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Introduction: Pike perch (Sander Lucioperca) is a predatory freshwater fish, which is highly popular amongst consumers, owing to its white flesh with a delicate structure and mild flavor. Compared to wild pike perch, the diet of farmed ones has shifted fromnatural food to artificial feeds. These changes would affect the gut flora of the pike perch. Endogenous metabolites of the intestinal flora are transferred through the gut-liver axis, which affects the physiological functions of the host. By studying wild and farmed individuals of the pike perch, novel insights into the stability of the intestinal flora can be provided. Methods and results: In this study, we measured various immune parameters in the blood, liver and intestine of wild and farmed pike perch using enzyme activity assays and real-time fluorescence quantitative PCR. Gut microbes were also collected for 16S rRNA gene sequencing. Our results showed that the serum lowdensity lipoprotein cholesterol (LDL-C) levels were twice as high in the wild group as in the farmed group. Furthermore, the activities of glutamate pyruvate transaminase (GPT) and glutamate oxaloacetate transaminase (GOT) in the intestinal tissues of the wild group were 733.91 U/g and 375.35 U/g, which were significantly higher than those of the farmed group. Expression of IL10 in the liver of farmed pike perch was also 4-fold higher than that of wild pike perch. The expression of genes related to the p53-BAX/Bcl2 signaling pathway was higher in both intestinal and liver tissues of wild pike perch compared with farmed. 16S rRNA gene analysis of the gut microflora showed a high relative abundance of Cetobacterium in the gut of farmed pike perch. Conclusion: As a result, our study indicates that dietary differences affect the diversity, composition and relative abundance of the gut flora of the pike perch. Meanwhile, it affects the glycolipid metabolism and immunomodulation of pike perch. [ABSTRACT FROM AUTHOR]

Simple Summary: This study reports an unusual case of hermaphroditism in Japanese flounder captured from the Bohai Sea. In this study, the results showed that the heterozygosity of the intersex Japanese flounder was 0.632, with the synchronous maturation of the testis and ovary, and eggs and the sperm were capable of fertilization. The levels of reproduction-related hormones were intermediate; the activity of 21-hydroxylase was reduced by approximately 20.0%. Japanese flounder is usually gonochoristic, with gonads that are either testes or ovaries. Here, we report an unusual case of hermaphroditism in Japanese flounder captured from the Bohai Sea. In the intersex flounder, the membrane of the upper ovary was closely connected to the abdominal muscles and internal organs, and the eggs filled the entire abdomen. The lower ovary was small and closely connected to the testes. The testes contained few fully mature sperm. Both eggs and sperm were capable of fertilization. The levels of several reproduction-related hormones (17β-estradiol, 11-ketotestosterone, 17α, 20β-dihydroxyprogesterone, luteinizing hormone, follicle-stimulating hormone, and testosterone) in the intersex flounder were intermediate, between those in females and males. The results showed that the heterozygosity of the intersex flounder was 0.632, and there were 28 single-nucleotide polymorphisms in the cyp21a gene. Compared with that of wild flounder, the activity of 21-hydroxylase was reduced by approximately 20.0%, and expressions of cyp19a, amh, and dmrt1 differed. We present the first report of its kind, detailing the anatomy, hormonal endocrinology, molecular biology, and physiology of the intersex Japanese flounder. [ABSTRACT FROM AUTHOR]

Leukemia is a form of cancer that affects the bone marrow and lymphatic system, and it requires complex treatment strategies that vary with each subtype. Due to the subtle morphological differences among these types, monitoring gene expressions is crucial for accurate classification. Manual or pathological testing can be time-consuming and expensive. Therefore, data-driven methods and machine learning algorithms offer an efficient alternative for leukemia classification. This study introduced a novel super learning model that leverages heterogeneous machine learning models to analyze gene expression data and classify leukemia cells. The proposed approach incorporates an entropy-based feature importance technique to identify the gene profiles most significant to the labeling process. The strength of this super learning model lies in its final super learner, Random Forest, which effectively classifies cross-validated data from the candidate learners. Validation on a gene expression monitoring dataset demonstrates that this model outperforms other state-of-the-art models in predictive accuracy. The study contributes to the knowledge regarding the use of advanced machine learning techniques to improve the accuracy and reliability of leukemia classification using gene expression data, addressing the challenges of traditional methods that rely on clinical features and morphological examination. [ABSTRACT FROM AUTHOR]

Aims: Rotator cuff tear (RCT) is the leading cause of shoulder pain, primarily associated with age-related tendon degeneration. This study aimed to elucidate the potential differential gene expressions in tendons across different age groups, and to investigate their roles in tendon degeneration. Methods: Linear regression and differential expression (DE) analyses were performed on two transcriptome profiling datasets of torn supraspinatus tendons to identify age-related genes. Subsequent functional analyses were conducted on these candidate genes to explore their potential roles in tendon ageing. Additionally, a secondary DE analysis was performed on candidate genes by comparing their expressions between lesioned and normal tendons to explore their correlations with RCTs. Results: We identified 49 genes in torn supraspinatus tendons associated with advancing age. Among them, five age-related genes showed DE in lesioned tendons compared to normal tendons. Functional analyses and previous studies have highlighted their specific enrichments in biological functions, such as muscle development (e.g. myosin heavy chain 3 (MYH3)), transcription regulation (e.g. CCAAT enhancer binding brotein delta (CEBPD)), and metal ion homeostasis (e.g. metallothionein 1X (MT1X)). Conclusion: This study uncovered molecular aspects of tendon ageing and their potential links to RCT development, offering insights for targeted interventions. These findings enhance our understanding of the mechanisms of tendon degeneration, allowing potential strategies to be made for reducing the incidence of RCT. Cite this article: Bone Joint Res 2024;13(9):474–484.

Abstract Leukemia is a form of cancer that affects the bone marrow and lymphatic system, and it requires complex treatment strategies that vary with each subtype. Due to the subtle morphological differences among these types, monitoring gene expressions is crucial for accurate classification. Manual or pathological testing can be time-consuming and expensive. Therefore, data-driven methods and machine learning algorithms offer an efficient alternative for leukemia classification. This study introduced a novel super learning model that leverages heterogeneous machine learning models to analyze gene expression data and classify leukemia cells. The proposed approach incorporates an entropy-based feature importance technique to identify the gene profiles most significant to the labeling process. The strength of this super learning model lies in its final super learner, Random Forest, which effectively classifies cross-validated data from the candidate learners. Validation on a gene expression monitoring dataset demonstrates that this model outperforms other state-of-the-art models in predictive accuracy. The study contributes to the knowledge regarding the use of advanced machine learning techniques to improve the accuracy and reliability of leukemia classification using gene expression data, addressing the challenges of traditional methods that rely on clinical features and morphological examination.

