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

Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae

To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.

Gene co-expression patterns shared between chemobrain and neurodegenerative disease models in rodents

Chemotherapy-related cognitive impairment (CRCI), is a well-recognized phenomenon in cancer patients who have undergone chemotherapy but the exact molecular mechanisms underpinning CRCI remain elusive. Symptoms reported by people with CRCI resemble those experienced by people with age-related neurodegenerative disorders (ARNDDs), yet no clear connection between CRCI and ARNDDs has been reported to date. The existence of shared mechanisms between these conditions offers opportunities for repurposing drugs already approved for the treatment of ARNDDs to improve symptoms of CRCI. Given that there is no available microarray or RNA-Seq data from the brains of people who have experienced CRCI, we investigated to what extent brain gene expression perturbations from validated rodent models of CRCI induced by chemotherapy compared with validated rodent models of Alzheimer's disease and Parkinson's disease. We utilized multiple bioinformatic analyses, including functional enrichment, protein-protein interaction network analyses, gene ontology analyses and identification of hub genes to reveal connections between comparable gene expression perturbations observed in these conditions. Collectively 165 genes overlapped between CRCI and Parkinson's disease and/or Alzheimer's disease, and 15 overlapped between all three conditions. The joint genes between Alzheimer's disease, Parkinson's disease and CRCI demonstrate an average of 83.65% nucleotide sequence similarity to human orthologues. Gene ontology and pathway enrichment analyses suggest mechanisms involved in neural activity and inflammatory response as the key components of the studied neuropathological conditions. Accordingly, genes in which expression was comparably affected in all three condition models could be attributed to neuroinflammation, cell cycle arrest, and changes in physiological neural activity.

Effect of Low-Intensity Pulsed Ultrasound on Post-Traumatic Intra-Articular Knee Adhesions in Rats

OBJECTIVE

Intra-articular adhesions (IAA) caused by trauma or surgical invasion commonly elicit pain and motor dysfunction. However, effective treatments for preventing IAA remain elusive. This study investigated the effects of low-intensity pulsed ultrasound (LIPUS) therapy on IAA after immobilization following trauma.

METHODS

A knee adhesion model was established in male Wistar rats, which were divided into LIPUS and sham groups. LIPUS was applied for 20 min/d (30 mW/cm2 [spatial average temporal average], 1 MHz, duty cycle 20%, 5 times/wk, for 1, 2 and 3 wk). Another group of rats was treated with the same parameters for 3 or 7 d. After the treatment period, we evaluated the range of motion (ROM) of the knee joint, the length of the adhesion and the posterior knee joint capsule. RNA-seq and RT-quantitative polymerase chain reaction were performed to investigate the molecular mechanisms underlying the effects of LIPUS.

RESULTS

The knee ROM was significantly improved, and the adhesion length was reduced in the LIPUS group. RNA-seq identified 113 and 776 differentially expressed genes on days 3 and 7, respectively, highlighting pathways related to inflammatory, immune and fibrotic responses. IL-6 mRNA in the LIPUS group was significantly upregulated on day 3 and significantly downregulated at 1 wk. The TNFα, TGFβ and HIF1α levels did not differ between all groups. COL1A1 expression in the sham group significantly increased on day 7.

CONCLUSION

These results indicate that LIPUS therapy may affect inflammatory and fibrotic pathways and may serve as a rehabilitation approach to prevent the development of IAA.

Chromosome-level genome assembly and annotation of the maize weevil (Sitophilus zeamais Motschulsky)

The maize weevil, Sitophilus zeamais Motschulsky, is one of the most destructive pests of stored grains worldwide, posing a significant threat to global food security. To better understand the biology, resistance mechanism, and adaptive evolution of this species, we presented a high-quality chromosome-level genome assembly of S. zeamais using PacBio sequencing and Hi-C technologies. The size of the final assembled genome was 693.21 Mb with scaffold N50 of 61.03 Mb, and 631.97 Mb were successfully anchored into 11 pseudochromosomes. In total, 15,161 protein-coding genes were annotated, of which 98.89% obtained functional descriptions. Additionally, 377.50 Mb of sequences were identified as repeat elements, accounting for 54.46% of the genome. BUSCO analysis revealed a high level of completeness in both the genome assembly and annotation, with scores of 98.17% and 97.22%, respectively. The chromosome-level genome of S. zeamais provides valuable genomic insights that deepen our understanding of the evolution and ecology of Sitophilus species, while also contributing to the development of targeted and innovative control strategies for stored-product pests.

Transcriptomic Profiling of Quinoa Reveals Distinct Defense Responses to Exogenous Methyl Jasmonate and Salicylic Acid

Plant defense responses are mediated by hormones such as jasmonic acid (JA) and salicylic acid (SA). JA and SA are known to trigger a range of different defense responses in model plants but little is described in crops like quinoa. Here, we present the first molecular description of JA and SA signaling at the transcriptomic level in quinoa. The transcriptomes of quinoa cv. Kurmi seedlings treated with 100 µM methyl JA or 1 mM SA for 4 h were analyzed, using on average 4.1 million paired-end reads per sample. Quinoa plants treated with JA showed 1246 differentially expressed (DE) genes and plants treated with SA showed 590 DE genes. The response to JA included the induction of genes for the biosynthesis of JA (8/8 genes) and lignin (10/11 genes), and displayed a strong association with treatments with Trichoderma biocontrol agents. The SA treatment triggered the upregulation of genes for the biosynthesis of monoterpenoids and glucosinolates, both having defense properties. Overall, this suggest that JA and SA promotes the biosynthesis of lignin polymers and chemical defense compounds, respectively. Overall, the DE genes identified can be used as molecular markers in quinoa for tracking plant-hormone pathway involvements in defense responses.

Developmental landscape and asymmetric gene expression in the leaf vasculature of Brassica rapa revealed by single-cell transcriptome

Leaf vasculature not only acts as a channel for nutrients and signaling information but also influences leaf morphology. It consists of several distinct cell types with specialized functions. Cell type-specific characterizations based on single-cell RNA sequencing technology could aid in understanding the identities of vascular tissues and their roles in leaf morphogenesis in Brassica rapa. Here, we generated a single-cell transcriptome landscape of the Chinese cabbage leaf vasculature. A total of 12 cell clusters covering seven known cell types were identified. Different vascular cell types were characterized by distinct identities. The xylem parenchyma and companion cells exhibited an active expression pattern of amino acid metabolism genes. Tracheary elements and sieve elements were enriched in many genes related to cell wall biosynthesis, and the phloem parenchyma was enriched in many sugar transporter-encoding genes. Pseudo-time analyses revealed the developmental trajectories of the xylem and phloem and the potential roles of auxin and ethylene in xylem development. Furthermore, we identified key candidate regulators along the differentiation trajectory of the sieve elements and companion cells. Most of the homoeologous genes in the syntenic triads from the three subgenomes showed asymmetric gene expression patterns in different vascular cell types. Collectively, our study revealed that Chinese cabbage leaf vasculature cells had highly heterogeneous transcriptomes, providing new insights into the complex processes of leaf vasculature development in B. rapa leafy vegetables and other Brassica crops.

Qarles: a web server for the quick characterization of large sets of genes

The characterization of gene sets is a recurring task in computational biology. Identifying specific properties of a hit set compared to a reference set can reveal biological roles and mechanisms, and can lead to the prediction of new hits. However, collecting the features to evaluate can be time consuming, and implementing an informative but compact graphical representation of the multiple comparisons can be challenging, particularly for bench scientists. Here, I present Qarles (quick characterization of large sets of genes), a web server that annotates Saccharomyces cerevisiae gene sets by querying a database of 31 features widely used by the yeast community and that identifies their specific properties, providing publication-ready figures and reliable statistics. Qarles has a deliberately simple user interface with all the functionality in a single web page and a fast response time to facilitate adoption by the scientific community. Qarles provides a rich and compact graphical output, including up to five gene set comparisons across 31 features in a single dotplot, and interactive boxplots to enable the identification of outliers. Qarles can also predict new hit genes by using a random forest trained on the selected features. The web server is freely available at https://qarles.org.

