Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 649 records · Page 36Linked to original sources

bioRxiv2025

An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal

Introns play a critical role in regulating alternative splicing. However, identifying functional intronic motifs is challenging due to their short and degenerate sequence composition. Massively parallel reporter assays have provided insights into cis-regulatory logic governing alternative splicing, but these approaches are generally performed in cell culture, limiting their ability to capture tissue-specific contexts. Here, we implemented in vivo Parallelized Reporter Assays in C. elegans neurons and muscle cells to screen for intronic enhancer and silencer motifs among thousands of randomized sequences. We identified nearly 200 sequences regulating splicing in these tissues. We uncovered core sub-sequences with tissue-biased enhancing and silencing activity, including motifs recognized by well-characterized RNA-binding proteins, and orphan motifs with no obvious cognate binding protein. Mapping our PRA-derived motifs to native introns flanking tissue-biased alternative exons revealed their conservation across nematodes, supporting their functional relevance. Additionally, individual intronic regions frequently contained diverse combinations of these motifs, indicative of complex engagement of these sequences by RNA-binding proteins. Finally, we performed targeted mutagenesis of PRA-derived intronic enhancers flanking a neuronal microexon, identifying key cis-regulatory determinants of microexon splicing. Together, our study provides a framework to explore the role of intronic regions in tissue-specific splicing regulation within a multicellular organism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/670696v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@84d5daorg.highwire.dtl.DTLVardef@f3f625org.highwire.dtl.DTLVardef@a53739org.highwire.dtl.DTLVardef@ccbb03_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

C-6 Modified 2-F-Fucose Derivatives as Inhibitors of Fucosyl Transferases

Fluorinated analogs of guanosine-diphosphate-{beta}-L-fucose (GDP-Fuc) have received considerable attention for the development of inhibitors of fucosyltransferases (FUTs). These compounds can be recognized by FUTs but do not or slowly transfer the fluorinated fucosyl residue because the electron-withdrawing fluorine(s) destabilize the oxocarbenium-like transition state. Fluorinated GDP-Fuc analogs can also act as feedback inhibitor of the de novo biosynthesis pathway of GDP-Fuc. To investigate the biological significance of distinct glycoconjugate classes, it is important to develop inhibitors that can selectively target specific FUT enzymes. Here, we report the design, synthesis, and biological evaluation of a series of GDP-2-F-Fuc analogs modified at C-6 of Fuc by various amides and ethers. We also prepared and examined corresponding prodrugs as potential FUT inhibitors of cellular glycosylation. Our findings reveal that two of the inhibitors potently inhibited FUT1, 3, 6, and 9, while displaying minimal activity against FUT8. However, the corresponding prodrugs did not inhibit cellular fucosylation, which is probably due to a lack of GDP-fucose pyrophosphorylase activity. The results demonstrate that modifications at the C-6 position of Fuc can confer selectivity, although further investigations of alternative functional groups are required to enhance cellular tolerance and efficacy.

biochemistry↗

bioRxiv2025

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-matched reference panel to model protein expression using genetic variants as features and determine the proteins impact on phenotype. However, reference panels from underrepresented populations remain relatively limited. In this study, we developed an analytic framework that borrows information from potentially multiple ancestries to boost the protein abundance prediction accuracy in an underrepresented population. We illustrate the frameworks utility and reproducibility through application to PWAS in East Asians: BioBank Japan (BBJ), Korean Genome and Epidemiology Study (KoGES), and Taiwan Biobank (TWB). An ensemble of information-sharing approaches was integrated to build the Multi-Ancestry-based Best-performing Model (MABM). MABM substantially improved the prediction performance with higher performance observed in both cross-validation and an external validation dataset (Tongji-Huaxi-Shuangliu Birth Cohort). Leveraging the BBJ, we identified three times as many significant PWAS associations with MABM as with the baseline Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced gene/protein prioritization for downstream functional validation by (1) confirming a greater number of well-established gene/protein-trait associations and (2) identifying previously uncharacterized trait-associated genes. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research, develop a new reference resource of genetic models of protein abundance, and facilitate trait-relevant protein discovery in underrepresented populations.

genomics↗

bioRxiv2025

Single-Cell Super-Resolution Quantification of Oxidative DNA Damage via Aptamer-Assisted DNA-PAINT