Aeromonas hydrophila is an important etiologic agent, triggering an increased trend of disease outbreak in fish farming. In this investigation, we evaluated pathological response in the midgut and liver of three types of grass carps after gut infection. Severe pathological levels of tissue necrosis were observed in common grass carp (GC) and gynogenetic grass carp (GGC), but mild pathological symptom was detected in hybrid grass carp (DRGC), along with the dramatically increased number of goblet cells. Moreover, three types of grass carps showed upregulated levels of immune gene patterns and antioxidant abilities, whereas inflammatory cytokine expression levels in hybrid grass carp (DRGC) were lower than that of gynogenetic grass carp (GGC) and common grass carp (GC). These results suggested that DRGC may exhibit a disease tolerance against A. hydrophila-induced tissue inflammation. [ABSTRACT FROM AUTHOR]

Simple Summary: The journey of discovering melanoma—the most dangerous type of skin cancer—biomarkers is never-ending. Under that assumption, this study attempts to partially fill a gap in that journey by identifying melanoma-related biomarkers. This research paper studied the genetic and molecular profiling of melanoma. A transcriptome-wide association study (TWAS) was conducted to reveal the significant biomarkers associated with melanoma. A molecular network was constructed to represent the significant interactions between genes and microRNAs (miRNAs). The related biological processes, the enriched pathways, and the associated diseases were identified. The hotspot biomarkers were discovered to elucidate further the mechanism of these genes and miRNAs in melanoma pathogenesis. This work reveals the pathogenesis and biologically important molecular interactions of melanoma and provides new insights into the molecular mechanisms of melanoma. A transcriptome-wide association study (TWAS) was conducted on genome-wide association study (GWAS) summary statistics of malignant melanoma of skin (UK Biobank dataset) and The Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM) gene expression weights to identify melanoma susceptibility genes. The GWAS included 2465 cases and 449,799 controls, while the gene expression testing was conducted on 103 cases. Afterward, a gene enrichment analysis was applied to identify significant TWAS associations. The melanoma's gene–microRNA (miRNA) regulatory network was constructed from the TWAS genes and their corresponding miRNAs. At last, a disease enrichment analysis was conducted on the corresponding miRNAs. The TWAS detected 27 genes associated with melanoma with p-values less than 0.05 (the top three genes are LOC389458 (RBAK), C16orf73 (MEIOB), and EIF3CL). After the joint/conditional test, one gene (AMIGO1) was dropped, resulting in 26 significant genes. The Gene Ontology (GO) biological process associated the extended gene set (76 genes) with protein K11-linked ubiquitination and regulation of cell cycle phase transition. K11-linked ubiquitin chains regulate cell division. Interestingly, the extended gene set was related to different skin cancer subtypes. Moreover, the enriched pathways were nsp1 from SARS-CoV-2 that inhibit translation initiation in the host cell, cell cycle, translation factors, and DNA repair pathways full network. The gene-miRNA regulatory network identified 10 hotspot genes with the top three: TP53, BRCA1, and MDM2; and four hotspot miRNAs: mir-16, mir-15a, mir-125b, and mir-146a. Melanoma was among the top ten diseases associated with the corresponding (106) miRNAs. Our results shed light on melanoma pathogenesis and biologically significant molecular interactions. [ABSTRACT FROM AUTHOR]

Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and β-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.Key message: We identified transcription factors, ACREs, that bind to the CMSRE-1, essential for sugarresponsive gene expression, and activate in a CMSRE-1-dependent manner, and ACREs may be widely conserved among plant species. [ABSTRACT FROM AUTHOR]

Oncogenic growth signal regulates glucose, glutamine and lipid metabolism to provide the bioenergy and biosynthetic requirements of rapidly dividing tumor cells. A class of membrane-bound transcription factors known as sterol regulatory element-binding proteins (SREBPs) activate the genes encoding the enzymes required to produce cholesterol and unsaturated fatty acids. In this study, we discussed the anticancer role of SREBP and its target genes, lipid and cholesterol metabolism enzymes in the development of endometrial cancer. This study comprised 45 patients with endometrial adenocarcinoma, who were further categorized into Grade 1 (n = 15), Grade 2 (n = 15), and Grade 3 (n = 15). The control group consisted of 29 endometrial tissues without an endometrial cancer diagnosis. SREBP, ATP-citrate lyase (ACLY), acetyl-CoA carboxylase (ACC), fatty acid synthase (FASN), acetyl CoA acetyltransferase (ACAT) and 3-hydroxy-3- methylglutaryl-CoA reductase (HMGCR) gene expressions were examined using the real-time polymerase chain reaction (RT-PCR) method. The gene expressions of the patient group were higher than the control group (P <0.05), and there were differences between the grades of the patient group (P <0.05). In general comparison, it was observed that SREBP expression increased in the patient group compared to the control group. While the SREBF1 increased in grade 2 (p=0.0001), the SREBF2 increased in grade 1(p=0.0001). The findings imply that whereas lipogenesis might exhibit various tissue-specific behaviours linked to a few pathways, it might also have a direct connection to endometrial cancer. [ABSTRACT FROM AUTHOR]

Aims: The present study investigated receptor activator of nuclear factor kappa-Β ligand (RANKL), osteoprotegerin (OPG), and Runt-related transcription factor 2 (RUNX2) gene expressions in giant cell tumour of bone (GCTB) patients in relationship with tumour recurrence. We also aimed to investigate the influence of CpG methylation on the transcriptional levels of RANKL and OPG. Methods: A total of 32 GCTB tissue samples were analyzed, and the expression of RANKL, OPG, and RUNX2 was evaluated by quantitative polymerase chain reaction (qPCR). The methylation status of RANKL and OPG was also evaluated by quantitative methylation-specific polymerase chain reaction (qMSP). Results: We found that RANKL and RUNX2 gene expression was upregulated more in recurrent than in non-recurrent GCTB tissues, while OPG gene expression was downregulated more in recurrent than in non-recurrent GCTB tissues. Additionally, we proved that changes in DNA methylation contribute to upregulating the expression of RANKL and downregulating the expression of OPG, which are critical for bone homeostasis and GCTB development. Conclusion: Our results suggest that the overexpression of RANKL/RUNX2 and the lower expression of OPG are associated with recurrence in GCTB patients. Cite this article: Bone Joint Res 2024;13(2):84–91.

Abstract Background Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. Results Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. Conclusions SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.

Aims: Transcription factor nuclear factor kappa B (NF-κB) plays a major role in the pathogenesis of chronic inflammatory diseases in all organ systems. Despite its importance, NF-κB targeted drug therapy to mitigate chronic inflammation has had limited success in preclinical studies. We hypothesized that sex differences affect the response to NF-κB treatment during chronic inflammation in bone. This study investigated the therapeutic effects of NF-κB decoy oligodeoxynucleotides (ODN) during chronic inflammation in male and female mice. Methods: We used a murine model of chronic inflammation induced by continuous intramedullary delivery of lipopolysaccharide-contaminated polyethylene particles (cPE) using an osmotic pump. Specimens were evaluated using micro-CT and histomorphometric analyses. Sex-specific osteogenic and osteoclastic differentiation potentials were also investigated in vitro, including alkaline phosphatase, Alizarin Red, tartrate-resistant acid phosphatase staining, and gene expression using reverse transcription polymerase chain reaction (RT-PCR). Results: Local delivery of NF-κB decoy ODN in vivo increased osteogenesis in males, but not females, in the presence of chronic inflammation induced by cPE. Bone resorption activity was decreased in both sexes. In vitro osteogenic and osteoclastic differentiation assays during inflammatory conditions did not reveal differences among the groups. Receptor activator of nuclear factor kappa Β ligand (Rankl) gene expression by osteoblasts was significantly decreased only in males when treated with ODN. Conclusion: We demonstrated that NF-κB decoy ODN increased osteogenesis in male mice and decreased bone resorption activity in both sexes in preclinical models of chronic inflammation. NF-κB signalling could be a therapeutic target for chronic inflammatory diseases involving bone, especially in males. Cite this article: Bone Joint Res 2024;13(1):28–39.