Expression of poplar sex-determining gene affects plant drought tolerance and the underlying molecular mechanism

It is frequently observed that plant sexes differ in their response to environmental stress. Poplars are dioecious plants, and sex separation of poplars is triggered by the sex-limited expression of the poplar sex-determining gene FERR. In this study, we over-expressed FERR in a male poplar and knocked it out in a female poplar. The over-expression lines exhibited distinct morphological and physiological changes rendering the transformed plants more tolerant to drought stress. By contrast, no obvious change in drought tolerance was observed in the knockout lines. Transcriptome sequencing and molecular interaction analysis demonstrated that the effect of FERR on drought tolerance was conferred by competitive interaction with protein phosphatase 2C and SNF1-related protein kinase 2 (SnRK2). Under drought stress, an FERR-SnRK2s-ARR5 complex forms and activates the ABA signaling pathway. Our results provide direct evidence that the expression of the poplar sex-determining gene pleiotropically affects plant drought tolerance.

The enigma of introns: Intronic miRNA-directed mechanisms and alternative splicing diversify alternative oxidase potential in Vitis vinifera

Alternative oxidase (AOX) transcript levels were associated with efficiently balanced respiration and validated to assist selection on multiple-resilience. Consistently, AOX has also been identified as a target for weakening the survival capabilities of parasites and microorganisms responsible for severe human diseases. Despite the unique features of AOX in Vitis vinifera, particularly intense constitutive expression of AOX2 in the presence of unusually large introns that challenge the dogma of gene expression in eukaryotes, V. vinifera has been overlooked in AOX research. This study uncovered two distinct alternative splicing variants of the AOX: AOX1a-Alternative variant attributed to unusual retention of the intron-4 in the 3´UTR, and AOX2-Alternative variant, which is intron-1-dependent, involving the skipping of exon-1. The AOX2-Alternative variant differed in that cystine-I changed to serine, which is linked to different metabolite stimulation. However, molecular docking suggested that AOX2 and the variant proteins exhibit the same catalytic activities and binding affinities for ubiquinol. The unique large introns in AOX2 exhibited 16 miRNAs, including the master regulator of development and stress responses, mir-398. Among these, nine were conserved and validated in other plant species, whereas seven were considered potential novel miRNA candidates. Transcriptome analyses revealed down- and up-regulation of AOX1a-Alternative during shrivelling and water deficiency, and up-regulation of AOX2-Alternative with increasing temperatures. Consistent with previous studies, AOX1a and AOX1d were linked to biotic and abiotic stress, whereas AOX2 showed constitutive or developmental regulation. This study encourages hypothesis-driven advanced research on early mechanisms and functionality of newly discovered alternative splicing events and intronic miRNAs. Given functional marker-assisted breeding, it strengthened the requirement to consider overall AOX transcript levels as markers for predicting multiple-resilient phenotypes.

Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that diversifies gene expression by generating messenger RNA isoforms with varying 3' untranslated regions. Accurate identification and quantification of transcriptome-wide polyadenylation site (PAS) usage are essential for understanding APA-mediated gene regulation and its biological implications. In this review, we first review the landscape of computational tools developed to identify APA events from RNA sequencing (RNA-seq) data. We then benchmarked five PAS prediction tools and seven APA detection algorithms using five RNA-seq datasets derived from clear cell renal cell carcinoma (ccRCC) and adjacent normal tissues. By evaluating tool performance across genes with either single or multiple PASs, we revealed substantial variation in accuracy, sensitivity, and consistency among the tools. Based on this comparative analysis, we offer practical guidelines for tool selection and propose considerations for improving APA detection accuracy. Additionally, our analysis identified CCNL2 as a candidate gene exhibiting significant APA regulation in ccRCC, highlighting its potential as a disease-associated biomarker.

Deubiquitinating enzyme USP2 regulates brown adipose tissue thermogenesis via controlling EBF2 stabilization

OBJECTIVE

The activation of brown adipose tissue (BAT) promotes energy expenditure is recognized as a promising therapeutic strategy for combating obesity. The deubiquitinating enzyme family members are widely involved in the process of energy metabolism. However, the specific deubiquitinating enzyme member that affects the BAT thermogenesis remains largely unexplored.

METHODS

Adeno-associated virus, lentivirus and small molecule inhibitor were applied to generate USP2 gain- or loss-of-function both in vivo and in vitro. OxyMax comprehensive laboratory animal monitoring system, seahorse and transmission electron microscopy were used to determine the energy metabolism. Quantitative proteomics, immunofluorescence staining and co-immunoprecipitation were performed to reveal the potential substrates of USP2.

RESULTS

USP2 is upregulated upon thermogenic activation in adipose, and has a close correlation with UCP1 mRNA levels in human adipose tissue. BAT-specific Usp2 knockdown or systemic USP2 inhibition resulted in impaired thermogenic programs both in vivo and in vitro. Conversely, overexpression of Usp2 in BAT conferred protection against high-fat diet-induced obesity and associated metabolic disorders. Proteome-wide analysis identified EBF2 as the substrate of USP2 that mediates the thermogenic function of USP2 in BAT.

CONCLUSIONS

Our data demonstrated the vital role of USP2 in regulating BAT activation and systemic energy homeostasis. Activation of USP2-EBF2 interaction could be a potential therapeutic strategy against obesity.

Dataset of a de novo transcriptome assembly for the leaves and rhizomes of a five-year-old Atractylodes chinensis

Atractylodes (A.) chinensis (DC.) Koidz. is a traditional Chinese medicinal plant. The rhizome contains its medicinal component, which consists of abundant essential oils. Sesquiterpene and atractylodin are the main active ingredients in these essential oils. On the other hand, the leaves contain less medicinal active ingredients. Thus far, studies on the formation mechanism of the active ingredients, especially atractylodin, are still limited. This study used RNA sequencing to reveal the de novo transcriptome of the leaves and rhizomes of a five-year old A. chinensis plant with divided leaves. High-throughput sequencing data was acquired using the Illumina NovaSeq X Plus system (Illumina, USA) in PE150 mode. After the data was corrected and filtered, the clean data was used for subsequent analysis. Based on the assembled sequence file, the differentially expressed unigenes between the rhizomes and leaves of A. chinensis were analyzed. The assembled unigene file and table including these differentially expressed unigenes was deposited in the "Mendeley Data" database. The raw SRA data was deposited in the National Center of Biotechnology Information (NCBI) Sequence Read Archive (SRA) database.

Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data

The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.

Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations

Human mediated intra-continental exchange of genetic material among domesticated organisms has never been restricted to a single direction. The introduction of pig breeds between China and Europe aims to enhance economically important traits in local populations. However, the reciprocal introgression pattern, specifically the role of introgressed genes and structural variations (SVs), remains underexplored. A global collection of whole-genome resequencing data is utilized from 418 pigs to generate comprehensive dataset, including single-nucleotide polymorphisms (SNPs) as well as SVs. The analysis reveals incomplete linkage disequilibrium between SVs and adjacent SNPs, highlighting the limitations of conventional SNP-based analyses in capturing the genetic effects of SVs. By examining both population-level SNPs and SVs, bidirectional introgression between Chinese and European pig populations is characterized. It is identified 3558 bidirectional introgressed genomic segments and 30 SVs, with haplotypes at BMP2, which are associated with improved body size. The origin and allele frequency trajectory of the BMP2 segment are further validated using ancient genomes, suggesting that the body size-enhancing haplotype likely originated from ancient European populations and has since maintained a relatively high allele frequency. Overall, the results highlight the significant role of bidirectional introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.

