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The present study investigated the effects of black mulberry (Morus nigra) syrup supplementation on growth performance, hematological, serum biochemical, innate immune parameters, immune and antioxidant related gene expression responses, and disease resistance of Nile tilapia, Oreochromis niloticus. Five isonitrogenous and isoenergetic diets were formulated to contain black mulberry syrup at levels of 0%, 0.75%, 1.5%, 2.0%, and 3.0%. Fish were fed experimental diets for 60 days. Dietary black mulberry syrup increased activities of serum lysozyme, myeloperoxidase, superoxide dismutase and catalase, and increased the expression levels of immune-related genes (interleukin 1, beta, tumor necrosis factor, immunoglobulin M, interferon gamma and heat shock protein 70) in the spleen and antioxidant-related genes (superoxide dismutase, catalase and glutathione peroxidase) in the liver of fish fed especially with 1.5%, 2.0%, and 3.0% black mulberry syrup supplemented diets. Furthermore, at 2.0% incorporation level, growth performance increased. The findings of the present study indicate that Nile tilapia fed with diet containing 2.0% black mulberry might be adequate to improve the growth performance, innate immune parameters, antioxidant related gene expression responses, and disease resistance against Aeromonas veronii., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The great Gambusia affinis (G. affinis) is considered as an important animal model to study the endocrine disruption, ecological behavior, and environmental pollutant. The present study aims to build a new promising infection model with Aeromonas hydrophila (A. hydrophila) in aquaculture. The mRNA expression of Rac1, MyD88, IRAK4, TAK1, IKKβ, and IL-1β in G. affinis were significance higher (P < 0.05) in the liver of G. affinis than that of brain and intestine. And the PI3K mRNA expression level was significant lower (P < 0.05) in the intestine than that of brain and liver. The mRNA levels of AKT3 were significant higher (P < 0.05) in the brain than that of liver and intestine. And then the brain, liver, and intestine were collected at different time points (0 h, 3 h, 9 h, 18 h, 24 h, 48 h) after post injection of LD 50 of A. hydrophila. The 0.85% NaCl was used as a negative control for the LD 50 of A. hydrophila. The RT-PCR results showed that mRNA expressions of TLR2/4 pathway downstream genes MyD88, IRAK4, TAK1, Rac1, IKKβ, and IL-1β were firstly significantly up-regulated (P < 0.05) and were then backed to the 0 h group levels in three tissues. In contrast, mRNA expressions of TLR2/4 pathway downstream genes PI3K and AKT3 were firstly significantly decreased (P < 0.05) and were then increased to the 0 h group levels in brain and intestine. In summary, the results indicated that A. hydrophila could cause inflammatory reaction in intestinal and brain. In addition, the liver showed a provocative reaction when infected with A. hydrophila., Competing Interests: Declaration of competing interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Introduction: Omega-3 polyunsaturated fatty acids (PUFAs) have been proven critical in the development and management of major depressive disorder (MDD) by a number of epidemiological, clinical and preclinical studies, but the molecular mechanisms underlying this therapeutic action are yet to be understood. Although eicosapentaenoic acid (EPA) seems to be the active component of omega-3 PUFAs' antidepressant effects, the biological research about the difference of specific genetic regulations between EPA and docosahexaenoic acid (DHA), the two main components of omega-3 PUFAs, is still lacking in human subjects., Methods: We conducted a 12-week randomized-controlled trial comparing the effects of EPA and DHA on gene expressions of phospholipase A2 (cPLA2) and cyclooxygenase-2 (COX2), serotonin transporter (5HTT), and Tryptophan hydroxylase 2 (TPH-2) in 27 MDD patients. In addition, the erythrocyte PUFA compositions and the candidate gene expressions were also compared between these 27 MDD patients and 22 healthy controls., Results: EPA was associated with a significant decrease in HAM-D scores (CI: -13 to -21, p<0.001) and significant increases in erythrocyte levels of EPA (CI: +1.0% to +2.9%, p=0.001) and DHA (CI: +2.9% to +5.6%, p=0.007). DHA treatment was associated with a significant decrease in HAM-D scores (CI: -6 to -14, p<0.001) and a significant increase in DHA levels (CI: +0.2% to +2.3%, p=0.047), but not of EPA levels. The cPLA2 gene expression levels were significantly increased in patients received EPA (1.9 folds, p=0.038), but not DHA (1.08 folds, p=0.92). There was a tendency for both EPA and DHA groups to decrease COX-2 gene expressions. The gene expressions of COX-2, cPLA2, TPH-2 and 5-HTT did not differ between MDD cases and healthy controls., Conclusions: EPA differentiates from DHA in clinical antidepressant efficacy and in upregulating cPLA2 gene regulations, which supports the clinical observation showing the superiority of EPA's antidepressant effects., Trial Registration: ClinicalTrials.gov identifier: NCT02615405., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Liver biopsy is the gold standard to assess pathological features (eg inflammation grades) for hepatitis B virus-infected patients although it is invasive and traumatic; meanwhile, several gene profiles of chronic hepatitis B (CHB) have been separately described in relatively small hepatitis B virus (HBV)-infected samples. We aimed to analyse correlations among inflammation grades, gene expressions and clinical parameters (serum alanine amino transaminase, aspartate amino transaminase and HBV-DNA) in large-scale CHB samples and to predict inflammation grades by using clinical parameters and/or gene expressions., Methods: We analysed gene expressions with three clinical parameters in 122 CHB samples by an improved regression model. Principal component analysis and machine-learning methods including Random Forest, K-nearest neighbour and support vector machine were used for analysis and further diagnosis models. Six normal samples were conducted to validate the predictive model., Results: Significant genes related to clinical parameters were found enriching in the immune system, interferon-stimulated, regulation of cytokine production, anti-apoptosis, and etc. A panel of these genes with clinical parameters can effectively predict binary classifications of inflammation grade (area under the ROC curve [AUC]: 0.88, 95% confidence interval [CI]: 0.77-0.93), validated by normal samples. A panel with only clinical parameters was also valuable (AUC: 0.78, 95% CI: 0.65-0.86), indicating that liquid biopsy method for detecting the pathology of CHB is possible., Conclusions: This is the first study to systematically elucidate the relationships among gene expressions, clinical parameters and pathological inflammation grades in CHB, and to build models predicting inflammation grades by gene expressions and/or clinical parameters as well., (© 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Introduction: The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials., Methods: This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations., Results: The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models., Conclusions: The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Background: Zinc finger homeodomain (ZF-HD) belongs to the plant-specific transcription factor (TF) family and is widely involved in plant growth, development and stress responses. Despite their importance, a comprehensive identification and analysis of ZF-HD genes in the soybean (Glycine max) genome and their possible roles under abiotic stress remain unexplored. Results: In this study, 51 ZF-HD genes were identified in the soybean genome that were unevenly distributed on 17 chromosomes. All GmZF-HD genes contained a conserved ZF-HD_dimer domain and had diverse physicochemical features. Furthermore, the GmZF-HD gene structures exhibited 3 to 10 conserved motifs, and most of them showed intronless gene structures. Phylogenetic analysis categorized them into eight major groups with the highest closeness to dicots including Brassica rapa and Malus domestica. The cis-element analysis recognized plant growth and development (10%), phytohormones (31%) and stress-responsive (59%) elements. Synteny analysis identified 73 segmental and 1 tandem duplicated genes that underwent purifying selection. The collinearity analysis revealed that GmZF-HD genes showed higher homology with dicot species, indicating common ancestors with close evolutionary relationships. A total of 94 gma-miRNAs from 41 diverse miRNA families were identified, targeting 40 GmZF-HD genes, with GmZF-HD6 being most targeted by 7 miRNAs, and gma-miR4993 emerging as the dominant miRNA family. Different TFs including ERF, LBD, BBR-BPC and MYB, etc., were predicted in all 51 GmZF-HD genes upstream regions and visualized in the network. Expression profiling through RNA-Seq showed diverse expressions of GmZF-HD genes in different tissues including seeds, roots, shoots and leaves under diverse conditions. Further, the qRT-PCR analysis demonstrated that all tested GmZF-HD genes were significantly induced in soybean leaves, mainly the GmZF-HD5/6/13/39 and GmZF-HD45 genes were significantly upregulated (2.5 to 8.8 folds) under the tested stress treatments compared to control, highlighting their potential roles in response to stresses in soybean. Conclusion: Overall, this study reveals comprehensive insights into the ZF-HD genes in soybeans and provides a valuable contribution towards functional studies for soybean improvement under stress conditions. [ABSTRACT FROM AUTHOR]

