Search Results (435)

Hydrogen-rich water (HRW) is an aqueous solution containing dissolved molecular hydrogen. This study evaluated its effects on juvenile largemouth bass (Micropterus salmoides) under acute low-temperature stress. A total of 480 juveniles (2.4 ± 0.5 g) were randomly assigned to four groups: the control group was reared in standard water; the treatment groups were exposed to different hydrogen concentrations, specifically H1 (0.3 mg/L), H2 (0.5 mg/L), and H3 (0.9 mg/L). The fry were reared at 26 ± 0.5 °C for 30 days, followed by acute low-temperature stress (11 ± 0.5 °C) for 48 h. Samples were collected at 0, 8, 24, and 48 h. Results showed that after 30 days of HRW rearing, the final body weight (FBW), specific growth rate (SGR), and condition factor (CF) of the H1 group were significantly increased, while the H3 group only increased CF. No significant differences were observed in hepatopancreas somatic index (HSI) and survival rate (SR) among groups. Acute low-temperature stress induced liver and intestinal damage, which were alleviated in the H1 group. The H1 group exhibited significantly increased SOD, CAT, and GSH-Px activities in the liver, as well as CAT and SOD in the intestine and gills, while reducing MDA levels, thereby enhancing the antioxidant capacity. The H1 group significantly upregulated the antioxidant genes expression (sod, cat, and gsh-px mRNA levels) in the liver and gills but downregulated them in the intestine. 16S rDNA analysis revealed that HRW increased intestinal microbiota and the relative abundance of Bacillota. In conclusion, the H1 group significantly improved growth performance, mitigated acute low-temperature damage, enhanced antioxidant capacity, and increased the relative abundance of Bacillota in the intestines. This provides an innovative, safe, and effective solution for aquaculture industries confronting low-temperature challenges. Full article

Background/Objectives: Genomic testing has transformed rare-disease diagnostics, yet a substantial proportion of individuals remain without a molecular diagnosis even after short-read exome sequencing (SR-ES) or short-read genome sequencing (SR-GS) and repeated conventional analysis. Methods: To address this persistent gap, we evaluated a coordinated multimodal reanalysis framework for deeply investigated families with suspected monogenic disease. Six families (20 individuals; 8 affected individuals) that had remained unsolved after prior comprehensive testing were reviewed prospectively in weekly interdisciplinary case conferences over one year. Available data included SR-ES, SR-GS, long-read genome sequencing (LR-GS), RNA-seq, optical genome mapping, mobile-element analysis, and mitochondrial genome analysis. The goal was not to test a single modality in isolation, but to assess whether systematic escalation across complementary assays plus continued reinterpretation could improve case resolution. Results: Three families (50%) achieved a reportable molecular diagnosis, two (33%) yielded strong candidate findings requiring additional evidence, and one (17%) remained without a definitive new molecular diagnosis, although reinterpretation of a previously identified NOTCH3 variant provided a possible partial explanation. Resolved cases included compound-heterozygous variants in KLHL40, a 119 kb multi-exon deletion in TTN, and a recurrent insertion in RNU4-2. Candidate findings included biallelic NARS2 variants and a 1.3 kb intragenic deletion involving ZEB2. Functional transcriptomic analyses supported the KLHL40 and TTN diagnoses but did not demonstrate a splicing consequence for the candidate NARS2 intronic variant in cardiac tissue. Conclusions: This small pilot cohort is not intended to estimate general diagnostic yield, but it demonstrates that a coordinated multimodal framework can reveal different sources of added value, including structural variant discovery, orthogonal functional support, and reinterpretation of existing short-read data as knowledge evolves. These findings underscore that archived short-read exome and genome data can retain substantial diagnostic value years after initial testing, particularly when reanalyzed with updated pipelines, expanded disease gene knowledge, and orthogonal multimodal evidence. Adoption of iterative, team-based multimodal strategies may help resolve the most complex unsolved rare-disease cases. Full article

