Biology subjects

Pan, Y.-H.

Publications and source records attributed to Pan, Y.-H..

13 recordsLinked to original sources

bioRxiv2026

Accelerated lung evolution associated with end-Permian and end-Triassic mass extinctions

The end-Permian and end-Triassic mass extinctions, driven by massive catastrophic volcanism and prolonged hypoxia, fundamentally reshaped life on Earth. However, the genomic impacts of these two biodiversity crises on living organisms remain largely unknown. Here, we performed a genome-wide screening to identify accelerated evolved regions in the ancestral lineage of mammals that survived both extinction events. Nearly all (20/21) of these accelerated regions were located in protein-coding sequences, and 81% (17/21) were found to be associated with lung function. We further extended our analysis to three additional vertebrate lineages that experienced either one or both of the mass extinctions. Similar genomic signatures, involving accelerated evolution of lung-related genes, were also observed in these non-mammalian lineages. Collectively, these findings suggest that adaptation of lung-related genes to prolonged hypoxia may have occurred during the two mass extinction events, potentially driving a second evolutionary stage of the lung following the vertebrate transition to land.

evolutionary biology↗

bioRxiv2025

Targeting Putrescine Homeostasis with Lactiplantibacillus plantarum PS128 to Mitigate Autism-like Behaviors in Fmr1 KO Mice

BackgroundAutism spectrum disorder (ASD) is biologically heterogeneous and has limited mechanism-informed interventions targeting core behavioral symptoms. Emerging evidence suggests that gut microbial metabolism shapes neurobehavioral outcomes, yet the specific metabolic pathways linking gut ecology to brain function remain incompletely understood. One candidate pathway is polyamine metabolism, which links microbial amino acid metabolism to host regulation and represents a plausible but underexplored contributor to ASD-related phenotypes. Notably, the psychobiotic Lactiplantibacillus plantarum PS128 has been reported to improve social behaviors in individuals with ASD, although the molecular basis for these effects is unclear. In this study, we used Fragile X mental retardation 1 knockout (Fmr1 KO) mice, a well-established ASD model, to investigate microbiota-dependent metabolic mechanisms underlying autism-like behaviors. ResultsWe found that autism-like behaviors in Fmr1 KO mice were associated with gut dysbiosis, impaired intestinal barrier integrity, disruption of the arginine-ornithine-polyamine pathway, and elevated putrescine in the prefrontal cortex (PFC). Supplementation with PS128 remodeled the gut microbiota, reduced inflammation- and disease-associated taxa, improved intestinal structure and permeability, and restored polyamine homeostasis. Targeted metabolomics revealed an increased PFC-to-serum putrescine ratio in KO mice, which was normalized following PS128 intervention. This correction was accompanied by reduced expression of polyamine transporters in the PFC, including ATP13A family members. Causal experiments supported a functional role for putrescine, as peripheral elevation of putrescine induced autism-like behaviors in wild-type mice, whereas pharmacological inhibition of putrescine synthesis ameliorated behavioral deficits in Fmr1 KO mice. ConclusionsThese findings identify putrescine metabolic dysregulation as a key contributor to autism-like phenotypes and support the existence of an ASD subtype defined by disruption of the arginine-ornithine-polyamine axis. Integrated multi-omics and causal perturbation analyses support a model in which microbiota-targeted intervention rebalances systemic polyamine regulation along the gut-brain axis, thereby improving ASD-relevant behaviors. Our work provides mechanistic evidence linking microbial metabolism to neurochemical homeostasis and highlights the translational potential of metabolic stratification in ASD. Graphical AbstractWe identify dysregulated microbiota-driven polyamine homeostasis as a causal contributor to autism-like behaviors in Fmr1 knockout mice. A psychobiotic intervention restores gut-brain metabolic balance and rescues social and repetitive behavioral deficits through coordinated microbial and host transport regulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/694366v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@e1e780org.highwire.dtl.DTLVardef@125a3baorg.highwire.dtl.DTLVardef@201228org.highwire.dtl.DTLVardef@1880650_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Interaction of Carbamoyl-Phosphate Synthase 1 with Agmatinase in the Liver of Torpid Bats

