Potential Functional Genes Research Articles

Identifying novel chemical-related susceptibility genes for five psychiatric disorders through integrating genome-wide association study and tissue-specific 3'aQTL annotation datasets.

The establishment of 3'aQTLs comprehensive database provides an opportunity to help explore the functional interpretation from the genome-wide association study (GWAS) data of psychiatric disorders. In this study, we aim to search novel susceptibility genes, pathways, and related chemicals of five psychiatric disorders via GWAS and 3'aQTLs datasets. The GWAS datasets of five psychiatric disorders were collected from the open platform of Psychiatric Genomics Consortium (PGC, https://www.med.unc.edu/pgc/ ) and iPSYCH ( https://ipsych.dk/ ) (Demontis et al. in Nat Genet 51(1):63-75, 2019; Grove et al. in Nat Genet 51:431-444, 2019; Genomic Dissection of Bipolar Disorder and Schizophrenia in Cell 173: 1705-1715.e1716, 2018; Mullins et al. in Nat Genet 53: 817-829; Howard et al. in Nat Neurosci 22: 343-352, 2019). The 3'untranslated region (3'UTR) alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) summary datasets of 12 brain regions were obtained from another public platform ( https://wlcb.oit.uci.edu/3aQTLatlas/ ) (Cui et al. in Nucleic Acids Res 50: D39-D45, 2022). First, we aligned the GWAS-associated SNPs of psychiatric disorders and datasets of 3'aQTLs, and then, the GWAS-associated 3'aQTLs were identified from the overlap. Second, gene ontology (GO) and pathway analysis was applied to investigate the potential biological functions of matching genes based on the methods provided by MAGMA. Finally, chemical-related gene-set analysis (GSA) was also conducted by MAGMA to explore the potential interaction of GWAS-associated 3'aQTLs and multiple chemicals in the mechanism of psychiatric disorders. A number of susceptibility genes with 3'aQTLs were found to be associated with psychiatric disorders and some of them had brain-region specificity. For schizophrenia (SCZ), HLA-A showed associated with psychiatric disorders in all 12 brain regions, such as cerebellar hemisphere (P = 1.58 × 10-36) and cortex (P = 1.58 × 10-36). GO and pathway analysis identified several associated pathways, such as Phenylpropanoid Metabolic Process (GO:0009698, P = 6.24 × 10-7 for SCZ). Chemical-related GSA detected several chemical-related gene sets associated with psychiatric disorders. For example, gene sets of Ferulic Acid (P = 6.24 × 10-7), Morin (P = 4.47 × 10-2) and Vanillic Acid (P = 6.24 × 10-7) were found to be associated with SCZ. By integrating the functional information from 3'aQTLs, we identified several susceptibility genes and associated pathways especially chemical-related gene sets for five psychiatric disorders. Our results provided new insights to understand the etiology and mechanism of psychiatric disorders.

Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data.

The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

JAK/STAT signaling regulated intestinal regeneration defends insect pests against pore-forming toxins produced by Bacillus thuringiensis.

A variety of coordinated host-cell responses are activated as defense mechanisms against pore-forming toxins (PFTs). Bacillus thuringiensis (Bt) is a worldwide used biopesticide whose efficacy and precise application methods limits its use to replace synthetic pesticides in agricultural settings. Here, we analyzed the intestinal defense mechanisms of two lepidopteran insect pests after intoxication with sublethal dose of Bt PFTs to find out potential functional genes. We show that larval intestinal epithelium was initially damaged by the PFTs and that larval survival was observed after intestinal epithelium regeneration. Further analyses showed that the intestinal regeneration caused by Cry9A protein is regulated through c-Jun NH (2) terminal kinase (JNK) and Janus tyrosine kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathways. JAK/STAT signaling regulates intestinal regeneration through proliferation and differentiation of intestinal stem cells to defend three different Bt proteins including Cry9A, Cry1F or Vip3A in both insect pests, Chilo suppressalis and Spodoptera frugiperda. Consequently, a nano-biopesticide was designed to improve pesticidal efficacy based on the combination of Stat double stranded RNA (dsRNA)-nanoparticles and Bt strain. This formulation controlled insect pests with better effect suggesting its potential use to reduce the use of synthetic pesticides in agricultural settings for pest control.

