The fungus Ustilaginoidea virens, which impacts rice spikes, causes rice false smut (RFS), a significant prevalent disease in rice cultivation regions globally. Cytochrome P450 genes are known to be involved in secondary metabolism and pathogenesis in various species, but studies on CYP450 genes in U. virens are limited. In this research, a P450 family gene, CYP503, was found up-regulated during invasion stage of U. virens. Observation of fluorescence indicated that UvCYP503-GFP is situated within cytoplasm of hyphae. Disruption of CYP503 led to decreased hyphal development, conidiation, and pathogenicity. Additional RNA-seq assay revealed that UvCYP503 affects the transcript of genes associated with pathogenicity, various stress responses, and other CYP450 genes. In alignment with RNA-seq results, compared with wild-type, ΔUvcyp503 mutants showed increased sensitivity to cell wall stresses, but reduced sensitivity to osmotic and hyperosmotic stressors. Moreover, ΔUvcyp503 mutants exhibited decreased sensitivity to the fungicides difenoconazole and tebuconazole. This study represents a phenome-based functional analysis of a CYP503 gene in U. virens and provides valuable genetic resources for further research in filamentous fungi and other plant pathogens.

Adipose-derived stem cells (ADSCs) are a type of stem cell found in adipose tissue with the capacity to differentiate into multiple lineages, including osteoblasts. The differentiation of ADSCs into osteoblasts underlies osteogenic and pathological cellular basis in osteoporosis, bone damage and repair.

Focused on ADSCs osteogenic differentiation, we conducted mRNA, microRNA expression and bioinformatics analysis, including gene differential expression, time series-based trend analysis, functional enrichment, and generates potential nuclear activating miRNAs (NamiRNA) regulatory network. The screened mRNAs in NamiRNA regulatory network were validated with correlation analysis.

The NamiRNA Regulatory Network reveals 4 mRNAs (C12orf61, MIR31HG, NFE2L1, and PCYOX1L) significantly downregulated in differentiated group and may be associated with ADSCs stemness. Furthermore, the significantly upregulated 10 genes (ACTA2, TAGLN, LY6E, IFITM3, NGFRAP1, TCEAL4, ATP5C1, CAV1, RPSA, and KDELR3) were significantly enriched in osteogenic-related pathways, and negatively correlated with ADSCs cell stemness in vitro.

These findings uncover potential genes related to ADSCs osteogenic differentiation, and provide theoretical basis for underlying ADSCs osteogenic differentiation and related diseases.

MicroRNAs (miRNAs) have acquired an increased recognition to unravel the complex molecular mechanisms underlying Diminished Ovarian Reserve (DOR), one of the main responsible for infertility. To investigate the impact of miRNA profiles in granulosa cells and follicular fluid, crucial players in follicle development, this study employed a computational network theory approach to reconstruct potential pathways regulated by miRNAs in granulosa cells and follicular fluid of women suffering from DOR. Available data from published research were collected to create the FGC_MiRNome_MC, a representation of miRNA target genes and their interactions. 365 hubs were identified within the network, representing potential key regulators, and 210 nodes that act as both hubs and bottlenecks (H&BN nodes), suggesting that they may control the information flow within the network. GO enrichment analysis of the 210 H&BN nodes revealed their involvement in fundamental cellular processes relevant to ovarian function. In particular, the cluster analysis identified several shared pathways between cluster 1 and cluster 2 involved in the RAS/MAPK pathway, which plays a critical role in cell proliferation, differentiation and survival. These findings suggest that miRNAs play a significant role in DOR and highlight the potential of the RAS/MAPK pathway as a target for further investigation. Additionally, the genes identified as both hubs and bottlenecks revealed interesting connections to reproductive health in KO mice models. This in silico approach provides valuable insights into potential biomarkers and therapeutic targets for age-related reproductive disorders.

Busulfan is the most commonly used drug for the treatment of chronic myelogenous leukemia and pretreatment for hematopoietic stem cell transplantation, which can damage the reproductive and immune system. However, little is known about the protein expression profiling in busulfan treated testis.

This research studies the proteomics for busulfan-induced spermatogenesis disorder. The model of busulfan-induced mouse spermatogenesis disorder was subjected to label-free quantification proteomics analysis. Clustering heatmap, gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein interaction analyses were performed and validated by molecular experiments.

The busulfan-treated mouse model showed abnormal testis morphology and reduced sperm number and testis weight. Testicular and sperm damage was most severe at 30 days after busulfan treatment. The busulfan-treated mouse testes were subjected to label-free quantification proteomics, which revealed 190 significantly downregulated proteins including lactate dehydrogenase A like 6B (LDHAL6B) and ubiquitin-specific protease 7 (USP7). In addition, the testis and spermatozoa in the epididymis progressively improved from 70 to 80 days after busulfan treatment, and that the testis weight and spermatozoa number gradually increased from 40 to 80 days after busulfan treatment. Western blotting revealed that LDHAL6B protein significantly increased at 10 days, decreased from 20 to 60 days, and then gradually elevated from 70 to 80 days after busulfan treatment.

We revealed 190 significantly downregulated proteins in busulfan-treated mouse testes at 30 days and indicated that 70 days is the cut-off point of spermatogenic recovery for busulfan-treated mouse testis, increasing our understanding of this reproductive disorder model. An increased understanding of busulfan's toxic effect will help to prevent and treat reproductive diseases.