The purpose of the study was to demonstrate how soybean peptides (SBP) protect against H2O2 -induced injury in intestinal porcine epithelial cells (IPEC-J2). SBP were prepared by protease hydrolysis, in which the molecular weights of 95.76% SBP were smaller than 3 kDa. Cell experiment included four groups: Control group (IPEC-J2 cells were treated with HGDMEM), SBP group (100 μg/mL SBP incubation for 13 h), H2O2 treatment group (1 mM H2O2 treatment for 1 h), SBP + H2O2 group (100 μg/mL SBP pretreatment for 12 h followed by 1 mM H2O2 treatment for 1 h). This study showed that that treatment with single 1 mM H2O2 for 1 h significantly reduced cell viability to 52.99% (p < 0.05), up-regulated Bax and Caspase-3 gene expressions (p < 0.05), and down-regulated gene expressions of ZO-1, CAT, SOD1, HO-1 and Nrf2 (p < 0.05), compared with the control group. However, pretreatment with SBP followed by H2O2 inducement significantly increased cell viability to 72.99%, decreased cell apoptosis, increased SOD, CAT and GSH-Px activity (p < 0.05), down-regulated Bax and Caspase-3 gene expressions (p < 0.05), and up-regulated the gene expressions of ZO-1, Claudin-1, Occludin, catalase, glutathione GPX1, SOD1, HO-1, NQO1 and Nrf2, compared with the single H2O2–induced cells. According to the study, SBP pretreatment reduced H2O2-induced oxidative stress in cells and preserved the integrity of intestinal cells. [ABSTRACT FROM AUTHOR]

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]

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]

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]

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.

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]

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]

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]

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]

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]

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]

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]

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]

Genetic engineering has made sizeable contributions to technical innovation, agriculture, and the development of pharmaceuticals. Various approaches were evolved to control the genetic cloth of cells using both viral and nonviral vector architectures. Gene therapy aims to reverse pathological traits with the aid of the use of viral and nonviral gene shipping mechanisms. Gene transfer motors have made massive strides in becoming more environmentally pleasant, much less risky, and nonimmunogenic, as well as making an allowance for lengthy-time period transgene expression. One of the most tough components of correctly enforcing gene healing treatments in the clinical putting is adjusting gene expression extremely tightly and constantly as and while it's required. This research work will cognizance on using viral vectors for gene concentrated on biological applications with various gene expressions. Due to improvements in viral vector engineering and superior gene regulatory systems to permit and adjust tightly therapeutic gene expression, the technology for using genes to offer a preferred treatment has confirmed to be an effective approach. [ABSTRACT FROM AUTHOR]