Transformation to small cell lung cancer is irrespective of EGFR and accelerated by SMAD4-mediated ASCL1 transcription independently of RB1 in non-small cell lung cancer

ObjectivesHistological transformation to small cell lung cancer (SCLC) has been identified as a mechanism of TKIs resistance in EGFR-mutant non-small cell lung cancer (NSCLC). We aim to explore the prevalence of transformation in EGFR-wildtype NSCLC and the mechanism of SCLC transformation, which are rarely understood.MethodsWe reviewed 1474 NSCLC patients to investigate the NSCLC-to-SCLC transformed cases and the basic clinical characteristics, driver gene status and disease course of them. To explore the potential functional genes in SCLC transformation, we obtained pre- and post-transformation specimens and subjected them to a multigene NGS panel involving 416 cancer-related genes. To validate the putative gene function, we established knocked-out models by CRISPR-Cas 9 in HCC827 and A549-TP53-/- cells and investigated the effects on tumor growth, drug sensitivity and neuroendocrine phenotype in vitro and in vivo. We also detected the expression level of protein and mRNA to explore the molecular mechanism involved.ResultsWe firstly reported an incidence rate of 9.73% (11/113) of SCLC transformation in EGFR-wildtype NSCLC and demonstrated that SCLC transformation is irrespective of EGFR mutation status (P = 0.16). We sequenced 8 paired tumors and identified a series of mutant genes specially in transformed SCLC such as SMAD4, RICTOR and RET. We firstly demonstrated that SMAD4 deficiency can accelerate SCLC transition by inducing neuroendocrine phenotype regardless of RB1 status in TP53-deficient NSCLC cells. Further mechanical experiments identified the SMAD4 can regulate ASCL1 transcription competitively with Myc in NSCLC cells and Myc inhibitor acts as a potential subsequent treatment agent.ConclusionsTransformation to SCLC is irrespective of EFGR status and can be accelerated by SMAD4 in non-small cell lung cancer. Myc inhibitor acts as a potential therapeutic drug for SMAD4-mediated resistant lung cancer.9vNWjpNbo9djtsBQF6k7BHVideo

Pseudomonas weihenstephanensis through the iron metabolism pathway promotes in situ spoilage capacity of prepared beef steaks during cold storage

In this study, we evaluated the histomorphology, reactive oxygen species (ROS), protein degradation, and iron metabolism characteristics and differential expression analysis of genes for siderophores synthesis and protease secretion in prepared beef steaks inoculated alone or co-inoculated with P. weihenstephanensis, B. thermotrichothrix and M. caseolyticus at 4 °C for 12 days. The results showed that the P. weihenstephanensis was the key bacteria that degraded protein in the process of prepared beef steaks spoilage, which led to protein oxidation by promoting ferritin degradation to release free iron and inducing ROS accumulation. The highest expression of FpvA and AprE was detected in the P. weihenstephanensis group by comparing qRT-PCR of the different inoculation groups. Both qRT-PCR and Western blot revealed that ferritin heavy polypeptide and ferritin light chain polypeptide gene and protein expressions were significantly higher in the P. weihenstephanensis inoculation group compared to the other inoculation groups. Results suggested that FpvA and AprE might play roles in meat spoilage and were potential positional, physiological and functional candidate genes for improving the quality traits of prepared beef steaks. This work may provide insights on controlling food quality and safety by intervening in spoilage pathways targeting iron carrier biosynthesis or protease secretion genes.