Aims: Knee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA. Methods: First, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expression Omnibus (GEO). Several datasets were standardized by merging and removing batch effects. Then, we used unsupervised clustering to divide OA into three subtypes. The gene ontology and pathway enrichment of three subtypes were analyzed. CIBERSORT was used to evaluate the infiltration of immune cells in different subtypes. Finally, OA-related genes were obtained from the Molecular Signatures Database for validation, and diagnostic markers were screened according to clinical characteristics. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to verify the effectiveness of markers. Results: C1 subtype is mainly concentrated in the development of skeletal muscle organs, C2 lies in metabolic process and immune response, and C3 in pyroptosis and cell death process. Therefore, we divided OA into three subtypes: bone remodelling subtype (C1), immune metabolism subtype (C2), and cartilage degradation subtype (C3). The number of macrophage M0 and activated mast cells of C2 subtype was significantly higher than those of the other two subtypes. COL2A1 has significant differences in different subtypes. The expression of COL2A1 is related to age, and trafficking protein particle complex subunit 2 is related to the sex of OA patients. Conclusion: This study linked different tissues with gene expression profiles, revealing different molecular subtypes of patients with knee OA. The relationship between clinical characteristics and OA-related genes was also studied, which provides a new concept for the diagnosis and treatment of OA. Cite this article: Bone Joint Res 2023;12(12):702–711.

Japanese flounder is usually gonochoristic, with gonads that are either testes or ovaries. Here, we report an unusual case of hermaphroditism in Japanese flounder captured from the Bohai Sea. In the intersex flounder, the membrane of the upper ovary was closely connected to the abdominal muscles and internal organs, and the eggs filled the entire abdomen. The lower ovary was small and closely connected to the testes. The testes contained few fully mature sperm. Both eggs and sperm were capable of fertilization. The levels of several reproduction-related hormones (17β-estradiol, 11-ketotestosterone, 17α, 20β-dihydroxyprogesterone, luteinizing hormone, follicle-stimulating hormone, and testosterone) in the intersex flounder were intermediate, between those in females and males. The results showed that the heterozygosity of the intersex flounder was 0.632, and there were 28 single-nucleotide polymorphisms in the cyp21a gene. Compared with that of wild flounder, the activity of 21-hydroxylase was reduced by approximately 20.0%, and expressions of cyp19a, amh, and dmrt1 differed. We present the first report of its kind, detailing the anatomy, hormonal endocrinology, molecular biology, and physiology of the intersex Japanese flounder.

Background: Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. Results: Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. Conclusions: SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA. [ABSTRACT FROM AUTHOR]

The primary neuronal and astrocyte culture described here is from the stress-hyperreactive Wistar Kyoto (WKY) More Immobile (WMI) rat with premature aging-related memory deficit, and its nearly isogenic control, the Less Immobile (WLI) strain. Primary WMI hippocampal neurons and cortical astrocytes are significantly more sensitive to oxidative stress (OS) generated by administration of H2O2 compared to WLI cells as measured by the trypan blue cell viability assay. Intrinsic genetic vulnerability is also suggested by the decreased gene expression in WMI neurons of catalase (Cat), and in WMI cortical astrocytes of insulin-like growth factor 2 (Igf2), synuclein gamma (Sncg) and glutathione peroxidase 2 (Gpx2) compared to WLI. The expressions of several mitochondrial genes are dramatically increased in response to H2O2 treatment in WLI, but not in WMI cortical astrocytes. We propose that the vulnerability of WMI neurons to OS is due to the genetic differences between the WLI and WMI. Furthermore, the upregulation of mitochondrial genes may be a compensatory response to the generation of free radicals by OS in the WLIs, and this mechanism is disturbed in the WMIs. Thus, this pilot study suggests intrinsic vulnerabilities in the WMI hippocampal neurons and cortical astrocytes, and affirm the efficacy of this bimodal in vitro screening system for finding novel drug targets to prevent oxidative damage in illnesses. [ABSTRACT FROM AUTHOR]

Simple Summary: Fenugreek seeds, a natural source of bioactive compounds, were tested for their effects on the immune system and gut bacteria of broiler chickens. Broilers were fed three diets: control, low fenugreek seed powder (5 g/kg), and high fenugreek seed powder (10 g/kg). The results showed that fenugreek seeds downregulated genes related to inflammation and antimicrobial defense, suggesting reduced inflammation, and improved immune response. Fenugreek increased the "good" Firmicutes bacteria and decreased the "bad" Actinobacteriota, Gemmatimonadota, and Verrucomicrobiota. It also boosted beneficial Alistipes, Bacteriodes, and Prevotellaceae bacteria. In conclusion, fenugreek seeds positively impact broiler chickens' immune systems and gut bacteria, possibly by influencing how these two systems interact. This suggests the potential for fenugreek as a natural health promoter in poultry production. Fenugreek seeds (FSs) are a natural source of bioactive compounds that may modulate the immune system and gut microbiota in broilers. This study examined the effects of dietary fenugreek seed powder on immune-related gene expression and cecal microbiota composition in broilers. A total of 144 broiler chickens were randomly allocated to three dietary groups, CON (0 g/kg FS, FS5 (5 g/kg FS) and FS10 (10 g/kg FS), each with 6 replicates of 8 birds. Ileum tissues and cecal contents were collected on day 42 for the mRNA expression of inflammation and antimicrobial defense-related genes and cecal microbiome diversity, respectively. The results indicated that fenugreek seeds downregulated mRNA-level inflammation and antimicrobial defense-related genes: IL6, IL8L2, CASP6, PTGS2, IRF7, AvBD9, AvBD10, and AvBD11. Moreover, fenugreek seeds altered the cecal microbial community by increasing the population of Firmicutes and decreasing the population of Actinobacteriota, Gemmatimonadota and Verrucomicrobiota at the phylum level and increasing Alistipes, Bacteriodes and Prevotellaceae at the genera level. These findings suggest that fenugreek seeds have a positive impact on the immunological profile and microbiome of broiler chickens, possibly through the interplay of the immune system and the gut microbiome. [ABSTRACT FROM AUTHOR]

Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans. [ABSTRACT FROM AUTHOR]

Despite the high amount of indigestible carbohydrates in rice husk as a natural source of prebiotics, it cannot be used directly in fish diet whose diet is more carnivorous. Hence, the aim of this research was conducted to investigation of rice husk extract on growth performance and expression of related genes (GH and IGF-1) in ozone fish fingerlings. For this aim, the number of 120 pieces of healthy ozone fish fingerlings (50 ± 2.6 g) was purchased and then was randomly transferred in tanks with a water volume of 1000 liters. They were fed for 60 days with different levels of rice husk extract in the basic diet (crud protein: 44.5%) including 0.5, 1 and 2 g Kg-1 of diet along with a control group (with three replicates) at the rate of 5% of body weight. At the end of the trial, growth performance was evaluated by biometrical assay completely randomly. Also, brain tissue was sampled to investigate the expression of genes involved in growth (GH, IGF-1). The results showed that feeding ozone fish fingerlings with different levels of rice husk extract had a significant effect on the growth performance and the expression of related genes in treatments compared to the control group (P<0.05). So that the best results were observed in treatment fed with 2 g of rice husk extract in per kilogram of diet (P<0.05). In general, the results showed that using rice husk extract was able to improve the growth performance and the expression of related genes involved in growth in ozone fish fingerlings, and the best level recommended in this study was 2 grams in per kilogram of diet. [ABSTRACT FROM AUTHOR]