The aim was to identify the gene expressions of human cytomegalovirus (HCMV)-infected human umbilical vein endothelial cells (HUVECs) and to study its possible pathogenic mechanism on atherosclerosis using microarray technology. The gene expression differences in HCMV AD169 strain-infected HUVECs were studied by the microarray technology to explore the potential molecular mechanism of HCMV infection. The qPCRs were performed to verify the transcriptome results. A total of 2,583 differentially expressed genes, including 407 down-regulated genes and 2,176 up-regulated genes, were detected by the systematic bioinformatics analysis. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the significantly differentially expressed genes were mainly involved in regulating protein kinase activity, inflammatory response, ubiquitination, protein phosphorylation, cell metabolism, and exosomes, among which 12 genes had significant changes and were screened by protein-protein interaction (PPI) analysis and verified by qPCR. The experimental qPCR results were consistent with the microarray results. The GO and KEGG analyses revealed that the regulation of protein kinase activity, inflammatory response, ubiquitination, protein phosphorylation, and cell metabolism played important roles in the process of endothelial cell infection. Furthermore, 12 genes were involved in the process of HCMV infection of endothelial cells and contributed to the current understanding of the infection and pathogenic mechanisms of atherosclerosis. [ABSTRACT FROM AUTHOR]

The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance. [ABSTRACT FROM AUTHOR]

The purpose of this study was to look into the effects of pinacidil and glibenclamide on HCN1, KCNT1, Kir 6.1, and SUR1 gene expression in epileptic rats hippocampus and cortex. Male Wistar-Albino rats were used in this study. The drugs pinacidil and glibenclamide were utilized. Control, Epilepsy, Epilepsy-O, and Epilepsy-B were the five groups formed. The epileptic focus was created by intracortical administration of penicillin at a dose of 500 IU/2 µl. Hippocampus and Cortex are removed from all animals and Kir 6.1, SUR1, HCN1, and KCNT1 gene expression levels were determined by qPCR. The SPSS 21 program was used for statistics. HCN1 gene expression level is equal in the hippocampus and cortex (p<0.05). KCNT1, SUR1, and KIR6.1 are more expressed in the hippocampus than in the cortex (p<0.05). In epilepsy groups, HCN1 gene expression level was found to be higher than KCNT1, SUR1, and KIR6.1 gene expression levels (p<0.05). KIR6.1, SUR1, gene expression levels decreased with the application of pinacidil and glibenclamide (p<0.05). SUR1 and KIR6.1 gene expression levels were considerably lower in the epilepsy pinacidil group compared to the other groups. The gene expression levels in the hippocampus were found to be considerably higher than in the cortex group, according to this study. The fact that HCN1 gene expression levels are significantly greater in both the brain and the hippocampus 24 hours following the commencement of epileptic convulsions suggests that preventive medication may be possible. [ABSTRACT FROM AUTHOR]

We tested the hypothesis that gene expressions from biopsies of locally advanced head and neck squamous cell carcinoma (HNSCC) patients can supplement dose-volume parameters to predict dysphagia and xerostomia following primary radiochemotherapy (RCTx). A panel of 178 genes previously related to radiochemosensitivity of HNSCC was considered for nanoString analysis based on tumour biopsies of 90 patients with locally advanced HNSCC treated by primary RCTx. Dose-volume parameters were extracted from the parotid, submandibular glands, oral cavity, larynx, buccal mucosa, and lips. Normal tissue complication probability (NTCP) models were developed for acute, late, and for the improvement of xerostomia grade ≥2 and dysphagia grade ≥3 using a cross-validation-based least absolute shrinkage and selection operator (LASSO) approach combined with stepwise logistic regression for feature selection. The final signatures were included in a logistic regression model with optimism correction. Performance was assessed by the area under the receiver operating characteristic curve (AUC). NTCP models for acute and late xerostomia and the improvement of dysphagia resulted in optimism-corrected AUC values of 0.84, 0.76, and 0.70, respectively. The minimum dose to the contralateral parotid was selected for both acute and late xerostomia and the minimum dose to the larynx was selected for dysphagia improvement. For the xerostomia endpoints, the following gene expressions were selected: RPA2 (cellular response to DNA damage), TCF3 (salivary gland cells development), GBE1 (glycogen storage and regulation), and MAPK3 (regulation of cellular processes). No gene expression features were selected for the prediction of dysphagia. This hypothesis-generating study showed the potential of improving NTCP models using gene expression data for HNSCC patients. The presented models require independent validation before potential application in clinical practice. [ABSTRACT FROM AUTHOR]

This study evaluates the effects of longan seed powder (LS) on the growth performance, immunological response, and immune-antioxidant related gene expression of Nile tilapia (Oreochromis niloticus). Three hundred fish (13.82 ± 0.06 g) were divided into five experiments and fed 5 diets, including the basal diet (control without LS) and basal diet containing 10 (LS10), 20 (LS20), 40 (LS40), and 80 (LS80) g kg−1 LS for eight weeks. A completely randomized design (CRD) with three replications was utilised. The growth performance and immune response were measured at weeks 4 and 8 post feeding, while the gene expressions were determined at the end of the feeding trial. The results revealed that administration of LS could significantly (P < 0.05) improve specific growth rate (SGR), weight gain (WG), and feed conversion ratio (FCR) in Nile tilapia as compared to the control group. However, no significant differences (P > 0.05) were observed in survival rates among treatments. LS-supplemented diets showed enhanced serum peroxidase activity (SPA), serum lysozyme activity (SLA), skin mucus lysozyme activity (MLA), and skin mucus peroxidase activity (MPA) at weeks 4 and 8 post-feeding, with the highest values observed in the LS20 diet (P < 0.05). Additionally, LS-supplemented diets significantly up-regulated (P < 0.05) immune and antioxidant related gene expressions (IL1, IL8, LBP, GSTa, GPX, and GSR) in the liver and intestine, with highest values observed in the LS20 treatment. The present results confirmed the beneficial effects of LS as a functional feed additive and immunostimulant for Nile Tilapia culture in a biofloc system. [Display omitted] • Longan seed powder (LS) (20 g kg−1 – LS20) supplemented diet significantly improved growth rate and FCR of Nile tilapia. • No significant differences in survival rate were observed in fish fed LS diets. • Significantly improved skin mucus and serum immunities were noted in fish fed LS20. • Up-regulation IL-1, IL-8, LBP, GSTa, GPX, and GSR were observed in fish LS20. [ABSTRACT FROM AUTHOR]