Identification of pathogenic-specific open reading frames in staphylococci species

Background Bacteria within the Staphylococcus genus are notorious for causing a wide range of infections, and they possess genes that play a pivotal role in determining their pathogenicity. In this study, we characterized open reading frames (ORFs), which represent potential functional gene sequences, from selected staphylococcal genomes. Methods Our study involved the extraction, categorization, and annotation of ORFs using diverse analytical methods. This approach unveiled distinct ORFs in both pathogenic and non-pathogenic species, with some commonalities. To assess the conservation of these ORFs and their relevance to pathogenicity, we employed tblastn and Clustal Omega-Multiple Sequence Alignment (MSA) methods. Results Remarkably, we identified 23 ORFs that displayed high conservation among pathogenic staphylococci, with five of them extending beyond the Staphylococcus genus. These particular ORFs may encode products associated with RNA catabolism and could potentially function as regulatory small open reading frames (smORFs). Of particular interest, we found a single smORF situated within a conserved locus of the 50S ribosomal protein L1, present in 200 genomes, including 102 pathogenic strains. Conclusions Our findings highlight the existence of ORFs with highly conserved elements, proposing the existence of 23 novel smORFs that may play a role in the pathogenicity of Staphylococcus species.

Characterization of rice aspartic protease genes and induced expression by phytohormones and Xanthomonas oryzae pv. oryzae

Aspartic proteases (APs) are present in both monocotyledonous and dicotyledonous plants. APs consist of nine different families of proteolytic enzymes. APs play important functions in several physiological processes including defense. However, there are limited reports on APs in disease resistance in rice (Oryza sativa). Here, we report that 104 APs were discovered in rice genome. They can be classified into three clades (I, II and III) with APs from Arabidopsis thaliana, and Nymphaea colorata according to phylogenetic relationships. Tandem and segmental duplications were observed to lead to the expansion of OsAP genes in rice. Analysis of gene structure revealed that numerous OsAPs contain multiple exons and introns, however, several OsAPs harbor a single exon and no introns. Synteny analyses demonstrated that four AP genes among O. sativa, A. thaliana, and N. colorata may evolve from a common ancestor of land plants. Ten conserved motifs of amino acids were uncovered from the OsAPs, and two of the motifs are the catalytic sequences, with the conserved Asp-Thr and Ser-Gly amino acids. Within the OsAP promoter sequences, cis-regulatory elements responsive to light, abscisic acid, auxin, gibberellins, methyl jasmonate, and salicylic acid were identified. Stress-responsive elements and tissue-specific expressed elements were also found. Majority of OsAP genes were found to be expressed in diverse tissues and organs. Some of the OsAP genes were observed to be induced by brassinosteroids, jasmonic acid, and salicylic acid. Further, some OsAP genes can be induced by Xanthomonas oryzae pv. oryzae (Xoo), the cause of rice bacterial leaf blight. Among them, OsAP21 was strongly activated by the pathogen, suggesting its potential function in response to the bacterial agent. The results shed light in the potential functions of OsAP genes in rice disease resistance to Xoo.

TRIB3, as a robust prognostic biomarker for HNSC, is associated with poor immune infiltration and cancer cell immune evasion.

As a pseudokinase, Tribbles Pseudokinase 3 (TRIB3) is implicated in a wide array of biological processes, including cell signal transduction, metabolic regulation, stress responses, and immune regulation. While its significant role in the immune regulation of certain cancers is well-established, the specific functions and impact of TRIB3 in head and neck squamous cell carcinoma (HNSC) remain unclear. The data of RNA-sequence was acquired from the TCGA database to analyze the expression patterns of TRIB3 and elucidate its prognostic value in HNSC patients. Furthermore, the correlation between TRIB3 and tumor mutation burden, clinical data, immune checkpoint genes, and immune cell infiltration was explored. Moreover, the TRIB3 location in tumor tissues and subcellular structures was identified via Tisch in the HPA database, and the potential protein interaction molecules for TRIB3 were elucidated in the STRING database. The potential TRIB3 gene function was assessed using gene set enrichment analysis (GSEA), whereas the TRIB3 expression levels in clinical HNSC samples were verified by RT-qPCR and immunohistochemistry. the role of TRIB3 in enhancing the malignant behavior of HNSC cells was validated in vitro through a series of methods including RT-qPCR, CCK8 assay, wound healing assay, and transwell assay. It was revealed that TRIB3 was significantly overexpressed in the nucleus and cytoplasm of HNSC. Furthermore, this overexpression markedly enhanced the migration ability of tumor cells. As an independent prognostic factor, TRIB3 was associated with advanced tumor T stage and was significantly involved with tumor mutation burden and immune cell infiltration in HNSC. Moreover, it was observed that TRIB3 was not a predicted factor for PD1/PDL1 and ATL4 inhibitor treatment; however, it was substantially correlated with various immune evasion-related genes in HNSC. TRIB3 could serve as a potential prognostic marker for HNSC and might be a key gene mediating HNSC immune evasion.

