Search Results (5,888)

Soapstock (SS), a by-product of vegetable oil refining, is a promising source of a mixture of mono-, di-, triglycerides, and free fatty acids (MDTG-FFA), a valuable feedstock for biodiesel production. In this study, the selective extraction of MDTG-FFA from SS using green solvents (ethyl acetate, ethyl formate, methyl acetate, isopropyl acetate, and isobutanol) was investigated. Ethyl acetate showed the highest efficiency, allowing the elimination of the phosphatide (PL) precipitation step with acetone. The process optimization was carried out by response surface methodology with central composite design. Statistical analysis confirmed the significance of the obtained models: F-values were 4.55 (p = 0.013) for MDTG-FFA and 9.62 (p = 0.00074) for PL. Regression analysis revealed a good fit of the experimental data with quadratic models for MDTG-FFA and PL, with coefficients of determination (R²) of 0.804 and 0.897, respectively. The optimum extraction parameters were a solvent-to-dry-matter-of-SS ratio 5:1, time 10.2 min, and initial extraction temperature 21.7 °C. Under these conditions, maximum MDTG-FFA yields of 12.6% and 13.4% were achieved for the two batches of SS, respectively, with minimum PL yields of 0.02% and 0.1%. The obtained MDTG-FFA extracts rich in free fatty acids represent a promising feedstock for biodiesel production. The proposed method provides a rational, resource-efficient, and environmentally preferable extraction of valuable components from SS. Full article

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and fibromyalgia (FM) are debilitating disorders with overlapping symptoms such as chronic pain and fatigue. Dysregulation of the endogenous opioid system, particularly µ-opioid receptor function, may contribute to their pathophysiology. This study examined whether epigenetic modifications, specifically µ-opioid receptor 1 gene (OPRM1) promoter methylation, play a role in this dysfunction. Using a repeated-measures design, 28 ME/CFS/FM patients and 26 matched healthy controls visited the hospital twice within four days. Assessments included blood sampling for epigenetic analysis, a clinical questionnaire battery, and quantitative sensory testing (QST). Global DNA (hydroxy)methylation was quantified via liquid chromatography–tandem mass spectrometry, and targeted pyrosequencing was performed on promoter regions of OPRM1, COMT, and BDNF. ME/CFS/FM patients reported significantly worse symptom outcomes. No differences in global (hydroxy)methylation were found. Patients showed significantly higher OPRM1 promoter methylation, which remained after adjusting for symptom severity and QST findings. Across timepoints, OPRM1 methylation consistently correlated with BDNF Promoter I and Exon III methylation. This is, to the best of our knowledge, the first study examining OPRM1 methylation in ME/CFS/FM. Increased OPRM1 methylation in patients, independent of symptoms or pain sensitivity measures, supports the hypothesis of dysregulated opioidergic signaling in these conditions. Full article

Lugana DOC is an Italian PDO white wine from the south coast of Lake Garda, produced with ‘Trebbiano di Lugana’ grapes (synonym of ‘Trebbiano di Soave’ and ‘Verdicchio bianco’) and characterised by tropical fruit, citrus, and balsamic notes due to the presence of volatile thiols and methyl salicylate, respectively. To deepen the knowledge of the aromatic profile of these wines and to study how they evolve during aging, the chemical and sensory profile of 12 Lugana DOC wines from the same winery in different consecutive vintages (2008–2019, evaluated in 2023) were analysed. Sensory analysis data were subjected to hierarchical cluster analysis, identifying four main groups that appropriately distinguished the aged wines from the young wines. Younger wines had a greenish yellow colour and were characterised mainly by fruity, citrus, floral, and flinty notes related to thiol compound contribution. Older wines, divided into three different clusters, shifted colour towards orange and were characterised by descriptors related to oxidative aging (e.g., cooked fruit, marsala-like, figs, nuts) or retained pleasant varietal and evolutionary notes (e.g., citrus, white flowers, flint, vanilla) confirmed by their chemical markers detected by GC-MS and LC-MS. Full article