Plant growth-promoting bacteria (PGPB) play an important role in improving agricultural production under several abiotic stress factors. PGPB can be used to increase crop growth and development through hormonal balance and increase nutrient uptake. The positive effect of PGPB may be due to its pivotal role in morphophysiological and biochemical characteristics like leaf number, leaf area, and stem length. Furthermore, relative water content, chlorophyll content, carotenoids, antioxidant enzymes, and plant hormones were improved with PGPB treatment. Crop yield and yield components were also increased with PGPB treatment in numerous crops. The anatomical structure of plant organs was increased such as lamina thickness, stem diameter, xylem vessel diameter, and number of xylem vessels as well as phloem thickness under treatment with PGPB. Additionally, PGPB can alleviate the negative effects of several abiotic stresses by regulating the antioxidant defense system to scavenge the reactive oxygen species resulting in an improvement of yield production in the stressed plants. Additionally, gene expressions were controlled by calcium ion modulation during secondary messengers that act upon calcium-dependent protein kinase and protein phosphatases. This includes many transcription factors such as MYB, AP2/ERF, bZIP, and NAC which regulate genes related to salinity stress signals. PGPB can demonstrate induction genes of signaling under abiotic stress conditions. This review gives an outline of the PGPB role in alleviating the harmful effects of abiotic factors such as salinity, drought, and heat associated with the improvement of the morpho-physiological and biochemical features especially, leaves and branches number, leaf area, antioxidant compounds, plant hormones, and relative water content. [ABSTRACT FROM AUTHOR]

Triphenyl phosphate (TPhP) is the predominant compound of organophosphate flame retardants (OPFRs), which can elicit a toxicological effect on physiological response and tissue development of fish. In this study, we investigated the effect of TPhP exposure on cell viability, antioxidant capacities, and apoptosis in EPC cells. Current study revealed that TPhP exposure could decrease cell viability and promote intracellular oxidative stress in EPC cells. In addition, high-dose TPhP exposure could facilitate antioxidant insults and cause mitochondrial collapse in a dose-dependent manner, along with increased gene expressions involved in apoptosis and unfolded protein response (UPR). These results indicated that reactive oxygen species (ROS)-induced cytotoxic stress and cell death were involved in antioxidant insults and apoptotic activation in TPhP-exposed fish cells. [ABSTRACT FROM AUTHOR]

Nitrogen (N) application is believed to improve photosynthesis in flag leaf ultimately increase final yield. The main results at 20–30 days after anthesis, the activities of superoxide dismutase (SOD) and peroxidase (POD) and soluble protein in flag leaves of N150 were found to be the most effective. Increased root weight density, root length density and root volume density at flowering stage, up to 10.6 %, 15.0 %, respectively. The root weight density, root length density and root bulk density at flowering and mature stages were the highest at the N180. Delaying the senescence physiology of post flowering leaves in the middle, and late stage, photosynthesis of leaves in the middle and late stage, improving the light energy interception of wheat, and then improving the light energy utilization efficiency. The stomatal conductance of flag leaves 15–30 days after anthesis, the maximum potential photochemical efficiency 20–30 days after anthesis, and the photochemical quenching of flag leaves 25–30 days after anthesis, and improved the light energy utilization efficiency by 9.6%–11.1 %. Yunhan-20410 the gene expressions of TaTZF1, TaNCY1, TaNCY3 and TaAKaGall in wheat flag leaves were significantly up-regulated YH-20410 gene expressions of N application treatment were significantly up-regulated compared with no N application treatment. The goal of high yield high efficiency, and high quality can be achieved by YH-20410 and combined to N180 kg ha−1. The senescence physiology and gene expression of post flowering leaves in the middle and late stage, prolonging the photosynthesis of leaves in the middle and late stage, improving the light energy interception of canopy, and then improving the light energy utilization efficiency.

High-pressure processing (HPP) is one of the non-thermal methods of food preservation considered to be safe but may cause an increase/decrease in virulence potential and antibiotic resistance. The aim of the present study was to evaluate the survival of L. monocytogenes isolates after high-pressure processing (200 and 400 MPa for 5 min) and to determine changes in phenotypic and genotypic antibiotic resistance and virulence after this treatment. The 400 MPa treatment was shown to be effective in reducing pathogens to safe levels; however, the potential for cell recovery during storage was observed. In addition, studies on changes in virulence indicated possibilities related to a decrease in actA gene expression, overexpression of the hly and osfX gene, and an increase in biofilm-forming ability. The studies on changes in antibiotic resistance of isolates showed that all isolates showing initial susceptibility to lincomycin, fosfomycin, trimethoprim/sulfamethoxazole, and tetracycline became resistant to these antibiotics, which was associated with an increase in the values of minimum inhibitory concentrations. An increase in the expression of antibiotic resistance genes (mainly tetA_1, tetA_3, tetC) was also observed (mainly after the application of 200 MPa pressure), which was isolate dependent. However, it is noteworthy that the induced changes were permanent, i.e., they persisted even after the restoration of optimal environmental conditions. The results presented in our work indicate that the stress occurring during HPP can affect both phenotypic and genotypic changes in the virulence and antibiotic resistance potential of pathogens isolated from food and food processing environments. The potential associated with cell recovery and persistence of changes may influence the spread of virulent isolates of pathogens with increased antibiotic resistance in the food and food processing environment. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila can pose a great threat to the survival of farmed fish. In current study, we investigated the pathological characteristics and immune response in gut–liver axis of white crucian carp (WCC) upon gut infection. WCC anally intubated with A. hydrophila exerted a tissue deformation in damaged midgut with elevated levels of goblet cells along with a significant decrease in tight junction proteins and villi length‐to‐width ratios. In addition, immune‐related gene expressions and antioxidant properties increased dramatically in gut–liver axis of WCC following gut infection with A. hydrophila. These results highlighted the immune modulation and redox alteration in gut–liver axis of WCC in response to gut infection. [ABSTRACT FROM AUTHOR]

