Biology subjects

Liu, K.

Publications and source records attributed to Liu, K..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Polarized ATP synthase in synaptic mitochondria induced by learning and plasticity signals

MINFLUX represents a state-of-the-art single-molecule localization microscopy technology that surpasses the conventional diffraction limit, enabling the visualization and analysis of nanostructures with exceptional precision. Despite its potential, the utilization of MINFLUX has been primarily confined to in vitro cultured cell environments. In this research, we have refined the sample preparation protocols to facilitate 3D MINFLUX imaging in fixed brain tissue sections, focusing on the mitochondrial distribution within dendritic spines and engram cells of the dentate gyrus. Probing single molecules in vivo reveals an interesting finding: the reorganization of mitochondrial inner membrane proteins during synaptic plasticity within dendritic spines of engram cells. Utilizing 3D MINFLUX nanoscopy, we identified a significant redistribution of -F1-ATP synthase, which correlates with learning related activities. This redistribution implies a pivotal function for polarized ATP synthesis in the vicinity of the postsynaptic zone, which may modulate both short-term and long-term synaptic modifications, thereby influencing synaptic plasticity and memory consolidation. Furthermore, dual-color 3D MINFLUX imaging has uncovered distinct patterns of mitochondrial reorganization involving both the inner and outer membranes within dendritic spines. These patterns, induced by plasticity signals, persist for up to 12 hours in neuronal cultures. This distinction highlights the presence of distinct regulatory mechanisms governing mitochondrial proteins during synaptic plasticity. These results offer new insights into the molecular mechanisms underlying synaptic plasticity and underscore the transformative potential of 3D MINFLUX imaging for studying neuronal processes in the brain.

neuroscience↗

bioRxiv2024

Reconstitution of SPO11-dependent double-strand break formation

Homologous meiotic recombination starts with DNA double-strand breaks (DSBs) generated by SPO11 protein1. SPO11 is critical for meiosis in most species but the DSBs it makes are also dangerous because of their mutagenic2 and gametocidal3 potential, so cells must foster SPO11s beneficial functions while minimizing its risks4. SPO11 mechanism and regulation remain poorly understood. Here we report reconstitution of DNA cleavage in vitro with purified recombinant mouse SPO11 bound to its essential partner TOP6BL. Similar to their yeast orthologs5,6, SPO11- TOP6BL complexes are monomeric (1:1) in solution and bind tightly to DNA. Unlike in yeast, however, dimeric (2:2) assemblies of mouse SPO11-TOP6BL cleave DNA to form covalent 5' attachments requiring SPO11 active site residues, divalent metal ions, and SPO11 dimerization. Surprisingly, SPO11 can also manifest topoisomerase activity by relaxing supercoils and resealing DNA that it has nicked. Structure modeling with AlphaFold37 illuminates the protein-DNA interface and suggests that DNA is bent prior to cleavage. Deep sequencing of in vitro cleavage products reveals a rotationally symmetric base composition bias that partially explains DSB site preferences in vivo. Cleavage is inefficient on complex DNA substrates, partly because SPO11 is readily trapped in DSB-incompetent (presumably monomeric) binding states that exchange slowly. However, cleavage is improved by using substrates that favor DSB-competent dimer assembly, or by fusing SPO11 to an artificial dimerization module. Our results inform a model in which intrinsically feeble dimerization restrains SPO11 activity in vivo, making it exquisitely dependent on accessory proteins that focus and control DSB formation so that it happens only at the right time and the right places.

biochemistry↗

bioRxiv2024

Spotiphy enables single-cell spatial whole transcriptomics across the entire section

Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole tissue sections1, but the approach remains dogged by the challenge of achieving single-cell resolution without sacrificing whole genome coverage2,3. Here we present Spotiphy (Spot imager with pseudo single-cell resolution histology), a novel computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. In evaluations with Alzheimers disease (AD) and normal mouse brains, Spotiphy delivers the most precise cellular compositions. For the first time, Spotiphy reveals novel astrocyte regional specification in mouse brains. It distinguishes sub-populations of DAM (Disease-Associated Microglia) located in different AD mouse brain regions. Spotiphy also identifies multiple spatial domains as well as changes in the patterns of tumor-tumor microenvironment interactions using human breast ST data. Spotiphy enables visualization of cell localization and gene expression in tissue sections, offering key insights into the function of complex biological systems.

systems biology↗

bioRxiv2024

Ophiostomatoid fungi associated with bark beetles infesting Pinus armandii, with characterizations of seven new species from western China

