Zoological Research

961−971

Authors: Xi Wang, Jing-Kun Jia, Qi Wang, Jing-Wen Gong, Ang Li, Jia Su, Peng Zhou

Bats, notable as the only flying mammals, serve as naturalreservoir hosts for various highly pathogenic viruses inhumans (e.g., SARS-CoV and Ebola virus). Furthermore,bats exhibit an unparalleled longevity among mammalsrelative to their size, particularly the Myotis bats, which canlive up to 40 years. However, the mechanisms underlyingthese distinctive traits remain incompletely understood. Inour prior research, we demonstrated that bats exhibitdampened STING-interferon activation, potentiallyconferring upon them the capacity to mitigate virus- oraging-induced inflammation. To substantiate thishypothesis, we established the first in vivo bat-mousemodel for aging studies by integrating Myotis davidii batSTING (MdSTING) into the mouse genome. We monitoredthe genotypes of these mice and performed a longitudinalcomparative transcriptomic analysis on MdSTING andwild-type mice over a 3-year aging process. Bloodtranscriptomic analysis indicated a reduction in aging-related inflammation in female MdSTING mice, asevidenced by significantly lower levels of pro-inflammatorycytokines and chemokines, immunopathology, andneutrophil recruitment in aged female MdSTING micecompared to aged wild-type mice in vivo. These resultsindicated that MdSTING knock-in attenuates the aging-related inflammatory response and may also improve thehealthspan in mice in a sex-dependent manner. Althoughthe underlying mechanism awaits further study, thisresearch has critical implications for bat longevityresearch, potentially contributing to our comprehension ofhealthy aging in humans.

983−989

Authors: Qiong Wu, Alexander G. Radchenko, Michael S. Engel, Xiao-Qin Li, Hong-Ru Yang, Xing-Ru Li, Chung-Kun Shih, Dong Ren, Tai-Ping Gao

Most described Mesozoic ants belong to stem groups thatexisted only during the Cretaceous period. Previously, theearliest known crown ants were dated to the Turonian(Late Cretaceous, ca. 94–90 million years ago (Ma))deposits found in the USA, Kazakhstan, and Botswana.However, the recent discovery of an alate male ant inKachin amber from the earliest Cenomanian (ca. 99 Ma),representing a new genus and species, Antiquiformicaalata, revises the narrative on ant diversification.Antiquiformica can be distinctly differentiated from allknown male stem ants by its geniculate antennae withelongated scape, extending far beyond the occipital marginof the head and half the length of the funiculus, as well asits partly reduced forewing venation. Furthermore, thecombination of a one-segmented waist with a well-developed node, elongated scape extending beyond theoccipital margin, and reduced forewing venation,particularly the completely reduced m-cu and rs-mcrossveins and absence of rm and mcu closed cells, firmlyplaces the fossil within the extant subfamily Formicinae.Fourier transform infrared spectroscopy (FTIR) confirmedthat the amber containing Antiquiformica alata originatedfrom the Kachin mines in Myanmar. This discoverysignificantly revises our understanding of the earlyevolution of Formicinae. The presence of Antiquiformica inCenomanian amber indicates that the subfamilyFormicinae emerged at least by the start of the LateCretaceous, with crown ants likely originating earlier duringthe earliest Cretaceous or possibly the Late Jurassic,although paleontological evidence is lacking to support thelatter hypothesis.

1001−1012

Authors: Li-Na Cha, Juan Yang, Jin-Ai Gao, Xin Lu, Xiao-Long Chang, Rebecca Caroline Thuku, Qi Liu, Qiu-Min Lu, Dong-Sheng Li, Ren Lai, Ming-Qian Fang

Thrombosis and inflammation are primary contributors tothe onset and progression of ischemic stroke. The contact-kinin pathway, initiated by plasma kallikrein (PK) andactivated factor XII (FXIIa), functions bidirectionally withthe coagulation and inflammation cascades, providing anovel target for therapeutic drug development in ischemicstroke. In this study, we identified a bat-derivedoligopeptide from Myotis myotis (Borkhausen, 1797),designated LE6 (Leu-Ser-Glu-Glu-Pro-Glu, 702 Da), withconsiderable potential in stroke therapy due to its effectson the contact kinin pathway. Notably, LE6 demonstratedsignificant inhibitory effects on PK and FXIIa, with inhibitionconstants of 43.97 μmol/L and 6.37 μmol/L, respectively.In vitro analyses revealed that LE6 prolonged plasmarecalcification time and activated partial thromboplastintime. In murine models, LE6 effectively inhibitedcarrageenan-induced mouse tail thrombosis, FeCl3-induced carotid artery thrombosis, and photochemicallyinduced intracerebral thrombosis. Furthermore, LE6significantly decreased inflammation and stroke injury intransient middle cerebral artery occlusion models. Notably,the low toxicity, hemolytic activity, and bleeding risk ofLE6, along with its synthetic simplicity, underscore itsclinical applicability. In conclusion, as an inhibitor of FXIIaand PK, LE6 offers potential therapeutic benefits in stroketreatment by mitigating inflammation and preventingthrombus formation.

1027−1036

Authors: Chao Bian, Rui-Han Li, Zhi-Qiang Ruan, Wei-Ting Chen, Yu Huang, Li-Yue Liu, Hong-Ling Zhou, Cheong-Meng Chong, Xi-Dong Mu, Qiong Shi

Glass catfish (Kryptopterus vitreolus) are notable in theaquarium trade for their highly transparent body pattern.This transparency is due to the loss of most reflectiveiridophores and light-absorbing melanophores in the mainbody, although certain black and silver pigments remain inthe face and head. To date, however, the molecularmechanisms underlying this transparent phenotype remainlargely unknown. To explore the genetic basis of thistransparency, we constructed a chromosome-levelhaplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-codinggenes, using PacBio and Hi-C sequencing technologiesand standard assembly and annotation pipelines. Analysisrevealed a premature stop codon in the putative albinism-related tyrp1b gene, encoding tyrosinase-related protein 1, rendering it a nonfunctional pseudogene. Notably, asynteny comparison with over 30 other fish speciesidentified the loss of the endothelin-3 (edn3b) gene in theglass catfish genome. To investigate the role of edn3b, wegenerated edn3b−/− mutant zebrafish, which exhibited aremarkable reduction in black pigments in body surfacestripes compared to wild-type zebrafish. These findingsindicate that edn3b loss contributes to the transparentphenotype of the glass catfish. Our high-quality chromosome-scale genome assembly and identification ofkey genes provide important molecular insights into thetransparent phenotype of glass catfish. These findings notonly enhance our understanding of the molecularmechanisms underlying transparency in glass catfish, butalso offer a valuable genetic resource for further researchon pigmentation in various animal species.

1048−1060

Authors: Xiao-Xiao Li, Dan-Chen Zhang, Yan Wang, Jian Wen, Xing-Ju Wang, Yu-Lu Cao, Ru Jiang, Jia-Rui Li, Yi-Nuo Li, He-He Liu, Wen-Hai Xie, Zheng-Feng Xu, Ping Hu, Kang Zou

Extracellular membrane proteins are crucial for mediatingcell attachment, recognition, and signal transduction in thetesticular microenvironment, particularly germline stemcells. Cadherin 18 (CDH18), a type II classical cadherin, isprimarily expressed in the nervous and reproductivesystems. Here, we investigated the expression of CDH18in neonatal porcine prospermatogonia (ProSGs) andmurine spermatogonial stem cells (SSCs). Disruption ofCDH18 expression did not adversely affect cellmorphology, proliferation, self-renewal, or differentiation incultured porcine ProSGs, but enhanced cell adhesion andprolonged cell maintenance. Transcriptomic analysisindicated that the down-regulation of CDH18 in ProSGssignificantly up-regulated genes and signaling pathwaysassociated with cell adhesion. To further elucidate thefunction of CDH18 in germ cells, Cdh18 knockout micewere generated, which exhibited normal testicularmorphology, histology, and spermatogenesis.Transcriptomic analysis showed increased expression ofgenes associated with adhesion, consistent with theobservations in porcine ProSGs. The interaction of CDH18with β-catenin and JAK2 in both porcine ProSGs andmurine SSCs suggested an inhibitory effect on thecanonical Wnt and JAK-STAT signaling pathways duringCDH18 deficiency. Collectively, these findings highlight thecrucial role of CDH18 in regulating cell adhesion in porcineProSGs and mouse SSCs. Understanding this regulatorymechanism provides significant insights into the testicularniche.