Lentiviral transduction remains the gold standard in adoptive modified cellular therapy, such as CAR-T; however, genome integration is not always desirable, such as when treating non-fatal autoimmune disease or for additional editing steps using CRISPR to produce allogeneic CAR-modified cells. Delivering in vitro-transcribed (IVT) mRNA represents an alternative solution but the labile nature of mRNA has led to efforts to improve half-life and translation efficiencies using a range of approaches including chemical and structural modifications. In this study, we explore the role of N⁶–methyladenosine (m6A) in a CD19-CAR sequence when delivered to T cells as an IVT mRNA. In silico analysis predicted the presence of four m6A consensus (DRACH) motifs in the CAR coding sequence and treating T cells with an inhibitor of the m6A methyltransferase (METTL3) resulted in a significant reduction in CAR protein expression. RNA analysis confirmed m6A bases at three of the predicted sites, indicating that the modification occurs independently of nuclear transcription. Synonymous mutation of the DRACH sites reduced the levels of CAR protein from 15 to >50% depending on the T cell donor. We also tested a panel of CAR transcripts with different UTRs, some containing m6A consensus motifs, and identified those which further improved protein expression. Furthermore, we found that the methylation of consensus m6A sites seems to be somewhat sequence-context-dependent. These findings demonstrate the importance of the m6A modification in stabilising and enhancing expression from IVT-derived mRNA and that this occurs within the cell, meaning targeted in vitro chemical modification during mRNA manufacturing may not be necessary. Full article

Tremella mesenterica, commonly known as the yellow brain or golden jelly fungus, has been traditionally used for its medicinal properties. In this study, we elucidated the structural characteristics of T. mesenterica polysaccharide (TMP) and evaluated its potential moisturizing mechanism in vitro, comparing it to Tremella fuciformis polysaccharide (TFP) and hyaluronic acid (HA). TMP was isolated through enzyme assisted extraction and it has a molecular weight (MW) of approximately 143 kDa. We investigated the composition of mannose, xylose, glucuronic acid, and glucose as a ratio of 59.8 ± 0.3, 24.0 ± 1.2, 11.0 ± 0.8, 5.2 ± 0.0, respectively. Through methylation and GC-MS analysis, we discovered TMP was composed of a main chain of β-(1→3)-linked mannopyranoside, substituted with various side chains such as xylopyranoside, glucuronopyranoside, glucopyranoside at the C-2 or C-4 positions of the backbone. TMP upregulated the expression of key moisturizing-related factors compared to TFP and HA, such as aquaporin-3 (AQP3) with 55% and 57% at 25 and 50 μg/mL and hyaluronic acid synthase-2 (HAS2) with 22% at 25 μg/mL, as confirmed through qRT-PCR analysis. Additionally, TMP significantly enhanced the expression of filaggrin (FLG), a critical protein involved in skin barrier function, with 22% at 25 μg/mL. Immunocytochemistry (ICC) analysis further revealed that TMP achieved the highest improvement in hyaluronic acid synthase-3 (HAS3) protein levels by 475% at 50 μg/mL. While further in vivo studies are required to substantiate its functional moisturizing efficacy, these findings suggest that TMP serves as a promising moisturizing agent. The structural and functional properties of TMP provide a potential foundation for its application in diverse industries, including cosmetics, food, biopolymers, and pharmaceuticals. Full article

(1) Background: Modifications of histone methylation could alter chromatin structure and thereby have an impact on gene expressions. (2) Methods: To investigate whether ORY-1001 delay retinal photoreceptor degeneration, rd10 mice were intraperitoneally injected with ORY-1001 (0.075 mg/kg) every second day from the 14th to the 24th day after birth. Full-field electroretinogram detection (ff ERG), optical coherence tomography (OCT), visual behavioral testing, retinal tissue morphology observation, and protein expression detection experiments were performed on the 25th day. Simultaneously, ATAC-seq and RNA-seq were used to test the mice’s retinal tissues, and metabolomics detection and quantitative real-time polymerase chain reaction (qRT-PCR) were carried out. (3) Results: Compared with the rd10 group, in the treatment group, the function in the electroretinogram response and the visual behavioral responses were improved, the nuclear layer morphology of retinal tissue was reserved more, and the protein expression of H3K4me2 and CoREST was increased. Conjoint analysis of our ATAC-seq and RNA-seq results showed that chromatin accessibility was changed, as was gene expression which was involved in metabolism changes. In addition, the effector gene in the retina was Gnat1. (4) Conclusions: ORY-1001 delays retinal photoreceptor degeneration by inhibiting H3K4me2 demethylation in rd10 mice, which suggests that ORY-1001, as a novel epigenetic modifier, has potential for treating RP. Full article

Glioblastoma (GBM) is the most prevalent and devastating form of primary brain tumors in adults, with dismal survival despite advancements in treatment modalities. The current study sought to develop clinically significant prognostic models for GBM patients by comprehensively profiling MGMT, NUPR1, NDRG2, and GLI1 gene promoter methylation in GBM tissues vs. non-neurooncological disease (NND) and their association with clinical characteristics and therapeutic outcome. This was further evaluated by in silico functional enrichment analysis. NUPR1, NDRG2, and GLI1 gene promoter methylation were significant epigenetic discriminators between GBM and NND. However, NDRG2 methylation was the sole independent predictor for neoplastic lesions (OR = 1.71, 95% CI [1.25–3.57], p = 0.028). Multivariable Cox regression analysis revealed that NUPR1 promoter hypermethylation was significantly correlated with a lower risk of mortality (HR = 0.96, 95% CI [0.96–0.99], p = 0.002), while multiple tumor sites were linked to an increased risk of mortality in the univariate model (HR = 4.44, 95% CI [1.42–13.88], p = 0.01). A heatmap correlation matrix identified a robust positive correlation among the MGMT and NUPR1 methylation status (r = 0.93, p < 0.001). NUPR1 and MGMT promoter hypermethylation was associated with a favorable response to temozolomide therapy. Patients with NUPR1 and MGMT hypermethylation exhibited extended OS and PFS compared to those with hypomethylation levels, whereas GLI1 and NDRG2 hypermethylation were linked to shorter PFS. In conclusion, the multi-faceted epigenetic panel adopted in the current study captures different aspects of GBM biology and moves towards a more comprehensive model that reflects the molecular heterogeneity of GBM as insights for personalized therapy. Full article

Liquid biopsy is moving beyond mutation-centric assays to multimodal frameworks that integrate cell-free DNA (cfDNA) signals with additional analytes such as circulating tumor cells (CTCs) and extracellular vesicles (EVs). In this review, we summarize emerging technologies across analytes for early cancer detection, emphasizing sequencing and error-suppression strategies and the growing evidence for multi-cancer early detection (MCED), tissue-of-origin (TOO) inference, diagnostic triage, and longitudinal surveillance. At low tumor fractions, fragmentomic and methylation features preserve tissue and chromatin context; when combined with radiomics using deep learning, they support blood-first, high-specificity risk stratification, increase positive predictive value (PPV), reduce unnecessary procedures, and enhance early prediction of treatment response and relapse. Building on these findings, we propose a pathway-aware workflow: initial blood-based risk scoring, followed by organ-directed imaging, and targeted secondary testing when indicated. We further recommend that model reports include not only discrimination metrics but also calibration, decision-curve analysis, PPV/negative predictive value (NPV) at fixed specificity, and TOO accuracy, alongside multi-site external validation and blinded dataset splits to improve generalizability. Overall, liquid biopsy is transitioning from signal discovery to deployable multimodal decision systems; standardized pre-analytical and analytical workflows, robust error suppression, and prospective real-world evaluations will be pivotal for clinical implementation. Full article

The quality of different coffee varieties varies, and the corresponding bioactive value of coffee processing byproducts is often overlooked. For that, we employed HPLC, GC-MS, and electronic sensory analyses to evaluate the key bioactive components, antioxidant potential, and flavor traits of green coffee bean and coffee processing byproducts of seven coffee varieties. The results showed that green coffee beans (Oe+Ie) and exocarp (Ep) possessed strong antioxidant activity and high total phenolic content (TPC), caffeine and trigonelline content. Among the varieties, DR390 contained higher levels of total phenols, caffeine, and trigonelline, whereas DR402 was rich in caffeine and chlorogenic acid. In addition, RY3 exhibited higher TPC, total flavonoid content (TFC), caffeine, and chlorogenic acid. The parchment (Pc) layer was rich in soluble sugars (1.83–5.43%), while the silverskin (Sk) contained relatively high levels of chlorogenic acid (3.58–4.69 mg/g). Flavor analysis identified eleven classes of volatile compounds in green coffee bean (Oe+Ie) and byproducts (Ep, Pc, Sk), with esters, ketones, alcohols, and aldehydes being the most prevalent. Seven key aroma compounds, including methyl salicylate, phenethyl alcohol, nonanal, and benzaldehyde, were identified across the various structural tissues of coffee fruit. Distinct flavor profiles were observed among the coffee fruit parts: green coffee bean (Oe+Ie) was nutty; the Ep showed fruity and cocoa-like aromas; the Pc and Sk exhibited papery and nutty aromas, respectively. Varieties DR397, DR402, and RY3 exhibited pronounced aroma profiles. Comprehensive analysis showed that DR402 and RY3 had higher overall scores for bioactive and flavor components than other varieties in their groups. In summary, green coffee bean (Oe+Ie) exhibited strong antioxidant activity and high levels of bioactive compounds. Coffee byproducts, such as the Ep, hold potential for extracting natural antioxidants and bioactive compounds to develop specialty products or for other high-value utilization. Full article

Severe acute respiratory syndrome coronavirus (SARS-CoV) assembles and buds from the Golgi apparatus or the ER membrane, but the specific membrane microdomains utilized during this process remain underexplored. Here, we show that co-expression of the SARS-CoV structural proteins S, M, and N in HEK-293T cells is sufficient to generate genome-free SARS-CoV-like virus-like particles (VLPs), which preferentially bud from glycolipid-enriched membrane lipid raft microdomains. Immunofluorescence microscopy using raft-selective dyes (DiIC16) and spike-specific antibodies revealed strong co-localization of VLPs with lipid rafts. Detergent-resistant membrane analysis and sucrose gradient centrifugation further confirmed the presence of S protein in buoyant, raft-associated fractions alongside the raft marker CD44. Importantly, pharmacological disruption of rafts with methyl-β-cyclodextrin reduced VLP budding and S protein partitioning into raft domains, underscoring the requirement for intact lipid rafts in assembly. Additionally, our data support lipid raft-associated proteins’ (e.g., FNRA, VIM, CD59, RHOA) roles in modulating cellular responses conducive to viral replication and assembly. These findings highlight lipid rafts as crucial platforms for SARS-CoV morphogenesis and suggest new avenues for vaccine and antiviral development using VLPs and raft-targeting therapeutics. Full article

Background/Objectives: DNA methylation is a key epigenetic process that regulates gene expression and is often disrupted in colorectal cancer (CRC). Aberrant methylation of promoter CpG islands can silence tumor suppressor genes and drive tumorigenesis. A subset of CRCs exhibits the CpG Island Methylator Phenotype (CIMP), characterized by widespread hypermethylation and distinct clinical outcomes. Identifying genes whose expression is epigenetically regulated by methylation is important for prioritizing candidate biomarkers and therapeutic targets in CRC. Methods: We developed and compared a series of computational approaches to identify genes whose expression is regulated by DNA methylation in The Cancer Genome Atlas (TCGA) cohort of Colon Adenocarcinoma (COAD) patients. Samples were stratified according to their CpG Island Methylator Phenotype (CIMP) level to capture distinct epigenetic subgroups. The proposed framework integrates methylation and transcriptomic data to systematically detect methylation–expression associations indicative of epigenetic regulation. Results: The best-performing method identified gene sets strongly associated with promoter methylation–expression relationships and enriched for pathways relevant to colorectal cancer progression and patient stratification. To evaluate the robustness and transferability of the approach, it was further validated on independent datasets, including Stomach Adenocarcinoma (STAD), Glioblastoma Multiforme (GBM), and Mesothelioma (MESO), supporting its robustness and potential generalizability across multiple tumor types. Conclusions: Our study highlights the potential of computational pipelines to uncover epigenetically regulated genes in colorectal cancer. The identified candidate genes provide a hypothesis-generating foundation for refining molecular stratification and guiding future studies aimed at epigenetic biomarker discovery and therapeutic hypothesis development. Full article

Gliomas are notoriously difficult to treat owing to their pronounced heterogeneity and highly variable treatment responses. This reality drives the development of precise diagnostic and prognostic methods. This review explores the modern arsenal of bioinformatic tools aimed at refining diagnosis and stratifying glioma patients by different malignancy grades and types. We perform a comparative analysis of software solutions for processing whole-exome sequencing data, analyzing DNA methylation profiles, and interpreting transcriptomic data, highlighting their key advantages and limited applicability in routine clinical practice. Special emphasis is placed on the contribution of bioinformatics to fundamental oncology, as these tools aid in the discovery of new biomarker genes and potential targets for targeted therapy. The ninth section discusses the role of computational models in predicting immunotherapy efficacy. It demonstrates how integrative data analysis—including tumor mutational burden assessment, characterization of the tumor immune microenvironment, and neoantigen identification—can help identify patients who are most likely to respond to immune checkpoint inhibitors and other immunotherapeutic approaches. The obtained data provide compelling justification for including immunotherapy in standard glioma treatment protocols, provided that candidates are accurately selected based on comprehensive bioinformatic analysis. The tools discussed pave the way for transitioning from an empirical to a personalized approach in glioma patient management. However, we also note that this field remains largely in the preclinical research stage and has not yet revolutionized clinical practice. This review is intended for biological scientists and clinicians who find traditional bioinformatic tools difficult to use. Full article

Transposable elements (TEs) are ubiquitous components of plant genomes that profoundly influence plant diversity, adaptation, and genome structure. Transposition of TEs is primarily suppressed by distinct DNA methylation systems. However, the distribution of DNA methylation at the level of individual TEs in plants remains poorly understood. Here, we address this question by generating per-base cytosine methylation maps of individual long terminal repeat retrotransposons (LTR-RTEs) for the large sunflower (Helianthus annuus L.) and the small Arabidopsis thaliana genomes. A. thaliana was selected as the model species, for which genome-wide DNA methylation profiles have been extensively characterized in prior studies. Our analysis revealed significant heterogeneity in methylation patterns both between and within individual LTR-RTE lineages. We also found that the sunflower genes harboring intact or fragmented LTR-RTE insertions exhibit altered DNA methylation and expression profiles, with intact LTR-RTE insertions enriched in stress-response and regulatory pathways. Our interspecies comparison of DNA methylation patterns indicates that methylation patterns are intrinsic features of LTR-RTE lineages, conserved across diverse plant species but influenced by factors such as insertion age, element length, and proximity to genes. Furthermore, we identified epigenetically distinct clusters of Tork and Athila sunflower elements corresponding to separate phylogenetic clades, suggesting a link between epigenetic regulation and the genetic diversity of plant LTR-RTEs. Full article

Potato is a globally important non-cereal crop in which infection with potato spindle tuber viroid (PSTVd) can cause stunted growth and significantly reduce tuber yield. We previously showed that PSTVd induces accumulation of the plant hormone jasmonic acid (JA) and alters antioxidant responses in potato plants. To clarify the role of JA in response to PSTVd, we analyzed disease development in transgenic JA-deficient opr3 and JA-insensitive coi1 lines compared to the wild-type. Transcriptomic analysis using RNA-Seq revealed that most genotype-specific differentially expressed genes (DEGs) in all comparisons were enriched in plant hormone signal transduction, plant-pathogen interaction, and MAPK signaling pathways, although the number of DEGs varied. These differences were confirmed by independent data from RT-qPCR, hormone, and hydrogen peroxide (H₂O₂) analyses. After PSTVd infection, opr3 plants showed enhanced JA signaling and increased abscisic acid (ABA) and auxin (AUX) content. In contrast, coi1 plants showed reduced ABA, AUX, and salicylic acid content. Both opr3 and coi1 plants showed reduced JA and H₂O₂ content and lower expression of defense-related genes, resulting in milder symptoms but increased viroid accumulation. In addition, treatment with methyl jasmonate alleviated symptoms in infected wild-type plants. Together, these results indicate a modulatory role for JA and JA signaling in basal immune responses and symptom development in the potato-PSTVd interaction. Full article

Volatile fingerprint analysis using Gas Chromatography–Ion Mobility Spectrometry (GC-IMS) was applied to differentiate cowhide (22 samples), sheepskin (6 samples), and pigskin (6 samples). A total of 126 signal peaks were detected from the whole GC-IMS dataset, with 96 volatile compounds identified. Principal Component Analysis (PCA) revealed distinct clustering: cowhide exhibited unique volatile profiles, separating itself clearly from sheepskin and pigskin, which showed significant similarity. This was confirmed by Hierarchical clustering, K-means clustering (optimal k = 2), and Partial Least Squares Discriminant Analysis (PLS-DA) (R² = 0.9836, Q² = 0.9040). Cowhide was characterized by exclusive compounds (2-Hexanone, alpha-Thujene, Butyl acetate, 3-Methyl-2-butanol, 2-Heptanone, Hexyl methyl ether-monomer, Diethyl disulfide). Sheepskin and pigskin shared exclusive compounds (2-Methyl propanol, Isobutyl acetate, 2-Pentyl acetate, 3-Penten-2-one, 2,5-Dimethylfuran). Orthogonal PLS-DA (OPLS-DA) further differentiated sheepskin (Ethyl isobutanoate-dimer, Pentyl acetate-dimer, 3-Methyl-2-butanol, 2-Pentanone, 2-Methylbutanol-dimer, 3-Methyl-1-butanol, 2,5-Dimethylfuran, Propan-2-ol, Ethanol-dimer, and alpha-Thujene) and pigskin (Butan-2-one, Pentanal-dimer, 1-Pentanal-monomer, Ethyl vinyl ether, Z-2-Heptene, and Butyronitrile), identifying alpha-Thujene, 3-Methyl-2-butanol, and 2,5-Dimethylfuran as universal discriminatory markers. GC-IMS coupled with chemometric analysis provides a robust approach for leather authentication. Full article