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Liu, H.

Publications and source records attributed to Liu, H..

At least 217 records · Page 12Linked to original sources

EHMT2 Controls Neural Crest-Derived Craniofacial Development but is Dispensable in Limb Development

Post-translational modifications of histones, such as methylation of histone H3 at lysine 9 (H3K9), play critical roles in regulating chromatin structure and gene expression. EHMT2 (also called G9A), a histone methyltransferase, mediates H3K9 mono- and dimethylation and has been implicated in both transcriptional repression and context-specific gene activation. Although global knockout of the mouse Ehmt2 gene results in early embryonic lethality, tissue-specific knockouts have uncovered diverse roles in organ development. However, how EHMT2 contributes to skeletal development in a lineage-specific manner remains to be fully elucidated. Here, we investigated the role of EHMT2 in skeletal development by conditionally inactivating Ehmt2 in neural crest-derived and mesoderm-derived progenitors using Wnt1-Cre and Prx1-Cre mouse lines, respectively. Loss of Ehmt2 function in neural crest cells led to postnatal growth failure and craniofacial defects, including delayed intramembranous ossification and malformations of the jaw and cranial base. Transcriptomic analysis of neural crest cells revealed disrupted chromatin regulatory networks, reduced expression of proliferation-associated genes, and upregulation of inflammatory pathways. In contrast, inactivation of Ehmt2 in Prx1-expressing mesodermal progenitors had minimal impact on limb and cranial bone development, with no significant alterations in bone mass or osteoblast function. Together, these results reveal a lineage-specific requirement for EHMT2 in neural crest-derived skeletal tissues, suggesting that distinct progenitor populations exhibit differential dependency for bone development.

cell biology↗

Mating-Type Imputation (MTI) provides an efficient tool for the mating-type inference of tetrapolar fungi

Mating-type identification is fundamental for the genetic diversity and genetic breeding study in fungi, especially for tetrapolar basidiomycetes, whose mating-types are determined by two multiallelic loci A and B. Traditional mating-type identification of monokaryons relies on manual inference based on their hybridization experiments; however, the process is rather complex, time-consuming and error-prone for large-scale hybridization experiments. In this study, we developed the Mating-Type Imputation (MTI) software for automatic, rapid and accurate monokaryon mating-type inference for tetrapolar fungi using a combinatorial pruning traversal algorithm. Taking the compatibility matrix from 435 hybridization experiments of 30 Flammulina velutipes monokaryons as an example, MTI takes a few minutes to infer the accurate mating-types of all monokaryons, which might take several days for manual inference by experienced investigators. Furthermore, MTI enables us to investigate how false-positives and false-negatives influence mating-type inference results. Using simulated compatibility matrix, we found that MTI could accurately detect potential false-negatives in compatibility and successfully infer the true mating-type combination with limited false-negatives, but the tool could be misled by any false-positives to result in a wrong mating-type combination, indicating that false-positives records in hybridization experiments should be strictly obviated for mating-type inferences. In summary, MTI provides an efficient tool for mating-type inference of tetrapolar fungi, offering technical support for the research paradigm in mating-type studies of edible and medicinal fungi and holding significant theoretical value and broad application prospects in the fields of fungal genetic diversity and breeding studies.

genetics↗

Ergothioneine and a new food supplement product protectagainst cyclophosphamide-induced premature ovarianfailure in rats

Premature ovarian failure (POF) is characterized by disrupted estrous cycles and impaired folliculogenesis due to oxidative stress and inflammation. In this study, a cyclophosphamide (CTX)-induced POF rat model was used to evaluate the protective effects of ergothioneine (EGT) and a nutraceutical formula (FineNutri Cellular Vitality Capsules) containing EGT. CTX treatment markedly prolonged the estrous cycle, reduced estrus duration, decreased ovarian weight, impaired follicular development, and increased granulosa cell apoptosis. Serum estradiol (E2) and anti-Mullerian hormone (AMH) levels decreased, whereas luteinizing hormone (LH) and follicle-stimulating hormone (FSH) increased, reflecting disruption of the hypothalamic-pituitary-ovarian axis by CTX. CTX treatment induced oxidative stress, with reduced catalase (CAT), superoxide dismutase (SOD) activity, and glutathione (GSH) content, and increased malondialdehyde (MDA) in ovarian tissue. The EGT and the nutraceutical formula restored estrous cycles, increased ovarian weight, improved primordial follicle counts, and reduced atretic follicles and granulosa cell apoptosis. Hormonal balance was partially restored, with increased E2 and AMH and reduced LH and FSH levels. Oxidative stress was alleviated with higher CAT, SOD, and GSH levels and reduced MDA concentrations. In addition, EGT and the formula reduced inflammation in skin tissue. These findings suggest that EGT and the nutraceutical formula could protect against CTX-induced POF and help preserve ovarian function, probably by mitigating oxidative stress.