Phenolic compounds are plant secondary metabolites with strong antioxidant potential. They are involved in stress tolerance, plant defense mechanism, and protection against environmental factors. Due to their medicinal and antioxidant properties, they have been part of the human diet for centuries. They also affect the overall quality of the grapes for commercial use. Fruit color is one quality attribute that is directly influenced by the production of anthocyanins in the berry skin. The production of anthocyanins is, however, linked with the production of abscisic acid. This review is focused on the production of different phenolic compounds in grapes, the role of abscisic acid in the production of anthocyanin contents through the phenylpropanoid pathway, and its effect on color development and final quality. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to investigate the effect of Curcumin nanoparticles and alcoholic extract of Falcaria vulgaris on the growth rate, biofilm, and gene expression in Pseudomonas aeruginosa isolated from burn wound infection. Methods: The alcoholic extract of Falcaria vulgaris was purchased from Pasargad Company. Curcumin nanoparticles were synthesized. Antibacterial activity of Curcumin nanoparticles and alcoholic extract of Falcaria vulgaris was investigated by microdilution method alone and in combination. Biofilm inhibitory was investigated by microtitrplate method. Effect of Curcumin nanoparticles and alcoholic extract of Falcaria vulgaris were evaluated on algD gene expression via Real-Time PCR. Cytotoxicity was evaluated by MTT assay on HDF cell line. Then, the data were analyzed using SPSS software. Results: Synthesized Curcumin nanoparticles were approved by Fourier Transform Infrared (FTIR), and Scanning Electron Microscope. The alcoholic extract of Falcaria Vulgaris showed significant antibacterial activity against multidrug resistance (MDR) P. aeruginosa isolates at a concentration of 156.25 µg/mL. Moreover, MIC of the curcumin nanoparticle for isolates was 625 µg/mL. Based on fraction inhibition concentration, synergy, and the additive effect were shown against %7.7, and %93.3 of MDRs, respectively. The sub-MIC concentration of the binary compound reduced biofilms and algD gene expression in P. aeruginosa isolates. The Biological function of HDF cell lines was desirable after the effect of the binary compound. Conclusions: Regarding our results, this combination can be suggested as a promising agent in terms of biofilm inhibitory and antimicrobial properties. [ABSTRACT FROM AUTHOR]

An 8-week feeding trial was executed to evaluate the efficacy of four functional feed additives in replacing antibiotics in juvenile olive flounder, Paralichthys olivaceus, fed with a low-fish-meal diet. A basal diet without feed additives was used as a control (CON); other diets were formulated by supplementing 0.50% taurine (TW), 0.30% peptide (PT), 0.23% mineral water (MW), 0.35% yeast-extracted nucleotides (GRO), 0.35% GRO + 0.50% taurine (GROTW), 0.35% GRO + 0.30% peptide (GROPT) and 0.35% GRO + 0.23% mineral water (GROMW) into the basal diet; in addition, one diet was supplemented with oxytetracycline (OTC) at 0.5% as a positive control. Triplicate groups of 25 fish with an average weight of 5.15 ± 0.06 g (mean ± SD) were fed one of the nine experimental diets. At the end of the feeding trial, the weight gain, specific growth rate and protein efficiency ratio of fish fed the GRO, GROMW, GROPT and GROTW diets were significantly higher than those of fish fed the CON diet (p < 0.05). The feed efficiency of fish fed the GRO, GROMW, GROPT and GROTW diets was significantly higher than that of fish fed the TW and OTC diets. However, the survival, hepatosomatic index, viscerosomatic index and condition factor of fish, as well as their whole-body proximate composition, were not significantly affected by the experimental diets (p > 0.05). The serum glutamic pyruvic transaminase of fish fed the GROPT diet was significantly lower than that of fish fed the CON diet. However, glutamic oxaloacetic transaminase, glucose and total protein were not significantly affected by the experimental diets (p > 0.05). The serum superoxide dismutase activity of fish fed the PT, TW, GRO, GROMW, GROPT and GROTW diets was significantly higher than that of fish fed the CON diet. The lysozyme activity of fish fed the PT, GRO, GROMW, GROPT and GROTW diets was significantly higher than that of fish fed the CON and OTC diets. The myeloperoxidase activity of fish fed the TW, GRO, GROMW, GROPT and GROTW diets was significantly higher than that of fish fed the CON, PT and MW diets (p < 0.05). The flounder growth hormone gene expression of fish fed the TW, GRO, GROMW, GROPT, GROTW and OTC diets was significantly higher than that of fish fed the CON, PT and MW diets (p < 0.05). The interleukin 1β and interleukin 10 gene expressions of fish fed the GRO, GROMW, GROPT and GROTW diets were significantly higher than those of fish fed the CON, PT, TW and MW diets (p < 0.05). Intestinal histology showed a significantly higher villi length for fish fed the GRO, GROMW, GROPT and GROTW diets compared to that of fish fed the CON diet (p < 0.05). Digestive enzyme activities such as trypsin activity were significantly higher in fish fed the GROMW, GROPT and GROTW diets than those in the rest of the diet groups (p < 0.05). Amylase activity in fish fed the MW, GRO, GROMW, GROPT, GROTW and OTC diets was significantly higher than that of fish fed the PT, TW and CON diets (p < 0.05). On the other hand, the lipase activity of fish fed the TW, GRO, GROMW, GROPT and GROTW diets was significantly higher than that of fish fed the CON, PT, MW and OTC diets (p < 0.05). The cumulative survival rate of fish fed the PT, GROTW, GROPT and GROMW diets was significantly higher than that of fish fed the CON, TW and MW diets after thirteen days of the challenge testing. Overall, the results demonstrate that the GRO, GROMW, GROPT and GROTW diets could be beneficial feed additives to replace antibiotics in juvenile olive flounder fed low-fish-meal diets. [ABSTRACT FROM AUTHOR]

Abstract Background In the current genomic era, gene expression datasets have become one of the main tools utilized in cancer classification. Both curse of dimensionality and class imbalance problems are inherent characteristics of these datasets. These characteristics have a negative impact on the performance of most classifiers when used to classify cancer using genomic datasets. Results This paper introduces Reduced Noise-Autoencoder (RN-Autoencoder) for pre-processing imbalanced genomic datasets for precise cancer classification. Firstly, RN-Autoencoder solves the curse of dimensionality problem by utilizing the autoencoder for feature reduction and hence generating new extracted data with lower dimensionality. In the next stage, RN-Autoencoder introduces the extracted data to the well-known Reduced Noise-Synthesis Minority Over Sampling Technique (RN- SMOTE) that efficiently solve the problem of class imbalance in the extracted data. RN-Autoencoder has been evaluated using different classifiers and various imbalanced datasets with different imbalance ratios. The results proved that the performance of the classifiers has been improved with RN-Autoencoder and outperformed the performance with original data and extracted data with percentages based on the classifier, dataset and evaluation metric. Also, the performance of RN-Autoencoder has been compared to the performance of the current state of the art and resulted in an increase up to 18.017, 19.183, 18.58 and 8.87% in terms of test accuracy using colon, leukemia, Diffuse Large B-Cell Lymphoma (DLBCL) and Wisconsin Diagnostic Breast Cancer (WDBC) datasets respectively. Conclusion RN-Autoencoder is a model for cancer classification using imbalanced gene expression datasets. It utilizes the autoencoder to reduce the high dimensionality of the gene expression datasets and then handles the class imbalance using RN-SMOTE. RN-Autoencoder has been evaluated using many different classifiers and many different imbalanced datasets. The performance of many classifiers has improved and some have succeeded in classifying cancer with 100% performance in terms of all used metrics. In addition, RN-Autoencoder outperformed many recent works using the same datasets.

