Biology subjects

Liao, M.

Publications and source records attributed to Liao, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Dendritic Morphology Constrains Microtubule Dynamics and Organization

Neuronal dendrites form highly branched morphologies supported by spatially patterned microtubule arrays that are essential for intracellular transport and structural stability, yet how this organization is established and maintained remains unclear. Here we analyze microtubule behavior in Drosophila sensory neurons using live-cell imaging, deep learning-based analysis, and genetic perturbations. We find that microtubules are shorter and fewer in thin distal branches and progressively longer and more abundant in thicker proximal branches. Locally, polymerization slows in narrow branches due to soluble tubulin depletion, while catastrophe frequency increases near branch points upon cortical encounter. A physical model incorporating these morphology-dependent constraints reproduces both local microtubule dynamics and global organization. Inverting the textbook view that microtubule dynamics shape cell morphology, our results demonstrate that, on short timescales, cell morphology instead constrains microtubule dynamics, thereby determining large-scale cytoskeletal organization.

biophysics↗

bioRxiv2026

Chemistry and Structure of Birch Bark Support Passive Radiative Cooling

White-barked birches extend to the northern limit of tree growth, and their bark is known to reduce solar damage during winter and early-spring by limiting solar heating and the incidence of harmful freeze-thaw events. The physical basis for this protection, however, has remained unclear. Here, we show that extracted betulin, the dominant triterpenoid responsible for the bark's whiteness, and Himalayan birch bark, both exhibit passive radiative cooling. Under low solar irradiance, bark and betulin-pellets reach temperatures below that of a shaded reference, and pellets cool more than bark. The cooling arises from high solar reflectance, which suppresses solar heating, and substantial mid-infrared emission, which drives radiative heat loss toward outer space. These findings help explain how bark-whiteness may contribute to protecting birch trees from solar-induced thermal stress.

plant biology↗

bioRxiv2026

Vegetation change and functional composition shifts in southwestern China during late MIS 3 to LGM

The climatic transition from Marine Isotope Stage 3 (MIS3) to the Last Glacial Maximum (LGM) had caused widespread vegetation change. Despite the dynamic equilibrium between vegetation and climate, the specific role of functional composition in vegetations response to climate change was inadequately understood. Here, we analyzed the long-term trajectories of palynological diversity, vegetation coverage and community-weighted-mean (CWM) functional traits based on EH22 pollen record (35-18 cal ka BP) from Erhai Lake, southwestern China. The results disclosed a vegetation transition from temperate deciduous broadleaf forest dominance in late MIS3 to cold coniferous and mixed broadleaved/coniferous forests in LGM. This vegetation dynamic involved functional composition shifts from competitive-driven functional convergence to partial recovery via niche differentiation during the late MIS3, and finally to a low-diversity but functional differentiation state through trait complementarity and diversification strategies during the cold LGM. Our results likely support a function-mediated climate filtering process whereby climate change regulated long-term vegetation dynamics during the MIS3-LGM transition primarily through shifts in CWM functional composition. These findings underscore the potential of pollen-based trait approaches to reconstruct ecosystem properties and advance our understanding of ecosystem change over decadal to millennial time-scales.

ecology↗

bioRxiv2026

Rapid vegetation reorganization in Hengduan Mountains driven by high climatic oscillations

The accelerating global climate change has been triggering large-scale vegetation reorganizations, yet our understanding of how mountain ecosystems respond to rapid climatic oscillations is critically constrained. Here, we present a high-resolution palynological record from Erhai Lake, southwestern China, revealing eight episodes of rapid vegetation reorganizations in the Hengduan Mountains (HMs) over the past 35,200 years. These reorganizations closely tracked the rhythms of rapid climate oscillations, particularly during the Last Glacial Maximum and the Last Deglacial Period. We find that while the timing of rapid vegetation reorganizations were synchronous with Atlantic Meridional Overturning Circulation (AMOC) anomalies that modulated global climate variability, the magnitude of these reorganizations did not exhibit a linear correlation with AMOC strength; instead, they were governed by local heat and moisture availability mediated through teleconnections. This demonstrates a strong natural regulatory capacity of mountain vegetation in HMs, enabling resilience to intense climatic fluctuations. However, when using the Erhai record as a benchmark, we project that rapid reorganizations under the high-emission pathway (SSP585) will likely surpass the intensities observed during historical events. These findings reveal the high climatic sensitivity and strong natural regulatory capacity of mountain ecosystems, highlighting the critical necessity of climate mitigation actions and nature-based solutions to safeguard subalpine and alpine biodiversity against unprecedented future climate change.

