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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.

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]

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]

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]

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]

"Big omics data" provoke the challenge of extracting meaningful information with clinical benefit. Here, we propose a two-step approach, an initial unsupervised inspection of the structure of the high dimensional data followed by supervised analysis of gene expression levels, to reconstruct the surface patterns on different subtypes of acute myeloid leukemia (AML). First, Bayesian methodology was used, focusing on surface molecules encoded by cluster of differentiation (CD) genes to assess whether AML is a homogeneous group or segregates into clusters. Gene expressions of 390 patient samples measured using microarray technology and 150 samples measured via RNA-Seq were compared. Beyond acute promyelocytic leukemia (APL), a well-known AML subentity, the remaining AML samples were separated into two distinct subgroups. Next, we investigated which CD molecules would best distinguish each AML subgroup against APL, and validated discriminative molecules of both datasets by searching the scientific literature. Surprisingly, a comparison of both omics analyses revealed that CD339 was the only overlapping gene differentially regulated in APL and other AML subtypes. In summary, our two-step approach for gene expression analysis revealed two previously unknown subgroup distinctions in AML based on surface molecule expression, which may guide the differentiation of subentities in a given clinical–diagnostic context. [ABSTRACT FROM AUTHOR]

There are shreds of evidence that osteoarthritis is a risk factor for cardiovascular disease. Regular exercise and ozone therapy independently can prevent such diseases; however, their combined effect was not investigated until now. The current study was aimed to compare the independent and combined effects of aerobic training and ozone therapy on mitochondrial fission 1 protein (FIS1) and mitofusin 2 (MFN2) gene expressions, KI67 protein expression, and percentage collagen deposition in the heart tissue of rats with osteoarthritis. Thirty rats were randomly divided into five groups (six per group), named healthy control, osteoarthritis control, osteoarthritis training, osteoarthritis ozone, and osteoarthritis training + ozone. The interventions were performed according to the group name (aerobic training: run on the treadmill five sessions/week, 30 – 50 min/session for 8 weeks; ozone therapy: 20 μg/mL, once/week, for three weeks). Rat heart tissue was collected 48 h after the last intervention. Data were analyzed using two-way ANOVA and P < 0.05 was considered as significant effect. The results showed that osteoarthritis intervention significantly increased the expression of FIS-1 and MFN-2 genes as well as the percentage of collagen degradation in heart tissue. Osteoarthritis also decreased expression of the heart KI67 protein. Aerobic training and ozone therapy independently positively affect mentioned variables; however, the synergic effect was seen just for the percentage of collagen degradation. In conclusion, the present study confirms effectiveness of the aerobic exercise and ozone therapy concerning research variables and shows that combination of the exercise and ozone therapy had a greater effect than using either alone in improving collagen degradation. [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]

Streptococcus iniae and Aeromonas hydrophila are the two major pathogens of tilapia, and considered a significant problem with huge economic losses in global aquaculture. Infections by these pathogens can be prevented via vaccination. This study measures the expression of immune genes and the subsequent systemic and mucosal immune responses following administration of a feed-based bivalent vaccine against streptococcosis and motile aeromonad septicemia (MAS) in red hybrid tilapia. A total of 1176 healthy red hybrid tilapias were dispersed into four experimental groups with triplicates. Group BI was vaccinated with a bivalent vaccine containing killed S. iniae and A. hydrophila that were mixed into feed. Group MS was similarly vaccinated with a monovalent vaccine containing killed S. iniae, group MA was vaccinated with a monovalent vaccine containing killed A. hydrophila, while group control was fed the normal feed that contained no vaccine. The vaccines were delivered orally at 5% of bodyweight for 5 consecutive days, and the double booster doses were administered in same manner on 14 and 42 days post-vaccination (dpv). Quantitative real-time PCR revealed significant (P < 0.05) upregulation of IL-1β, C-type lysozyme, TNF-α, TGF-β, CD4, MHC-I, MHC-II, and IgT in the spleen, head kidney, and hindgut of the BI and MS groups. The highest expressions of IL-1β, TNF-α, and IgT were observed in the spleen (3.91-fold), head kidney (3.61-fold), and hindgut (8.85-fold) of the BI fish. Lysozyme activity increased significantly (P < 0.05) on days 21, 35, 63, and 105 in BI group, while phagocytic activity was significantly (P < 0.05) higher on days 7, 63, and 77 in BI group than other vaccinated groups. The current experiment showed the upregulation of immune genes in systemic and mucosal tissues of immunized fish with subsequent higher immune activities. Thus, the feed-based bivalent vaccine was able to stimulate the innate and adaptive immune responses against streptococcosis and MAS. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is one of the most harmful phytopathogens. It causes big problems for potatoes and other important crops around the world. Nanoclays have been extensively studied for various biomedical applications. However, reports on their interactions with phytopathogens, particularly viral infections, are still limited. In this study, the protective activity of Egyptian nanoclay (CE) and standard nanoclay (CS) against PVY was evaluated on potato (Solanum tuberosum L.) plants. Their physicochemical and morphological properties were examined with scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), and energy dispersive spectrometer (EDS). SEM and TEM analyses revealed that CE has a spherical and hexagonal structure ranging from 20 to 80 nm in size, while CS has boulder-like and tubular structures of about 320 nm in size. FTIR and EDS showed that both nanoclay types have different functional groups and contain many vital plant nutrients that are necessary for every stage and process of the plant, including development, productivity, and metabolism. Under greenhouse conditions, a 1% nanoclay foliar application enhanced potato growth, reduced disease symptoms, and reduced PVY accumulation levels compared with non-treated plants. Significant increases in levels of antioxidant enzymes (PPO and POX) and considerable decreases in oxidative stress markers (MDA and H2O2) were also reported. Moreover, a significant increase in the transcriptional levels of defense-related genes (PAL-1, PR-5, and CHI-2) was observed. All experiment and analysis results indicate that the CE type is more effective than the CS type against PVY infection. Based on these results, the foliar applications of nanoclay could be used to manage plant viral infections in a way that is both effective and environmentally friendly. To our knowledge, this is the first report of the antiviral activity of the foliar application of nanoclay against PVY infection. [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]

