Biology subjects

Zhao, T.

Publications and source records attributed to Zhao, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

MTARC1 Regulates Lipid Droplet Degradation via Phospholipid Remodeling in Metabolic Fatty Liver Disease

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a spectrum of liver disease, including simple fatty liver, hepatic steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma, with limited treatment options. MTARC1 p.A165T variant is associated with reduced risk of MASLD. We previously showed that this variant promotes MTARC1 protein degradation, suggesting MTARC1 inactivation may represent a potential therapeutic strategy. Here, we report that global or liver specific Mtarc1 knockout markedly suppresses diet-induced hepatic TG accumulation, liver injury, inflammation, and fibrosis in a manner dependently on lipolysis and lipophagy. MTARC1 inactivation post-transcriptionally upregulates PEMT and CEPT1 expression, consequently elevating GPL levels, including PC, PE, and lyso-PE, three major GPLs of hepatic LDs. Furthermore, we observed that MTARC1-deficient hepatocytes exhibited smaller but more numerous LDs compared to controls, under comparable cellular TG levels during lipolysis/lipophagy inhibition. Importantly, inhibition of CEPT1 or PEMT could attenuated the hepatoprotective effect of MTARC1 deficiency. Mechanistically, subcellular GPL remodeling induced by MTARC1 deficiency reduce LD size while increase their surface-to-volume ratio, which in turn promote TG degradation through lipolysis and lipophagy. Collectively, our findings identify MTARC1-GPL biosynthesis-LD degradation axis as a key regulator of fatty liver disease and highlight MTARC1 inhibition as a promising therapeutic strategy for MASLD.

cell biology↗

bioRxiv2025

DrugLM: A Unified Framework to Enhance Drug-Target Interaction Predictions by Incorporating Textual Embeddings via Language Models

MotivationAccurate prediction of drug-target interactions (DTIs) is central to computational drug discovery, offering the potential to reduce experimental costs and accelerate development timelines. While existing deep learning approaches such as Graph Neural Networks and Transformers have shown promise, they often overlook the rich semantic information embedded in textual descriptions of drugs and targets. These descriptions encode critical biomedical knowledge, including mechanisms of action, biological pathways involved, and therapeutic effects of drugs, which can enhance DTI prediction performance. ResultsWe introduce DrugLM, a unified framework that integrates embeddings derived from large language models (LLMs) into DTI-specific model architectures. DrugLM leverages textual descriptions of drugs and targets to generate semantic embeddings using a range of pretrained LLMs. These embeddings can be seamlessly incorporated into existing DTI models. We systematically evaluate multiple LLMs on benchmark DTI datasets and demonstrate strong performance even without fine-tuning. Moreover, supervised parameter-efficient fine-tuning of the LLMs further improves embedding quality, leading to enhanced prediction accuracy. Notably, a simple multilayer perceptron (MLP) using only LLM-derived embeddings surpasses several established DTI methods, underscoring the power of semantic features. Our findings highlight the practical value of integrating LLMs into DTI pipelines and offer a straightforward recipe for improved drug discovery: LLM embeddings of drugs and targets are both effective and easy to use. AvailabilityOur code and dataset are available at https://github.com/ShPhoebus/DrugLM

bioinformatics↗

bioRxiv2025

Central nervous system atlas of larval zebrafish constructed using the morphology of single excitatory and inhibitory neurons

Single-neuron morphology mapping is fundamental for deciphering brain architecture and function, yet in vertebrates it remains limited in spatial coverage and cell-type information. Here we present a nervous system-wide single-neuron morphology atlas of larval zebrafish with annotated excitatory/inhibitory identity and dendrite-axon polarity. The atlas comprises >20,000 reconstructed neurons from >13,400 animals, spanning the central and peripheral nervous system and representing [~]24.5% of the total excitatory and inhibitory neurons in the brain, all integrated into a common physical space with neuroanatomical parcellations. We define >500 excitatory and inhibitory neuronal morphotypes and construct putative inter-cell-type and interregional connectomes. Projection and morphotype analyses reveal distinct laterality and directionality biases and modular innervation patterns in excitatory and inhibitory neurons, while network analyses uncover fundamental connectivity motifs, hubs, and sensorimotor pathways. Accessible through custom-built interactive platform ZExplorer, this atlas provides a foundational resource for multimodal data integration, circuit analysis, computational modeling, and hypothesis-driven research.