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease often leading to rapidly progressive glomerulonephritis. Oxidative stress plays a critical role in the development and progression of ANCA-associated glomerulonephritis (AAGN), but the underlying mechanisms remain poorly understood. Targeting genes related to oxidative stress may provide novel insights and supplementary therapeutic benefits for AAGN. In the current study, we obtained differentially expressed genes from AAGN-related microarray datasets in the Gene Expression Omnibus database, and oxidative stress-related genes (OSRGs) from the GeneCards and Gene Ontology databases to identify differentially expressed OSRGs. Then, by integrating weighted gene co-expression network analysis, and machine learning algorithms, we identified four upregulated hub OSRGs (all p < 0.01) with strong diagnostic potential (all AUC > 0.9)-CD44, ITGB2, MICB, and RAC2 - in the AAGN glomerular training dataset GSE104948 and validation dataset GSE108109, along with two hub OSRGs (all p < 0.05) with better diagnostic potential (all AUC > 0.7) - upregulated gene VCAM1 and downregulated gene VEGFA-in the AAGN tubulointerstitial training dataset GSE104954 and validation dataset GSE108112. The GSEA analysis suggested that these hub genes may play a role in inflammatory and immune response processes. Moreover, we constructed regulatory networks and identified drugs that potentially target these hub genes. It's to be noted that RAC2 and ITGB2 were associated with cyclophosphamide in the AAGN glomerular compartment, while VCAM1 and VEGFA were associated with dexamethasone in the tubulointerstitial compartment. This study offers novel insights into immune-associated OSRGs within the glomerular and tubulointerstitial compartments of AAGN which may serve as innovative targets for diagnosing and treating AAGN.

Stroke is a leading cause of disability and death worldwide. In this study, we identified potential therapeutic targets for stroke using a data mining, network analysis, enrichment, and docking analysis approach. We first identified 1991 genes associated with stroke from two publicly available databases: GeneCards and DisGeNET. We then constructed a protein-protein interaction (PPI) network using the STRING database and identified 1301 nodes and 5413 edges. We used Metascape to perform GO enrichment analysis and KEGG pathway enrichment analysis. The results of these analyses identified ten hub genes (TNF, IL6, ACTB, AKT1, IL1B, TP53, VEGFA, STAT3, CASP3, and CTNNB1) and five KEGG pathways (cancer, lipid and atherosclerosis, cytokine-cytokine receptor interaction, AGE RAGE signaling pathway in complications, and TNF signaling pathway) that are enriched in stroke genes. We then performed molecular docking analysis to screen potential drug candidates for these targets. The results of this analysis identified several promising drug candidates that could be used to develop new therapeutic strategies for stroke.

Thraustochytrids are heterotrophic marine protists known for their ability to produce valuable lipids such as docosahexaenoic acid (DHA). However, like many non-model organisms, they present challenges for transcriptomic studies due to the limited reliable reference genomes and compatibility with curated protein databases, complicating the respective assembly and annotation. This study presents a de novo transcriptome assembly and functional annotation for the recently isolated thraustochytrid strain Ulkenia visurgensis Lng2 using solely free access software and code available in public domain repositories. The assembled transcriptome presented 45,867 unique gene models, with a total of 66,623 transcripts and a contig N50 of 3162. Functional annotations highlighted high amounts of transcripts related to the biosynthesis of relevant lipidic molecules, as well as stress-adaptive features including catalytic and xenobiotic degrading activity. Likewise, 2381 transcripts were linked to enzymes with potential biotechnological applications. Notably, several transcripts corresponding to uncommon enzymatic activities in thraustochytrids, including laccases, cellulases, and chitinases, were identified. Additionally, evidence for a potential lactamase activity was found, marking the first report of such activity in thraustochytrids. Overall, this study offers a simple free-access procedural strategy for a de novo transcriptome assembly and functional annotation in non-model organisms. These results provide valuable insights into the biotechnological potential of thraustochytrids, while also expanding the limited transcriptomic data available for these protists. Notably, it represents the first transcriptomic analysis of the Ulkenia genus.

In central nervous system (CNS) diseases characterized by late-onset neurodegeneration, the interplay between innate and adaptive immune responses remains poorly understood. This knowledge gap is exacerbated by the prolonged protracted disease course as it complicates the delineation of brain-resident and infiltrating cells. Here, we conducted comprehensive profiling of innate and adaptive immune cells in a murine model of spastic paraplegia 15 (SPG15), a complicated form of hereditary spastic paraplegia. Using fate-mapping of bone marrow-derived cells, we identified microgliosis accompanied by infiltration and local expansion of T cells in the CNS of Spg15-/- mice. Single-cell analysis revealed an expansion of disease-associated microglia (DAM) and effector CD8+ T cells prior to neuronal loss. Analysis of potential cell-cell communication pathways suggested bidirectional interactions between DAM and effector CD8+ T cells, potentially contributing to disease progression in Spg15-/- mice. In summary, we identified a shift in microglial phenotypes associated with the recruitment and expansion of T cells as a new characteristic of Spg15-driven neuropathology.

The mitochondrion is a highly dynamic organelle capable of adapting to external stimuli and the energetic demands of the cell. As the primary source of cellular ATP, generating approximately 90 % of the total, mitochondrion facilitates the association of respiratory complexes I, III2, and IV into supramolecular structures called respirasomes. This supramolecular organization enhances protein density within the mitochondrial inner membrane, enabling homogenous energy production. In this study, we investigate the subunits composition and the kinetic characterization of digitonin-solubilized respirasomes and the free complex I from Yarrowia lipolytica as well as their role in reactive oxygen species (ROS) production. The NADH:DBQ oxido reductase activity of respirasome and free complex I was similar. Respiration by respirasome was inhibited with rotenone, antimycin A, or cyanide, simultaneously to an increase in the ROS production. A value of 1.6 ± 0.2 for the NADH oxidized/oxygen reduced ratio was determined for the respirasome activity. The role of interaction between complexes in the function of the respirasome is discussed.

Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H. contortus, highlighting its value for comparative studies with the free-living nematode Caenorhabditis elegans. Key themes include recent developments in genomic, transcriptomic and proteomic technologies and resources, which are illuminating critical molecular pathways, including the ubiquitination pathway, protease/protease inhibitor systems and the secretome of H. contortus. Some of these insights are providing a foundation for identifying essential genes and exploring their potential as targets for novel anthelmintics or vaccines, particularly in the face of widespread anthelmintic resistance. Advanced bioinformatic tools, such as machine learning (ML) algorithms and artificial intelligence (AI)-driven protein structure prediction, are enhancing annotation capabilities, facilitating and accelerating analyses of gene functions, and biological pathways and processes. This review also discusses the integration of these tools with cutting-edge single-cell sequencing and spatial transcriptomics to dissect host-parasite interactions at the cellular level. The discussion emphasises the importance of curated databases, improved culture systems and functional genomics platforms to translate molecular discoveries into practical outcomes, such as novel interventions. New research findings and resources not only advance research on H. contortus and related nematodes but may also pave the way for innovative solutions to the global challenges with anthelmintic resistance.

Cutaneous wound healing remains a common health problem. Metal-organic frameworks (MOFs) have emerged as an advanced therapeutic platform for promoted wound healing. However, there is a lack of MOF particles possessing excellent stability, biocompatibility, and reactive oxygen species (ROS) scavenging ability for tight orchestration of wound healing. Herein, we synthetize therapeutic MOF particles named PgC3Zn and employ them as skin sprays for wound repair. At the inflammatory stage, the pH- and ROS-responsive Zn2+ release of PgC3Zn alleviates oxidative stress and exerts antibacterial and anti-inflammatory efficacy. During the proliferation stage, PgC3Zn promote the migration and proliferation of fibroblasts, the re-epithelialization of keratinocytes, and the angiogenesis of endothelial cells. During the remodeling stage, PgC3Zn effectively facilitate the wound closure and collagen deposition. Moreover, multiple endogenous growth factors have been identified to contribute to the wound healing process. Importantly, PgC3Zn exhibit excellent biocompatibility and remarkably accelerate the healing process in both acute and infected rat full-thickness skin wound models in vivo. Consistently, transcriptomic data illustrate the multi-stage and multi-functional regulation effects of PgC3Zn in promoting wound healing. This study proposes versatile and biocompatible PgC3Zn MOF particles with potentials for enhancing the management of acute and infected skin wounds.

This study optimized hydraulic retention time (HRT) to improve p-cresol and chemical oxygen demand (COD) removal and promote algal-bacterial granular sludge (ABGS) formation in Chinese fermented liquor wastewater treatment. At an HRT of 4 h, no granules formed in the sequential batch reactor, and after 30 days, the removal efficiencies were low for both COD (58.5 %) and p-cresol (21.6 %). In contrast, compact granules developed at HRT 8 and 12 h. The HRT of 8 h achieved the highest removal efficiencies (COD: 96.0 %, p-cresol: 91.3 %), outperforming the HRT of 12 h (COD: 95.1 %, p-cresol: 82.7 %). Microbial analysis identified Rhodobacteraceae and Pseudomonas as key p-cresol degraders. Metagenomic analysis revealed a higher abundance of benzoate degradation genes at an HRT of 8 h compared to 12 h, with Acidovorax predominantly contributing at 8 h and Hydrogenophaga at 12 h. These findings provide insights into the optimization of liquor wastewater treatment.

The partitioning and metabolism of carbohydrates and lignin in leaves are essential for numerous physiological functions, growth and development of plants. This study was aimed to characterize these processes in four leaf types (i.e., autumn-, summer-, spring- and current-year spring shoots) of two citrus hybrids (loose-skin mandarin cultivars OP (i.e., cultivars 'Orah' (OR) Citrus reticulata Blanco and 'Ponkan' (PO) Citrus reticulata Blanco and the sweet orange cultivars NT 'Newhall navel orange' (NO) Citrus sinensis (L.) Osbeck and 'Tarocco' (TA) Citrus sinensis (L.) Osbeck) differing in fruit maturation under field conditions. For this purpose, we analyzed the levels of foliar structural, non-structural carbohydrates and lignin and the expression of related genes. Our results showed that the contents of structural, non-structural carbohydrates and lignin measured in the two hybrids and its partitioning were mostly determined by differences in gene expression recorded in hybrids, cultivars and leaf type. Particularly, differences between leaf types were largely attributed to up- and down-regulation of the expression of genes of cellulose synthesis, lignin precursor synthesis, the Calvin cycle, glycolysis, the tricarbonic acid and starch synthesis and degradation pathways. These differences between leaf types required more complex transcriptional regulation than differences between hybrids and cultivars. The present results indicated that the two citrus hybrids studied differed in the expression of structural, non-structural carbohydrates and lignin-related genes. Future studies have to show if the differences observed in foliar partitioning and metabolism of carbohydrates and lignin are translated into partitioning and metabolism of carbohydrates and lignin in the roots.

Astyanax lacustris is a model of laboratory native fish species. Reproductive studies of this species have already been performed. Nevertheless, there is a relative shortcoming of gene sequence information available in public databases, which hinder their use in more comprehensive investigations that employ sensitivity molecular biology techniques to assess gene expression profile for biomarker identification. In this data article, we report the first de novo transcriptome assembly of A. lacustris testicles, ovaries and male / female pituitary gland improving gene sequence data available for this fish species and transcriptome of male liver. Illumina sequencing generated 808,023,356 raw reads, filtered in 752,739,866 high-quality reads. Initially, a de novo assembly was filtered to include protein coding elements only in each tissue sample, which were merged in a final pantranscriptome (PAN) containing 109,232 contigs. The PAN was functionally annotated against a custom Actinopterygii proteins dataset and EggNOG terms with the aid of EnTAP, retrieving homology queries for about 90 % of all transcripts. Therefore, in this study we provide a PAN and a custom blast tool that can help discovery genomic information on metabolism pathways and their related genes in A. lacustris, enabling future research and molecular studies using this fish species as a model.

