Search Results (96)

Fistulina hepatica (Schaeff.) With. and Clitocybe nuda (Bull.) H.E. Bigelow & A.H. Sm. are wild edible mushrooms with nutritional and functional potential that remain insufficiently characterized. This study provides the first comparative assessment of their nutritional profiles, phenolic composition, and antioxidant activity, using specimens collected from Montesinho Natural Park (Portugal). Proximate composition, organic and phenolic acids, free sugars, and fatty acids were analyzed by chromatographic methods, and antioxidant capacity was assessed through OxHLIA and TBARS assays. F. hepatica showed higher carbohydrates (9.3 ± 0.2 g/100 g fw) and estimated energy values (43 ± 1 kcal/100 g fw), increased phenolic acids content (2.7 ± 0.1 mg/g extract), and the exclusive presence of p-coumaric and cinnamic acids, along with OxHLIA activity (IC₅₀ = 126 ± 5 µg/mL at Δt = 60 min). C. nuda displayed higher protein (2.5 ± 0.1 g/100 g dw) and quinic acid contents (4.13 ± 0.02 mg/g extract), a PUFA-rich profile, and greater TBARS inhibition (EC₅₀ = 303 ± 17 µg/mL). These findings highlight distinct and complementary bioactive traits, supporting their valorization as natural functional ingredients. Their compositional features offer promising applications in sustainable food systems and nutraceutical development, encouraging further investigations into safety, bioaccessibility, and formulation strategies. Notably, F. hepatica is best consumed at a young developmental stage, as its sensory properties tend to decline with maturity. Full article

Type 10 17β-hydroxysteroid dehydrogenase (17β-HSD10) is the HSD17B10 gene product. It plays an appreciable part in the carcinogenesis and pathogenesis of neurodegeneration, such as Alzheimer’s disease and infantile neurodegeneration. This mitochondrial, homo-tetrameric protein is a central hub in various metabolic pathways, e.g., branched-chain amino acid degradation and neurosteroid metabolism. It can bind to other proteins carrying out diverse physiological functions, e.g., tRNA maturation. It has also previously been proposed to be an Aβ-binding alcohol dehydrogenase (ABAD) or endoplasmic reticulum-associated Aβ-binding protein (ERAB), although those reports are controversial due to data analyses. For example, the reported k_m value of some substrate of ABAD/ERAB was five times higher than its natural solubility in the assay employed to measure k_m. Regarding any reported “one-site competitive inhibition” of ABAD/ERAB by Aβ, the k_i value estimations were likely impacted by non-physiological concentrations of 2-octanol at high concentrations of vehicle DMSO and, therefore, are likely artefactual. Certain data associated with ABAD/ERAB were found not reproducible, and multiple experimental approaches were undertaken under non-physiological conditions. In contrast, 17β-HSD10 studies prompted a conclusion that Aβ inhibited 17β-HSD10 activity, thus harming brain cells, replacing a prior supposition that “ABAD” mediates Aβ neurotoxicity. Furthermore, it is critical to find answers to the question as to why elevated levels of 17β-HSD10, in addition to Aβ and phosphorylated Tau, are present in the brains of AD patients and mouse AD models. Addressing this question will likely prompt better approaches to develop treatments for Alzheimer’s disease. Full article