1073−1087

Authors: Jing-Wei Ye, Tanveer Abbas, Jian-Teng Zhou, Jing Chen, Meng-Lei Yang, Xiong-Heng Huang, Huan Zhang, Hui Ma, Ao Ma, Bo Xu, Ghulam Murtaza, Qing-Hua Shi, Bao-Lu Shi

Infertility represents a significant health concern, withsperm quantity and quality being crucial determinants ofmale fertility. Oligoasthenoteratozoospermia (OAT) ischaracterized by reduced sperm motility, lower spermconcentration, and morphological abnormalities in spermheads and flagella. Although variants in several geneshave been implicated in OAT, its genetic etiologies andpathogenetic mechanisms remain inadequatelyunderstood. In this study, we identified a homozygousnonsense mutation (c.916C>T, p.Arg306*) in the coiled-coil domain containing 146 (CCDC146) gene in an infertilemale patient with OAT. This mutation resulted in theproduction of a truncated CCDC146 protein (amino acids1–305), retaining only two out of five coiled-coil domains.To validate the pathogenicity of the CCDC146 mutation,we generated a mouse model (Ccdc146mut/mut) with asimilar mutation to that of the patient. Consistently, theCcdc146mut/mut mice exhibited infertility, characterized bysignificantly reduced sperm counts, diminished motility,and multiple defects in sperm heads and flagella.Furthermore, the levels of axonemal proteins, includingDNAH17, DNAH1, and SPAG6, were significantly reducedin the sperm of Ccdc146mut/mut mice. Additionally, bothhuman and mouse CCDC146 interacted with intraflagellartransport protein 20 (IFT20), but this interaction was lost inthe mutated versions, leading to the degradation of IFT20.This study identified a novel deleterious homozygousnonsense mutation in CCDC146 that causes maleinfertility, potentially by disrupting axonemal proteintransportation. These findings offer valuable insights forgenetic counseling and understanding the mechanismsunderlying CCDC146 mutant-associated infertility inhuman males.

1108−1115

Authors: Qiran Chen, Wei Sun, Lin Jin, Yingjie Zhou, Fang Li, Chutian Ge

In reptiles, such as the red-eared slider turtle (Trachemysscripta elegans), gonadal sex determination is highlydependent on the environmental temperature duringembryonic stages. This complex process, which leads todifferentiation into either testes or ovaries, is governed bythe finely tuned expression of upstream genes, notably thetestis-promoting gene Dmrt1 and the ovary-promotinggene Foxl2. Recent studies have identified epigeneticregulation as a crucial factor in testis development, withthe H3K27me3 demethylase KDM6B being essential forDmrt1 expression in T. s. elegans. However, whetherKDM6B alone can induce testicular differentiation remainsunclear. In this study, we found that overexpression ofKdm6b in T. s. elegans embryos induced the maledevelopment pathway, accompanied by a rapid increase inthe gonadal expression of Dmrt1 at 31°C, a temperaturetypically resulting in female development. Notably, this sexreversal could be entirely rescued by Dmrt1 knockdown.These findings demonstrate that Kdm6b is sufficient forcommitment to the male pathway, underscoring its role asa critical epigenetic regulator in the sex determination ofthe red-eared slider turtle.

1131−1146

Authors: Ai-Li Lin, Ming-Ming Zou, Li-Jun Cao, Fumio Hayashi, Ding Yang, Xing-Yue Liu

Unraveling the phylogeographic histories of speciesremains a key endeavor for comprehending theevolutionary processes contributing to the rich biodiversityand high endemism found in East Asia. In this study, weexplored the phylogeographic patterns and demographichistories of three endemic fishfly and dobsonfly species(Neochauliodes formosanus, Protohermes costalis, andNeoneuromus orientalis) belonging to the holometabolanorder Megaloptera. These species, which share a broadand largely overlapping distribution, were analyzed usingcomprehensive mitogenomic data. Our findings revealed aconsistent influence of vicariance on the populationisolation of Neoc. formosanus and P. costalis betweenHainan, Taiwan, and the East Asian mainland during theearly Pleistocene, potentially hindering subsequentcolonization of the later diverged Neon. orientalis to theseislands. Additionally, we unveiled the dual function of themajor mountain ranges in East Asia, serving both asbarriers and conduits, in shaping the population structureof all three species. Notably, we demonstrated that theseco-distributed species originated from Southwest,Southern, and eastern Central China, respectively, thensubsequently migrated along multi-directional routes,leading to their sympatric distribution on the East Asianmainland. Furthermore, our results highlighted thesignificance of Pleistocene land bridges along the easterncoast of East Asia in facilitating the dispersal of mountain-dwelling insects with low dispersal ability. Overall, thisstudy provides novel insight into the synergistic impact ofPleistocene geological and climatic events in shaping thediversity and distribution of aquatic insects in East Asia.

1161−1174

Authors: Jin Miao, Huanhuan Zhu, Junni Wang, Jianghua Chen, Fei Han, Weiqiang Lin

Acute kidney injury (AKI) and chronic kidney disease(CKD) are significant public health issues associated witha long-term increase in mortality risk, resulting fromvarious etiologies including renal ischemia, sepsis, drugtoxicity, and diabetes mellitus. Numerous preclinicalmodels have been developed to deepen our understandingof the pathophysiological mechanisms and therapeuticapproaches for kidney diseases. Among these, rodentmodels have proven to be powerful tools in the discoveryof novel therapeutics, while the development of kidneyorganoids has emerged as a promising advancement inthe field. This review provides a comprehensive analysis ofthe construction methodologies, underlying biologicalmechanisms, and recent therapeutic developments acrossdifferent AKI and CKD models. Additionally, this reviewsummarizes the advantages, limitations, and challengesinherent in these preclinical models, thereby contributingrobust evidence to support the development of effectivetherapeutic strategies.

711−723

Authors: Weitao Chen, Nicolas Hubert, Yuefei Li, Shuli Zhu, Jun Wang, Denggao Xiang, Shang Gao, Chunni Kou, Jilong Wang, Tai Wang, Zhiqiang Liang, Junjie Wu, Xinhui Li, Jie Li

The genus Silurus, an important group of catfish, exhibitsheterogeneous distribution in Eurasian freshwatersystems. This group includes economically important andendangered species, thereby attracting considerablescientific interest. Despite this interest, the lack of acomprehensive phylogenetic framework impedes ourunderstanding of the mechanisms underlying the extensivediversity found within this genus. Herein, we analyzed 89newly sequenced and 20 previously publishedmitochondrial genomes (mitogenomes) from 13morphological species to reconstruct the phylogeneticrelationships, biogeographic history, and species diversityof Silurus. Our phylogenetic reconstructions identified eightclades, supported by both maximum-likelihood andBayesian inference. Sequence-based species delimitationanalyses yielded multiple molecular operational taxonomicunits (MOTUs) in several taxa, including the Silurus asotuscomplex (four MOTUs) and Silurus microdorsalis (twoMOTUs), suggesting that species diversity isunderestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimateof the most recent common ancestor of approximately37.61 million years ago (Ma), with divergences amongclades within the genus occurring between 11.56 Ma and29.44 Ma, and divergences among MOTUs within speciesoccurring between 3.71 Ma and 11.56 Ma. Biogeographicreconstructions suggested that the ancestral area for thegenus likely encompassed China and the KoreanPeninsula, with multiple inferred dispersal events toEurope and Central and Western Asia between 21.78 Maand 26.67 Ma and to Japan between 2.51 Ma and 18.42Ma. Key factors such as the Eocene-Oligocene extinctionevent, onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuationshave likely played significant roles in shaping theevolutionary history of the genus Silurus.

