KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Intracellular HIV-1 Tat regulator induces epigenetic changes in the DNA methylation landscape

Introduction

The HIV regulatory protein Tat enhances viral transcription and also modifies host gene expression, affecting cell functions like cell cycle and apoptosis. Residual expression of Tat protein is detected in blood and other tissues even under antiretroviral treatment. Cohort studies have indicated that, despite virologic suppression, people with HIV (PWH) are at increased risk of comorbidities linked to chronic inflammation, accelerated immune ageing, and cellular senescence, sometimes associated with abnormal genomic methylation patterns. We analysed whether Tat influences DNA methylation and subsequently impacts the transcriptional signature, contributing to inflammation and accelerated ageing.

Methods

We transfected Jurkat cells with full-length Tat (Tat101), Tat's first exon (Tat72), or an empty vector (TetOFF). We assessed DNA methylation modifications via the Infinium MethylationEPIC array, and we evaluated transcriptomic alterations through RNA-Seq. Methylation levels in gene promoters or body regions were correlated to their expression data, and subsequently, we performed an overrepresentation analysis to identify the biological terms containing differentially methylated and expressed genes.

Results

Tat101 expression caused significant hyper- and hypomethylation changes at individual CpG sites, resulting in slightly global DNA hypermethylation. Methylation changes at gene promoters and bodies resulted in altered gene expression, specifically regulating gene transcription in 5.1% of differentially expressed genes (DEGs) in Tat101- expressing cells. In contrast, Tat72 had a minimal impact on this epigenetic process. The observed differentially methylated and expressed genes were involved in inflammatory responses, lipid antigen presentation, and apoptosis.

Discussion

Tat expression in HIV infection may constitute a key epigenetic modelling actor that contributes to HIV pathogenesis and chronic inflammation. Clinical interventions targeting Tat blockade may reduce chronic inflammation and cellular senescence related to HIV infection comorbidities.

In situ diversification and adaptive introgression in Taiwanese Scutellaria

Island habitats provide unique opportunities to study speciation. Recent work indicates that both ex situ origination and in situ speciation contribute to island species diversity. However, clear evidence of local adaptation of endemic plant species on islands requires in-depth studies, which are scarce. This study underscores the importance of local adaptation in maintaining species boundaries by examining how adaptive introgression, hybridization, and local adaptation contribute to genetic variation in island species. Multilocus genome scanning of 51 nuclear genes was used to investigate the evolutionary relationships of the Scutellaria species complex on Taiwan Island and assess the role of in situ diversification in generating high endemism and genetic diversity. Interspecies introgressions were detected by phylogenetic networks and ABBA-BABA-based analysis, suggesting ongoing or recent speciation processes. Coalescent-based simulation identified hybrid speciation in Scutellaria taiwanensis and Scutellaria hsiehii, with evidence of hybridization between more than two parental species. Genotype-environment association studies revealed that the influence of climate, particularly precipitation- and temperature-related factors, contributed to adaptive genetic divergence between species. Additionally, adaptive introgression related to environmental pressures that may have facilitated the colonization of new island habitats were identified. This research illustrates how hybridization, introgression, and adaptation shaped the evolutionary histories and divergence of this island-endemic plant species complex and sheds light on the multifaceted mechanisms of speciation on semi-isolated islands.

Proteomic insights into nematode-trapping fungi Arthrobotrys oligospora after their response to chitin

Introduction

Nematode-trapping fungi (NTFs) can produce various chitinases to degrade nematode body wall and eggshell chitin during predation. However, the regulatory mechanisms of their expression of chitinases still remain unclear. The primary objective of this study was to elucidate the differential protein profile of A. oligospora, an NTF, in response to chitin.

Material and Methods

Colloidal chitin was added to induce the culture of A. oligospora, and the phenotypic differences before and after induction were observed under inverted microscope. The differential proteins before and after mycelium induction were screened by liquid chromatography-tandem mass spectrometry. The differentially expressed chitinase was expressed in Pichia yeast, and the recombinant enzyme was incubated with Caenorhabditis elegans and its egg suspension to explore its biological activity.

Results

It was found that there was a significant acceleration in the mycelial growth post chitin interaction in A. oligospora. A total of 1,124 differentially expressed proteins (DEPs) were identified between the control group (AO-c) and the experimental group (AO-e), with 183 upregulated and 941 downregulated. Gene Ontology analysis revealed that the DEPs acted in various metabolic processes with catalysis and binding functions. Kyoto Encyclopedia of Genes and Genomes analysis associated these proteins primarily with signalling pathways related to glucose metabolism. Three chitinases were significantly modulated among DEPs. Moreover, enzymatic activity assays demonstrated that one of them effectively degraded C. elegans and its eggs.

Conclusion

These findings suggest that A. oligospora can significantly alter its protein expression profile in response to chitin, thereby facilitating its sugar metabolism and mycelial development. Our study provided new insights into the regulatory mechanisms of nematode predation in A. oligospora.

TSG-6 Protects Against Cerebral Ischemia-Reperfusion Injury via Upregulating Hsp70-1B in Astrocytes

AIMS

This study aimed to investigate the relationship between tumor necrosis factor alpha-induced protein (TNFAIP6/TSG-6) and astrocytes in cerebral ischemia/reperfusion (I/R) injury.

METHODS

Utilizing in vivo and in vitro cerebral I/R models, cerebral infarct volumes, neurobehavioral outcomes, blood-brain barrier (BBB) permeability, as well as indicators of astrocyte apoptosis, reactivity, and A1 phenotype were assessed to evaluate the effects of recombinant rattus TSG-6 (rrTSG-6) on astrocytes in acute cerebral I/R injury. Following mRNA sequencing of all astrocyte groups, astrocyte apoptosis and reactivity were analyzed through a combined intervention of rrTSG-6 and Apoptozole, a heat shock protein 70-1B (Hsp70-1B) inhibitor, in vitro.

RESULTS

The findings demonstrated that rrTSG-6 significantly reduced cerebral infarct volumes by nearly half, improved neurobehavioral outcomes, mitigated BBB damage, and suppressed the expressions of astrocyte apoptosis markers, reactivity indicators, and A1 phenotype markers. mRNA sequencing revealed that the Hsp70-1B protein level increased to approximately 1.6 times that of the rrTSG-6 non-intervention group. Furthermore, Apoptozole impeded the expressions of astrocyte apoptosis markers, reactivity indicators, and A1 phenotype markers.

CONCLUSION

TSG-6 inhibited nuclear factor kappa-B (NF-κB) phosphorylation by upregulating Hsp70-1B in oxygen-glucose deprivation/reoxygenation (OGD/R)-induced astrocytes, thereby exerting a protective effect through anti-apoptotic mechanisms and the suppression of astrocyte reactivity and A1 transformation following cerebral I/R injury.

The Genome of the Lima Bean Variety Baiyu Bean Highlights Its Evolutionary Characteristics

The baiyu bean (Phaseolus lunatus), also known as the lima bean, is a plant belonging to the Fabaceae family, has a long and distinguished history of cultivation in China and is a highly regarded local variety of lima bean. In the current study, we present the reference genome of the baiyu bean variety, which has a scaffold N50 length of 47.545 Mb. A comparative genomic analysis was conducted using genomes of seven legume species, and the results demonstrated that 1564 and 1275 genes of baiyu bean exhibited expansion and contraction, respectively. Moreover, 543 genes were identified as exclusive to the baiyu bean. The analysis of adaptive evolution genes revealed the presence of 61 genes under adaptive evolution between P. lunatus and the common bean P. vulgaris. An examination of the branch model revealed the presence of five genes undergoing adaptive evolution in the P. lunatus branch. Additionally, the evolutionary selective pressure acting on other branches of legume plants was analyzed. A comprehensive analysis of structural variations (SVs) between the baiyu bean and G27455 genome was conducted, resulting in the identification of 5549 SVs. Among these, 333 genes were identified as high-impact SV genes. The acquisition of the genome sequence of this excellent variety will facilitate the exploration and utilization of its characteristics, providing a foundation for the genetic improvement of the lima bean.

Ginger exosome-like nanoparticle-derived miRNA therapeutics: A strategic inhibitor of intestinal inflammation

INTRODUCTION

MicroRNAs (miRNAs) involve in destabilising messenger RNA or repressing translation of target molecules. Ginger-derived exosome-like nanoparticles (GELNs) play a crucial role in modulating intestinal inflammation. Moreover, GELNs contain highly heterogeneous miRNA. However, the role of miRNAs derived from GELNs in immunomodulation remains unclear.

OBJECTIVES

This study aimed to elucidate the molecular basis of the unique biological effects mediated by miRNA derived from GELNs on macrophages.