Magenta Cherry or Eugenia (Syzygium paniculatum Gaertn) is an underutilized berry species with an interesting source of functional components. This study aimed to evaluate these berries’ morphometric, nutritional, and phytochemical characteristics at two ripening stages, CM: consumer maturity (CM) and OM: over-maturity. Morphometric analysis revealed size and weight parameters comparable to commercial berries such as blueberries. Fresh fruits were processed into pulverized material, and in this, a proximate analysis was evaluated, showing high moisture content (88.9%), dietary fiber (3.56%), and protein (0.63%), with negligible fat, indicating suitability for low-calorie diets. Phytochemical screening by HPLC identified gallic acid, chlorogenic acid, hydroxycinnamic acid, ferulic acid, quercetin, rutin, and condensed tannins. Ethanol extracts showed stronger bioactive profiles than aqueous extracts, with significant antioxidant capacity (up to 803.40 µmol _Trolox/g via Ferric Reducing Antioxidant Power (FRAP assay). Fourier-transform infrared spectroscopy (FTIR) and Raman spectroscopic analyses established structural transformations of hydroxyl, carbonyl, and aromatic groups associated with ripening. These changes were supported by observed variations in anthocyanin and flavonoid contents, both higher at the CM stage. A notable pigment loss in OM fruits could be attributed to pH changes, oxidative degradation, enzymatic activity loss, and biotic stressors. Antioxidant assays (DPPH, ABTS, and FRAP) confirmed higher radical scavenging activity in CM-stage berries. Elemental analysis identified minerals such as potassium, calcium, magnesium, iron, and zinc, although in moderate concentrations. In summary, Syzygium paniculatum Gaertn fruit demonstrates considerable potential as a source of natural antioxidants and bioactive compounds. These findings advocate for greater exploration and sustainable use of this native berry species in functional food systems. Full article

Dirigent proteins (DIRs) are pivotal regulators of lignin/lignan biosynthesis and play multifaceted roles in plant development and stress adaptation. Despite their functional significance, DIR genes remain unexplored in Rosa chinensis, a globally important woody ornamental species. This study identified 33 RcDIRs through whole-genome analysis, including their chromosomal distribution, phylogenetic relationships, collinearity, protein and gene structure, conserved motifs, and cis-acting element distribution, and classified them into three phylogenetically independent subgroups (DIR-a, DIR-b/d, and DIR-e). Notably, the DIR-e subgroup includes an exclusive tandem cluster comprising RcDIR7-RcDIR12, representing the largest lineage-specific RcDIR expansion in R. chinensis. Structural characterization revealed that most RcDIRs exhibit a conserved single-exon architecture. Promoter cis-element analysis uncovered abundant stress-/hormone-responsive elements and three pollen-specific motifs (AAATGA, POLLEN1LELAT52, GTGANTG10), with RcDIR12 from the DIR-e cluster showing high pollen-specific regulatory potential. Experimental validation included cloning the RcDIR12 promoter from R. chinensis ‘Old Blush’, constructing proRcDIR12::GUS vectors, and conducting histochemical GUS assays with pollen viability/DAPI staining in transgenic Arabidopsis. Histochemical assays demonstrated GUS activity localization in mature trinucleate pollen grains, marking the first experimental evidence of pollen-specific DIRs in rose. Our findings not only elucidate the DIR family’s genomic organization and evolutionary innovations in R. chinensis but also establish proRcDIR12 as a molecular tool for manipulating pollen development in plants. Full article

Most eukaryotic genes express more than one mature mRNA, defined as transcript variants. This complex phenomenon arises from various mechanisms, such as using alternative transcription start sites and alternative post-transcriptional processing events. The resulting transcript variants can lead to synthesizing proteins that possess distinct functional domains or may even generate noncoding RNAs, each with unique roles in cellular processes. The generation of these transcript variants is not merely a random occurrence; it is cell-type specific and varies with developmental stages, aging processes, or pathogenesis of diseases. This highlights the biological significance of transcript variants in regulating gene expression and their potential impact on cellular functionality. Despite the biological importance, investigating transcript variants has been hampered by challenges associated with detecting their expression. This review article addresses the advancements in molecular techniques in detecting transcript variants. Traditional methods such as RT-PCR and RT-qPCR can easily detect known transcript variants using primers that target unique exons associated with the variants. Other techniques like RACE-PCR and hybridization-based methods, including Northern blotting, RNase protection assays, and microarrays, have also been utilized to detect transcript variants. Nevertheless, RNA sequencing (RNA-Seq) has emerged as a powerful technique for identifying transcript variants, especially those with previously unknown sequences. The effectiveness of RNA sequencing in transcript variant detection depends on the specific sequencing approach and the precision of data analysis. By understanding the strengths and weaknesses of each laboratory technique, researchers can develop more effective strategies for detecting mRNA transcript variants. This ability will be crucial for our comprehensive understanding of gene regulation and the implications of transcript diversity in various biological contexts. Full article