Immune disease-associated non-coding SNPs, which often locate in tissue-specific regulatory elements, are emerging as key factors in gene regulation. Among these elements, long non-coding RNAs (lncRNAs) participate in many cellular processes, and their characteristics make these molecules appealing therapeutic targets. In this study, we have studied lncRNA LOC339803 in the context of neuronal cells, which is located in autoimmunity-associated region 2p15 and recently described to have a proinflammatory role in intestinal disorders. Using human brain samples and a wide variety of in vitro techniques, we have showed a differential function of this lncRNA in neuronal cells. We have further demonstrated the role of LOC339803 in maintaining hexokinase 2 (HK2) levels and thus mitochondrial integrity, partially explaining the implication of the lncRNA in multiple sclerosis (MS) pathogenesis. Our results show the importance of cell-type-specific studies in the case of regulatory lncRNAs. We present LOC339803 as a candidate for further studies as a mitochondrial dysfunction marker or possible therapeutic target in neurodegeneration.

Algal-bacterial granules (ABGs) system represents a promising technology for organic wastewater treatment due to its high settleability, efficient oxygen transfer, and low-energy consumption. However, the secretion of extracellular polymeric substances (EPS) in algae, which played a key role in self-assembly of ABGs, would be inhibited by concentrated organic wastewater. This study proposed a novel strategy for developing ABGs by inducing bacterial N-acyl-homoserine lactone (AHL) variation through high-strength pyridine application. Results showed that bacterial long-chain AHL concentrations significantly increased in response to high-strength pyridine at 550 mg L-1, inducing the secretion of algal extracellular aromatic proteins and facilitating ABGs construction. The ABGs system achieved over 99 % pyridine removal efficiency and 82 % settleability. Moreover, the proportions of β-sheet and α-helix structures in the extracellular aromatic proteins of ABGs increased, while the random coil structures decreased. This shift in protein structure lowered the surface free energy and energy barriers, which in turn enhanced the surface hydrophobicity and promoted cell adhesion. Furthermore, based on metatranscriptomic analysis, the mechanism for AHL-regulated physiological and behavioral responses between algae and bacteria in ABGs was proposed. This study provides an economically feasible approach to develop efficient and sustainable ABGs systems for industrial wastewater treatment.

Despite the availability of Pap tests and HPV vaccines, Cervical Cancer continues to be a significant factor contributing to women's deaths. It poses severe consequences to women's health. The disease's severity lies in its potential to progress silently in its early stages, mainly detected in its advanced stage, and clinical treatment is challenging due to drug resistance. This study aims to identify multitargeted lead molecules based on the interactome of Cervical Cancer-related crucial genes, which can help develop drug-resistant therapies. We have considered 9 crucial Cervical Cancer genes, namely BUBR1, CCNB1, FEN1, MAD2, MCM10, MCM6, ITGB8, POLE, and TPX2, to perform gene network analysis and Gene Ontology enrichment studies to identify the potential hub genes and their role. Further, we performed multitarget screening using multisampling algorithms HTVS, SP, and XP to screen the protein products of the 9 genes for their binding affinity for the FDA-approved drugs library. The binding affinities of the compounds were evaluated using MM\GBSA that identified multitargeted potential inhibitor as a Levophed for Cervical Cancer, and the docking results showed a range of MM/GBSA scores, varying from -8.35 to -5.38 kcal/mol for docking, and -43.41 to -19.37 kcal/mol for MM/GBSA scoring. The protein residues that interact the most with Levophed are ALA, THR, ILE, ASN, GLY, ASP, LEU, LYS, VAL, GLN, PRO, CYS, GLU, and TYR. The pharmacokinetic properties and WaterMap computations also support the idea that the compound can potentially become a drug candidate. Furthermore, all 9 complexes were simulated for 100ns, resulting in cumulative deviation and fluctuation of <2 Å, with many intermolecular interactions and binding free energy computations supporting the studies. The study shows that Levophed could treat Cervical Cancer without encountering drug resistance- however, experimental studies are needed to confirm the accuracy.

Light quality exerts a vital influence on the accumulation of secondary metabolites in medicinal plants. Atropa belladonna L. serves as a primary source plant of tropane alkaloids (TAs). Nevertheless, in agricultural production, its application is restricted due to the relatively low content of alkaloids. This study explored the impacts of red, yellow, blue, and white light on the growth of A. belladonna and the biosynthesis of TAs. Through phenotypic and physiological analyses, it was found that red-light had the most significant effect on A. belladonna. Red-light remarkably increased the content of TAs, enlarged the leaf area, extended the stomatal length, and elevated the ammonium nitrogen level. It also enhanced the activities of ornithine decarboxylase, nitrate reductase, and glutamine synthetase, which are essential for nitrogen assimilation. Transcriptomic analysis identified GDHA, At2g42690, and PAO5 as key genes with upregulated expression in the putrescine biosynthesis pathway, where putrescine is an important precursor of TAs. Metabolomic data confirmed that the levels of scopolamine, hyoscyamine, and their precursors increased under red-light. Subsequent qPCR verification under red/white light treatments consistently showed the upregulation of these genes, further confirming their roles in the synthesis of TAs. Moreover, red-light activated photosynthesis-related genes and transcription factors, indicating a coordinated regulatory relationship between light signal transduction and metabolic pathways. This study has preliminarily elucidated the potential mechanism by which red-light promotes the accumulation of TAs through enhancing nitrogen metabolism and precursor synthesis, providing a theoretical basis for improving the quality of A. belladonna and optimizing agricultural production.