Mammalian torpor imposes unique metabolic constraints, yet the mechanisms of nitrogen metabolism during this state remain unclear. In this study, we show that the urea cycle is selectively regulated rather than broadly suppressed in torpid bats. A significantly increased abundance of carbamoyl-phosphate synthase 1 (CPS1) maintained its functional capacity during torpor and arousal in Myotis ricketti. Proteomic analyses and confocal microscopy identified a specific association and co-localization between CPS1 and agmatinase (AGMAT), an ATP-independent enzyme involved in nitrogen metabolism. Co-localization of CPS1 and AGMAT was also observed in torpid Rhinolophus ferrumequinum, a phylogenetically distant species. Fluorescence resonance energy transfer (FRET) further supported an indirect CPS1-AGMAT interaction. Most urea cycle enzymes exhibited stable or only moderately reduced expression during bat torpor, and metabolic profiling demonstrated sustained nitrogen flux. Together, these findings reveal a conserved adaptive mechanism that maintains urea cycle function, potentially enhancing osmotic stability and energy efficiency during prolonged fasting and water scarcity.

zoology↗

bioRxiv2025

Ancient human extinction risk: Implications from high-precision computation and fossil evidence

Reconstructing ancient population size history is essential for understanding the evolutionary origin of Homo sapiens. Using the fast infinitesimal time coalescent process (FitCoal), which precisely computes the expected site frequency spectrum (SFS), we revisited the debated population bottleneck that occurred approximately 930 thousand years ago. By benchmarking FitCoal against mushi and ten billion coalescent simulations, we demonstrate that FitCoal achieves both superior speed and accuracy in expected SFS estimation. Analyses of simulated datasets confirmed that FitCoal reliably recovered the bottleneck, whereas mushi failed under identical conditions. Independent fossil and paleoclimate evidence further corroborates the timing and evolutionary impact of this bottleneck, linking it to hominin dispersals, speciation events, and a subsequent increase in brain size. These findings refine the demographic history of Homo during the Pleistocene and highlight the importance of high-precision SFS computation for revealing critical evolutionary transitions that shaped modern human ancestry.

evolutionary biology↗

bioRxiv2024

Pre-rRNA spatial distribution and functional organization of the nucleolus

The self-organized nucleolus is where the pre-ribosomal RNA (pre-rRNA) processing and pre-ribosomal ribonucleoprotein (RNP) assembly take place. Here we present the spatiotemporal distribution of pre-rRNA intermediates in the human nucleolus, revealing a segregated spatial distribution of small subunit (SSU) and large subunit (LSU) precursors. Notably, the 5 external transcribed spacer (5 ETS)-containing SSU pre-rRNAs are retained across FC-DFC-PDFC regions, while the internal transcribed spacer 2 (ITS2)-containing LSU pre-rRNAs move to PDFC-GC regions for processing. Inhibiting 5 ETS processing disrupts the SSU pre-rRNA distribution and the nested FC-DFC sub-nucleolar structure. Cells in amniotes possess a multi-layered nucleolus, whereas anamniotes have only a bipartite structure with a merged FC-DFC. Kinetic labeling of pre-rRNA outflow shows a 7-fold higher pace in tetrapartite nucleoli over that in bipartite nucleoli, indicating that the emergence of the nested FC-DFC may facilitate an efficient SSU pre-rRNA processing over the course of evolution. Collectively, depicting the spatiotemporal distribution of pre-rRNAs reveals a key role of processing steps in organizing the multi-layered nucleolus and suggests a possible evolutionary advantage of the multi-layered structure in amniotes.