Background/Objectives: In pregnancy threatened by preterm birth, antenatal corticosteroids (ACS) are administered to accelerate fetal lung maturation. However, they have side effects, including the production of reactive oxygen species that can impact cytochrome P450 (CYP) activity. We hypothesised that antioxidants could protect a fetus treated with ACS during gestation and prevent the programming of altered hepatic CYP activity in the offspring. The primary outcome of our study was the impact of different maternal treatments on the activity of hepatic drug-metabolising enzymes in offspring. Methods: At 100 ± 1 days gestational age (dGA, term = 147 dGA), 73 ewes were randomly allocated to the following: saline (5 mL IV daily 105–137 ± 2 dGA, n = 17), ACS (Dexamethasone (Dex); 12 mg IM at 115 and 116 dGA; n = 25), MitoQ (6 mg/kg MS010 IV, daily bolus 105–137 ± 2 dGA; n = 17) or Dex and MitoQ (Dex+MitoQ; n = 14). CYP activity and protein abundance were assessed using functional assays and Western blot. Results: Dex decreased the hepatic activity of fetal CYP3A (−56%, P_Dex = 0.0322), and 9 mo lamb CYP1A2 (−22%, P_Dex = 0.0003), CYP2B6 (−36%, P_Dex = 0.0234), CYP2C8 (−34%, P_Dex = 0.0493) and CYP2E1 (−57%, P_Dex = 0.0009). For all, except CYP1A2, activity returned to control levels with Dex+MitoQ in 9 mo lambs. In 9 mo lambs, MitoQ alone increased activity of CYP2B6 (+16%, P_MitoQ = 0.0011) and CYP3A (midazolam, +25%, P_MitoQ = 0.0162) and increased CAT expression (P_MitoQ = 0.0171). Dex+MitoQ increased CYP3A4/5 activity (testosterone, +65%, P_Intx < 0.0003), decreased CYP1A2 activity (−14%, P_Intx = 0.0036) and decreased mitochondrial abundance (P_Intx = 0.0051). All treatments decreased fetal hepatic DRP1, a regulator of mitochondrial fission (P_Dex = 0.0055, P_MitoQ = 0.0006 and P_Intx = 0.0034). Conclusions: Antenatal Dex reduced activity of only one CYP in the fetus but programmed the reduced activity of several hepatic CYPs in young adult offspring, and this effect was ameliorated by combination with MitoQ. Full article

Runx2 is an essential transcription factor for osteoblast differentiation and chondrocyte maturation. The spatiotemporal expression of Runx2 is regulated by enhancers. We previously identified a 1.3 kb osteoblast-specific enhancer; however, mice with this deletion showed no phenotypes. A 0.8 kb conserved region detected near the 1.3 kb enhancer did not exhibit enhancer activity in reporter assays, whereas four tandem repeats of 452 bp (452 × 4) containing the most conserved region of 0.8 kb induced strong reporter activity in chondrocyte cell lines. However, chondrocytes of enhanced green fluorescent protein (EGFP) reporter mice using 452 × 4 did not express EGFP. When 452 × 4 was combined with the 1.3 kb enhancer, hypertrophic chondrocytes highly expressed EGFP. Moreover, the 0.8 kb region combined with the 1.3 kb enhancer induced EGFP expression in prehypertrophic and hypertrophic chondrocytes. The deletion of both the 1.3 kb enhancer and the 0.8 kb conserved region slightly reduced Runx2 expression in the limbs. However, neither homozygous nor heterozygous deletions in the Runx2^+/− background showed phenotypes. The 0.8 kb conserved region itself lacked enhancer activity, but when combined with the 1.3 kb enhancer, EGFP expression was induced in chondrocytes with a similar expression pattern to Runx2. Therefore, the 0.8 kb conserved region has a novel function as a subenhancer. Full article

