High-throughput Bioinformatics Research Articles

Identification and validation of lung adenocarcinoma (LUAD)-associated targets for monascin from the extracts of Monascus purpureus-fermented rice: Compound preparation, high-throughput genome sequencing and bioinformatics analysis

Despite the remarkable bioactivities exhibited by monascin against several tumors, its therapeutic targets remain unexplored. In this study, our objective is to identify therapeutic targets based on the antitumor activity of monascin against lung adenocarcinoma (LUAD) A549 cells. The compound monascin was derived from extracts of Monascus purpureus-fermented rice. Its chemical structure was determined using spectroscopic methods, while the physicochemical properties of monascin were investigated through thermal behavior analysis. Herein, antitumor studies indicated that monascin significantly inhibited the viability of A549 cells, with an IC50 value of 2.05 μM; RNA-sequencing revealed 12 up-regulated and 29 down-regulated genes as differentially expressed genes (DEGs) for A549 cells in response to monascin; RT-qPCR validation supported the plausibility of the RNA-sequencing results. Moreover, utilizing data from the Cancer Genome Atlas (TCGA) database, univariate and multivariate Cox regression analyses provided evidence supporting GPR37 and FAM83A as potential candidate genes for predicting disease progression in LUAD patients. Additionally, the LASSO Cox regression and nomogram analyses confirmed that FAM83A and GPR37 genes had the potential to predict overall survival for LUAD patients. Finally, molecular docking studies suggested that monascin could interact with both GPR37 and FAM83A proteins through the hydrogen bonding and hydrophobic interactions; Western blotting assays indicated that monascin inhibited the expression levels of both GPR37 and FAM83A proteins. Overall, the clinical prognosis of GPR37 and FAM83A highlights the rationale for targeting these specific genes with monascin. Additionally, there findings provide compelling evidence for the ploypharmacological properties of monascin against LUAD.

Characteristics and Functions of Rhizosphere Bacterial Communities of Camelli sinensis cv. Shifocui with Cold Resistance Characteristics in Anhui Province, China.

The rhizosphere bacterial community of plants has a crucial effect on healthy plant growth, and each rhizosphere has a specific microbial community. Camellia sinensis cv. Shifocui (C. sinensis cv. Shifocui) is a tea plant distributed in the Dabie Mountains of Anhui Province. It has the characteristics of high yield, good quality, strong cold resistance, and a high amino acid content. This study was the first to use 16S rRNA high-throughput sequencing technology and bioinformatics methods to explore the characteristics and functions of the rhizosphere bacterial community of the cold-tolerant tea tree C. sinensis cv. Shifocui, providing an important basis for the development and utilization of rhizosphere microbial resources. The dominant phylum in the rhizosphere microbes of the C. sinensis cv. Shifocui rhizosphere microorganisms were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteria. Network analysis showed significant positive and negative correlations among the rhizosphere bacterial groups of C. sinensis cv. Shifocui, among which Candidatus _ Xiphinematobacter, Acidobacteriale, Bradyrhizobium, Subgroup _ 2, Candidatus_Udaeobacter, Gemmataceae, and Gaiellales were notable nodes in theinteraction networks. Functional prediction of FAPROTAX indicated that C. sinensis cv. Shifocui was rich in chemoheterotrophic, cellulose hydrolysis, and oxidative heterotrophic conditions, indicating that the dominant bacterial flora was enriched in its rhizosphere microbes and played an important role in plant growth and development. These results lay a foundation for exploring the mechanism of interaction between C. sinensis cv. Shifocui and rhizosphere microorganisms and provide a research basis for the development and utilization of tea plant microbial resources.

The T2T Genome of the Domesticated Silkworm Bombyx mori.