METHODS

GELNs were isolated using a combination of commercial exosome isolation kits and the differential centrifugation method, and the lipid composition of GELNs was determined using liquid chromatography-mass spectrometry. Subsequently, PKH26 labelled GELNs were taken up by macrophages. Furthermore, the modulation of inflammatory and immune responses by GELNs or osa-miR164d was assessed through the RNA-seq, RT-qPCR, online databases, and dual luciferase reporter assays to explore the underlying mechanisms of osa-miR164d. Biomimetic exosomes loaded with osa-miR164d were prepared using a microfluidic mixing device and systematically characterized. The therapeutic effects of osa-miR164d on relieving colitis were evaluated.

RESULTS

We report for the first time that GELNs-derived osa-miR164d is a regulatory factor of reprogramming macrophage polarization, thereby inhibiting the intestinal inflammatory response. Mechanistically, osa-miR164d directly targets the 3'-UTRs of TAB1, which regulates macrophage polarization through the downregulation of NF-κB expression. In addition, We have designed a biomimetic exosome mimicking GELNs to deliver osa-miR164d (osa-miR164d-MGELNs). Notably, the osa-miR164d-MGELNs can efficiently reprogram macrophages to alleviate colitis-related symptoms.

CONCLUSION

Our findings enhance the systematic understanding of how GELNs-derived osa-miR164d mediates cross-kingdom communication and provide an original engineering paradigm for mimicking GELNs to transfer miRNA.

Whole genome and transcriptome analyses in dairy goats identify genetic markers associated with high milk yield

Milk production is the most important economic trait of dairy goats and a key indicator for genetic improvement and breeding. However, milk yield is a complex phenotypic trait, and its genetic mechanisms are still not fully understood. This study focuses on dairy goats and non-dairy goats. By analyzing the population structure of these two groups, we found that there is a significant genetic distance between the populations of dairy goats and non-dairy goats. Using SNP and Indel analyses to identify selection signals, we identified several genes associated with milk production traits, including MPP7, PRPF6, DNAJC5, TPD52L2, HNF4G, LAMA3, FAM13A, and EPHA5. Through longitudinal GWAS of the milk production traits of 298 dairy goats, we discovered additional genes such as TRNAS-GGA-102, TTC39C, LAMA3, ANKRD29, NPC1, C24H18orf8, LOC108633789, RIOK3, TMEM241, CABLES1, LOC108633781, and RBBP8. Transcriptome sequencing of breast tissues at different lactation stages reveals dynamic LAMA3 expression changes. Three non-synonymous mutations in LAMA3 are identified, with the TT genotype at one site correlating significantly with average milk production in dairy goats. Our study discovered new genetic markers for improving dairy goat genetics and provided valuable insights into the genetic mechanisms underlying complex traits.

Comprehensive analysis reveals the prognostic and immunological role of PSMD13 in hepatocellular carcinoma

Immune cell infiltration in liver hepatocellular carcinoma (LIHC) is promising for immunotherapy. However, effective predictive markers to accurately predict a tumour's immune status are lacking. PSMD13, a native component of the 26 S proteasome subunit involved in intracellular metabolism, has an unclear association with cancer and immunity. Using bioinformatics analysis of data from the TCGA, we investigated the expression patterns, prognostic values, gene functions, and tumour immune relationships of PSMD13 in LIHC. We developed a prognostic model that incorporates PSMD13 for LIHC and validated the biological functions of PSMD13 in LIHC cells. Furthermore, we analysed the associations between PSMD13 expression and the tumour immune markers CD206 and CD8 in 101 paired liver tissues using immunohistochemistry. PSMD13 was upregulated in LIHC and served as a prognostic biomarker of LIHC. The knockdown of PMSD13 significantly affected the proliferation, migration, and colony formation of LIHC cells. PSMD13 was closely associated with the infiltration of M2 macrophages and the expression of various tumour immune checkpoints. Our study revealed that PSMD13 is a crucial component contributing to the malignant behaviour of LIHC, indicating its essential role in both the prognosis and potential immune microenvironment profile of LIHC.

Linalool and 1,8-Cineole as Constitutive Disease-Resistant Factors of Norway Spruce Against Necrotrophic Pathogen Heterobasidion Parviporum

Norway spruce is an important coniferous species in boreal forests. Root and stem rot diseases caused by the necrotrophic pathogen Heterobasidion parviporum threaten the wood production of Norway spruce which necessitates the search for durable control and management strategies. Breeding for resistant traits is considered a viable long-term strategy. However, identification of potential resistant traits and markers remains a major challenge. In this study, short-term disease resistance screening was conducted using 218 Norway spruce clones from 17 families. Disease resistance was evaluated based on the size of necrosis lesion length following infection with the pathogen. A subset of needles/branches from clones with small (partial resistant) or large (susceptible) lesions were used for terpene analysis and transcriptomic profiling. The results revealed that the content of monoterpene linalool and 1,8-cineole and their respective encoded genes were significantly more abundant and highly expressed in the partial resistant group. Furthermore, linalool and 1,8-cineole were demonstrated to have inhibitory effect on the growth of the pathogen H. parviporum, with morphological distortion of the hyphae. RNAseq analysis revealed that transcript of pathogen genes involved in the regulation of carbohydrate metabolism and stress responses were significantly decreased in presence of the terpenes. The results suggest the relevance of monoterpenes together with jasmonic acid precursor and some genes involved in phenylpropanoid biosynthesis, as constitutive tolerance factors for Norway spruce tolerance against necrotrophic pathogen. The high level of necrosis related cell death gene expression might be factors critical for host susceptibility and disease development.

Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen)

Rhamdia quelen is a catfish widely distributed throughout South America, characterized by a complex taxonomic history. This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotropical region. Population genomics studies supported two main lineages latitudinally distributed (North and South) in the Neotropical basins Río de la Plata and Laguna Merín based on current genetic isolation and signals of local adaptation. In this study, we characterized the R. quelen transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. After filtering, a comprehensive catalog of 24,433 transcripts was annotated, providing insights into the immune function of head kidney and liver, the association of brain with the endocrine system, and the metabolic function of liver. Skeletal muscle and brain expressed genes associated with growth were also identified. Transcriptomic differences suggestive of adaptation to temperature and salinity were revealed between North and South genomic lineages. A total of 100,045 SNPs loci were identified within transcripts, most of them (78.8%) showing low genetic differentiation between lineages (FST ≤ 0.100). However, 2504 loci (2.5%) showed high differentiation (FST ≥ 0.800), some of them located within genes associated with putative adaptation of genomic lineages to environmental factors such as temperature and salinity. These SNPs represent useful gene markers for future functional and population genomic studies for sustainable management of wild populations and their application in breeding programs.

Three regulatory elements upstream of LMO4 are strongly associated with intermittent fertilization intensity in Chicken

Intermittent fertilization intensity (IFI) is closely related to higher fertilization in chicken hens. Recent studies have identified genes influencing sperm-oocyte interactions and immune regulation that impact the fertilization process in chickens. This research aims to identify key candidate genes and variants regulating IFI through transcriptomic analysis and dual luciferase assays. Our study's transcriptomic analysis of 12 individuals exhibiting extreme IFI revealed several key candidate genes. Validation using quantitative PCR highlighted PRSS12, DNER, WIF1, and NRXN1 as potential contributors to variations in IFI. Notably, we observed significant differences in the expression of LMO4, located 247.2 kb downstream of IFI-associated genomic regions. To explore variants potentially involved in the regulation of LMO4, we conducted short variant annotation and SV-GWAS, but found no significant associations with IFI. Further motif analysis and dual luciferase validation uncovered three regulatory elements within the associated region that exhibited enhanced promoter or enhancer activity following significant SNP mutations. In conclusion, our findings indicate that LMO4, PRSS12, DNER, WIF1, and NRXN1 serve as primary candidate genes for regulating IFI. Additionally, three regulatory elements significantly associated with IFI were identified upstream of LMO4. These variants hold promise for use in selecting low-IFI lines.

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.

