Search Results (426)

Vibrio parahaemolyticus is a major foodborne pathogen worldwide, responsible for seafood-associated poisoning. Among its toxin genes, tdh2 is the most critical. To investigate the role of tdh2 in V. parahaemolyticus under gastrointestinal conditions, we constructed tdh2 deletion and complementation strains and compared their survival under acid (pH 3 and 4) and bile stress (2%). The results showed that tdh2 expression was significantly upregulated under cold (4 °C) and bile stress (0.9%). Survival assays and PI staining revealed that the tdh2 mutant strain (VP: △tdh2) was more sensitive to acid and bile stress than the wild-type (WT), and this sensitivity was rescued by tdh2 complementation. These findings suggest that tdh2 plays a protective role in enhancing V. parahaemolyticus tolerance to acid and bile stress. In the VP: △tdh2 strain, seven genes were significantly upregulated and six were downregulated as a result of tdh2 deletion. These genes included VPA1332 (vtrA), VPA1348 (vtrB), VP2467 (ompU), VP0301 and VP1995 (ABC transporters), VP0527 (nhaR), and VP2553 (rpoS), among others. Additionally, LC-MS/MS analysis identified 12 differential metabolites between the WT and VP: △tdh2 strains, including phosphatidylserine (PS) (17:2 (9Z,12Z) /0:0 and 20:1 (11Z) /0:0), phosphatidylglycerol (PG) (17:0/0:0), flavin mononucleotide (FMN), and various nucleotides. The protective mechanism of tdh2 may involve preserving cell membrane permeability through regulation of ompU and ABC transporters and enhancing electron transfer efficiency via regulation of nhaR. The resulting reduction in ATP, DNA, and RNA synthesis—along with changes in membrane permeability and electron transfer due to decreased FMN—likely contributed to the reduced survival of the VP: △tdh2 strain. Meanwhile, the cells actively synthesized phospholipids to repair membrane damage, leading to increased levels of PS and PG. This study provides important insights into strategies for preventing and controlling food poisoning caused by tdh⁺ V. parahaemolyticus. Full article

Variants in ELAC2, a gene encoding the mitochondrial RNase Z enzyme essential for mitochondrial tRNA processing, have been associated with severe pediatric-onset mitochondrial dysfunction, primarily presenting with developmental delay, hypertrophic cardiomyopathy (HCM), and lactic-acidosis. We hereby report the case of a 25-year-old young woman presenting with dilated cardiomyopathy (DCM) and peripheral sensorimotor polyneuropathy, harboring a homozygous variant in ELAC2. The same variant has been reported only once so far in a case of severe infantile-onset form of HCM and mitochondrial respiratory chain dysfunction, with in vitro data showing a moderate reduction in the RNase Z activity and supporting the current classification as C4 according to the American College of Medical Genetics (ACMG) criteria (PS3, PM2, PM3, PP4). Our extensive clinical, imaging, histological, and genetic investigations support a causal link between the identified variant and the patient’s phenotype, despite the fact that the latter might be considered atypical according to the current state of knowledge. A detailed review of the existing literature on ELAC2-related disease is also provided, highlighting the molecular mechanisms underlying tRNA maturation, mitochondrial dysfunction, and the variable phenotypic expression. Our case further expands the clinical spectrum of ELAC2-related cardiomyopathies to include a relatively late onset in young adulthood and underscores the importance of comprehensive genetic testing in unexplained cardiomyopathies with multisystem involvement. Full article