AlliumDB: a central portal for comparative and functional genomics in Allium.

The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion, garlic, bunching onion, and leek, used as vegetables, spices, and traditional medicines. The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding. With the growing accumulation of genomic, resequencing, transcriptome, and phenotypic data, the demand for an integrative Allium database is increasing. Here we present a user-friendly database, AlliumDB (https://allium.qau.edu.cn), as a functional genomics hub integrating public and in-house data. The database contains all currently available nuclear and organelle genomes for Allium species, with genes comprehensively annotated based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, orthology, gene families, protein families (Pfam), and non-coding RNA families (Rfam). Transcriptome and variation profiles are integrated into dynamic visualization tools. We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide, which are included in the database. We incorporated JBrowse for the visualization of gene structures, RNA sequencing data, and variation data. Analysis tools such as the basic local alignment search tool (BLAST), sequence fetch, enrichment, and motif analyses are available to explore potential gene functions. This database incorporates comprehensive Allium genotypic and phenotypic datasets. As the community assembles new genomes and generates resequencing data for Allium germplasms, the database will be improved and continuously updated with these multi-omics data and comparative genomic studies. We expect the AlliumDB database to become a key resource for the study of Allium crops.

Biochar Mitigates the Negative Effects of Microplastics on Sugarcane Growth by Altering Soil Nutrients and Microbial Community Structure and Function.

Microplastic pollution in sugarcane areas of China is severe, and reducing the ecological risks is critical. Biochar has been widely used in soil remediation. This study aims to explore the effects and mechanisms of microplastics combined with or without biochar on sugarcane biomass, soil biochemical properties in red soil through a potted experiment. The results show that, compared with control (CK), treatments with microplastics alone reduced the dry biomass of sugarcane, soil pH, and nitrogen (N) and phosphorus (P) contents by an average of 8.8%, 2.1%, 1.1%, and 2.0%, respectively. Interestingly, microplastics combined with biochar could alleviate the negative effects of microplastic accumulation on sugarcane growth and soil quality. There were significant differences in the bacterial community alpha diversity indices and compositions among different treatments. Compared with CK, treatments with microplastics alone obviously decreased the observed operational taxonomic units (OTUs) and the Chao1 and Shannon indices of soil total bacteria (16S rRNA gene-based bacteria) while increasing them in phoD-harboring bacteria. Microplastics combined with biochar treatments significantly increased the abundance of Subgroup_10 for the 16S rRNA gene and treatments with microplastics alone significantly increased the relative abundance of Streptomyces for the phoD gene compared to CK. Moreover, compared with microplastics alone, the treatments with microplastics combined with biochar increased the relative abundance of Subgroup_10, Bacillus, Pseudomonas in soil total bacteria, and Amycolatopsis and Bradyrhizobium in phoD-harboring bacteria, most of which can inhibit harmful bacteria and promote plant growth. Additionally, different treatments also changed the abundance of potential microbial functional genes. Compared to CK, other treatments increased the abundance of aerobic ammonia oxidation and denitrification but decreased the abundance of nitrate respiration and nitrogen respiration; meanwhile, these four functional genes involved in N cycling processes were obviously higher in treatments with microplastics combined with biochar than in treatments with microplastics alone. In conclusion, microplastics combined with biochar could alleviate the negative effects of microplastic accumulation on sugarcane biomass by altering soil nutrients and microbial community structure and function.