WISP1 inhibition of YAP phosphorylation drives breast cancer growth and chemoresistance via TEAD4 activation

Wnt1-inducible signaling pathway protein 1 (WISP1) promotes breast cancer. The Hippo signaling pathway demonstrates a potential connection with WISP1, necessitating an exploration of their interaction. This study hypothesized that WISP1 boosts breast cancer by modulating the Hippo signaling pathway. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to analyze WISP1 expression and Hippo signaling in breast cancer patients. WISP1, yes-associated protein (YAP), and domain family member 4 (TEAD4) were overexpressed or silenced in breast cancer cells. Epithelial-mesenchymal transition (EMT), and chemoresistance of breast cancer cells were evaluated. Immunofluorescence, PCR, immunoprecipitation, and western blot were used to detect the expression of WISP1 and key Hippo signaling factors and their interactions. Enrichment analysis indicated activation of WISP1 and Hippo signaling pathway and correlated with a worse prognosis in breast cancer. WISP1 overexpression facilitated EMT and chemotherapy resistance in breast cancer. Importantly, overexpression of WISP1 promoted YAP's nuclear translocation. TEAD4 expression in YAP precipitates from nuclear of WISP1-overexpressing MCF-7 cells increased. The promoting effect of WISP1 on breast cancer was counteracted by silencing YAP or TEAD4. Moreover, in WISP1 small interfering RNA-transfected MCF-7 cells, p-YAP expression increased, while interaction between YAP and TEAD4 decreased. WISP1 silencing led to ubiquitin increase and TEAD reduction in the p-YAP precipitates. In conclusion, WISP1 promotes YAP nuclear translocation and binding with TEAD4 by inhibiting YAP phosphorylation, reducing ubiquitin recruitment, and participating in transcriptional regulation in breast cancer.

Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites

Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.

Dynamic molecular responses of the sea urchin Strongylocentrotus intermedius to pathogen infection: Insights from a serial comparative transcriptome analysis

To explore the dynamic molecular responses to pathogen infection in sea urchins, the sea urchin Strongylocentrotus intermedius were infected by a causative pathogen strain of sea urchin black peristomial membrane disease. Specimens were collected at 0, 6, 12, 24, 48, 72, and 96 h post-infection (hpi), and comparative transcriptome analysis were performed. The results showed that 1) a total of 771, 1437, 3477, 8417, 1566, and 2171 differentially expressed genes (DEGs) were identified at 6, 12, 24, 48, 72, and 96 hpi compared with the 0 hpi (as the control), respectively. 2) The number of upregulated DEGs was higher than that of downregulated DEGs at each time point after infection. The largest number of DEGs was obtained at 48 hpi. 3) Among identified DEGs, percent cellular process, binding, and metabolic process related DEGs account for 57.9 %, 49.9 %, and 45.5 %, respectively. Main Rho-GTPase family members (RhoA, Rac1, and Cdc42) exhibited a general upregulated expression trend during the examined infection process, the same as Caspase family members (Casp3, Casp6 and Casp7). 4) Cell cycle and apoptosis pathways are the most affected pathways, the DEG enrichment level of which remained in the top 30 (cell cycle pathways) and top 50 (apoptosis pathways) throughout the whole examined infection process. To sum up, all findings from this study will not only deepen our understanding of the dynamic molecular expression mechanisms of sea urchins in response to pathogen infection, but also provide new clues for elutriating the profound mechanisms of serial gene expression in innate immunity.

Multi-disciplinary evidence illuminates the speciation history of a monophyletic yet dimorphic lily group

Species boundaries are dynamic and constantly challenged by gene flow. Understanding the strategies different lineages adopt to maintain ecological and genetic distinctiveness requires employing an integrative species concept that incorporates data from a variety of sources. In this study, we incorporated genetic, ecological, and environmental evidence to assess the extent of speciation or evolutionary divergence within a monophyletic yet dimorphic group (i.e., clade Leucolirion consisting of six species) within the genus Lilium. This clade consists of two lineages that exhibit unexpectedly distinct perianth appearances: whitish trumpet (funnel form, encompassing four species) and orange recurved (reflex form, including two species), respectively, which are separated by completely different pollination syndromes. Transcriptome-based nuclear and plastome datasets indicate that these two lineages are isolated, with only weak ancient gene flow between them. Within each lineage, several taxa with incomplete isolation have diverged, as indicated by weak genetic structure, strong gene flow, and conflicts between nuclear and chloroplast phylogenies, especially in the trumpet lineage. Although these taxa are not entirely independent, our evidence indicates that they are diverging, with recent gene flow disappearing and multiple isolation strategies emerging, such as differences in flowering time and niche specialization. Taken together, our findings suggest that species divergence and maintenance in Lilium are driven by a combination of adaptive and non-adaptive processes, highlighting the complex interplay of historical climate changes, ecological adaptation, and gene flow in shaping biodiversity within this genus.

Adaptive Divergence and Functional Convergence: The Evolution of Pulmonary Gene Expression in Amphibians of the Qingzang Plateau

The Qingzang Plateau, with its harsh environmental conditions-low oxygen, high ultraviolet radiation and significant temperature fluctuations-demands specialised adaptations for survival. While genetic adaptations have been extensively studied, gene expression's role in amphibian adaptation to high elevations remains understudied. This study analysed pulmonary gene expression in 119 amphibians across the plateau to explore how genetic and environmental factors shape expression evolution. Transcriptomic analyses revealed significant interspecies variation, driven by environmental factors like temperature, oxygen levels, UVB radiation and precipitation. Principal Component and Mantel analyses found no significant correlation between gene expression divergence and genetic distance. Instead, species-specific traits and environmental pressures were pivotal in shaping expression patterns. PERMANOVA analysis showed environmental factors had varying impacts on species. For instance, Bufo gargarizans exhibited a strong gene expression response to multiple environmental factors, while Scutiger boulengeri was less influenced, reflecting diverse adaptive strategies. Functional enrichment analysis highlighted convergence in key biological processes, such as energy metabolism, apoptosis and autophagy, despite species-specific gene expression differences. These processes are critical for surviving the plateau's extremes. The findings suggest that gene expression evolution in amphibians on the Qingzang Plateau is shaped by both genetic diversity and environmental pressures. Although gene expression profiles vary, they converge on essential functions, offering insights into adaptation mechanisms in extreme environments.

SRF Facilitates Transcriptional Inhibition of Gem Expression by m6A Methyltransferase METTL3 to Suppress Neuronal Damage in Epilepsy

A bioinformatics analysis was conducted to screen for relevant expression datasets of the transcription factor SRF knockout mice. The aim was to investigate the relationship between SRF and m6A-related genes, predict how SRF regulates the m6A modification of GEM genes mediated by METTL3, and explore potential molecular mechanisms associated with neurotrauma. Disease gene databases such as GeneCards, DisGeNET, and Phenolyzer, and transcription factor databases TFDB and TRRUST, were used to obtain epilepsy-related genes and transcription factors. The intersection was then selected. Expression data of SRF knockout epilepsy mice were obtained from the GEO database and used to filter differentially expressed genes. Important module genes related to the disease were selected through WGCNA co-expression analysis. The intersection between these genes and the differentially expressed genes was performed, followed by PPI network analysis and GO/KEGG enrichment analysis. Furthermore, the core genes were selected using the cytoHubba plugin of the Cytoscape software. Differential expression analysis was performed on m6A-related factors in the GEO dataset, and the relationship between SRF and m6A-related factors and core genes was analyzed. The m6A binding sites of SRF with the METTL3 promoter and target gene Gem were predicted using the AnimalTFDB and SRAMP websites, respectively. We found that the transcription factor SRF may be a key gene in epilepsy during neuronal development. Further WGCNA analysis showed that 129 module genes were associated with SRF knockout epilepsy, and these differentially expressed genes were mainly enriched in the neuroactive ligand-receptor interaction pathway. The final results indicate that knocking out SRF may inhibit the transcription of METTL3, thereby inhibiting the m6A modification of Gem and leading to upregulation of Gem expression, thereby playing an important role in neuronal damage. Knocking out the SRF gene may inhibit the transcription of m6A methyltransferase METTL3, thereby inhibiting the m6A modification of GEM genes mediated by METTL3, promoting GEM gene expression, and leading to the occurrence of epilepsy-related neuron injury. Further investigation revealed that SRF overexpression can potentially enhance the transcription of METTL3, thus promoting m6A modification of GEM, resulting in downregulation of GEM expression. This process regulates oxidative stress in epileptic mouse neurons, suppresses inflammatory responses, and mitigates associated damage. Additionally, an in vitro neuronal epileptic model was established, and experimental techniques such as qRT-PCR and WB were employed to assess the expression of SRF, METTL3, and GEM in hippocampal tissues and neurons. The experimental results were consistent with our predictions, demonstrating that overexpression of SRF can inhibit the development of epilepsy-related neuronal damage. This study reveals that knockout of the SRF gene may suppress the transcription of m6A methyltransferase METTL3, thereby inhibiting m6A modification of the GEM gene mediated by METTL3 and subsequently promoting the expression of the GEM gene, leading to the occurrence of epilepsy-related neuronal damage.

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds

BACKGROUND

Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N'Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds.

RESULTS

Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from Bos taurus and Bos indicus. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1).

CONCLUSIONS

This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.

A cysteine-rich transmembrane module peptide GhCYSTM9 is involved in cold stress response

BACKGROUND

Cysteine-rich transmembrane module (CYSTM) peptides, which are widely distributed and highly conserved in eukaryotes, are largely involved in stress response and defence. However, the role of cotton CYSTM genes in the stress response has not been functionally characterized.