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and developmentspecific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants. [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]

Vibrio parahaemolyticus is a common pathogen in aquatic products, such as shellfishes. Laboratory-based simulated studies demonstrated that V. parahaemolyticus can tolerate high hydrostatic pressure (HHP) up to 20 MPa. However, the molecular mechanisms of high-pressure adaptation remain unclear. Herein, we analyzed the physiological changes and transcriptomic responses of V. parahaemolyticus ATCC 17,802 under HHP conditions to determine the possible survival mechanisms. Under HHP conditions, the morphology of V. parahaemolyticus was notably changed exhibiting the coccoid microbial cells. The transcriptome analysis revealed that there were 795 differentially expressed genes (DEGs) under the 20 MPa condition, including 406 upregulated DEGs and 389 downregulated DEGs. Most of the downregulated DEGs encoded proteins related to energy metabolism, such as citrate synthase (gltA), pyruvate kinase (pyk), and glyceraldehyde-3-phosphate dehydrogenase (gapA). Many of the upregulated DEGs encoded proteins related to adhesion and virulence factors, such as RNA polymerase σ factor (rpoE), L-threonine 3-dehydrogenase, and bacterial nucleotide signal c-di-GMP (WU75_RS02745 and WU75_RS07185). In our proposed mechanism model, V. parahaemolyticus responds to HHP stress through RNA polymerase σ factor RpoE. These findings indicate that V. parahaemolyticus cells may adopt a complex adaptation strategy to cope with HHP stress. Key points: •The transcriptomic response of Vibrio parahaemolyticus under HHP conditions was studied for the first time. •V. parahaemolyticus may adopt a complex adaptation strategy to cope with HHP stress. •ToxRS and RpoE played an important role in sensing and responding the HHP signal. [ABSTRACT FROM AUTHOR]

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Caffeine, Toxicant Responsive Genes and PD In Vivo Study In 2008, Singh and team investigated the roles of nicotine and caffeine on toxicant responsive gene expression in MPTP-induced PD [[48]]. Neuroprotective Mechanisms of Caffeine x Gene Interaction for the Amelioration of PD The promising molecular integration linking caffeine, gene expressions and PD is currently under investigation. Keywords: caffeine; coffee; complementary medicine; gene expressions; nutrigenomic; Parkinson's disease EN caffeine coffee complementary medicine gene expressions nutrigenomic Parkinson's disease N.PAG N.PAG 15 08/29/22 20220801 NES 220801 1. Heavy caffeine intake with CC genotype reduced PD risk by 47%, while having GRIN2A rs4998386 T allele with light caffeine intake showed a trend of protectiveness, and the combination of heavy caffeine intake and GRIN2A rs4998386 TC genotype was associated with an overall 64% PD risk reduction. [Extracted from the article]