Ziziphus lotus (L.) Lam. (Rhamnaceae), a key shrub species native to North Africa, is commonly found in arid and semi-arid regions. Renowned for its resilience under harsh conditions, it forms vegetation clusters that influence the surrounding environment. These clusters create microhabitats that promote biodiversity, reduce soil erosion, and improve soil fertility. However, in agricultural fields, Z. lotus is often regarded as an undesirable species. This study investigated the bacterial diversity and community composition along spatial gradients around Z. lotus patches in barley-planted and non-planted fields. Using 16S rRNA gene sequencing, 84 soil samples were analyzed from distances of 0, 3, and 6 m from Z. lotus patches. MiSeq sequencing generated 143,424 reads, representing 505 bacterial ASVs across 22 phyla. Alpha-diversity was highest at intermediate distances (3 m), while beta-diversity analyses revealed significant differences in community composition across distances (p = 0.035). Pseudomonadota dominated close to the shrub (44% at 0 m) but decreased at greater distances, whereas Bacillota and Actinobacteriota displayed distinct spatial patterns. A core microbiome comprising 44 ASVs (8.7%) was shared across all distances, with the greatest number of unique ASVs identified at 3 m. Random forest analysis highlighted Skermanella and Rubrobacter as key discriminatory taxa. These findings emphasize the spatial structuring of bacterial communities around Z. lotus patches, demonstrating the shrub’s substantial influence on bacterial dynamics in arid ecosystems. Full article

Plastid division regulatory genes play a crucial role in the morphogenesis of chloroplasts and amyloplasts. Chloroplasts are the main sites for photosynthesis and metabolic reactions, while amyloplasts are the organelles responsible for forming and storing starch granules. The proper division of chloroplasts and amyloplasts is essential for plant growth and yield maintenance. Therefore, this study aimed to examine the J175 (FtsZ2-2) gene, cloned from an ethyl methanesulphonate (EMS) mutant involved in chloroplast and amyloplast division in maize, through map-based cloning. We found that J175 encodes a cell division protein, FtsZ (filamentous temperature-sensitive Z). The FtsZ family of proteins is widely distributed in plants and may be related to the division of chloroplasts and amyloplasts. The J175 protein is localized in plastids, and its gene is expressed across various tissues. From the seedling stage, the leaves of the j175 mutant exhibited white stripes, while the division of chloroplasts was inhibited, leading to a significant increase in volume and a reduction in their number. Measurement of the photosynthetic rate showed a significant decrease in the photosynthetic efficiency of j175. Additionally, the division of amyloplasts in j175 grains at different stages was impeded, resulting in irregular polygonal starch granules. RNA-seq analyses of leaves and kernels also showed that multiple genes affecting plastid division, such as FtsZ1, ARC3, ARC6, PDV1-1, PDV2, and MinE1, were significantly downregulated. This study demonstrates that the maize gene j175 is essential for maintaining the division of chloroplasts and amyloplasts and ensuring normal plant growth, and provides an important gene resource for the molecular breeding of maize. Full article

A 56-day trial was conducted to assess the effects of rice straw (RS) and bamboo flour (BF) on growth performance, water quality, gill histology, and the bacterial community of water and the intestine of mandarin fish (Siniperca chuatsi) in biofloc technology systems. The results showed that mandarin fish in the RS and BF groups had comparable survival rates of 100.00 ± 0.00 and 93.33 ± 3.85%; feed conversion ratios of 1.13 ± 0.02 and 1.40 ± 0.15; and weight gain rates of 112.21 ± 1.56 and 100.92 ± 6.45%, respectively. From days 11 to 56 of the farming period, the BF group was more effective than the RS group in removing total ammonia nitrogen (TAN) and NO₂⁻-N, maintaining TAN levels below 0.24 ± 0.05 mg/L. During the early stage of the experiment, the TAN level in the RS group was higher; however, with the supplementation of a carbon source, it gradually decreased and eventually stabilized at 0.13 ± 0.03 mg/L later in the farming period. The secondary gill lamella in the RS group was curved and showed hyperplasia, and the basal gill lamellae showed an increase in the volume of interlamellar cell mass in the BF group. Genes related to denitrification (narG, napA, nirS, nirK, and nosZ) and anammox showed higher expression levels in the BF group than in the RS group, although the differences were not statistically significant (p > 0.05). The results of 16S rRNA sequencing research showed that both treatment groups’ intestinal and water bacterial communities had comparable levels of richness and diversity. Pseudomonas mosselii was the dominant bacterial species in the water. In the BF group, the dominant intestinal species were Bacillus halodurans and Caldalkalibacillus thermarum, while in the RS group, the dominant species was Plesiomonas shigelloides. In conclusion, rice straw and bamboo flour are applicable in BFT systems for mandarin fish culture, with good growth performance and water quality. The BF group showed higher nitrogen removal efficiency and denitrification gene expression than the RS group. Full article