In this study, we introduce an artificial intelligent method for addressing the batch effect of a transcriptome data. The method has several clear advantages in comparison with the alternative methods presently in use. Batch effect refers to the discrepancy in gene expression data series, measured under different conditions. While the data from the same batch (measurements performed under the same conditions) are compatible, combining various batches into 1 data set is problematic because of incompatible measurements. Therefore, it is necessary to perform correction of the combined data (normalization), before performing biological analysis. There are numerous methods attempting to correct data set for batch effect. These methods rely on various assumptions regarding the distribution of the measurements. Forcing the data elements into pre-supposed distribution can severely distort biological signals, thus leading to incorrect results and conclusions. As the discrepancy between the assumptions regarding the data distribution and the actual distribution is wider, the biases introduced by such "correction methods" are greater. We introduce a heuristic method to reduce batch effect. The method does not rely on any assumptions regarding the distribution and the behavior of data elements. Hence, it does not introduce any new biases in the process of correcting the batch effect. It strictly maintains the integrity of measurements within the original batches. [ABSTRACT FROM AUTHOR]

Fenugreek seeds (FSs) are a natural source of bioactive compounds that may modulate the immune system and gut microbiota in broilers. This study examined the effects of dietary fenugreek seed powder on immune-related gene expression and cecal microbiota composition in broilers. A total of 144 broiler chickens were randomly allocated to three dietary groups, CON (0 g/kg FS, FS5 (5 g/kg FS) and FS10 (10 g/kg FS), each with 6 replicates of 8 birds. Ileum tissues and cecal contents were collected on day 42 for the mRNA expression of inflammation and antimicrobial defense-related genes and cecal microbiome diversity, respectively. The results indicated that fenugreek seeds downregulated mRNA-level inflammation and antimicrobial defense-related genes: IL6, IL8L2, CASP6, PTGS2, IRF7, AvBD9, AvBD10, and AvBD11. Moreover, fenugreek seeds altered the cecal microbial community by increasing the population of Firmicutes and decreasing the population of Actinobacteriota, Gemmatimonadota and Verrucomicrobiota at the phylum level and increasing Alistipes, Bacteriodes and Prevotellaceae at the genera level. These findings suggest that fenugreek seeds have a positive impact on the immunological profile and microbiome of broiler chickens, possibly through the interplay of the immune system and the gut microbiome.

The primary neuronal and astrocyte culture described here is from the stress-hyperreactive Wistar Kyoto (WKY) More Immobile (WMI) rat with premature aging-related memory deficit, and its nearly isogenic control, the Less Immobile (WLI) strain. Primary WMI hippocampal neurons and cortical astrocytes are significantly more sensitive to oxidative stress (OS) generated by administration of H2O2 compared to WLI cells as measured by the trypan blue cell viability assay. Intrinsic genetic vulnerability is also suggested by the decreased gene expression in WMI neurons of catalase (Cat), and in WMI cortical astrocytes of insulin-like growth factor 2 (Igf2), synuclein gamma (Sncg) and glutathione peroxidase 2 (Gpx2) compared to WLI. The expressions of several mitochondrial genes are dramatically increased in response to H2O2 treatment in WLI, but not in WMI cortical astrocytes. We propose that the vulnerability of WMI neurons to OS is due to the genetic differences between the WLI and WMI. Furthermore, the upregulation of mitochondrial genes may be a compensatory response to the generation of free radicals by OS in the WLIs, and this mechanism is disturbed in the WMIs. Thus, this pilot study suggests intrinsic vulnerabilities in the WMI hippocampal neurons and cortical astrocytes, and affirm the efficacy of this bimodal in vitro screening system for finding novel drug targets to prevent oxidative damage in illnesses.

Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.

AimsWe aimed to develop a gene signature that predicts the occurrence of postmenopausal osteoporosis (PMOP) by studying its genetic mechanism.MethodsFive datasets were obtained from the Gene Expression Omnibus database. Unsupervised consensus cluster analysis was used to determine new PMOP subtypes. To determine the central genes and the core modules related to PMOP, the weighted gene co-expression network analysis (WCGNA) was applied. Gene Ontology enrichment analysis was used to explore the biological processes underlying key genes. Logistic regression univariate analysis was used to screen for statistically significant variables. Two algorithms were used to select important PMOP-related genes. A logistic regression model was used to construct the PMOP-related gene profile. The receiver operating characteristic area under the curve, Harrell’s concordance index, a calibration chart, and decision curve analysis were used to characterize PMOP-related genes. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of the PMOP-related genes in the gene signature.ResultsWe identified three PMOP-related subtypes and four core modules. The muscle system process, muscle contraction, and actin filament-based movement were more active in the hub genes. We obtained five feature genes related to PMOP. Our analysis verified that the gene signature had good predictive power and applicability. The outcomes of the GSE56815 cohort were found to be consistent with the results of the earlier studies. qRT-PCR results showed that RAB2A and FYCO1 were amplified in clinical samples.ConclusionThe PMOP-related gene signature we developed and verified can accurately predict the risk of PMOP in patients. These results can elucidate the molecular mechanism of RAB2A and FYCO1 underlying PMOP, and yield new and improved treatment strategies, ultimately helping PMOP monitoring.Cite this article: Bone Joint Res 2022;11(8):548–560.

Black rockfish (Sebastes schlegelii) is a marine fish with high financial value; however, the frequent occurrence of bacterial diseases has caused a production decline and economic losses. This study found that hyperemia, hemorrhage, and ascites were common in S. schlegelii during the V. parahaemolyticus infection. Inflammation, degeneration, and necrosis in the liver could be observed. The epithelial mucosal integrity, the intestine epidermis thickness, the villus heights, and the number of mucous cells in the intestine were decreased after infection. Apparent differences in most of the hematological parameters between the two groups were observed, such as the corpuscular volume (CV) and NaCl concentrations of the beginning hemolysis were decreased remarkably (P < 0.01) after infecting with V. parahaemolyticus. However, the white blood cell count (WBC), lysozyme (LZM), malondialdehyde (MDA), K+, Cl−, and Ca2+ were increased significantly (P < 0.01) after infection. In addition, the mRNA expressions in four tissues (gills, liver, blood, spleen) of eleven immune-related genes were investigated. The results showed that C1r, C1s, and C1inh expression varied considerably among tissues. Caspase 10 expression was reduced in four tissues after infection, but MyD88, TNF receptor, TNF-α, BAFF, IL-1β, IL-8, and IL-10 showed increased expression profiles within 24 h after infection. In particular, IL-1β expression in the liver and spleen increased 123.67 and 104.94-fold at 6 hpi, respectively. Therefore, in addition to pathology, the hematological detection and gene expression profiles could be used in the evaluation of healthy status in fish, and this study provided a preliminary basis for the diagnosis of S. schlegelii infecting with V. parahaemolyticus. [ABSTRACT FROM AUTHOR]

A novel form of nanocomposite based on bioactive glass (BG) and CuAl LDH has been devised and manufactured for the first time in this paper. The produced nanocomposites, BG@CuAl LDH and BG@CuAl LDH@RO, were employed to examine the ability of the alkaline phosphatase activity to regulate the expression of COL 1, OCN and RUNX2 (ALP) gene expressions. The role of leaf extracts (Rosmarinus officinalis [RO]) on enhanced osteogenic gene expression has been investigated. Also, the relative cell viability has been analyzed by MTT assay on the hBMSCs, HEK‐293 and PC12 cell lines after 24 and 48 hours of treatment. The results showed significantly increased gene expressions in different microenvironments, the presence and absence of ascorbic acid and low cytotoxicity towards different cell lines. In the case of the hBMSCs cell lines, the synthesized nanomaterials' cell attachment and proliferation findings proved completely successful. [ABSTRACT FROM AUTHOR]