Effects of microplastics on litter decomposition in wetland soil

Microplastics (MPs) may interfere with the primary ecological processes of soil, which has become a growing global environmental issue. In terrestrial ecosystems, litter decomposition is the main process of nutrient cycling, particularly for carbon (C) and nitrogen (N). However, how microplastic pollution could alter wetland litter decomposition has barely been investigated. Therefore, a 100-day lab-scale litter decomposition experiment was conducted using Shengjin Lake wetland soil, which was treated with two types of MPs (polyethylene, PE and polyvinyl chloride, PVC) at three concentrations (0.1%, 0.5%, and 2.5%, w/w), to explore if and how MPs accumulation could affect wetland litter decomposition processes. According to our research, the PE and PVC greatly slowed the decomposition rate of wetland litter. Compared with control treatments, the addition of MPs decreased litter quality (high C:N), reduced litter decomposition-related soil enzyme activity, decreased the diversity of bacteria, and altered microbial community structure and potential functional gene abundance linked to litter decomposition. These findings revealed that MPs could affect the main process of C and N cycling in wetland ecosystems, providing important cues for further research on the wetland ecosystem function.

Elucidation of the complete degradation mechanism of N,N-dimethylformamide (DMF) and substrate preference within a synthetic bacterial consortium (DMFsyn) formed via a “top-down” strategy

The challenge posed by the chemical stability of N,N-dimethylformamide (DMF) renders its biological treatment a complex endeavor. Despite the isolation and characterization of numerous DMF-degrading bacterial strains, their limited adaptability to diverse environments has resulted in suboptimal efficacy in the treatment of actual DMF-containing wastewater. This research aims to address this predicament by employing a “top-down” approach to engineer a synthetic bacterial community termed DMFsyn. The mineralization of 0.5 % (v/v) DMF (∼4725 mg L−1) was efficiently carried out by DMFsyn within 4 days. Notably, robust DMF degradation capabilities across a broad spectrum of environmental conditions were observed. In scenarios where N,N-dimethylacetamide (DMAC) and N-methylpyrrolidone (NMP) coexisted with DMF, degradation followed a sequential pattern: NMP > DMAC > DMF. Through 16S rRNA gene sequencing, and metagenomic analysis, potential functional genes and species responsible for DMF degradation were unveiled. The active DMF degraders in DMFsyn, including Paracoccus aminovorans bin8, Hyphomicrobium sulfonivorans bin2, Hyphomicrobium zavarzinii bin0, Paracoccus zhejiangensis bin23, and Aquamicrobium lusatiense bin4, were substantiated by metaproteomic analysis. Furthermore, another DMF-mineralizing bacterium Aminobacter niigataensis DMFA1 was isolated from DMFsyn. Molecular dynamics simulations indicated that the preference for DMAC over DMF at the community level is dictated by the substrate specificity of DMFases from Sphingosinicella microcystinivorans bin6. By harnessing a multi-omics approach, conducting pure culture studies, and employing molecular simulations, an intricate mechanism governing DMF degradation and substrate preference within the DMFsyn was elucidated.

Genome wide association analysis identifies candidate genes for fruit quality and yield in Actinidia eriantha

Quality and yield are the primary concerns in kiwifruit breeding, but research on the genetic mechanisms of fruit size, shape, and ascorbic acid (ASA) content is currently very limited, which restricts the development of kiwifruit molecular breeding. In this study, we obtained a total of 8.88 million highly reliable single nucleotide polymorphism (SNP) markers from 140 individuals from the natural hybrid offspring of Actinidia eriantha cv. ‘White’ using whole genome resequencing technology. A genome-wide association study was conducted on eight key agronomic traits, including single fruit weight, fruit shape, ASA content, and the number of inflorescences per branch. A total of 59 genetic loci containing potential functional genes were located, and candidate genes related to single fruit weight, fruit length, ASA content, number of inflorescences per branch and other traits were identified within the candidate interval, such as AeWUSCHEL, AeCDK1 (cell cycle dependent kinase), AeAO1 (ascorbic oxidase) and AeCO1 (CONSTANS-like 4). After constructing an RNAi vector for AeAO1 and injecting it into the fruit of cv. ‘Midao 31’ to interfere with the expression of the AeAO1 gene, the results showed that the activity of ascorbic oxidase in the fruit of ‘Midao 31’ significantly decreased, while the content of ASA significantly increased. This study provides valuable insights into the genetic basis of variation in A. eriantha fruit traits, which may benefit molecular marker-assisted breeding efforts.

Natural killer cell-related prognosis signature predicts immune response in colon cancer patients.