Accurately quantifying oxidative DNA damage at the single-cell level remains a major challenge due to the limitations of conventional ensemble-based assays, which obscure cell-to-cell variability and lack molecular specificity. To address this, we developed a super-resolution imaging strategy that combines an 8-oxo-dG-specific DNA aptamer with DNA-PAINT, enabling quantitative visualization of 8-oxo-dG lesions with [~]22 nm spatial resolution in individual cells. Our approach reliably detects 8-oxo-dG clusters, distinguishes oxidative damage levels across cells, and exhibits superior specificity and labeling efficiency compared to antibody-based methods. Furthermore, it enables direct evaluation of the repair efficiency of hOGG1 and its catalytic mutants at the single-cell level, overcoming the confounding effects of variable transfection efficiency. This method also serves as a platform for assessing the effects of pharmacological modulators and antioxidants on DNA repair. Looking forward, this strategy can be extended to map other small molecular targets, such as epigenetically modified DNA or RNA bases, with single-cell precision.

biochemistry↗

bioRxiv2025

Molecular insights into ligand recognition and signaling of GPR99/OXGR1

GPR99/OXGR1 is a G protein-coupled receptor (GPCR) with two endogenous agonists, the tricarboxylic acid cycle derivative oxoglutarate and the inflammatory lipid mediator leukotriene E4 (LTE4). How GPR99/OXGR1 recognizes two distinct ligands is a biologically important question relevant to therapeutic development due to its established roles in asthma, allergy and inflammation. Here we present cryo-EM structures of GPR99/OXGR1-Gq complex with oxoglutarate and LTE4, respectively. The oxoglutarate-bound structure shows a binding pocket surrounded by the transmembrane domains (TM), with a primary site and an accessory site for simultaneous binding of two oxoglutarate molecules for full activation of the receptor. The TM binding pocket, however, is too small to accommodate the "Y" shaped structure of LTE4, a cysteinyl leukotriene. Alanine substitution of key residues for oxoglutarate binding had little impact on LTE4-induced signaling. An alternative site in between TM3/4/5 just above intracellular loop 2 was identified in the cryo-EM structure of GPR99/OXGR1-Gq complex formed with LTE4, but the densities were less well defined. Alanine substitution of amino acids potentially involved in LTE4 interaction at this site abrogated LTE4-induced receptor activation, with no effect on oxoglutarate-induced signaling. Both ligands activated GPR99/OXGR1 primarily through the Gq pathway, but LTE4 also induced inhibition of cAMP accumulation that was sensitive to pertussis toxin. These findings illustrate the structural basis for GPR99/OXGR1 interaction with oxoglutarate and suggest the presence of a distinct binding site for LTE4.

biochemistry↗

bioRxiv2025

scSTAR2: a multiomics integration algorithm to reveal disease specific cellular signatures by bridging single-cell resolution features and clinical metadata

Single-cell techniques, pivotal in characterizing intricate cell and spatial structures within tissues, face challenges in contextualizing clinical phenotypes. Currently, most investigations of the clinical phenotype related cell/spatial heterogeneities relied on the phenotype information from single-cell data. However, a wealth of underutilized clinical metadata exists within conventional bulk sequencing data. Current methods for correlating clinical information with individual cells or spatial regions remain limited and lack robustness. Here we present scSTAR2, a novel algorithm that transcends existing limitations by reconstructively integrating multiomics data to identify cells associated with clinical phenotypes. Unlike existing methods, scSTAR2 reconstructs single-cell data guided by specific phenotypes, significantly reducing interference from irrelevant noise. By employing scSTAR2 to integrate scRNA-seq, scATAC-seq, and spatial transcriptomics and bulk RNA-seq, we not only confirmed a new heat-shock Treg subtype in tumors but also more sensitively identified TLS (tertiary lymphoid structure) areas than traditional methods. In conclusion, scSTAR2 has proven to significantly enhance single-cell data interpretation across diverse clinical scenarios.

bioinformatics↗

bioRxiv2025

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↗

bioRxiv2025

Helicobacter pylori genome aggregation database reveals complex evolutionary forces shaping its genomic landscape and clinical impact in East Asia

We assembled HPgnomAD, a comprehensive global genome aggregation database of Helicobacter pylori (H. pylori) featuring 7,544 high-quality genomes from 278 populations, along with the first species-wide haplotype reference panel for genotype imputation. The panel provides high accuracy across diverse H. pylori populations, including those from low-coverage data, and is openly accessible with integrated analysis tools (https://www.hpgnomad.top/). Variant discovery revealed 1.82 million SNPs and 0.65 million InDels, with African strains exhibiting the most tremendous diversity and East Asian strains showing unexpectedly high novel variation. Fine-scale analysis of the hpEAsia lineage revealed six new sublineages shaped by altitude-, latitude-related divergence and region-specific admixture. Phylogenomic dating revealed two divergence waves in East Asia, paralleling Upper Paleolithic settlement and Neolithic human expansions, with highland-lowland separation at [~]18.8 kya, followed by the formation of complex geography-related population substructures. Genome-wide scans revealed adaptive loci related to metal acquisition, nitrogen metabolism, surface adhesion, and membrane transport, including altitude-associated highly differentiated variants linked to antibiotic resistance and gastric disease. By integrating genomic, evolutionary, environmental, and clinical data, HPgnomAD offers a framework for understanding H. pylori evolution, host-pathogen adaptation, and precision medicine worldwide.

