Search Results (493)

Mushrooms are eukaryotic organisms with absorptive heterotrophic nutrition, capable of feeding on organic matter rich in cellulose and lignocellulose. Since ancient times, they have been considered allies and, in certain cultures, they were seen as magical beings or food of the gods. Of the great variety of edible mushrooms identified worldwide, less than 2% are traded on the market. Although mushrooms have been valued for their multiple nutritional and healing benefits, some cultures perceive them as toxic and do not accept them in their culinary practices. Despite the existing skepticism, several researchers are promoting the potential of edible mushrooms. There are two main methods of mushroom cultivation: solid-state fermentation and submerged fermentation. The former is the most widely used and simplest, since the fungus grows in its natural environment; in the latter, the fungus grows suspended without developing a fruiting body. In addition, submerged fermentation is easily monitored and scalable. Both systems are important and have their limitations. This article discusses the main methods used to increase the performance of submerged fermentation with emphasis on the modes of operation used, types of bioreactors and application of morphological bioengineering of filamentous fungi, and especially the use of intelligent automatic control technologies and the use of non-invasive monitoring in fermentation systems thanks to the development of machine learning (ML), neural networks, and the use of big data, which will allow more accurate decisions to be made in the fermentation of filamentous fungi in submerged environments with improvements in production yields. Full article

Background: Fowl typhoid (FT), a septicemic infection caused by Salmonella Gallinarum (SG), and H9N2 avian influenza are two economically important diseases that significantly affect the global poultry industry. Methods: We exploited the live attenuated Salmonella Gallinarum (SG) mutant JOL3062 (SG: ∆lon ∆pagL ∆asd) as a delivery system for H9N2 antigens to induce an immunoprotective response against both H9N2 and FT. To enhance immune protection against H9N2, a prokaryotic and eukaryotic dual expression plasmid, pJHL270, was employed. The hemagglutinin (HA) consensus sequence from South Korean avian influenza A virus (AIV) was cloned under the Ptrc promoter for prokaryotic expression, and the B cell epitope of neuraminidase (NA) linked with matrix protein 2 (M2e) was placed for eukaryotic expression. In vitro and in vivo expressions of the H9N2 antigens were validated by qRT-PCR and Western blot, respectively. Results: Oral immunization with JOL3121 induced a significant increase in SG and H9N2-specific serum IgY and cloacal swab IgA antibodies, confirming humoral and mucosal immune responses. Furthermore, FACS analysis showed increased CD4+ and CD8+ T cell populations. On day 28 post-immunization, there was a substantial rise in the hemagglutination inhibition titer in the immunized birds, demonstrating neutralization capabilities of immunization. Both IFN-γ and IL-4 demonstrated a significant increase, indicating a balance of Th1 and Th2 responses. Intranasal challenge with the H9N2 Y280 strain resulted in minimal to no clinical signs with significantly lower lung viral titer in the JOL3121 group. Upon SG wildtype challenge, the immunized birds in the JOL3121 group yielded 20% mortality, while 80% mortality was recorded in the PBS control group. Additionally, bacterial load in the spleen and liver was significantly lower in the immunized birds. Conclusions: The current vaccine model, designed with a host-specific pathogen, SG, delivers a robust immune boost that could enhance dual protection against FT and H9N2 infection, both being significant diseases in poultry, as well as ensure public health. Full article

Background: The N⁶-methyladenosine (m⁶A) modification of eukaryotic mRNA is the most prevalent of such epigenetic modifications and has recently been identified as a potential player in the pathogenesis and progression of hepatocellular carcinoma (HCC). With the increasing emergence of immunotherapy in the treatment of HCC, we have evaluated the potential of m⁶A-related genes in predicting overall survival and the therapeutic efficacy of immunotherapy in HCC patients. Methods: We employed transcriptomic data from TCGA-LIHC and GSE76427, comprising a total of 485 HCC patients, as the training set. Based on 23 recognized m⁶A regulators, we performed clustering analysis on HCC patients. The intersecting differentially expressed genes (DEGs) among subtypes were used in least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression analyses to construct the risk model. For the quantification of a risk model of HCC patients, a risk score was developed and correlated with clinical and immunological parameters. Furthermore, a single-cell transcriptomic atlas was used to analyze the relationship between model genes and immune cell subpopulations. Mechanistic studies included in vitro assays to validate the association between the m⁶A-related gene ANLN and the progression of HCC. Results: Internal (TCGA and GEO) and external validation (ICGC) suggested that an 8-gene risk score provides an accurate and stable prognostic assessment for HCC. Furthermore, the high-risk score, characterized by elevated TP53 mutation frequency, tumor mutation burden (TMB), and tumor stem cell characteristics indicated a poor prognosis. The prognostic signature was associated with immune cell infiltration in HCC. Those patients with a high-risk score had lower immune tolerance with a better prediction of the efficacy of immunotherapy. The risk model helps to assess and predict the response and prognosis of HCC patients to immune checkpoint inhibitors (ICIs). Additionally, single-cell RNA sequencing data revealed that the high-risk group had a higher proportion of T cells and fewer immunosuppressive T cells, potentially correlating with a better response to immunotherapy. Finally, in vitro experiments showed that ANLN, an m⁶A-related gene, promoted the proliferation and migration of HCC cells. Conclusions: In this study, we identified and validated an m⁶A gene signature consisting of eight genes that can be used to predict prognosis and immunotherapy efficacy in HCC patients. Full article