neuroscience↗

bioRxiv2025

A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies

Single-domain antibodies (sdAbs) have emerged as powerful therapeutic agents due to their small size, high stability, and superior tissue penetration. However, unlike conventional monoclonal antibodies (mAbs), sdAbs lack an Fc domain, limiting their functional versatility and manufacturability. To address this challenge, we developed TFDesign-sdAb, a deep learning-based generative-ranking framework that enables rational engineering of sdAbs with tailored functionalities. Our framework integrates a structure-aware diffusion model (IgGM) for large-scale candidate generation and a fine-tuned sorter (A2binder) that evaluates and prioritizes them based on predicted functionality. Unlike traditional CDR-focused approaches, TFDesign-sdAb optimizes both complementarity-determining regions (CDRs) and framework regions (FRs), allowing sdAbs to acquire new functional properties while maintaining antigen specificity. We validated our approach by conferring Protein A binding to human VHs and nanobodies that originally lacked this feature, achieving high expression rates, strong binding affinities, and successful purification via industry-standard Protein A affinity chromatography. High-resolution structural characterization (1.49 [A] and 2.0 [A]) of the redesigned sdAb-Protein A complexes revealed conserved FR-mediated binding motifs that recapitulate natural Fc-Protein A interactions, validating the accuracy of our model. Furthermore, our pipeline streamlined the antibody engineering process, achieving a 100% success rate in generating Protein A-binding sdAbs while maintaining their original antigen-binding affinity. This work demonstrates the power of AI-driven design in overcoming long-standing limitations in antibody engineering and presents a scalable, generalizable solution for enhancing sdAb functionality.

bioinformatics↗

bioRxiv2025

Genome-Wide Identification of Conditionally Essential Genes Supporting Streptococcus suis Growth in Serum and Cerebrospinal Fluid

Streptococcus suis is a major cause of sepsis and meningitis in pigs, and zoonosis through the emergence of disease-associated lineages. The ability of S. suis to adapt and survive in host environments, such as blood and cerebrospinal fluid (CSF), is important for pathogenesis. Here, we used Tn-Seq coupled with Nanopore sequencing to identify conditionally essential genes for growth of S. suis P1/7 in active porcine serum (APS) and CSF derived from choroid plexus organoids (Zhao et al., 2025). Through comparative fitness analyses we identified 33 conditionally essential genes (CEGs) supporting growth in APS and 25 CEGs in CSF, highlighting the importance of pathways involved in amino acid transport, nucleotide metabolism, and cell envelope integrity. Notably, the LiaFSR regulatory system and multiple ABC transporters were important for proliferation. We also identified several genes of unknown function as essential for growth, pointing to previously unrecognized genetic factors involved in S. suis adaptation during infection. These findings provide new insights into the genetic requirements for S. suis survival in host-like environments and a deeper understanding of its ability to adapt to distinct physiological niches.

microbiology↗

bioRxiv2025

Interrupting Elmsan1 repression of nuclear Acetyl-CoA production therapeutically reprograms cancer cells

Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we combined phenotypic chemical screen and genome-wide CRISPR screen to demonstrate a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. While previously thought that nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively active, we found that nPDC is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprogramming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo, including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy.

cancer biology↗

bioRxiv2025

Fluorescence Characterization of Extracellular Vesicles using Single-Molecule Confocal Microscopy