evolutionary biology↗

bioRxiv2025

Suppression of interferon signaling via small molecule modulation of TFAM

The mitochondrial transcription factor A (TFAM) is essential for mitochondrial genome maintenance. It binds to mitochondrial DNA (mtDNA) and determines the abundance, packaging and stability of the mitochondrial genome. Because its function is tightly associated with mtDNA, TFAM has a protective role in mitochondrial diseases and supportive studies demonstrate reversal of disease phenotypes by TFAM overexpression. In addition, TFAM deficiency has been shown to cause release of mtDNA into the cytosol and activation of the cGAS/STING innate immune response pathway. As such, TFAM presents as a unique target for therapeutic intervention, but limited efforts for activators have been reported. Herein we disclose novel TFAM small molecule modulators with sub-micromolar activity. Our results demonstrate that these compounds result in increase of TFAM protein levels and mtDNA copy number. This results in inhibition of a mtDNA stress-mediated inflammatory response by preventing mtDNA escape into the cytosol. Furthermore, we see beneficial effects in cellular disease models in which boosting TFAM activity has been advanced as a disease modifying strategy including improved energetics in MELAS cybrid cells and a decrease of fibrotic markers in Systemic Sclerosis (SSc) fibroblasts. These results highlight the therapeutic potential of using small molecule TFAM activators in indications characterized by mitochondrial dysfunction.

cell biology↗

bioRxiv2025

Light-Activated Nucleic Acid Amplification Systems Using Photo-caged DNA Polymerase or Primers

Precise control over nucleic acid amplification is essential for achieving reliable, quantitative, high-throughput, and multiplexed molecular diagnostics, particularly in point-of-care and field settings. However, conventional isothermal amplification methods, especially rapid assays at ambient temperature such as recombinase-aided amplification (RAA), suffer from spontaneous initiation and lack of synchronization across parallel reactions. Here, we report light-activatable RAA systems employing two distinct photocaging strategies to achieve spatiotemporal control. In the first, a photocaged DNA polymerase was engineered via site-specific incorporation of p-azido-L-phenylalanine and conjugation with a 2-nitrobenzyl-modified ssDNA blocker through click chemistry. This approach offers high stability, making it advantageous for long-term storage and lyophilized formats. In the second, 5'-nitrobenzyl-modified primers were synthesized to block hybridization or extension until UV activation, offering operational simplicity and rapid integration into existing workflows. Both strategies independently suppressed background activity in the dark and restored full amplification efficiency upon 365 nm UV exposure. The systems exhibited high sensitivity, low background, and compatibility with portable diagnostics. A custom-built device integrating UV activation and real-time fluorescence detection enabled seamless, on-demand operation. This modular platform provides flexible light-gated amplification solutions, allowing the selection of polymerase- or primer-based caging according to storage stability or workflow requirements, thereby advancing precise and field-ready molecular diagnostics.

molecular biology↗

bioRxiv2025

Distinct Flower signaling domains orchestrate cellular fitness via secreted vesicles in Aβ-induced neurodegeneration

Cellular fitness surveillance preserves tissue integrity, yet its regulation within the mammalian brain remains poorly understood. We identify a bifurcated mechanism in the transmembrane protein Flower--encoding both survival-promoting ("win") and apoptosis-inducing ("lose") isoforms. We demonstrate that astrocytes secrete specialized extracellular vesicles (EVs), termed "fitness vesicles," carrying Flower to facilitate competitive selection across distal cell populations. The N-terminal Flower domain acts extrinsically via these EVs to drive the elimination of less-fit neighbors. Conversely, the "win"-specific C-terminal domain functions as a cell-intrinsic module; it translocates to the nucleus under stress to repress Caspase-3 and provide resilience. In Alzheimers disease (AD) models and human AD brains, Flower-positive astrocytes accumulate around amyloid-{beta} (A{beta}) plaques. Under A{beta} stress, the "win" isoform reprograms astrocytes toward a neuroprotective state that enhances plaque clearance while ensuring cell-intrinsic survival. Our findings reveal how Flower couples long-range, EV-mediated cellular selection with cell-autonomous protection to coordinate astrocyte quality control and tissue resilience in neurodegeneration.