Sugar beet cultivation in Europe is threatened by two vector-borne diseases: syndrome “basses richesses”, caused by the phloem-limited pathogen ‘Candidatus Arsenophonus phytopathogenicus’, and phytoplasmoses associated with ‘Ca. Phytoplasma solani’ subgroup 16SrXII-A and the related subgroup 16SrXII-P. Infections lead to reduced sugar yield, biomass and growth abnormalities. In Germany, Pentastiridius leporinus represents the main vector. Despite their importance, genetic diversity remains poorly understood. During a two-year survey, barcoded amplicons were generated from infected sugar beet samples from Germany and neighbouring countries using the phytoplasma markers 16S rRNA-ITS-23S rRNA, tuf, and groEL-stamp-nadE, as well as rplO-secY-rpmJ and groEL for ‘Ca. A. phytopathogenicus’. Amplicon pools underwent single-molecule real-time sequencing and amplicon-sequence-variant inference. Additionally, planthopper samples from sugar beet in Germany were analysed and compared to sugar beet data for ‘Ca. A. phytopathogenicus’. No genetic diversity of ‘Ca. A. phytopathogenicus’ was detected, whereas 16SrXII-A and -P showed variation below the subgroup level. 16SrXII-A exhibited higher diversity than 16SrXII-P. In Germany, 16SrXII-A formed a single cluster, while 16SrXII-P comprised two clusters based on 16S rRNA-ITS-23S rRNA. In neighbouring countries, only 16SrXII-A showed diversity, resolving up to four clusters by groEL-stamp-nadE. These results provide a basis for the identification of dominant strains supporting comparative variety evaluation for tolerance. Full article

In this study, we systematically analyzed the dynamic changes in chromatin accessibility and the transcriptional responses in the spleen of largemouth bass (Micropterus salmoides) following infection with iridovirus (LMBV) using the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq). Based on post-infection survival status, largemouth bass were classified into a resistant group (SR) and a susceptible group (SS). A total of 11,317 differentially accessible regions were identified between the two groups, among which the chromatin accessibility of core promoter regions was entirely increased in the SR group, suggesting that chromatin remodeling in these regions may directly participate in the transcriptional regulation of immune-related genes. Functional enrichment analysis revealed that genes associated with differentially accessible regions were significantly enriched in immune-related pathways such as autophagy, apoptosis, Toll-like receptor signaling, and NOD-like receptor signaling. Motif analysis further identified that transcription factors significantly enriched in the SR group included CTCF and heterodimers composed of multiple members of the ETS and FOX transcription factor families. Through integrative analysis, seven transcription factors (CTCF, Spi1, ETV2::FOXI1, FOXJ2::ELF1, FOXO1::ELK1, SPIC, and FOXO1::ELF1) were found to be significantly enriched in core promoter regions. To further screen for differentially expressed genes directly regulated by chromatin accessibility changes, an overlapping analysis was performed between 629 predicted target genes and 2656 differentially expressed genes (DEGs), resulting in the identification of 71 candidate genes. Among these, three immune-related genes (irf4a, btk, and nfil3-2) belonging to the ETS and FOX families were identified. This study reveals the dynamic chromatin accessibility landscape of largemouth bass in response to LMBV infection and demonstrates that increased chromatin accessibility in core promoter regions is closely associated with the resistant phenotype. Heterodimers of ETS and FOX family transcription factors may participate in antiviral immune responses by regulating the expression of key immune genes such as irf4a, btk, and nfil3-2, providing potential epigenetic molecular markers for disease resistance breeding in fish. Full article