Hematopoiesis and blood diseases include leukemia and unclassified blood disorders (UBDs). Leukemia, one of the leading causes of cancer death in the world, is divided into four major types including acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). The SHP gene group belongs to the protein tyrosine phosphatase (PTP) family, which plays an important role in preventing cancer growth. This group consists of two main genes, SHP-1 and SHP-2. In this study, experiments were conducted to determine the expression of SHP-1 and SHP-2 genes in patients with leukemia and UBDs using real-time PCR. Results showed that while SHP-1 gene expression was significantly decreased in all patient samples compared to control samples, SHP-2 gene expression was significantly increased in patients with CML and other blood disorders but decreased in ALL patients compared to healthy subjects. These results are important for disease diagnosis and combination therapy based on SHP-1 and SHP-2 target genes. [ABSTRACT FROM AUTHOR]

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, Elephant search (ESA) based optimization is proposed to select best gene expressions from the large volume of microarray data. Firefly search (FFS) is also used to understand the effectiveness of the Elephant search method in feature selection process. Stochastic gradient descent based Deep Neural Network as Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on ten most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning approach are compared with the most recent published article for its suitability in future Bioinformatics research. Finally, Statistical significance test by one-way ANOVA with post hoc Tukey's test is conducted to deduce a number of insights on the selection of the best classification model. [ABSTRACT FROM AUTHOR]

Sunitinib (SUN) is an oral tyrosine kinase inhibitor approved in 2006 as a first-line treatment for metastatic renal cell cancer. However, weak selectivity to kinase receptors and cardiotoxicity have limited the use of sunitinib. Rivaroxaban (RIVA) is a Factor Xa inhibitor with cardioprotective action. It inhibits atherosclerosis and numerous inflammatory cascades. The present study was designed to investigate the cardioprotective effects of RIVA in sunitinib-induced cardiotoxicity. Thirty male Wistar rats were divided into five groups. Group 1 was the normal control (control). Group 2 was administered i.p. SUN 25 mg kg−1 thrice weekly for 3 weeks. Groups 3 and 4 received the same treatment as Group 2 followed by the administration of RIVA 5 mg kg−1 day−1 and 10 mg kg−1 day−1, respectively, for 3 weeks. Group 5 received only 10 mg kg−1 day−1 RIVA for 3 weeks. Serum levels of Ca2+, Mg2+, Fe3+/Fe2+, lipid profiles, and cardiac enzymes were measured. Cardiac tissues were isolated for the measurements of oxidant/antioxidant balance gene and protein expressions. Relative to the controls, the administration of SUN significantly altered serum levels of (Ca2+, Mg2+, Fe3+/Fe2+, lipid profiles, and cardiac enzymes), intracellular antioxidant enzymes, and the expression levels of the genes encoding certain proteins. RIVA treatment significantly restored these parameters to near-normal levels. RIVA treatment significantly mitigated SUN-induced cardiac injuries by restoring antioxidant enzyme levels and attenuating the proinflammatory cascades resulting from SUN-induced cardiac injuries. [ABSTRACT FROM AUTHOR]

[Display omitted] • Autism spectrum disorders ASD have a major adverse impact on social interactions. • Male dominance in ASD, with females receiving late diagnosis or remain undiagnosed. • There is a link between ASD and the "female brain" or "male brain" • Very recently, mutations in micro RNA (miRNA) have become apparent in ASD. • fMRI sheds light on the details of neural connectivity, important in ASD. Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by social deficits, repetitive behaviours and lack of empathy. Its significant genetic heritability and potential comorbidities often lead to diagnostic and therapeutic challenges. This review addresses the biological basis of ASD, focusing on the sex differences in gene expression and hormonal influences. ASD is more commonly diagnosed in males at a ratio of 4:1, indicating a potential oversight in female-specific ASD research and a risk of underdiagnosis in females. We consider how ASD manifests differently across sexes by exploring differential gene expression in female and male brains and consider how variations in steroid hormones influence ASD characteristics. Synaptic function, including excitation/inhibition ratio imbalance, is influenced by gene mutations and this is explored as a key factor in the cognitive and behavioural manifestations of ASD. We also discuss the role of micro RNAs (miRNAs) and highlight a novel mutation in miRNA-873, which affects a suite of key synaptic genes, neurexin, neuroligin, SHANK and post-synaptic density proteins, implicated in the pathology of ASD. Our review suggests that genetic predisposition, sex differences in brain gene expression, and hormonal factors significantly contribute to the presentation, identification and severity of ASD, necessitating sex-specific considerations in diagnosis and treatments. These findings advocate for personalized interventions to improve the outcomes for individuals with ASD. [ABSTRACT FROM AUTHOR]