The epigenetic mechanisms underlying early-onset acute myocardial infarction (AMI) remain insufficiently characterized. The present study aims to elucidate the pathophysiology of early-onset AMI by investigating its epigenetic features as molecular indicators.

A comparative differential methylation analysis was performed on whole blood samples from 298 patients with early-onset AMI with clinical follow-up and 247 controls using targeted bisulfite sequencing. Clusters of differentially methylated sites (CDMSs) were defined to highlight regions of concentrated methylation changes in patients with early-onset AMI. Cox proportional hazards regression was conducted to evaluate the prognostic significance of the methylation biomarkers.

A total of 692 differentially methylated sites (DMSs) were identified as biomarkers associated with early-onset AMI. Among these, 396 DMSs were grouped into 147 CDMSs. Notably, the UHRF1 and STIMATE genes, which regulate synthetic and osteoblast-like vascular smooth muscle cell phenotypes, respectively, contained CDMSs with the highest number of significant DMSs. UHRF1 demonstrated a CDMS with 10 significant DMSs within a 117-bp region, while STIMATE included a 264-bp CDMS with 10 significant DMSs. Both regions also exhibited consistent methylation patterns in coronary tissues, comparing human coronary plaque to normal coronary artery samples. Additionally, the HIPK3 gene, which modulates STAT3 (signal transducer and activator of transcription 3) expression, thereby promoting osteoblast-like transformation in vascular smooth muscle cells, showed a CDMS with 5 significant DMSs within a 123-bp region, with further validation in the corresponding tissues. Furthermore, over 66% biomarkers demonstrated significant associations with mortality in patients with early-onset AMI, providing evidence of the impact of these biomarkers on the pathophysiology of the disease.

This innovative epigenomic study into early-onset AMI not only identifies biomarkers associated with the disease and its mortality but also highlights the critical role of vascular smooth muscle cell phenotype regulation in early-onset AMI pathogenesis. Our findings suggest that changes in vascular smooth muscle cell phenotypes toward synthetic and osteoblast-like states play a crucial role in early-onset AMI.

Background: Sepsis is a life-threatening condition driven by a dysregulated immune response to infection. Identifying the genetic factors underlying sepsis pathogenesis remains a major challenge in developing effective treatments. Methods: The Summary data-based Mendelian Randomization method was used to integrate Genome-Wide Association Studies and expression quantitative trait loci data to identify sepsis-related genes. These genes were intersected with prognostic gene sets from Gene Expression Omnibus transcriptomic datasets and validated using an independent dataset. Comprehensive single-cell RNA sequencing analysis, including cell clustering, differential expression analysis, cell-cell communication mapping, and pseudotime trajectory analysis, was performed to explore the roles of the identified genes within the sepsis microenvironment. Results: Intersection of Summary data-based Mendelian Randomization and Gene Expression Omnibus gene sets, followed by validation, identified two risk genes and five protective genes as significantly differentially expressed. The risk gene BEND7, predominantly expressed in platelets, was further analyzed using single-cell RNA sequencing, revealing strong interactions with immune cells, particularly monocytes and neutrophils, via the intercellular adhesion molecule signaling pathway. Functional enrichment analysis suggested that BEND7-positive platelets play a role in immune modulation and platelet activation. Conclusion: BEND7 was identified as a platelet-specific gene involved in immune regulation during sepsis. Targeting BEND7-positive platelets may present new therapeutic opportunities in sepsis management.

Existing single-cell clustering methods are based on gene expressions that are susceptible to dropout events in single-cell RNA sequencing (scRNA-seq) data. To overcome this limitation, we proposed a pathway-based clustering method for single cells (scPathClus). scPathClus first transforms the single-cell gene expression matrix into a pathway enrichment matrix and generates its latent feature matrix. Based on the latent feature matrix, scPathClus clusters single cells using the method of community detection. Applying scPathClus to pancreatic ductal adenocarcinoma (PDAC) scRNA-seq datasets, we identified two types of cancer-associated fibroblasts (CAFs), termed csCAFs and gapCAFs, which highly expressed complement system and gap junction-related pathways, respectively. Spatial transcriptome analysis revealed that gapCAFs and csCAFs are located at cancer and non-cancer regions, respectively. Pseudotime analysis suggested a potential differentiation trajectory from csCAFs to gapCAFs. Bulk transcriptome analysis showed that gapCAFs-enriched tumors are more endowed with tumor-promoting characteristics and worse clinical outcomes, while csCAFs-enriched tumors confront stronger antitumor immune responses. Compared to established CAF subtyping methods, this method displays better prognostic relevance.

Cell-free DNA (cfDNA) is a marker of organ injury and immune response. DNA methylation is an epigenetic regulator of gene expression. Here, we elucidate total plasma cfDNA methylation from kidney transplant recipients in presence versus absence of rejection. In doing so, we exploit cfDNA as a real-time biomarker to define molecular pathways of rejection. Twenty plasma cfDNA samples from pediatric kidney transplant recipients were collected at allograft biopsy. Differentially methylated cytosine residues (>20 % methylation difference, q-value <0.05) were identified in presence (N = 7) versus absence (N = 9) of acute rejection. Separate analyses were performed comparing borderline rejection (N = 4) to rejection and non-rejection. In rejection versus non-rejection, there were 1269 differentially methylated genes corresponding to 533 pathways. These numbers were 4-13× greater than comparisons against borderline samples. Enriched pathways between rejection and non-rejection samples were related to immune cell/inflammatory response, lipid metabolism, and tryptophan-kynurenine metabolism, suggesting differential methylation of these pathways contributes to rejection.