Extracellular vesicles (EVs) are small, membrane-bound particles released by cells into the extracellular environment. They play a pivotal role in cell communication and have recently gained prominence as biomarkers. However, their low abundance and high heterogeneity challenges their accurate characterization using conventional approaches. To enable the specific detection of individual EVs, we coupled EV-specific antibodies labeled with two different fluorophores with fast-flow microfluidics and single-molecule confocal microscopy. This allowed us to determine the concentration of EVs down to femtomolar levels ([~]107 EVs/mL), and we demonstrated the approachs capacity to detect EVs even in the presence of other lipid vesicles. We highlighted the ability to quantify EVs in serum and plasma samples, without the need for purification. Furthermore, we compared the yield of EVs extracted from both serum and plasma using ultracentrifugation and various size exclusion chromatography approaches. Overall, our method offers a highly specific, sensitive and easy-to-use solution for characterizing EVs from different sources.

biophysics↗

bioRxiv2025

Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development

Mammalian lung development is a complex, highly orchestrated process involving the precise coordination of diverse cell types. Despite significant advances, the spatial gene expression patterns and regulatory mechanisms within the developmental niches of different lung structures remain incompletely understood. In this study, we present a comprehensive spatial transcriptomic atlas of mouse lung development, spanning from the early pseudoglandular to the alveolar stage. We further uncover transcription factor (TF) regulation landscapes by integrating spatial epigenome, including novel TF-eRegulons critical for epithelial progenitors during early lung development. Our analysis also identifies hundreds of spatiotemporally dynamic cell-cell communications, such as BMP8B-mediated ligand-receptor signaling enriched in airway branching. Notably, we delineate the distinct developmental trajectories of alveolar AT1 and AT2 cells and reveal that collagen pathways facilitate their spatial convergence, forming primary alveoli during the canalicular-saccular transition. Together, this spatial transcriptomic atlas provides a foundational resource for understanding the complex cellular and molecular orchestration underlying mammalian lung development.

developmental biology↗

bioRxiv2025

Longitudinal analysis of antibody titers after primary and booster mRNA COVID-19 vaccination can identify individuals at risk for breakthrough infection

A key issue in the post-COVID-19 era is the ongoing administration of COVID-19 vaccines. Repeated vaccination is essential for preparing against currently circulating and newly emerging SARS-CoV-2 variants while enabling people to continue with daily life. Optimizing vaccination strategies is crucial to efficiently manage medical resources and establish an effective vaccination framework. Therefore, it is important to quantitatively understand vaccine-induced immunity dynamics and to be able to identify poor responders with lower sustained antibody titers as potential priorities for revaccination. We investigated longitudinal antibody titer data in a cohort of 2,526 people in Fukushima, Japan, from April 2021 to November 2022 for whom basic demographic and health information was available. Using mathematical modeling and machine learning, we stratified the time-course patterns of antibody titers after 2 primary doses and 1 booster dose of mRNA COVID-19 vaccines. We identified 3 notable populations, which we refer to as the durable, the vulnerable, and the rapid-decliner populations, approximately half of which remained in the same population after the booster dose. Notably, the rapid-decliner population experienced earlier infections than the others. Furthermore, when comparing IgG(S) titers, IgA(S) titers, and T-spot counts between participants who experienced breakthrough infections after booster vaccination and those who did not, we found that IgA(S) titers were significantly lower in breakthrough infected participants during the early stage after booster vaccination. Our computational approach is adaptable to various types of vaccinations. This flexibility can inform policy decisions on vaccine distribution to enhance immunity both in future pandemics and in the post-COVID-19 era.

immunology↗

bioRxiv2025

An integrated system for comprehensive mouse peripheral vestibular function evaluation based on Vestibulo-ocular Reflex