Proteomic insights into cell signaling and stress response mechanisms in Chaetoceros muelleri under nitrogen limitation

Microalgae are often called "green factories" because they can perform photosynthesis, converting sunlight into biomass and high-value metabolites. Nitrogen concentration is a critical factor influencing protein accumulation. Unfortunately, nitrogen deprivation often negatively impacts biomass production. Understanding the relationship between nitrogen concentration and protein accumulation is crucial for harnessing the potential of microalgae in various industries and addressing environmental challenges. Here, we quantitatively compared the proteomic profiles of Chaetoceros muelleri diatom, grown in two Nitrogen-deficient conditions and control treatment by employing a Tandem Mass Tag-based quantitative proteomic approach. Proteins involved in photosynthesis were differentially accumulated under moderately nitrogen-deficient conditions. In contrast, proteins involved in cell signaling and protection mechanisms were differentially accumulated under severely nitrogen-limited conditions. Proteins associated with nitrogen metabolism, carbohydrate metabolism, and protein biosynthesis were differentially decreased in severely nitrogen-limited conditions, indicating differential response mechanisms of C. muelleri to varying nitrogen conditions. Our results show that C. muelleri employs distinct strategies in response to nitrogen limitation. These results provide valuable insights into the adaptive strategies of C. muelleri under nitrogen limitation, offering potential applications in optimizing microalgal cultures for the enhanced production of target metabolites in industrial bioreactors. BIOLOGICAL SIGNIFICANCE: The marine diatom Chaetoceros muelleri accumulates lipids and carbohydrates under low nitrogen conditions without affecting its biomass. Response to nitrogen limitation in C. muelleri was examined by isobaric labelling-based proteomics. We identified changes mainly focused on photosynthesis pathways, cell signaling and protection mechanisms, nitrogen and carbohydrate metabolism, as well as protein biosynthesis. Our results indicate that C. muelleri activate unique strategies in response to different nitrogen concentrations, and this differential response represents a key factor for inducing metabolite accumulation without affecting biomass production.

FTO regulates ELK3-mediated metabolic rewiring and represents a unique therapeutic target in T cell leukemia

Understanding the regulation of N6-methyladenosine (m6A), the prominent internal modification in mRNA, fosters the development of potential therapeutic strategies for human cancers. While the m6A demethylases FTO and ALKBH5 are recognized for their crucial roles in various cancers, their impact on lymphoid leukemia remains uncertain. Using T cell acute lymphoblastic leukemia (T-ALL) as a model system, we identify FTO as a unique vulnerability in T cell leukemia. Knockout of FTO, but not ALKBH5, significantly suppresses leukemia initiation and progression. Mechanistic analysis reveals that FTO heightens ELK3 mRNA stability in an m6A-dependent manner. Elevated ELK3 in turn transcriptionally activates the expression of glycolytic genes. Pharmacological inhibition of FTO suppresses ELK3 expression, hampers glycolysis and manifests remarkable antileukemia efficacy. Our findings unravel the crucial role of FTO in T-ALL and highlight the FTO-ELK3 axis as a key nodule during leukemogenesis, thereby providing a fundamental basis to harness selective FTO antagonist for T-ALL therapeutics.

A meta-analysis of genome-wide association studies revealed significant QTL and candidate genes for loin muscle area in three breeding pigs

Loin muscle area (LMA) is an important production trait in pigs and is highly correlated with lean meat percentage. However, the genetic architecture of LMA has not yet been fully elucidated. This study conducted genome-wide association studies (GWAS) and meta-analyses of LMA in Duroc (n = 337), Landrace (n = 662), and Yorkshire pigs (n = 3,176) using imputed whole-genome sequencing to identify new QTLs and candidate genes associated with LMA traits. A total of 108, 34, and 232 significant variants were identified in the Duroc, Landrace, and Yorkshire populations, respectively. The meta-analysis revealed 143 genome-wide significant SNPs and 276 suggestive SNPs, among which 213 were not identified in single population GWAS. Notably, 229 and 413 SNPs were located on SSC16 in the Yorkshire population and meta-analysis, respectively. Based on the 2-LOD drop-off interval, the SSC16 QTL in the Yorkshire population was further narrowed to a 679.835 kb interval (from 32.818 Mb to 33.498 Mb). The most significant variant within this QTL, 16_33228254 (P = 4.45 × 10-9), explained 1.11% phenotypic variance, representing a potential novel locus for LMA. Further bioinformatics analysis determined seven promising candidate genes (NDUFS4, ARL15, FST, ADAM12, DAB2, PLPP1, and SGMS2) with biological processes such as myoblast fusion and positive regulation of transforming growth factor beta receptor signaling pathway. Among them, ARL15 was previously reported in LMA studies, while the other six genes represent novel candidate genes. These findings reveal potential functional genes and pathways associated with LMA, providing valuable insights for future genetic improvement in pigs.

Integrating multi-omics and biomarkers to reveal the stress mechanisms of high fluoride on earthworms

Excessive fluorine accumulation poses a significant threat to soil ecology and even human health, yet its impact on soil fauna, especially earthworms, remains poorly understood. This study employed multi-omics and biomarkers to investigate high fluorine-induced biochemical changes that cause tissue damages in Eisenia fetida. The results demonstrated that earthworms exhibited obvious damage with fluorine addition exceeding 200 mg kg-1, with stress levels escalating as fluorine contents increased. Further analysis of the underlying mechanisms revealed that fluorine could upregulate genes encoding mitochondrial respiratory chain complexes I-III and downregulate those for IV-V, leading to reactive oxygen species (ROS) accumulation despite antioxidant system activation. The resulting ROS interfered with deoxyribonucleoside triphosphate synthesis, prompting homologous recombination as the main DNA repair mechanism. Additionally, fluorine-induced ROS also attacked and disrupted protein and lipid related metabolisms ultimately causing oxidative damages. These cumulative oxidative damages from high fluorine contents subsequently triggered autophagy or apoptosis, resulting in tissue ulceration and epithelial exfoliation. Therefore, high fluorine could threaten earthworms by inducing ROS accumulation and subsequent biomolecule damages.

Differential Methylation Analysis of Hypermelanosis in Chinese Tongue Sole (Cynoglossus semilaevis)

Hypermelanosis on the blind side is a major concern in tongue sole (Cynoglossus semilaevis) aquaculture in China and causes great economic loss for farmers. To investigate the relationship between DNA methylation and hypermelanosis, different skin tissues on both the ocular and blind sides of both normal and hypermelanotic fish were used in this study, and set analysis was utilized to narrow and filter the possible, potential, and direct differentially methylated regions (DMRs). A total of 2278, 1015, and 6740 DMRs were discovered, which belonged to 1786, 908, and 4210 genes, for possible, potential, and direct methylation types, respectively. Enrichment analysis revealed that the genes harboring DMRs associated with hypermelanosis were involved in the development of the skeletal system and embryonic organs during morphogenesis. Tens of key genes were mutually found by comparing methylation results with reported transcriptomic, ncRNA, and genetic studies. These results implied that hypermelanosis on the blind side in tongue sole is a complex trait that is affected by both genetic factors and environmental conditions and is regulated by a complicated gene network.

SRSF10 regulates oligodendrocyte differentiation during mouse central nervous system development by modulating pre-mRNA splicing

We characterized the role and regulation mechanism of a pre-mRNA splicing factor, SRSF10, in the development of oligodendrocyte lineage cells (OLCs) and the myelination process during mouse central nervous system (CNS) development. We found that depletion of SRSF10 specifically in OLCs induces hypomyelination and a decrease in OLCs in the developing mouse CNS, whereas depletion of SRSF10 only in differentiated OLCs does not significantly affect these processes. More detailed in vivo and in vitro analyses revealed that SRSF10 primarily regulates the earlier differentiation stages of OLCs, while the proliferation and apoptosis of OLCs were not affected. Mechanistically, RNA-seq and RIP-Seq transcript analyses identified a series of genes whose alternative splicing (AS) was directly regulated by SRSF10. Among these genes, compensating for the AS phenotype of Myo5a using antisense oligonucleotides (ASOs) reversed the inhibition of OLCs differentiation induced by SRSF10 depletion. In summary, we revealed for the first time that SRSF10 is a key regulator in the early differentiation of OLCs, likely via modulating the AS patterns of target genes such as Myo5a. This research provides significant implications for understanding OLC development and exploring potential therapeutic strategies for dysmyelination-related diseases.

Meiosis-associated expression patterns during starvation-induced cell fusion in the protist Fisculla terrestris

BACKGROUND

Unicellular eukaryotes were widely considered to r eproduce without sex. However, recent findings suggest that meiosis, and by extension (sometimes cryptic) sexual reproduction, might be present in almost all eukaryotic lineages.

RESULTS

Here, we investigate the transcriptomic response underlying starvation-induced fusion in the Rhizaria protist Fisculla terrestris. Investigations of differentially expressed genes (DEGs) with a particular focus on the expression of meiosis-associated genes suggest that some form of meiosis and recombination might occur in these Rhizaria.