Class B scavenger receptor BI splice variants (SR-BI) and BII (SR-BII) internalize lipoproteins but also bind and internalize bacteria. Their individual roles in sepsis are unknown. We overexpressed human SR-BI or BII in transgenic mice, primarily in the liver, but also in the kidney and in bone marrow-derived macrophages, and then performed cecal ligation and puncture (CLP) surgery. SR-BI and BII transgenic mice had significantly worse survival compared to WT mice. Twenty-four hours after CLP, liver injury markers and histological damage were elevated in both SR-BI and BII transgenic mice, whereas kidney damage was similar. Systemic inflammatory cytokines were markedly increased in SR-BI and BII transgenic mice; parallel increases were seen in liver mRNA expression, but not in the kidney. The highest degree of neutrophil infiltration was observed in the liver of SR-BI. Human SR-BI and BII dramatically decreased bacterial accumulation in the liver. Green fluorescent protein-labeled E. coli were efficiently phagocytosed in hepatic macrophages of SR-BI and BII transgenic mice; phagocytosis was more prominent in SR-BII transgenic mice. Finally, human SR-BI overexpression reduced systemic HDL-C levels, eliminated adrenal cortex lipid droplets, and dampened the systemic increase of corticosterone after CLP. Supplementation with glucocorticoid and mineralocorticoid improved survival in SR-BI but not in SR-BII transgenic mice after CLP. In summary, our findings suggest human SR-BI and BII overexpression contributes to higher mortality after CLP by different mechanisms: excessive inflammatory response due to adrenal insufficiency (SR-BI) or hyperactive phagocytosis (SR-BII) in the liver. Full article

Neurotensin (NTS) binds to the G protein-coupled receptors (GPCRs) NTSR1 and NTSR2. NTSR1 regulates transactivation of the EGFR, HER2, and HER3, but its effects on HER4 are unknown. By Western blot, NTSR1 and HER4 were present in six lung cancer cell lines examined. In NCI-H522 or NCI-H661 cells, adding NTS increased phosphorylation (P) of tyrosine (Y) 1284 on HER4. Because SR48692 antagonized NTS’s ability to increase P-HER4 or P-ERK, NTSR1 may play an important role in NSCLC. SR48692, HER4 siRNA, reactive oxygen species inhibitors, and the tyrosine kinase inhibitor ibrutinib inhibited NTS-induced P-HER4. Adding NTS to NCI-H661 cells increased the formation of HER4/HER4, HER4/ EGFR, and HER4/HER2 dimers. Adding NTS to NSCLC cells increased both P-ERK and P-AKT, which were inhibited by PD98059 and LY294002, respectively. The growth of NCI-H522 or NCI-H661 cells was stimulated by NTS or neuregulin 1 (NRG1), a HER4 ligand, but inhibited by SR48692 or ibrutinib. The results indicate that NTSR1 regulates HER4 transactivation, thereby increasing the proliferation of lung cancer cells. Full article

Saskatoon berry (SB), a traditional food of Indigenous people, has been associated with cardiometabolic benefits in animal models; however, its effects on humans remain unclear. This study investigated the effects of dried SB consumption on cardiometabolic outcomes, gut microbiota, and short-chain fatty acids (SCFAs) profiles in healthy adults. In a 10-week, single-arm, and open-label trial, 20 healthy adults consumed 40 g/day of freeze-dried whole SB. Biochemical measures, physical exams, dietary records, participant feedback, and fecal samples were collected before and after the intervention. Gut microbiota composition and fecal SCFAs were profiled using 16S-rRNA sequencing and gas chromatography–mass spectrometry, respectively. SB intake significantly reduced fasting plasma glucose, total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-c), non-high-density lipoprotein-cholesterol (non-HDL-c), systolic blood pressure, and high-sensitivity C-reactive protein, while increasing dietary fiber intake. Fiber intake was negatively correlated with TC, LDL-c and non-HDL-c (p < 0.05). The relative abundance of fecal Prevotellaceae increased after SB consumption and was positively correlated with multiple fecal SCFAs (p < 0.05–0.0001), while being negatively associated with lipid profiles and blood pressure. No adverse cardiovascular, hepatic, or renal dysfunction were observed; however, the significant increase in sugar intake may pose a risk for elevated blood glucose. Therefore, limiting other high-sugar foods during SB supplementation may be advisable for individuals with glucose intolerance. Overall, SB intake improved glucose and lipid metabolism and lowered blood pressure and inflammatory markers in healthy adults. These cardiometabolic benefits may be mediated by fiber and anthocyanins in SB and through modulation of gut microbiota and SCFA production; however, further confirmation is needed in subsequent randomized controlled trials. Full article