RESULTS

In this study, we identified GhCYSTM9 as a cold stress-responsive CYSTM member from upland cotton. Compared with that in control cotton plants, GhCYSTM9 silencing in cotton resulted in reduced tolerance under cold stress, accompanied by higher MDA contents and lower proline contents and SOD activities in leaves. Overexpressing GhCYTMS9 in Arabidopsis significantly increased the seed germination rates and root elongation at the germination stage. Compared with wild-type seedlings, GhCYSTM9-overexpressing seedlings presented lower MDA contents and greater proline contents in leaves under cold stress. Transcriptome analysis of transgenic Arabidopsis revealed that GhCYSTM9 may contribute to the cold response by regulating oxidative stress-related genes to mediate ROS levels. Yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that GhCYSTM9 interacted with the light-harvesting chlorophyll a/b-binding protein GhLHBC2A1.

CONCLUSIONS

Overall, our results revealed a positive role of GhCYSTM9 in cold stress defence and suggested candidate genes for the genetic breeding of cold defence.

Transposable Element Landscape in the Monotypic Species Barthea barthei (Hance) Krass (Melastomataceae) and Its Role in Ecological Adaptation

Transposable elements (TEs) are crucial for genome evolution and ecological adaptation, but their dynamics in non-model plants are poorly understood. Using genomic, transcriptomic, and population genomic approaches, we analyzed the TE landscape of Barthea barthei (Melastomataceae), a species distributed across tropical and subtropical southern China. We identified 64,866 TE copies (16.76% of a 235 Mb genome), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). A genome-wide analysis revealed 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response. We identified 3859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress response, and secondary metabolism. A transcriptome analysis of the flower buds identified 343 differentially expressed TEs between the ecotypes, 30 of which were near or within differentially expressed genes. The non-random distribution (primarily within 5 kb of genes) and association with adaptive traits suggest a significant role in B. barthei's successful colonization of diverse habitats. Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forests, particularly through their influence on regulatory networks governing stress response and development.

Dynamic molecular regulation of salt stress responses in maize (Zea mays L.) seedlings

Introduction

Maize ranks among the most essential crops globally, yet its growth and yield are significantly hindered by salt stress, posing challenges to agricultural productivity. To utilize saline-alkali soils more effectively and enrich maize germplasm resources, identifying salt-tolerant genes in maize is essential.

Methods

In this study, we used a salt-tolerant maize inbred line, SPL02, and a salt-sensitive maize inbred line, Mo17. We treated both lines with 180 mmol/L sodium chloride (NaCl) for 0 days, 3 days, 6 days, and 9 days at the three-leaf growth stage (V3). Through comprehensive morphological, physiological, and transcriptomic analyses, we assessed salt stress effects and identified hub genes and pathways associated with salt tolerance.

Results

Our analysis identified 25,383 expressed genes, with substantial differences in gene expression patterns across the salt treatment stages. We found 8,971 differentially expressed genes (DEGs)-7,111 unique to SPL02 and 4,791 unique to Mo17-indicating dynamic gene expression changes under salt stress. In SPL02, the DEGs are primarily associated with the MAPK signaling pathway, phenylpropanoid biosynthesis, and hormone signaling under salt treatment conditions. In Mo17, salt stress responses are primarily mediated through the abscisic acid-activated signaling pathway and hormone response. Additionally, our weighted gene co-expression network analysis (WGCNA) pinpointed five hub genes that likely play central roles in mediating salt tolerance. These genes are associated with functions including phosphate import ATP-binding protein, glycosyltransferase, and WRKY transcription factors.

Discussion

This study offers valuable insights into the complex regulatory networks governing the maize response to salt stress and identifies five hub genes and pathways for further investigation. These findings contribute valuable knowledge for enhancing agricultural resilience and sustainability in saline-affected environments.

Unveiling the secrets of lotus seed longevity: insights into adaptive strategies for extended storage

Seed longevity is crucial for long-term storage, but prolonged unfavorable conditions can lead to loss of viability. This study integrated theoretical and experimental techniques to elucidate the inherent mechanisms underlying the unique ability of lotus seeds to maintain stable viability over many years. Transcriptome analysis and microscopy revealed a sturdy structure of the lotus seed pericarp, which predominantly expressed cellulose synthase genes involved in cell wall biogenesis. The cotyledon serves as a nutrient source for seeds during long-term storage. Additionally, the inactivation of chlorophyll degradation pathways may allow for the retention of chlorophyll in the lotus seed plumule, potentially enhancing the environmental adaptability of lotus seedlings. Reduced abundance of transcripts corresponding to heat shock protein genes could impact protein processing and consequently diminish the vitality of aging lotus seeds. Moreover, an expansion in the number of seed maturation and defense response genes was observed in the lotus genome compared with 11 other species, which might represent an adaptive strategy against long-term adverse storage conditions. Overall, these findings are crucial for understanding the mechanisms underlying lotus seed longevity and may inform future improvements in the extended storage periods of seed crops.

Reduction of intestinal RIPK1 ameliorates HFD-induced metabolic disorders in female mice

In modern society, excessive nutrient intake from food is a major factor contributing to the development of a series of metabolic disorders and cardiovascular diseases. Further investigation of the mechanisms underlying nutrient absorption in the intestine will help to better understand and develop preventive or therapeutic strategies. In this study, using receptor-interacting protein kinase 1 (Ripk1) intestine-specific heterozygous knockout mice (Ripk1 IEC+/-) and high-fat diet (HFD)-feeding mouse model, we report that HFD-induced shift in the transcriptional profile of the ileum toward that of the jejunum, characterized by increased expression of jejunal feature genes in the ileum, are attenuated in Ripk1 IEC+/- female mice, but not in males. Accordingly, HFD-induced metabolic disorders, including obesity, impaired glucose tolerance, insulin resistance, and dyslipidemia, are significantly ameliorated in the Ripk1 IEC+/- female mice. These findings demonstrate a new, sex-specific intestinal regulatory mechanism and highlight the critical role of intestinal RIPK1 in regulating HFD-induced metabolic disorders in females.

miRNome analysis reveals mir-155-5p as a protective factor to dengue infection in a resistant Thai cohort

Dengue virus (DENV) is a global health threat, with approximately 390 million infections annually, ranging from mild dengue fever to severe dengue hemorrhagic fever and shock syndrome. MicroRNA (miRNA) are crucial post-transcriptional regulators which may regulate host resistance to DENV infection. This study aimed to identify miRNAs involved in natural resistance to DENV infection. Individuals from a dengue-endemic area were classified as susceptible (SD) or resistant (RD) according to their anti-DENV antibody status. RD individuals were seronegative despite high local DENV infection prevalence. Monocytes susceptibility to DENV infection was assessed in vitro. The miRNome profiles of the monocytes from 7 individuals per group were assessed upon mock or DENV-2 infection. The antiviral effect of differentially expressed miRNAs was analyzed using miRNA mimics in HeLa cells followed by infection with DENV-1, DENV-2, DENV-3, and DENV-4 serotypes. We performed RNA-seq on miRNA mimic-transfected cells to identify miRNA-targeted genes interacting with DENV proteins. Monocytes from RD individuals exhibit lower DENV-2 production in vitro. The miRNAs miR-155, miR-132-3p, miR-576-5p were overexpressed in monocytes from RD group upon DENV-2 infection. The transfection of miR-155-5p mimic reduced DENV infection and viral production in HeLa cells, regulating 18 genes interacting with DENV proteins and downregulating target genes involved in interferon response, TP53 regulation, apoptosis, and vesicle trafficking (e.g. HSD17B12, ANXA2). Therefore, we show that monocytes from RD individuals show a distinct miRNA expression profile and reduced viral production. In vitro miR-155-5p upregulation induces an antiviral state, revealing potential therapeutic targets to treat dengue.

β-lapachone suppresses carcinogenesis of cervical cancer via interaction with AKT1

Introduction

Cervical cancer is one of the most prevalent malignant tumors affecting women worldwide, and affected patients often face a poor prognosis due to its high drug resistance and recurrence rates. β-lapachone, a quinone compound originally extracted from natural plants, is an antitumor agent that specifically targets NQO1.

Methods

CC cells were treated with varying concentrations of β-lapachone to examine its effects on glucose metabolism, proliferation, metastasis, angiogenesis, and EMT in vitro. The targets and action pathways of β-lapachone were identified using network pharmacology and molecular docking, with KEGG pathway enrichment analysis. Its effects and toxicity were verified in vivo using a nude mouse xenograft model.