(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions of the same sample to generate combined multi-omics. This process is a source of bias, mainly in the field of immunology on cells originating from pluripotent hematopoietic stem cells with high flexibility during maturation. (2) Methods: Although new multi-omics approaches have been developed to use the advantages of cellular and molecular barcoding and next-generation sequencing to solve this issue, one of the main current challenges is intracellular proteomics, which should be combined with other omics data with high importance for immune system studies. We designed this study to evaluate previously recommended minimal permeabilization and fixation methods on the quality and quantity of transcriptomics and proteomics data generated by the BD Rhapsody™ Single-Cell Analysis System. (3) Results: Our findings showed that high-throughput sequencing with advanced quality and read-out is required for the combination of multi-omics outcomes from a permeabilized single cell. Therefore, the HiseqX platform was selected for further analysis. The effect of immune stimulation was observed clearly as the separated clusters of helper and cytotoxic T cells using unsupervised clustering. Importantly, fixation and permeabilization did not affect the general expression profile of unstimulated cells. However, fixation and permeabilization were proved to negatively impact the detection of the whole transcriptome for single-cell assay. Nevertheless, about 60% of the transcriptomic signature of the stimulation was detected. If the measurement of combined surface and intracellular markers is required to be achieved, the modified fixation and permeabilization method is recommended because of a lower transcriptomic loss and more precise proteomic fingerprint detected. (4) Conclusions: The findings of this study support the potential possibility for integrating intracellular proteomics, which needs to be optimized and tested with newly designed oligonucleotide-tagged antibodies targeting intracellular proteins. Full article

Sugars will eventually be exported transporters (SWEETs) are essential transmembrane proteins involved in plant growth, stress responses, and plant–pathogen interactions. Despite their importance, systematic studies on SWEETs in blueberries (Vaccinium corymbosum L.) are limited. Blueberries are recognized for their rapid growth and the significant impact of sugar content on fruit flavor, yet the role of the SWEET gene family in sugar accumulation during fruit development remains unclear. In this study, 23 SWEET genes were identified in blueberry, and their phylogenetic relationships, duplication events, gene structures, cis-regulatory elements, and expression profiles were systematically analyzed. The VcSWEET gene family was classified into four clades. Structural and motif analysis revealed conserved exon–intron organization within each clade. RT-qPCR analysis showed widespread expression of VcSWEETs across various tissues and developmental stages, correlating with promoter cis-elements. VcSWEET6a, in particular, was specifically expressed in fruit and showed reduced expression during fruit maturation. Subcellular localization indicated that VcSWEET6a is located in the endoplasmic reticulum. Functional assays in yeast confirmed its role in glucose and fructose uptake, with transport activity inhibited at higher sugar concentrations. Overexpression of VcSWEET6a in blueberries resulted in reduced sugar accumulation. These findings offer valuable insights into the role of VcSWEETs in blueberry sugar metabolism. Full article

ERF56, a member of the APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor (TF) family, was reported to be an early nitrate-responsive TF in Arabidopsis. But the function of ERF56 in nitrate signaling remains not entirely clear. This study aimed to investigate the role of ERF56 in nitrate-dependent plant growth and nitrate signaling. We confirmed with reverse transcription quantitative PCR (RT-qPCR) that the transcription of ERF56 is quickly induced by nitrate. ERF56 overexpressors displayed decreased nitrate-dependent plant growth, while erf56 mutants exhibited increased plant growth. Confocal imaging demonstrated that ERF56 is localized into nuclei. Assays with the glucuronidase (GUS) reporter showed that ERF56 is mainly expressed at the region of maturation of roots and in anthers. The dual-luciferase assay manifested that the transcription of ERF56 is not directly regulated by NIN-LIKE PROTEIN 7 (NLP7). The transcriptome analysis identified 1038 candidate genes regulated by ERF56 directly. A gene ontology (GO) over-representation analysis showed that ERF56 is involved in the processes of water transport, inorganic molecule transmembrane transport, secondary metabolite biosynthesis, and cell wall organization. We revealed that ERF56 represses nitrate-dependent growth through regulating the processes of inorganic molecule transmembrane transport, the secondary metabolite biosynthesis, and cell wall organization. Full article