In the realms of both vestibular and auditory research, conducting vestibular function tests is essential. However, unlike the auditory function tests which utilize standard equipment such as the Auditory Brainstem Response (ABR) device, there is no equivalent widely adopted apparatus for vestibular tests. This is largely due to the intricate nature of the vestibular system and the challenges associated with assessing its functions. Vestibulo-ocular reflexes (VORs) are the compensatory ocular reflexes that ensure stable vision during head motion. VORs are widely used in clinics for diagnosing the vestibular deficit. In the research field, VORs, including angular VOR (aVOR) or off-vertical axis rotation (OVAR) tests, have been used by various groups to evaluate the mouse vestibular function. However, the effectiveness of VOR tests has not been systematically evaluated with proper animal models, and the lack of commercial equipment hampers its accessibility, confining vestibular testing to a select few labs. In this study, we developed an integrated instrument system with both aVOR and OVAR modes for evaluating mouse vestibular function. To demonstrate its efficacy, peripheral vestibular animal models, 1) Vestibulotoxicity drugs 3,3-iminodiproprionitrile (IDPN, 2 mg/g and 4 mg/g) induced; 2) Critical MET-related mutant (Cdh23v2J/v2J and TMC1-/-); 3) Vestibulo-specific mutant (Zpld1-/- for semicircular canal dysfunction and Otop1tlt/tlt for otoconia deficient; 4) Unilateral vestibular lesion (UVL) model by injecting gentamicin into horizontal semicircular canal, were constructed and evaluated with the system. The results showed 1) Quantification of the vestibular deficit is achieved in a daily manner; 2) Both the otolith organ and semicircular canals can be assessed respectively; and 3) The lesion side of UVL can be identified. During an 8-week study of IDPN vestibulotoxicity, the vestibular function of 3 groups of 20 animals was evaluated at 15 test days. These test results reveal the potential of our system as a standard system for evaluating common vestibular deficits in mice.

neuroscience↗

bioRxiv2025

Machine learning ensemble identifies distinct age-related response to spaceflight in mammary tissue

BackgroundSpaceflight presents unique environmental stressors, such as microgravity and radiation, that significantly affect biological systems at the molecular, cellular, and organismal levels. Astronauts face an increased risk of developing cancer due to exposure to ionizing radiation and other spaceflight-related factors. Age plays a crucial role in the bodys response to the cellular stresses that lead to cancer, with younger organisms generally exhibiting more efficient response mechanisms than older ones. The vast majority of research investigating breast cancer risk from spaceflight is done in vitro, using cell lines exposed to simulated radiation and microgravity. ObjectivesThe primary objective of this observational study is to characterize the response to spaceflight of in vivo murine mammary tissue and identify the molecular biomarkers enriched in this response using mice flown on the International Space Station. The secondary objective is to determine if age plays a role in this response. MethodsThe NASA Open Science Data Repository (OSDR) has curated transcriptomic data obtained from murine mammary tissue in a controlled experiment (OSD-511) which includes 43 young and old female mice. In this study, we utilized an ensemble of four machine learning binary classifiers (logistic regression, support vector machine, random forest, and single-layer perceptron) to analyze gene expression profiles to predict age (old vs young) and condition (spaceflight vs ground control). Using the genes our ensemble identified as most predictive, we performed pathway enrichment analysis to investigate the molecular pathways involved in spaceflight-related health risks, particularly in the context of breast cancer. ResultsAll space-flown mice responded to spaceflight with evidence of systemic metabolic reprogramming and mitochondrial adaptation to microgravity and radiation as compared to their 33 ground control counterparts. For the 10 mice flown in space, older mice exhibited chronic, significantly enriched pathways related to cell adhesion and extracellular matrix (ECM) structure, while younger mice showed acute activation of pathways involved in cortisol synthesis and adrenergic stress response (with false discovery rate adjusted q-values < .001). These results provide putative biomarkers for monitoring and treating breast cancer. ConclusionsThese findings highlight the critical role of age in modulating the response to spaceflight-induced stress and suggest that these molecular pathways may contribute to differential outcomes in tissue homeostasis, metabolic disorders, and breast cancer tumorigenesis. Moreover, our computational methodology may be applied to several unexplored datasets in OSDR and beyond.

bioinformatics↗

bioRxiv2025

Hematopoietic stem cells undergo bidirectional fate transitions in vivo.