Results

β-lapachone significantly inhibited the proliferation and metastasis of cervical cancer cells by regulating glucose metabolism, reducing tumor angiogenesis, and suppressing epithelial-mesenchymal transition (EMT) in cells with high NQO1 expression. Furthermore, we identified the inactivation of the PI3K/AKT/mTOR pathway as the key mechanism underlying these effects. AKT1 was identified as a potential target of β-lapachone in modulating glucose metabolism and EMT in cervical cancer cells.

Conclusion

These findings suggest that β-lapachone inhibits the malignant progression of cervical cancer by targeting AKT1 to regulate glucose metabolism in NQO1-overexpressing cells, providing a theoretical basis for developing novel therapeutic strategies for cervical cancer.

Luteolin alleviates olfactory dysfunction in eosinophilic chronic rhinosinusitis through modulation of the TLR4/NF-κB signaling pathway

OBJECTIVES

Eosinophilic chronic rhinosinusitis (ECRS) is characterized by early, severe olfactory dysfunction and a high recurrence rate, with inadequate treatments. This article aims to elucidate the potential mechanisms by which luteolin may treat olfactory dysfunction in the context of ECRS.

METHODS

Thirty C57 BL/6 mice were randomly assigned to five groups: a control group and four experimental groups (ECRS, ECRS + Luteolin (Low, Medium, High Dose)). We conducted RNA sequencing, behavioral testing, ELISA, PCR, HE staining, Western blot analysis, and immunofluorescence staining. Additionally, human olfactory epithelial Cells (HOEPCs) were treated with Luteolin, TAK-242, QNZ, and Luteolin + LPS to investigate the underlying mechanisms.

RESULTS

Luteolin significantly reduced IL-4, IL-5, and IL-13 levels in the nasal lavage fluid (NLF) of ECRS mice, improving olfactory function and restoring OMP+ mature and Gap43+ immature olfactory sensory neurons (OSNs). RNA sequencing revealed the involvement of the TLR4/NF-κB pathway in ECRS-related olfactory dysfunction and luteolin's therapeutic effects. Luteolin reduced TLR4+ cells, P65 nuclear translocation, and decreased protein levels of IL-1β, TLR4, MyD88, p-P65, P65, and p-P38. The treatment also lowered OSNs cell apoptosis by decreasing the levels of cleaved caspase-3 and caspase-9 levels, and increasing Bcl-2 protein. Antioxidant enzymes SOD, CAT, and GSH-Px were elevated, while MDA levels decreased. In ECRS HOEPCs, luteolin's anti-apoptotic effects on OSNs were reversed by LPS-induced TLR4/NF-κB activation.

CONCLUSIONS

Luteolin ameliorates olfactory dysfunction associated with ECRS by modulating the TLR4/NF-κB signaling pathway. This modulation results in a reduction of TH2-type inflammation, oxidative stress, and apoptosis in OSNs.

Huqi formula suppresses hepatocellular carcinoma growth by modulating the PI3K/AKT/mTOR pathway and promoting T cell infiltration

BACKGROUND

Hepatocellular carcinoma (HCC) poses ongoing difficulties for public health systems due to its high incidence and poor prognosis. Huqi formula (HQF), a well-known prescription in traditional Chinese medicine, has demonstrated notable clinical effectiveness in the treatment of HCC. However, the mechanisms underlying its therapeutic effects have yet to be completely elucidated.

PURPOSE

This study aimed to investigate the anti-HCC effects of HQF and its underlying mechanisms.

METHODS

Chemical profiling and quantification of HQF were conducted by LC-MS and HPLC. Orthotopic and subcutaneous tumor models were established through hydrodynamic injection of Akt/Nras plasmids and subcutaneous injection of c-Met/sgPten cells, respectively, to evaluate the therapeutic effects of HQF on HCC. Network pharmacology, RNA-Seq, molecular docking, Western blot, and flow cytometry were employed to assess the anti-HCC mechanisms.

RESULTS

LC-MS analysis identified 41 components, with HPLC quantification showing salvianolic acid B as the most abundant compound (0.303%). In Akt/Nras and c-Met/sgPten-induced HCC models, HQF significantly reduced tissue damage, improved liver function, and inhibited HCC progression. Mechanistic studies revealed that HQF induced apoptosis in HCC cells by downregulating p-PI3K, p-AKT, and p-mTOR expression, with molecular docking indicating the strongest binding affinity between salvianolic acid B and PI3K. HQF further enhanced CD4+ and CD8+ T cell infiltration within the tumor microenvironment. When combined with PD-1 therapy, HQF improved therapeutic efficacy against HCC. Finally, toxicity assays confirmed the safety profile of HQF.

CONCLUSION

HQF demonstrated significant anti-HCC effects and a synergistic effect with PD-1, could be used as an alternative therapeutic agent for HCC.

Integration of Multiomics Data Reveals Selection Characteristics of ITGB1 That Are Associated with Size Differentiation in Pigs

Min pigs, a prominent local breed from Northeast China, have diverged into two distinct breeds, Ermin (EM) pigs and Hebao (HB) pigs, through prolonged natural and artificial selection. Although these two breeds exhibit distinct differences in body size, the genetic mechanisms underlying this variation remain poorly understood. In this study, we performed whole-genome resequencing and transcriptome analysis on EM and HB pigs to elucidate the genetic basis of body size variation in Min pigs through genome-wide selection signal analysis and the identification of differentially expressed genes (DEGs). The analysis of genetic diversity and population genetic structure across 14 pig breeds revealed that, compared with other breeds, Min pigs present relatively high genetic diversity and a unique genetic structure. Notably, EM pigs exhibited significant genetic differentiation from HB pigs. Integrated analysis of whole-genome resequencing and transcriptome data revealed candidate genes associated with body size variation in Min pigs, including ENPP1, ENPP3, SPP1, CLU, ITGA11, ITGB1, IQGAP2, BMP7, and F2RL2. These genes are enriched primarily in pathways related to ECM-receptor interactions; pantothenate and CoA biosynthesis; starch and sucrose metabolism; nicotinate and nicotinamide metabolism; pyrimidine metabolism; nucleotide metabolism; cellular responses to lipids; biomineral tissue development; biomineralization; and other pathways related to cell signaling, metabolic responses, lipid deposition, and skeletal development. Notably, ITGB1 on chromosome 10 showed strong positive selection in EM pigs, with an SNP locus exhibiting a significant G/A allele frequency difference between EM pigs (G = 52.94%, A = 47.06%) and HB pigs (G = 0%, A = 100%). Our findings suggest that Min pigs potentially modulate lipid metabolism efficiency in adipose tissue through variations in the expression of the ITGB1 gene, potentially contributing to body size differences. These results provide new insights into the genetic mechanisms underlying body size variation in domestic pigs and serve as a valuable reference for identifying and breeding pig breeds with distinct body sizes.

Single-nucleus transcriptomes reveal the underlying mechanisms of dynamic whitening in thermogenic adipose tissue in goats

BACKGROUND

Thermogenic adipose tissue, both beige and brown, experiences whitening as animals are exposed to warmth and age, but the potential mechanisms are not fully understood. In this study, we employed single-nucleus RNA-seq to construct a cell atlas during whitening progression and identified the characteristics of thermogenic adipocytes.

RESULTS

Our histological studies and bulk transcriptome gene expression analysis confirmed that both perirenal and omental adipose tissues (pAT and oAT) exhibited progressive whitening in goats. Compared to the classic brown adipocytes in mice, goat thermogenic adipocytes were more closely related in gene expression patterns to human beige adipocytes, which was also confirmed by adipocyte type- and lineage-specific marker expression analysis. Furthermore, trajectory analysis revealed beige- and white-like adipocytes deriving from a common origin, coexisting and undergoing the transdifferentiation. In addition, differences in gene expression profiles and cell communication patterns (e.g., FGF and CALCR signaling) between oAT and pAT suggested a lower thermogenic capacity of oAT than that of pAT.

CONCLUSIONS

We constructed a cell atlas of goat pAT and oAT and descripted the characteristics of thermogenic adipocytes during whitening progression. Altogether, our results make a significant contribution to the molecular and cellular mechanisms behind the whitening of thermogenic adipocytes, and providing new insights into obesity prevention in humans and cold adaptation in animals.