Parabens are widely used in various industries, which are including chemical, pharmaceutical, food, cosmetic, and plastic processing industries. Among these, methyl paraben (MP) serves as an antimicrobial preservative in processed foods, pharmaceuticals, and cosmetics, and it is particularly detected in baby care products. Studies indicate that MP functions as an endocrine-disrupting compound with estrogenic properties, negatively affecting mitochondrial bioenergetics and antioxidant activity in testicular germ cells. However, limited information exists regarding studies on the effects of MP in oocytes. The aim of this study was to investigate the specific mechanism and the toxic effects of MP during oocyte maturation cultured in vitro using a porcine oocyte model. The results indicated that MP (50 μM) inhibited oocyte expansion, significantly reducing the expression of expansion-related genes MAPK1 and ERK1, and decreased the first polar body extrusion significantly as well. ATP levels decreased, reactive oxygen species (ROS) levels remained unchanged, and glutathione (GSH) levels decreased significantly, resulting in an elevated ROS/GSH ratio. The expression of antioxidant genes SOD1 and GPX was significantly decreased. Additionally, a significant decrease in levels of mitochondrial production and biosynthesis protein PGC1α+β, whereas levels of antioxidant-related protein Nrf2 and related gene expression were significantly increased. Autophagy protein LC3B and gene expression significantly decreased, and apoptosis assay indicated a significant increase in levels of caspase3 protein and apoptosis-related genes. These results demonstrated the negative effect of MP on oocyte maturation. In conclusion, our findings indicate that MP disrupts redox balance and induces mitochondrial dysfunction during meiosis in porcine oocytes, resulting in the inhibition of meiotic progression. The present study reveals the mechanism underlying the effects of methyl para-hydroxybenzoate on oocyte maturation. Full article

Background/Objectives: The non-canonical GC-5′ splice sites (5′ss) are the most common exception (~1%) to the classical GT/AG splicing rule. They constitute weak 5′ss and can be regulated by splicing factors, so they are especially sensitive to genetic variations inducing the misrecognition of their respective exons. We aimed to investigate the GC-5′ss of the breast/ovarian cancer susceptibility genes, ATM (exon 50), BRIP1 (exon 1), and PALB2 (exon 12), and their dysregulation induced by DNA variants. Methods: Splicing assays of the minigenes, mgATM_49-52, mgBRIP1_1-2, and mgPALB2_5-12, were conducted to study the regulation of the indicated GC-5′ss. Results: A functional map of the splicing regulatory elements (SRE) formed by overlapping exonic microdeletions revealed three essential intervals, ATM c.7335_7344del, PALB2 c.3229_3258del, and c.3293_3322del, which are likely targets for spliceogenic SRE-variants. We then selected 14 ATM and 9 PALB2 variants (Hexplorer score < −40) located at these intervals that were assayed in MCF-7 cells. Nine ATM and three PALB2 variants affected splicing, impairing the recognition of exons 50 and 12, respectively. Therefore, these variants likely disrupt the active SREs involved in the inclusion of both exons in the mature mRNA. DeepCLIP predictions suggested the participation of several splicing factors in exon recognition, including SRSF1, SRSF2, and SRSF7, involved in the recognition of other GC sites. The ATM spliceogenic variants c.7336G>T (p.(Glu2446Ter)) and c.7340T>A (p.(Leu2447Ter)) produced significant amounts of full-length transcripts (55–59%), which include premature termination stop codons, so they would inactivate ATM through both splicing disruption and protein truncation mechanisms. Conclusions: ATM exon 50 and PALB2 exon 12 require specific sequences for efficient recognition by the splicing machinery. The mapping of SRE-rich intervals in minigenes is a valuable approach for the identification of spliceogenic variants that outperforms any prediction software. Indeed, 12 spliceogenic SRE-variants were identified in the critical intervals. Full article

Genome instability relies on preserving the chromatin structure, with any histone imbalances threating DNA integrity. Histone synthesis occurs in the cytoplasm, followed by a maturation process before their nuclear translocation. This maturation involves protein folding and the establishment of post-translational modifications. Disruptions in this pathway hinder chromatin assembly and contribute to genome instability. JMJD1B, a histone demethylase, not only regulates gene expression but also ensures a proper supply of histones H3 and H4 for the chromatin assembly. Reduced JMJD1B levels lead to the cytoplasmic accumulation of histones, causing defects in the chromatin assembly and resulting in DNA damage. To investigate the role of JMJD1B in regulating genome stability and the malignancy of melanoma tumors, we used a JMJD1B/KDM3B knockout in B16F10 mouse melanoma cells to perform tumorigenic and genome instability assays. Additionally, we analyzed the transcriptomic data of human cutaneous melanoma tumors. Our results show the enhanced tumorigenic properties of JMJD1B knockout melanoma cells both in vitro and in vivo. The γH2AX staining, Micrococcal Nuclease sensitivity, and comet assays demonstrated increased DNA damage and genome instability. The JMJD1B expression in human melanoma tumors correlates with a lower mutational burden and fewer oncogenic driver mutations. Our findings highlight JMJD1B’s role in maintaining genome integrity by ensuring a proper histone supply to the nucleus, expanding its function beyond gene expression regulation. JMJD1B emerges as a crucial player in preserving genome stability and the development of melanoma, with a potential role as a safeguard against oncogenic mutations. Full article

Immune responses demand the rapid and precise regulation of gene protein expression. Splicing is a crucial step in this process; ~95% of protein-coding gene transcripts are spliced during mRNA maturation. Alternative splicing allows for distinct functional regulation, as it can affect transcript degradation and can lead to alternative functional protein isoforms. There is increasing evidence that splicing can directly regulate immune responses. For several genes, immune cells display dramatic changes in isoform-level transcript expression patterns upon activation. Recent advances in long-read RNA sequencing assays have enabled an unbiased and complete description of transcript isoform expression patterns. With an increasing amount of cell types and conditions that have been analyzed with such assays, thousands of novel transcript isoforms have been identified. Alternative splicing has been associated with autoimmune diseases, including arthritis. Here, GWASs revealed that SNPs associated with arthritis are enriched in splice sites. In this review, we will discuss how alternative splicing is involved in immune responses and how the dysregulation of alternative splicing can contribute to arthritis pathogenesis. In addition, we will discuss the therapeutic potential of modulating alternative splicing, which includes examples of spliceform-based biomarkers for disease severity or disease subtype, splicing manipulation using antisense oligonucleotides, and the targeting of specific immune-related spliceforms using antibodies. Full article

Inflammasomes are multiprotein complexes that trigger processes through caspase-1 activation, leading to the maturation of proinflammatory cytokines, such as IL-1β and IL-18. The gene encoding the inflammasome stimulatory protein NLRP3 is conserved in canines. Caspase-1/4 homologues have been identified in multiple carnivores, including canines, and caspase-1 activity has been shown in humans. The NLRP3 inflammasome has also been described in some canine inflammatory diseases. Andrographolide, a labdane diterpene, is the principal active ingredient in the herb Andrographis paniculate. The objective of this study was to determine the effect of andrographolide on the gene expression of the components of the NLRP3 inflammasome, proinflammatory cytokines, and IL-1β secretion in canine peripheral blood mononuclear cells. For this, MTT assays and real-time PCR were employed to assess the cytotoxicity and gene expression. Further, an ELISA test was performed to measure the IL-1β concentration. The findings reveal that andrographolide significantly reduces the expression of NLRP3, caspase-1/4, IL-1β, and IL-18. Additionally, it decreases the secretion of IL-1β and other proinflammatory cytokines, including IL-6, IL-8, and TNF-α. The results show that andrographolide decreases the expression of NLRP3, caspase-1/4, IL-1β, and IL-18. Andrographolide also reduces proinflammatory cytokines expression, and decreases IL-1β secretion. This indicates that andrographolide can interfere with the activation and function of the inflammasome, resulting in a decrease in the inflammatory response in canines. Research in this area is still budding, and more studies are necessary to fully understand andrographolide’s mechanisms of action and its therapeutic potential in relation to the NLRP3 inflammasome in dogs. Full article