pharmacology and toxicology↗

Automated analysis of C. elegans behavior by LabGym: an open-source, AI-powered platform

The genetic tractability, well-mapped circuitry, and diverse behavioral repertoire of the nematode C. elegans make it an ideal model for physiological and behavioral studies. A wide range of methods has been developed for analyzing C. elegans behaviors, evolving with advances in technology such as videography and computer-assisted analysis. Here, we introduce LabGym--an open-source, artificial intelligence (AI)-based platform we recently developed--to the C. elegans research community. We trained deep learning models in LabGym capable of automatically categorizing and quantifying multiple user-defined parameters of worm locomotion behavior in multi-worm videos with high accuracy. Furthermore, we demonstrated their efficacy in quantifying locomotion changes in aging worms. Our work offers a cost-effective, user-accessible approach to behavioral analysis in C. elegans.

animal behavior and cognition↗

Site- and Structure-Specific Characterization of Glycoproteins of H11: Potent Vaccine Candidates against Parasitic Worm Haemonchus

Parasitic worms (helminths) infections pose significant threats to global health and livestock economies. While mass spectrometry (MS)-based glycomics have revealed that helminths express complex, immunomodulatory N-glycans, site- and structure-specific characterization of intact glycopeptides remain challenging. Here we employed advanced MS-based intact glycoproteomics to explore the N-glycosylation profile of H11 antigen - an important vaccine antigen from pathogenic parasite Haemonchus contortus. We successfully identified seven glycosylated aminopeptidases carrying 19 N-glycosylation sites with 31 distinct N-glycan structures. Notably, 13 N-glycopeptides were significantly enriched by H11-induced protective IgG antibodies. Our findings revealed a high degree of structural heterogeneity and abundant core fucosylation among the identified N-glycopeptides. Additionally, molecular docking studies demonstrated those IgG-recognized N-glycopeptides are situated on the protein surface or adjacent to the substrate-access channels, strongly indicating their potential as antigenic epitopes. Overall, our work represents the first comprehensive glycoproteome of an economically important parasitic worm. These results hold important implications for the rational design of vaccines against H. contortus and other related metazoan parasites.

pathology↗

Male germline vulnerability to DNA damage causes sex-biased mutation

In many vertebrates the male germline mutation rate is higher than that of females, so-called male mutation bias, the causes of which are central to numerous molecular evolution debates including the relationship between life history traits and the mutation rate and the cause of the generation time effect. The male bias was classically considered a consequence of the higher number of cell divisions in the male germline, but recently multiple lines of evidence find this to be an inadequate explanation. The revived damage-induced hypothesis posits that males are either more prone to germline damage or less likely to repair damage, leading to more mutations. The model predicts that, when males and females are treated with approximately equal levels of mutagenic stress, the male germline will accumulate more mutations. Here we provide the first test of the damage hypothesis by exposing male and female mice to mutagenic chemicals with both untreated and a non-mutagenic (PBS) controls, assaying de novo mutations via parent-offspring whole-genome sequencing. As predicted, in the instances where the mutagens caused a net increase to the mutation rate, it went up more in male germline. Comparison with established mutational signatures reveals differential involvement of the base excision repair (BER) pathway. Similarly, transcriptome analysis finds higher expression levels of DNA repair genes in ovary compared to testis for those genes in the BER pathway, a difference that becomes more extreme on administration of mutagens. As parental age, hence number of germline cell divisions, is controlled, we conclude that the male mutation bias is, at least in part, owing to differential damage repair with lower base excision repair in males playing a significant role.

evolutionary biology↗

Aromatic amino acids in the orthosteric region regulate cannabinoid receptor 1 conformation transitions