ecology↗

bioRxiv2025

Mining of natural diversity enables efficient and expressible peptide asparaginyl ligases

Peptide asparaginyl ligases (PALs) are powerful tools for protein engineering but are limited by natural rarity and poor expression. We mined 23 cyclotide-rich Viola species, uncovering 29 new PALs that expanded the known repertoire to 47. A dual-objective screen identified VdiPAL1 as the best-performed natural PAL, with twice efficiency of wt-VyPAL2 and 12 mg L-1 soluble expression in E. coli. A broad P2 specificity including Trp/Ile/Leu/Phe/Tyr/Met was discovered across diverse PALs, which enables sequential click-compatible liposome dual-functionalization. 1.8L[A] crystal structure of VdiPAL1 reveals a pre-organized near-attack conformation (NAC), supported by constant-pH MD simulations linking pH-dependent reactivity to NAC geometry. Our homology- and structure-based design yielded VyOpt1, a quintuple mutant of VyPAL2 with over 24-fold improved expression via enhanced cap-domain foldability in a single design-test cycle. This work expands the PAL family and demonstrates a transferable cap-domain-based engineering strategy, highlighting natural diversity as a powerful driver of enzyme discovery and optimization. TOC summaryMining of cyclotide-rich Viola genus expanded the total number of natural peptide asparaginyl ligases (PALs) to 47, including the discovery of highly expressible VdiPAL1. Its high-resolution structure provided new insights for mechanism, and its sequence guided us to a generalized PAL engineering strategy, leading to 24-fold increment in VyPAL2 expression.

biochemistry↗

bioRxiv2025

Global shifts in vegetation compositional resilience over the past 8,000 years

Vegetation resilience is critical for sustaining biodiversity and ecosystem services, yet its long-term dynamics and underlying drivers remain poorly resolved. Here, we assess changes in continental-scale vegetation compositional resilience over the past 8,000 years by applying established leading indicators (including autocorrelation, standard deviation, skewness, and kurtosis) to 482 fossil pollen records from all major landmasses except Antarctica. Using a machine learning approach, we evaluate the relative contributions of anthropogenic land cover change (ALCC) and climatic parameters (annual mean temperature, temperature seasonality, annual precipitation, and precipitation seasonality) in driving resilience shifts across continents. We further employ structural equation modeling (SEM) to disentangle how abiotic factors (ALCC and climatic variables) and biotic factors (species richness, evenness, synchrony, and temporal {beta} diversity) jointly shape long-term trends in vegetation resilience at the continental scale. Our results reveal a persistent, millennia-scale decline in resilience during the past 1.6 to 4.4 thousand years before present, with intensified anthropogenic land-use change identified as the dominant global driver. This finding suggests that the global decline in vegetation resilience observed over recent decades likely represents a continuation of the long-term trend established during the preceding Holocene. Notably, North America exhibited a resurgence in resilience over the past 1,200 years, primarily attributed to enhanced resilience in tundra and savanna ecosystems. SEM analyses uncover complex pathways through which abiotic and biotic predictors interact to shape millennial-scale resilience changes across continents. Despite the complexity of these underlying mechanisms, the analyses demonstrate that biotic factors collectively exert substantial, and often predominant, influences on long-term resilience dynamics. This underscores the indispensable role of biotic attributes in modulating long-term vegetation resilience, highlighting their potential as critical targets for ecosystem conservation and restoration.