Genome-Wide Association Study Pinpoints Novel Candidate Genes Associated with the Gestation Length of the First Parity in French Large White Sows

Gestation length (GL) is a critical indicator of reproductive performance in sows and is closely associated with other reproductive traits, such as total number born (TNB) and number born alive (NBA). Despite its importance, the genetic mechanisms underlying GL and its impact on reproductive traits remain poorly understood. In this study, we investigated the relationship between GL and reproductive traits using 7013 farrowing records and conducted an imputed whole-genome sequence-based genome-wide association study (GWAS) for GL in first-parity sows, involving 3005 French Large White sows. Our findings revealed that the heritability of GL ranged from 0.22 to 0.26. Both excessively short and long GLs were associated with negative impacts on TNB, NBA, and other reproductive traits. A total of 64 SNPs exceeded the significance threshold, leading to the identification of two novel quantitative trait loci (QTLs) on chromosome 5 (QTL-1: 15.29-15.39 Mb and QTL-2: 12.86-12.94 Mb) and three promising candidate genes: TROAP, RFX4, and ADCY6. Gene ontology and KEGG pathway enrichment analyses revealed that these candidate genes are enriched in key biological processes, including ovarian steroidogenesis, the GnRH signaling pathway, and the regulation of cAMP biosynthesis, all of which are crucial for gestation and pregnancy maintenance. These findings improve our understanding of the genetic architecture of GL in sows and offer valuable genetic markers for enhancing reproductive efficiency in breeding programs.

Genome assembly, gene content, and plastic gene expression responses to salinity changes in the Brackishwater Clam (Corbicula japonica) from a dynamic estuarine environment

Estuaries are dynamic transition zones between marine and freshwater environments, where salinity varies greatly on spatial and temporal scales. The temporal salinity fluctuations of these habitats require organisms to rapidly regulate ionic concentrations and osmotic pressure to survive in these dynamic conditions. Understanding the extent of plasticity of euryhaline animals is vital for predicting their responses and resilience to salinity change. We generated the first high-resolution genome and transcriptome sequences of C. japonica. In comparison with 11 other molluscan genomes, the C. japonica genome displayed striking expansions of putative neuron-related genes and gene families. The involvement of these genes in the glutamate/GABA-glutamine and glycine cycle suggests a possible contribution to the excitation of neuronal networks, particularly under high salinity conditions. This study contributes to our understanding of mechanisms underlying the rapid responses of estuarine species to changing conditions and raises many intriguing hypotheses and questions for future investigation.

Better Transcriptomic Stability and Broader Transcriptomic Thermal Response Range Drive the Greater Thermal Tolerance in a Global Invasive Turtle Relative to Native Turtle

Greater thermal tolerance of invasive species benefits their survival and spread under extreme climate events, especially under global warming. Revealing the mechanisms underlying the interspecific differences in thermal tolerance between invasive and native species can help understand the invasion process and predict potential invaders. Here, we link the changes in global transcriptomics and antioxidant defense at multiple temperatures with the differences in thermal limits in the juveniles of a successful globally invasive turtle, Trachemys scripta elegans, and a native turtle in China, Mauremys reevesii. The two species show different thermal tolerances and have co-existed in habitats with the risk of overheating. The majority of the transcriptional response to thermal stress is conserved in the two turtle species, including protein folding or DNA damage responses activated under relatively moderate thermal stress and regulation of the cell cycle and apoptosis during severe thermal stress. Greater thermal tolerance of T. scripta elegans can be associated with a more stable global transcriptome during thermal stress, except for necessary stress responses, and a broader thermal range of continuous up-regulation of the core mechanisms promoting survival under thermal stress, mainly protein folding and negative regulation of apoptosis. Under extreme hot conditions, the opposite change trends of genes involved in survival mechanisms during thermal stress between invasive and native turtles can be due to differences in energy turnover. The present study provides insights into the mechanisms of physiological differences between invasive and native species given global transcriptional changes and helps understand successful invasion and predict potential invasive species.

Gyral peak variations between HCP and CHCP: functional and structural implications

Significant culture and ethnic diversity play an important role in shaping brain structure and function. Many attempts have been undertaken to connect ethnic variations with brain function, which, however, fluctuates over time and is costly, limiting its utility to identify consistent brain markers as well as its application to a broad population. In contrast, brain anatomy is less altered during a short period of time, but it is not fully understood whether it could serve as the ethnicity-sensitive landmark, or its variation is associated with functional one. In this study, We utilized gyral peaks, a set of early cortical folds, as cortical landmarks to explore the role of ethnic factors in brain anatomy and their relationship to brain function. Comparative experiments were conducted using the Human Connectome Project and the Chinese Human Connectome Project. In populations with similar ethnic backgrounds, gyral peak patterns showed greater consistency. For groups with significantly different ethnic backgrounds, we identified both shared peaks and peaks unique to each group. Compared to shared peaks, unique peaks showed significant differences in anatomical and functional network attributes and were spatially associated with working memory networks, which exhibited increased activation in their presence. Gene enrichment analysis provided additional support, suggesting that the unique peaks are associated with genes linked to working memory functions. These findings could provide new knowledge to understanding how ethnic diversity interplay with brain functions and associate with brain shapes.

ctdsp2 Knockout Induces Zebrafish Craniofacial Dysplasia via p53 Signaling Activation

Hemifacial microsomia (HFM) is a rare congenital craniofacial deformity that significantly impacts the appearance and hearing. The genetic etiology of HFM remains largely unknown, although genetic factors are considered to be primary contributors. We previously identified CTDSP2 as a potential causative gene in HFM cases. Utilizing CRISPR/Cas9, we knocked out ctdsp2 in zebrafish and analyzed the spatiotemporal expression of ctdsp2 and neural crest cell (NCC) markers through in situ hybridization (ISH). Craniofacial cartilage and chondrocyte phenotypes were visualized using Alcian blue and wheat germ agglutinin (WGA) staining. Cell proliferation and apoptosis were assessed via immunofluorescence with PH3 and TUNEL. RNA sequencing was performed on ctdsp2-/- embryos and control siblings, followed by rescue experiments. Knockout of ctdsp2 in zebrafish resulted in craniofacial defects characteristic of HFM. We observed abnormalities in NCC apoptosis and proliferation in the pharyngeal arches, as well as impaired differentiation of chondrocytes in ctdsp2-/- embryos. RNA-Seq analysis revealed significantly higher expression of genes in the p53 signaling pathway in mutants. Furthermore, ctdsp2 mRNA injection and tp53 knockout significantly rescued pharyngeal arch cartilage dysplasia. Our findings suggest that ctdsp2 knockout induces zebrafish craniofacial dysplasia, primarily by disrupting pharyngeal chondrocyte differentiation and inhibiting NCC proliferation through p53 signaling pathway activation.

Every Gain Comes With Loss: Ecological and Physiological Shifts Associated With Polyploidization in a Pygmy Frog

Polyploidization plays a pivotal role in vertebrate evolution and diversification. However, the effects of polyploidization on animals across various biological levels, and how these differences drive ecological shifts, remain unclear. Through karyotype analysis and whole-genome sequencing, we identified an autotetraploid Microhyla fissipes from Hainan Island, which shows reproductive isolation and geographic differentiation from its diploid counterpart. Tetraploids exhibited larger cell size, improved tadpole growth rates, and greater whole-body size, along with reduced cell cycle activity. Rather than being simple scaled-up diploids, tetraploids showed shifts in physiological performance, organ allometry, gene expression profiles, and metabolic patterns. Tetraploid adults demonstrated superior jumping ability and increased reproductive investment (e.g. larger gonads and steeper slopes in the relationship between gonadal weight and body weight), suggesting a potential competitive advantage over diploids. However, tetraploids exhibited higher energy expenditure at elevated temperatures, reduced hepatic energy storage, and altered pulmonary regulatory metabolites at 25 °C. Males had smaller relative heart sizes, and females showed flatter slopes in the relationship between heart and lung weight and body weight, indicating reduced investment in cardiopulmonary system. These variations suggest an increased risk of metabolic constraints under heat stress, putting tetraploids at a disadvantage in warmer regions. Importantly, the physiological tradeoffs associated with polyploidization help explain the geographical differentiation between diploids and tetraploids, which reflects a climatic boundary, with tetraploids occupying cooler northeastern areas. Our findings identify an autotetraploid frog, report the first autotetraploid genome in amphibians, and demonstrate how vertebrate polyploids physiologically and ecologically diverge from their diploid counterparts.

Omics Data Integration of Rhynchophorus Ferrugineus Reveals High-Potential Targeted Pathways for the Development of Pest Control Management

Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Dryophthoridae), commonly known as the red palm weevil (RPW), is a globally significant pest that threatens economically important palm trees. Its cryptic infestation behavior leads to irreversible damage and eventual host plant death. Current control methods using broad-spectrum insecticides are largely ineffective due to resistance development and their adverse effects on nontarget organisms, necessitating novel strategies. This study integrates proteomics and transcriptomics data to explore the molecular landscape of RPW and identify pathways for targeted pest management. A total of 16,954 transcripts and 983 proteins were identified across three developmental stages (larvae, male adults, and female adults), with a notable decline in protein numbers from larvae to adult. Differential expression analysis revealed 7540 proteins varying significantly between developmental stages. Through subtractive analysis, 218 proteins meeting stringent inclusion and exclusion criteria were identified. These proteins underwent pathway enrichment analysis, mapping to 39 enriched pathways (p-value and an FDR of < 0.01). Among these, two pathways involving three key enzymes were highlighted as high-potential targets for developing insect-specific insecticides and diet-specific control strategies. This is the first comprehensive proteomics study analyzing the whole body of RPW across its developmental stages. The findings emphasize critical pathways, their enzyme components, and the regulation of these enzymes, offering novel insights for sustainable and targeted pest management solutions.