‘Candidatus Phytoplasma rubi’ (elm yellows group, 16SrV-E phytoplasma subgroup) is the causal agent of rubus stunt disease, a disorder affecting economically important plants—raspberries and blackberries. Although this phytoplasma has been extensively studied in cultivated Rubus crops, its occurrence and molecular identity in wild Rubus species populations in North-Eastern Europe remain poorly documented. In this study, phytoplasmas associated with symptomatic wild Rubus idaeus L. and Rubus nessensis Hall plants were investigated in natural forest ecosystems of the Curonian Spit, Lithuania. A total of 65 symptomatic plants were surveyed, and phytoplasma infection was detected in 30 samples by nested PCR targeting the 16S rRNA gene. Positive samples were characterized using a multilocus molecular approach based on sequence analysis of the additional cpn60 and secA genes. All strains showed high nucleotide sequence similarity across the analysed loci and consistently clustered with reference strains of ‘Candidatus Phytoplasma rubi’. Virtual RFLP profiles derived from the 16S rRNA and cpn60 genes were nearly identical to those of established 16SrV-E phytoplasma subgroup reference strains and clearly distinct from other 16SrV phytoplasma subgroups. These results provide not only the first detailed multilocus molecular characterization of ‘Candidatus Phytoplasma rubi’-related strains infecting wild Rubus species in Lithuania but also represent the first report of this phytoplasma in naturally occurring R. idaeus and R. nessensis plants in the country, thereby extending the known geographical occurrence of this pathogen and documenting its presence in wild Rubus hosts from unmanaged forest habitats in the Eastern Baltic region of Northern Europe. Full article

The artificially cultivated edible mushroom Stropharia rugosoannulata is widely promoted and cultivated in China because of its ability to efficiently decompose agricultural and forestry waste. However, methods for CRISPR/Cas9 genome editing have not yet been established for S. rugosoannulata. In this study, we identified three SrU6 promoters in S. rugosoannulata and constructed the CRISPR/Cas9 expression vector GPiE-SrU6. Moreover, we found that mutant strains were obtained only when the expression of the single guide RNA (sgRNA) was driven by the SrU6-3 promoter. We subsequently employed a tandemly repeated SrU6-tRNA-sgRNA module to knock out two sites within the ura3 gene. The expression vector was introduced into the mycelium via Agrobacterium-mediated transformation (ATMT). Following dual selection with 60 μg/mL hygromycin (Hyg) and 0.2 mg/mL 5-fluoroorotic acid (5-FOA), stable transformants were obtained and subcultured. The mutation efficiency at the targeted ura3 locus was subsequently assessed. The CRISPR/Cas9 system successfully disrupted the target marker gene (ura3), achieving an editing efficiency of 14.9%. In summary, this study reports the first successful establishment of a CRISPR/Cas9 genome editing system in S. rugosoannulata. This study not only meets a future need for genetic manipulation tools for S. rugosoannulata but also provides a robust platform for engineering superior strains for eco-circular agriculture. Full article

SHORT INTERNODE (SHI)-related sequence (SRS) transcription factors are plant-specific zinc-finger proteins increasingly implicated in growth and abiotic stress responses. Despite their diverse vital role in plants, they are largely unexplored in bread wheat. In this study, we identified 15 TaSRS genes and classified them into five homoeologous groups in the bread wheat genome. Each TaSRS protein consisted of conserved RING-like zinc-finger and IGGH domains. The synteny and phylogenetic analyses provided insight into the evolutionary divergence and conservation of TaSRS proteins. Promoter analysis revealed the presence of stress-responsive cis-regulatory elements along with various transcription factor binding sites, indicating their plausible roles in drought and salinity stress responses and signalling. Additionally, the predicted regulation of a few TaSRS genes through certain miRNAs involved in hormone and stress responses, plant development, and nutrient uptake suggested their diverse functions. In silico protein–protein interaction and gene ontology analyses further anticipated an association of TaSRS proteins with organ development and hormone and stress response. High-throughput transcriptomic profiling revealed differential expression of TaSRS genes across various vegetative and reproductive stages and abiotic stress conditions. The qRT-PCR analyses confirmed the stress-responsive role of TaSRS1-1D, TaSRS2-3D, TaSRS4-7A, and TaSRS5-7A under drought and salinity conditions. These results indicated the potential role of TaSRS genes in stress adaptation and opened up opportunities for their detailed functional characterization and applications in the development of salinity and drought resilience in crops. Full article