ecology↗

bioRxiv2025

AniMarkerDB: a comprehensive database for exploring cell types and marker genes in livestock and poultry at single-cell resolution

Single-cell RNA sequencing (scRNA-seq) has dramatically advanced the understanding of cellular heterogeneity. While numerous marker gene databases are available for humans and mice, a lack of systematic resources for livestock and poultry species remains, limiting progress in functional genomics, immunology, and breeding.. To address this challenge, we developed AniMarkerDB (https://animarkerdb.bio), a comprehensive and curated database dedicated to marker genes and immune-related epitopes in economically animals, including chicken, pig, and duck. AniMarkerDB integrates 7,010 marker gene across 37 tissues and 846 cell types, together with 71,442 immune epitope records from IEDB. All entries undergo rigorous literature curation, manual validation, and multi-level quality control, with standardized nomenclature and annotation to ensure data consistency and reusability. The platform supports flexible queries by species, tissue, cell type, or gene. It offers analytical tools for cross-species comparison model organisms such as human and mouse, interactive single-cell atlas visualization, and user-defined cell type annotation. Additionally, AniMarkerDB provides dynamic visualizations and export options, enabling researchers to efficiently obtain large-scale marker and epitope data for downstream applications such as infectious disease research, vaccine target design, and comparative immunology. Looking ahead, AniMarkerDB will expand species coverage and incorporate additional modalities, including single-cell atlases from healthy and disease models, establishing itself as a comprehensive and authoritative platform for animal cell biology, disease modeling, and translational research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/682327v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@af7e7borg.highwire.dtl.DTLVardef@198d114org.highwire.dtl.DTLVardef@1c69ed2org.highwire.dtl.DTLVardef@e4fc43_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Characterization of a C9orf72 Knockout Danio rerio model for ALS and cross-species validation of potential therapeutics screened in Caenorhabditis elegans.

Intronic hexanucleotide repeat expansions in the C9orf72 gene represent the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. This expansion decreases C9orf72 expression in affected patients, indicating that loss of C9orf72 function (LOF) acts as a pathogenic mechanism. Several models using Danio rerio (zebrafish) for C9orf72 depletion have been developed to explore disease mechanisms and the consequences of C9orf72 LOF. However, inconsistencies exist in reported phenotypes, and many have yet to be validated in stable germline ablation models. To address this, we created a zebrafish C9orf72 knockout model using CRISPR/Cas9. The C9orf72 LOF model demonstrates, in a generally dose-dependent manner, increased larval mortality, persistent growth reduction, and motor deficits. Additionally, homozygous C9orf72 LOF larvae exhibited mild overbranching of spinal motoneurons. To identify potential therapeutic compounds, we performed a screen on an established Caenorhabditis elegans (C. elegans) C9orf72 homologue (alfa-1) LOF model, identifying 12 compounds that enhanced motility, reduced neurodegeneration, and alleviated paralysis phenotypes. Motivated by the shared motor phenotype, 2 of those compounds were tested in our zebrafish C9orf72 LOF model. Pizotifen malate was found to significantly improve motor deficits in C9orf72 LOF zebrafish larvae. We introduce a novel zebrafish C9orf72 knockout model that exhibits phenotypic differences from depletion models, providing a valuable tool for in vivo C9orf72 research and ALS therapeutic validation. Furthermore, we identify pizotifen malate as a promising compound for further preclinical evaluation. Author SummaryAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the progressive loss of motor neurons, with no curative treatments currently available. The most common genetic cause is a hexanucleotide repeat expansion in the C9orf72 gene, which reduces its expression and implicates loss-of-function (LOF) as a disease mechanism. However, the complete functions of C9orf72 and its role in ALS remain unclear. Zebrafish models with indirect partial reduction of C9orf72 expression have shown promise in recapitulating key aspects of ALS, but inconsistencies have been observed across these models. To address these challenges, we developed a stable genetic C9orf72 LOF zebrafish model to study the effects of its LOF, validate previous findings, and test potential ALS therapeutics. Our model displays swimming activity deficits, reduced growth, increased mortality, and mild spinal motor neuron abnormalities. We demonstrated that pizotifen malate significantly improved motor function in both our model and a similar well-established worm model. These results underscore the differences between indirect depletion and direct genetic LOF models while identifying pizotifen malate as a promising candidate for preclinical testing. This zebrafish model serves as a valuable tool for understanding C9orf72-associated ALS mechanisms and advancing therapeutic development.