The genomic landscape of short tandem repeats in cattle

Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5'UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (R = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes

Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.

Genomic insights into drought adaptation of the forage shrub Caragana korshinskii (Fabaceae) widely planted in drylands

The Korshinsk peashrub (Caragana korshinskii), known for its exceptional drought tolerance, is widely cultivated in arid and semi-arid regions for vegetation restoration and as a vital forage plant. To elucidate the genomic basis of its drought tolerance, we generated a chromosomal-scale genome sequence of C. korshinskii. Our synteny analysis disputes the previously hypothesized genus-specific whole-genome duplication event, as suggested by earlier transcriptome study of this species and its congeners. We identified that tandem duplications were critical for the expansion of gene families, such as early light-induced protein, heat shock protein 100, and Dehydrin, which are involved in cellular protection processes. These expansions are likely pivotal to the superior drought tolerance observed in C. korshinskii, as evidenced by the elevated gene expression of these genes under drought conditions. Furthermore, overexpression studies of seven tandemly duplicated DHN genes revealed a substantial enhancement in drought survival rates of seedlings, likely attributable to increased gene dosage effects. Conversely, gene silencing via virus-induced gene silencing demonstrated opposing effects. Additionally, we have established the CakorDB, a genomic resource database for C. korshinskii (https://bis.zju.edu.cn/cakordb/), accessible freely to the scientific community. Collectively, our study not only provides a valuable genomic resource for the Korshinsk peashrub but also highlights the genetic adaptations that enable C. korshinskii to thrive in desert environments, positioning its stress-responsive genes as a valuable genetic reservoir for breeding drought-resistant crops.

Molecular mechanisms of libido influencing semen quality in geese through the hypothalamic-pituitary-testicular-external genitalia axis

Libido plays a crucial role in influencing semen quality, yet the underlying regulatory mechanisms remain unclear. As a central axis in male goose reproduction, the hypothalamic-pituitary-testicular-external genitalia (HPTE) axis may contribute to the regulation of this process. In this study, we established a rating scale for goose libido based on average number of massages to erection (ANM) and the erection type, and evaluated semen quality across the entire flock. Correlation analyses showed that ANM was negatively correlated with sperm concentration (SC), acrosome integrity (AI), and semen quality factor (SQF), while positively correlated with morphological abnormal sperm (MAS) (P < 0.01). A comparison of semen quality and testicular histology between high libido (HG) and low libido (LG) groups showed that SC and SQF were significantly higher and MAS was lower in HG (P < 0.05). The lumen diameter of seminiferous tubules (LD) (P < 0.01) and the number of Sertoli cells (Sc) (P < 0.05) were also significantly greater in HG. Further, the number of spermatogonia (Sg) was significantly (P < 0.01) lower, and spermatocyte (Sp) and elongated spermatid (Se) were significantly higher in HG (P < 0.05). Through transcriptome sequencing (RNA-seq), we identified 98, 163, 2,474 and 400 differentially expressed genes (DEGs) in the hypothalamus, pituitary, testis and external genitalia, respectively. Gene Ontology (GO) analysis indicated that the term "male gonad development" was significantly enriched in the hypothalamus. Here, the expression of LHX9 was positively correlated with ANM, and negatively correlated with SC and SQF (P < 0.05). Additionally, WNT4 was positively correlated with ANM and MAS (P < 0.01), and negatively correlated with SC (P < 0.05), suggesting that LHX9 and WNT4 might serve as key upstream regulatory genes. Further analysis through Weighted Gene Co-Expression Network Analysis (WGCNA) showed that the yellow module (R = 0.89, P = 7e-09) was strongly associated with testicular development, with genes predominantly involved in male reproductive process. Based on these findings, we screened genes significantly correlated with LHX9 and WNT4 from the yellow module (|Cor |≥0.6, P < 0.05). These genes were significantly enriched in 8 pathways, primarily associated with metabolic processes, including drug metabolism - other enzymes, metabolism of xenobiotics by cytochrome P450, metabolic pathways, pyrimidine metabolism, glycerolipid metabolism, and riboflavin metabolism. Using the Maximal Clique Centrality (MCC) algorithm in the CytoHubba plug-in, SYCP3, DDX4, STRA8, AMH, MEIOB, CDT1, BCL2, PRIM1, and DLGAP5 were identified as hub genes. In conclusion, within the HPTE axis, libido might influence metabolism-related signaling pathways (mainly involving genes such as SYCP3, DDX4, STRA8, AMH, MEIOB, CDT1, BCL2, PRIM1, and DLGAP5) through LHX9 and WNT4 to regulate the development of the seminiferous tubules and germ cell number, ultimately affecting SC and MAS in geese. These findings offer practical insights into libido rating and shed light on the mechanisms by which libido regulates semen quality, potentially aiding in the improvement of goose breeding capacity.

Mild hypothermia therapy attenuates early BBB leakage in acute ischemic stroke

Reperfusion therapy inevitably leads to brain-blood barrier (BBB) disruption and promotes damage despite its benefits for acute ischaemic stroke (AIS). An effective brain cytoprotective treatment is still needed as an adjunct to reperfusion therapy. Here, we explore the potential benefits of therapeutic hypothermia (HT) in attenuating early BBB leakage and improving neurological outcomes. Mild HT was induced during the early and peri-recanalization stages in a mouse model of transient middle cerebral artery occlusion and reperfusion (tMCAO/R). The results showed that mild HT attenuated early BBB leakage in AIS, decreased the infarction volume, and improved functional outcomes. RNA sequencing data of the microvessels indicated that HT decreased the transcription of the actin polymerization-related pathway. We further discovered that HT attenuated the ROCK1/MLC pathway, leading to a decrease in the polymerization of G-actin to F-actin. Arachidonic acid (AA), a known structural ROCK agonist, partially counteracted the protective effects of HT in the tMCAO/R model. Our study highlights the importance of early vascular protection during reperfusion and provides a new strategy for attenuating early BBB leakage by HT treatment for ischaemic stroke.

TMT-Based quantitative proteomic analysis reveals age-related changes in eggshell matrix proteins and their correlation with eggshell quality in Xinyang blue-shelled laying hens

The decline in eggshell quality with increasing hen age may be related to changes in ultrastructure and chemical composition, with matrix proteins playing key roles in these changes. However, research on blue-shelled eggs remains limited. This study investigated the effects of hen age (35, 55, 75, and 85 weeks) on the physical, mechanical, and chemical properties of eggshells in the Xinyang blue-shelled laying hens, as well as their ultrastructural and nanostructural characteristics. Subsequently, a comparative proteomic analysis was performed to elucidate the differential protein profiles in eggshells from hens at 35 and 85 weeks of age. Results showed that egg weight, eggshell weight, and eggshell surface area increased with hen age, whereas eggshell stiffness decreased (p < 0.05). As the age advanced, the eggshell organic matter content declined (p < 0.05). The effective layer ratio, mammillae density, as well as the porosity and total pore area in the mammillary layer also decreased with age, whereas the ratio of the mammillary layer increased (p < 0.05). Compared to eggshells collected from 35-week-old hens, those from 85-week-old hens showed increases in egg weight, eggshell weight, surface area, and both the ratio and thickness of the mammillary layer (p < 0.05). However, significant decreases were observed in eggshell stiffness, organic matter content, phosphorus content, effective layer ratio, mammillae density, as well as the porosity and total pore area in the mammillary layer (p < 0.05). Additionally, eggshell stiffness, phosphorus content, and organic matter content were significantly correlated with each other (p < 0.05). Proteomic analysis identified 37 downregulated and 68 upregulated differentially expressed proteins (DEPs, FC > 1.2 or < 0.83, with a p-value < 0.05) in eggshells from 85-week-old hens compared to those from 35-week-old hens. These DEPs are associated with functions such as biomineralization, calcium transport, immunity, and proteases and protease inhibitors. Mantel and Pearson correlations suggest that these functions may be involved in regulating eggshell stiffness, phosphorus content, and organic matter content. Overall, the eggshell stiffness decreased from 35 to 85 weeks of age, which may be attributed to the reductions in eggshell organic matter and phosphorus contents, as well as the deteriorations in eggshell ultrastructure. The proteins associated with biomineralization, calcium transport, immunity, and proteases and protease inhibitors may contribute to these changes.