Maize is a cold-sensitive crop, and it exhibits severe retardation of growth and development when exposed to cold snaps during and right after seedling emergence. Although different agronomic, physiological, and molecular approaches have been tried to overcome the problems related to cold stress in recent years, the mechanisms causing cold resistance in maize are still unclear. Screening and breeding of varieties for cold resistance may be a sustainable option to boost maize production under low-temperature environments. Herein, seedlings of 39 different maize genotypes were treated under both 10 °C low temperature and 22 °C normal temperature conditions for 7 days, to assess the changes in seven growth parameters, two membrane characteristics, two reactive oxygen species (ROS) levels, and four antioxidant enzymes activities. The changes in ten photosynthetic performances, one osmotic substance accumulation, and three polyamines (PAs) metabolisms were also measured. Results indicated that significant differences among genotypes, temperature treatments, and their interactions were found in 29 studied traits, and cold–stressed seedlings were capable to enhance their cold resistance by maintaining high levels of membrane stability index (66.07%); antioxidant enzymes activities including the activity of superoxide dismutase (2.44 Unit g−1 protein), peroxidase (1.65 Unit g−1 protein), catalase (0.65 μM min−1 g−1 protein), and ascorbate peroxidase (5.45 μM min−1 g−1 protein); chlorophyll (Chl) content, i.e., Chl a (0.36 mg g−1 FW) and Chl b (0.40 mg g−1 FW); photosynthetic capacity such as net photosynthetic rate (5.52 μM m−2 s−1) and ribulose 1,5–biphosphate carboxylase activity (6.57 M m−2 s−1); PAs concentration, mainly putrescine (274.89 nM g−1 FW), spermidine (52.69 nM g−1 FW), and spermine (45.81 nM g−1 FW), particularly under extended cold stress. Importantly, 16 traits can be good indicators for screening of cold–resistant genotypes of maize. Gene expression analysis showed that GRMZM2G059991, GRMZM2G089982, GRMZM2G088212, GRMZM2G396553, GRMZM2G120578, and GRMZM2G396856 involved in antioxidant enzymes activity and PAs metabolism, and these genes may be used for genetic modification to improve maize cold resistance. Moreover, seven strong cold–resistant genotypes were identified, and they can be used as parents in maize breeding programs to develop new varieties. [ABSTRACT FROM AUTHOR]

Carbendazim (CBZ) is one of the most common fungicides used to fight plant fungal diseases, otherwise, it leaves residue on fruits, vegetables, and soil that contaminate the environment, water, animal, and human causing serious health problems. Several studies have reported the reproductive and endocrine pathological disorders induced by CBZ in several animal models, but little is known about its neurotoxicity. So that, the present study aimed to explain the possible mechanisms of CBZ induced neurotoxicity in rats. Sixty male Wistar rats were divided into 4 groups (n = 15). Group (1) received normal saline and was kept as the negative control group, whereas groups (2, 3, 4) received CBZ at 100, 300, 600 mg/kg b.wt respectively. All rats received the aforementioned materials daily via oral gavage. Brain tissue samples were collected at 7, 14, 28 days from the beginning of the experiment. CBZ induced oxidative stress damage manifested by increasing MDA levels and reducing the levels of TAC, GSH, CAT in some brain areas at 14 and 28 days. There were extensive neuropathological alterations in the cerebrum, hippocampus, and cerebellum with strong caspase-3, iNOS, Cox-2 protein expressions mainly in rats receiving 600 mg/kg CBZ at each time point. Moreover, upregulation of mRNA levels of NF-κB, TNF-α, IL-1B genes and downregulation of the transcript levels of both AchE and MAO genes were recorded in all CBZ receiving groups at 14 and 28 days especially those receiving 600 mg/kg CBZ. Our results concluded that CBZ induced dose- and time-dependent neurotoxicity via disturbance of oxidant/antioxidant balance and activation of NF-κB signaling pathway. We recommend reducing the uses of CBZ in agricultural and veterinary fields or finding other novel formulations to reduce its toxicity on non-target organisms and enhance its efficacy on the target organisms. [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]

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

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]

Hickory (Carya cathayensis) is a critical tree species of the genus Carya from the Juglandaceae family that contains nutrient-rich nuts. Due to large-scale soil degradation, the pests and diseases of hickory are becoming more and more serious. Thaumatin-like proteins (TLPs) are vital proteins involved in the complex defense process of plant pathogens. In this study, 40 CcTLP genes were identified genome-widely and phylogenetically grouped into three subfamilies. The sequence of CcTLPs had a conservative pattern, such as eight stable disulfide bonds, REDDD, and G-X-[GF]-X-C-X-T-[GA]-D-C-X(1,2)-G-X-(2,3)-C structure. In total, 57 cis -elements related to stress-responsive, light-responsive, phytohormone-responsive, and plant-responsive were discovered. Under salicylate (SA), methyl jasmonate (MeJA), and ethephon (ETH) treatments, the expressions of CcTLP28, CcTLP29, CcTLP30, CcTLP31, CcTLP32, CcTLP33, CcTLP37, CcTLP38 , and CcTLP39 had different patterns. This is an indication that most of the TLP genes were upregulated by SA and downregulated by MeJA. Notably, seven TLP genes were significantly upregulated under the Botryosphaeria dothidea inoculation, especially CcTLP31 , with an over 20-fold change. Nine genes were shown by subcellular localization analysis to be located at the plasma membrane and cytoplasm. The knowledge of the disease-resistant function of the CcTLP family in hickory is promoted by these results. A foundation reference for the molecular breeding of this plant in the future is provided by our findings. [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.