Salt stress severely restricts grape (Vitis vinifera L.) production. Serine/arginine-rich (SR) proteins, as a class of RNA-binding proteins, play important roles in plant growth, development and stress responses. However, the function and regulatory mechanism of VvSR34a in grape salt tolerance remain unclear. In this study, grape callus and cutting seedlings were used as materials to explore the role and molecular mechanism of VvSR34a in grape salt stress response. The results showed that, under 100 mM NaCl treatment, the relative level of VvSR34a in grape callus exhibited a ‘first increase and then decrease’ pattern, reaching a peak at 2 h, and the gene was localized in the nucleus. Transgenic experiments confirmed that the overexpression of VvSR34a significantly enhanced salt tolerance in grape callus and cuttings, as evidenced by better growth status, higher chlorophyll content and root activity, as well as lower electrolyte leakage and malondialdehyde (MDA) content under salt stress. In contrast, the silencing of VvSR34a significantly increased salt sensitivity in grapes. Y2H and LCI assays verified that VvSR34a physically interacts with VvCOP9. VvCOP9 may play a negative regulatory role in the salt stress response of the grapevine, and through the loss of the high salt-tolerant phenotype in the VvSR34a/VvCOP9-RNAi lines, it demonstrated that VvCOP9 is genetically upstream of VvSR34a. Furthermore, the ubiquitination and degradation assay demonstrated that VvCOP9 can significantly promote the degradation of VvSR34a. RNA-seq analysis showed that a total of 2834 differentially expressed genes and 202 alternative splicing events were detected in VvSR34a overexpression lines. These differentially expressed genes were significantly enriched in ATPase activity, redox and hormone signaling pathways. This study demonstrates that VvSR34a positively regulates salt tolerance in grapes, providing an important theoretical basis for molecular breeding of salt-tolerant grapevines. Full article

Background/Objectives: Early-life skeletal growth is critical for achieving optimal peak bone mass. This study aimed to investigate whether synbiotic supplementation with 2′-fucosyllactose (2′-FL) and Lactiplantibacillus plantarum Hi188 (Hi188) influences bone development in growing mice and its potential association with gut microbial modulation. Methods: Three-week-old BALB/c mice were orally supplemented with 2′-FL, Hi188, or their combinations at low and medium doses for 7 weeks. Bone length, microarchitecture and mechanical properties were analyzed. Serum bone turnover markers and osteogenic gene expression were analyzed by ELISA and qRT-PCR, respectively. Gut microbiota composition, and short-chain fatty acid (SCFA) production were analyzed by 16S-rRNA sequencing and GC-FID, respectively. Correlation associations among microbial taxa, SCFAs, and skeletal parameters were also assessed. Results: Medium-dose synbiotic supplementation significantly increased tibial and spine length without altering body weight or intestinal histology. Trabecular bone density and volume fraction were elevated, accompanied by reduced trabecular separation and improved mechanical strength. Serum BALP levels were increased and TRACP-5b levels were reduced, together with upregulation of osteogenesis- and matrix-related genes. Synbiotic treatment also modulated gut microbial composition, enriched SCFA-associated taxa, and significantly enhanced total and individual SCFA levels. Correlation analyses revealed selective associations among specific microbial taxa, SCFAs, and skeletal structural and molecular parameters. Conclusions: Medium doses of synbiotic supplementation were associated with improved skeletal growth and bone quality during development, alongside coordinated modulation of bone remodeling and gut microbial metabolic activity. These findings suggest its potential as a functional nutritional strategy for supporting early bone health. Full article