Background: Natural killer (NK) cells are crucial components of the innate immune system that fight tumors and viral infections. Patients with colorectal cancer (CRC) have a poor prognosis, and immunotherapeutic tools play a key role in the treatment of CRC. Methods: Public data on CRC patients was collected from the TCGA and the GEO databases. Tissue data of CRC patients were collected from Guangxi Medical University Affiliated Cancer Hospital. An NK-related prognostic model was developed by the least absolute shrinkage and selection operator (LASSO) and Cox regression method. Validation data were collected from different clinical subgroups and an external independent validation cohort to verify the model's accuracy. In addition, multiple external independent immunotherapy datasets were collected to further examine the value of NK-related risk scores (NKRS) in the prediction of immunotherapy response. Potential biological functions of key genes were examined by methods of cell proliferation, apoptosis and Western blotting. Results: A novel prognostic model for CRC patients based on NK-related genes was developed and NKRS was generated. There was a significantly poorer prognosis among the high-NKRS group. Based on immune response prediction, patients with low NKRS may be more suitable for immunotherapy and they are more sensitive to immunotherapy. The proliferation rate of CRC cells was significantly reduced and apoptosis of CRC cells was increased after SLC2A3 was knocked down. SLC2A3 was also found to be associated with the TGF-β signaling pathway. Conclusion: NKRS has potential applications for predicting prognostic status and response to immunotherapy in CRC patients. SLC2A3 has potential as a therapeutic target for CRC.

N-carbamylglutamate supplementation induces functional egg production in layers by modulating liver transcriptome profiles

Eggs rich in polyunsaturated fatty acids (PUFA), known as functional eggs, are animal products deemed beneficial to human health and possess high economic value. The production of functional eggs involves supplementing exogenous additives with the ability to regulate lipid metabolism. As N-Carbamylglutamate (NCG) serves as an endogenous arginine synthesizer, and arginine acts as the substrate for the formation of nitric oxide (NO), the biological function of NCG is partially mediated by NO. NO is a key regulatory molecule in lipid metabolism, suggesting that NCG may also have the ability to modulate lipid metabolism. In order to assess the capacity of NCG in regulating liver lipid metabolism and its potential application in producing functional eggs, we conducted a study to investigate the effects of dietary supplementation of NCG on production performance, serum, and liver NO levels, yolk fatty acid composition, and the liver transcriptome of layers. In this study, we utilized 30 layers of the Jinghong No.1 breed, all aged 45 wk. All the birds were randomly divided into 2 groups. Each group had 5 replicates, and each replicate had 3 birds. We provided them with different diets: one group received the basic diet, and the other group's diet was supplemented with 0.08% NCG. The experiment lasted for 14 wk. The results did not reveal any positive impact of NCG on production performance. However, NCG supplementation elevated NO levels in serum and liver, along with an increase in yolk PUFA, ω-3, and ω-6 fatty acids. Liver transcriptome analysis identified 124 upregulated differentially expressed genes (DEGs) and 43 downregulated DEGs due to NCG supplementation. Functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database highlighted 3 upregulated DEGs (CPT1A, MOGAT1, and CHKA) and 2 downregulated DEGs (FASN and ETNPPL) associated with lipid metabolism. Pathway enrichment analysis revealed that CPT1A was enriched in the AMPK signaling pathway and the PPAR signaling pathway, while FASN was enriched in the AMPK signaling pathway. Thus, CPT1A and FASN are potential functional genes related to lipid metabolism facilitated by NCG supplementation. In summary, our study suggests that NCG supplementation modulates liver lipid metabolism, leading to the production of functional eggs in layers.

Genome-Wide Identification and Expression Analysis of bZIP Family Genes in Stevia rebaudiana.