Background/Objectives: High-fat-diet (HFD) consumption drives chronic liver injury via gut dysbiosis and metabolic disturban. Apple cider vinegar, rich in polyphenols and organic acids, shows potential in metabolic regulation. This study aimed to investigate whether apple cider vinegar powder (ACVP) alleviates HFD-induced liver injury by modulating the gut–liver axis. Methods: For 12 weeks, C57BL/6 J mice received daily ACVP gavage while being fed a HFD. A series of biological assessments were conducted, including systemic metabolic evaluations (body weight, serum alanine aminotransferase (ALT)/aspartate aminotransferase (AST), and lipid/glucose levels), hepatic steatosis (hematoxylin and eosin (H&E) staining), intestinal microbiome characterization (16S rRNA gene genomic analysis), and comprehensive metabolite profiling of cecal contents (non-targeted metabolomics). Pearson correlation networks integrated multi-omics data. Results: ACVP attenuated HFD-induced weight gain by 26.3%, hepatomegaly and dyslipidemia, as well as reduced hepatic lipid vacuoles and serum ALT (48%)/AST (21.5%). ACVP restored gut microbiota diversity, enriching Muribaculaceae. Cecal metabolomics identified 38 HFD-perturbed metabolites reversed by ACVP, including indolelactate, hyocholate, and taurocholic acid. the Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed ACVP-mediated recovery of linoleic acid metabolism. Correlation networks linked Akkermansia to anti-inflammatory metabolites (e.g., trans-ferulic), while Desulfobacterota correlated with pro-inflammatory oxylipins (e.g., 12,13-dihydroxy-9Z-octadecenoic acid (DHOME)). Conclusions: ACVP mitigates HFD-induced liver injury by remodeling gut microbiota, restoring microbial metabolites, and enhancing gut–liver crosstalk. Full article

Polyembryonic maize, capable of producing multiple seedlings from a single kernel, holds great potential value in agricultural and industrial applications, but the seedling quality needs to be improved. In this study, seedlings of two waxy maize (Zea mays L. sinensis Kulesh) inbred lines, D35 (a polyembryonic line with twin shoots) and N6110 (single-shoot), exhibited similar relative growth rates during 1 to 5 days post-germination. UPLC-MS/MS profiling of 3- to 5-day-old seedling roots and shoots revealed that H2JA, MeSAG, and IAA-Val-Me were the common differentially accumulated metabolites (DAMs) of the 3-day-old vs. 5-day-old seedlings of D35 and N6110 in the same tissues, and MeSAG, tZ9G, cZROG, and DHZROG were identified in D35 vs. N6110 across the same tissues and the same periods. RNA-seq analyses showed various processes involved in seedling development, including DNA replication initiation, rhythmic processes, the cell cycle, secondary metabolic processes, and hormone biosynthetic regulation. The differentially expressed genes (DEGs) between D35 and N6110 were significantly enriched in organic hydroxy compound biosynthetic, alcohol biosynthetic, organic hydroxy compound metabolic, abscisic acid biosynthetic, and apocarotenoid biosynthetic processes. The KEGG-enriched pathways of DAMs and DEGs identified that AUX1, AHP, A-ARR, JAR1, SIMKK, ERF1, and GID2 might be conserved genes regulating seedling growth. The integrated analyses revealed that 98 TFs were potentially associated with multiple hormones, and 24 of them were identified to be core genes, including 11 AP2/ERFs, 4 Dofs, 2 bZIPs, 2 MADS-box genes, 2 MYBs, 1 GATA, 1 LOB, and 1 RWP-RK member. This study promotes a valuable understanding of the complex hormone interactions governing twin-shoot seedling growth and offers potential targets for improving crop establishment via seedling quality. Full article