molecular biology↗

bioRxiv2024

Sociability genetically separable from social hierarchy in amniotes

The emergence of social structure and organization is essential for the evolution of amniotes, including human beings. Sociability and social hierarchy are two key features to form a social group. However, it remains unknown whether sociability and social hierarchy are genetically separable. In this study, we examined the social hierarchy, social and social novelty preference of PAS1 (placental-accelerated sequence 1) knock-out and knock-in mice. PAS1 is a social enhancer that modulates social hierarchy. We found that PAS1 knock-out mice lack social hierarchy while wallaby/chicken PAS1 knock-in mice establish stable social ranks. Moreover, social and social novelty preference was observed in all PAS1-mutated mice. PAS1 knock-in mice have stronger preference to interact with other mice than wild-type mice (C57BL/6). No aggressive alteration was found in PAS1-mutated mice. Overall, our results showed that PAS1 is an indispensable regulatory element in the formation of social hierarchy while PAS1 regulates one of pathways modulating sociability. Therefore, sociability is genetically separable from social hierarchy in amniotes, providing insights into how social structure and organization evolved. HighlightsPAS1, a social enhancer, is indispensable for amniotes to establish social hierarchy. PAS1 modulates sociability in amniotes. Sociability and social hierarchy are regulated differently in amniotes. The frequency of PAS1 allele was not rare when social hierarchy first appeared.

animal behavior and cognition↗

bioRxiv2023

ASD mutation of Katnal2 impairs ependymal ciliary motion and causes hydrocephalus

Katanin catalytic subunit A1 like 2 (KATNAL2) is a high-risk gene associated with autism spectrum disorders (ASD), however its impact on brain development and disease remains unclear. The present study revealed an unexpected role of KATNAL2 in regulating ependymal ciliary motion and cerebrospinal fluid flow during brain development, an important contributing factor for ASD. We discovered a distinct expression pattern of KATNAL2 in multiciliated ependymal cells of both human and mouse brains. Notably, an ASD-associated mutation of Katnal2 disrupted its molecular function and resulted in ASD-related behavioral deficits in mice. Additionally, this mutation affected the polarized organization and beating of ependymal cilia, leading to delayed cerebrospinal fluid flow and sustained ventricular enlargement from the early postnatal stage. Conditional ablation of Katnal2 specifically in the ependymal cells of neonatal mice is sufficient to cause ventricular dilation, whereas no such effect was observed in adult mice. Our findings highlight the importance of ependymal motile cilia and hydrocephalus in ASD, offering insights into its pathogenesis and potential intervention.

neuroscience↗

bioRxiv2023

A non-image-forming visual circuit mediates the innate fear of heights

The neural basis of fear of heights remains largely unknown. In this study, we investigated the fear response to heights in mice and observed characteristic aversive behaviors resembling human height vertigo. We identified visual input as a critical factor in mouse reactions to heights, while peripheral vestibular input was found to be nonessential for fear of heights. Unexpectedly, we found that fear of heights in naive mice does not rely on image-forming visual processing by the primary visual cortex. Instead, a subset of neurons in the ventral lateral geniculate nucleus (vLGN), which connects to the lateral/ventrolateral periaqueductal gray (l/vlPAG), drives the expression of fear associated with heights. Additionally, we observed that a subcortical visual pathway linking the superior colliculus to the lateral posterior thalamic nucleus inhibits the defensive response to height threats. These findings highlight a rapid fear response to heights threat through a subcortical visual and defensive pathway from the vLGN to the l/vlPAG.

neuroscience↗

bioRxiv2021

Genomic inference of a human super bottleneck in the Early Stone Age

The demographic history is a foundation of human evolutionary studies. However, the ancient demographic history during the Mid-Pleistocene is poorly investigated while it is essential for understanding the early origin of humankind. Here we present the fast infinitesimal time coalescent (FitCoal) process, which allows the analytical calculation of the composite likelihood of a site frequency spectrum and provides the precise inference of demographic history. We apply it to analyze 3,154 present-day human genomic sequences. We find that African populations have passed through a population super bottleneck, a small effective size of approximately 1,280 breeding individuals between 930 and 813 thousand years ago. Further analyses confirm the existence of the super bottleneck on non-African populations although it cannot be directly inferred. This observation, together with simulation results, indicates that confounding factors, such as population structure and selection, are unlikely to affect the inference of the super bottleneck. The time interval of the super bottleneck coincides with a gap in the human fossil record in Africa and possibly marks the origin of Homo heidelbergensis. Our results provide new insights into human evolution during the Mid-Pleistocene.