The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors widely distributed in eukaryotic organisms. In plants, they are not only involved in growth and development, defense and stress responses and regulation of physiological processes but also play a pivotal role in regulating secondary metabolism. To explore the function related to the bZIP gene family in Stevia rebaudiana Bertoni, we identified 105 SrbZIP genes at the genome-wide level and classified them into 12 subfamilies using bioinformation methods. Three main classes of cis-acting elements were found in the SrbZIP promoter regions, including development-related elements, defense and stress-responsive elements and phytohormone-responsive elements. Through protein-protein interaction network of 105 SrbZIP proteins, SrbZIP proteins were mainly classified into four major categories: ABF2/ABF4/ABI5 (SrbZIP51/SrbZIP38/SrbZIP7), involved in phytohormone signaling, GBF1/GBF3/GBF4 (SrbZIP29/SrbZIP63/SrbZIP60) involved in environmental signaling, AREB3 (SrbZIP88), PAN (SrbZIP12), TGA1 (SrbZIP69), TGA4 (SrbZIP82), TGA7 (SrbZIP31), TGA9 (SrbZIP95), TGA10 (SrbZIP79) and HY5 (SrbZIP96) involved in cryptochrome signaling, and FD (SrbZIP72) promoted flowering. The transcriptomic data showed that SrbZIP genes were differentially expressed in six S. rebaudiana cultivars ('023', '110', 'B1188', '11-14', 'GP' and 'GX'). Moreover, the expression levels of selected 15 SrbZIP genes in response to light, abiotic stress (low temperature, salt and drought), phytohormones (methyl jasmonate, gibberellic acid and salicylic acid) treatment and in different tissues were analyzed utilizing qRT-PCR. Some SrbZIP genes were further identified to be highly induced by factors affecting glycoside synthesis. Among them, three SrbZIP genes (SrbZIP54, SrbZIP63 and SrbZIP32) were predicted to be related to stress-responsive terpenoid synthesis in S. rebaudiana. The protein-protein interaction network expanded the potential functions of SrbZIP genes. This study firstly provided the comprehensive genome-wide report of the SrbZIP gene family, laying a foundation for further research on the evolution, function and regulatory role of the bZIP gene family in terpenoid synthesis in S. rebaudiana.

Identification of miRNAs Involved in Intracranial Aneurysm Rupture in Cigarette-Smoking Patients.

Smoking is an independent risk factor for the formation and rupture of intracranial aneurysms (IA). However, the underlying mechanism remains unclear. In this study, we performed miRNA sequencing on plasma from 10 smoking patients with IA, 10 non-smoking patients with IA, and 10 healthy controls. The differentially expressed miRNAs (DE miRNAs) between smoking and non-smoking patients with IA were identified. Functional and pathway enrichment analysis is employed to investigate the potential functions of those DE miRNA target genes. The correlations with the clinical parameters were assessed using receiver operating characteristic curve (ROC) analysis. In total, we identified 428 DE miRNAs. Functional enrichment analysis showed the target genes were significantly enriched in biological aspects related to cell characteristics, such as cell cycle, cell differentiation, and cell migration. Pathway analysis showed DE miRNAs mainly enriched in the PI3K-Akt signaling pathway, Focal adhesion, and JAK-STAT signaling pathway. The expressions of miR-574-5p, miR-151a-3p, and miR-652-3p correlated well with aneurysm parameters. The AUC of miR-574-5p, miR-151a-3p, and miR-652-3p were 97%, 92%, and 99%, respectively. Our study indicated that smoking significantly altered the plasma miRNA profile in patients with IA. The expression of miR-574-5p, miR-151a-3p, and miR-652-3p correlated with aneurysm parameters, which may play a significant role in the formation and rupture of IA.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

Transcriptional analysis of human peripheral blood mononuclear cells stimulated by Mycobacterium tuberculosis antigen.