CONCLUSIONS

We showed that starvation triggered changes in gene expression of meiosis-associated genes in F. terrestris. However, if these processes are coupled with sexual reproduction remains to be investigated.

Syntaxin-6 restricts SARS-CoV-2 infection by facilitating virus trafficking to autophagosomes

Despite the diminishing global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus continues to circulate and undergo mutations, posing ongoing challenges for public health. A comprehensive understanding of virus entry mechanisms is crucial for managing new epidemic strains. However, the cellular processes post-endocytosis remain largely unexplored. This study employs proximity labeling to examine proteins near ACE2 post-viral infection and identified syntaxin-6 (STX6) as a factor that inhibits SARS-CoV-2 infection by impeding the endocytic release of the virus. SARS-CoV-2 infection enhances early endosome recruitment of STX6. STX6 appears to hinder the maturation of viral particles-laden early endosomes into late endosomes, from which the virus could escape. Instead, it promotes the trafficking of the virus toward the autophagy-lysosomal degradation pathway. STX6 exhibits a broad-spectrum effect against various SARS-CoV-2 variants and several other viruses that enter via endocytosis. We report for the first time the function of STX6 as a restrictive factor in viral infection.IMPORTANCEVirus entry is the first step of the virus life cycle, and the exploitation of the endo-lysosome pathway for cellular entry by viruses has been well documented. Meanwhile, the intrinsic defense present within cells interferes with virus entry. We identified STX6 as a host restriction factor for viral entry by facilitating the virus trafficking to the autophagy-lysosomal degradation pathway. Notably, STX6 exhibits broad-spectrum antiviral activity against diverse severe acute respiratory syndrome coronavirus 2 variants and other viruses employing endocytosis for entry.

Cadmium Exposure Disrupts Uterine Energy Metabolism and Coagulation Homeostasis During Labor in Institute of Cancer Research Mice: Insights from Transcriptomic Analysis

Background: Cadmium (Cd) is a highly toxic heavy metal. There are very few studies about the effects of Cd on reproductive health and metabolism, and even fewer on metabolic disorders in the uterus of mice in labor. This study is the first to establish a model of Cd exposure in the uterus of laboring mice and investigate the underlying metabolic mechanisms through transcriptomic analysis. Methods: Pregnant mice received intraperitoneal injections of CdCl2 (1.5 mg/kg) on gestational days 12.5, 14.5, and 16.5 were set up as the experimental group (Cd group), and pregnant mice injected with saline were set up as the control group (CT group). A total of 738 differentially expressed genes (DEGs) were screened using DESeq2 software, including 326 upregulated genes and 412 downregulated genes. Results: Through enrichment databases including the KEGG, GO, Reactome, and PANTHER, we identified 76 metabolism-related DEGs and performed protein-protein interaction (PPI) network analysis. The PPI results were visualized using Cytoscape software and further analyzed, with 18 hub genes (maximum clique centrality score > 10) identified through the MCC algorithm of the Cytohubba plugin. The results showed that the highest-scoring hub genes included mt-Co2, mt-Co3, mt-Atp6, mt-Atp8, mt-Nd3, and mt-Nd4l, which are involved in mitochondrial energy metabolism. The remaining lower-scoring hub genes were primarily associated with coagulation processes. Pathway analysis revealed hub genes predominantly involved in oxidative phosphorylation, complement and coagulation cascades, the cGMP-PKG signaling pathway, and thermogenesis. Conclusion: This study successfully established a Cd exposure-induced uterine injury model, providing valuable references for human reproductive health research.

Liver and intestine transcriptome analysis reveals molecular mechanisms of phytase-driven nutrient utilization and metabolic regulation in hybrid catfish

The use of phytase in aquafeeds has gained increasing attention as a strategy to enhance nutritional value and mitigate the adverse effects of phytic acid, especially for diets containing plant-based ingredients. Notwithstanding examples of phytase-induced phenotypic changes, the molecular mechanisms underlying phytase supplementation are not well understood. The present study evaluated the effects of phytase on the transcriptomic profiles in the liver and intestine, as well as on growth, feed conversion ratio (FCR), and hematological parameters of Jubilee × D&B hybrid catfish. Over a 140-day feeding trial, phytase supplementation (2500 phytase units/kg diet) significantly improved growth, FCR, red blood cell count, hematocrit, and total cell count in the blood compared with fish fed the basal diet. By comparing the transcriptomic profiles of phytase-supplemented and control fish, we identified a distinct gene expression profile relative to controls. This profile was characterized by differentially expressed genes (DEGs) associated with mineral metabolism (including iron), energy homeostasis, protein synthesis, carbohydrate and lipid metabolism, and immune response. The putative roles of key DEGs, including their interactions in different metabolic pathways, are discussed. The current study explains the benefits of phytase supplementation on hybrid catfish performance on the molecular level, uncovers the transcriptomic mechanisms controlling these benefits, and provides valuable information for customized functional feeds in aquaculture.

Ticagrelor inhibits the growth of lung adenocarcinoma by downregulating SYK expression and modulating the PI3K/AKT pathway

Lung cancer is one of the malignant tumors with the highest morbidity and mortality in China. Despite the use of some targeted therapies in lung cancer treatment, the prognosis remains suboptimal, highlighting the urgent need for new, effective drugs to enhance outcomes. Ticagrelor, a marketed anti-platelet drug, has been reported to have anti-tumor effects. This study primarily investigates the inhibitory effect of Ticagrelor on lung adenocarcinoma in both in vivo and in vitro models, as well as its molecular mechanisms. Firstly, the effects of ticagrelor on the proliferation (CCK-8 and Edu staining), migration (scratch test), and invasion (Transwell chamber) of lung adenocarcinoma cells were evaluated using a variety of lung adenocarcinoma cell models. Secondly, the efficacy of ticagrelor on lung adenocarcinoma in vivo was evaluated by A549, H1975 tumor-bearing mouse models. Finally, transcriptomic sequencing (RNA-Seq) and immunohistochemistry were used to explore the molecular mechanism of the intervention effect of ticagrelor on lung cancer. Ticagrelor significantly inhibits the proliferation, migration and invasion of various lung cancer cells in vitro, and markedly suppressed tumor growth in A549 and NCI-H1975 CDX model in vivo. The pathological results showed that the number of tumor cells in the intervention group was significantly reduced, with large area necrosis, and the expression of Ki-67 in the intervention group was significantly decreased by immunohistochemistry. RNA-seq sequencing results from NCI-H1975 xenograft showed that several integrin-related pathways were down-regulated in the Ticagrelor treatment group, along with a significant reduction in spleen tyrosine kinase (SYK), a pivotal protein related to integrin signaling. Furthermore, we demonstrated that ticagrelor inhibits lung adenocarcinoma by down-regulating SYK and regulating PI3K/AKT pathway using WB. Ticagrelor has obvious inhibitory effect on a variety of lung adenocarcinoma cell lines and cell line transplanted tumors, and its antitumor effect may be related to the inhibition of SYK signaling pathway and PI3K/AKT pathway.

Combined Analysis of Transcriptomes and Metabolomes Reveals That MeJA-Mediated Flavonoid Biosynthesis Is Crucial for Pigment Deposition in Naturally Colored Green Cotton Fibers

Background: Green cotton fibers (GCFs) are valued for their natural coloration and eco-friendly properties, but their pigmentation mechanisms remain unclear, limiting their wider application in the textile industry. This study aims to uncover the key regulatory genes and metabolic pathways involved in GCF coloration. Methods: We conducted transcriptome and metabolome profiling of green and white cotton fibers at different developmental stages to identify differences in gene expression and metabolite accumulation related to pigmentation. Results: Transcript analysis revealed significant enrichment in α-linolenic acid metabolism, flavonoid biosynthesis and phenylpropane metabolism pathways during late pigmentation stages. Key genes in methyl jasmonate (MeJA) biosynthesis and flavonoid biosynthesis (LOX, JMT, ANS, C4H, DFR, F3H) were upregulated. The MYB transcription factor showed the most significant increase during fiber development. Metabolomic analysis identified 12 metabolites that accumulated specifically in green fibers. MeJA treatment promoted the expression of MYB genes and flavonoid biosynthesis genes (DFRs, ANSs, F3H, C4H), as well as the accumulation of Luteolin, Gallocatechin, Cyanidin and Chrysanthemum metabolites. Conclusions: Our study demonstrates that MeJA-mediated flavonoid biosynthesis, regulated by MYB transcription factors, is the central pathway controlling pigment deposition in GCFs. These findings provide valuable insights for developing improved colored cotton materials.