neuroscience↗

bioRxiv2025

Divergent ontogeny of Tissue Resident Memory and Tissue Resident Exhausted CD8+ T cells underlies distinct functional potential

Persistent antigen stimulation promotes differentiation of exhausted CD8+ T (TEX) cells. TEX cells are distinct from circulating memory T (TCIRCM) cells but share many features with tissue-resident memory (TRM) cells established following infection resolution. CD8+ T cells co-expressing residency- and exhaustion-associated molecules in chronic diseases often correlate with clinical outcomes. However, the relationship between these cells and conventional TRM or TEX cells remains unclear. Here, we show that chronic antigen stimulation drives development of tissue-resident TEX (TR-TEX) cells that are ontologically and functionally distinct from TRM cells generated after antigen clearance. TR-TEX phenotypically resembled TRM cells but were regulated by distinct transcriptional networks and were uniquely dependent on Tox for residency programming. Although TEX progenitor cells acquired residency features upon entering chronically infected tissues, they failed to generate conventional TRM cells after antigen withdrawal. Conversely, TRM cells were able to differentiate into TEX cells during chronic antigen stimulation. Deriving cell-state specific transcriptional signatures revealed a selective association of TR-TEX cells with patient responses to immune checkpoint blockade, and only TR-TEX but not TRM cells responded to PD-1 pathway inhibition in vivo. These data suggest that TR-TEX and TRM cells are developmentally distinct cell types that share a tissue-residency program but have distinct roles in disease control.

immunology↗

bioRxiv2025

Renal Coenzyme A (CoA) Production Fuels Stem Cell Proliferation and Tumor Growth

Coenzyme A (CoA), derived from Vitamin B5 (VB5; also called pantothenate), is essential for lipid metabolism, energy production, and cell proliferation. While the intracellular functions of CoA are well-characterized, much less is known about its tissue-specific regulation and systemic physiological roles. Here, using Drosophila melanogaster, we uncover a gut-renal circuit in which dietary VB5 fuels CoA biosynthesis specifically in the Malpighian tubules (MTs, the fly kidney), non-autonomously impacting gut homeostasis. We show that, in the MTs, Myc boosts renal CoA production by directly upregulating the pantothenate kinase Fbl (human PANK1-3 ortholog) and downregulating CG5828, which we characterize as the functional ortholog of the metabolite phosphatase and CoA synthesis suppressor PANK4 (dPANK4). Elevated CoA biosynthesis enhances the mevalonate-isoprenoid pathway activity in the gut, promoting intestinal stem cell proliferation. We further demonstrate that renal CoA production is required for gut tumor growth in a fly model. Consistently, MYC and genes within the CoA-isoprenoid axis display strong association with clinical outcomes in human cancers. Together, our findings establish that Myc-driven CoA metabolism generates an inter-organ signal that couples VB5 availability to stem cell control and tumor growth, and identify the CoA-isoprenoid axis as a targetable metabolic vulnerability in cancer.

genetics↗

bioRxiv2025

Bottlebrush Polymer Conjugates for Enhanced Antisense Oligonucleotide Therapy in Myotonic Dystrophy Type 1

Oligonucleotides are a promising genetic medicine for myotonic dystrophy type 1 (DM1), the most common adult-onset muscular dystrophy. However, poor muscle distribution of nucleic acid drugs after systemic administration has hindered drug development, and no curative treatment exists. Additionally, DM1 pathology requires drug localization to the nucleus, where pathogenic mutant RNA is trapped, posing challenges after endocytosis and endosomal escape. Here, we show that a locked nucleic acid oligonucleotide targeting mutant CUGexp RNA tracts, conjugated to a bottlebrush polymer, exhibited improved muscle distribution and potent correction of DM1-associated splicing at low nanomolar doses in a DM1 mouse model. Significant improvements in myotonia, body weight, and grip strength were observed. The conjugates were well tolerated after 12 weeks of weekly intravenous dosing. These results suggest that bottlebrush polymer bioconjugates may overcome key limitations of traditional antisense drugs for muscular dystrophies, with the potential as potent, durable, and cost-efficient DM1 therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/668589v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@e3961corg.highwire.dtl.DTLVardef@194225dorg.highwire.dtl.DTLVardef@5c470dorg.highwire.dtl.DTLVardef@3cc46a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

