scale fusion strategy with a domain adversarial neural network (DANN) loss function that induces biased pattern reconstruction, by strengthening the features relevant to the retinal vasculature reference while weakening the irrelevant features. VasNet delivers outputs of "Structure + X", where X refers to multi-dimensional features such as blood flows, the distinguishment of blood dilation and its suspicious counterparts, and the dependence of new pattern emergence on a disease progression, which may assist the discovery of novel diagnostics. Therefore, explainable imaging output from VasNet and other algorithm extensions hold the promise to revolutionize the practice of medical diagnosis, as it improves performance while reduces the cost on human expertise, equipment exquisite and time consumption.

bioengineering↗

bioRxiv2019

Paired design of ATP bioluminescence method and colony counting method: whether it is suitable for evaluating the disinfection effect of environmental surface?

ATP bioluminescence method has been used as a on-site rapid detection method in nosocomial infections control more and more. In this study, a paired design between four methods/detectors were performed to detect the environmental surface after disinfection. Two methods were ATP bioluminescence method and colony counting method (C), and ATP bioluminescence method included three kinds of detectors (B, P and N). Every surface was performed by two methods/detectors. ATP content per surface from ICU had no statistically significant difference with internal medicine wards of B and P, of which p was 0.435 and 0.260. By Spearman rank correlation coefficients, with the exception of better correlation between ATP content detected by B and P, the correlation between the remaining methods/detectors was poor or had no correlation. And the differences between detectors are statistically significant. Therefor, ATP bioluminescence method may not be suitable for the evaluation of disinfection effect, but be more appropriate for evaluating the cleanliness of environmental surface.

microbiology↗