Hickory (Carya cathayensis) is a critical tree species of the genus Carya from the Juglandaceae family that contains nutrient-rich nuts. Due to large-scale soil degradation, the pests and diseases of hickory are becoming more and more serious. Thaumatin-like proteins (TLPs) are vital proteins involved in the complex defense process of plant pathogens. In this study, 40 CcTLP genes were identified genome-widely and phylogenetically grouped into three subfamilies. The sequence of CcTLPs had a conservative pattern, such as eight stable disulfide bonds, REDDD, and G-X-[GF]-X-C-X-T-[GA]-D-C-X(1,2)-G-X-(2,3)-C structure. In total, 57 cis-elements related to stress-responsive, light-responsive, phytohormone-responsive, and plant-responsive were discovered. Under salicylate (SA), methyl jasmonate (MeJA), and ethephon (ETH) treatments, the expressions of CcTLP28, CcTLP29, CcTLP30, CcTLP31, CcTLP32, CcTLP33, CcTLP37, CcTLP38, and CcTLP39 had different patterns. This is an indication that most of the TLP genes were upregulated by SA and downregulated by MeJA. Notably, seven TLP genes were significantly upregulated under the Botryosphaeria dothidea inoculation, especially CcTLP31, with an over 20-fold change. Nine genes were shown by subcellular localization analysis to be located at the plasma membrane and cytoplasm. The knowledge of the disease-resistant function of the CcTLP family in hickory is promoted by these results. A foundation reference for the molecular breeding of this plant in the future is provided by our findings.

Cotton is one of the most important natural fiber crops. 20% of cultivated land worldwide and 33% of irrigated farmland is subject to salinity, and this area is increasing by 10% annually. It is known that salt stress has a negative effect on all main physiological and phenotypic parameters of cotton, including the main trait - fiber quality. To reduce negative effects of salt stress on cotton, two complementary approaches are used: creation of salt-tolerant varieties and improvement of agrotechnological methods using different biostimulants. In this connection the effect of biostimulants on fiber quality parameters and expression of gens responsible for development of this trait was studied. Our studies have shown that the use of microbial fertilizers has a positive effect on fiber quality parameters. In this case the preparation Rizokom-1 had the greatest positive effect. This preparation increased one of the most important fiber quality parameters - fiber length. Besides, Rizokom-1 maximally increases fiber strength of cotton without reduction of its homogeneity index. The morphological data were confirmed by the results of expression of corresponding genes. Thus, Rizokom-1 and Micro-1 preparations significantly affected the expression level of genes responsible for synthesis of sugars (SPS and SuSy) and unsaturated fatty acids (FAD2), as well as for synthesis of cell wall polysaccharides (CESA2). The mechanism of action of the preparation Hosyl on fiber quality is mainly due to its effect on the expression level of genes regulating hormone biosynthesis involved in cotton fiber development.

Pesticides commonly occur as mixtures in an aqueous environment, causing deleterious effects on human health and the environment. However, the mechanism underlying the combined effects on aqueous organisms remains largely unknown, especially at low concentrations. In the current study, we inspected the interactive toxicity of tebuconazole (TEB), a triazole fungicide, and bifenthrin (BIF), a pyrethroid insecticide, to zebrafish (Danio rerio) using various toxicological assays. Our data revealed that the 96 h-LC50 (lethal concentration 50) values of BIF to fish at different life periods (embryonic, larval, juvenile, and adult periods) ranged from 0.013 (0.011–0.016) to 0.41 (0.35–0.48) mg a.i. L−1, which were lower than that of TEB ranging from 1.1 (0.88–1.3) to 4.8 (4.1–5.7) mg a.i. L−1. Combination of TEB and BIF induced synergetic acute toxicity to embryonic fish. Activities of T-SOD, POD, and GST were distinctly altered in most individual and joint administrations. Expressions of 16 genes associated with oxidative stress, cellular apoptosis, immune system, and endocrine system at the mRNA level were evaluated, and the information revealed that embryonic zebrafish were impacted by both individual compounds and their combinations. Six genes (cas9, P53, gr, TRα, IL-8, and cxcl-clc) exhibited greater changes when exposed to pesticide mixtures. Therefore, the joint effects induced by the pesticides at low concentrations should be considered in the risk assessment of mixtures and regulated as priorities for mixture risk management in the aqueous ecosystem. More research is needed to identify the threshold concentrations of the realistic pesticide mixtures above which synergistic interactions occur.

The biological contents of the white button mushroom including(lectin and polysaccharides) were extracted from its dried fruiting bodies and purified through Q-Sepharose column which was considered a strong anion for adsorption of lectin with high performance. The purified lectin has a great hemagglutinating activity (HA) that was considered a specific feature for lectin and inhibited by GlcNAc which was a specific binding sugar receptor. In this study, we reported that lectin agglutinated all blood groups without specificity, was active below 70 and 80°C and it had no activity at that temperature degrees. The best pH media for HA within range (6 to 9) for 24hr the purified lectin had molecular weight 16KDa that was determined by SDS PAGE ELECTROPHORESIS. Gene expressions by RT-PCR of the white button mushroom showed that the lectin upregulated Bax (pro-apoptotic gene). Lectin had apoptotic activity on HepG-2 cell line. The cell toxicity assay showed that mushroom's lectin has high toxicity on malignant cells with very low toxicity on WI-38 (normal cells). White button mushroom lectin had antiproliferative & toxic effects on HepG-2 with IC50; 41.90 ug/ml while had very weak toxicity on WI-38(normal cells) with IC50 (98.54 ug/ml). The lectin of edible mushroom can be utilized in human eating regimens and recommended for malignancy with a safety margin in clinical pathological research with different concentrations starting from 200g fruiting bodies mushroom & 98.44 ug/ml lectin concentration. [ABSTRACT FROM AUTHOR]