Maternal malnutrition induces inflammatory pathways and oxidative stress in the dorsolateral prostate of male offspring rats

Maternal conditions during pregnancy can influence the long-term health of offspring. In particular, maternal malnutrition (MM), such as protein restriction, affects the development of several organs, including the male reproductive system. This study examined how a low-protein maternal diet impacts the structure and function of the dorsolateral prostate (DLP) in aging male rats. Male offspring were divided into two groups: A control group (CTR), whose mothers received a normal protein diet (17%) during pregnancy and lactation, and a low-protein group (GLLP), whose mothers received a low-protein diet (6%) during the same period. At 540 days of age, the offspring were euthanized, and the DLPs were collected for analysis. The GLLP group showed significant structural changes in the DLP, including increased epithelial and reduced stromal compartments. These rats also had lower levels of probasin (a prostate-specific protein), along with a higher number of mast cells, CD68 + macrophages, and IL-10 protein expression, indicating inflammation. Antioxidant balance was disrupted: Glutathione (GSH) levels increased, while catalase (CAT) and superoxide dismutase (SOD) decreased. The expression of SIRT1, a protein linked to aging and oxidative stress control, was reduced. In silico analysis using human prostate cancer data (PRAD-TCGA) revealed that biological pathways related to oxidative stress, immune response, and tissue remodeling were disrupted in both the rat model and human prostate cancer. In summary, maternal protein restriction leads to long-term changes in the dorsolateral prostate of aging male offspring, including inflammation, oxidative stress, and tissue remodeling. The reduced expression of SIRT1 may play a key role in these effects.

Integrating network pharmacology and experimental validation to advance psoriasis treatment: Multi-target mechanistic elucidation of medicinal herbs and natural compounds

BACKGROUND

Psoriasis, a chronic immune-mediated inflammatory disease (IMID), presents significant therapeutic challenges, necessitating exploration of alternative treatments like medicinal herbs (MH) and natural compounds (NC). Network pharmacology offers predictive insights, yet a systematic evaluation connecting these predictions with experimental validation outcomes specifically for MH/NC in psoriasis is lacking. This review specifically fills this gap by comprehensively integrating and analyzing studies that combine network pharmacology predictions with subsequent experimental validation.

METHODS

A systematic literature search identified 44 studies employing both network pharmacology and in vitro or in vivo experimental methods for MH/NC targeting psoriasis. This review provides a systematic analysis of the specific network pharmacology platforms, predicted targets/pathways, in vivo and in vitro experimental validation models, and key biomarker changes reported across these integrated studies. Methodological approaches and the consistency between predictions and empirical findings were critically evaluated.

RESULTS

This first comprehensive analysis reveals that network pharmacology predictions regarding MH/NC mechanisms in psoriasis are frequently corroborated by experimental data. Key signaling pathways, including the IL-17/IL-23 axis, MAPK, and NF-κB, emerge as consistently predicted and experimentally validated targets across diverse natural products. The review maps the specific network pharmacology tools and experimental designs utilized, establishing a methodological benchmark for the field and highlighting the successful synergy between computational prediction and empirical verification.

CONCLUSION

By systematically integrating and critically assessing the linkage between network pharmacology predictions and experimental validation for MH/NC in psoriasis, this review offers a unique clarification of the current, validated state-of-the-art, differentiating it from previous literature. It confirms network pharmacology's predictive power for natural products, identifies robustly validated therapeutic pathways, and provides a crucial benchmark, offering data-driven insights for future research into artificial intelligence-enhanced natural product-based therapies for psoriasis and other IMIDs.

Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China

Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.

The CNV map construction and ROH analysis of Pinan cattle

Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by VST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.

Multiomics analysis uncovers host-microbiota interactions regulate hybrid vigor traits in geese

Economic hybridization represents a predominant breeding strategy for enhancing poultry quality. In this study, we bred hybrid geese (ZF) by crossing Xianghai Flying geese (FG) as paternal lines with Zi geese (ZG) as maternal lines. ZF exhibited integrated superior traits, including increased body weight and breast muscle index, reduced abdominal fat, and improved meat quality (enhanced tenderness, deeper red meat color), with notably higher ileal villus height than parental lines. Integrated phenotypic, transcriptomic, gut microbiome and metabolomic analyses systematically revealed regulatory mechanisms underlying heterosis. The analysis showed 87 differentially expressed genes common between ZF and both parents, mainly enriched in energy metabolism and cytoskeletal and cell adhesion-related pathways. Protein-protein interaction networks revealed KDR, CS, PDHA1, IDH2, and GAPDH as key candidate genes (fold change > 2 and P < 0.0001) regulating the host phenotype. Meanwhile, ZF exhibited microbiome reconfiguration, characterized by the dominance of Bacteroides producing short-chain fatty acids (SCFAs), along with beneficial genera such as Megamonas, Romboutsia, and Subdoligranulum. Additionally, there was a depletion of the pathogenic genus Desulfovibrio. Integrated multi-omics analyses demonstrated that host genes and microbiota interact closely, synergistically governing hybrid vigor traits. The findings provide the first theoretical basis for revealing the potential molecular mechanisms by which the host-gut microbiota interactions regulate hybrid vigor traits in geese.

CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer

Single-cell transcriptome sequencing technology has been applied to decode the cell types and functional states of immune cells, revealing their tissue-specific gene expression patterns and functions in cancer immunity. Comprehensive assessments of immune cells within and across tissues will provide us with a deeper understanding of the tumor immune system in general. Here, we present Cross-tissue Immune cell type or state Enrichment analysis of gene lists for Cancer (CIEC), the first web-based application that integrates database and enrichment analysis to estimate the cross-tissue immune cell types or states. CIEC version 1.0 consists of 480 samples covering primary tumor, adjacent normal tissue, lymph node, metastasis tissue, and peripheral blood from 323 cancer patients. By applying integrative analysis, we constructed an immune cell type/state map for each context, and adopted our previously developed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) algorithm to estimate the enrichment for context-specific immune cell types/states. In addition, CIEC also provides an easy-to-use online interface for users to comprehensively analyze the immune cell characteristics mapped across multiple tissues, including expression map, correlation, similar gene detection, signature score, and expression comparison. We believe that CIEC will be a valuable resource for exploring the intrinsic characteristics of immune cells in cancer patients and for potentially guiding novel cancer-immune biomarker development and immunotherapy strategies. CIEC is freely accessible at http://ciec.gene.ac/.

Establishment, identification, and transcriptome analysis of a Sertoli cell line from ovoviviparous black rockfish Sebastes schlegelii

Black rockfish (Sebastes schlegelii) is an economically important species with a unique ovoviviparous reproductive mode, in which reproduction is limited by incomplete fertilization. In order to understand the mechanism of spermatogenesis of black rockfish, a cell line derived from the testis, named SSTC, was successfully established and cultured in L-15 medium at 25 °C, and it was passaged to the 50th generation. The SSTC exhibited fibroblast-like and epithelial-like morphology during in vitro culture, and 62% of the SSTC retained the diploid karyotype with 48 chromosomes by the 30th passage (P30). To evaluate the ability of SSTC to express exogenous genes, lipofection and electrotransfection were performed, achieving transfection efficiencies of 9% and 12%, respectively. Transcriptome analysis showed that SSTC at P15 and P30 scarcely expressed germ cell and Leydig cell marker genes, while only expressing the Sertoli cell marker genes sox9a, amh, krt18 and fasl, indicating that SSTC mainly consists of Sertoli cells. GO and KEGG enrichment analyses revealed that, compared to the primary cells, the MAPK, TGF-β, and Wnt signaling pathways, which are crucial for spermatogenesis in Sertoli cells, were significantly upregulated in SSTC after passaging. Additionally, cell cycle-related pathways were upregulated, while pathways associated with cell adhesion, extracellular matrix, cell communication and membrane signal transduction were significantly downregulated. This study demonstrated that SSTC can be used as a tool for exploring the molecular mechanisms of gonadal differentiation and development in black rockfish, providing an effective platform for research on reproduction and endocrinology in this species.