Potato purple top is a complex phytoplasma disease that poses a serious threat to potato cultivation worldwide. To verify the presence of different phytoplasma strains in potato disease outbreaks in Iran, six major potato-growing provinces in the central and western regions of the country were surveyed, and a total of 270 potato plants, 230 symptomatic and 40 asymptomatic, was sampled. Nested PCR analysis revealed the phytoplasma presence in 45% of symptomatic and 7% of asymptomatic plants. Molecular analysis was performed, analyzing the sequences of the 16S rRNA gene and the ribosomal protein rp, secY, and tufB genes. Four ‘Candidatus Phytoplasma’ species were identified in the tested potato samples: ‘Ca. P. asteris’ (16SrI-B), ‘Ca. P. tritici’ (16SrI-R), ‘Ca. P. trifolii’ (16SrVI-A), and ‘Ca. P. solani’ (16SrXII-A). The ‘Ca. P. solani’ strains were prevalent, occurring in all the surveyed provinces, whereas the ‘Ca. P. tritici’ strains were restricted to the Chaharmahal and Bakhtiari province. Phylogenetic and multilocus sequence analyses provided a finer resolution, distinguishing among some of the closely related phytoplasma strains. This study represents the first comprehensive molecular survey of potato-infecting phytoplasmas across a wide geographical region of Iran. The findings will aid studies regarding insect vector(s), pathogen biology, host range and disease management strategies. Full article

Deoxynivalenol (DON), a Fusarium-derived mycotoxin widely found in grain-based feed, has become a major global environmental contaminant. Reproductive toxicity is one of its most important toxic effects, yet systematic investigations covering both male and female reproductive injury remain limited. This study aimed to establish a combined strategy of network toxicology, molecular docking, molecular dynamics simulation, and single-cell RNA sequencing to evaluate the reproductive toxicity of DON. AKT1, EGFR, PIK3CA, PIK3R1, and SRC were identified as key targets involved in DON-induced reproductive injury. For testicular injury, the prolactin, Ras, HIF-1, and AGE-RAGE signaling pathways were closely associated with DON toxicity. For ovarian injury, the PI3K-Akt, HIF-1, prolactin, insulin, and AGE-RAGE signaling pathways were strongly implicated. Molecular docking demonstrated favorable binding affinities between DON and the hub targets, while molecular dynamics simulation further confirmed the stability of the DON–PIK3CA complex. Single-cell RNA sequencing analysis revealed that these five hub genes were highly expressed in both testicular (SRA667709:SRS3065430) and ovarian (SRA638923:SRS2797100) tissues. These findings deepen current understanding of DON-induced reproductive toxicity, provide new insights into the effects of environmental toxins on reproductive health, and offer a theoretical basis for future studies integrating DON exposure with in vivo validation of core targets and signaling pathways. Full article

Sesame is an oilseed crop threatened by a phyllody disease associated with the presence of phytoplasmas, which can reduce yields by up to 80%. The molecular identification of these bacteria in crops located in Western Iran was achieved from samples showing symptoms of diverse intensity and types. For biological characterization, the pathogen was also dodder-transmitted to periwinkle plants. After nucleic acid extraction and nested PCR using phytoplasma-specific primer pairs amplifying part of the 16S rRNA gene, it was possible to amplify DNA fragments from both symptomatic sesame samples and dodder-inoculated periwinkle plants. The virtual RFLP pattern from the 16S rRNA gene sequences using iPhyClassifier indicated the presence of phytoplasma strains in 16SrII-D and 16SrIX-C subgroups. The identity percentage values of the obtained amplified sequences corroborated by the phylogenetic analysis identified them as ‘Candidatus Phytoplasma australasiaticum’ and ‘Ca. P. phoenicium’, respectively. The two phytoplasma strains were detected in different sesame samples collected in the same field. The coexistence of two phytoplasmas may influence the observed differences in disease severity and suggests appropriate management strategies, since diverse insect vectors were reported alongside diverse phytoplasmas associated with this disease. Moreover, the widespread disease presence strongly suggests the breeding of resistant varieties. Full article