Genome sequences contain the fundamental genetic information that largely determines the biology of a species. Over the past 20 years, advancements in high-throughput sequencing technologies and bioinformatics tools have matured, facilitating genome assembly and ushering in the telomere-to-telomere (T2T) era. Bombyx mori is renowned as a silk-producing insect and serves as an important model organism extensively studied across various fields of biology. In this study, we present the first assembled T2T genome by integrating HiFi, ultra-long ONT, NGS, and Hi-C data. This assembly comprises 450,267,439 base pairs from 28 chromosomes and includes annotations for a total of 18,253 protein-coding genes. A completeness evaluation revealed that 99.1% of conserved single-copy genes were included, as determined by a BUSCO analysis. Furthermore, the consensus quality (QV) assessed through Merqury was recorded at 59.88. The proportion of repeat sequence achieved 60.77%, marking it as the highest reported value for B. mori to date. In comparison to previously published genomes, our assembly offers a more complete and higher quality representation, particularly concerning highly homologous tandem regions such as telomeres, rDNA clusters, and Gr family regions. Furthermore, our extensive experience in genome assembly, including sample preparation experience and assembly strategies to reduce complexity, will provide valuable references for other species aiming to achieve their own T2T genome assemblies.

BIRC3 induces the phosphoinositide 3-kinase-Akt pathway activation to promote trastuzumab resistance in human epidermal growth factor receptor 2-positive gastric cancer.

Trastuzumab-targeted therapy is currently the standard of care for advanced human epidermal growth factor receptor 2 (HER2)-positive gastric cancer. However, the emergence of resistance to trastuzumab poses significant challenges. To identify the key genes associated with trastuzumab resistance. These results provide a basis for the development of interventions to address drug resistance and improve patient outcomes. High-throughput sequencing and bioinformatics were used to identify the differentially expressed pivotal gene BIRC3 and delineate its potential function and pathway regulation. Tumor samples were collected from patients with HER2-positive gastric cancer to evaluate the correlation between BIRC3 expression and trastuzumab resistance. We established gastric cancer cell lines with both highly expressed and suppressed levels of BIRC3, followed by comprehensive in vitro and in vivo experiments to confirm the involvement of BIRC3 in trastuzumab resistance and to elucidate its underlying mechanisms. In patients with HER2-positive gastric cancer, there is a significant correlation between elevated BIRC3 expression in tumor tissues and higher T stage, tumor node metastasis stage, as well as poor overall survival and progression-free survival. BIRC3 is highly expressed in trastuzumab-resistant gastric cancer cell lines, where it inhibits tumor cell apoptosis and enhances trastuzumab resistance by promoting the phosphorylation and activation of the phosphoinositide 3-kinase-Akt (PI3K-AKT) pathway in HER2-positive gastric cancer cells, both in vivo and in vitro. This study revealed a robust association between high BIRC3 expression and an unfavorable prognosis in patients with HER2-positive gastric cancer. Thus, the high expression of BIRC3 stimulated PI3K-AKT phosphorylation and activation, stimulating the proliferation of HER2-positive tumor cells and suppressing apoptosis, ultimately leading to trastuzumab resistance.

Nonselective beta blockade enhances gut microbiome diversity in a rodent model of trauma, hemorrhage, and chronic stress

BACKGROUND Traumatic injury leads to gut dysbiosis with changes in microbiome diversity and conversion toward a “pathobiome” signature characterized by a selective overabundance of pathogenic bacteria. The use of non-selective beta antagonism in trauma patients has been established as a useful adjunct to reduce systemic inflammation. We sought to investigate whether beta-adrenergic blockade following trauma would prevent the conversion of microbiome to a “pathobiome” phenotype. METHODS Sprague-Dawley rats (n = 6–8/group) were subjected to routine daily handling (naïve), lung contusion with hemorrhagic shock (LCHS), or LCHS with daily chronic stress (LCHS/CS), each with or without administration of intraperitoneal propranolol (BB) (10 mg/kg/day). Fecal microbiome was measured on Days 0, 7, and 14 using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Alpha- and beta-diversity and microbiome composition were assessed with significance defined as *p < 0.05. RESULTS Use of propranolol following LCHS or LCHS/CS demonstrated a significant increase in the number of bacterial species (Chao1 index), as well as overall richness and evenness (Shannon index) compared with their untreated counterparts at Day 7. By Day 14, these differences were no longer apparent between BB and untreated groups subjected to LCHS/CS. There was an abundance of commensal bacteria such as Oscillospiraceae and Clostridia in LCHS and LCHS/CS treated with BB after 7 days which persisted at 14 days. CONCLUSION These findings suggest a role for beta-antagonism in altering the diversity of the gut microbiome and the need for further studies to elucidate the cellular and molecular mechanisms underlying this intriguing connection of microbiome with trauma and beta-blockade.