MiaA is responsible for the addition of the isopentyl modification to adenine 37 in the anticodon stem loop of specific tRNAs in Escherichia coli. Mutants in miaA have pleotropic effects on the cell in E. coli and play a role in virulence gene regulation. In addition, MiaA is necessary for stress response gene expression by promoting efficient decoding of UUX-leucine codons, and genes with elevated UUX-leucine codons may be a regulatory target for i⁶A-modified tRNAs. Understanding the temporal nature of the i⁶A modification status of tRNAs would help us determine the regulatory potential of MiaA and its potential interplay with leucine codon frequency. In this work, we set out to uncover additional information about the synthesis of the MiaA. MiaA synthesis is primarily driven at the transcriptional level from multiple promoters in a complex operon. However, very little is known about the post-transcriptional regulation of MiaA, including the role of sRNAs in its synthesis. To determine the role of small RNAs (sRNAs) in the regulation of miaA, we constructed a chromosomal miaA-lacZ translational fusion driven by the arabinose-responsive P_BAD promoter and used it to screen against an Escherichia coli sRNA library (containing sRNAs driven by the IPTG-inducible P_Lac promoter). Our genetic screen and quantitative β-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators of miaA expression in E. coli. Consistent with our hypothesis that CsrA regulates miaA post-transcriptional gene expression through binding to the miaA mRNA 5′ UTR, and CsrB binds and regulates miaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion of csrA significantly reduced expression of the reporter fusion as well as reducing miaA mRNA levels. These results suggest that under conditions where CsrA is inhibited, miaA mRNA translation and thus MiaA-dependent tRNA modification may be limited. Full article

LncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley remains incomplete. To elucidate the coordination of drought stress responses in Tibetan hulless barely by lncRNAs, we analyzed the previously published RNA-seq data from two cultivars of hulless barley, drought-tolerant (Z772) and drought-sensitive (Z013), subjected to varying durations of drought treatment (0, 1, and 5 h). Initially, we identified a total of 2877 lncRNAs through a strict pipeline, of which 2179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we utilized WGCNA and uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring PCGs were co-clustered in key control modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as TFs. Two of these pairs were validated by qRT-PCR in the Tibetan hulless barley cultivar Kunlun 14. These findings suggested that lncRNAs may participate in regulatory networks involved in drought adaptation in Tibetan hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties. Full article

Ovarian cancer is the most lethal gynecological cancer. Up to 75% of cases are high-grade serous ovarian cancer (HGSOC) that have high chemosensitivity to first-line platinum-based therapies. However, 75% of patients will become chemoresistant following relapse. The underlying mechanism for developing resistance to chemotherapy in HGSOC is poorly understood. In this study, we employed Matrix-Assisted Laser Desorption/Ionization–Mass Spectrometry Imaging (MALDI-MSI) on matching formalin-fixed paraffin-embedded (FFPE) HGSOC tissues at the time of diagnosis and following relapse with chemotherapy-resistant disease (n = 4). We identified m/z values that were differentially abundant in the matching diagnosis and relapse HGSOC tissues. These were matched to proteins using nano-liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified upregulated proteins in the HGSOC relapse tissues, including COL12A1, FUBP1, PLEC, SLC4A1, and TKT. These proteins were validated by immunohistochemistry (IHC) and gene expression using online databases. IHC showed COL12A1, FUBP1, PLEC, SLC4A1, and TKT protein abundance were significantly elevated in HGSOC relapse tissues compared to matching tissues at diagnosis. COL12A1, FUBP1, PLEC, and TKT mRNA expression levels were significantly increased in HGSOC compared to normal ovary and associated with poor prognosis in HGSOC. We confirmed that higher protein abundance of both COL12A1 and PLEC correlated with reduced progression-free survival in HGSOC patients. Furthermore, both COL12A1 and PLEC mRNA and protein levels were significantly associated with chemotherapy resistance. In summary, using MALDI-MSI, we have identified proteins, including COL12A1 and PLEC, associated with chemotherapy resistance to be further evaluated as HGSOC biomarkers and/or therapeutic targets. Full article