Background: N6-methyladenosine (m6A) is the most prevalent chemical modification of eukaryotic RNA, playing a crucial role in regulating plant growth and development, stress responses, and other essential biological processes. The enzymes involved in m6A modification—methyltransferases (writers), demethylases (erasers), and recognition proteins (readers)—have been identified in various plant species; however, their roles in the economically significant tree species Populus deltoides × P. euramericana (NL895) remain underexplored. Results: In this study, we identified 39 m6A-related genes in the NL895 genome, comprising 8 writers, 13 erasers, and 18 readers. Evolutionary analysis indicated that the expansion of writers and readers primarily resulted from whole-genome duplication events. Purifying selection pressures were observed on all duplicated gene pairs, suggesting their essential roles in functional differentiation. Phylogenetic analysis revealed that writers, erasers, and readers are categorized into six, four, and two groups, respectively, with these genes being more conserved among dicotyledonous plants. Gene structure, protein domains, and motifs exhibited greater conservation within the same group. Promoter analysis of m6A-related genes showed enrichment of cis-acting elements associated with responses to light, phytohormones, and stress, indicating their potential involvement in gene expression regulation. Under cadmium treatment, the expression of all writers was significantly upregulated in both the aboveground and root tissues of NL895. Conclusions: This study systematically identified m6A-related gene families in Populus deltoides × P. euramericana (NL895), elucidating their evolutionary patterns and expression regulation characteristics. These findings provide a theoretical foundation for analyzing the molecular mechanisms of m6A modification in poplar growth, development, and stress adaptation, and offered candidate genes for molecular breeding in forest trees. Full article

The large portion of the eukaryotic genomes was considered non-functional and called the “dark matter” of the genome, now appearing as regulatory hubs coding for RNAs without the potential for making proteins, known as non-coding RNA. Long non-coding RNA (lncRNA) is defined as functional RNA molecules having lengths larger than 200 nucleotides without the potential for coding for proteins. Thousands of lncRNAs are identified in different plants and animals. LncRNAs are characterized by a low abundance, fewer exons than mRNA, tissue-specific expression, and low sequence conservation compared to protein-coding genes (PCGs). LncRNAs, like PCGs, are regulated by promoters and enhancers with characteristic chromatin signatures, DNA methylation, multiple exons, introns, and alternate splicing. LncRNAs interact with DNA, mRNA, microRNA, and proteins, including chromatin/histone modifiers, transcription factors/repressors, epigenetic regulators, spliceosomal, and RNA-binding proteins. Recent observations indicate that lncRNAs code for small peptides, also called micropeptides (<100 amino acids), and are involved in the development and growth of plants, suggesting the bi-functional activities of lncRNAs. LncRNAs have emerged as the major regulators of diverse functions, principally by altering the transcription of target genes. LncRNAs are involved in plant growth, development, immune responses, and various physiological processes. Abiotic, biotic, nutrient, and other environmental stresses alter the expressions of numerous lncRNAs. Understanding the mechanisms of actions of lncRNAs opens up the possibility of improving agronomic traits by manipulating lncRNAs. However, further studies are required in order to find the interactions among the deregulated lncRNAs and validate the findings from high-throughput studies to harness their potential in crop improvement. Full article