Ophiostomatoid fungi mainly refer to the order Ophiostomatales (Ascomycota), which are known to be symbiotic with bark beetles infesting pine trees. These fungi are primarily associated with Dendroctonus armandi and other bark beetles, significantly impacting the local pines Pinus armandii in western China. However, this fungal diversity must be further explored. This study aims to identify Ophiostomatoid fungi associated with P. armandii in Ningshaan, Shaanxi Province. A total of 225 Ophiostomatalean isolates were obtained from 46 gallery samples, accounting for 77.6 % of the total number of isolated strains. Twenty species were identified based on the phylogenetic analyses of ITS, LSU, {beta}-tubulin, and EF-1, as well as morphological characteristics. These include seven new taxa, Ceratocystiopsis rugosa, Graphilbum prolificum, G. ramosus, Masuyamyces huoditangensis, Ophiostoma flavescens, O. lenta, O. mediotumida, and thirteen known species. This study laid a theoretical foundation for understanding the relationship between the beetles and the ophiostomatalean fungi in the Ningshan region, China.

microbiology↗

bioRxiv2024

Ophiostomatalean fungi associated with Cyrtogenius luteus infested Pinus massoniana, including characterization of Masuyamyces qingyuanensis sp. nov. in China

Ophiostomatalean fungi refers to the species in the order Ophiostomatales of Ascomycota. This group of fungi comprises wood blue-stain agents and some species that are important pathogens of trees, nematodes, or humans. Most species in the Ophiostomatales have beneficial relationships with wood-boring insects such as bark beetles. Recent surveys were conducted to investigate the diversity of Ophiostomatoid fungi associated with Cyrtogenius luteus infesting Pinus massoniana in some areas of Guangdong, China. This study, 382 fungal strains were obtained, and 224 were identified as belonging to the Ophiostomatales order. Identification of these strains revealed that they spanned seven distinct genera. A new species, Masuyamyces qingyuanensis sp. nov., was discovered and identified through a combination of morphological and phylogenetic analyses across four gene regions: beta-tubulin (TUBB), internal transcribed spacer (ITS), large subunit ribosomal RNA (LSU), and translation elongation factor 1 alpha (EF1A).

microbiology↗

bioRxiv2024

Ophiostomatalean fungi associated with bark beetles infesting Pinus koraiensis, including the description of Ceratocystiopsis fushunensis sp. nov. in China

Fungi of Ophiostomatales (Sordariomycetes, Ascomycota) always have a symbiotic relationship with bark beetles (Coleoptera: Scolytinae). In this study, we investigated the fungi associated with Cryphalus piceae and Hylastes sp in Fushun. Based on the four gene fragments of TUB, ITS, LSU, and TEF and morphological characteristics, 206 strains of Ophiostomatales were identified to be distributed in 21 taxa; these included an undescribed taxon. Here, we described it as Ceratocystiopsis fushunensis sp. nov. The results of this study provided valuable information on the relationship between fungi and bark beetles.

microbiology↗

bioRxiv2024

SCAD Delivery Platform: A Novel Approach for Efficient CNS and Extrahepatic Oligonucleotide Therapeutics

Oligonucleotide therapeutics, including antisense oligonucleotides (ASOs) and duplex RNAs like siRNA, saRNA, and miRNA, hold immense potential for treating genetic and acquired diseases by modulating gene expression in a target-specific manner. However, effective delivery to extrahepatic tissues, particularly the central nervous system (CNS), remains a significant challenge. While GalNAc conjugation has enabled liver-specific delivery, leading to several approved siRNA drugs for hepatic targets, CNS delivery lags. ASOs, on the other hand, can self-deliver to the CNS when administered locally, as seen with nusinersen and tofersen. To address this disparity, weve developed the Smart Chemistry Aided Delivery (SCAD) platform which enables duplex RNA delivery by conjugating it to an accessory oligonucleotide (ACO), which acts as an aptamer to mediate protein binding and facilitate cellular uptake. Through extensive screening, we identified an optimal SCAD architecture that demonstrates enhanced cell-free protein binding and in vitro activity. In rodent models, local administration of SCAD-siRNA conjugates resulted in broad biodistribution throughout the CNS and sustained mRNA knockdown for over five months, with a favorable safety profile. The SCAD platform also exhibited efficient delivery to other tissues, including the eye, the lung and the joint. These features support its potential for broader clinical applications, as evidenced by an ongoing trial targeting amyotrophic lateral sclerosis (ALS) associated with mutations in the SOD1 gene. The modular design of SCAD allows it to easily adapt to any duplex RNA, making it a powerful tool for advancing oligonucleotide therapeutics.