Community assembly and potential function analysis of the endophyte in Eucommia ulmoides

Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.

Unraveling the genetic and physiological potential of donkeys: insights from genomics, proteomics, and metabolomics approaches.

Donkeys (Equus asinus) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultural, and medical industries. Despite their critical importance, research on donkeys has historically been overshadowed with studies on horses. However, recent advancements in high-throughput sequencing and bioinformatics have significantly deepened our understanding of the molecular landscape of donkey genome, uncovering their unique adaptations, genetic diversity, and potential therapeutic applications. Microsatellite and mitochondrial DNA (mtDNA) markers have proven effective in assessing the genetic diversity of donkeys across various regions of the world. Additionally, significant strides have been made in characterizing differentially abundant genes, proteins, and metabolic profiles in donkey milk, meat, and skin, and in identifying specific genes/proteins/metabolites associated with sperm quality, motility, and reproduction. Advanced genomic technologies, such as genome-wide association studies and the identification of selection signatures, have also been instrumental in delineating genomic regions associated with phenotypic and adaptive traits. This review integrates data from diverse studies, including those on genetic diversity, transcriptomics, whole genome sequencing, protein analysis, and metabolic profiling, to provide a comprehensive overview of donkey biology. It underscores the unique characteristics of donkeys and emphasizes the importance of continued research to improve their genetic management, conservation, and agricultural use, ensuring their ongoing contribution to human societies.

Beyond chromosomal rearrangements: The expanding landscape of gene fusions and chimeric RNAs

BCR–ABL, the pioneering gene fusion resulting from chromosomal translocation, has marked a major milestone in understanding genetic alterations in cancer. Initially, gene fusions were linked solely to chromosomal rearrangements, serving as diagnostic markers and cancer drivers. However, advancements in high-throughput sequencing and bioinformatics have revealed additional mechanisms underlying gene fusion. The term “gene fusion” primarily refers to fusion events at the DNA level, whereas “chimeric RNA” encompasses a wide range of transcripts containing exons from different parental genes, including gene fusion transcripts. Recent developments have identified numerous chimeric RNAs in various cancer types, extending even to non-cancerous tissues. Chimeric RNAs, originating from events such as trans-splicing, read-through, and intergenic splicing, form a complex landscape with varied functions. While some chimeric RNAs have defined roles and therapeutic potential, a comprehensive understanding of their diverse functions remains a priority. Exploring the full spectrum of chimeric RNA activities is crucial for revealing their clinical and therapeutic implications. In addition, chimeric RNAs are key players in tumorigenesis, affecting cellular processes, and driving cancer progression. Understanding their intricate interactions with cellular pathways is essential for developing targeted therapies and precision medicine approaches. The dynamic nature of chimeric RNAs highlights the need for ongoing research to fully harness their diagnostic and therapeutic potential.

Characteristics of the IgM Repertoires in the Peripheral Blood of Early Rheumatoid Arthritis Patients.

Rheumatoid arthritis is a common autoimmune disease, but little is known about the characteristics of the B cell repertoires in the peripheral blood. In this study, the peripheral IgM repertoires of early rheumatoid arthritis (ERA) patients were analyzed by high-throughput sequencing and bioinformatics analyses. Clonal expansion was observed in IgM repertoires of ERA patients. Interestingly, a subset of the dominant clones in ERA repertoires showed self- and poly-reactivity to several autoantigens. The clones were also present in IgM repertoires of healthy adults but they were not expanded, suggesting that may stem from the natural auto-reactive B cell repertoire. Additionally, the ERA repertoires exhibited a greater extent of somatic hypermutations, particularly in the ERA dominant clones, resulting in an enrichment of amino acids important for antigen-antibody interaction. The in-depth analysis of B-cell repertoires improved our knowledge of the IgM repertoires in early rheumatoid arthritis, offering potential insights into the disease's pathogenesis.

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions.