747−766

Authors: Hong-Yi Zheng, Tian-Zhang Song, Yong-Tang Zheng

The distribution of the immune system throughout the bodycomplicates in vitro assessments of coronavirus disease2019 (COVID-19) immunobiology, often resulting in a lackof reproducibility when extrapolated to the whole organism.Consequently, developing animal models is imperative fora comprehensive understanding of the pathology andimmunology of severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) infection. This reviewsummarizes current progress related to COVID-19 animalmodels, including non-human primates (NHPs), mice, andhamsters, with a focus on their roles in exploring themechanisms of immunopathology, immune protection, andlong-term effects of SARS-CoV-2 infection, as well as theirapplication in immunoprevention and immunotherapy ofSARS-CoV-2 infection. Differences among these animalmodels and their specific applications are also highlighted,as no single model can fully encapsulate all aspects ofCOVID-19. To effectively address the challenges posed byCOVID-19, it is essential to select appropriate animalmodels that can accurately replicate both fatal and non-fatal infections with varying courses and severities.Optimizing animal model libraries and associated researchtools is key to resolving the global COVID-19 pandemic,serving as a robust resource for future emerging infectiousdiseases.

781−790

Authors: Neng-Song Luo, Yu-Xiang Cai, Zeng-Peng Han, Xiao-Kai Sui, Wen-Jia Yuan, Zi-Lian Zhang, Hao-Dong Guo, Jie Wang, Kun-Zhang Lin, Fu-Qiang Xu

Precise targeting of specific regions within the centralnervous system (CNS) is crucial for both scientificresearch and gene therapy in the context of braindiseases. Adeno-associated virus 13 (AAV13) is known forits restricted diffusion range within the CNS, making it anideal choice for precise labeling and administration withinsmall brain regions. However, AAV13 mediates relativelylow expression of target genes. Here, we introducedspecifically engineered modifications to the AAV13 capsidprotein to enhance its transduction efficiency. We firstconstructed AAV13-YF by mutating tyrosine tophenylalanine on the surface of the AAV13 capsid. Wethen inserted the 7m8 peptide, known to enhance celltransduction, into positions 587/588 and 585/586 of theAAV13 capsid, resulting in two distinct variants namedAAV13-587-7m8 and AAV13-585-7m8, respectively. Wefound that AAV13-YF exhibited superior in vitro infectivityin HEK293T cells compared to AAV13, while AAV13-587-7m8 and AAV13-585-7m8 showed enhanced CNSinfection capabilities in C57BL/6 mice, with AAV13-587-7m8 infection retaining a limited spread range. Thesemodified AAV13 variants hold promising potential forapplications in gene therapy and neuroscience research.

805−820

Authors: Wei Yan, Zi-Jie Li, Zi-Yi Lin, Shu-Qin Ji, William Ka Fai Tse, Zhi-Qiang Meng, Chang Liu, Lei Li

The organ-specific toxicity resulting from microplastic (MP)exposure has been extensively explored, particularlyconcerning the gut, liver, testis, and lung. However, undernatural conditions, these effects are not restricted tospecific organs or tissues. Investigating whether MPexposure presents a systemic threat to an entire organism,impacting factors such as lifespan, sleep, and fecundity, isessential. In this study, we investigated the effects ofdietary exposure to two different doses of MPs (1–5 μm)using the terrestrial model organism Drosophilamelanogaster. Results indicated that the particles causedgut damage and remained within the digestive system.Continuous MP exposure significantly shortened thelifespan of adult flies. Even short-term exposure disruptedsleep patterns, increasing the length of daytime sleepepisodes. Additionally, one week of MP exposure reducedovary size, with a trend towards decreased egg-laying inmated females. Although MPs did not penetrate the brainor ovaries, transcriptome analysis revealed altered geneexpression in these tissues. In the ovary, Gene Ontology(GO) analysis indicated genotoxic effects impactinginflammation, circadian regulation, and metabolicprocesses, with significant impacts on extracellularstructure-related pathways. In the brain, GO analysisidentified changes in pathways associated with proteolysisand carbohydrate metabolism. Overall, this study providescompelling evidence of the systemic negative effects ofMP exposure, highlighting the urgent need to address andmitigate environmental MP pollution.

831−832

Authors: P. J. Hore

 

845−856

Authors: Qunxian Wang, Yanshuang Jiang, Zijun Meng, Xiangjun Dong, Dongjie Hu, Liangye Ji, Weihui Zhou, Weihong Song

SIL1, an endoplasmic reticulum (ER)-resident protein, isreported to play a protective role in Alzheimer’s disease(AD). However, the effect of SIL1 on amyloid precursorprotein (APP) processing remains unclear. In this study,the role of SIL1 in APP processing was explored both invitro and in vivo. In the in vitro experiment, SIL1 was eitheroverexpressed or knocked down in cells stably expressingthe human Swedish mutant APP695. In the in vivoexperiment, AAV-SIL1-EGFP or AAV-EGFP wasmicroinjected into APP23/PS45 mice and their wild-typelittermates. Western blotting (WB), immunohistochemistry,RNA sequencing (RNA-seq), and behavioral experimentswere performed to evaluate the relevant parameters.Results indicated that SIL1 expression decreased inAPP23/PS45 mice. Overexpression of SIL1 significantlydecreased the protein levels of APP, presenilin-1 (PS1),and C-terminal fragments (CTFs) of APP in vivo and invitro. Conversely, knockdown of SIL1 increased the proteinlevels of APP, β-site APP cleavage enzyme 1 (BACE1),PS1, and CTFs, as well as APP mRNA expression in2EB2 cells. Furthermore, SIL1 overexpression reduced thenumber of senile plaques in APP23/PS45 mice.Importantly, Y-maze and Morris Water maze testsdemonstrated that SIL1 overexpression improved cognitiveimpairment in APP23/PS45 mice. These findings indicatethat SIL1 improves cognitive impairment in APP23/PS45mice by inhibiting APP amyloidogenic processing andsuggest that SIL1 is a potential therapeutic target for ADby modulating APP processing.

875−876

Authors: Jing Cao, Yun-Wu Zhang

 

910−923

Authors: Jin-Bo Xiong, Hao-Nan Sha, Jiong Chen

Litopenaeus vannamei is the most extensively culturedshrimp species globally, recognized for its scale,production, and economic value. However, its aquacultureis plagued by frequent disease outbreaks, resulting in rapidand massive mortality. etiological research often lagsbehind the emergence of new diseases, leaving the causalagents of some shrimp diseases unidentified and leadingto nomenclature based on symptomatic presentations,especially in cases involving co- and polymicrobialpathogens. Comprehensive data on shrimp diseasestatuses remain limited. In this review, we summarizecurrent knowledge on shrimp diseases and their effects onthe gut microbiome. Furthermore, we also propose aworkflow integrating primary colonizers, “driver” taxa in gutnetworks from healthy to diseased states, disease-discriminatory taxa, and virulence genes to identifypotential polymicrobial pathogens. We examine bothabiotic and biotic factors (e.g., external and internalsources and specific-disease effects) that influence shrimpgut microbiota, with an emphasis on the “holobiome”concept and common features of gut microbiota responseto diverse diseases. After excluding the effects ofconfounding factors, we provide a diagnosis model forquantitatively predicting shrimp disease incidence usingdisease common-discriminatory taxa, irrespective of thecausal agents. Due to the conservation of functional genesused in designing specific primers, we propose a practicalstrategy applying qPCR-assayed abundances of diseasecommon-discriminatory functional genes. This reviewupdates the roles of the gut microbiota in exploring shrimpetiology, polymicrobial pathogens, and disease incidence,offering a refined perspective for advancing shrimpaquaculture health management.