Eukaryotic cells double their mass and divide at the same rate, allowing cells to maintain a uniform cell size over many cell divisions. We hypothesize that aneuploid cancer cells are more sensitive to forced overgrowth, more than doubling their mass during a single longer-duration cell division cycle, relative to healthy diploid cells. This hypothesis stems from the observation that cancer cells are under proteotoxic stress, during which heat-shock proteins become rate-limiting and the unfolded-protein response network has a growth-suppressive phenotype. Forced overgrowth will lead to the production of more individual proteins per cell division cycle and increase the duration of time during which any mis-folded or aggregated proteins might disrupt the function of properly folded proteins. To induce these potential forced overgrowth effects, we suggest targeting the cell division cycle regulatory enzyme, the anaphase-promoting complex/cyclosome (APC/C), to suppress—but not inhibit—its activity. We conclude by proposing experiments to test this hypothesis in which an APC/C inhibitor, such as a low level of proTAME, is combined with the clinically approved heat-shock protein 90 (HSP90)-inhibitor pimitespib (TAS-116) or the pre-clinical molecule tanespimycin, which, to the best of our knowledge, are combinations that have not been investigated before. Full article

Background: Casein kinase I-like (CKL) protein is a member of the serine/threonine kinase CKI family and plays a pivotal regulatory role in various eukaryotic cellular processes, including stress responses. Objectives: This study aims to systematically identify the CKL gene family in the tomato genome and investigate its responsiveness to abiotic stress. Methods: Members of SlCKL were identified through genome-wide bioinformatics analysis, and their physicochemical properties, chromosomal localization, gene structure, conserved domains, phylogenetic relationships, cis-acting elements, cross-species collinearity, and tissue expression profiles were comprehensively analyzed. The expression patterns of SlCKL genes under abiotic stress were validated using real-time quantitative PCR. Results: A total of 16 SlCKL genes were identified and classified into three subfamilies (I–III), which are unevenly distributed across nine chromosomes, predominantly clustered at the ends. The gene structure, motifs, and functional domains exhibit high conservation. Collinearity analysis revealed stronger synteny between tomato and Arabidopsis thaliana or pepper compared to rice, maize, or tobacco, suggesting a common ancestral origin. The tissue expression profile indicates that SlCKLs are preferentially transcribed in roots. Promoter analysis and qRT-PCR validation demonstrated differential responses of SlCKLs to various abiotic stresses, such as drought, salt, heat, cold, and ABA treatment. Conclusions: This study represents the first systematic identification of the tomato SlCKL gene family, elucidating its evolutionary relationships, structural characteristics, tissue-specific expression patterns, and differential responsiveness to abiotic stress, thereby providing a critical foundation for further investigation into the molecular mechanisms underlying CKL-mediated abiotic stress adaptation in tomatoes. Full article

Background: Basic (region) leucine zippers (bZIPs) make up one of the largest families and are some of the most prevalent evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. Plant bZIP family members are involved in seed germination, vegetative growth, flower development, light response, and various biotic/abiotic stress response pathways. Nevertheless, a detailed identification and genome-wide analysis of the bZIP family genes in broomcorn millet have not been conducted. Methods: In this research, we performed genome-wide identification, phylogenetic analysis, cis-elements analysis, and expression pattern analysis. Results: 144 bZIP transcription factors were identified from the P. miliaceum genome and classified into eleven subfamilies using a phylogenetic analysis. Motif and bZIP domain sequence alignment analyses indicated that the members in each subfamily were relatively conserved. Furthermore, a promoter analysis revealed that bZIP transcription factor family genes were responsive to multiple hormones and environmental stresses. Additionally, cis-element MYB binding sites were identified in the promoters of most PmbZIP genes. A gene expression analysis showed that 18 PmbZIP genes were differentially expressed during seed germination in salt stress, with 7 being significantly downregulated and 11 upregulated, thus suggesting that these PmbZIP genes may play an important role in the salt stress response and seed germination. Conclusions: Current research provides valuable information for further functional analyses of the PmbZIP gene family and as a reference for future studies on broomcorn millet’s stress response. Full article