Exploring novel preservation strategies for blue honeysuckle through high-throughput sequencing and bioinformatics analysis

Berries’ metabolic activities continue post-harvest, and their quality and safety are affected by various external and internal factors, with microbial contamination being one of the major influences. Refrigeration is necessary to preserve freshness and increase shelf life; however, understanding the changes in microbial communities on berries during refrigeration still is in its infancy. This study examines the diversity and dynamics of epidermal microbes on blue honeysuckle during refrigeration. Blue honeysuckle was refrigerated at 4 °C for 0, 4, 8, and 12 d, with microbial communities analyzed via Illumina Novaseq sequencing. Species distribution revealed dominant Ascomycota and Basidiomycota in fungi, Proteobacteria and Firmicutes in bacteria, with fluctuating abundance over time. Through tissue isolation, Alternaria alternata and Irpex lacteus were successfully separated and validated as predominant decay-causing fungi. Additionally, lactobacilli were isolated and screened for inhibiting decay-causing fungi, with Enterococcus faecium showing significant efficacy. Factors influencing its activity were evaluated, with temperature and pH impacting efficacy. Enzyme treatments indicated the role of peptides in inhibition. In vivo tests demonstrated preservation efficacy, highlighting bio-preservation potential for quality maintenance during storage. The study's workflow emphasizes exploring microbial ecological interventions that can be implemented in bio-preservation strategies, thereby enhancing understanding and management of post-harvest quality in berries, particularly blue honeysuckle.

Deciphering Immunotoxicity in Animal-Derived Biomaterials: A Genomic and Bioinformatics Approach

Immunotoxicity evaluation has been crucial in preclinical testing for implantable animal-derived biomaterials due to their prolonged contact with the human body, which requires stringent safety assessments. By creating experimental models with varying levels of immunotoxicity, this study reveals the decisive role of decellularization treatment in diminishing the immunogenicity of materials, thus ensuring clinical safety. Employing cutting-edge differential gene expression analysis, the research not only accurately quantifies gene expression alterations in immune responses but also, through pathway enrichment analysis, identifies gene networks associated with oncogenesis. This offers novel insights into the mechanisms of immune responses following biomaterial implantation. Additionally, the study highlights the importance of developing highly sensitive immunotoxicity testing methods and validates the efficacy of high-throughput sequencing and bioinformatics tools in assessing biomaterial safety, providing robust scientific support for future preclinical evaluations.

Regulation of hippocampal miRNA expression by intestinal flora in anxiety-like mice

This study investigated the possible interaction between gut flora and miRNAs and the effect of both on anxiety disorders. The model group was induced with chronic restraint stress (CRS) and each group was tested for anxiety-like behaviour by open field test and elevated plus maze test. Meanwhile, the gut flora was analysed by 16S rRNA high-throughput sequencing. The miRNAs in hippocampus were analysed by high-throughput sequencing, and the key miRNAs were obtained by using the method of bioinformatics analysis. PCR was used to verify the significantly related key miRNAs. Spearman correlation analysis was used to explore the correlation between behaviour, key miRNAs and differential gut microbiota. The 16S rRNA high-throughput sequencing result showed that the gut flora was dysregulated in the model group. In particular, Verrucomicrobia, Akkermansia, Anaerostipes, Ralstonia, Burkholderia and Anaeroplasma were correlated with behaviour. The results of miRNA high-throughput sequencing analysis and bioinformatics analysis showed that 7 key miRNAs influenced the pathogenesis of anxiety, and qRT-PCR results were consistent with the high-throughput sequencing results. Mmu-miR-543-3p and mmu-miR-26a-5p were positively correlated with Verrucomicrobia, Akkermansia and Anaerostipes. Therefore, we infer that chronic stress caused the decrease of Akkermansia abundance, which may aggravate the decrease of mmu-miR-543-3p and mmu-miR-26a-5p expression, leading to the increase of SLC1A2 expression. In conclusion, gut flora has played an important influence on anxiety with changes in miRNAs.

Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis

The discovery of Lactylation may pave the way for novel approaches to investigating sepsis. This study focused on the prognostic and diagnostic significance of lactylated genes in sepsis. RNA sequencing was performed on blood samples from 20 sepsis patients and 10 healthy individuals at Southwest Medical University in Luzhou, Sichuan, China. Genes associated with sepsis were identified through analysis of RNA sequencing data. Afterward, the genes that were expressed differently were compared with the lactylation genes, resulting in the identification of 55 lactylation genes linked to sepsis. The overlapping genes underwent analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Protein-Protein Network Interactions were used to screen for the core genes. The datasets GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233 were obtained from the GEO database to validate core genes. Survival analysis evaluated the predictive significance of central genes in sepsis, while Receiver Operating Characteristic (ROC) Curve analysis was employed to establish the diagnostic value of genes. Additionally, a meta-analysis was conducted to confirm the precision of RNA-seq data. We obtained five peripheral blood samples, including two from healthy individuals, one from a patient with systemic inflammatory response syndrome (SIRS), and two from patients with sepsis. These samples were used to identify the specific location of core genes using 10×single-cell sequencing. High-throughput sequencing and bioinformatics techniques identified two lactylation-related genes (S100A11 and CCNA2) associated with sepsis. Survival analysis indicated that septic patients with reduced levels of S100A11 had a decreased 28-day survival rate compared to those with elevated levels. Conversely, individuals exhibiting decreased CCNA2 levels demonstrated a greater likelihood of surviving for 28 days than those in the high expression category, indicating a favorable association with survival rates among sepsis patients (P < 0.05). Both genes showed high sensitivity and specificity based on the ROC curve, with AUC values of 0.961 for S100A11 and 0.890 for CCNA2. The meta-analysis revealed that S100A11 exhibited high levels of expression in the sepsis survivors, whereas it displayed low levels of expression in the non-survivors; on the other hand, CCNA2 demonstrated low expression in the sepsis survivors and high expression in the non-survivors (P < 0.05). Single-cell RNA sequencing ultimately showed that monocyte macrophages, T cells, and B cells exhibited high expression levels of the crucial genes associated with sepsis-induced lactylation. In conclusion, the lactylation genes S100A11 and CCNA2 are strongly linked to sepsis and could be valuable markers for diagnosing, predicting outcomes, and providing guidance for sepsis.

The Modifications of Longevity Regulating Pathway Resulting from Endurance Effort in Arabian Horses

Abstract Recent studies have shown a highly positive effect of physical exercise on the overall condition of the body. The observed changes occur at the cellular level – proliferation, oxidative respiration, ROS degradation, whole-organism homeostasis improvement and ageing inhibition. The longevity regulating pathway is a broad term encompassing all the biochemical actions that contribute to keeping the organism in good condition and prolonging life duration. The overall aim of the present study was to describe the correlation between intensive physical activity and the expression of genes involved in biochemical processes related to longevity. A group of n=10 Arabian horses taking part in an endurance ride for 120 km were included in the study. Blood samples from the horses were taken before and after the ride to perform comparative analyses of the transcriptome profiles. Using high-throughput NGS and bioinformatics tools, the group of 9 genes with the highest up- and downregulation fold change (FC) rates were identified: PTEN, IRS2, SESN2, CCND1, TBC1D1, FOXO1, KL, TP53, and SOD2. The results of this study could lead to the identification of a genetic marker for hot-blooded horse breeding.

Honokiol Exhibits Anti-Tumor Effects in Breast Cancer by Modulating the miR-148a-5p-CYP1B1 Axis.

Breast cancer (BC) is the most frequently diagnosed malignancy in female patients. There is a significant lack of therapeutic strategies for BC, particularly triple-negative breast cancer (TNBC). Honokiol (HNK), a lignin extracted from the Magnolia genus plant, has demonstrated numerous pharmacological effects. Therefore, this study aims to investigate the antitumor effect of HNK on BC cells and employ high-throughput sequencing to elucidate its potential mechanism. We found that HNK significantly inhibited proliferation and induced apoptosis on BC cell lines in a dose-dependent manner. Moreover, HNK treatment suppressed migration and colony formation and initiated the intrinsic apoptotic pathway specifically in MDA-MB-231 cells. High-throughput sequencing and bioinformatics analysis revealed that miR-148a-5p expression was significantly up-regulated, whereas CYP1B1 expression was down-regulated following HNK treatment. Importantly, survival analysis based on TCGA database showed high miR-148a-5p expression was correlated with a better prognosis for BC patients. Inhibition of miR-148a-5p by inhibitor not only increased cell viability but also attenuated apoptosis induced by HNK.Finally, a strong synergistic effect between HNK and paclitaxel was observed in vitro. In conclusion, our study validated the antitumor efficacy of HNK against human BC cells and elucidated its underlying mechanism through high-throughput sequencing, thereby providing compelling evidence for further exploration of the potential clinical application of HNK towards the treatment of BC.