We build personalized relevance parameterization method (prep-ad) based on artificial intelligence (ai) techniques to compute Alzheimer's disease (ad) progression for patients at the mild cognitive impairment (mci) stage. Expressions of ad related genes, mini mental state examination (mmse) scores, and hippocampal volume measurements of mci patients are obtained from the Alzheimer‘s Disease Neuroimaging Initiative (adni) database. In evaluation of cognitive changes under pharmacological therapies, patients are grouped based on available clinical measurements and the type of therapy administered, namely donepezil monotherapy and polytherapy of donepezil with memantine. Average leave one out cross validation (loocv) error rates are calculated for prep-ad results as less than 8 percent when mmse scores are used to compute disease progression for a 60 month period, and 3 percent with hippocampal volume measurements for 12 months. Statistical significance is calculated as p = 0.003 for using ad related genes in disease progression and as p < 0. 05 for the results computed by prep-ad. These relatively small average loocv errors and p-values suggest that our prep-ad methods employing gene expressions, mmse scores and hippocampal volume loss measurements can be useful in supporting pharmacologic therapy decisions during early stages of ad. [ABSTRACT FROM AUTHOR]

The aim of the present study was to define whether elevated rumen‐undegradable protein (RUP) and tannin‐rich peanut skin (PS) supplementation would affect animal growth performance, average daily gain (ADG), blood metabolites, carcass traits associated with lipogenic and immune‐related gene expressions in meat goats grazing winter wheat (WW). Thirty‐six Kiko‐crossbreed male goats at approximately 6 months of age were blocked by body weight (BW; 25.6 ± 1.1 kg) and randomly assigned to one of the four treatments with two replicates based on a 2 × 2 factorial design. Diets contained PS replacing alfalfa meal (ALM), without or with RUP supplementation. Both PS and ALM were incorporated into grain mix portion of the diet and pelletized, with remaining diets fed ad libitum of WW forage for a period of 51 days. Lipogenic genes examined included SCD, ACLY, YWHAZ, PPIA and FABP4, while immune‐related genes examined included ACTB (as a control gene), H3F3A, PPIA, IRF3, STAT2, HERC3 and IFIT3 antibody genes. The meat goats on PS‐pellet‐supplemented group with or without RUP supplementation grew 38.5% faster ADG (p <.001) when compared to control‐supplemented group. When goats received PS diet, empty body weight, hot carcass, cold carcass, shoulder, hind shank, rack, loin and fat thickness were greater (p <.05) than control diet. Animals on PS‐pellet had higher ACLY, YWHAZ, PPIA and FABP4 gene expression (p <.05) when compared to ALM‐pellet control, with RUP by PS‐pellet interactions (p <.01). Goats receiving additional RUP supplementation had increased (p <.05) STAT2 gene expression, whereas goats receiving PS‐pellet supplementation showed increased STAT2 (p <.05) and a tendency to increase IRF3 (p =.07) gene expressions. In conclusion, the addition of PS‐pellet or RUP supplementation has the potential to improve ADG and altered selected lipogenic and immune‐related gene expressions. [ABSTRACT FROM AUTHOR]

Errors‐in‐variables models in high‐dimensional settings pose two challenges in application. First, the number of observed covariates is larger than the sample size, while only a small number of covariates are true predictors under an assumption of model sparsity. Second, the presence of measurement error can result in severely biased parameter estimates, and also affects the ability of penalized methods such as the lasso to recover the true sparsity pattern. A new estimation procedure called SIMulation‐SELection‐EXtrapolation (SIMSELEX) is proposed. This procedure makes double use of lasso methodology. First, the lasso is used to estimate sparse solutions in the simulation step, after which a group lasso is implemented to do variable selection. The SIMSELEX estimator is shown to perform well in variable selection, and has significantly lower estimation error than naive estimators that ignore measurement error. SIMSELEX can be applied in a variety of errors‐in‐variables settings, including linear models, generalized linear models, and Cox survival models. It is furthermore shown in the Supporting Information how SIMSELEX can be applied to spline‐based regression models. A simulation study is conducted to compare the SIMSELEX estimators to existing methods in the linear and logistic model settings, and to evaluate performance compared to naive methods in the Cox and spline models. Finally, the method is used to analyze a microarray dataset that contains gene expression measurements of favorable histology Wilms tumors. [ABSTRACT FROM AUTHOR]

This study was to investigate the effect of zinc pectin oligosaccharides chelate (Zn-POS) on growth performance, serum enzyme activities, tissue zinc accumulation, metallothionein (MT) concentrations, and gene expression of zinc transporters (ZnT) in broilers. Five hundred forty 1-d-old Arbor Acres broiler chicks were randomly assigned to 5 dietary groups with 6 replicates of 18 birds per replicate. The diets were formulated with the same supplemental Zn level (80 mg/kg diet) but different amount of the Zn-POS: 0, 200, 400, 600, and 800 mg Zn-POS/kg diet. ZnSO4 was used to adjust to the desired amount of the Zn (80 mg/kg) in the Zn-POS diets. Broilers were fed with the experimental diets for 42 d including the starter (days 1 to 21) and grower (days 22 to 42) phases. Our results showed that dietary supplementation of Zn-POS linearly and quadratically increased (P < 0.05) the average daily gain and gain-to-feed ratio during 22 to 42 d and 1 to 42 d as well as body weight on day 42, whereas reduced (P < 0.05) the sum of mortality and lag abnormalities in broilers on day 42. Besides, serum alkaline phosphatase and copper-zinc superoxide dismutase activities increased (P < 0.05) linearly and quadratically in response to dietary Zn-POS supplemental level on day 42. Dietary Zn-POS supplementation increased Zn accumulation in serum (linear, P < 0.05), liver (linear, P < 0.05), and pancreas (linear and quadratic, P < 0.05). In addition, Zn-POS supplementation linearly and quadratically increased (P < 0.01, P < 0.05, respectively) MT concentrations in liver and pancreas of broilers. Pancreatic mRNA levels of MT, ZnT-1, and ZnT-2 increased (P < 0.05) linearly and quadratically, and the mRNA expression of metal response element-binding transcription factor-1 increased linearly (P < 0.05), in response to dietary Zn-POS supplementation. In conclusion, supplementation of Zn-POS in the diet increases Zn enrichment in the metabolic organs such as liver and pancreas and promotes productive performance in broilers. [ABSTRACT FROM AUTHOR]