Glycine has the greatest rate of deposition in whole-body proteins among all amino acids in neonates, but its provision from sow’s milk meets only 20% of the requirement of suckling piglets. The results of our recent studies indicate that piglets with intrauterine growth restriction (IUGR) have a reduced ability to synthesize glycine. The present study determined the role of glycine in the growth of sow-reared IUGR piglets. In Experiment 1, 56 newborn piglets (postnatal day 0) with a low birth weight (<1.10 kg) were selected from 14 litters, providing 4 IUGR piglets/litter that were allotted randomly into one of four treatment groups (14 piglets/group). Piglets received oral administration of either 0, 0.1, 0.2 or 0.4 g glycine/kg body weight (BW) twice daily (i.e., 0, 0.2, 0.4 or 0.8 g glycine/kg BW/day) between 0 and 14 days of age. L-Alanine was used as the isonitrogenous control. The BWs of all piglets were recorded each week during the experiment. Two weeks after the initiation of glycine supplementation, blood and tissue samples were collected for biochemical analyses. In Experiment 2, rates of muscle protein synthesis in tissues were determined on day 14 using the ³H-phenylalanine flooding dose technique. Compared with piglets in the control group, oral administration of 0.2, 0.4 and 0.8 g glycine/kg BW/day did not affect their milk intake (p > 0.05) but increased (p < 0.05) concentrations of glycine in plasma by 1.52-, 1.94-, and 2.34-fold, respectively, and body weight by 20%, 37%, and 34%, respectively. The dose of 0.4 g glycine/kg BW/day was the most cost-effective. Consistent with its growth-promoting effect, glycine supplementation stimulated (p < 0.05) the phosphorylation of mechanistic target of rapamycin (MTOR), eukaryotic initiation factor 4E binding protein 1 (4E-BP1), and ribosomal protein S6 kinase beta-1 (p70^S6K) as well as protein synthesis in skeletal muscle, compared with the control group. Collectively, oral administration of glycine activated the MTOR signaling pathway in skeletal muscle and enhanced the growth performance of IUGR piglets. These results indicate that endogenous synthesis of glycine is inadequate to meet the needs of IUGR piglets during the suckling period and that oral supplementation with glycine to these compromized neonates can improve their growth performance. Full article

The ubiquitin-proteasome pathway performs a strictly controlled degradation of specific protein substrates within the eukaryotic cell. This catabolic mechanism allows the rapid removal of proteins damaged in any way, and therefore potentially capable of compromising cellular homeostasis, as well as the constant turnover of all cellular proteins, in order to balance their synthesis and thus maintain the correct levels of proteins required by the cell at any given time. Consequently, the ubiquitin-proteasome system plays a fundamental role in regulating essential cellular processes, such as the cell cycle, apoptosis, immune responses, and inflammation, whose dysregulation or malfunction can lead to neoplastic transformation. Not surprisingly, therefore, alterations in the activity and regulatory mechanisms of the proteasome are common not only in various types of tumors, but often represent a contributing cause of oncogenesis itself. Among proteasome modulators, PA28γ, due to its function in promoting cell growth and proliferation, while inhibiting apoptosis and cell-mediated immune responses, has received great attention in recent years for its well established pro-tumoral activity. Conversely, the role played in oncogenesis by the second paralogue of the PA28 family of proteasome activators, namely PA28αβ, is less clearly defined, which is also related to the lower level of general understanding of its cellular activities and biological functions. However, increasing experimental evidence has demonstrated that PA28αβ also plays a non-secondary role in the process of neoplastic transformation and tumor growth, both by virtue of its regulatory function on class I cell-mediated immune responses and through activity promoting cell duplication and growth. This review aims to summarize the current knowledge and evidence on the molecular mechanisms and cellular functions through which PA28αβ may support development and growth of cancer. Full article

Meiotic recombination is essential for chromosomal segregation and facilitates the exchange between homologs, which leads to the transmission of new combinations of linked alleles to the progeny. The eukaryotic meiotic machinery is generally highly conserved, but the frequency of crossover occurrence can vary dramatically across species and populations, between individuals, and across sexes. The chicken and the guinea fowl exhibit interspecific variation in the distribution of crossovers along their largest chromosomes. In many organisms, an association has been observed between the preferred crossover location and certain sequence parameters, such as high GC content, CpG islands, or gene promoters. Here, we compared the distribution of these genomic parameters with the recombination landscape, represented by MLH1 focus frequencies, in the two birds. We found an association between GC content density and recombination in the chicken, but the remaining parameters showed weak or no association with recombination, especially in the guinea fowl. We conclude that despite the different broad-scale crossover distribution, the investigated genomic parameters remained remarkably similar in these two species. We suggest that the density of these genomic features is more likely related to microscale variations in recombination rates, such as those determined by open chromatin configurations. Full article