Earthworms are important in agriculture in the process of soil fertilization and influence its physicochemical properties. The taxonomic classification of earthworms using morphological characteristics requires experts, is difficult, and can require specimen dissection to extract detailed anatomical studies. Molecular techniques are time-consuming and expensive. The objective of this study was to distinguish earthworms belonging to different genera, Eisenia, Dendrobaena, and Lumbricus, using an innovative approach involving machine learning models built based on image texture parameters from individual color channels R, G, B, L, a, b, X, Y, Z, U, V, and S. The earthworms Eisenia fetida, Dendrobaena ssp., and Lumbricus terrestris were used as research materials. Image acquisition was performed using a flatbed scanner on a black background. In the case of each earthworm, 2172 texture parameters from images in individual color channels R, G, B, L, a, b, X, Y, Z, U, V, and S were extracted. Textures after selection were used to develop classification models using machine learning algorithms. The earthworms Eisenia fetida, Dendrobaena ssp., and Lumbricus terrestris were distinguished with the accuracy reaching 100% for models built using Logistic, Ensemble, and Narrow Neural Network. All earthworms were correctly classified. Also, in the case of other models, earthworm classes were distinguished with high accuracies, such as 99% (Naive Bayes, Random Forest, SVM, KNN), 97% (Simple Logistic), and 94% (KStar). For the most important species, E. fetida, the correctness of the species identification was confirmed by direct RNA sequencing. The application of image analysis and machine learning turned out to be a non-destructive, inexpensive, and objective approach to distinguishing earthworms belonging to different genera. Full article

This study investigates the main insects and endophytic fungi that promote the formation of agarwood in Aquilaria sinensis (Lour.) Spreng. and elucidates the effects and mechanisms of different ‘insect + fungus’ combinations on agarwood formation. The results showed that 16 strains of endophytic fungi were isolated from A. sinensis. Fusarium solani, Penicillium chrysogenum, Fusarium equiseti, and Phaeoacremonium alvesii were identified as dominant fungi promoting agarwood formation, while Nadezhdiella cantori was recognized as the dominant insect facilitating this process. The optimal ‘insect + fungus’ combination was Nadezhdiella cantori + Fusarium equiseti. The average agarotetrol contents were 0.046% and 0.054% in February and June, respectively, which were significantly higher than those in cold drilling, fungal-only, and insect-only treatments. RNA sequencing revealed 23,801 differentially expressed unigenes in cjYB1Z4 (optimal combination) versus control BMZ. Upregulated unigenes were enriched in isoflavone biosynthesis, flavonoid biosynthesis, and sesquiterpenoid and triterpene biosynthesis. Fifty sesquiterpene-related differential unigenes encoded seven key enzymes in the MVA pathway, seven key enzymes in the MEP pathway, and seven terpene synthases. Co-expression network analysis indicated that transcription factors (e.g., WRKY33, ABF, WRKY2) potentially regulate agarwood sesquiterpene formation. This work elucidates preliminary effects and molecular mechanisms of insect- and fungi-induced agarwood formation in A. sinensis, advancing agarwood induction technology. Full article