This study was to investigate the effect of zinc pectin oligosaccharides chelate (Zn-POS) on growth performance, serum enzyme activities, tissue zinc accumulation, metallothionein (MT) concentrations, and gene expression of zinc transporters (ZnT) in broilers. Five hundred forty 1-d-old Arbor Acres broiler chicks were randomly assigned to 5 dietary groups with 6 replicates of 18 birds per replicate. The diets were formulated with the same supplemental Zn level (80 mg/kg diet) but different amount of the Zn-POS: 0, 200, 400, 600, and 800 mg Zn-POS/kg diet. ZnSO4 was used to adjust to the desired amount of the Zn (80 mg/kg) in the Zn-POS diets. Broilers were fed with the experimental diets for 42 d including the starter (days 1 to 21) and grower (days 22 to 42) phases. Our results showed that dietary supplementation of Zn-POS linearly and quadratically increased (P < 0.05) the average daily gain and gain-to-feed ratio during 22 to 42 d and 1 to 42 d as well as body weight on day 42, whereas reduced (P < 0.05) the sum of mortality and lag abnormalities in broilers on day 42. Besides, serum alkaline phosphatase and copper-zinc superoxide dismutase activities increased (P < 0.05) linearly and quadratically in response to dietary Zn-POS supplemental level on day 42. Dietary Zn-POS supplementation increased Zn accumulation in serum (linear, P < 0.05), liver (linear, P < 0.05), and pancreas (linear and quadratic, P < 0.05). In addition, Zn-POS supplementation linearly and quadratically increased (P < 0.01, P < 0.05, respectively) MT concentrations in liver and pancreas of broilers. Pancreatic mRNA levels of MT, ZnT-1, and ZnT-2 increased (P < 0.05) linearly and quadratically, and the mRNA expression of metal response element-binding transcription factor-1 increased linearly (P < 0.05), in response to dietary Zn-POS supplementation. In conclusion, supplementation of Zn-POS in the diet increases Zn enrichment in the metabolic organs such as liver and pancreas and promotes productive performance in broilers. [ABSTRACT FROM AUTHOR]

• An elite climate resilient cold tolerant Ocimum genotype CIM Shishir developed with linalool rich high essential oil yield. • During cold stress CIM-Shishir demonstrated better adaptive tolerance along with variation in trichomes. • This study reveals adaptive cold stress tolerance mechanisms in CIM-Shishir hybrid variety, elucidating gene expression regulation. • Physiological activity under low temperature stress in new variety demonstrates cold tolerant behavior. • Macropropagation technique was developed in Ocimum for QPM production. The newly released interspecific hybrid variety CIM-Shishir, resulting from a cross between Ocimum basilicum and Ocimum kilimandscharicum claims to be a multicut, lodging resistant, cold tolerant, high essential oil yielding with linalool rich variety. It has a purple-green stem and has a unique feature and advantage of better survival in the winter season than other O. basilicum varieties, illustrating its physiological mechanisms for cold tolerance. In this study, we subjected both the CIM-Shishir variety and a control plant to cold stress to investigate the impact of low temperatures on various physiological, trichome developments, secondary metabolite constitution aspects related to essential oil production, and gene expression. The analysis revealed a significantly higher density and altered morphology of trichomes on the leaf surface of the variety subjected to low temperatures, indicating its adaptation to cold conditions. Furthermore, when comparing the treated plants under low-temperature stress, it was observed that the relative electrolyte leakage and Malondialdehyde (MDA) contents substantially increased in the control in contrast to the CIM-Shishir variety. This finding suggests that CIM-Shishir exhibits superior cold tolerance. Additionally, an increase in proline content was noted in the variety exposed to low temperatures compared to the control. Moreover, the chlorophyll and anthocyanin content gradually increased with prolonged exposure to low-temperature stress in the newly developed variety, indicating its ability to maintain photosynthetic capacity and adapt to cold conditions. The activities of superoxide dismutase (SOD) also increased under low-temperature conditions in the CIM-Shishir variety, further highlighting its cold tolerance behaviour. In our research, we investigated the comprehensive molecular mechanisms of cold response in Ocimum. We analyzed the expression of key genes associated with cold tolerance in two plant groups: the newly developed hybrid variety known as CIM-Shishir Ocimum, which exhibits cold tolerance, and the control plants susceptible to cold climates that include WRKY53, ICE1, HOS1, COR47, LOS15, DREB5, CBF4, LTI6, KIN , and ERD2. These genes exhibited significantly higher expression levels in the CIM-Shishir variety compared to the control, shedding light on the genetic basis of its cold tolerance. The need for climate-smart, resilient high-yielding genotype is of high importance due to varied climatic conditions as this will hit the yield drastically and further to the economic sectors including farmers and many industries that are dependent on the bioactive constituents of Ocimum. [ABSTRACT FROM AUTHOR]