Development and Application of a 40 K Liquid Capture Chip for Beef Cattle

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective genotyping platform essential for molecular breeding of livestock. In this study, we developed a liquid SNP capture chip suitable for five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. The panel consisted of 42,686 SNPs (~40 K). These SNPs were evenly distributed on each bovine chromosome, with the majority of SNPs having minor allele frequencies >0.05 and located within intergenic regions. The performance evaluation of this SNP chip panel was proceeded by genotyping 200 individuals, revealing that this panel has a high SNP call rate of 99.48%. The SNP chip panel was further used to examine the population structure of a beef cattle population with 205 individuals and demonstrated the ability to differentiate between foreign and indigenous cattle breeds. The SNP chip was also used to determine the runs of homozygosity (ROH) within a local Hubei beef cattle population of 195 individuals. We identified 2547 ROH and several genes associated with economically important traits in the study population. Our findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value.

Genome-wide identification of long non-coding RNAs reveals potential association with Phytophthora infestans asexual and sexual development

Long non-coding RNAs (lncRNAs) play pivotal roles in regulating diverse biological processes across plants, mammals, and fungi. However, the information on lncRNAs in oomycete asexual and sexual reproduction, which are two pivotal processes in the pathogenic cycle, has not been elucidated. In this present study, strand-specific RNA sequencing data of Phytophthora infestans with asexual development and sexual reproduction were reanalyzed, and a total of 4,399 lncRNAs were systematically identified. Compared to messenger RNAs (mRNAs), lncRNAs had a higher proportion of transcripts containing more than one exon, shorter nucleotide lengths, and lower expression levels. Target analysis showed that although only 280 lncRNA-mRNA pairs were shared, the functional pathways in which cis and trans targets participated were similar. Weighted gene co-expression network analysis of differentially expressed lncRNAs (DElncRs) and differentially expressed mRNAs (DEmRs) of asexual development stages indicated that lncRNAs might participate in different asexual stages and transformation of the growth stages via regulating functional genes. Expression trend analysis of DElncRs and DEmRs showed that lncRNAs may promote asexual development via upregulating mRNAs encoding development- and invasion-related proteins, such as INF6, triosephosphate isomerase, and glycoprotein elicitor. Co-expression analysis of DElncRs and DEmRs of sexual reproduction showed that lncRNAs could increase the level of mRNAs related to mating, such as M96 mating-specific protein and Crinkler family protein, which meant that lncRNAs might participate in sexual reproduction by regulating mating-related genes. Our study conducted a comprehensive analysis of lncRNAs in P. infestans and suggested a potential function of lncRNAs in asexual and sexual development.

IMPORTANCE

This study systematically analyzed lncRNAs in Phytophthora infestans, revealing the associations between lncRNAs and functional genes. The potential regulatory roles of lncRNAs in the asexual and sexual reproduction stages were clarified, providing a new perspective for in-depth understanding of the reproductive regulatory network of oomycetes. This not only expands the understanding of the functions of non-coding RNAs in different biological groups but also provides potential targets for the development of new disease prevention and control strategies, promoting related research in the fields of agriculture and biology.

Transcriptomic comparison analysis across seven developmental stages of the Triatoma rubrofasciata, a vector of Chagas disease

BACKGROUND

Triatoma rubrofasciata is an obligate hematophagous insect and a primary vector of Trypanosoma cruzi, the etiological agent of Chagas disease, with a widespread global distribution. In addition to Try. cruzi, T. rubrofasciata also serves as a vector for various other pathogens, including Try. lewisi, Try. conorhini, and Bartonella species. Despite its increasing epidemiological relevance in the transmission of multiple diseases, research on T. rubrofasciata remains limited.

RESULTS

Differentially expressed genes (DEGs) were associated with growth, development, carbohydrate metabolism, and immunity. Notably, homeobox protein genes, including homeobox protein Nkx-6.2-like, homeobox protein abdominal-B isoform X1, homeobox protein Hox-A3-like, and Hox-B4-like, along with E3 ubiquitin protein ligase genes and sexual differentiation-related genes, such as male-specific lethal 1-like 1 isoform X3 (MSL), transformer-2 protein homolog beta-like isoform X2 (tra-2), and doublesex- and mab-3-related transcription factor A2-like (dsx), were highly expressed in the egg stage. Additionally, venom-related genes, including venom histidine phosphatase-like protein 1 and venom serine carboxypeptidase-like, were predominantly expressed in nymphal stages 4 and 5, while cytochrome P450 CYP425A1v2 exhibited high expression levels in the adult stages. Among these DEGs, we propose that homeobox protein genes, dsx, tra-2, and others may serve as candidate genes involved in growth, development, and sexual differentiation. This study provides valuable insights into gene expression dynamics during T. rubrofasciata development and establishes a foundation for future functional research on this species.

CONCLUSIONS

In this study, we sequenced the complete developmental stages of T. rubrofasciata using HiSeq technology. Our findings offer novel insights into the molecular mechanisms underlying development and sex regulation in this species. Furthermore, the identified differentially expressed genes (DEGs) may serve as potential targets for innovative pest control strategies.

Genome-wide analysis of the BoBZR1 family genes and transcriptome analysis in Brassica oleracea

The BRASSINAZOLE-RESISTANT 1 genes play a crucial role as key regulators in Brassinosteroid (BR) signaling, which affects various plant developmental and stress-responsive aspects. Understanding regulatory mechanisms via BZR1 in modulating target genes has become a main point in research on plant BR signaling networks. Despite this, the BZR1 functioning in B. oleracea is not elucidated. A complete genome-wide analysis identified 12 BZR1 genes in B. oleracea, categorized into three groups based on their gene motif and structural features. These BoBZR1s were found on eight different chromosomes. Synteny analysis between B. oleracea, Arabidopsis, and potato provided perception into their evolutionary characteristics. Promoter regions of BoBZR1 family genes in B. oleracea have shown specific cis-elements associated with hormones, stress, and plant development. The expression analysis toward cuticular wax biosynthesis revealed that BoBZR1-1, BoBZR1-6, BoBZR1-7, and BoBZR1-10 were upregulated in response to cuticular wax biosynthesis. Differential expressions of BoBZR1 genes were observed for all seven different tested tissues. The whole study involved systematic characterization of the BoBZR1 family, and expression patterns, in BR signaling and its extensive involvement in developmental processes in B. oleracea. Results establish a theoretical foundation for deeper investigation of BoBZR1 structure and functions in B. oleracea, specifically toward regulating plant stress.

Analysis of stress response in multiple bacterial pathogens using a network biology approach

Stress response in bacterial pathogens promotes adaptation, virulence and antibiotic resistance. In this study, a network approach is applied to identify the common central mediators of stress response in five emerging opportunistic pathogens; Enterococcus faecium Aus0004, Staphylococcus aureus subsp. aureus USA300, Klebsiella pneumoniae MGH 78,578, Pseudomonas aeruginosa PAO1, and Mycobacterium tuberculosis H37Rv. A Protein-protein interaction network (PPIN) was constructed for each stressor using Cytoscape3.7.1 from the differentially expressed genes obtained from Gene expression omnibus datasets. A merged PPIN was constructed for each bacterium. Hub-bottlenecks in each network were the central stress response proteins and common pathways enriched in stress response were identified using KOBAS3.0. 31 hub-bottlenecks were common to each individual stress response, merged networks in all five pathogens and an independent cross stress (CS) response dataset of Escherichia coli. The 31 central nodes are in the RpoS mediated general stress regulon and also regulated by other stress response systems. Analysis of the 20 common metabolic pathways modulating stress response in all five bacteria showed that carbon metabolism pathway had the highest crosstalk with other pathways like amino acid biosynthesis and purine metabolism pathways. The central proteins identified can serve as targets for novel wide-spectrum antibiotics to overcome multidrug resistance.