Differentiation of haematopoietic stem and progenitor cells (HSPCs) is widely considered unidirectional in vivo. Here, we developed clonal phylogenetic tracing (CP-tracer) by sequential genetic barcoding, which enabled high-resolution analysis of 181,695 subclones derived from 847 individually labelled HSPCs. This approach uncovered bidirectional fate transitions between myeloid-biased (My-) and lineage-balanced haematopoietic stem cells (HSCs). Individual HSC clones, distinguished by temporally unique serial barcodes, exhibited durable lineage bidirectionality, with dynamics favouring progressive accumulation of My-HSCs over time. CRISPR-Cas9 screening identified the homeobox gene Hhex as a suppressor of myeloid differentiation that enables pivoting toward balanced output. Hhex function is age-dependent, with its expression declining in aged HSCs. Together, these findings demonstrate unexpected plasticity in HSC differentiation, modulated in part by Hhex-mediated repression, that shifts over time to drive the myeloid bias characteristic of ageing.

cell biology↗

bioRxiv2024

Iridescent structural coloration in a crested Cretaceous enantiornithine bird from Jehol Biota

A combination of sectioning and microscopy techniques, along with the application of finite-difference-time-domain modeling on a fossil feather, results in the novel estimation of the range of iridescent colors from the fossilized melanosome type and organization preserved in the elongate head crest feathers of a new Cretaceous enantiornithine bird. The densely packed rod-like melanosomes are estimated to have yielded from red to deep blue iridescent coloration of the head feathers. The shape and density of these melanosomes also may have further increased the feathers structural strength. This occurrence on a likely male individual is highly suggestive of both a signaling function of the iridescent crest, and a potential behavioral role in adjusting the angle of light incidence to control the display of this iridescent structural coloration.

evolutionary biology↗

bioRxiv2024

Unveiling the potato cultivars with microbiome interactive traits for sustainable agricultural production

Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive traits (MITs), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MITs. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MITs. By examining the distribution of low, medium, and high MITs, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.

microbiology↗

bioRxiv2024

S-RNase Evolution in Self-Incompatibility: Phylogenomic Insights into Synteny with S-Like Genes

S-RNases are essential in the gametophytic self-incompatibility (GSI) system of many flowering plants, where they act as stylar-S determinants. Despite their significance, the syntenic genomic origin and evolutionary trajectory of S-RNase genes in eudicots have remained largely unclear. Here, we performed large-scale phylogenetic and microsynteny network analyses of RNase T2 genes across 130 angiosperm genomes, encompassing 35 orders and 56 families. Based on the connections observed in the synteny network, particularly the persisting synteny block in none-SI Cucurbitaceae species, we infer that well-characterized S-RNase genes (Class III-A RNase genes) were duplicated and evolved from Class I S-like RNase genes, possibly as a result of the gamma triplication event shared by core eudicots. Additionally, we identified frequent lineage-specific gene transpositions of S-RNase genes across diverse angiosperm lineages, including Rosaceae, Solanaceae, and Rutaceae families, accompanied by a significant increase in transposable element (TE) activity near these genes. Our findings delineate the precise genomic origin and evolutionary path of eudicot S-RNase genes, enhancing our understanding of the evolution of the S-RNase-based GSI system.

evolutionary biology↗

bioRxiv2024

Amidase and Lysozyme Dual Functions in TseP Reveal a New Family of Chimeric Effectors in the Type VI Secretion System