genetics↗

bioRxiv2025

A comprehensive benchmark and guide for sequence-function interpretable deep learning models in genomics

The development of sequence-based deep learning methods has greatly increased our understanding of how sequence determines function. In parallel, numerous interpretable algorithms have been developed to address complex tasks, such as elucidating sequence regulatory syntax and analyzing non-coding variants from trained models. However, few studies have systematically compared and evaluated the performance and interpretability of these algorithms. Here, we introduce a comprehensive benchmark framework for evaluating sequence-to-function models. We systematically evaluated multiple models and DNA language foundation models using 369 ATAC-seq datasets, employing diverse training strategies and evaluation metrics to uncover their critical strengths and limitations. Our benchmark study highlights that different model architectures and interpretability methods are better suited to specific scenarios. Negative samples derived from naturally inactive regions outperform synthetic sequences, whereas single-cell tasks require specialized models. Additionally, we demonstrate that interpretable sequence-function models can complement traditional sequence alignment methods in studying cross-species enhancer regulatory logic. We also provide a pipeline to help researchers select the optimal sequence-function prediction and interpretability algorithms.

bioinformatics↗

bioRxiv2024

Development of a monoclonal antibody against duck IFN-γ protein and the application for Intracellular Cytokine Staining

ABSTRACTInterferon-{gamma} (IFN-{gamma}), a member of the type II IFN family, is a crucial cytokine in the immune system and serves as an important indicator of immune response. Intracellular Cytokine Staining (ICS) is a technique used to analyze the production of cytokines within individual cells, and it has a wide range of applications in the fields of immunological monitoring, vaccine trials, and the study of infectious diseases. This study aimed to prepare monoclonal antibodies against duck IFN-{gamma} protein and to establish an ICS protocol for detecting the duck IFN-{gamma} protein. The duIFN-{gamma}-His or duIFN-{gamma}-Fc gene was cloned into the pEE12.4 expression vector and expressed as a recombinant protein of size 20.2 KDa or 54.9 KDa in 293F cells. The purified recombinant proteins were inoculated into BALB/c mice to generate splenic lymphocytes capable of secreting anti-duIFN-{gamma} antibodies, and hybridoma cells were obtained after fusion with SP2/0 cells. A new hybridoma cell line named 24H4, which stably secreted IgG3 {kappa} subtype antibody against duck IFN-{gamma}. This monoclonal antibody (mAb) was identified by Western Blot to recognize duck IFN-{gamma} antibodies, and the indirect ELISA results showed that its ability to recognize IFN-{gamma} protein reached 0.001 g/ml. The established ICS method was used to stain PBMCs after ConA stimulation, and duck IFN-{gamma} protein was successfully detected by flow cytometry, indicating that the ICS method was successfully established. This study we use the monoclonal antibody, 24H4, provides a crucial tool for subsequent research on duck cellular immune responses.

immunology↗

bioRxiv2024

Environmental DNA vs. Community Science: Strengths and Limitations for Urban Odonata Surveys