Background: In the current genomic era, gene expression datasets have become one of the main tools utilized in cancer classification. Both curse of dimensionality and class imbalance problems are inherent characteristics of these datasets. These characteristics have a negative impact on the performance of most classifiers when used to classify cancer using genomic datasets. Results: This paper introduces Reduced Noise-Autoencoder (RN-Autoencoder) for pre-processing imbalanced genomic datasets for precise cancer classification. Firstly, RN-Autoencoder solves the curse of dimensionality problem by utilizing the autoencoder for feature reduction and hence generating new extracted data with lower dimensionality. In the next stage, RN-Autoencoder introduces the extracted data to the well-known Reduced Noise-Synthesis Minority Over Sampling Technique (RN- SMOTE) that efficiently solve the problem of class imbalance in the extracted data. RN-Autoencoder has been evaluated using different classifiers and various imbalanced datasets with different imbalance ratios. The results proved that the performance of the classifiers has been improved with RN-Autoencoder and outperformed the performance with original data and extracted data with percentages based on the classifier, dataset and evaluation metric. Also, the performance of RN-Autoencoder has been compared to the performance of the current state of the art and resulted in an increase up to 18.017, 19.183, 18.58 and 8.87% in terms of test accuracy using colon, leukemia, Diffuse Large B-Cell Lymphoma (DLBCL) and Wisconsin Diagnostic Breast Cancer (WDBC) datasets respectively. Conclusion: RN-Autoencoder is a model for cancer classification using imbalanced gene expression datasets. It utilizes the autoencoder to reduce the high dimensionality of the gene expression datasets and then handles the class imbalance using RN-SMOTE. RN-Autoencoder has been evaluated using many different classifiers and many different imbalanced datasets. The performance of many classifiers has improved and some have succeeded in classifying cancer with 100% performance in terms of all used metrics. In addition, RN-Autoencoder outperformed many recent works using the same datasets. [ABSTRACT FROM AUTHOR]

Simple Summary: The effects of seasonal transition and temperature humidity index (THI) on a number of variables representing physiological, hematological and molecular responses of lactating dairy cows reared under natural environmental conditions were assessed. The study revealed significant impact of seasonal transition and THI on most of these variables. The physiological, hematological and molecular alterations highlight adaptive responses of bovine traits to climatic stressors. The results of this study contribute to a deeper understanding of the adaptive mechanisms of dairy cows under challenging environmental conditions, indicating their potential as heat stress biomarkers. A comprehensive study was conducted to assess the effects of seasonal transition and temperature humidity index (THI) on the adaptive responses in crossbred dairy cows reared in a tropical savanna region. A total of 40 lactating dairy cattle reared by small-scale dairy farmers in Bengaluru, India, were selected for this study. The research period comprised the transitioning season of summer to monsoon, wherein all traits were recorded at two points, one representing late summer (June) and the other early monsoon (July). A set of extensive variables representing physiological responses (pulse rate, respiration rate, rectal temperature, skin surface temperature), hematological responses (hematological profile), production (test day milk yield, milk composition) and molecular patterns (PBMC mRNA relative expression of selective stress response genes) were assessed. A significant effect of seasonal transition was identified on respiration rate (RR), skin surface temperature, mean platelet volume (MPV), platelet distribution width (PDWc), test day milk yield and on milk composition variables (milk density, lactose, solids-not-fat (SNF) and salts). The THI had a significant effect on RR, skin surface temperature, platelet count (PLT), plateletcrit (PCT) and PDWc. Lastly, THI and/or seasonal transition significantly affected the relative PBMC mRNA expression of heat shock protein 70 (HSP70), interferon beta (IFNβ), IFNγ, tumor necrosis factor alpha (TNFα), growth hormone (GH) and insulin-like growth factor-1 (IGF-1) genes. The results from this study reveal environmental sensitivity of novel physiological traits and gene expressions to climatic stressors, highlighting their potential as THI-independent heat stress biomarkers. [ABSTRACT FROM AUTHOR]

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Rice sheath blight is caused by the necrotrophic soil-borne fungus Rhizoctonia solani Kühn. It is one of the most destructive rice disease. Jasmonic acid (JA) plays a vital role in plant defense mechanisms. This study aims to increase the understanding of JA in plant defense mechanisms against R. solani. In this study, we applied four different JA concentrations: 0.01, 0.1, 0.5, and 1 mM. JA application significantly increased the plant resistance against R. solani. The highest relative control of 82.38% was achieved by plants treated with a concentration of 0.1 mM. JA concentration of 0.1 mM is the most suitable treatment and above this concentration, the lesion length started to increase which indicates the reduction of plant resistance. Treatment 0.1 mM JA is further used to investigate defense-related enzymes and the expression of genes. 0.1 mM JA treatment effectively increases the activity of enzymes involved in plant defense mechanisms such as phenylalanine ammonia-lyase (PAL), peroxidase (POD), and β-1,3-glucanase, JA also lowers the malondialdehyde (MDA) content which proves its effectiveness against R. solani. The POX, PAL, and OsPR1b genes are the key marker genes for the plant defense, and the application of JA positively increases the relative expressions of these genes. These results confirm the significance of JA in plant defense mechanisms. [ABSTRACT FROM AUTHOR]

Several gene expressions are related to the success of spermatogenesis. Protamine plays an important role in sperm DNA packaging, spermatogenesis, and sperm quality. This study aimed to isolate RNA from spermatozoa and determine the gene expression profiles of protamine 1 (PRM1) and protamine 2 (PRM2). Six Pasundan bulls aged 5-8 years with a body weight of 380 kg-430 kg were used for this study. The Pasundan bulls were classified into group A (70%-79%) and group B (80%-89%) based on their sperm motility in fresh semen. In this study, correlation analysis was performed between fresh semen characteristics (volume, motility, concentration, abnormality, viability, intact plasma membrane (IPM), DNA integrity) and frozen semen characteristics after thawing (motility, viability, IPM, and DNA integrity). Total RNA was isolated from the frozen sperm pellet, and cDNA was synthesized. Specific PCR primers were used for the transcription of PRM1 and PRM2 from sperm. PRM1 and PRM2 gene expressions were evaluated by qRT-PCR, and ACTB was used as a control. The results showed that progressive sperm motility in the fresh sperm positively correlated with sperm viability and IPM. PRM1 and PRM2 were higher (p<0.05) in group B than in group A. This condition indicates the existence and influence of protamine on the parameters of progressive sperm motility. The expression of PRM1 and PRM2 genes could use as markers of semen quality in Pasundan bulls. [ABSTRACT FROM AUTHOR]