Objective: Genetic contribution is thought to be involved in the pathophysiology of pelvic organ prolapse (POP). We aimed to study the gene expression profiles of the genes HomeoboxA11 (HOXA11), HomeoboxA13 (HOXA13), Collagen Type I (COL1A), Collagen Type III (COL3A), estrogen receptor genes (ESR1 and ESR2) of round (RL) and uterosacral ligaments (USL) in postmenopausal women with uterine prolapse.Study Design: Gene expressions of 32 postmenopausal women with prolapse were analysed according to gene expressions of 8 postmenopausal women without prolapse. Quantitative real-time PCR (qRT-PCR) method was used for the detection of expression levels of the genes. Student's t-Test and Mann-Whitney U test were used for statistical analysis.Results: In the USL specimens of all women with uterine prolapse HOXA13 and ESR1 gene expressions were decreased compared to controls (0.5 fold, p = 0.04 and 0.82 fold, p = 0.04, respectively). In the RL specimens, ESR2 gene expression was decreased 0.7 fold in women with prolapse when compared to controls (p = 0.04). In the USL specimens of women with advanced stages of prolapse (stage ≥3), HOXA13 and COL3A gene expressions were decreased compared to controls (0.44 fold, p = 0.043 and 0.39 fold, p = 0.045, respectively). In the RL specimens, ESR2 gene expression was decreased 0.65 fold in women with prolapse when compared to controls (p = 0.052).Conclusion: The significant decrease in the expression of the genes HOXA13, COL3A in the USL and ESR2 in the RL especially in advanced stages of prolapse, implicate that these gene expressions may play a role in the development of uterine prolapse. [ABSTRACT FROM AUTHOR]

Objective: To Evaluate the viability of cells against exposure to the Methanol Extract of Gladiolus segetum (MEGS) by various colorimetric detection tests (Alamar Blue, WST-1) and the trypan blue exclusion test in Human Leukemia Monocytes THP-1 and Using reverse transcription-polymerase chain reaction assays. Methods: Human THP-1 monocytic cell line was exposed to 25 to 800 μg/mL concentrations of MEGS for 24 h and cellular viability was estimated using Alamar Blue, WST-1 and trypan blue tests. Gene expressions were performed using reverse transcription-polymerase chain reaction assays and the measurement of Caspase-3 enzyme activity. Results: A decrease of viability was observed with a dose-dependent effect of MEGS on THP-1. In addition, a differential expression involved in the different genes tested. Moreover, it has been shown overexpression of casp3 for an exposure to 25 μg/ml and 100 μg/ml of MEGS. Conclusion: Our results show that the MEGS present a toxicity to THP-1 cells, especially with regard to apoptosis processes. [ABSTRACT FROM AUTHOR]

Objectives: Pendimethalin and trifluralin are commonly used in many countries to control broadleaf weeds and grassy weed species because of their inhibitor effects on growth and cell division. In this study, we examined the apoptotic and anti-apoptotic potentials of pendimethalin and trifluralin on A549 human non-small lung cancer cells with several concentrations in vitro. Materials and Methods: The expression levels of apoptosis-related genes BCL-2, BAX, CAS3, CAS9, P53, BIRC, and PPIA were examined using quantitative RT-PCR after 24 h treatment of 1, 10, 50, 100 and 500 μM pendimethalin and trifluralin. Results: The effects of pendimethalin were found more repressive than trifluralin on all studied concentrations. Twenty-four hours' exposure with 100 μM pendimethalin and trifluralin altered the gene expressions, suppressing apoptosis and allowing cancer cells to grow and proliferate. Conclusion: Care should be taken not to exceed the permissible values and residue limits in food during pendimethalin and trifluralin use in order to reduce the possible carcinogenic effects on humans. [ABSTRACT FROM AUTHOR]

Acute myeloid leukemia (AML) is a heterogeneous group of hematopoietic malignancies. Magnet assisted transfection (MATRA) is one of the most effective non-viral transfection methods. We aimed to evaluate the apoptotic effect of resveratrol (RES), MDM2, RUNX3, RB gene expression exchanges and MicroRNA- 150 (miR-150) transfected with MATRA to HL-60 cells. MATRA was used as non-viral vector carrier for miR-150 transfection. IC50 dose of RES was determineted by Fahri et al. Resveratrol and miR-150 transfected cells were performed apoptosis and MDM2, RUNX3, RB gene expression assays in Human promyelocytic leukemia (HL-60) cells. IC50 dose of RES was used as 5 µM. In HL-60 cells, it was found that miR-150, miR150-Resveratrol combination, resveratrol alone induces apoptosis by 6.48, 6.93 and 4.54 fold, respectively, compared to the control cells. Compared to control cells, MDM2, RUNX3, RB, gene expressions decreased (miR-150) 1.7, 1.3 and 1.4 fold, (miR-150-resveratrol) MDM2 expression increased 2.73 fold, RUNX3 and RB expression decreased 6.1, 1.07 fold, respectively. Combination with resveratrol, MDM2, RB decreased 2.9 and 1.4 fold, respectively. Non-viral miR-150 transfection may be effective in leukemia cells, induction of apoptotic effects and gene expression changes, following treatment with resveratrol and miR-150-resveratrol combinations. [ABSTRACT FROM AUTHOR]

Two experiments were designed to investigate the effects of Mn source and concentration on the mRNA expression and enzymatic activities of fatty acid synthase (FAS) and malic enzyme (ME) in cultured primary broiler hepatocytes. In Expt 1, primary broiler hepatocytes were treated with 0 (control), 0·25, 0·50 or 0·75 mmol/l of Mn as inorganic manganese chloride (MnCl2.4H2O) for 24 and 48 h. In Expt 2, primary broiler hepatocytes were incubated with 0 (control), 0·25 or 0·50 mmol/l of Mn as either manganese chloride or Mn–amino acid chelate for 48 h. The mRNA levels and activities of FAS and ME in the hepatocytes were measured in Expts 1 and 2. The results in Expt 1 showed that only at 48 h mRNA expression levels of FAS and ME in the hepatocytes decreased linearly (P<0·001) and quadratically (P<0·02) as supplemental Mn concentrations increased. In Expt 2, compared with the control, Mn supplementation reduced (P<0·01) the activities of FAS, mRNA expression levels of FAS and ME in the hepatocytes, and the efflux of lactic dehydrogenase to the medium. The supplemental Mn at 0·5 mmol/l showed a lower (P<0·03) ME mRNA expression level compared with the Mn group at 0·25 mmol/l. However, Mn source and the interaction between Mn source and concentration had no impacts (P>0·33) on any of the measured cellular parameters. The results suggested that Mn might reduce cell damage and regulate FAS and ME expression at a transcriptional level in primary cultured broiler hepatocytes. [ABSTRACT FROM PUBLISHER]