Sea buckthorn (Hippophae rhamnoides) is a valuable plant rich in biologically active compounds, mainly found in its berries and leaves. The harvesting process, which includes pruning, freezing, and shaking, leaves behind large amounts of biomass and juice-pressing residues, typically composted. The aim of this study is to expand knowledge of the valorization of sea buckthorn secondary raw materials by applying an innovative pressure cyclic solid–liquid (PCSL) extraction method and to develop value-added functional food products. Extraction was performed in 20 and 60 cycles, each lasting from 2 to 10 min. The highest concentrations of proanthocyanidins (5.51 g_CE/L) and total phenolics (12.42 g_GAE/L) were obtained under prolonged conditions, but the L-4 extract (20 cycles × 2 min) was selected for kombucha production due to its favorable balance between efficiency and sustainability. Microbial safety evaluation showed that kombucha with sea buckthorn leaf extract exhibited significantly stronger antimicrobial activity against tested pathogens compared to green tea kombucha. Additionally, sensory analysis revealed higher consumer acceptability of beverages enriched with sea buckthorn extracts. Shotgun metagenomic analysis identified high microbial diversity in the M. gisevii MI-2 starter culture and fermented kombucha products (227 bacteria and 44 eukaryotes), most of which (92.5% bacteria, 77.8% eukaryotes) remain viable and contribute to fermentation dynamics. New biotechnological strategies and genetic modifications raise concerns about the safe use of microorganisms in food production. To address these issues, these findings provide a foundation for future strategies aimed at the safe application of beneficial microorganisms in food biotechnology and support the long-term goals of the European Green Deal by promoting sustainable biomass valorization and circular economy advancement in the food sector. Full article

Chromatin remodeling factors efficiently and precisely establish, maintain, regulate, and distinguish between chromatin states in eukaryotes. DECREASE in DNA METHYLATION 1 (DDM1) is an important heterochromatin remodeling factor in plants that is responsible for maintaining heterochromatin DNA methylation and suppressing most transposable elements. Previous studies have predominantly focused on the effects of DDM1 on chromatin, with only a few focusing on its remodeling mechanisms. However, recent studies have greatly advanced understanding of the remodeling functions of DDM1 and, in particular, have clarified the mechanisms involved. In this review, we discuss the newly identified remodeling functions and mechanisms of DDM1. As DDM1 is closely involved in histone variant exchange, we first introduce the main histone variants associated with chromatin states in plants. Next, we focus on how DDM1 promotes the deposition of specific histone variants and describe its other remodeling functions. We propose that the core function of DDM1 is the regulation of histone variant distribution. DDM1 maintains heterochromatin by regulating the deposition of H2A and H3 variants, particularly by facilitating the exchange of specific histone variants. Full article

SINEs are one type of the most frequently found DNA repetitive sequences in the eukaryotic genome. The polymorphism generated by SINE insertion may affect proximal host genes and even cause phenotypic variations in domestic animals. Glycine N-acyltransferase-like 3 (GLYATL3) is a member of the N-acyltransferase family which may play a role in amino acid and fatty acid metabolism. Previous studies have identified short interspersed nuclear element (SINE) insertion sites in the 5′UTR region of GLYATL3. This study investigated the effects of the 294 bp SINE insertion on GLYATL3 expression and phenotypic variation. The polymerase chain reaction (PCR) was used to determine the distribution of GLYATL3-SINE-RIP in 15 pig breeds. SINE insertions were absent in hybrid pigs and present in all purebred pigs. Correlation analysis further revealed significant differences in SINE+/+ and SINE−/− individuals when they reached 30 kg of body weight. In light of these findings, qPCR revealed that the SINE insertion significantly increased GLYATL3 expression in the cerebellum of Mi pigs. Additionally, dual-luciferase reporter assays confirmed that the SINE insertion significantly enhanced the activity of the Oct4 promoter. Preliminary evidence indicates the SINE insertion may modulate an increase in the growth rate of pigs through transcriptional regulation of GLYATL3. As a new type marker, this SINE-insertion polymorphism may assist genetic selection to optimize growth traits in porcine breeding programs. Full article

Cellular senescence plays a pivotal role in aging and stress response mechanisms. Controlling cellular senescence is essential for developing novel techniques to prevent aging or aging-related diseases and promote a healthy lifespan. This study explores the efficiency of cold atmospheric microplasma (CAM) for controlling cellular senescence in yeast Saccharomyces cerevisiae. Reactive oxygen and nitrogen species (RONS) generated by CAM influence key processes, such as the regulation of oxidative stress, alterations in membrane potential, and senescence-related epigenetic modifications. As a marker of cellular senescence, the expression of β-galactosidase was assessed in response to different plasma treatments. At a frequency of 1 kHz and a discharge voltage of 5 kV_p-p, a significant reduction in β-galactosidase activity was observed in cells treated for 10 s and 30 s compared to the control, indicating a reduction in cellular senescence. Additionally, cell viability, metabolic activity, and plasma membrane potential were also found to be higher for the treated cells compared to the control under the same conditions. This study confirms that a physiologically tolerable level of ROS and RNS is sufficient for cellular signaling, but not for damage induction. The findings from this study provide insights on the potential of microplasma as a tool for controlling cellular senescence and the development of therapeutic innovations involving eukaryotic cells. Full article