937−950

Authors: Yi-Fu Zhu, Rong-Hua Yu, Shuai Zhou, Pei-Pei Tang, Rui Zhang, Yu-Xin Wu, Ran Xu, Jia-Ming Wei, Ying-Ying Wang, Jia-Li Zhang, Meng-Ke Li, Xiao-Jing Shi, Yu-Wei Zhang, Guang-Zhi Liu, Rick F. Thorne, Xu Dong Zhang, Mian Wu, Song Chen

Autophagy plays a pivotal role in diverse biologicalprocesses, including the maintenance and differentiation ofneural stem cells (NSCs). Interestingly, while completedeletion of Fip200 severely impairs NSC maintenance anddifferentiation, inhibiting canonical autophagy via deletionof core genes, such as Atg5, Atg16l1, and Atg7, orblockade of canonical interactions between FIP200 andATG13 (designated as FIP200-4A mutant or FIP200 KI)does not produce comparable detrimental effects. Thishighlights the likely critical involvement of the non-canonical functions of FIP200, the mechanisms of whichhave remained elusive. Here, utilizing genetic mousemodels, we demonstrated that FIP200 mediates non-canonical autophagic degradation of p62/sequestome1,primarily via TAX1BP1 in NSCs. Conditional deletion ofTax1bp1 in fip200hGFAP conditional knock-in (cKI) mice ledto NSC deficiency, resembling the fip200hGFAP conditionalknockout (cKO) mouse phenotype. Notably, reintroducingwild-type TAX1BP1 not only restored the maintenance ofNSCs derived from tax1bp1-knockout fip200hGFAP cKI micebut also led to a marked reduction in p62 aggregateaccumulation. Conversely, a TAX1BP1 mutant incapableof binding to FIP200 or NBR1/p62 failed to achieve thisrestoration. Furthermore, conditional deletion of Tax1bp1in fip200hGFAP cKO mice exacerbated NSC deficiency andp62 aggregate accumulation compared to fip200hGFAP cKOmice. Collectively, these findings illustrate the essentialrole of the FIP200-TAX1BP1 axis in mediating the non-canonical autophagic degradation of p62 aggregatestowards NSC maintenance and function, presenting noveltherapeutic targets for neurodegenerative diseases.

451−463

Authors: Bin Hu, Jia-Min Wang, Qing-Xun Zhang, Jing Xu, Ya-Nan Xing, Bo Wang, Shu-Yi Han, Hong-Xuan He

The gut microbiota significantly influences host physiologyand provides essential ecosystem services. While diet canaffect the composition of the gut microbiota, the gutmicrobiota can also help the host adapt to specific dietaryhabits. The carrion crow (Corvus corone), an urbanfacultative scavenger bird, hosts an abundance ofpathogens due to its scavenging behavior. Despite this,carrion crows infrequently exhibit illness, a phenomenonrelated to their unique physiological adaptability. Atpresent, however, the role of the gut microbiota remainsincompletely understood. In this study, we performed acomparative analysis using 16S rRNA ampliconsequencing technology to assess colonic content in carrioncrows and 16 other bird species with different diets inBeijing, China. Our findings revealed that the dominant gutmicrobiota in carrion crows was primarily composed ofProteobacteria (75.51%) and Firmicutes (22.37%).Significant differences were observed in the relativeabundance of Enterococcus faecalis among groups,highlighting its potential as a biomarker of facultativescavenging behavior in carrion crows. Subsequently, E.faecalis isolated from carrion crows was transplanted intomodel mice to explore the protective effects of thisbacterial community against Salmonella enterica infection.Results showed that E. faecalis down-regulated theexpression of pro-inflammatory cytokines tumor necrosisfactor alpha (TNF-α), interferon gamma (IFN-γ), andinterleukin 6 (IL-6), prevented S. enterica colonization, andregulated the composition of gut microbiota in mice,thereby modulating the host’s immune regulatory capacity.Therefore, E. faecalis exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged inscavenging behavior, offering a representative case of howthe gut microbiota contributes to the protection of hostswith specialized diets.

468−477

Authors: Yanqi Zhang, Peng Zhang, Junjun Wang, Jing Zhang, Tianyang Tong, Xiujuan Zhou, Yajie Zhou, Mengke Wei, Chuanlin Feng, Jinqian Li, Xin Zhang, Can Xie, Tiantian Cai

Iron-sulfur clusters (ISC) are essential cofactors forproteins involved in various biological processes, such aselectron transport, biosynthetic reactions, DNA repair, andgene expression regulation. ISC assembly protein IscA1(or MagR) is found within the mitochondria of mosteukaryotes. Magnetoreceptor (MagR) is a highlyconserved A-type iron and iron-sulfur cluster-bindingprotein, characterized by two distinct types of iron-sulfurclusters, [2Fe-2S] and [3Fe-4S], each conferring uniquemagnetic properties. MagR forms a rod-like polymerstructure in complex with photoreceptive cryptochrome(Cry) and serves as a putative magnetoreceptor forretrieving geomagnetic information in animal navigation.Although the N-terminal sequences of MagR vary amongspecies, their specific function remains unknown. In thepresent study, we found that the N-terminal sequences ofpigeon MagR, previously thought to serve as amitochondrial targeting signal (MTS), were not cleavedfollowing mitochondrial entry but instead modulated theefficiency with which iron-sulfur clusters and irons arebound. Moreover, the N-terminal region of MagR wasrequired for the formation of a stable MagR/Cry complex.Thus, the N-terminal sequences in pigeon MagR fulfil moreimportant functional roles than just mitochondrial targeting.These results further extend our understanding of thefunction of MagR and provide new insights into the originof magnetoreception from an evolutionary perspective.

491−505

Authors: Yue Yu, Shi-Ming Wan, Cheng-You Huang, Shuang-Meng Zhang, Ai-Li Sun, Jun-Qi Liu, Shun-Yao Li, Yong-Fu Zhu, Shu-Xin Gu, Ze-Xia Gao

Coilia nasus, a migratory fish species found in the middleand lower reaches of the Yangtze River and along offshoreareas of China, possesses considerable aquacultural andeconomic potential. However, the species faceschallenges due to significant variation in the gonadaldevelopment rate among females, resulting in inconsistentovarian maturation times at the population level, anextended reproductive period, and limitations on fishgrowth rate due to ovarian prematurity. In the presentstudy, we combined genome-wide association study(GWAS) and comparative transcriptome analysis toinvestigate the potential single nucleotide polymorphisms(SNPs) and candidate genes associated with population-asynchronous ovarian development in C. nasus.Genotyping of the female population based on whole-genome resequencing yielded 2 120 695 high-qualitySNPs, 39 of which were suggestively associated withovarian development. Of note, a significant SNP peak onLG21 containing 30 suggestively associated SNPs wasidentified, with cpne5a determined as the causal gene ofthe peak. Therefore, single-marker and haplotypeassociation analyses were performed on cpne5a, revealingfour genetic markers (P<0.05) and seven haplotypes(r2>0.9) significantly associated with the phenotype.Comparative transcriptome analysis of precociously andnormally maturing individuals screened out 29 and 426overlapping differentially expressed genes in the brain andovary, respectively, between individuals of different bodysizes. Integrating the GWAS and transcriptome analysisresults, this study identified genes and pathways related tohypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix, angiogenesis, and gap junctionsinvolved in population-asynchronous ovarian development.The insights gained from this study provide a basis for adeeper understanding of the molecular mechanismsunderlying ovarian development in fish and may facilitatethe genetic breeding of C. nasus strains exhibitingpopulation-synchronous ovarian development in the future.