Osmoregulatory evolution of gills promoted salinity adaptation following the sea-land transition of crustaceans

The sea-land transition is one of the most dramatic evolutionary changes and requires an adaptive genetic response to salinity changes and osmotic stress. Here, we used multi-species genomes and multi-tissue transcriptomes of the talitrid crustaceans, a living sea-land transition model, to investigate the adaptive genetic changes and osmoregulatory organs that facilitated their salinity adaptation. Genomic analyses detected numerous osmoregulatory genes in terrestrial talitrids undergoing gene family expansions and positive selection. Gene expression comparisons among species and tissues confirmed the gill being the primary organ responsible for ion transport and identified the genetic expression variation that enable talitrids to adapt to marine and land habitats. V-type H+-ATPases related to H+ transport play a crucial role in land adaptations, while genes related to the transport of inorganic ions (Na+, K+, Cl-) are upregulated in marine habitats. Our results demonstrate that talitrids have divergent genetic responses to salinity change that led to the uptake or excretion of ions in the gills and promoted habitat adaptation. These findings suggest that detecting gene expression changes in talitrids presents promising potential as a biomarker for salinity monitoring.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-025-00298-6.

High relative humidity mitigates the adverse effects of excessive light by protecting photosynthetic machinery in flowering Chinese cabbage

Increasing canopy relative air humidity (RH) facilitates the resistance of flowering Chinese cabbage plants against excessive light exposure in a plant factory with artificial lighting (PFAL), thereby completely inhibiting leaf burn occurrence. To clarify this high RH-mediated resistance mechanism, we further analyzed the transcriptomes, gas exchange parameters, and chlorophyll fluorescence of flowering Chinese cabbage plants subjected to two levels of canopy RH (70% and 90%). Transcriptomic data revealed a significant enrichment of photosynthesis antenna proteins pathway, which was notably downregulated in both the cotyledons and the first true leaves of the plants grown at 70% RH from the 10th to the 14th day after sowing. However, the downregulation of the photosynthesis-antenna proteins pathway in the first true leaves was notably attenuated by increasing the RH from 70% to 90%, consequently inhibiting the down-regulated expression of all light-harvesting complex I- and II-subunit-encoding mRNAs. The 70% RH-treated seedlings exhibited serious photoinhibition, as indicated by relatively lower non-photochemical quenching (NPQ), maximal quantum yield of photosystem I and II, and adaptation of the photosynthetic apparatus to high irradiance. The 90% RH treatment greatly lessened the reduction of NPQ and relative electron transport rates, which favored dissipating the excess excited energy, protected the photosynthetic apparatus against photodamage, and ultimately completely inhibited leaf burn occurrence. Overall, our results indicate that high canopy RH could improve the resistance of plants to intense light by maintaining efficient photosynthesis, thereby minimizing reliance on supplemental artificial lighting.

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs

Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted comprehensive genome-wide association studies (GWAS) followed by a cross-breed meta-analysis for 232 complex traits and a within-breed meta-analysis for 12 traits, using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds. We identified 6878 quantitative trait loci (QTL) for 139 complex traits. Leveraging the Pig Genotype-Tissue Expression resource, we systematically investigated the biological context and regulatory mechanisms behind these trait-QTLs, ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits. For instance, rs344053754 regulates UGT2B31 expression in the liver and intestines, potentially by modulating enhancer activity, ultimately influencing litter weight at weaning in pigs. Furthermore, we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs. Overall, our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.

Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis

During lactation, dairy cattle's digestive tract requires significant adaptations to meet the increased nutrient demands for milk production. As we attempt to improve milk-related traits through selective pressure, it is crucial to understand the biological functions of the epithelia of the rumen, small intestine, and colonic tissues in response to changes in physiological state driven by changes in nutrient demands for milk synthesis. In this study, we obtained a total of 108 transcriptome profiles from three tissues (epithelia of the colon, duodenum, and rumen) of five Holstein cows, spanning eight time points from the early, mid, late lactation periods to the dry period. On average 97.06% of reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We analyzed 27,607 gene expression patterns at multiple periods, enabling direct comparisons within and among tissues during different lactation stages, including early and peak lactation. We identified 1645, 813, and 2187 stage-specific genes in the colon, duodenum, and rumen, respectively, which were enriched for common or specific biological functions among different tissues. Time series analysis categorized the expressed genes within each tissue into four clusters. Furthermore, when the three tissues were analyzed collectively, 36 clusters of similarly expressed genes were identified. By integrating other comprehensive approaches such as gene co-expression analyses, functional enrichment, and cell type deconvolution, we gained profound insights into cattle lactation, revealing tissue-specific characteristics of the gastrointestinal tract and shedding light on the intricate molecular adaptations involved in nutrient absorption, immune regulation, and cellular processes for milk synthesis during lactation.

Advances in artificial intelligence-envisioned technologies for protein and nucleic acid research

Artificial intelligence (AI) and machine learning (ML) have revolutionized pharmaceutical research, particularly in protein and nucleic acid studies. This review summarizes the current status of AI and ML applications in the pharmaceutical sector, focusing on innovative tools, web servers, and databases. This paper highlights how these technologies address key challenges in drug development including high costs, lengthy timelines, and the complexity of biological systems. Furthermore, the potential of AI in personalized medicine, cancer drug response prediction, and biomarker identification is discussed. The integration of AI and ML in pharmaceutical research promises to accelerate drug discovery, reduce development costs, and ultimately lead to more effective and personalized therapeutic strategies.

16S rRNA and transcriptome analysis revealed the regulatory mechanism of Romboutsia lituseburensis on serum immunoglobulin levels in geese

Romboutsia is a dominant genus in the goose intestine. Recent studies have suggested that Romboutsia lituseburensis might regulate serum immunoglobulin levels in female geese, although the underlying mechanisms remain unclear. In this study, we administered Romboutsia lituseburensis (R. lituseburensis) orally to female geese, leading to successful colonization of the ileum. Subsequent analysis showed that the levels of IgM, IgA, and IgG in the serum significantly decreased after colonization (P < 0.01). 16S rRNA sequencing revealed that R. lituseburensis significantly altered the microbial composition and increased the relative abundance of Jeotgalicoccus (P < 0.01), Turicibacter, and Bacillus (P < 0.05) in the ileum. Transcriptome sequencing further identified 263 differentially expressed genes (DEGs) in the ileum (146 upregulated, 117 downregulated) and 725 DEGs in the spleen (300 upregulated, 425 downregulated). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these DEGs were enriched in 17 pathways in the ileum and 21 pathways in the spleen. Notably, the "Intestinal immune network for IgA production" pathway was significantly enriched in the spleen (P < 0.05). Further, Short Time-series Expression Miner (STEM) analysis grouped the DEGs in these 2 tissues into 49 clusters, with clusters 27 and 29 showing the highest significance and similar expression patterns. Pathway analysis confirmed that the "Intestinal immune network for IgA production" pathway was enriched in both clusters. Furthermore, a protein-protein interaction (PPI) network of these 2 clusters, along with correlation analysis between microbiota abundance and gene expression, highlighted KEL, SERPING1, CALR, and OSTN as key hub genes. Overall, R. lituseburensis significantly increased the abundance of Jeotgalicoccus, Turicibacter, and Bacillus in the ileum. Concurrently, it might downregulate the "Intestinal immune network for IgA production" pathway in the spleen (CCR9, TNFRSF13B, AICDA) via KEL, SERPING1, CALR, and OSTN, thereby contributing to the reduction of serum immunoglobulin levels. These findings offer new insights into how R. lituseburensis influences immune function in female geese and provide a theoretical basis for further research into its other physiological roles in geese.

Whole-genome resequencing reveals the population structure and domestication processes of endemic endangered goose breeds (Anser cygnoides)

In recent years, the dwindling population of these endangered geese has hindered our understanding of their phenotypic variations and the genes associated with important traits. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 90 individuals from a conservation farm were obtained using the Illumina 6000 paired-end platform. The research results indicate that each locally endangered goose variety has formed a monophyletic population. The Baizi (BZ), Lingxian White (LX), and Xupu (XP) geese exhibiting higher genetic diversity than the other goose breeds. Tree-Mix analysis revealed the presence of five gene flows events between goose populations, with Yangjiang (YJ) geese consistently exhibiting significant genetic distance from the other breeds. Under strong pressures from the natural environment and artificial selection, whole-genome selective scanning revealed 394 overlapping genes. Gene Ontology (GO) enrichment analysis of the putative candidate genes (PCGs) revealed significant enrichment of 20 terms (P < 0.05). Similarly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant enrichment of PCGs in 23 terms (P < 0.05). Examination of overlapping genes identified through at least two selection methods revealed a set of genes associated with key traits, including growth and development (CCND1, DES, CCNO, SMC5, and NUBP1), immunity (ABCA2, ABCC8, UHRF2, and ABCA1), and body aging (KAT6B). Our findings provide insights into the genetic basis of endangered geese at the whole-genome level, laying the foundation for future molecular research on genetic variation and phenotypic changes. In summary, our results provide invaluable resources for delineating the uniqueness of endangered goose breeds.