Peptidoglycan (PG) serves as an essential target for antimicrobial development. An overlooked reservoir of antimicrobials lies in the form of PG-hydrolyzing enzymes naturally produced for polymicrobial competition, particularly those associated with the type VI secretion system (T6SS). Here we report that a T6SS effector TseP, from Aeromonas dhakensis, represents a family of effectors with dual amidase-lysozyme activities. In vitro PG-digestion coupled with LC-MS analysis revealed the N-domains amidase activity, which is neutralized by either catalytic mutations or the presence of the immunity protein TsiP. The N-domain, but not the C-domain, of TseP is sufficient to restore T6SS secretion in T6SS-defective mutants, underscoring its critical structural role. Using pull-down and secretion assays, we showed that these two domains interact directly with a carrier protein VgrG2 and can be secreted separately. Homologs in Aeromonas hydrophila and Pseudomonas syringae exhibited analogous dual functions. Additionally, N- and C-domains display distinctive GC contents, suggesting an evolutionary fusion event. By altering the surface charge through structural-guided design, we engineered the TsePC4+ effector that successfully lyses otherwise resistant Bacillus subtilis cells, enabling the T6SS to inhibit B. subtilis in a contact-independent manner. This research uncovers TseP as a new family of bifunctional chimeric effectors targeting PG, offering a potential strategy to harness these proteins in the fight against antimicrobial resistance. Significance StatementAntimicrobial resistance urgently demands global interventions, and the bacteria cell wall remains a promising target. Our research introduces a novel family of bifunctional, cell-wall-damaging T6SS effectors. More importantly, we demonstrate an effective strategy to enable an otherwise ineffective enzyme to target both Gram-negative and Gram-positive bacteria. Our findings highlight a promising path forward using cell-wall-damaging effectors, a largely untapped resource, in the fight against antimicrobial resistance.

microbiology↗

bioRxiv2024

Alleviation of salt stress in strawberries by hydrogen-rich water: physiological, transcriptomic and metabolomic responses

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/605184v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1aa6488org.highwire.dtl.DTLVardef@1ae580borg.highwire.dtl.DTLVardef@11656bcorg.highwire.dtl.DTLVardef@1985c7b_HPS_FORMAT_FIGEXP M_FIG C_FIG With the continuous advancement of climate change and human activities, cultivable land is becoming increasingly susceptible to the influence of salt ions. Therefore, it is crucial to mitigate the salt stress on plants through various approaches. In this study, strawberry seedlings were selected as the experimental plants, and a comprehensive transcriptomic and metabolomic analysis was conducted to elucidate the effects of hydrogen-rich water (HRW) on strawberries under salt stress. The results indicated that HRW significantly promoted plant growth, particularly increasing root biomass by 49.50%. Additionally, HRW regulated the levels of soluble sugars, malondialdehyde (MDA), and antioxidant enzymes, enhancing the cellular uptake of potassium ions and the expulsion of sodium ions. The levels of Ca2+ and Mg2+ in organelles increased by 2.06 and 2.45-fold, respectively. Transcriptomic analysis revealed that HRW substantially altered gene expression in strawberry roots; under salt stress, HRW up-regulated beneficial biological processes. Furthermore, genes related to ion absorption and transport, antioxidant enzymes, and cell wall biosynthesis were screened. Meanwhile, key common pathways were identified in differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs) related to phenylpropane biosynthesis, alanine, aspartate, and glutamate metabolism, amino and nucleotide sugar metabolism, and galactose metabolism. A molecular mechanism for mitigating salt stress in strawberry seedlings by HRW was provided by the integrated approaches in this research, reflecting the potential applications of hydrogen gas in agriculture.

physiology↗

bioRxiv2024

CREEPING STEM1 Regulates Directional Auxin Transport for Lodging Resistance in Soybean

Soybean, a staple crop on a global scale, frequently encounters challenges due to lodging under high planting densities, which results in significant yield losses. Despite extensive research, the fundamental genetic mechanisms governing lodging resistance in soybeans remain elusive. In this study, we identify and characterize the Creeping Stem 1 (CS1) gene, which plays a crucial role in conferring lodging resistance in soybeans. The CS1 gene encodes a HEAT-repeat protein that modulates hypocotyl gravitropism by regulating amyloplast sedimentation. Functional analysis reveals that the loss of CS1 activity disrupts polar auxin transport, vascular bundle development, and the biosynthesis of cellulose and lignin, ultimately leading to premature lodging and aberrant root development. Conversely, increasing CS1 expression significantly enhances lodging resistance and improves yield under conditions of high planting density. Our findings shed light on the genetic mechanisms that underlie lodging resistance in soybeans and highlight the potential of CS1 as a valuable target for genetic engineering to improve crop lodging resistance and yield.

plant biology↗