Autophagy plays a crucial role in innate and adaptive immunity against invading microorganisms. However, the mechanism underlying autophagy in Macrobrachium rosenbergii remains largely unknown. Here, we demonstrate that Aeromonas hydrophila activates autophagy in M. rosenbergii, according to Western blot, qRT-PCR, and transmission electron microscopy observations. Rapamycin treatment to activate autophagy in M. rosenbergii followed by stimulation with A. hydrophila significantly decreased the A. hydrophila OmpA copy number in the gills of M. rosenbergii. Furthermore, high-throughput RNA-seq analysis of M. rosenbergii gills treated with rapamycin revealed 1684 upregulated and 1500 downregulated differentially expressed genes (DEGs), most of which regulate metabolic pathways. A comprehensive joint analysis of the two transcriptomic databases for A. hydrophila infection and rapamycin treatment identified 15 upregulated and 25 downregulated DEGs, respectively. These genes enhance the immune defense of M. rosenbergii by negatively regulating metabolic pathways and promoting immune pathways. Our results provide a theoretical basis for further exploration of the antibacterial mechanism of M. rosenbergii.

Opsariichthys bidens is a unique economically important freshwater fish in China. Male O. bidens grow faster than females, and male fish have attractive blue-green stripes on the body surface during the breeding period. The breeding of all-male stocks can significantly improve the efficiency of breeding. To accelerate the breeding of all-male stocks, additional studies of the mechanism regulating sex differentiation and gonad development are needed. In this study, transcriptome sequencing of the ovaries and testes of O. bidens was performed using Illumina high-throughput sequencing. The results revealed a total of 21,703 differentially expressed genes, including 8645 up-regulated genes and 5880 down-regulated genes expressed in the ovary compared with the testis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed multiple differentially expressed genes involved in sex differentiation and gonad development. Eight differentially expressed genes (zp3, cyp19a, hsd17b1, msh4, dmrt1, rspo2, kif23, and gdf9) that play a key role in sex differentiation and gonadal development were selected for RT-qPCR validation. The expression levels of selected genes in the testes and ovaries were significantly different (P < 0.05). zp3, cyp19a, hsd17b1, and gdf9 were female-biased genes, and msh4, dmrt1, rspo2, and kif23 were male-biased genes. zp3, cyp19a, hsd17b, and msh4 were only slightly expressed in the kidney and liver, and dmrt1, rspo2, kif23, and gdf9 were all expressed in gill, kidney, and liver tissue. None of the genes were expressed in the heart or muscle. In this study, differentially expressed genes related to the sex determination and differentiation of O. bidens were identified. Overall, our findings provide important data for future studies of the molecular mechanisms of sex differentiation and gonad development of O. bidens and will aid the breeding of all-male species.

In the face of advancements in osteosarcoma research, existing preclinical models - including in vitro (i.e., two- and three-dimensional cell cultures, organoids) and in vivo approaches (i.e., xenografts, animal models) - are often characterised by low translatability, limiting their predictive power for clinical outcomes. This study investigated the potential use of a 3D-printed β-tricalcium phosphate (β-TCP) scaffold as a bone-mimicking environment in an advanced in vitro osteosarcoma preclinical model. The compatibility of the scaffold with osteosarcoma cell spheroids, endothelial cells, and primary bone marrow-derived mesenchymal stem cells (pBMSCs) was evaluated along with its physicochemical characteristics. Transcriptomic analysis of pBMSCs on the scaffolds revealed gene expression profiles indicating pronounced extracellular matrix organisation and minor osteogenic activity. The model effectively replicated significant aspects of the tumour microenvironment in a tri-culture system, with dynamic perfusion enhancing metabolic activity. The developed scaffold-based model was employed in the doxorubicin cytotoxicity test. The physiological significance of the tri-culture was demonstrated by its distinct doxorubicin accumulation, in contrast to spheroid monocultures. Despite the limitations of the proposed approach regarding efficient vascularisation of the model, this study highlights the potential of 3D-printed β-TCP scaffolds in tumour modelling to support physiologically relevant preclinical models.

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.

The field of Natural Language Processing (NLP) within the life sciences has exploded in its capacity to aid the extraction and analysis of data from scientific texts in recent years through the advancement of Artificial Intelligence (AI). Drug discovery pipelines have been innovated and accelerated by the uptake of AI/Machine Learning (ML) techniques.

The authors provide background on Named Entity Recognition (NER) in text - from tagging terms in text using ontologies to entity identification via ML models. They also explore the use of Knowledge Graphs (KGs) in biological data ingestion, manipulation, and extraction, leading into the modern age of Large Language Models (LLMs) and their ability to maneuver complex and abundant data. The authors also cover the main strengths and weaknesses of the many methods available when undertaking NLP tasks in drug discovery. Literature was derived from searches utilizing Europe PMC, ResearchRabbit and SciSpace.

The mass of scientific data that is now produced each year is both a huge positive for potential innovation in drug discovery and a new hurdle for researchers to overcome. Notably, methods should be selected to fit a use case and the data available, as each method performs optimally under different conditions.

Aims This study assessed sex-specific proteomic profiles by cardiovascular disease (CVD) phenotype (coronary artery disease [CAD] vs coronary microvascular dysfunction [CMD]) and describe their role in sex-specific pathways.

In a secondary biobank analysis of the Yale-CMD registry, adults with ischemic symptoms who underwent cardiac positron emission test/computed tomography were categorized as a) controls (normal coronary flow reserve (CFR) > 2 without perfusion defect or coronary calcification), b) having CMD (CFR < 2 without defect or calcification), or c) having CAD (known CAD or new perfusion defect). Using proximity extension assays (Olink® Explore 3072), we examined 2944 proteins. Differential protein expression was assessed using linear regression models, adjusting for age, race, body mass index, diabetes, dyslipidemia, hypertension, or smoking.