Cannabinoid receptor 1 (CB1) is a class A G protein-coupled receptor that exhibits constitutive activity by spontaneously sampling both active and inactive states in the absence of ligand binding. Structural studies have identified a domain of aromatic residues, F2003.36, W3566.48, and W2795.43, that modulates receptor function and ligand engagement; however, their mechanistic roles remain unclear. Here, we use equilibrium and targeted molecular dynamics simulations to investigate how alanine substitutions at these positions alter CB1 dynamics. Our results show that mutations, especially the F200A+W356A combination, enhanced conformational flexibility and shifted the receptor toward inactive-like states. W3566.48 emerged as a structural pivot essential for active-state stability, F2003.36 acted as a late-stage kinetic barrier to inactivation, and W2795.43 modulated orthosteric pocket packing and flexibility, amplifying destabilization when combined with F2003.36 or W3566.48 mutations. Targeted simulations showed that mutation of this aromatic domain lowers energetic barriers and rewires the inactivation pathway. These findings define the structural logic of CB1 toggle-switch control and provide a mechanistic framework for designing modulators that tune basal activity in CB1.

biophysics↗

The claudin-like molecule CLC-3 regulates neuromuscular function in Caenorhabditis elegans by modulating cholinergic signalling

Cell adhesion molecules (CAMs play important roles in neurons, contributing to nervous system development, synapse formation, and activity-dependent plasticity. Claudins, the cell-adhesion molecules known for their roles at tight junctions in epithelial and endothelial cells, remain underexplored in neurons, particularly in vertebrates. In contrast, emerging studies in Caenorhabditis elegans have begun to reveal neuronal functions of claudin-like proteins. However, a systematic analysis of their neuronal expression has not been performed. We conducted a transcriptional reporter screen of all claudin-like genes in C. elegans and identified several candidates with previously unreported neuronal expression, highlighting a broader role of this family in the nervous system. One candidate, clc-3, showed robust expression in head, tail, and ventral cord neurons, with no detectable expression in non-neuronal tissues. Functional analyses of clc-3 mutants revealed increased body-bend amplitude and elevated evoked postsynaptic currents at the cholinergic neuromuscular synapses. Imaging and molecular interaction studies demonstrated that CLC-3 localises to the presynaptic membranes in cholinergic neurons, where it interacts with the actin-binding protein NAB-1 and regulates cholinergic signalling. This presynaptic role of CLC-3 likely contributes to the regulation of sinusoidal movement in C. elegans. Our findings identify CLC-3 as a neuronally expressed claudin that regulates motor system output by influencing synaptic vesicle organization and illustrate how changes in synaptic organization are coupled to whole-animal behaviour.

neuroscience↗

Paclitaxel Alleviates Pulmonary Arterial Hypertension by Modulating Macrophage M2a Polarization via the NF-κB Pathway

BackgroundPulmonary arterial hypertension (PAH) is primarily associated with vascular remodeling, in which macrophage polarization is considered to play a major role. Paclitaxel(PTX) has been shown to modulate macrophage polarization in tumors. We investigated whether PTX could alleviate PAH by altering macrophage polarization, particularly M2a macrophages. MethodsTo establish PAH, rats underwent left pneumonectomy followed by monocrotaline (MCT) injection. In vitro, THP-1 cells were differentiated into macrophages using PMA and polarized with LPS+IFN-{gamma} (M1), IL-4 (M2a), or IL-10 (M2c), followed by PTX intervention. Hemodynamic parameters (mPAP) and right ventricular hypertrophy index (RVHI) were measured. Pathological changes were assessed via HE staining. Single-cell RNA sequencing analyzed macrophage subsets in lung tissues. Macrophage polarization and NF-{kappa}B pathway activity were evaluated using immunohistochemistry, qPCR, cytokine profiling and Western blot. ResultsIn a severe PAH model induced by left pneumonectomy plus monocrotaline, pulmonary interstitial macrophages initially exhibited a predominant M1-polarized phenotype in the early stage, which transitioned to an M2a-polarized phenotype in the later stage and eventually stabilized. Low-dose PTX alleviated severe PAH by reducing perivascular macrophage infiltration. Cytological studies confirmed that PTX inhibited M2a polarization via suppression of NF-{kappa}B, thereby attenuating its proliferative effects on pulmonary arterial smooth muscle cells (PASMCs). ConclusionM2a macrophages play a crucial role in PAH progression. PTX may alleviate PAH by suppressing M2a polarization via the NF-{kappa}B pathway.

immunology↗

Hypobaric hypoxia drives citrate cycle reprogramming to suppress tumor progression