evolutionary biology↗

bioRxiv2021

Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7

Three prevalent SARS-CoV-2 Variants of Concern (VOCs) were emerged and caused epidemic waves. It is essential to uncover the key genetic changes that cause the high transmissibility of VOCs. However, different viral mutations are generally tightly linked so traditional population genetic methods may not reliably detect beneficial mutation. In this study, we proposed a new pandemic-scale phylogenomic approach to detect mutations crucial to transmissibility. We analyzed 3,646,973 high-quality SARS-CoV-2 genomic sequences and the epidemiology metadata. Based on the sequential occurrence order of mutations and the instantaneously accelerated furcation rate, the analysis revealed that two non-coding mutations at the position of 28271 (g.a28271-/t) might be crucial for the high transmissibility of Alpha, Delta and Omicron VOCs. Both two mutations cause an A-to-T change at the core Kozak site of the N gene. The analysis also revealed that the non-coding mutations (g.a28271-/t) alone are unlikely to cause high viral transmissibility, indicating epistasis or multilocus interaction in viral transmissibility. A convergent evolutionary analysis revealed that g.a28271-/t, S:P681H/R and N:R203K/M occur independently in the three-VOC lineages, suggesting a potential interaction among these mutations. Therefore, this study unveils that non-synonymous and non-coding mutations could affect the transmissibility synergistically.

evolutionary biology↗

bioRxiv2021

New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

Accelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 x 10-11 ~ 9.03 x 10-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.

evolutionary biology↗

bioRxiv2020

Identification of CDH11 as an ASD risk gene by matched-gene co-expression analysis and mouse behavioral studies

A large number of putative risk genes of autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and a causal relationship between their variations and autism traits has not been established. The aim of this study is to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high confidence ASD risk genes (hcASDs). Results showed that three gene features, including gene size, mRNA abundance, and guanine-cytosine content, affect genome-wide co-expression profiles of hcASDs. To circumvent the interference of these gene features on gene co-expression analysis (GCA), we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. Results of analysis of two recently reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlighted the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.

neuroscience↗

bioRxiv2018

A GYS2/p53 negative feedback loop restricts tumor growth in HBV-related hepatocellular carcinoma

Hepatocarcinogenesis is attributed to the reprogramming of cellular metabolism as consequence of the alteration in metabolite-related gene regulation. Identifying the mechanism of aberrant metabolism is of great potential to provide novel targets for the treatment of hepatocellular carcinoma (HCC). Here, we demonstrated that glycogen synthase 2 (GYS2) restricted tumor growth in HBV-related HCC via a negative feedback loop with p53. Expression of GYS2 was significantly downregulated in HCC and correlated with decreased glycogen content and unfavorable patient outcomes. GYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 expression. GYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation. Furthermore, GYS2 enhanced the p300-induced acetylation of p53 at K373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex. In summary, our findings suggest that GYS2 serves as a prognostic factor and functions as a tumor suppressor in HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.\n\nSynopsisThis study elucidate the role of GYS2 in glycogen metabolism and the progression of HCC. The newly identified HBx/GYS2/p53 axis is responsible for the deregulation of glycogen metabolism and represents a promising therapeutic target for the clinical management of HCC.\n\nO_LIDecrease of GYS2 was significantly correlated with decreased glycogen content and unfavorable patient outcomes in a large cohort containing 768 patients with HCC.\nC_LIO_LIGYS2 overexpression suppressed, whereas GYS2 knockdown facilitated cell proliferation in vitro and tumor growth in vivo via modulating p53 signaling pathway.\nC_LIO_LIGYS2 competitively bound to MDM2 to prevent p53 from MDM2-mediated ubiquitination and degradation.\nC_LIO_LIGYS2 enhanced the p300-induced acetylation of p53 at Lys373/382, which in turn inhibited the transcription of GYS2 in the support of HBx/HDAC1 complex.\nC_LI

pathology↗