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

Structural assembly of maize CRY-GL2 photosignaling complex provides insights into its regulatory role in cuticular wax biosynthesis

Cryptochromes (CRYs) are blue-light photoreceptors in plants that regulate diverse physiological processes through oligomerization-dependent interactions with downstream effectors. While numerous light-inducible CRY-binding proteins have been identified, the structural basis for photoactivated CRY-effector assembly remains poorly understood. Here we report the crystal structure of a constitutively active maize CRY1c photolyase homology region (ZmCRY1c-PHRW368A) in complex with ZmGL2, a BAHD ptotein directing very-long-chain fatty acid (VLCFA) elongation for cuticular wax biosynthesis. Structural analysis reveals that light-activated ZmCRY1c forms a homotetrameric scaffold generating four symmetric binding sites at subunit interfaces. Each ZmCRY1c protomer engages one ZmGL2 molecule through conformational reorganization of its 16-17 loop and 17 helix, establishing a 4:4 hetero-octameric photosignaling complex validated by mutational profiling and optical design. Remarkably, structural alignment with the ZmCER6-ZmGL2 complex reveals substantial overlap (78%) in ZmGL2 binding interfaces. Biochemical quantification demonstrates that ZmCRY1c suppresses ZmCER6-GL2 enzyme activity in a dose dependent manner, unveiling a light-dependent regulatory switch controlling VLCFA elongation efficiency, though in vivo physiological investigation is awaited. Collectively, our work not only establishes the atomic model of light-activated plant CRY-effector assembly, but also uncovers a previously unrecognized spatial competition between photoreceptor and metabolic enzyme complexes that might function as a photoregulatory paradigm in cuticular wax biosynthesis.

plant biology↗

bioRxiv2025

On the Utility of Virtual Staining for Downstream Applications as it relates to Task Network Capacity

Virtual staining, or in-silico-labeling, has been proposed to computationally generate synthetic fluorescence images from label-free images by use of deep learning-based image-to-image translation networks. In most reported studies, virtually stained images have been assessed only using traditional image quality measures such as structural similarity or signal-to-noise ratio. However, in biomedical imaging, images are typically acquired to facilitate an image-based inference, which we refer to as a downstream biological or clinical task. This study systematically investigates the utility of virtual staining for facilitating clinically relevant downstream tasks (like segmentation or classification) with consideration of the capacity of the deep neural networks employed to perform the tasks. Comprehensive empirical evaluations were conducted using biological datasets, assessing task performance by use of label-free, virtually stained, and ground truth fluorescence images. The results demonstrated that the utility of virtual staining is largely dependent on the ability of the segmentation or classification task network to extract meaningful task-relevant information, which is related to the concept of network capacity. Examples are provided in which virtual staining does not improve, or even degrades, segmentation or classification performance when the capacity of the associated task network is sufficiently large. The results demonstrate that task network capacity should be considered when deciding whether to perform virtual staining.

bioinformatics↗

bioRxiv2025

ZmCRY1s interact with GL2 in a blue light dependent manner to regulate epidermal wax composition in Zea mays

Cryptochromes (CRYs) are photolyase-like blue-light / ultraviolet-A (UV-A) receptors that regulate diverse aspects of plant growth. Maize (Zea mays), a major crop often grown under high UV-B radiation, possesses four copies of CRY. However, it remains unclear whether the multiple copies of CRY in maize have evolved to improve UV tolerance or to acquire new functions. In this study, CRISPR-Cas9-engineered Zmcry mutants were used to investigate the functions of four cryptochromes (ZmCRYs) in maize. The findings revealed that ZmCRYs play a redundant role in mediating blue light signaling and in inhibiting the elongation of the mesocotyl. The results also demonstrated that ZmCRYs mediated blue light-enhanced UV-B stress tolerance in Zea mays by upregulating the expression of genes involved in UV-B stress tolerance-related metabolites such as phenylpropanoid, flavonoid, and fatty acid biosynthesis. Furthermore, blue light was found to influence both the accumulation and composition of epidermal waxes, suggesting that blue light enhances epidermal wax accumulation for UV-B stress tolerance. Additionally, it was discovered that ZmCRY1 directly interacted with GLOSSY2 (GL2) in a blue light dependent manner to mediate blue light promoted C32 aldehyde accumulation, shedding new light on the enigma of aldehyde-forming. These results highlight the critical roles of ZmCRY1s in mediating blue light regulated epidermal wax biosynthesis and UV-B tolerance in Zea mays.

plant biology↗