neuroscience↗

bioRxiv2024

CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells

FOXP3-expressing regulatory T (Treg) cells play a pivotal role in maintaining immune homeostasis and tolerance, with their activation being crucial for preventing various inflammatory responses. However, the mechanisms governing the epigenetic program in Treg cells during their dynamic activation remain unclear. In this study, we demonstrate that CXXC finger protein 1 (CXXC1) interacts with the transcription factor FOXP3 and facilitates the regulation of target genes by modulating H3K4me3 deposition. Cxxc1 deletion in Treg cells leads to severe inflammatory disease and spontaneous T-cell activation, with impaired immunosuppressive function. As a transcriptional regulator, CXXC1 promotes the expression of key Treg functional markers under steady-state conditions, which are essential for the maintenance of Treg cell homeostasis and their suppressive functions. Epigenetically, CXXC1 binds to the genomic regulatory regions of Treg program genes in mouse Treg cells, overlapping with FOXP3 binding sites. Given its critical role in Treg cell homeostasis, CXXC1 presents itself as a promising therapeutic target for autoimmune diseases.

immunology↗

bioRxiv2024

Isolating the Direct Effects of Growth Hormone on Lifespan and Metabolism

Prior studies show that disrupting somatotropic axis components extends laboratory mouse lifespan, but confounding effects of additional genes and hormones obscure the specific impact of growth hormone (GH) on longevity. We address this issue by using mice with a specific knockout of the GH gene, revealing that disrupting GH alone substantially increases lifespan. The longevity effects are accompanied by altered metabolic fuel utilization, directly linking GH action to aging mechanisms.

physiology↗

bioRxiv2024

Two new species of Graphium (Microascales, Ascomycota) associated with pine-infesting bark beetles in China

Graphium is a genus of fungi that falls under the order Microascales of Ascomycota. Some species in this genus can establish a unique symbiotic relationship with the pine-infesting bark beetles, while others are typically found in wood or soil habitats. To comprehensively investigate the diversity of species of these fungi, recent field trips were conducted in seven provinces (Fujian, Guangdong, Guizhou, Guangxi, Liaoning, Shaanxi, and Shandong) in China. 96 pure isolates of Graphium were obtained by sequences from 361 samples. Nineteen representative strains were carefully selected to generate sequencing data from four gene regions (ITS, LSU, EF1A and TUBB), then used to construct phylogenetic trees for the genus. The results revealed the discovery of two new species, namely G. armandii sp. nov. and G. massoniana sp. nov., and G. pseudoumiticum was the most common species in various pine hosts.

microbiology↗

bioRxiv2024

3D Molecular Pretraining via Localized Geometric Generation

Self-supervised learning on 3D molecular structures is gaining importance in data-driven scientific research and applications due to the high costs of annotating bio-chemical data. However, the strategic selection of semantic units for modeling 3D molecular structures remains underexplored, despite its crucial role in effective pre-training--a concept well-established in language processing and computer vision. We introduce Localized Geometric Generation (LEGO), a novel approach that treats tetrahedrons within 3D molecular structures as fundamental building blocks, leveraging their geometric simplicity and widespread presence across chemical functional patterns. Inspired by masked modeling, LEGO perturbs tetrahedral local structures and learns to reconstruct them in a self-supervised manner. Experimental results demonstrate LEGO consistently enhances molecular representations across biochemistry and quantum property prediction benchmarks. Additionally, the tetrahedral modeling and pretraining generalize from small molecules to larger molecular systems, validating by protein-ligand affinity prediction. Our results highlight the potential of selecting semantic units to build more expressive and interpretable neural networks for scientific AI applications.

bioinformatics↗

bioRxiv2024

Discordance in acute gastrointestinal toxicity between synchrotron-based proton and linac-based electron ultra-high dose rate irradiation

PurposeProton FLASH has been investigated using cyclotron and synchrocyclotron beamlines but not synchrotron beamlines. We evaluated the impact of dose rate (ultra-high [UHDR] vs. conventional [CONV]) and beam configuration (shoot-through [ST] vs. spread-out-Bragg-peak [SOBP]) on acute radiation-induced gastrointestinal toxicity (RIGIT) in mice. We also compared RIGIT between synchrotron-based protons and linac-based electrons with matched mean dose rates. Methods and MaterialsWe administered abdominal irradiation (12-14 Gy single fraction) to female C57BL/6J mice with an 87 MeV synchrotron-based proton beamline (2 cm diameter field size as a lateral beam). Dose rates were 0.2 Gy/s (S-T pCONV), 0.3 Gy/s (SOBP pCONV), 150 Gy/s (S-T pFLASH), and 230 Gy/s (SOBP pFLASH). RIGIT was assessed by the jejunal regenerating crypt assay and survival. We also compared responses to proton [pFLASH and pCONV] with responses to electron CONV (eCONV, 0.4 Gy/s) and electron FLASH (eFLASH, 188-205 Gy/s). ResultsThe number of regenerating jejunal crypts at each matched dose was lowest for pFLASH (similar between S-T and SOBP), greater and similar between pCONV (S-T and SOBP) and eCONV, and greatest for eFLASH. Correspondingly, mice that received pFLASH SOBP had the lowest survival rates (50% at 50 days), followed by pFLASH S-T (80%), and pCONV SOBP (90%), but 100% of mice receiving pCONV S-T survived (log-rank P = 0.047 for the four groups). ConclusionsOur findings are consistent with an increase in RIGIT after synchrotron-based pFLASH versus pCONV. This negative proton-specific FLASH effect versus linac-based electron irradiation underscores the importance of understanding the physical and biological factors that will allow safe and effective clinical translation.

cancer biology↗

bioRxiv2024

Paired C-type lectin receptors mediate specific recognition of divergent oomycete pathogens in C. elegans.

Innate immune responses can be initiated through the detection of pathogen or damage-associated molecular patterns by host receptors that are often present on the surface of immune cells. While certain invertebrates like Caenorhabditis elegans lack professional immune cells, they still respond to infection in a pathogen-specific manner. It has been debated for years whether homologues of the canonical pathogen recognition receptors are also functioning in the nematode. Here we show that C-type lectin receptors mediate species-specific recognition of divergent oomycetes in C. elegans. A CLEC-27/CLEC-35 pair is essential for recognition of the oomycete Myzocytiopsis humicola, while a CLEC-26/CLEC-36 pair is required for detection of Haptoglossa zoospora. Both clec pairs are transcriptionally regulated through a shared promoter by the conserved PRD-like homeodomain transcription factor CEH-37/OTX2 and act in sensory neurons and the anterior intestine to trigger a protective immune response in the epidermis. This system enables redundant tissue sensing of oomycete threats through canonical CLEC receptors and host defense via cross-tissue communication. HighlightsO_LIA CLEC-27/CLEC-35 pair is required for recognition of the oomycete Myzocytiopsis humicola C_LIO_LIA CLEC-26/CLEC-36 pair is required for recognition of the oomycete Haptoglossa zoospora C_LIO_LIBoth CLEC pairs are co-regulated by the homeodomain transcription factor CEH-37/OTX2 C_LIO_LIBoth CLEC pairs function redundantly in sensory neurons and the intestine for host defense C_LI

immunology↗

bioRxiv2024

Differential splice isoforms of mouse CDK2 play functionally redundant roles during mitotic and meiotic division

In most mammals, the cell cycle kinase; cyclin-dependent kinase 2 (CDK2) is expressed as two major isoforms due to the inclusion or exclusion of an alternatively spliced exon. The shorter CDK2 isoform: CDK2S, is expressed constitutively during the cell cycle and can be detected in many different tissue types. In contrast, the longer isoform: CDK2L, shows preferential expression in meiotically dividing cells of the germ cells and upon S-phase entry during mitotic cell division. Both CDK2L and CDK2S form heteromeric complexes with cyclins A2 and E1 in vitro. However, complexes comprised of each isoform differ considerably in their kinase activity towards known CDK substrates. It is currently unknown whether the long and short isoforms of CDK2 play functionally different roles in vivo during either mitotic and meiotic divisions as conventional knockout methodology leads to the loss of both isoforms. In this study, we find that both CDK2L and CDK2S are sufficient to support both mitotic and meiotic division when expressed in the absence of the other. This data contributes to the explanation of the apparent tolerance of the evolutionary loss of CDK2L expression in humans.

cell biology↗

bioRxiv2024

Leveraging Multi-Modal Feature Learning for Predictions of Antibody Viscosity

The shift towards the subcutaneous administration route for biologics therapeutics has gained momentum due to its patient-friendly nature, convenience, reduced healthcare burden, and improved compliance compared to traditional intravenous infusions. However, one of the potentially significant challenges with this transition is managing the viscosity of the administered solutions. High viscosity can pose substantial development and manufacturability challenges, directly impacting the patient by increasing injection time and pain at the injection site. Moreover, high viscosity formulations can prolong residence time at the injection site, affecting absorption kinetics and potentially altering the intended pharmacological profile and therapeutic efficacy of the biologic candidate. This publication explores the application of a multimodal feature learning workflow for predicting the viscosity of antibodies in therapeutics discovery, integrating multiple data sources such as sequence, structural, physicochemical properties, and embeddings from a language model. This approach enables the model to learn from various underlying rules, including physicochemical rules from molecular simulations and molecular protein evolutionary rules by large, pre-trained deep learning foundation models. By comparing the effectiveness of this approach against other selected published viscosity prediction methods, this study offers insights on their intrinsic viscosity predictive potential and usability in therapeutics antibody early development pipelines.