High altitude residents present lower tumor incidence and mortality than plain residents, suggesting that hypobaric hypoxia displays protective effect against tumor development. The results of our studies showed that hypobaric hypoxia exposure significantly suppressed tumor progression in subcutaneous bearing and lung metastasis tumor models. With single-cell transcriptome analysis, we identified HIF-1 pathway was significantly downregulated in tumor tissues with high altitude hypoxia, leading to decreased glycolysis and angiogenesis and improved antitumor immune response. Mechanistically, systemic hypoxia rewired citric acid cycle, with enhanced CS and IDH2 expression and reduced OGDH and SUCLG2 expression, to induce -ketoglutarate accumulation and succinate decline in tumor microenvironment, further mediating HIF-1 pathway inhibition. Moreover, hypobaric hypoxia treatment significantly improved the antitumor effects of adjuvant therapies (including chemotherapy, anti-angiogenic therapy and immunotherapy). Our findings reveal the role and mechanism of hypobaric hypoxia for tumor regression and yield new insights into tumor therapy.

cancer biology↗

HerbComb: an integrated database for the discovery of novel combinational therapies from herbal medicines

Drug combinations have gained increasing interest due to their potential for optimal efficacy and the ability to overcome drug resistance. Herbal medicine is a complex system with multiple ingredients and has illustrated apparent therapeutic effects through thousands of years of clinical experience, offering a rich resource for combinational therapies. However, the underlying mechanism of their synergistic therapeutic effects for disease treatment remains obscure for most herbal medicines. To fill this gap, we developed an integrated database named HerbComb (https://herbcomb.com/) to discover combinatorial therapies in herbal medicine, featuring three unique functions: drug prepositioning, customized combinatorial analysis, and biological and pharmacological features. Additionally, transcriptional gene signatures and ADMET properties were also interrogated as interactive functionalities to facilitate combinational analysis. Using Tongxinluo for Stroke as a case study, we identified and validated Oleanolic acid and Ferulic acid as synergistic ingredients. In summary, HerbComb is a versatile data exploration platform designed to characterize synergistic interactions among herbal medicines, enhancing the understanding of synergistic mechanisms and facilitating the discovery of effective drug combinations.

pharmacology and toxicology↗

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↗

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↗

Complementary cortical and thalamic contributions to cell-type-specific striatal activity dynamics during movement

Coordinated motor behavior emerges from information flow across brain regions. How long-range inputs drive cell-type-specific activity within motor circuits remains unclear. The dorsolateral striatum (DLS) contains direct- and indirect-pathway medium spiny neurons (dMSNs and iMSNs) with distinct roles in movement control. In mice performing skilled locomotion, we recorded from dMSNs, iMSNs, and their cortical and thalamic inputs identified by monosynaptic rabies tracing. An RNN classifier and clustering analysis revealed functionally heterogeneous subpopulations in each population, with dMSNs preferentially activated at movement onset and offset, and iMSNs during execution. Cortical and thalamic inputs were preferentially activated during onset/offset and execution, respectively, though dMSN- and iMSN-projecting neurons in each region showed similar patterns. Locomotion phase-specific rhythmic activity was found in a subset of thalamic dMSN-projecting neurons and dMSNs. Cortex or thalamus inactivation reduced MSN activity. These findings suggest that corticostriatal and thalamostriatal inputs convey complementary motor signals via shared and cell-type-specific pathways.

neuroscience↗

Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids

A bioengineered kidney using a decellularized kidney scaffold (DKS) offers a promising solution to the kidney shortage. However, the transplantation of bioengineered kidneys using DKS recellularized with human endothelial, renal cells or others has not yet successfully achieved the vascular and renal reconstruction in vivo. In this study, we identified another type of stem cells, designated as human placenta-derived angiogenic stem cells (hPASCs), which serve as seeding cells for the vascularization of DKS. These hPASCs encompass angiogenic subpopulations, exhibit both stem cell properties and the capacity for vascular differentiation. Human fetal kidney organoids (KIO) were established as a source of renal parenchymal cells, comprising renal, immune, and vascular cell populations. We developed a vascularized bioengineered kidney by recellularizing DKS with hPASCs and KIO using a circulation perfusion culture system. The hPASCs bioengineered kidney demonstrated enhanced angiogenesis and reconstructed renal architecture in vivo, by transplantation into rat models of renal subcapsular and partial nephrectomy. Furthermore, immunofluorescence and single-cell analyses revealed that the hPASCs revascularized bioengineered kidney regenerated both vascular and renal parenchymal cells within the host. This study offers another strategy for kidney bioengineering and regeneration.

bioengineering↗

Secretory carrier membrane proteins assist with aquaporin trafficking in Arabidopsis.