Uncovering the relationships between the content and compositions of olive oil, environmental factor, and developmental stages can lead to the effective cultivation choices and maximizing productivity. Fatty acid contents of 4 olive cultivars are screened at 5 developmental stages during 2 cropping seasons. Moreover, the transcript abundance of 4 fatty acids and triacylglycerol biosynthesis genes are evaluated in 2 cultivars displaying distinct oil content and composition. Thought, all studied cultivars display a rise in oil content and a decline in oleic/linoleic acid as maturity advances, the fatty acid content, however changes in a cultivar‐dependent manner. In contrast to other cultivars, "Mari" shows an increasing trend for oleic acid and fruit RH, and steady state pattern for linoleic acid during fruit development. All these characteristics result in a unique oil quality in "Mari". Accordingly, there are slight differences in the oil related‐attributes in 2 cropping years at different sampling dates which are also cultivar dependent. The expression patterns of oil biosynthesis genes are well‐paralleled with oil accumulation and compositions in the studied olive cultivars; as OeSAD2 and OeDGAT2 experience a significant higher expression in "Mari", while "Shengeh" has higher levels for OeFAD2‐2 and OeDGAT1 during most sampling times. Practical Applications: According to these data, the lower expression of OeFAD2‐2, as well as, substantially higher expression of OeSAD2 and OeDGAT2 are suggested as the major players for higher oil and oleic acid production in "Mari". Results obtained from this study improve knowledge about oil biosynthesis in olive drupe in relation to fruit ripening and environmental factors. These data are useful for both growers and experts enabling them to make more appropriate planting and harvest decisions, as well as, to design suitable breeding programs to achieve olive improvement objectives. [ABSTRACT FROM AUTHOR]

Bacterial drug resistance to antibiotics is growing globally at unprecedented levels, and strategies to overcome treatment deficiencies are continuously developing. In our approach, we utilized metal nanoparticles, silver nanoparticles (AgNPs), known for their wide spread and significant anti-bacterial actions, and the high-dose regimen of lincosamide antibiotic, lincomycin, to demonstrate the efficacy of the combined delivery concept in combating the bacterial resistance. The anti-bacterial actions of the AgNPs and the lincomycin as single entities and as part of the combined mixture of the AgNPs–lincomycin showed improved anti-bacterial biological activity in the Bacillus cereus and Proteus mirabilis microorganisms in comparison to the AgNPs and lincomycin alone. The comparison of the anti-biofilm formation tendency, minimum bactericidal concentration (MBC), and minimum inhibitory concentration (MIC) suggested additive effects of the AgNPs and lincomycin combination co-delivery. The AgNPs' MIC at 100 μg/mL and MBC at 100 μg/mL for both Bacillus cereus and Proteus mirabilis, respectively, together with the AgNPs–lincomycin mixture MIC at 100 + 12.5 μg/mL for Bacillus cereus and 50 + 12.5 μg/mL for Proteus mirabilis, confirmed the efficacy of the mixture. The growth curve test showed that the AgNPs required 90 min to kill both bacterial isolates. The freshly prepared and well-characterized AgNPs, important for the antioxidant activity levels of the AgNPs material, showed radical scavenging potential that increased with the increasing concentrations. The DPPH's best activity concentration, 100 μg/mL, which is also the best concentration exhibiting the highest anti-bacterial zone inhibition, was chosen for evaluating the combined effects of the antibiotic, lincomycin, and the AgNPs. Plausible genotoxic effects and the roles of AgNPs were observed through decreased Bla gene expressions in the Bacillus cereus and BlaCTX-M-15 gene expressions in the Proteus mirabilis. [ABSTRACT FROM AUTHOR]

Response by plants to drought occurs through a series of mechanisms that involve transcription regulation. This research was conducted to study transcription factors (TF) and physiological changes in the drought response of local rice cultivars from East Nusa Tenggara (Nusa Tenggara Timur, NTT) during drought stress. Using three NTT local rice cultivars (Boawae Seratus Malam (BSM), Gogo Jak (GJ), and Kisol Manggarai (KM)) and the fraction of transpirable soil water (FTSW) method with two treatment levels, FTSW 1 (control) and FTSW 0.2 (severe stress), we analyzed the TF expression of OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6. Based on the result, the highest level of TF expression occurred in the BSM, followed by the GJ and KM cultivars. Analysis of physiological characteristics showed an association between TF expression levels and physiological response, with the BSM cultivar showing high pigment levels, high proline content, and lower H2O2 levels. A linkage was also found in relation to water conservation, as indicated by the higher relative water content and cell membrane stability index in the BSM cultivar in contrast to lower electronic leakage and malondialdehyde percentage when exposed to drought. Based on the results, it can be concluded that the BSM cultivar can be considered as a drought‐tolerant local cultivar according to morpho‐physiological analysis. In this study, all NTT local rice cultivars showed a subtle upregulation of stress‐responsive transcription factors OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6 as responses to drought stress.

High-pressure processing (HPP) is one of the non-thermal methods of food preservation considered to be safe but may cause an increase/decrease in virulence potential and antibiotic resistance. The aim of the present study was to evaluate the survival of L. monocytogenes isolates after high-pressure processing (200 and 400 MPa for 5 min) and to determine changes in phenotypic and genotypic antibiotic resistance and virulence after this treatment. The 400 MPa treatment was shown to be effective in reducing pathogens to safe levels; however, the potential for cell recovery during storage was observed. In addition, studies on changes in virulence indicated possibilities related to a decrease in actA gene expression, overexpression of the hly and osfX gene, and an increase in biofilm-forming ability. The studies on changes in antibiotic resistance of isolates showed that all isolates showing initial susceptibility to lincomycin, fosfomycin, trimethoprim/sulfamethoxazole, and tetracycline became resistant to these antibiotics, which was associated with an increase in the values of minimum inhibitory concentrations. An increase in the expression of antibiotic resistance genes (mainly tetA_1, tetA_3, tetC) was also observed (mainly after the application of 200 MPa pressure), which was isolate dependent. However, it is noteworthy that the induced changes were permanent, i.e., they persisted even after the restoration of optimal environmental conditions. The results presented in our work indicate that the stress occurring during HPP can affect both phenotypic and genotypic changes in the virulence and antibiotic resistance potential of pathogens isolated from food and food processing environments. The potential associated with cell recovery and persistence of changes may influence the spread of virulent isolates of pathogens with increased antibiotic resistance in the food and food processing environment.

High-altitude environments impose intense stresses on living organisms and drive striking phenotypic and genetic adaptations, such as hypoxia resistance, cold tolerance, and increases in metabolic capacity and body mass. As one of the most successful and dominant mammals on the Qinghai-Tibetan Plateau (QHTP), the plateau pika (Ochotona curzoniae) has adapted to the extreme environments of the highest altitudes of this region and exhibits tolerance to cold and hypoxia, in contrast to closely related species that inhabit the peripheral alpine bush or forests. To explore the potential genetic mechanisms underlying the adaptation of O. curzoniae to a high-altitude environment, we sequenced the heart tissue transcriptomes of adult plateau pikas (comparing specimens from sites at two different altitudes) and Gansu pikas (O. cansus). Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify differentially expressed genes (DEGs) and their primary functions. Key genes and pathways related to high-altitude adaptation were identified. In addition to the biological processes of signal transduction, energy metabolism and material transport, the identified plateau pika genes were mainly enriched in biological pathways such as the negative regulation of smooth muscle cell proliferation, the apoptosis signalling pathway, the cellular response to DNA damage stimulus, and ossification involved in bone maturation and heart development. Our results showed that the plateau pika has adapted to the extreme environments of the QHTP via protection against cardiomyopathy, tissue structure alterations and improvements in the blood circulation system and energy metabolism. These adaptations shed light on how pikas thrive on the roof of the world. [ABSTRACT FROM AUTHOR]