The study of insect decline remains a major frontier in insect biodiversity and conservation. Despite growing concern about accelerating rates of insect decline generally, relatively little data has been compiled about species of aquatic insects. Data is particularly lacking on the distribution of aquatic insects in urban ecosystems. Here, we compare environmental DNA (eDNA) metabarcoding and community science observation as means of monitoring Odonata within an urban system in Southwest Idaho. We show that the distribution of Odonata across this urban landscape is not uniform and that both monitoring methods have different strengths and weaknesses. We found that eDNA metabarcoding was very sensitive to the identification of genera from underrepresented families in the region, but was unable to distinguish between closely related genera, particularly from localities where eDNA could accumulate more damage. On the other hand, community science observations effectively identified the presence of genera from more speciose families but missed the presence of relatively rare species, and those that had a short flight season. These findings suggest that, in our study system, eDNA and community science are highly complementary of each other. In cases where only one method is employed for a monitoring or conservation project, care should be given to account for the biases of each approach.

ecology↗

bioRxiv2024

Contributions of genetic variation in astrocytes to cell and molecular mechanisms of risk and resilience to late onset Alzheimer's disease

Reactive astrocytes are associated with Alzheimers disease (AD), and several AD genetic risk variants are associated with genes highly expressed in astrocytes. However, the contribution of genetic risk within astrocytes to cellular processes relevant to the pathogenesis of AD remains ill-defined. Here we present a resource for studying AD genetic risk in astrocytes using a large collection of induced pluripotent stem cell (iPSC) lines from deeply phenotyped individuals with a range of neuropathological and cognitive outcomes. IPSC lines from forty-four individuals were differentiated into astrocytes followed by unbiased molecular profiling using RNA sequencing and tandem mass tag-mass spectrometry. We demonstrate the utility of this resource in examining gene- and pathway-level associations with clinical and neuropathological traits, as well as in analyzing genetic risk and resilience factors through parallel analyses of iPSC-astrocytes and brain tissue from the same individuals. Our analyses reveal that genes and pathways altered in iPSC-derived astrocytes from AD individuals are concordantly dysregulated in AD brain tissue. This includes increased prefoldin proteins, extracellular matrix factors, COPI-mediated trafficking components and reduced proteins involved in cellular respiration and fatty acid oxidation. Additionally, iPSC-derived astrocytes from individuals resilient to high AD neuropathology show elevated basal levels of interferon response proteins and increased secretion of interferon gamma. Correspondingly, higher polygenic risk scores for AD are associated with lower levels of interferon response proteins. This study establishes an experimental system that integrates genetic information with a heterogeneous set of iPSCs to identify genetic contributions to molecular pathways affecting AD risk and resilience.

neuroscience↗

bioRxiv2024

RFC1 regulates the expansion of neural progenitors in the developing zebrafish cerebellum

DNA replication and repair are basic yet essential molecular processes for all cells. RFC1 encodes the largest subunit of the Replication Factor C (RFC), which is a clamp-loader during DNA replication and repair. Intronic repeat expansion in RFC1 has recently been associated with so-called RFC1-related disorders, which mainly encompass late-onset cerebellar ataxias. However, the mechanisms that make certain tissues more susceptible to defects in these universal pathways remain mysterious. In this study, we provide the first investigation of RFC1 gene function in vivo using zebrafish. We showed that RFC1 is expressed in neural progenitor cells within the developing cerebellum and that it is necessary to maintain these cells genomic integrity during neurogenic maturation. Accordingly, RFC1 loss-of-function leads to a severe cerebellar phenotype due to impaired neurogenesis of both Purkinje and granule cells. Our data thus point to a specific role of RFC1 in the developing cerebellum, paving the way for a better understanding of the pathogenic mechanisms underlying RFC1-related disorders.