Background/Objectives: Intraventricular hemorrhage (IVH) frequently occurs in premature infants and adults with intracerebral or subarachnoid hemorrhage. It is a major cause of cerebral palsy in premature infants and a risk factor for poor outcome in adult cerebral hemorrhage. Posthemorrhagic hydrocephalus is a common complication of IVH and aggravates brain damage. Hemoglobin (Hb), released from the hemorrhage after IVH, has been implicated in IVH-induced hydrocephalus. The aim of the current study was to examine the impact of Hb on the choroid plexuses (CPs) that reside in the ventricular system. Methods: Experiments were performed in freshly isolated CPs, in primary cultures of CP epithelial cells (CPECs), and in the Z310 cell line exposed to Hb with MTT assay, scratch wound healing assay, cell counting/total cell protein measurement and RT-qPCR. Results: We found that Hb significantly induced CPEC proliferation (e.g., 37–65% higher than control by MTT assay and 56% higher than control by cell counting), and upregulated mRNA expression of growth factors in isolated CP tissue (e.g., IGF-2 and NGF were 39% and 79% higher than control by RT-PCR). Hb also remarkably induced mRNA expression of NKCC1 (50%) and claudin-2 (154%), two proteins involved in CSF secretion, in isolated CP tissue. Conclusions: These results indicate that Hb-induced growth factor-mediated CP proliferation and upregulation of CSF secretion-related proteins might contribute to PHH and suggest there may be alternate therapeutic targets for PHH. Full article

Background: Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder caused by mutations in the SERPINA1 gene, leading to reduced levels or impaired alpha-1 antitrypsin (AAT) function. This condition predominantly affects the lungs and liver. The Z allele, a specific mutation in the SERPINA1 gene, is the most severe form and results in the production of misfolded AAT proteins. The misfolded proteins accumulate in the endoplasmic reticulum (ER) of liver cells, triggering ER stress and activating the unfolded protein response (UPR), a cellular mechanism designed to restore ER homeostasis. Currently, there is limited knowledge regarding specific nutritional recommendations for patients with AATD. The liver is essential for the regulation of zinc homeostasis, with zinc widely recognized for its hepatoprotective properties. However, the effects of AATD on zinc metabolism remain poorly understood. Similarly, the potential benefits of zinc supplementation for individuals with AATD have not been thoroughly investigated. Objective: This study explored the relationship between AATD and zinc metabolism through a combination of in vitro experiments and computational analysis. Results: The expression of the mutant Z variant of ATT (ATZ) in cultured mouse hepatocytes was associated with decreased labile zinc levels in cells and dysregulation of zinc homeostasis genes. Analysis of two data series from the Gene Expression Omnibus (GEO) revealed that mice expressing ATZ (PiZ mice), a murine model of AATD, exhibited significant differences in mRNA levels related to zinc homeostasis and UPR when compared to wildtype mice. Bayesian network analysis of GEO data uncovered novel gene-to-gene interactions among zinc transporters, as well as between zinc homeostasis, UPR, and other associated genes. Conclusions: The findings provide valuable insights into the role of zinc homeostasis genes in UPR processes linked to AATD. Full article

Background: The Polyplacophora class, which includes all chitons, is distinguished by its unique eight-piece interlocking armor, showcasing a vast diversity in marine environments. However, the detailed evolutionary relationships within the Chitonidae family remain largely unknown. The mitochondrial genome is essential for understanding these relationships, but there has been a significant lack of such genomic information, especially for the Liolophura genus. Methods: We generated the first mitogenome of Liolophura japonica by assembling Illumina reads with GetOrganelle, polishing with Pilon, annotating genes with MitoZ and MITOS2, and inferring phylogeny from 13 concatenated protein-coding genes (PCGs) using MAFFT and IQ-TREE. Results: The mitogenome is 15,209 base pairs long and includes 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The mitogenome exhibited a slight AT bias common in Chitonidae and showcased structural uniqueness with no control region found. Notably, all protein-coding genes demonstrated evidence of purifying selection, with Ka/Ks ratios below 1, highlighting evolutionary conservation. Phylogenetic analysis reveals a close relationship between L. japonica, Acanthopleura loochooana Broderip & Sowerby 1829, and Acanthopleura vaillantii Rochebrune, 1882, potentially warranting future taxonomic re-evaluation. This research emphasizes the crucial role of mitochondrial genomes in mollusk phylogeny and sets the stage for advanced genetic studies within this group. Conclusions: The significance of this study lies in its contribution to understanding the mitochondrial genome of L. japonica, a key species within the Polyplacophora class. By analyzing its mitogenome, we aim to enhance our understanding of evolutionary processes in chitons and other mollusks. Full article