Lycoris longituba is an important ornamental and medicinal plant and contains various Amaryllidaceae alkaloids such as galanthamine (GAL), lycorine (LYC), and lycoramine (LYCM), which have been reported to exhibit medicinal values. However, the effects of light quality on L. longituba are unknown. The present study aimed to explore the effects of different light emitting diode (LED) light quality on growth, physiological characteristics, and alkaloid accumulations in the seedlings. Lycoris longituba seedlings were cultured under different ratios of blue and red LEDs. The results showed that compared to CK, RB (1:2) treatment improved growth, biomass accumulation, and the synthesis of photosynthetic pigments and reduced membrane lipid peroxidation. Blue light increased GAL, LYC, and LYCM contents which were 2.45-, 1.74-, and 1.92-fold higher than CK, respectively. Most of Amaryllidaceae alkaloids biosynthetic pathway genes including PAL, C4H, NBS, TYDC, OMT, and CYP96T1 were upregulated under B treatment. In general, RB (1:2) was the optimal light quality condition for the growth of L. longituba seedlings. B treatment could promote the accumulation of alkaloids and related gene expressions. This study has established the theoretical foundation and technical support for the use of LED light quality control technology in the production of high-quality L. longituba seedlings. [ABSTRACT FROM AUTHOR]

Remedies toward sustainable aquaculture rely upon research that unveils the molecular mechanisms behind host immunity and their interactions with pathogens. Antiviral defense is a major innate immune response in fish. The antiviral protein GCHV-induced gene-2 (Gig2), a member of the interferon-stimulated gene (ISG), was identified and characterized from rockfish (Sebastes schlegelii). Gig2 exists in two isoforms, namely, SsGig2-I1 and SsGig2-I2 , in rockfish with lengths of 163 and 223 bp, respectively. Bioinformatic analysis indicated the availability of poly (ADP-ribose) polymerase domain in both proteins, and 51.3% identity and 71.3% similarity between both isoforms were observed. The basal expression pattern revealed the highest tissue-specific expression in rockfish gills for both isoforms. The immune challenge experiment disclosed a distinctive and strong expression of each transcript in the presence of poly I:C. Both isoforms are localized in the endoplasmic reticulum. Interferon (IFN) pathway gene analysis revealed no significant upregulation of IFN related genes. Viral hemorrhagic septicemia virus (VHSV) gene expression analysis revealed strong downregulation of viral transcripts after 48 h of infection in the presence of Gig2 isoforms. Collectively, these results indicate the protective role of Gig2 in rockfish against VHSV infection and help broaden our understanding of the innate immunity of fish. • SsGig2-I1 and SsGig2-I2 were cloned and characterized. • SsGig2-I1 and SsGig2-I2 showed tissue-specific expression in the gill of rockfish. • Poly(I:C) stimulation up regulated both isoforms in the blood. • SsGig2-I1 and SsGig2-I2 overexpression significantly inhibited the replication of VHSV. [ABSTRACT FROM AUTHOR]

Cancer classification using gene expressions is extremely challenging given the complexity and high dimensionality of the data. Current classification methods typically rely on samples collected from a single tissue type and perform a prerequisite of gene feature selection to avoid processing the full set of genes. These methods fall short in taking advantage of genome-wide next generation sequencing technologies which provide a snapshot of the whole transcriptome rather than a predetermined subset of genes. We propose a deep learning framework for cancer diagnosis by developing a multi-tissue cancer classifier based on whole-transcriptome gene expressions collected from multiple tumor types covering multiple organ sites. We introduce a new Convolutional Neural Network architecture called Gene eXpression Network (GeneXNet), which is specifically designed to address the complex nature of gene expressions. Our proposed GeneXNet provides capabilities of detecting genetic alterations driving cancer progression by learning genomic signatures across multiple tissue types without requiring the prerequisite of gene feature selection. Our model achieves 98.9% classification accuracy on human samples representing 33 different cancer tumor types across 26 organ sites. We demonstrate how our model can be used for transfer learning to build classifiers for tumors lacking sufficient samples to be trained independently. We introduce visualization procedures to provide biological insight on how our model is performing classification across multiple tumors.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study’s findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions.

Endometriosis is a common, benign, and hormone-dependent gynaecological disorder that displays altered immunoinflammatory profiles. Myeloid-derived suppressor cells (MDSCs) suppressed immunosurveillance in endometriosis in human and mouse model. Receptor tyrosine kinase inhibitor Sunitinib can induce MDSC apoptosis and suppress the progression of cancer. However, the effects of Sunitinib on MDSCs in endometriosis and the underlying mechanism are not clear. In this study, we employed an animal study of the endometriosis model in mice for treatment of Sunitinib. After syngeneic endometrium transplantation and treatment, endometriotic lesion volume, weight, and histology were compared. Peritoneal fluid, peripheral blood, and bone marrow MDSC subsets and their molecular signaling were monitored by flow cytometry. Peritoneal cytokines were assayed by ELISA. The gene expression profiles of isolated CD11b+Ly6G+Ly6Clo cells were studied by RNA sequencing. We found that Sunitinib significantly decreased the endometriotic lesion size and weight after 1 and 3 weeks, and decreased p-STAT3 activation in MDSCs after 1 week of treatment. In the first week, Sunitinib specifically increased the G-MDSC population in peritoneal fluid but the isolated CD11b+Ly6G+Ly6Clo MDSCs after Sunitinib treatment were presented as mature polynuclear MDSCs, while the control group had immature mononuclear MDSCs. Importantly, we found Sunitinib differentially suppressed gene expressions of immunosuppressive function and differentiation in peritoneal G-MDSCs. Apelin signaling pathway associated genes and inflammation related genes were upregulated, and amino acid metabolism regulator genes were downregulated in bone marrow G-MDSCs. For endometriotic lesions, the PPARG gene governing glucose metabolism and fatty acid storage, which is important for the development of endometriosis was upregulated. In conclusion, Sunitinib inhibited endometriotic lesions, by promoting peritoneal fluid MDSCs maturation and inhibiting the immunosuppressive function. These findings suggest that Sunitinib changed the immune microenvironment and inhibited the development of endometriosis, which has potential therapeutic effects as novel immunotherapy to promote MDSCs maturation, differentiation, and metabolism for the treatment of endometriosis.

The modified Cholesky decomposition (MCD) is a powerful tool for estimating a covariance matrix. The regularization can be conveniently imposed on the linear regressions to encourage the sparsity in the estimated covariance matrix to accommodate the high-dimensional data. In this paper, we propose a Cholesky-based sparse ensemble estimate for covariance matrix by averaging a set of Cholesky factor estimates obtained from multiple variable orderings used in the MCD. The sparse estimation is enabled by encouraging the sparsity in the Cholesky factor. The theoretical consistent property is established under some regular conditions. The merits of the proposed method are illustrated through simulation and a maize genes data set. [ABSTRACT FROM AUTHOR]

Endometriosis is a common, benign, and hormone-dependent gynaecological disorder that displays altered immunoinflammatory profiles. Myeloid-derived suppressor cells (MDSCs) suppressed immunosurveillance in endometriosis in human and mouse model. Receptor tyrosine kinase inhibitor Sunitinib can induce MDSC apoptosis and suppress the progression of cancer. However, the effects of Sunitinib on MDSCs in endometriosis and the underlying mechanism are not clear. In this study, we employed an animal study of the endometriosis model in mice for treatment of Sunitinib. After syngeneic endometrium transplantation and treatment, endometriotic lesion volume, weight, and histology were compared. Peritoneal fluid, peripheral blood, and bone marrow MDSC subsets and their molecular signaling were monitored by flow cytometry. Peritoneal cytokines were assayed by ELISA. The gene expression profiles of isolated CD11b+Ly6G+Ly6Clo cells were studied by RNA sequencing. We found that Sunitinib significantly decreased the endometriotic lesion size and weight after 1 and 3 weeks, and decreased p-STAT3 activation in MDSCs after 1 week of treatment. In the first week, Sunitinib specifically increased the G-MDSC population in peritoneal fluid but the isolated CD11b+Ly6G+Ly6Clo MDSCs after Sunitinib treatment were presented as mature polynuclear MDSCs, while the control group had immature mononuclear MDSCs. Importantly, we found Sunitinib differentially suppressed gene expressions of immunosuppressive function and differentiation in peritoneal G-MDSCs. Apelin signaling pathway associated genes and inflammation related genes were upregulated, and amino acid metabolism regulator genes were downregulated in bone marrow G-MDSCs. For endometriotic lesions, the PPARG gene governing glucose metabolism and fatty acid storage, which is important for the development of endometriosis was upregulated. In conclusion, Sunitinib inhibited endometriotic lesions, by promoting peritoneal fluid MDSCs maturation and inhibiting the immunosuppressive function. These findings suggest that Sunitinib changed the immune microenvironment and inhibited the development of endometriosis, which has potential therapeutic effects as novel immunotherapy to promote MDSCs maturation, differentiation, and metabolism for the treatment of endometriosis. [ABSTRACT FROM AUTHOR]

In the present study and under greenhouse conditions, tomato plants cv. Albium, grown in potted soil inoculated with the early blight fungus A. solani, were treated with abscisic acid (ABA), salicylic acid (SA), and potassium silicate (PS) abiotic inducers, singly, and in combination with the biotic inducer Trichoderma harzianum. The different tested inducers significantly decreased the intensity (severity) of early blight disease on tomato, as well as some growth characteristics, photosynthetic capacity, defense-related enzymes and expression analysis of the PR1, PR3 and PR5 genes using Real Time-q PCR. PS+ Trichoderma showed the lowest disease intensity, followed by ABA+ Trichoderma, and Trichoderma treatment had the highest disease intensity when compared to untreated inoculated control. PS + Trichoderma, ABA+ Trichoderma, and SA+ Trichoderma were also the most effective for the best growth characteristics (fresh shoot, dry shoot, fresh root, dry root weight, and total fruits weight/plant). Photosynthetic pigment content was significantly increased with all treatments by chemical inducer and T. harzianum compared with A. solani treatment. PS + Trichoderma was the most effective and significantly enhanced chlorophyll "A" and chlorophyll "B"content comparing with the A. solani treatment, while, the highest level of carotene content was observed with alt+ABA+ Trichoderma treatment at 2days post inoculation. Peroxidase (POD), polyphenol oxidase (PPO) and Phenylalanine Ammonia-Lyase (PAL) enzymes activity and PR1, PR2 and PR5 gene expressions were significantly increased in all treatments with chemical inducer comparing with the treatment by A.solani, In addition to the treatment by chemical inducer combined with Trichoderma were the most effective compared with chemical inducer alone. The maximum POD, PAL activities and PR1gene expression were observed with alt+PS + Trichoderma followed by alt+ABA+ Trichoderma while, PR2, PR5 gene expressions and POD activity reached the highest level with alt+PS+ Trichoderma followed by alt+SA+ Trichoderma and alt+ABA+ Trichoderma. Trichoderma was of the highest rate of the number of cfu in treatment with alt+PS+ Trichoderma with cfu was 5.9 x10, while the number of cfu in treatment with alt+ABA + Trichoderma was 3.77 x107 and the treatment with alt+SA + Trichoderma was 3.68 x107. [ABSTRACT FROM AUTHOR]

Recognizing the cancer genes from the microarray dataset is considered as the most essential research topic in bioinformatics and computational biology domain. Microarray dataset represents the state of each cell at the molecular level which is identified as the important diagnostic tool in medical field. Analyzing the microarray data may provide a huge support for cancer gene classification. Therefore recently a number of artificial intelligence and machine learning techniques are developed which utilize the microarray data for distinguishing the cancer and non-cancer cells. But still now these techniques does not achieved a satisfactory performance. Therefore, an efficient technique that provides a crisp output for cancer classification is required. To overcome such defect, an enhanced ANFIS (EANFIS) method is used in this proposed architecture for classifying the cancer genes. The convergence time of ANFIS gets increased during learning process, therefore to avoid such issue the Manta ray foraging optimization (MaFO) algorithm is hybrid along with ANFIS which improves the overall classification performance. The data given as an input to the classification process is pre-processed at the initial phase using the Ensemble Kalman Filter (EnKF) technique. After pre-processing, the genes having similar properties are clustered using an adaptive density-based spatial clustering with noise (ADBSCAN) clustering technique. Finally, the performance of proposed enhanced ANFIS is evaluated using the precision, accuracy, f-measure, recall, sensitivity, and specificity metrics. Further, the clustering based performance evaluation is also carried out using the cluster index metrics. Finally, the comparison with the state-of-the-art techniques is also performed to show the effectiveness of proposed approach. [ABSTRACT FROM AUTHOR]

BACKGROUND: The diamondback moth (Plutella xylostella) is one of the most destructive lepidopteran pests on cruciferous vegetables. However, resistance has emerged to current chemical and biological insecticides used for P. xylostella control, indicating the necessity of screening new targets on P. xylostella, and finding new insecticides against P. xylostella. In particular, octopamine receptors are representative G protein‐coupled receptors found only in invertebrates and are potential targets for identifying novel insecticides. RESULTS: A β‐adrenergic‐like octopamine receptor gene (PxOA2B1) was cloned, and its pharmacological characteristics in P. xylostella were studied. The results demonstrated that octopamine could activate the PxOA2B1 receptor, with a half‐maximal effective concentration (EC50) of 49.5 nm. Amitraz, an insecticide and acaricide, and its metabolite (N‐2,4‐dimethylphenyl‐N′‐methylformamidine; DPMF) were also found to act as PxOAB1R agonists. We synthesized phenyl imidazolidin‐2‐one derivatives 3a–h using DPMF as the lead compound, and compounds 3a–h showed similar antagonist activities as phentolamine, mianserin and chlorpromazine. In particular, 3d, with an EC50 of 25.2 nm, showed very similar antagonist activity to mianserin. CONCLUSION: This research found that PxOAB1R might be a potential target for P. xylostella control. Phenyl imidazolidin‐2‐ones could be novel potential antagonists targeted at octopamine receptors and would be useful tools for the design and development of novel insecticides. © 2021 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Caffeine is one of the predominant dietary components and psychostimulants present in coffee, a widely appreciated beverage. Corroborating epidemiological and laboratory evidence have suggested an inverse association between the dietary intakes of coffee and the risk of Parkinson’s Disease (PD). Growing attention has been paid to the impact of coffee consumption and genetic susceptibility to PD pathogenesis. Coffee is believed to play prominent roles in mediating the gene makeup and influencing the onset and progression of PD. The current review documents a current discovery of the coffee × gene interaction for the protective management of PD. The evidence underlying its potent impacts on the adenosine receptors (A2AR), estrogen receptors (ESR), heme oxygenase (HO), toxicant responsive genes, nitric oxide synthase (NOS), cytochrome oxidase (Cox), familial parkinsonism genetic susceptibility loci, bone marrow stromal cell antigen 1 (BST1), glutamate receptor gene and apolipoprotein E (APOE) genotype expressions is outlined. Furthermore, the neuroprotective mechanisms of coffee for the amelioration of PD are elucidated.