Objective: Human cytochrome P450 2C9 (CYP2C9), CYP2C19, and CYP2D6 (corresponding to rat CYP2C11, CYP2C6V, and CYP2D3, respectively) are the major enzymes responsible for the metabolism of a wide range of drugs and chemicals. Changes in CYP efficiency are associated with disease susceptibility that can lead to drug toxicity or ineffective therapy. We aimed to examine the effects of lipopolysaccharide (LPS)-induced endotoxemia on gene expressions of hepatic microsomal CYP enzymes in rats. Material and Methods: Male Wistar albino rats were allocated into two subgroups of control and LPS. Saline or LPS (10 mg/kg) of same volume (1 mL/kg) was intraperitoneally (i.p.) injected into rats. After 4 hours, liver tissues were removed. Hepatic mRNA expressions of the CYP enzymes were quantitatively analyzed using real-time polymerase chain reaction (PCR). Results: Hepatic gene expressions of CYP2C11 and CYP2C6V decreased (3.35 and 2.25 fold, respectively) in the endotoxemic rats; however, CYP2D3 expression did not change. Conclusion: Our results revealed that endotoxemia changes CYP2C11- and CYP2C6V-mediated drug metabolism. Therefore, drug dosage must be cautiously ad- justed in the patients with endotoxemia and sepsis. [ABSTRACT FROM AUTHOR]

Toxicity of Cd was tested with the hemocytes of the freshwater crab, Sinopotamon henanense , which were exposed to concentrations of 0, 0.725, 1.450, and 2.900 mg L −1 Cd for 7, 14 and 21 d. We investigated the effects of Cd on the total antioxidant capacity (TAC), and oxidative damage of biomarkers, such as malondialdehyde (MDA), protein carbonyl derivates (PCO), and DNA–protein crosslink (DPC). Transmission electron microscopy (TEM) was applied to assess ultrastructural changes of hemocytes. The mRNA expression levels of prophenoloxidase ( proPO ), lysozyme ( LSZ ), metallothionein ( MT ), and the activity of phenoloxidase (PO) were also determined. Our results showed that TAC was inhibited by Cd, resulting in an increase of MDA contents, PCO contents, and DPC levels in hemocytes, respectively. Ultrastructural observations revealed that chromatin condensation, nucleus deformation, mitochondrial dilation, rough endoplasmatic reticulum (rER) degranulation and secondary or tertiary lysosomes were observed in hemocytes of crabs exposed to Cd. Meanwhile, the expression levels of proPO were down-regulated, while the activity of PO was up-regulated in hemocytes. The expression levels of LSZ and MT were up-regulated to some extent. Our findings suggest these parameters could be used as biomarkers in the monitoring of heavy metal pollution and quantitative risk assessments of pollutant exposure. [ABSTRACT FROM AUTHOR]

We investigated the effects of α-tocopherol on oxidative stress-caused damage caused by copper II oxide nanoparticles (CuO NPs) on Oncorhynchus mykiss gonadal cells (RTG-2) for 24 and 48 h. α-Tocopherol reversed the cell death and alterations in the expressions of genes such as sod1, gpx1a, gpx4b, and igf2 caused by CuO NPs; it also supported the expressions of cat, igf1, and gapdh genes caused by CuO NPs for 24 h and promoted alterations in the expressions of the sod2, gh1 , and igf1 genes for 48 h. Additionally, α-tocopherol reversed the caspase 3/7 activity increased by CuO NPs for 24 h and supported it's decrease for 48 h. α-Tocopherol supported the increase in tail DNA (%) affected by CuO NPs for 24 h and reversed it for 48 h. Therefore, α-tocopherol may have the potential to protect against cellular alterations induced by CuO NPs in a time-dependent manner. • CuO NPs caused cytotoxicity, caspase 3/7 activity and tail DNA in the RTG-2 cells. • Tocopherol reduced cytotoxicity, caspase 3/7 activity induced by CuO NPs. • Tocopherol did not make a significant impact on antioxidant enzyme genes at 48 h. • Tocopherol supported the expressions of growth genes (gh1, igf1) changed by CuO NPs. • Tocopherol decreased the expression of the glycolytic gene compared to CuO NPs. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila can pose a great threat to fish survival. In this study, we investigated the differential immune and redox response in gut-liver axis of hybrid fish (WR) undergoing gut infection. WR anally intubated with A. hydrophila showed severe midgut injury with decreased length-to-width ratios of villi along with GC hyperplasia and enhanced antioxidant activities, but expression profiles of cytokines, chemokines, antibacterial molecules, redox sensors and tight junction proteins decreased dramatically. In contrast, immune-related gene expressions and antioxidant activities increased significantly in liver of WR following gut infection with A. hydrophila. These results highlighted the differential immune regulation and redox balance in gut-liver axis response to bacterial infection. [Display omitted] • Severe midgut injury with GC hyperplasia was observed in WR anally intubated with A. hydrophila. • Suppressions of tight junction molecules were observed in midgut of WR following gut infection. • WR receiving gut infection with A. hydrophila exhibited differential immune and redox response in gut-liver axis. [ABSTRACT FROM AUTHOR]