518−519

Authors: Yu-Fan Wang, Jiu-Lin Du

 

535−550

Authors: Laidong Yu, Fangfang Zeng, Mengshu Fan, Kexuan Zhang, Jingjing Duan, Yalu Tan, Panlin Liao, Jin Wen, Chenyu Wang, Meilin Wang, Jialong Yuan, Xinxin Pang, Yan Huang, Yangzhou Zhang, Jia-Da Li, Zhuohua Zhang, Zhonghua Hu

Proper regulation of synapse formation and elimination iscritical for establishing mature neuronal circuits andmaintaining brain function. Synaptic abnormalities, such asdefects in the density and morphology of postsynapticdendritic spines, underlie the pathology of variousneuropsychiatric disorders. Protocadherin 17 (PCDH17) isassociated with major mood disorders, including bipolardisorder and depression. However, the molecularmechanisms by which PCDH17 regulates spine number,morphology, and behavior remain elusive. In this study, wefound that PCDH17 functions at postsynaptic sites,restricting the number and size of dendritic spines inexcitatory neurons. Selective overexpression of PCDH17in the ventral hippocampal CA1 results in spine loss andanxiety- and depression-like behaviors in mice.Mechanistically, PCDH17 interacts with actin-relevantproteins and regulates actin filament (F-actin) organization.Specifically, PCDH17 binds to ROCK2, increasing itsexpression and subsequently enhancing the activity ofdownstream targets such as LIMK1 and thephosphorylation of cofilin serine-3 (Ser3). Inhibition ofROCK2 activity with belumosudil (KD025) ameliorates thedefective F-actin organization and spine structure inducedby PCDH17 overexpression, suggesting that ROCK2mediates the effects of PCDH17 on F-actin content andspine development. Hence, these findings reveal a novelmechanism by which PCDH17 regulates synapsedevelopment and behavior, providing pathological insightsinto the neurobiological basis of mood disorders.

567−574

Authors: Peng-Cheng Wang, Hao Deng, Rang Xu, Jiu-Lin Du, Rongkun Tao

Most viruses and transposons serve as effective carriersfor the introduction of foreign DNA up to 11 kb intovertebrate genomes. However, their activity markedlydiminishes with payloads exceeding 11 kb. Expanding thepayload capacity of transposons could facilitate moresophisticated cargo designs, improving the regulation ofexpression and minimizing mutagenic risks associated withmolecular therapeutics, metabolic engineering, andtransgenic animal production. In this study, we improvedthe Tol2 transposon by increasing protein expressionlevels using a translational enhancer (QBI SP163, ST) andenhanced the nuclear targeting ability using the nuclearlocalization protein H2B (SHT). The modified Tol2 and STtransposon efficiently integrated large DNA cargos intohuman cell cultures (H1299), comparable to the well-established super PiggyBac system. Furthermore, mRNAfrom ST and SHT showed a significant increase intransgene delivery efficiency of large DNA payloads (8 kb,14 kb, and 24 kb) into zebrafish (Danio rerio). This studypresents a modified Tol2 transposon as an enhancednonviral vector for the delivery of large DNA payloads intransgenic applications.

586−600

Authors: Guang-Hui Tan, Shi-Jie Liu, Ming-Le Dou, De-Feng Zhao, Ao Zhang, Heng-Kuan Li, Fu-Nong Luo, Tao Shi, Hao-Ping Wang, Jing-Yuan Lei, Yong Zhang, Yu Jiang, Yi Zheng, Fei Wang

The placenta plays a crucial role in successful mammalianreproduction. Ruminant animals possess a semi-invasiveplacenta characterized by a highly vascularized structureformed by maternal endometrial caruncles and fetalplacental cotyledons, essential for full-term fetaldevelopment. The cow placenta harbors at least twotrophoblast cell populations: uninucleate (UNC) andbinucleate (BNC) cells. However, the limited capacity toelucidate the transcriptomic dynamics of the placentalnatural environment has resulted in a poor understandingof both the molecular and cellular interactions betweentrophoblast cells and niches, and the molecularmechanisms governing trophoblast differentiation andfunctionalization. To fill this knowledge gap, we employedStereo-seq to map spatial gene expression patterns atnear single-cell resolution in the cow placenta at 90 and130 days of gestation, attaining high-resolution, spatiallyresolved gene expression profiles. Based on clusteringand cell marker gene expression analyses, keytranscription factors, including YBX1 and NPAS2, wereshown to regulate the heterogeneity of trophoblast cellsubpopulations. Cell communication and trajectoryanalysis provided a framework for understanding cell-cellinteractions and the differentiation of trophoblasts intoBNCs in the placental microenvironment. Differentialanalysis of cell trajectories identified a set of genesinvolved in regulation of trophoblast differentiation.Additionally, spatial modules and co-variant genes thathelp shape specific tissue structures were identified.Together, these findings provide foundational insights intoimportant biological pathways critical to the placentaldevelopment and function in cows.

617−632

Authors: Jing-Hang Jiang, Yi-Fu Wang, Jie Zheng, Yi-Ming Lei, Zhong-Yuan Chen, Yi Guo, Ya-Jie Guo, Bing-Qian Guo, Yu-Fang Lv, Hong-Hong Wang, Juan-Juan Xie, Yi-Xuan Liu, Ting-Wei Jin, Bi-Qi Li, Xiao-Shu Zhu, Yong-Hua Jiang, Zeng-Nan Mo

The Chinese tree shrew (Tupaia belangeri chinensis) hasemerged as a promising model for investigating adrenalsteroid synthesis, but it is unclear whether the same cellsproduce steroid hormones and whether their production isregulated in the same way as in humans. Here, wecomprehensively mapped the cell types and pathways ofsteroid metabolism in the adrenal gland of Chinese treeshrews using single-cell RNA sequencing, spatialtranscriptome analysis, mass spectrometry, andimmunohistochemistry. We compared the transcriptomesof various adrenal cell types across tree shrews, humans,macaques, and mice. Results showed that tree shrewadrenal glands expressed many of the same key enzymesfor steroid synthesis as humans, including CYP11B2,CYP11B1, CYB5A, and CHGA. Biochemical analysisconfirmed the production of aldosterone, cortisol, anddehydroepiandrosterone but not dehydroepiandrosteronesulfate in the tree shrew adrenal glands. Furthermore,genes in adrenal cell types in tree shrews were correlatedwith genetic risk factors for polycystic ovary syndrome,primary aldosteronism, hypertension, and related disordersin humans based on genome-wide association studies.Overall, this study suggests that the adrenal glands ofChinese tree shrews may consist of closely related cellpopulations with functional similarity to those of the humanadrenal gland. Our comprehensive results (publiclyavailable at http://gxmujyzmolab.cn:16245/scAGMap/)should facilitate the advancement of this animal model forthe investigation of adrenal gland disorders.

648−662

Authors: Dan Yang, Bin-Bin Nie, Jin-Gang He, Zong-Qiang Lv, Feng-Feng Mo, Si-Yi Ouyang, Jie Wang, JuXiang Chen, Tao Tao

Mild traumatic brain injury (mTBI)-induced post-traumaticheadache (PTH) is a pressing public health concern andleading cause of disability worldwide. Although PTH isoften accompanied by neurological disorders, the exactunderlying mechanism remains largely unknown.Identifying potential biomarkers may prompt the diagnosisand development of effective treatments for mTBI-inducedPTH. In this study, a mouse model of mTBI-induced PTHwas established to investigate its effects on cerebralstructure and function during short-term recovery. Resultsindicated that mice with mTBI-induced PTH exhibitedbalance deficits during the early post-injury stage.Metabolic kinetics revealed that variations inneurotransmitters were most prominent in the cerebellum,temporal lobe/cortex, and hippocampal regions during theearly stages of PTH. Additionally, variations in brainfunctional activities and connectivity were further detectedin the early stage of PTH, particularly in the cerebellumand temporal cortex, suggesting that these regions playcentral roles in the mechanism underlying PTH. Moreover,our results suggested that GABA and glutamate may serveas potential diagnostic or prognostic biomarkers for PTH.Future studies should explore the specific neural circuitsinvolved in the regulation of PTH by the cerebellum andtemporal cortex, with these two regions potentially utilizedas targets for non-invasive stimulation in future clinicaltreatment.

679−690

Authors: Gao-Lin Qiu, Li-Jun Peng, Peng Wang, Zhi-Lai Yang, Ji-Qian Zhang, Hu Liu, Xiao-Na Zhu, Jin Rao, Xue-Sheng Liu

General anesthesia is widely applied in clinical practice.However, the precise mechanism of loss of consciousnessinduced by general anesthetics remains unknown. Here,we measured the dynamics of five neurotransmitters,including γ-aminobutyric acid, glutamate, norepinephrine,acetylcholine, and dopamine, in the medial prefrontalcortex and primary visual cortex of C57BL/6 mice throughin vivo fiber photometry and genetically encodedneurotransmitter sensors under anesthesia to reveal themechanism of general anesthesia from a neurotransmitterperspective. Results revealed that the concentrations of γ-aminobutyric acid, glutamate, norepinephrine, andacetylcholine increased in the cortex during propofol-induced loss of consciousness. Dopamine levels did notchange following the hypnotic dose of propofol butincreased significantly following surgical doses of propofolanesthesia. Notably, the concentrations of the fiveneurotransmitters generally decreased during sevoflurane-induced loss of consciousness. Furthermore, theneurotransmitter dynamic networks were not synchronizedin the non-anesthesia groups but were highly synchronizedin the anesthetic groups. These findings suggest thatneurotransmitter dynamic network synchronization maycause anesthetic-induced loss of consciousness.

704−706

Authors: Cong Lin, Xiaohui Wang

 

709−710

Authors: Ji Hu, Ping Zheng

 

233−241

Authors: Peng Li, Ting Zhang, Ruo Wu, Jun-Yu Zhang, Yan Zhuo, Shan-Gang Li, Jiao-Jian Wang, WenTing Guo, Zheng-Bo Wang, Yong-Chang Chen

Neural tube defects (NTDs) are severe congenital neurodevelopmental disorders arising from incomplete neural tube closure. Although folate supplementation has been shown to mitigate the incidence of NTDs, some cases, often attributable to genetic factors, remain unpreventable. The SHROOM3 gene has been implicated in NTD cases that are unresponsive to folate supplementation; at present, however, the underlying mechanism remains unclear. Neural tube morphogenesis is a complex process involving the folding of the planar epithelium of the neural plate. To determine the role of SHROOM3 in early developmental morphogenesis, we established a neuroepithelial organoid culture system derived from cynomolgus monkeys to closely mimic the in vivo neural plate phase. Loss of SHROOM3 resulted in shorter neuroepithelial cells and smaller nuclei. These morphological changes were attributed to the insufficient recruitment of cytoskeletal proteins, namely fibrous actin (F-actin), myosin II, and phospho-myosin light chain (PMLC), to the apical side of the neuroepithelial cells. Notably, these defects were not rescued by folate supplementation. RNA sequencing revealed that differentially expressed genes were enriched in biological processes associated with cellular and organ morphogenesis. In summary, we established an authentic in vitro system to study NTDs and identified a novel mechanism for NTDs that are unresponsive to folate supplementation.

253−262

Authors: Yang Han, Jiale Zhou, Renquan Zhang, Yuru Liang, Liangxue Lai, Zhanjun Li

Animal models are extensively used in all aspects of biomedical research, with substantial contributions to our understanding of diseases, the development of pharmaceuticals, and the exploration of gene functions. The field of genome modification in rabbits has progressed slowly. However, recent advancements, particularly in CRISPR/Cas9-related technologies, have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases, including cardiovascular disorders, immunodeficiencies, aging-related ailments, neurological diseases, and ophthalmic pathologies. These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice. This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine, underscoring their impact and future potential in translational medicine.

275−283

Authors: Bofeng Han, Weien Liang, Xiao-Jiang Li, Shihua Li, Sen Yan, Zhuchi Tu

Huntington’s disease (HD) is a hereditary neurodegenerative disorder for which there is currently no effective treatment available. Consequently, the development of appropriate disease models is critical to thoroughly investigate disease progression. The genetic basis of HD involves the abnormal expansion of CAG repeats in the huntingtin (HTT) gene, leading to the expansion of a polyglutamine repeat in the HTT protein. Mutant HTT carrying the expanded polyglutamine repeat undergoes misfolding and forms aggregates in the brain, which precipitate selective neuronal loss in specific brain regions. Animal models play an important role in elucidating the pathogenesis of neurodegenerative disorders such as HD and in identifying potential therapeutic targets. Due to the marked species differences between rodents and larger animals, substantial efforts have been directed toward establishing large animal models for HD research. These models are pivotal for advancing the discovery of novel therapeutic targets, enhancing effective drug delivery methods, and improving treatment outcomes. We have explored the advantages of utilizing large animal models, particularly pigs, in previous reviews. Since then, however, significant progress has been made in developing more sophisticated animal models that faithfully replicate the typical pathology of HD. In the current review, we provide a comprehensive overview of large animal models of HD, incorporating recent findings regarding the establishment of HD knock-in (KI) pigs and their genetic therapy. We also explore the utilization of large animal models in HD research, with a focus on sheep, non-human primates (NHPs), and pigs. Our objective is to provide valuable insights into the application of these large animal models for the investigation and treatment of neurodegenerative disorders.

292−298

Authors: Chun-Yang Li, Xing-Chen Liu, Yu-Zhuo Li, Yan Wang, Yan-Hong Nie, Yu-Ting Xu, Xiao-Tong Zhang, Yong Lu, Qiang Sun

Mutations in mitochondrial DNA (mtDNA) are maternally inherited and have the potential to cause severe disorders. Mitochondrial replacement therapies, including spindle, polar body, and pronuclear transfers, are promising strategies for preventing the hereditary transmission of mtDNA diseases. While pronuclear transfer has been used to generate mitochondrial replacement mouse models and human embryos, its application in non-human primates has not been previously reported. In this study, we successfully generated four healthy cynomolgus monkeys (Macaca fascicularis) via female pronuclear transfer. These individuals all survived for more than two years and exhibited minimal mtDNA carryover (3.8%–6.7%), as well as relatively stable mtDNA heteroplasmy dynamics during development. The successful establishment of this non-human primate model highlights the considerable potential of pronuclear transfer in reducing the risk of inherited mtDNA diseases and provides a valuable preclinical research model for advancing mitochondrial replacement therapies in humans.

311−313

Authors: Xiao-Jiang Li, Liangxue Lai

 

329−340

Authors: Shao-Xuan Wu, Qi-Fan Zeng, Wen-Tao Han, Meng-Ya Wang, Hui Ding, Ming-Xuan Teng, Ming-Yi Wang, Pei-Yu Li, Xin Gao, Zhen-Min Bao, Bo Wang, Jing-Jie Hu

The leopard coral grouper (Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity (θπ) and fixation index (FST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

355−366

Authors: Jing-Yi Jia, Guang-Hui Chen, Ting-Ting Shu, Qi-Yong Lou, Xia Jin, Jiang-Yan He, Wu-Han Xiao, Gang Zhai, Zhan Yin

Testosterone is closely associated with lipid metabolism and known to affect body fat composition and muscle mass in males. However, the mechanisms by which testosterone acts on lipid metabolism are not yet fully understood, especially in teleosts. In this study, cyp17a1-/- zebrafish (Danio rerio) exhibited excessive visceral adipose tissue (VAT), lipid content, and up-regulated expression and activity of hepatic de novo lipogenesis (DNL) enzymes. The assay for transposase accessible chromatin with sequencing (ATAC-seq) results demonstrated that chromatin accessibility of DNL genes was increased in cyp17a1-/- fish compared to cyp17a1+/+ male fish, including stearoyl-CoA desaturase (scd) and fatty acid synthase (fasn). Androgen response element (ARE) motifs in the androgen signaling pathway were significantly enriched in cyp17a1+/+ male fish but not in cyp17a1-/- fish. Both androgen receptor (ar)-/- and wild-type (WT) zebrafish administered with Ar antagonist flutamide displayed excessive visceral adipose tissue, lipid content, and up-regulated expression and activity of hepatic de novo lipogenesis enzymes. The Ar agonist BMS-564929 reduced the content of VAT and lipid content, and down-regulated acetyl-CoA carboxylase a (acaca), fasn, and scd expression. Mechanistically, the rescue effect of testosterone on cyp17a1-/- fish in terms of phenotypes was abolished when ar was additionally depleted. Collectively, these findings reveal that testosterone inhibits lipid deposition by down-regulating DNL genes via Ar in zebrafish, thus expanding our understanding of the relationship between testosterone and lipid metabolism in teleosts.