Of 190 patients, 91 provided blood samples (mean age, 56 years; 66 %, females; 48 %, controls; 24 %, CAD; 27 %, CMD). Among controls, 15 proteins showed sex differences (5 proteins upregulated in females, 10 in males; false discovery rate [FDR < 0.05]). Upregulated in CAD patients were FSHB in females and INSL3 and EDDM3B in males (FDR < 0.05). Among CMD patients, SCGB3A1 and HGFAC were higher in females; INSL3, SPINT3, EDDM3B, and KLK3 were higher in males (FDR < 0.05). Per pathway analysis, females showed upregulation of immune pathways in CAD and lipid and glucose metabolism pathways in CMD. Males showed upregulated endothelial regulation of blood flow in CAD and increased angiogenesis in CMD.

Sex differences exist in the proteomic profiles of CAD and CMD patients, highlighting a need for precision medicine.

Biofilm formation on surfaces, tools and equipment can damage their quality and lead to high repair or replacement costs. Plasma-activated water (PAW), a new technology, has shown promise in killing biofilm and non-biofilm bacteria due to reactive oxygen and nitrogen species (RONS), particularly superoxide. However, the exact genetic mechanisms behind PAW's effectiveness against biofilms remain unclear. Here, we examined the stress responses of Escherichia coli biofilms exposed to sub-lethal PAW treatment using bulk RNA sequencing and transcriptomics. We compared gene expression in PAW-treated E. coli biofilms with and without superoxide removal, achieved by adding the scavenger Tiron. Biofilms treated with PAW exhibited a 40 % variation in gene expression compared to those treated with PAW-Tiron and controls. Specifically, PAW treatment resulted in 478 upregulated genes (>1.5 log2FC) and 186 downregulated genes (<-1.5 log2FC) compared to the control. Pathway and biological process enrichment analysis revealed significant upregulation of genes involved in sulfur metabolism, ATP-binding transporter, amino acid metabolism, hypochlorite response systems and oxidative phosphorylation in PAW-treated biofilms compared to control. Biofilm viability and intracellular RONS accumulation were tested for E. coli mutants lacking key genes from these pathways. Knockout mutants of thioredoxin (trxC), thiosulfate-binding proteins (cysP), and NADH dehydrogenase subunit (nuoM) showed significantly reduced biofilm viability after PAW treatment. Notably, ΔtrxC biofilms had the highest intracellular ROS accumulation, as revealed by 2',7'-dichlorofluorescin diacetate staining after PAW treatment. This confirms the importance of these genes in managing oxidative stress caused by PAW and highlights the significance of superoxide in PAW's bactericidal effects. Overall, our findings shed light on the specific genes and pathways that help E. coli biofilms survive and respond to PAW treatment, offering a new understanding of plasma technology and its anti-biofilm mechanisms.

End-stage kidney disease (ESKD) impacts over 740,000 individuals in the United States, with many patients relying on arteriovenous fistulae (AVF) for hemodialysis due to superior patency and reduced infections. However, AVF patency is reduced by thrombosis and neointimal hyperplasia, yielding a 1-yr patency of only 40%-50%. We hypothesized that tenascin-C (TNC), a regulator of inflammation and immune responses after injury, also regulates venous remodeling during AVF maturation. AVF were created in wild-type (WT) and Tnc knockout (Tnc-/-) mice, and proteomic analyses were conducted to identify protein changes between sham and AVF WT tissue. Immunofluorescence and Western blot assays compared venous tissue from WT and Tnc-/- mice. In vitro studies using human umbilical vein endothelial cells and human umbilical vein smooth muscle cells examined TNC-siRNA effects on thrombomodulin (THBD) and NF-κB. Macrophages from WT and Tnc-/- mice were assessed for anti-inflammatory phenotype polarization and tissue factor expression. TNC expression was spatially and temporally regulated in WT mice with AVF, and TNC colocalized with matrix remodeling but not with THBD expression; TNC expression was downregulated in patent AVF but sustained in occluded AVF, both in WT mice and human AVF specimens. Tnc-/- mice had reduced AVF patency, less wall thickening, and increased thrombosis, with increased THBD expression. In vitro, TNC-siRNA increased THBD and reduced NF-κB activation. Macrophages from Tnc-/- mice showed increased anti-inflammatory macrophage polarization and tissue factor expression, facilitating thrombosis. Sustained TNC expression drives neointimal hyperplasia and AVF failure by promoting a prothrombotic, inflammatory microenvironment. Targeting TNC pathways may enhance AVF patency and improve dialysis outcomes.NEW & NOTEWORTHY This study identifies Tenascin-C (TNC) as a key regulator of arteriovenous fistula (AVF) patency. TNC is spatially and temporally regulated, driving neointimal hyperplasia and thrombosis by promoting a prothrombotic, inflammatory microenvironment. In Tnc-/- mice, reduced TNC expression increased thrombomodulin and anti-inflammatory macrophage polarization but impaired wall thickening and AVF patency. These findings link sustained TNC expression to AVF failure and suggest that targeting TNC pathways could enhance AVF outcomes in patients requiring hemodialysis.

Glutamate transporters are important for regulating extracellular glutamate levels, impacting neural function and metabolic homeostasis. This study explores the behavioral, lifespan, and proteomic profiles in Caenorhabditis elegans strains with either glt-4 or glt-5 null mutations, highlighting contrasting phenotypes. Δglt-4 mutants displayed impaired mechanosensory and chemotactic responses, reduced lifespans, and decreased expression levels of ribosomal proteins and chaperonins involved in protein synthesis and folding. In contrast, Δglt-5 mutants displayed heightened chemorepulsion, extended lifespans, and upregulation of mitochondrial pyruvate carriers and cytoskeletal proteins. Proteomic profiling via mass spectrometry identified 53 differentially expressed proteins in Δglt-4 mutants and 45 in Δglt-5 mutants. Δglt-4 mutants showed disruptions in ribonucleoprotein complex organization and translational processes, including downregulation of glycogen phosphorylase and V-type ATPase subunits, while Δglt-5 mutants revealed altered metabolic protein expression, such as increased levels of mitochondrial pyruvate carriers and decreased levels of fibrillarin and ribosomal proteins. Gene ontology enrichment analysis highlighted differential regulation of protein biosynthesis and metabolic pathways between the strains. Overall, these findings underscore the distinct, tissue-specific roles of GLT-4 and GLT-5 in C. elegans, with broader implications for glutamate regulation and systemic physiology. The results also reinforce the utility of C. elegans as a model for studying glutamate transporters' impact on behavior, longevity, and proteostasis.

Aspergillus oryzae is the most widely used starter in koji-making of bean-based fermented foods due to its strong ability to produce proteolytic enzymes. However, the information of the key proteolytic enzymes in A. oryzae is still lacking. This study aimed to mine the key proteolytic enzymes from A. oryzae BL18 through genomic and transcriptomics analysis, to characterize their biochemical properties and to evaluate their application effect in soy sauce fermentation. Thirty-eight proteolytic enzyme genes with secretory ability were predicted while GME1689_g, GME238_g, GME3470_g and GME6033_g genes were found to have high expression levels among these genes during the koji-making process. After that, these four genes were heterologously expressed in Komagataella phaffii GS115 and their biochemical properties were characterized. The results showed that GME1689_g and GME238_g were optimal in neutral condition while GME3470_g and GME6033_g were acidic enzymes. Among these four enzymes, GME1689_g and GME238_g were more salt tolerant and had higher degradation degree towards globulin and albumin. Therefore, these two enzymes were applied in the initial stage of soy sauce fermentation individually or together. Compared to control group, the concentration of free amino acids in soy sauce fermented with addition of proteolytic enzymes were 20-25 % higher while more volatile flavor compounds (such as linolool and octen-3-ol) were enriched in both quantity and concentration. Through sensory evaluation, the addition of proteolytic enzymes, especially GME1689_g, could enhance the flavor of soy sauce with the average sensory score increasing from 7.5 to 8.0-8.5. The results obtained in this study could not only enhance our understanding of the proteolytic enzymes in A. oryzae but also provide possible solution for quality enhancement of soy sauce.

The rapid rise in drug-resistant tuberculosis poses a serious threat to public health and demands the discovery of new anti-mycobacterial agents. Medicinal plants are a proven potential source of bioactive compounds; however, identifying those responsible for the putative anti-mycobacterial action still remains a challenging task. In this study, we undertook a systematic network pharmacology approach to identify and evaluate anti-mycobacterial compounds from a traditional plant, Acacia nilotica, as a model system. The protein-protein interaction network revealed 17 key pathways in M. tuberculosis encompassing 40 unique druggable targets that are necessary for its growth and survival. The phytochemicals of A. nilotica were preferentially found to interfere with the cell division and cell wall biogenesis proteins, especially FtsZ and Mur. Notably, the compounds epigallocatechin, ellagic acid, chlorogenic acid, and D-pinitol were found to exhibit a potential polypharmacological effect against multiple proteins. Further, in vitro studies confirmed that the selected candidates, chlorogenic acid, and ellagic acid exhibited potent anti-mycobacterial activity (against M. smegmatis) with specific inhibition of purified M.tb FtsZ enzyme. Taken together, the present study demonstrates that network pharmacology combined with molecular docking can be utilized as an efficient approach to identify potential bioactive phytochemicals from natural products along with their mechanism of action. Hence, the compounds identified in this study can be potential lead candidates for developing novel anti-mycobacterial drugs, while the key proteins identified here can be potential drug targets.

Hepatocellular carcinoma (HCC) is a complex malignancy driven by the dysregulation of multiple cellular pathways. Survivin, a key member of the inhibitor of apoptosis (IAP) family, plays a central role in HCC tumorigenesis and progression. Despite significant research, a comprehensive understanding of the contributions of survivin to the hallmarks of cancer, its molecular network, and its potential as a therapeutic target remains incomplete. In this review, we integrated bioinformatics analysis with an extensive literature review to provide deeper insights into the role of survivin in HCC. Using bioinformatics tools such as the Human Protein Atlas, GEPIA, STRING, TIMER, and Metascape, we analyzed survivin expression and its functional associations and identified the top 20 coexpressed genes in HCC. These include TK1, SPC25, SGO2, PTTG1, PRR11, PLK1, NCAPH, KPNA2, KIF2C, KIF11, HJURP, GTSE1, FOXM1, CEP55, CENPA, CDCA3, CDC45, CCNB2, CCNB1 and CTD-2510F5.4. Our findings also revealed significant protein-protein interactions among these genes, which were enriched in pathways associated with the FOXM1 oncogenic signaling cascade, and biological processes such as cell cycle regulation, mitotic checkpoints, and diseases such as liver neoplasms. We also discussed the involvement of survivin in key oncogenic pathways, including the PI3K/AKT, WNT/β-catenin, Hippo, and JAK/STAT3 pathways, and its role in modulating cell cycle checkpoints, apoptosis, and autophagy. Furthermore, we explored its interactions with the tumor microenvironment, particularly its impact on immune modulation through myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages, and natural killer cell function in HCC. Additionally, we highlighted its involvement in alkylglycerone phosphate synthase (AGPS)-mediated lipid reprogramming and identified important gaps in the survivin network that warrant further investigation. This review also examined the role of survivin in cancer stemness, inflammation, and virally mediated hepatocarcinogenesis. We evaluated its potential as a diagnostic, prognostic, predictive, and pharmacodynamic biomarker in HCC, emphasizing its relevance in precision medicine. Finally, we summarized emerging survivin-targeted therapeutics and ongoing clinical trials, underscoring the need for novel strategies to effectively target survivin in HCC.