developmental biology↗

bioRxiv2024

DeepSS2GO: protein function prediction from secondary structure

Predicting protein function is crucial for understanding biological life processes, preventing diseases, and developing new drug targets. In recent years, methods based on sequence, structure, and biological networks for protein function annotation have been extensively researched. Although obtaining a protein in three-dimensional structure through experimental or computational methods enhances the accuracy of function prediction, the sheer volume of proteins sequenced by high-throughput technologies presents a significant challenge. To address this issue, we introduce a deep neural network model DeepSS2GO (Secondary Structure to Gene Ontology). It is a predictor incorporating secondary structure features along with primary sequence and homology information. The algorithm expertly combines the speed of sequence-based information with the accuracy of structure-based features, while streamlining the redundant data in primary sequences and bypassing the timeconsuming challenges of tertiary structure analysis. The results show that the prediction performance surpasses state-ofthe-art algorithms. It has the ability to predict key functions by effectively utilizing secondary structure information, rather than broadly predicting general Gene Ontology terms. Additionally, DeepSS2GO predicts five times faster than advanced algorithms, making it highly applicable to massive sequencing data. The source code and trained models are available at https://github.com/orca233/DeepSS2GO.

bioinformatics↗

bioRxiv2024

Molecular insights into the atypical activation mechanism of GPR156 in maintaining auditory function

The class C orphan GPCR GPR156, which lacks the typical extracellular region, plays a pivotal role in auditory function through Gi2/3. Here, we demonstrate that GPR156 with high constitutive activity is essential for maintaining auditory function, and we further present two cryo-EM structures of human GPR156. The GPR156 dimer in both the apo state and Gi3 protein-coupled state adopt a TM5/6-TM5/6 interface, indicating the high constitutive activity of GPR156 in the apo state. The C-terminus plays a dual role in promoting G protein binding within G-bound subunit while preventing the G-free subunit from binding to additional G protein. These observations explain how GPCR activity is maintained through dimerization and provide a mechanistic insight into the sustained role of GPR156 in maintaining auditory function.

molecular biology↗

bioRxiv2024

Structural basis of respiratory complexes adaptation to cold temperatures

In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain (1, 2). Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III2 (termed type 2) was identified with a [~]25{degrees} rotation of CIII2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.

cell biology↗

bioRxiv2023

Two transcriptional cascades orchestrate cockroach leg regeneration

The mystery of appendage regeneration has fascinated humans for centuries, while the regulatory mechanisms remain unclear. In this study, a transcriptional landscape of regenerating leg was established in the American cockroach, Periplaneta americana, an ideal model for appendage regeneration with remarkable regeneration capacity. Through a large-scale in vivo screening, we identified multiple signaling pathways and transcription factors (TFs) controlling leg regeneration. Specifically, zfh-2 and bowl, which have not been previously implicated in appendage regeneration, contributes to blastema proliferation and morphogenesis in two novel transcriptional cascades BMP/JAK-STAT-zfh-2-bab1/B-H2/Lim1 and Notch-drm/bowl-bab1. Notably, zfh-2 was found working as a direct target of BMP signaling to promote cell proliferation in the blastema. These mechanisms might be conserved in the appendage regeneration of vertebrates from an evolutionary perspective. Overall, our findings reveal that two crucial transcriptional cascades orchestrate distinct cockroach leg regeneration processes, significantly advancing the comprehension of molecular mechanism in appendage regeneration.

developmental biology↗

bioRxiv2023

The crystal and cryo-EM structures of PLCγ2 reveal dynamic inter-domain recognitions in autoinhibition

Abstract/SummaryPhospholipase C gamma 2 (PLC{gamma}2) plays important roles in cell signaling downstream of various membrane receptors. PLC{gamma}2 contains a multi-domain inhibitory region critical for its regulation, while it has remained unclear how these domains contribute to PLC{gamma}2 activity modulation. Here we determined three structures of human PLC{gamma}2 in autoinhibited states, which reveal dynamic interactions at the autoinhibition interface, involving the conformational flexibility of the SH3 domain in the inhibitory region, and its previously unknown interaction with a C-terminal helical domain in the core region. We also determined a structure of PLC{gamma}2 bound to the kinase domain of fibroblast growth factor receptor 1 (FGFR1), which demonstrates the recognition of FGFR1 by the nSH2 domain in the inhibitory region of PLC{gamma}2. Our results provide new structural insights into PLC{gamma}2 regulation that will facilitate future mechanistic studies to understand the entire activation process.

biochemistry↗