381−397

Authors: Xi-Dan Xu, Yue Zhou, Chong-Qing Wang, Xu Huang, Kun Zhang, Xiao-Wei Xu, Li-Wen He, Xin-Yue Zhang, Xin-Zhu Fu, Ming Ma, Qin-Bo Qin, Shao-Jun Liu

The autotetraploid Carassius auratus (4nRR, 4n=200, RRRR) is derived from whole-genome duplication of Carassius auratus red var. (RCC, 2n=100, RR). In the current study, we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin (red in RCC, brownish-yellow in 4nRR). To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR, we performed transcriptome profiling and molecular functional verification in RCC and 4nRR. Results revealed that scarb1, associated with carotenoid metabolism, underwent significant down-regulation in 4nRR. Efficient editing of this candidate pigment gene provided clear evidence of its significant role in RCC coloration. Subsequently, we identified four divergent scarb1 homeologs in 4nRR: two original scarb1 homeologs from RCC and two duplicated ones. Notably, three of these homeologs possessed two highly conserved alleles, exhibiting biased and allele-specific expression in the skin. Remarkably, after precise editing of both the original and duplicated scarb1 homeologs and/or alleles, 4nRR individuals, whether singly or multiply mutated, displayed a transition from brownish-yellow skin to a cyan-gray phenotype. Concurrently, the proportional areas of the cyan-gray regions displayed a gene-dose correlation. These findings illustrate the subfunctionalization of duplicated scarb1, with all scarb1 genes synergistically and equally contributing to the pigmentation of 4nRR. This is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploid fish, substantially enriching our understanding of coloration formation and change within this group of organisms.

415−428

Authors: Jiao-Na Zhang, Rui-Ting Wang, Francesca-Gioia Klinger, Shun-Feng Cheng, Wei Shen, Xiao-Feng Sun

In eukaryotic organisms, the most common internal modification of messenger RNA (mRNA) is N6-methyladenosine (m6A). This modification can be dynamically and reversibly controlled by specific enzymes known as m6A writers and erasers. The fat-mass and obesity-associated protein (FTO) catalyzes RNA demethylation and plays a critical role in various physiological and pathological processes. Our research identified dynamic alterations in both m6A and FTO during the assembly of primordial follicles, with an inverse relationship observed for m6A levels and nuclear-localized FTO expression. Application of Fto small interfering RNA (siRNA) altered the expression of genes related to cell proliferation, hormone regulation, and cell chemotaxis, and affected RNA alternative splicing. Overexpression of the full-length Fto gene led to changes in m6A levels, alternative splicing of Cdk5, cell proliferation, cell cycle progression, and proportion of primordial follicles. Conversely, overexpression of Fto lacking a nuclear localization signal (NLS) did not significantly alter m6A levels or primordial follicle assembly. These findings suggest that FTO, localized in the nucleus but not in the cytoplasm, regulates RNA m6A demethylation and plays a role in cell proliferation, cell cycle progression, and primordial follicle assembly. These results highlight the potential of m6A and its eraser FTO as possible biomarkers and therapeutic targets.

439−450

Authors: Yi Lu, Xin-Rong Xu, Bing-Yao Chen, Thomas A Jefferson, Holly Fearnbach, Guang Yang

As highly social animals, Indo-Pacific humpback dolphins (Sousa chinensis) exhibit community differentiation. Nevertheless, our understanding of the external and internal factors influencing these dynamics, as well as their spatiotemporal variations, is still limited. In the present study, variations in the social structure of an endangered Indo-Pacific humpback dolphin population in Xiamen Bay, China, were monitored over two distinct periods (2007–2010 and 2017–2019) to analyze the effects of habitat utilization and the composition of individuals within the population. In both periods, the population demonstrated a strikingly similar pattern of social differentiation, characterized by the division of individuals into two main clusters and one small cluster. Spatially, the two primary clusters occupied the eastern and western waters, respectively, although the core distribution area of the eastern cluster shifted further eastward between the two periods. Despite this distribution shift, the temporal stability of the social structure and inter-associations within the eastern cluster remained unaffected. A subset of 16 individuals observed in both periods, comprising 51.6% and 43.2% of the population in each respective period, emerged as a foundational element of the social structure and may be responsible for sustaining social structure stability, especially during the 2007–2010 period. These observations suggest that the composition of dominant individuals, an internal factor, had a more substantial influence on the formation of the social network than changes in habitat use, an external factor. Consequently, the study proposes distinct conservation measures tailored to each of the two main clusters.

1−12

Authors: Yong-Gang Niu, Deng-Bang Wei, Xue-Jing Zhang, Ti-Sen Xu, Xiang-Yong Li, Hai-Ying Zhang, Zhi-Fang An, Kenneth B. Storey, Qiang Chen

Changes in protein abundance and reversible protein phosphorylation (RPP) play important roles in regulating hypometabolism but have never been documented in overwintering frogs at high altitudes. To test the hypothesis that protein abundance and phosphorylation change in response to winter hibernation, we conducted a comprehensive and quantitative proteomic and phosphoproteomic analysis of the liver of the Xizang plateau frog, Nanorana parkeri, living on the Qinghai-Xizang Plateau. In total, 5170 proteins and 5695 phosphorylation sites in 1938 proteins were quantified. Based on proteomic analysis, 674 differentially expressed proteins (438 up-regulated, 236 down-regulated) were screened in hibernating N. parkeri versus summer individuals. Functional enrichment analysis revealed that higher expressed proteins in winter were significantly enriched in immune-related signaling pathways, whereas lower expressed proteins were mainly involved in metabolic processes. A total of 4251 modified sites (4147 up-regulated, 104 down-regulated) belonging to 1638 phosphoproteins (1555 up-regulated, 83 down-regulated) were significantly changed in the liver. During hibernation, RPP regulated a diverse array of proteins involved in multiple functions, including metabolic enzymatic activity, ion transport, protein turnover, signal transduction, and alternative splicing. These changes contribute to enhancing protection, suppressing energy-consuming processes, and inducing metabolic depression. Moreover, the activities of phosphofructokinase, glutamate dehydrogenase, and ATPase were all significantly lower in winter compared to summer. In conclusion, our results support the hypothesis and demonstrate the importance of RPP as a regulatory mechanism when animals transition into a hypometabolic state.

25−35

Authors: Xian-Hui Ning, Bing Han, Ye Peng, Shao-Wu Yin

Long non-coding RNAs (lncRNAs) function as key modulators in mammalian immunity, particularly due to their involvement in lncRNA-mediated competitive endogenous RNA (ceRNA) crosstalk. Despite their recognized significance in mammals, research on lncRNAs in lower vertebrates remains limited. In the present study, we characterized the first immune-related lncRNA (pol-lnc78) in the teleost Japanese flounder (Paralichthys olivaceus). Results indicated that pol-lnc78 acted as a ceRNA for pol-miR-n199-3p to target the sterile alpha and armadillo motif-containing protein (SARM), the fifth discovered member of the Toll/interleukin 1 (IL-1) receptor (TIR) adaptor family. This ceRNA network regulated the antibacterial responses of flounder via the Toll-like receptor (TLR) signaling pathway. Specifically, SARM acted as a negative regulator and exacerbated bacterial infection by inhibiting the expression of inflammatory cytokines IL-1β and tumor necrosis factor-α (TNF-α). Pol-miR-n199-3p reduced SARM expression by specifically interacting with the 3’ untranslated region (UTR), thereby promoting SARM-dependent inflammatory cytokine expression and protecting the host against bacterial dissemination. Furthermore, pol-lnc78 sponged pol-miR-n199-3p to ameliorate the inhibition of SARM expression. During infection, the negative regulators pol-lnc78 and SARM were significantly down-regulated, while pol-miR-n199-3p was significantly up-regulated, thus favoring host antibacterial defense. These findings provide novel insights into the mechanisms underlying fish immunity and open new horizons to better understand ceRNA crosstalk in lower vertebrates.