Mycobacterium tuberculosis antigen (Mtb-Ag) is a polypeptide component with a molecular weight of 10-14 kDa that is obtained from the supernatant of the H37Ra strain after heat treatment. It stimulates the activation and proliferation of γδT cells in the blood to produce an immune response against tuberculosis. Mtb-Ag is therefore crucial for classifying and detecting the central genes and key pathways involved in TB initiation and progression. In this study, we performed high-throughput RNA sequencing of peripheral blood mononuclear cells (PBMC) from Mtb-Ag-stimulated and control samples to identify differentially expressed genes and used them for gene ontology (GO) and a Kyoto Encyclopedia of Genomes (KEGG) enrichment analysis. Meanwhile, we used PPI protein interaction network and Cytoscape analysis to identify key genes and qRT-PCR to verify differential gene expression. Single-gene enrichment analysis (GSEA) was used further to elucidate the potential biological functions of key genes. Analysis of immune cell infiltration and correlation of key genes with immune cells after Mtb-Ag-stimulated using R language. We identified 597 differentially expressed genes in Mtb-Ag stimulated PBMCs. KEGG and GSEA enrichment analyzed the cellular pathways related to immune function, and DEGs were found to be primarily involved in the TNF signaling pathway, the IL-17 signaling pathway, the JAK-STAT signaling pathway, cytokine-cytokine receptor interactions, and the NF-κB signaling pathway. Wayne analysis using GSEA, KEGG, and the protein-protein interaction (PPI) network showed that 34 genes, including PTGS2, IL-1β, IL-6, TNF and IFN-γ etal., were co-expressed in the five pathways and all were up-regulated by Mtb-Ag stimulation. Twenty-four DEGs were identified using qRT-PCR, including fourteen up-regulated genes (SERPINB7, IL20, IFNG, CSF2, PTGS2, TNF-α, IL36G, IL6, IL10, IL1A, CXCL1, CXCL8, IL4, and CXCL3) and ten down-regulated genes (RTN1, CSF1R CD14, C5AR1, CXCL16, PLXNB2, OLIG1, EEPD1, ENG, and CCR1). These findings were consistent with the RNA-Seq results. The transcriptomic features associated with Mtb-Ag provide the scientific basis for exploring the intracellular immune mechanisms against Mtb. However, more studies on these DEGs in pathways associated with Mtb-Ag stimulation are needed to elucidate the underlying pathologic mechanisms of Mtb-Ag during Mtb infection.

Biomarkers associated with severity classification of asthma identified by comprehensive bioinformatics analysis

Using an integrated bioinformatics approach to find novel biomarkers that can predict asthma severity. From June 2022 to December 2022, this clinical medical study was conducted and completed in the Department of Allergy, Zhongnan Hospital of Wuhan University. The gene chip dataset GSE43696 was screened and downloaded from the high-throughput Gene Expression Omnibus (GEO) database, and the gene chip data preprocessing was completed using package "affy" in R and "rma" algorithm in turn. Use the the "edgeR" and "limma" packages to screen out the differentially expressed genes (DEGs) between normal controls, mild to moderate asthma patients and severe asthma patients, and then use the "clusterProfiler" package to perform GO enrichment analysis and KEGG pathway enrichment analysis of DEGs, finally use the STRING website to construct a protein-protein interaction (PPI) network of DEGs to further screen key genes. Using the R language "WGCNA" package, the weighted gene co-expression network analysis (WGCNA) was performed on the dataset GSE43696, and the modules significantly related to the severity of asthma were screened out, then the hub genes were obtained by intersecting the WGCNA analysis results with the DEGs screened by PPI. Datasets GSE43696 and GSE63142 were used to verify the expression of hub genes, and the diagnostic value was evaluated according to the ROC curve, then the potential function of hub genes in dataset GSE43696 was further clarified by gene set enrichment analysis (GSEA). The results showed that a total of 251 DEGs were screened, including 39 in the normal group and mild to moderate asthma group, 178 in the normal group and severe asthma group, and 34 in the mild to moderate asthma group and severe asthma group, mainly involved in biological processes such as response to toxic substance, response to oxidative stress, extracellular structure organization, extracellular matrix organization. Two modules significantly correlated with asthma severity were screened out (red module, P=7e-6, r=0.43; pink module, P=5e-8, r=-0.51), and finally six hub genes were obtained, including B3GNT6, CEACAM5, CCK, ERBB2, CSH1 and DPPA5. The comparison of gene expression levels and ROC curve analysis of datasets GSE43696 and GSE63142 further verified the six hub genes, which may associated with o-glycan biosynthesis, alpha linolenic acid metabolism, linoleic acid metabolism, pentose and glucoronate interconversions. In conclusion, through a variety of bioinformatics analysis methods, this study identified six hub genes significantly related to the severity of asthma, which potentially provided a new direction for the prediction and targeted therapy of asthma.