bioinformatics↗

bioRxiv2024

RNA functional control by hydrolysis reversible acylation

Reversible 2'-OH acylation is a powerful strategy for switching RNA function, but existing systems often rely on nonphysiological or cytotoxic triggers for deacylation. Here we present EST1A, a hydrolysis-responsive 2'-OH acylating reagent whose RNA adducts are efficiently removed by endogenous esterases in vitro and in cellulo. EST1A acylates model oligonucleotides, an EGFP-targeting antisense strand, and reporter mRNAs, thereby modulating their activity; notably, the acylated antisense strand shows enhanced EGFP knockdown in HepG2 cells. By tuning carboxylesterase and cholinesterase activity and comparing EST1A-acylated mCherry mRNA across noncancerous and cancer-derived cell lines, we reveal a positive correlation between intracellular esterase activity and functional recovery of acylated RNA. These results establish EST1A-mediated, hydrolysis-responsive 2'-OH acylation as a simple platform for enzyme-guided, cell-selective activation of RNA function and point toward esterase-activated RNA therapeutics. Entry for the Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/610419v2_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1cbce3org.highwire.dtl.DTLVardef@b51bc4org.highwire.dtl.DTLVardef@31e96dorg.highwire.dtl.DTLVardef@d42578_HPS_FORMAT_FIGEXP M_FIG Liu et al. introduce EST1A, a hydrolysis-responsive 2'-OH acylating reagent whose RNA adducts are removed by endogenous esterases or histidine, enabling reversible control of RNA function. By exploiting differences in esterase activity between noncancerous and cancer-derived cell lines, EST1A-treated mRNA exhibits enzyme-guided and cell-selective translational reactivation. C_FIG

cancer biology↗

bioRxiv2024

Survival of hepatocytes from executioner caspase activation promotes liver regeneration by enhancing JAK/STAT3 activity

Activation of executioner caspases, which is a key step in the apoptotic process, has been reported to promote tissue regeneration by sending pro-proliferation signals to the surrounding cells. However, whether executioner caspase activation (ECA) has cell-autonomous effect on tissue regeneration is not clear. Here, by generating transgenic mice carrying a lineage tracing system for cells that have experienced ECA, we demonstrate that transient ECA occurs in hepatocytes during liver regeneration after partial hepatectomy (PHx) or carbon tetrachloride (CCl4) treatment. Instead of committing apoptotic cell death, the majority of hepatocytes with ECA survive and proliferate to contribute to liver regeneration. Interestingly, inhibition of ECA in livers results in reduced hepatocyte proliferation and impaired regeneration, whereas increasing ECA to a level sufficient to kill hepatocytes also impedes regeneration, suggesting that ECA needs to be precisely controlled during liver regeneration. Mechanistic studies show that ECA promotes hepatocyte proliferation during regeneration through enhancing JAK/STAT3 activity. Our work reveals an essential role of survival of hepatocytes from ECA in liver regeneration.

developmental biology↗

bioRxiv2024

Transocular detection of premotor Parkinson's disease via retinal neurovascular coupling through functional OCT angiography

Early detection of Parkinsons disease (PD) is essential for timely initiating neuroprotective interventions before significant loss of dopaminergic (DAergic) neurons, but faces challenges in accurately and noninvasively detecting subtle neuronal changes in the midbrain. Here, we propose a transocular functional imaging method termed fOCTA-rNVC, which detects premotor PD by measuring alterations in retinal neurovascular coupling (rNVC) at the capillary level using specialized functional OCT angiography (fOCTA). Our findings demonstrate that capillary rNVC is significantly attenuated and delayed due to concurrent retinal dopaminergic degeneration in premotor PD mice. Notably, this PD-related rNVC attenuation can be temporarily reversed in acute levodopa challenge. Utilizing the functional characteristics of capillary rNVC in PD, we achieved an impressive accuracy of [~]100% in detecting premotor PD mice even with only [~]14.1% loss of midbrain DAergic neurons, at which stage prompt treatment offered superior outcomes. In contrast, no significant changes were observed in retinal thickness or vasculature in the premotor PD mice. These findings suggest that fOCTA-rNVC is a promising noninvasive solution for accurately detecting premotor PD and guiding early interventions.

bioengineering↗