Multiple, Single Trait GWAS and Supervised Machine Learning Reveal the Genetic Architecture of Fraxinus excelsior Tolerance to Ash Dieback in Europe

Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior requires further investigation. Here, we integrate quantitative genetics based on multiple replicates and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and of phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). Based on phenotypic data of 486 F. excelsior replicated genotypes we observed negative genotypic correlations between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Our results suggest that the examined traits are polygenic and using genomic prediction models, with ranked single nucleotide polymorphisms (SNPs) based on GWAS associations as input, a large proportion of the variation was predicted by unlinked SNPs. Based on 100 unlinked SNPs, we can predict 55% of the variation in disease tolerance among genotypes (as phenotyped in genetic trials), increasing to a maximum of 63% when predicted from 9155 SNPs. In autumn leaf yellowing, 52% of variation is predicted by 100 unlinked SNPs, reaching a peak of 72% using 3740 SNPs. Based on feature permutations within genomic prediction models, a total of eight nonsynonymous SNPs linked to ash dieback crown damage and autumn leaf yellowing (three and five SNPs, respectively) were identified, these were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). We did not find an overlap between genes associated with crown damage level and autumn leaf yellowing. Hence, our results shed light on the difference in the genomic basis of ADB tolerance and autumn leaf yellowing despite these two traits being correlated in quantitative genetic analysis. Overall, our methods show the applicability of genomic prediction models when combined with GWAS to reveal the genomic architecture of polygenic disease tolerance enabling the identification of ash dieback tolerant trees for breeding or conservation purposes.

Effects of Colony Breeding System and Nest Architecture on Soil Microbiome and Fertility in the Fungus-Growing Termite Macrotermes barneyi Light

Macrotermes barneyi is a typical fungus-growing termite that forms both monogynous (single queen) and polygynous (multiple queen) colonies in nature. This species influences the local soil fertility in part by redistributing nutrients across the landscape in its habitats. However, how the colony structure of M. barneyi affects nutrient cycling and microbial communities within the nest is not well understood. In this study, we compared the physicochemical properties and microbial communities across nest parts between monogynous and polygynous colonies of M. barneyi. Our results showed that the fungus garden is the most nutrient-rich part of the nest, with higher soil moisture, organic matter, ammonium nitrogen, nitrate nitrogen, available sulfur, available potassium, available silicon, and available boron than other nest parts. Notably, the fungus garden in monogynous colonies had higher nitrate nitrogen, available sulfur, and available silicon than those in the polygynous colonies. The microbial α-diversity in the fungus garden was lower than that in other parts of the nest. β-diversity analysis revealed a clear separation of microbial communities between monogynous and polygynous colonies across nest parts. Furthermore, the relative abundance of functional genes associated with "cell cycle control, cell division, and chromosome partitioning" was higher in the fungus garden of polygynous colonies compared to monogynous colonies. Our results suggest that the fungus garden plays a crucial role in maintaining colony stability in M. barneyi colonies. The rapid depletion of nutrients in the fungus garden to sustain the larger population in polygynous colonies likely influences microbial community dynamics and nutrient cycling.

Genome of a stage-dependent cave-dwelling frog reveals the genetic mechanism of an extremely divergent biphasic life cycle

Cave-dwelling species offer unique insights into adaptive evolution. The stage-dependent cave frog, Oreolalax rhodostigmatus (Orho), exhibits troglomorphic traits as a tadpole in Karst caves, transitioning to a troglophilic/trogloxenic lifestyle after metamorphosis, characterized by developed pigment and eyes. We present the Orho genome (3.16 Gb, 26,192 protein-coding genes), revealing extensive expansion and positive selection in gene families associated with olfactory, taste, visual, and pain perceptions. Orho tadpoles exhibit suppressed visual function while retaining crystalline lens development. Adult eyes demonstrate high light-induced plasticity in the visual cycle. Orho tadpoles display both developmental and light-induced melanogenesis, which is associated with distinctive tyrosinases. A stage-dependent amphibian-specific tyrosinase subfamily, reported here, underpins their ontogenetic pigmentation. Additionally, prominent hepatic fat storage and genetic/transcriptional variations in lipid metabolism genes characterize tadpole development. These findings unveil the molecular mechanisms behind Orho's stage-dependent cave adaptation, which differs mechanistically from cavefishes, offering valuable insights into the highly divergent biphasic life cycle.

Comprehensive aroma profiles and the underlying molecular mechanisms in six grape varieties with different flavors

Aroma is a critical factor in determining grape quality, develops through complex interactions among various volatile compounds. This study revealed the differences of the six grape varieties with three different aroma types though the HS-SPME/GC-MS and RNA-sequencing technologies. Muscat-type grapes ('Shine 13' and 'Shine Muscat') exhibited the highest monoterpene and C13-norisoprenoid level, correlating with elevated expression of DXS, TPS, and CCD4b genes in the MEP/MVA pathways. Strawberry-type cultivars (particularly 'Hutai 8') accumulated abundant esters linked to high AAT expression, while neutral aromatic varieties showed enriched C6/C9 compounds associated with upregulated LOXA and ADH2. Muscat-type grapes dominated monoterpenes with OAVs >1, which explained the abundant Muscat flavors, while neutral aromatic aroma cultivars had the most abundant C6/C9 compounds OAVs associated with leaf-like scents. Strawberry-type cultivars exhibited the highest esters OAVs with strawberry aroma profiles. WGCNA analysis revealed four specific modules correlated with aroma compound biosynthesis correlated with alcohols (88genes), carbonyl compounds (451genes), fatty acids (110 genes), and monoterpenes (790genes) accumulation in these grapes, respectively. These findings were expected to advance our understanding of the metabolic pathways responsible for grape aroma and could provide valuable recommendations for the enhancement of grape aromatic quality.

CircRNA profiling reveals circSMC1B that promotes bovine male germline stem cells proliferation and apoptosis via sponging let-7i

BACKGROUND

Despite significant advancements in artificial insemination techniques, male reproduction continues to pose a considerable challenge in cattle breeding. Circular RNAs (circRNAs), a class of non-coding RNAs (ncRNAs), play a crucial role in regulating testis growth and spermatogenesis. Therefore, it is essential to comprehend the involvement of circRNAs in bull reproduction for livestock production. However, the identification of differentially expressed circRNAs during testis development and their underlying mechanisms remains largely unknown.

RESULTS

In this study, RNA-seq was employed to investigate the expression of circRNAs in neonatal and sexually mature bovine testes. We identified 28,065 candidate circRNAs, of which 987 circRNAs showed differential expression between the two stages (P-adjust < 0.05). Notably, circSMC1B was significantly up-regulated in sexually mature testis. Overexpression of circSMC1B promoted the proliferation and apoptosis of bovine male germline stem cells (mGSCs). Further analysis revealed that circSMC1B acts as a molecular sponge for let-7i, while High mobility group AT-hook 1/Nuclear receptor subfamily 6 group A member 1 (HMGA1/NR6 A1) were identified as direct targets of let-7i. Furthermore, circSMC1B levels exhibited a significant positive correlation with HMGA1/NR6A1 mRNA expression in bovine mGSCs, highlighting the critical role of competing endogenous RNA (ceRNA) mechanisms.

CONCLUSION

Our research elucidates that circSMC1B, through let-7i binding, promotes bovine mGSCs proliferation and apoptosis by targeting HMGA1/NR6A1. These findings provide valuable resources for studying the functional aspects of circRNAs in testis development and enhance our understanding of the biological function of circSMC1B in promoting bull spermatogenesis.