39−54

Authors: Lan Zhao, Sheng-Nan Ji, Xiao-Bing Du, Jia-Hui Liu, Bo-Lun Zhang, Pei-Hua Li, Yi-Jun Yang, Bao-Guo Li, Yan-Qing Guo, Xiao-Guang Qi

The dynamics of animal social structures are heavily influenced by environmental patterns of competition and cooperation. In folivorous colobine primates, prevailing theories suggest that larger group sizes should be favored in rainforests with a year-round abundance of food, thereby reducing feeding competition. Yet, paradoxically, larger groups are frequently found in high-altitude or high-latitude montane ecosystems characterized by a seasonal scarcity of leaves. This contradiction is posited to arise from cooperative benefits in heterogeneous environments. To investigate this hypothesis, we carried out a six-year field study on two neighboring groups of golden snub-nosed monkey (Rhinopithecus roxellana), a species representing the northernmost distribution of colobine primates. Results showed that the groups adjusted their movement and habitat selection in response to fluctuating climates and spatiotemporal variability of resources, indicative of a dynamic foraging strategy. Notably, during the cold, resource-scarce conditions in winter, the large group occupied food-rich habitats but did not exhibit significantly longer daily travel distances than the smaller neighboring group. Subsequently, we compiled an eco-behavioral dataset of 52 colobine species to explore their evolutionary trajectories. Analysis of this dataset suggested that the increase in group size may have evolved via home range expansion in response to the cold and heterogeneous climates found at higher altitudes or latitudes. Hence, we developed a multi-benefits framework to interpret the formation of larger groups by integrating environmental heterogeneity. In cold and diverse environments, even smaller groups require larger home ranges to meet their dynamic survival needs. The spatiotemporal distribution of high-quality resources within these expanded home ranges facilitates more frequent interactions between groups, thereby encouraging social aggregation into larger groups. This process enhances the benefits of collaborative actions and reproductive opportunities, while simultaneously optimizing travel costs through a dynamic foraging strategy.

69−78

Authors: Shun Wang, Peng Zhang, Fan Fei, Tianyang Tong, Xiujuan Zhou, Yajie Zhou, Jing Zhang, Mengke Wei, Yanqi Zhang, Lei Zhang, Yulong Huang, Lin Zhang, Xin Zhang, Tiantian Cai, Can Xie

Birds exhibit extraordinary mobility and remarkable navigational skills, obtaining guidance cues from the Earth’s magnetic field for orientation and long-distance movement. Bird species also show tremendous diversity in navigation strategies, with considerable differences even within the same taxa and among individuals from the same population. The highly conserved iron and iron-sulfur cluster binding magnetoreceptor (MagR) protein is suggested to enable animals, including birds, to detect the geomagnetic field and navigate accordingly. Notably, MagR is also implicated in other functions, such as electron transfer and biogenesis of iron-sulfur clusters, raising the question of whether variability exists in its biochemical and biophysical features among species, particularly birds. In the current study, we conducted a comparative analysis of MagR from two different bird species, including the migratory European robin (Erithacus rubecula) and the homing pigeon (Columba livia) . Sequence alignment revealed an extremely high degree of similarity between the MagRs of these species, with only three sequence variations. Nevertheless, two of these variations underpinned significant differences in metal binding capacity, oligomeric state, and magnetic properties. These findings offer compelling evidence for the marked differences in MagR between the two avian species, potentially explaining how a highly conserved protein can mediate such diverse functions.

95−107

Authors: Hai-Yang Wang, Lan-Xiang Liu, Xue-Yi Chen, Yang-Dong Zhang, Wen-Xia Li, Wen-Wen Li, Lian Wang,  Xiao-Long Mo, Hong Wei, Ping Ji, Peng Xie

The gut microbiome interacts with the host to maintain body homeostasis, with gut microbial dysbiosis implicated in many diseases. However, the underlying mechanisms of gut microbe regulation of host behavior and brain functions remain unclear. This study aimed to elucidate the influence of gut microbiota on brain functions via post-translational modification mechanisms in the presence or absence of bacteria without any stimulation. We conducted succinylome analysis of hippocampal proteins in germ-free (GF) and specific pathogen-free (SPF) mice and metagenomic analysis of feces from SPF mice. These results were integrated with previously reported hippocampal acetylome and phosphorylome data from the same batch of mice. Subsequent bioinformatics analyses revealed 584 succinylation sites on 455 proteins, including 54 up-regulated succinylation sites on 91 proteins and 99 down-regulated sites on 51 proteins in the GF mice compared to the SPF mice. We constructed a panoramic map of gut microbiota-regulated succinylation, acetylation, and phosphorylation, and identified cross-talk and relative independence between the different types of post-translational modifications in modulating complicated intracellular pathways. Pearson correlation analysis indicated that 13 taxa, predominantly belonging to the Bacteroidetes phylum, were correlated with the biological functions of post-translational modifications. Positive correlations between these taxa and succinylation and negative correlations between these taxa and acetylation were identified in the modulation of intracellular pathways. This study highlights the hippocampal physiological changes induced by the absence of gut microbiota, and proteomic quantification of succinylation, phosphorylation, and acetylation, contributing to our understanding of the role of the gut microbiome in brain function and behavioral phenotypes.

125−135

Authors: Jian-Chao Liang, Zhi-Feng Ding, Chun-Lin Li, Yi-Ming Hu, Zhi-Xin Zhou, Gan-Wen Lie, Xiao-Nan Niu, Wen-Bin Huang, Hui-Jian Hu, Xing-Feng Si

Geographical background and dispersal ability may strongly influence assemblage dissimilarity; however, these aspects have generally been overlooked in previous large-scale beta diversity studies. Here, we examined whether the patterns and drivers of taxonomic beta diversity (TBD) and phylogenetic beta diversity (PBD) of breeding birds in China vary across (1) regions on both sides of the Hu Line, which demarcates China’s topographical, climatic, economic, and social patterns, and (2) species with different dispersal ability. TBD and PBD were calculated and partitioned into turnover and nestedness components using a moving window approach. Variables representing climate, habitat heterogeneity, and habitat quality were employed to evaluate the effects of environmental filtering. Spatial distance was considered to assess the impact of dispersal limitation. Variance partitioning analysis was applied to assess the relative roles of these variables. In general, the values of TBD and PBD were high in mountainous areas and were largely determined by environmental filtering. However, different dominant environmental filters on either side of the Hu Line led to divergent beta diversity patterns. Specifically, climate-driven species turnover and habitat heterogeneity-related species nestedness dominated the regions east and west of the line, respectively. Additionally, bird species with stronger dispersal ability were more susceptible to environmental filtering, resulting in more homogeneous assemblages. Our results indicated that regions with distinctive geographical backgrounds may present different ecological factors that lead to divergent assemblage dissimilarity patterns, and dispersal ability determines the response of assemblages to these ecological factors. Identifying a single universal explanation for the observed pattern without considering these aspects may lead to simplistic or incomplete conclusions. Consequently, a comprehensive understanding of large-scale beta diversity patterns and effective planning of conservation strategies necessitate the consideration of both geographical background and species dispersal ability.

138−151

Authors: Tao Jiang, Zhi-Min Zhou, Zi-Qi Ling, Qing Zhang, Zhong-Zi Wu, Jia-Wen Yang, Si-Yu Yang, Bin Yang Lu-Sheng Huang

Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.

160−175

Authors: Yu-Ran Li, Zheng-Wei Wang, Richard T. Corlett, Wen-Bin Yu

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.

189−200

Authors: Cui-Hong Tong, Zhi-Peng Huo, Lu Diao, Dan-Yu Xiao, Ruo-Nan Zhao, Zhen-Ling Zeng, Wen-Guang Xiong

Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs (P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy (r=0.72–0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

215−225

Authors: Zhan-Fei Wei, Kai-Wen Ta, Nan-Nan Zhang, Shan-Shan Liu, Liang Meng, Kai-Qiang Liu, Chong-Yang Cai, Xiao-Tong Peng, Chang-Wei Shao

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous (Ka) to synonymous (Ks) substitution ratio (Ka/Ks) suggested that the 14 protein-coding genes (PCGs) were under purifying selection, likely due to specific deep-sea environmental pressures. Correlation analysis of the median Ka/Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b (cyt b) and DNA mismatch repair protein (mutS) may be influenced by environmental factors in the context of deep-sea species formation. This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.

230−232

Authors: Wenhui Lee, Ren Lai