Revealing study and breeding implications for production traits and tail characteristics in Simmental cattle by GWAS

Simmental cattle are renowned for their dual purpose as meat and dairy breeds. The study recorded phenotype data from 183 Simmental cattle and performed a Genome-Wide Association Study (GWAS) analysis to elucidate the genetic mechanisms underlying milk production, body size traits, and tail characteristics. Statistical analysis of phenotype data showed that season, parity, and age at first calving (AFC) factors had a significant effect on milk production (P < 0.05). The results of GWAS on cattle linear traits revealed that the candidate genes SH3RF2, DCHS2, ADAMTS1, CAMK4, PPARGC1A, PRL, PRP6, and CORIN have been found to affect body circumference (BC) and cannon circumference (CC). Through GWAS analysis of tail traits, including Circumference over tail root (COTR) and Tail Length (TL) in Simmental cattle, candidate genes associated with tail length, such as KIF26B, ITPR2, SLC8A1, and SLIT3 were identified. Interestingly, candidate genes IL1RAP, AQP9, ITPR2, and PKD2 were also associated with metabolic inflammation in cattle tails. These genetic markers offer valuable insights into the traits of Simmental cattle, facilitating the development of molecular breeding strategies to enhance production value and provide references for breeding programs.

Jiedu Xiaozheng Yin extract targets cancer stem cells by Wnt signaling pathway in colorectal cancer

ETHNOPHARMACOLOGICAL RELEVANCE

The clinical application of the traditional Chinese medicinal formula Jiedu Xiaozheng Yin (JXY) for gastrointestinal tumors, particularly colorectal cancer (CRC), is well-established, yet the precise biological mechanism underlying its efficacy in CRC treatment remains elusive.

AIMS OF THE STUDY

This study endeavors to unravel the intricate mechanism through which JXY modulates colorectal cancer stem cells, thus elucidating the pathways by which it exerts its potent anti-tumor effects.

MATERIALS AND METHODS

In this study, the regulatory impact of JXY on the signaling pathway and function of CRC cells was analyzed through Network pharmacology. The ethyl acetate extract of JXY was detected the major compounds using HPLC and then treated the HCT-116 cells for RNA-Sequencing (RNA-Seq). Protein expression and stemness of HCT-15 and HCT-116 cells following JXY extract treatment were assessed using Western blot analysis and matrigel spheroid assays. Additionally, the β-catenin transcriptional activity was evaluated using a TOPflash reporter assay with or without Lithium chloride (LiCl) stimulation. Patient-derived organoids of CRC (CRC PDOs) were cultured using a stemness maintenance medium, and their viability was measured using ATP assays after treatment of JXY extract. Furthermore, the anti-tumor efficacy of JXY extract was assessed using a xenograft mice model derived from HCT-15 cells.

RESULTS

Network pharmacology emphasized the influence of JXY on cancer stem cells and the Wnt signaling pathway. HPLC analysis confirmed that the JXY extract contained the three most prevalent pharmaceutical compounds among the four herbs documented in the Chinese Pharmacopoeia (rosmarinic acid, quercetin, and kaempferol). RNA-Seq results further elucidated the effect of JXY extract, particularly targeting cancer stem cells and the Wnt signaling pathway. Furthermore, JXY extract inhibited spheroid formation in CRC cells and downregulated CRC CSC markers (CD133, DCLK1, and C-MYC). Additionally, JXY extract suppressed the β-catenin expression and transcriptional activity as well as the Wnt pathway target proteins, including C-MYC and Cyclin D1. Consistent with findings from cell lines, JXY extract suppressed the growth of CRC PDOs exhibiting stemness characteristics. And JXY extract demonstrated a significant inhibitory effect on tumor growth, C-MYC, and β-catenin protein levels in xenograft tumors.

CONCLUSIONS

These results highlight the novel function of JXY extract in targeting CRC CSCs by regulating Wnt signaling pathway, underscoring its potential as a therapeutic agent for treating CRC.

The Masculinizing gene is a candidate male pathway developmental factor in the mud crab Scylla paramamosain

The Masculinizer (Masc) gene plays a crucial role in masculinization during insect embryonic gonadal development. Nevertheless, the Masc expression pattern and function in crabs remain largely unknown. In the present study, we screened and validated the Masc gene from transcriptome data of mud crab S. paramamosain. The Masc relative transcript level in the testis was significantly higher than that of ovaries and other tissues, as measured by quantitative real-time PCR. In situ hybridization showed that Masc exhibited a significant signal throughout all stages of testicular development. The phylogenetic analysis revealed conservation in the evolution of crustaceans, potentially indicating its functional importance. Masc RNA interference showed that the expression of testis bias-related genes decreased significantly while the ovary bias-related genes increased significantly. Transcriptome data suggested that Masc regulates several signaling pathways, including the mTOR, Wnt, insulin, and other sex-related pathways. These results indicate that Masc may play a role in mud crab male development with possible application in sex control in aquaculture.

A comprehensive allele specific expression resource for the equine transcriptome

BACKGROUND

Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression.

RESULTS

An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were located in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE.

CONCLUSIONS

This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.

Quercetin, a natural flavonoid induced by the spider mite Tetranychus urticae or alamethicin, is involved in the defense of lima bean against spider mites

BACKGROUND

Phaseolus lunatus, commonly known as the lima bean, is a leguminous crop cultivated in various regions worldwide. It is native to tropical America and is extensively grown in both tropical and temperate climates. Lima beans are highly nutritious and versatile, serving not only as a food and vegetable, but also as a source of green manure. During cultivation, lima beans can be vulnerable to numerous pests, including the spider mite, Tetranychus urticae. In large-scale outbreaks, T. urticae can cause significant yield losses or even crop failure, posing a serious threat to agricultural production. The treatment of lima bean plants with T. urticae or alamethicin (ALA) has been shown to enhance their insect-resistant defense responses. Understanding the transcriptional and metabolic mechanisms underlying these defense responses to T. urticae and ALA is crucial for improving herbivore resistance in lima bean crops.

RESULT

By integrated analysis of transcriptomics and metabolomics data, we found that both T. urticae and ALA treatments significantly induced the flavonoid biosynthesis pathway. Both treatments increased the flavonoid content in lima bean leaves by upregulating the expression of key genes in this pathway, potentially contributing to enhanced resistance to phytophagous insects. Notably, quercetin has been shown to reduce the number of eggs per female and survival rate of T. urticae.

CONCLUSION

These findings provide a novel theoretical basis for understanding the response mechanisms of lima beans to T. urticae and ALA, while highlighting potential metabolites and genes that could be targeted to improve plant resistance to spider mite damage. © 2025 Society of Chemical Industry.

Highly efficient construction of monkey blastoid capsules from aged somatic cells

Blastoids-blastocyst-like structures created in vitro-emerge as a valuable model for early embryonic development research. Non-human primates stem cell-derived blastoids are an ethically viable alternative to human counterparts, yet the low formation efficiency of monkey blastoid cavities, typically below 30%, has limited their utility. Prior research has predominantly utilized embryonic stem cells. In this work, we demonstrate the efficient generation of blastoids from induced pluripotent stem cells and somatic cell nuclear transfer embryonic stem cells derived from aged monkeys, achieving an 80% formation efficiency. We also introduce a hydrogel-based microfluidics platform for the scalable and reproducible production of size-adjustable, biodegradable blastoid capsules, providing a stable 3D structure and mechanical protection. This advancement in the high-efficiency, scalable production of monkey blastoid capsules from reprogrammed aged somatic cells significantly enhances the study of embryonic development and holds promise for regenerative medicine.

Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958

Drought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. In this study, 2,911 genes, 32 conserved miRNAs, and 12 novel miRNAs showed a significantly differential expression under drought stress. Moreover, 6,340 target genes of 445 miRNAs were validated using degradome sequencing, forming 281 miRNA-mRNA pairs in control (CK) and drought-stressed (DS) library. These target genes were mainly involved in the plant hormone signal transduction and phenylpropanoid biosynthesis pathways. The integrated multi-omics analysis revealed that five DEmiRNA-mRNA pairs displayed negatively correlated expression patterns, which were also verified by qRT-PCR. Tissue-specific expression profile and regulatory network analysis revealed that miR528a/b-Zm00001d021850, miR408a/b-Zm00001d020794, and miR164e-Zm00001d003414 might be essential in root-specific drought stress response of maize Zhengdan958 seedlings. These worthwhile will promote the functional characterization of miRNA-mRNA modules response to drought stress, and potentially contribute to drought-resistance breeding of maize.