Alpha and beta-adrenoceptors (ADR-α1, 2, and β2) play a regulatory role in the folliculogenesis and steroidogenesis in the ovarian follicles. This study aimed to measure these adrenoceptors mRNA and its protein levels in cumulus cells (CCs) culture of poor ovarian reserve (POR) and polycystic ovarian syndrome (PCOS) infertile women (IVF candidate) and the effect of clonidine treatment at CCs culture. This case/control study was conducted in 2017 includes a control (donation oocytes) and two studies (PCO and POR) groups. The ovulation induction drugs were prescribed in all groups. After the oocyte puncture, the follicular fluid was collected and CCs were isolated were cultured. RNA was extracted and cDNA was synthesized and designed the primer for the ADR-α1, 2 and ADR-β2 gene expression. The protein levels were investigated by Western Blot. The results showed a high level of three adrenergic expressions in PCO women compared to the control group (p-value <.001), which can be reduced by clonidine. POR group showed a significant decrease in the gene expression of ADR-α1 (p-value =.004) and ADR-α2 (p-value =.003) compared to the control group and clonidine treatment had no effect. The significant increase of three adrenoceptors gene expression and protein levels in CCs culture indicate to the hyperactivity of the ovarian sympathetic nervous system at the receptor levels in women with PCOS, and clonidine confirmed it by reducing this expression. In POR women, the reduction of ADR-α1, 2 expressions maybe lead to the aging process in the ovary. [ABSTRACT FROM AUTHOR]

Introduction: Cervical cancer is the fourth most common cancer in women. The risk factors for cervical cancer include human papillomavirus (HPV) infection, age, smoking, number of pregnancies, use of oral contraceptives, and diet. However, long-term HPV infection appears to be the main risk factor for developing cervical cancer. This in-silico analysis aims to identify the expression network of proteins and the miRNAs that play a role in the development of HPV-induced cervical cancer., Methods: The critical proteins and miRNAs were extracted using the DisGeNET and miRBase databases. String and Gephi were applied to the network analysis. The GTEx web tool was utilized to Identify tissue expression levels. The Enrichr website was used to explore the molecular function and pathways of found genes., Results: Ten proteins, TP53, MYC, AKT1, TNF, IL6, EGFR, STAT3, CTNNB1, ESR1, and JUN, were identified as the most critical shared gene network among cervical cancer and HPV. Seven miRNAs were found, including hsa-mir-146a, hsa-mir-27, hsa-mir-203, hsa-mir-126, hsa-mir-145, hsa-mir-944, and hsa-mir-93, which have a common expression in cervical cancer and HPV., Conclusion: Overall, the gene network, including TP53, MYC, AKT1, TNF, IL6, EGFR, STAT3, CTNNB1, ESR1, and JUN, and Also, hsa-mir-145, hsa-mir-93, hsa-mir-203, and hsa-mir-126 can be regarded as a gene expression pathway in HPV-induced cervical cancer., Competing Interests: The authors declare no conflict of interest., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc.)

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn’s disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

10H-1,9-diazaphenothiazine was obtained in the sulphurisation reaction of diphenylamine with elemental sulphur and transformed into new 10-substituted derivatives, containing alkyl and dialkylaminoalkyl groups at the thiazine nitrogen atom. The 1,9-diazaphenothiazine ring system was identified with advanced 1H and 13C NMR techniques (COSY, NOESY, HSQC and HMBC) and confirmed by X-ray diffraction analysis of the methyl derivative. The compounds exhibited significant anticancer activities against the human glioblastoma SNB-19, melanoma C-32 and breast cancer MDA-MB-231 cell lines. The most active 1,9-diazaphenothiazines were the derivatives with the propynyl and N, N-diethylaminoethyl groups being more potent than cisplatin. For those two compounds, the expression of H3, TP53, CDKN1A, BCL-2 and BAX genes was detected by the RT-QPCR method. The proteome profiling study showed the most probable compound action on SNB-19 cells through the intrinsic mitochondrial pathway of apoptosis. The 1,9-diazaphenotiazine system seems to be more potent than known isomeric ones (1,6-diaza-, 1,8-diaza-, 2,7-diaza- and 3,6-diazaphenothiazine).

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. • Black mulberry increased the growth performance of Nile Tilapia. • Black mulberry improved the innate immune responses of fish. • Black mulberry significantly up-regulated the immune and antioxidant related genes of fish. • Black mulberry enhanced the protection of Nile Tilapia against Aeromonas veronii. [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]