Aquaporins belonging to the plasma membrane intrinsic protein (PIP) subfamily are channel proteins that control water flow across cells, allowing plants to rapidly adjust hydraulic conductivity and thereby sustain growth, gas exchange, and recovery from drought. We show that secretory carrier membrane proteins (SCAMP) regulate the abundance of the aquaporins and thereby water transport in Arabidopsis root cells. SCAMPs are evolutionarily conserved multi-spanning transmembrane proteins. In animal cells, they function in secretion, endocytosis and autophagy. Knowledge on their role in plants is restricted to localization and trafficking experiments in heterologous systems and few genetic perturbation experiments. Here, we analysed all five members of the Arabidopsis SCAMP family. We identified conserved tyrosine motifs assisting in transport to the plasma membrane and N-terminally located NPF motifs that are required for internalization. SCAMPs dimerize both at the plasma membrane and endosomes, and dimerization is required for their internalization. Functionally, several PIPs were identified as common targets of multiple SCAMP isoforms. Triple and quintuple scamp mutants show mild developmental delay under standard growth conditions, but they are less sensitive to drought-induced leaf wilting. This observation cannot be explained by altered stomatal dynamics or densities, nor by differential soil water content. However, scamp mutant root protoplasts contain less PIPs and swell less under hypotonic conditions compared to wild type, indicating reduced PIP plasma membrane levels. In conclusion, our research identifies the SCAMP membrane trafficking proteins as regulators of PIP abundance at the plasma membrane in root cells. We propose that the reduced PIP levels in the scamp mutants act as a priming mechanism, allowing them to respond better to conditions of reduced water availability.

plant biology↗

Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism

Hysteresis--where a system retains memory of a transient stimulus--is common in signaling but can also arise in intracellular organization. DNA repair foci, a type of biomolecular condensate, are initiated by the short-lived noncanonical nucleic acid poly(ADP-ribose) (PAR). PAR recruits proteins with prion-like domains (PrLDs), such as Fused in Sarcoma (FUS), and initiates their condensation, which persists even after PAR degradation. How FUS transitions from PAR-dependent to PAR-independent condensation remains unclear. Here, we show that PAR binding triggers a conformational switch in FUS, enabling sustained condensation. PAR binds to the C-terminal arginine-rich region of FUS, displacing intramolecular contacts, and exposing the N-terminal PrLD. This conformational opening allows PrLD interactions in trans, stabilizing condensates independently of PAR. FUS thus undergoes a regulated, nucleated conformational conversion--reminiscent of classical prions. This mechanism implies a paradigm of nucleic acid-induced conformational memory that may underlie hysteresis in intracellular organization in health and disease. HIGHLIGHTS[bullet] PAR-initiated FUS condensation follows a bi-modular mechanism involving both FUS termini. [bullet]Simulations predict and experiments confirm PAR disrupts FUS intramolecular contacts. [bullet]Upon condensation, FUS adopts a conformation with its N-terminus open for interactions. [bullet]N-terminal interactions maintain FUS condensation when PAR degrades during DNA repair.

molecular biology↗

Distinct functional potential of bacterial extracellular vesicles across biogeographic provinces of the South Pacific Ocean

Bacterial extracellular vesicles (BEVs) are nanoscale membranous structures released by diverse types of bacteria. Laboratory model systems indicate that these nanoparticles may play several roles in the ecophysiology of marine bacteria. However, their actual functionality in the environment remains unclear. Here we describe the proteomic composition of marine BEVs over more than 5,000 nautical miles of surface waters in the South Pacific, linking BEV cargoes to the bacterial communities producing them. BEVs were consistently present across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial cells. However, the protein content of the BEVs varied significantly between different ocean regions. The BEVs were enriched in carbohydrate transporters under phytoplankton bloom conditions, and contained iron and phosphate uptake-related proteins in nutrient-limited waters. This suggests that BEVs could enable cells to perform key extracellular functions in the marine environment. Our observations further highlight the prevalence of BEVs and the biogeographic patterns of their functional potential across oceanic scales.

microbiology↗