Insights into cytomegalovirus-associated T cell receptors in recipients following allogeneic hematopoietic stem cell transplantation

BackgroundCytomegalovirus (CMV) reactivation is a serious problem in recipients of allogeneic hematopoietic stem cell transplantation. Long-term latency depends on specific T cell immune reconstitution, which identifies various pathogens by T cell receptors (TCRs). However, the mechanisms underlying the selection of CMV-specific TCRs in recipients after transplantation remain unclear.MethodsUsing high-throughput sequencing and bioinformatics analysis, the T cell immune repertoire of seven CMV reactivated recipients (CRRs) were analyzed and compared to those of seven CMV non-activated recipients (CNRs) at an early stage after transplant.ResultsThe counts of unique complementarity-determining region 3 (CDR3) were significantly higher in CNRs than in CRRs. The CDR3 clones in the CNRs exhibit higher homogeneity compared to the CRRs. With regard to T cell receptor β-chain variable region (TRBV) and joint region (TRBJ) genotypes, significant differences were observed in the frequencies of TRBV6, BV23, and BV7–8 between the two groups. In addition to TRBV29–1/BJ1–2, TRBV2/BJ2–2, and TRBV12–4/BJ1–5, 11 V-J combinations had significantly different expression levels between CRRs and CNRs.ConclusionsThe differences in TCR diversity, TRBV segments, and TRBV-BJ combinations observed between CNRs and CRRs might be associated with post-transplant CMV reactivation and could serve as a foundation for further research.

Integrated analysis of circRNA regulation with ADARB2 enrichment in inhibitory neurons

This study investigates the regulation of circular RNAs (circRNAs) with Adenosine Deaminase RNA Specific B2 (ADARB2) enrichment specifically in inhibitory neurons. Using an integrated analysis combining high-throughput sequencing and bioinformatics approaches, we identified a group of circRNAs that are potentially enhanced by ADARB2. Our findings highlight the pivotal role of ADARB2 in circRNA synthesis within inhibitory neurons, likely through its specific binding to precursor RNAs, which facilitates circRNA biogenesis.

Biomimetic CO2 Capture Unlocked through Enzyme Mining: Discovery of a Highly Thermo- and Alkali-Stable Carbonic Anhydrase.

Taking immediate action to combat the urgent threat of CO2-driven global warming is crucial for ensuring a habitable planet. Decarbonizing the industrial sector requires implementing sustainable carbon-capture technologies, such as biomimetic hot potassium carbonate capture (BioHPC). BioHPC is superior to traditional amine-based strategies due to its eco-friendly nature. This innovative technology relies on robust carbonic anhydrases (CAs), enzymes that accelerate CO2 hydration and endure harsh industrial conditions like high temperature and alkalinity. Thus, the discovery of highly stable CAs is crucial for the BioHPC technology advancement. Through high-throughput bioinformatics analysis, we identified a highly thermo- and alkali-stable CA, termed CA-KR1, originating from a metagenomic sample collected at a hot spring in Kirishima, Japan. CA-KR1 demonstrates remarkable stability at high temperatures and pH, with a half-life of 24 h at 80 °C and retains activity and solubility even after 30 d in a 20% (w/v) K2CO3/pH 11.5 solution─a standard medium for HPC. In pressurized batch reactions, CA-KR1 enhanced CO2 absorption by >90% at 90 °C, 20% K2CO3, and 7 bar. To our knowledge, CA-KR1 constitutes the most resilient CA biocatalyst for efficient CO2 capture under HPC-relevant conditions, reported to date. CA-KR1 integration into industrial settings holds great promise in promoting efficient BioHPC, a potentially game-changing development for enhancing carbon-capture capacity toward industrial decarbonization.

Comparative Tissue Identification and Characterization of Long Non-Coding RNAs in the Globally Distributed Blue Shark Prionace glauca.

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark (Prionace glauca) from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high-confidence lncRNAs were identified, with 8984 and 3067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations.