Fold Change In Expression Research Articles

Neurotoxicity associated with oxidative stress and inflammasome gene expression induced by allethrin in SH-SY5Y cells.

Pyrethroids, including allethrin, have largely been used as commercial insecticides. The toxicity of allethrin is little known, but it is assumed that, as occurs with other pyrethroids, it could cause alterations of the nervous system and pose both occupational and non-occupational health hazards. To evaluate the neurotoxicity of allethrin we used the MTT assay of SH-SY5Y neuroblastoma cells to determine cell viability. Dose-dependent reductions of cell viability served to compare the vehicle-group and the IC50 for allethrin, which was 49.19μM. ROS production increased significantly at concentrations of 10-200μM of allethrin, and NO levels were significantly increased by the effect of allethrin at a minimum concentration of 50μM. Lipid peroxidation increased by the effect of allethrin at concentrations of 25, 50, 100, and 200μM. Caspase 3/7 activity was induced by allethrin concentrations of 50, 100, and 200μM. Here, we suggest that allethrin might affect the inflammasome complex (Caspase-1, NLRP3, and PYDC1) and apoptosis (Bax and Bcl-2) gene expression by mRNA fold change expression levels shown in Caspase-1 (2.46-fold), NLRP3 (1.57-fold), PYDC1 (1.48-fold), and Bax (2.1-fold). These results demonstrated that allethrin induced neurotoxicity effects on SH-SY5Y cells through activation of inflammasome pathways, cell death, and oxidative stress.

An SNN retrocopy insertion upstream of GPR22 is associated with dark red coat color in Poodles.

Pigment production and distribution is controlled through multiple genes, resulting in a wide range of coat color phenotypes in dogs. Dogs that produce only the pheomelanin pigment vary in intensity from white to deep red. The Poodle breed has a wide range of officially recognized coat colors, including the pheomelanin-based white, cream, apricot, and red coat colors, which are not fully explained by the previously identified genetic variants involved in pigment intensity. Here, a genome-wide association study for pheomelanin intensity was performed in Poodles which identified an association on canine chromosome 18. Whole-genome sequencing data revealed an SNN retrocopy insertion (SNNL1) in apricot and red Poodles within the associated region on chromosome 18. While equal numbers of melanocytes were observed in all Poodle skin hair bulbs, higher melanin content was observed in the darker Poodles. Several genes involved in melanogenesis were also identified as highly overexpressed in red Poodle skin. The most differentially expressed gene however was GPR22, which was highly expressed in red Poodle skin while unexpressed in white Poodle skin (log2 fold change in expression 6.1, P < 0.001). GPR22 is an orphan G-protein-coupled receptor normally expressed exclusively in the brain and heart. The SNNL1 retrocopy inserted 2.8 kb upstream of GPR22 and is likely disrupting regulation of the gene, resulting in atypical expression in the skin. Thus, we identify the SNNL1 insertion as a candidate variant for the CFA18 pheomelanin intensity locus in red Poodles.

Abstract 030: Aldosterone Promotes Nanoscale Colocalization Of Epithelial Sodium Channel Subunit Alpha And Sodium Calcium Exchanger In Neuro2a Cells

We previously reported that hypertensive patients have a higher concentration of sodium ([Na + ]) in their cerebrospinal fluid (CSF) compared with normotensive subjects but no difference in plasma [Na + ] was observed, suggesting the potential importance of CSF [Na + ] in hypertension. Epithelial sodium channels (ENaC) in the brain have been shown to be up regulated in salt-induced hypertension (SH). However, the molecular mechanisms of how brain ENaC contributes to SH development are not yet understood. We hypothesize that ENaC forms a nanoscale colocalization with the sodium-calcium exchanger (NCX) that mediates downstream signaling pathways leading to SH. To test our hypothesis, using self-labeling proteins we generated SNAP-ENaC-α and Halo-NCX1 constructs, enabling high-resolution imaging of surface expressed proteins. Expression of ENaC-α-SNAP and NCX1.5-Halo was confirmed by western blot showing an increase in expression (fold change) of ENaC-α (7.6 ± 1.7 vs. 1 ± 0.3, p<0.02) and NCX1.5 (10.1 ± 0.8 vs. 1 ± 0.4, p<0.0006) in transfected Neuro2A cells compared with controls. Transfected cells were treated with vehicle or aldosterone (100 nM) for 2 hours (n=15 cells from 3 repeat experiments/group) and imaged using ground-state depletion super-resolution microscopy. Data were analyzed using object-based analysis (OBA). Aldosterone treatment increased the density of individual ENaC-α clusters on the cell surface (12.4 ± 1.3 vs. 6.9 ± 1.08 clusters/μm 2 , p<0.002), supporting the functional role of aldosterone on increasing ENaC-α surface abundance. Importantly, the frequency (3.1 ± 0.34% vs 1.7 ± 0.22% colocalized /total clusters, p<0.001) and the density (0.5 ± 0.1 vs 0.2 ± 0.04 clusters/μm 2 of cell surface, p<0.009) of colocalized (< 40nm) ENaC-α and NCX 1.5 clusters were significantly increased in aldosterone treated cells. In sum, these data show aldosterone increases the number of ENaC-α channels on the cell surface and promotes its nanoscale colocalization with NCX, providing evidence for a functional role of ENaC-α and NCX1 coupling. Nanoscale colocalization of ENaC and NCX is potentially significant in SH, and future studies will focus on elucidating the functional importance and mechanisms.

Transcriptome analysis of the 2,4-dichlorophenoxyacetic acid (2,4-D)-tolerant cotton chromosome substitution line CS-B15sh and its susceptible parental lines G. hirsutum L. cv. Texas Marker-1 and G. barbadense L. cv. Pima 379.

The cotton chromosome substitution line, CS-B15sh, exhibits 41% lower injury from 2,4-D when applied at the field recommended rate of 1.12 kg ae ha−1 (1×) than does Texas Marker-1 (TM-1). CS-B15sh was developed in the genetic background of Gossypium hirsutum L. cv TM-1 and has chromosome introgression on the short arm of chromosome 15 from Gossypium barbadense L. cv. Pima 379. In a previous experiment, we observed reduced translocation of [14C]2,4-D outside the treated leaf tissue in CS-B15sh, which contrasted with an increased translocation of the herbicide in the tissues above and below the treated leaf in TM-1. Our results indicate a potential 2,4-D tolerance mechanism in CS-B15sh involving altered movement of 2,4-D. Here, we used RNA sequencing (RNA-seq) to determine the differential expression of genes between 2,4-D-challenged and control plants of the tolerant (CS-B15sh) and susceptible lines (TM-1 and Pima 379). Several components of the 2,4-D/auxin-response pathway—including ubiquitin E3 ligase, PB1|AUX/IAA, ARF transcription factors, and F-box proteins of the SCFTIR1/AFB complex—were upregulated with at least threefold higher expression in TM-1 compared with CS-B15sh, while both Pima 379 and TM-1 showed the same fold change expression for PB1|AUX/IAA mRNA. Some genes associated with herbicide metabolism, including flavin monooxygenase (Gohir.A01G174100) and FAD-linked oxidase (Gohir.D06G002600), exhibited at least a twofold increase in CS-B15sh than in TM-1 (the gene was not expressed in Pima 379), suggesting a potential relationship between the gene’s expression and 2,4-D tolerance. It is interesting to note that glutathione S-transferase was differentially expressed in both CS-B15sh and Pima 379 but not in TM-1, while cytochrome P450 and other genes involved in the oxidation–reduction process were significantly expressed only in CS-B15sh in response to 2,4-D. Gene set enrichment analysis on the union DEGs of the three cotton genotypes revealed the depletion of transcripts involved in photosynthesis and enrichment of transcripts involved in ABA response and signaling.

Abstract P3077: The Role Of Neutrophils In Initiating Type I Interferon Response In Myocardial Ischemia/reperfusion

Background: Inflammation succeeding myocardial ischemia/reperfusion (MI/R) plays a significant role in damaging cardiomyocytes and influencing infarct size, with neutrophils being the most rapid and most numerous cells in the post-MI/R heart. While neutrophils play a role in wound healing, they can cause further damage through the generation of reactive oxygen species, proteolytic enzymes, and neutrophil extracellular traps (NETs). We thus hypothesize that double stranded DNA stemming from these NETs activates cGAS-STING signaling in a murine model of MI/R, leading to the production of type I interferons by neutrophils, which worsens reperfusion injury. Methods: Single-cell RNA sequencing was performed on neutrophils isolated from the hearts of mice 24 hours post-MI/R. Additionally, mice underwent MI/R and heart tissues were harvested 6- and 24- hours after reperfusion for ELISA and qPCR analysis. Results: Utilizing single-cell RNA sequencing to better characterize the role of neutrophils and NETs in MI/R, we identified a significant population of neutrophils with a strong type I interferon (IFN) signature recruited to the area of infarct 24 hours post MI/R in a murine model. To further investigate the IFN response seen in this population of neutrophils, we preformed protein and gene expression analysis on heart tissue samples isolated from mice at timepoints in which neutrophils would be present in the area of infarct. Analysis by qPCR shows an increased fold change in gene expression of IFNα (7.22 ± 6.05, n = 3; 3.83 ± 2.22, n = 4) and IFNβ (6.74 ± 5.39, n = 3; 3.64 ± 2.25, n = 4) at 6- and 24- hours post MI/R respectively, compared to sham mice. Furthermore, analysis by ELISA shows a significant increase in IFNβ protein levels in the heart after 6- hours (0.41pg/mg ± 0.04, n =8) compared to sham mice (0.16 pg/mg ± 0.06, n = 7; p ≤ 0.01, Student’s t-test). Conclusions: These data show a rapid increase in type I IFN in the hearts of mice post-MI/R, which implicates neutrophils may be participating in the IFN signaling pathway. Identifying neutrophils as an early source of IFN can provide a potentially new therapeutic target in treating MI/R.

MiRNA Expression Profile in Ileocecal Adenocarcinoma Cells Infected with Cryptosporidium

Cryptosporidium spp. is an opportunistic protozoan transmitted by fecal-oral route via oocysts. The agent may cause severe infection especially in individuals with suppressed immune system, due to its intracellular location and ability to cause auto-infection. MicroRNAs (miRNAs) are non-translated endogenous RNA molecules with an average of 22 nucleotides in length that regulate the expression of genes involved in important biological functions such as proliferation, differentiation, apoptosis and immune response. Recent studies have focused on the role of miRNAs in pathogenesis of infectious diseases and their potential to be used as biomarkers. The aim of this study was to determine the miRNA profile of human ileocecal adenocarcinoma (HCT-8) cells at 24 hours of infection with Cryptosporidium spp. In the study, the HCT-8 cell line was infected with Cryptosporidium spp. that were isolated from infected human stool samples and RNA was isolated from the cells 24 hours after infection. After this process, cDNA synthesis was performed and the expression of 95 human miRNA profiles were investigated by polymerase chain reaction (PCR) method. Fold changes of expression were determined by comparison with Cryptosporidium spp. uninfected cell lines. Sequence information of miRNAs and their target genes were performed via TargetScanHuman7.1 and miRDB websites, while gene ontology (GO) pathways of target genes were analyzed with the mirPath v.3 program. It was detected that the expression of 10 miRNAs were upregulated and 11 of them were downregulated compared with the control group. It was observed that, this 21 differentially expressed miRNAs were mainly associated with apoptosis, mitotic cell cycle, and immune response. Hsa-miR-612, hsa-miR-6763-5p, hsa-miR-188-5p, hsa-miR-664b-3p, hsa-miR-210-3p, hsa-let-7e-5p hsa-let-7b-3p, hsa-miR-4787-3p, hsa-miR-548ab, hsa-miR-3714 and hsamiR-4803 were found to be associated with apoptosis; and hsa-miR-612, hsa-miR-664b-3p, hsa-miR210-3p, hsa-let-7e-5p, hsa-let-7b-3p, hsa-miR-548ab, and hsa-miR4803 were found to be associated with mitotic cell cycle. The balance of proliferation and apoptosis is very significant in the development of infection and cancer. It is thought that determination of the effect of miRNAs on proliferation-apoptosis balance could provide information related to the etiopathogenesis and prognosis of infections, and on the role of microorganisms in carcinogenesis. In this study, 12 differentially expressed miRNAs were found to be associated with immune response. This may emphasize the role of miRNAs in the prevention and treatment of infections. It was concluded that, miRNAs could be used in the diagnosis, treatment and prevention of infections with the determination of miRNA's role in the infection mechanism as a result of the increasing number of studies.

O107 Endotoxaemia rapidly impacts on skeletal muscle mrna expression under conditions of controlled nutrient availability in humans

Abstract Introduction Inflammation induces changes in muscle protein turnover and mass and dampens insulin stimulated glucose disposal and oxidation. Limited information is available regarding the molecular regulation of these events. We determined the acute effects of lipopolysaccharide (LPS) infusion on targeted muscle mRNA expression. Methods Seven healthy, males (age 21.9±0.6 yrs, BMI 23.4±1.2 kg.m-2) participated in this ethically approved randomised crossover design study. On 2 occasions separated by >2 weeks, subjects underwent a 4h hyperinsulinaemic euglycaemic clamp combined with a primed mixed amino-acid (6 g.h-1; to create a ‘fed-state’) infusion, immediately following bolus saline (control) or LPS (4 ng.kg-1) infusion. Vastus lateralis muscle biopsies were obtained at baseline, 120 and 240 min. Muscle mRNA expression was measured (191 targets deemed to be representative of insulin sensitivity, carbohydrate and fat metabolism, inflammation, and protein turnover) using microfluidics TaqMan array cards. Results Plasma [TNF alpha] was markedly elevated above control following 60 min of LPS infusion (P<0.05) and remained elevated. Following gene filtering (>1.5 fold change in muscle mRNA expression from baseline, P<0.05), Ingenuity Pathway Analysis identified several metabolic functions significantly altered from baseline after 120 and 240 min in control. The magnitude of change in each metabolic function (-log p value) and the size of each gene network was substantially greater after LPS. Conclusion Muscle mRNAs respond rapidly to insulin and amino acid infusion in humans, but the magnitude of response was greater in the presence of LPS and may underpin changes in muscle protein and fuel metabolism seen under these conditions. Take-home message Endotoxaemia acts rapidly (within 2 to 4 hours) to alter the expression levels of muscle mRNAs known to be intimately involved in the molecular regulation of muscle mass, insulin resistance and fuel oxidation in human volunteers under controlled conditions of insulin and nutrient availability. This may play a role in the changes in muscle metabolism seen under such conditions.

Genotyping Helicobacter pylori and fgf7 gene expression in gastric cancer.

Helicobacter pylori as the causative agent of the most common chronic bacterial infectious disease in human still involves a range of clinical challenging complications. In this meantime, the survey of the interaction between H. pylori virulence genes expression and its consequences on gastric antral epithelial cells is Controversial. This study surveyed the correlations between H. pylori cag Pathogenicity Island and virulence factors genes with Fgf7 gene expression as an angiogenic factor in developing gastric cancer in gastric antral epithelial cells of patients with H. pylori infection. Gastric antral biopsy samples collected from patients out of exclusion criteria, including consumption of tobacco, alchohol and anti-H. pylori drugs, were categorized into gastric cancer (case group n:53) and gastritis (control group n:50) with and without H. pylori infection to detect changes in cDNA of fgf7 in gastric antral epithelial cells by using Real Time RT PCR. Extracted total RNA from gastric antral biopsy samples was used to synthesize cDNA for real time PCR. Furthermore, the cDNA of H. pylori cag Pathogenicity Island and other virulence factors genes were detected by using specific designed primers and simple PCR. Fgf7 gene expression revealed a significantly increase in gastric antral epithelial cells of gastric cancer and H. pylori-positive patients in contrast with gastritis and H. pylori-negative patients (p < 0.05). In the meanwhile, cag Pathogenicity Island and hopQ genotypes showed a positive correlation with Fgf7 gene expression (fold changes of cDNA) in gastric antral epithelial cells (p < 0.05). This study revealed an obvious correlation between Fgf7 gene expression in gastric antral epithelial cells of patients with H. pylori carcinogenic genotypes infection and some host factors including age.

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.

SummaryIn biology, graph layout algorithms can reveal comprehensive biological contexts by visually positioning graph nodes in their relevant neighborhoods. A layout software algorithm/engine commonly takes a set of nodes and edges and produces layout coordinates of nodes according to edge constraints. However, current layout engines normally do not consider node, edge or node-set properties during layout and only curate these properties after the layout is created. Here, we propose a new layout algorithm, distance-bounded energy-field minimization algorithm (DEMA), to natively consider various biological factors, i.e., the strength of gene-to-gene association, the gene’s relative contribution weight and the functional groups of genes, to enhance the interpretation of complex network graphs. In DEMA, we introduce a parameterized energy model where nodes are repelled by the network topology and attracted by a few biological factors, i.e., interaction coefficient, effect coefficient and fold change of gene expression. We generalize these factors as gene weights, protein–protein interaction weights, gene-to-gene correlations and the gene set annotations—four parameterized functional properties used in DEMA. Moreover, DEMA considers further attraction/repulsion/grouping coefficient to enable different preferences in generating network views. Applying DEMA, we performed two case studies using genetic data in autism spectrum disorder and Alzheimer’s disease, respectively, for gene candidate discovery. Furthermore, we implement our algorithm as a plugin to Cytoscape, an open-source software platform for visualizing networks; hence, it is convenient. Our software and demo can be freely accessed at http://discovery.informatics.uab.edu/dema.Supplementary information Supplementary data are available at Bioinformatics online.

Differential Gene Expression and Withanolides Biosynthesis During in vitro and ex vitro Growth of Withania somnifera (L.) Dunal.

Ashwagandha (Withania somnifera L. Dunal) is a medicinally important plant with withanolides as its major bioactive compounds, abundant in the roots and leaves. We examined the influence of plant growth regulators (PGRs) on direct organogenesis, adventitious root development, withanolide biosynthetic pathway gene expression, withanolide contents, and metabolites during vegetative and reproductive growth phases under in vitro and ex vitro conditions. The highest shooting responses were observed with 6-benzylaminopurine (BAP) (2.0 mg L–1) + Kinetin (KIN) (1.5 mg L–1) supplementation. Furthermore, BAP (2.0 mg L–1) + KIN (1.5 mg L–1) + gibberellic acid (GA3) (0.5 mg L–1) exhibited better elongation responses with in vitro flowering. Half-strength MS medium with indole-3-butyric acid (IBA) (1.5 mg L–1) exhibited the highest rooting responses and IBA (1.0 mg L–1) with highest fruits, and overall biomass. Higher contents of withaferin A (WFA) [∼8.2 mg g–1 dry weight (DW)] were detected in the reproductive phase, whereas substantially lower WFA contents (∼1.10 mg g–1 DW) were detected in the vegetative phase. Cycloartenol synthase (CAS) (P = 0.0025), sterol methyltransferase (SMT) (P = 0.0059), and 1-deoxy-D-xylulose-5-phosphate reductase (DXR) (P = 0.0375) genes resulted in a significant fold change in expression during the reproductive phase. The liquid chromatography-mass spectrometry (LC-MS) analysis revealed metabolites that were common (177) and distinct in reproductive (218) and vegetative (167) phases. Adventitious roots cultured using varying concentrations of indole-3-acetic acid (IAA) (0.5 mg L–1) + IBA (1.0 mg L–1) + GA3 (0.2 mg L–1) exhibited the highest biomass, and IAA (0.5 mg L–1) + IBA (1.0 mg L–1) exhibited the highest withanolides content. Overall, our findings demonstrate the peculiarity of withanolide biosynthesis during distinct growth phases, which is relevant for the large-scale production of withanolides.

Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI).

Adverse event pathogenesis is often a complex process which compromises multiple events ranging from the molecular to the phenotypic level. In toxicology, Adverse Outcome Pathways (AOPs) aim to formalize this as temporal sequences of events, in which event relationships should be supported by causal evidence according to the tailored Bradford-Hill criteria. One of the criteria is whether events are consistently observed in a certain temporal order and, in this work, we study this time concordance using the concept of "first activation" as data-driven means to generate hypotheses on potentially causal mechanisms. As a case study, we analysed liver data from repeat-dose studies in rats from the TG-GATEs database which comprises measurements across eight timepoints, ranging from 3 hours to 4 weeks post-treatment. We identified time-concordant gene expression-derived events preceding adverse histopathology, which serves as surrogate readout for Drug-Induced Liver Injury (DILI). We find known mechanisms in DILI to be time-concordant, and show further that significance, frequency and log fold change (logFC) of differential expression are metrics which can additionally prioritize events although not necessary to be mechanistically relevant. Moreover, we used the temporal order of transcription factor (TF) expression and regulon activity to identify transcriptionally regulated TFs and subsequently combined this with prior knowledge on functional interactions to derive detailed gene-regulatory mechanisms, such as reduced Hnf4a activity leading to decreased expression and activity of Cebpa. At the same time, also potentially novel events are identified such as Sox13 which is highly significantly time-concordant and shows sustained activation over time. Overall, we demonstrate how time-resolved transcriptomics can derive and support mechanistic hypotheses by quantifying time concordance and how this can be combined with prior causal knowledge, with the aim of both understanding mechanisms of toxicity, as well as potential applications to the AOP framework. We make our results available in the form of a Shiny app (https://anikaliu.shinyapps.io/dili_cascades), which allows users to query events of interest in more detail.

Comprehensive Analysis of microRNA Expression During the Progression of Colorectal Tumors

BackgroundNo effective early diagnostic biomarkers are available for colorectal cancer (CRC). Therefore, we sought to identify new biomarkers that could identify CRC from progression as a pre-cancerous lesion to its invasive form. Recent studies have shown that microRNAs (miRs) are associated with the onset of cancer invasion and progression.AimsWe hypothesized that the identification of miRs associated with CRC might be useful to detect this disease at early stages.MethodsWe conducted an integrated analysis of 79 isolated colorectal tumor glands, including adenomas, intramucosal cancers, and invasive CRCs that showed a microsatellite stable phenotype using GeneChip miRNA 4.0 microarray assays. The colorectal tumors we examined were divided into 2 cohorts (42 in the first cohort and 37 in the second cohort).ResultsFirst, cluster analysis was performed to stratify expression patterns of multiple miRs that were pooled according to the following criteria: fold change in expression (< −2.0 or > 2.0), p < 0.05, and mature miRs. As a result, the expression patterns of pooled miRs were subdivided into 3 subgroups that were correlated with tumor grade. Each subgroup was characterized by specific miRs. In addition, we found that specific miRs, including miR-140-3p and miR-378i, were closely associated with cancer invasion. Finally, we analyzed paired dysregulated miRs between adenomatous and cancerous components present within the same tumor.DiscussionWe showed that several miRs were dysregulated during progression from adenoma to intramucosal cancer. Specific miRs may have key roles in progression from intramucosal tumor to invasive CRC.

Antioxidant Impact of Green Synthetized Magnetic Nanoparticle of Nigella Sativa Seed Alcoholic Extract in Male Rats

That experience was conducted for the purpose of known the impact antioxidant nanoparticles of Nigella sativa agonist oxidative stress of the Nanoparticles the iron in rats. The experience was conducted in veterinary medicine Al-Qadisiya university at the animal house. This study was carried out during a period from 20.11.2020 to 20.04.2021 (64) sixty four mature rat 90 days age. Wister rat average body weight (100-120) gram will be used in the preset study the rat will be kept under controlled hygienic condition with free access to food and water for two week before starting the experiment. The animal will be randomly assigned into 4equal groups 16 each and treated as follow. The following objective will be studied. Gene expression examination in 14 and 28 days. added Evaluation of liver alanine aminotransferase ALT and the alkaline phosphatase ALP, AST aspartate amino transferase gene expression level, And GSS (glutathione) and Sod 1(superoxide dismutase) gene expression. When gave mix groups (Nigella sativa and Iron) to male rats significant decrease fold change gene expression level compared with control groups. While gave Nigella sativa alone to male rats significant decease fold change (gene expression level) compared with control groups. Iron alone gave to male rats increase significant e fold change gene expression level compared with control group. Gene expression (fold change) (glutathione) and Sod 1(superoxide dismutase) gene expression. Examination in 14 and 28 days gave significant increase in mix group and Nigella sativa, significant decrease in Iron group.

A novel thaumatin-like protein from durum wheat, TdPR-5, is homologous to known plant allergens, responsive to stress exposure, and confers multiple-abiotic stress tolerances to transgenic yeast

Thaumatin-like proteins (TLPs) are highly complex group of Pathogenesis-Related proteins (PRs) recognized as human allergens. They are known to rapidly accumulate in high levels following stresses. Several members of TLPs were isolated from different plant species, but few were described in durum wheat. In this study, a PR-5 member, TdPR-5, was isolated from a Tunisian variety of durum wheat. Phylogenetic analysis showed that TdPR-5 protein shared high homology with TLPs isolated from several plant species. Allergenic assessment of TdPR-5, using Allermatch tool, revealed that TdPR-5 had significant identity with TLPs, known as plant allergens. qRT-PCR analysis revealed that TdPR-5 is robustly induced by drought, salt and heavy metals such as cadmium (Cd), copper (Cu) and zinc (Zn). Notably, TdPR-5 induction is concomitant with the induction of the durum wheat transcription factor TdSHN1 shown previously to control the expression of tobacco PR-5 gene when overexpressed in transgenic tobacco plants. Maximum fold-change in relative expression of TdPR-5 and TdSHN1 genes following stress treatments reached 6.5 times (mannitol 1 h) and 10 times (Cu 24 h), respectively. Heterologous expression of TdPR-5 in transgenic yeast conferred resistance to multiple abiotic stresses. These results indicated that TdPR-5 may play an important role in multiple abiotic stress tolerance in wheat. This study also provides valuable information regarding food safety. In fact, overexpression of strong transcription factors such as TdSHN1 or exposure of plants to stressful conditions can lead to an increase in the quantity of allergens in crops thereby increasing the risk for consumers with known allergy or sensitization.

Proteomic and Phosphoproteomic Changes of MAPK-Related Inflammatory Response in an Animal Model of Neuropathic Pain by Differential Target Multiplexed SCS and Low-Rate SCS.

IntroductionNeuropathic pain initiates an interplay of pathways, involving MAP kinases and NFκB-signaling, leading to expression of immune response factors and activation and inactivation of proteins via phosphorylation. Neuropathic pain models demonstrated that spinal cord stimulation (SCS) may provide analgesia by modulating gene and protein expression in neuroinflammatory processes. A differential target multiplexed programming (DTMP) approach was more effective than conventional SCS treatments at modulating these. This work investigated the effect of DTMP and low rate SCS (LR-SCS) on proteins associated with MAP kinases and NFκB-signaling relevant to neuroinflammation.MethodsAnimals subjected to the spared nerve injury model (SNI) of neuropathic pain were treated continuously (48h) with either DTMP or LR-SCS. No-SNI and No-SCS groups were included as controls. Proteomics and phosphoproteomics of stimulated spinal cord tissues were performed via liquid chromatography/tandem mass spectrometry. Proteins were identified from mass spectra using bioinformatics. Expression levels and fold changes (No-SCS/No-SNI and SCS/No-SCS) were obtained from spectral intensities.ResultsAnalyses identified 7192 proteins, with 1451 and 705 significantly changed by DTMP and LR-SCS, respectively. Eighty-one proteins, including MAP kinases, facilitating NFκB-signaling as part of inflammatory processes were identified. The pain model significantly increased expression levels of complement pathway-related proteins (LBP, NRG1, APP, CFH, C3, C5), which were significantly reversed by DTMP. Expression levels of other complement pathway-related proteins (HMGB1, S100A8, S100A9, CRP, C4) were decreased by DTMP, although not significantly affected by SNI. Other proteins (ORM1, APOE, NG2, CNTF) involved in NFκB-signaling were increased by SNI and decreased by DTMP. Expression levels of phosphorylated protein kinases involved in NFκB-signaling (including MAP kinases, PKC, MARK1) were affected by the pain model and reverse modulated by DTMP. LR-SCS modulated inflammatory-related proteins although to a lesser extent than DTMP.ConclusionProteomic analyses support the profound effect of the DTMP approach on neuroinflammation via MAP kinases and NFκB-mediated signaling to alleviate neuropathic pain.

Natural plant extracts mediated expression regulation of TGF-β receptors and SMAD genes in human cancer cell lines.

Transforming growth factor beta (TGF-β) superfamily has key role in cell proliferation which leads to tumor promoting activities at metastatic stage of cancer. Inhibition of transforming growth factor beta receptor (TGFβR) signaling pathway can provide better therapeutic strategy to control cancer. Natural products are best known for their safety, less toxic nature, antioxidant characteristics making them a promising candidate to inhibit TGFβR signaling pathway. Crude methanolic extracts (CMEs) of 16 selected plants were prepared by using maceration method and subjected to phytochemical assays for identification of major phytometabolites particularly cancer chemopreventive antioxidant constituents. Total flavonoid content of all plants CME was > 0.6mg/ml exhibiting the Cichorium intybus contains comparatively highest amount of total flavonoid content (0.53mg/ml). Scanvenging activity of all plants was determined having IC50 ranges between 2 and 88 (µg/ml) while Moringa oleifera revealed the maximum scavenging activity (IC50 2.03µg/ml). Comparative cytotoxicity of plant extracts was evaluated in HUH and MCF-7 cell lines using 3-(4,5-Dimethylthiazol-2-Yl)-2,5-Diphenyltetrazolium Bromide (MTT) colorimetric assay. The nine active plant extracts i.e. Fagonia cretica, Argemone Mexicana, Rubus fruticosus, M. oleifera, Punica granatum, Cichorium intybus, Xanthium strumarium, Carissa opaca, Cyperus rotundus were identified based on their high antiproliferative activity > 50% against cancer cell lines and subjected to relative expression studies. Modulation of TGFβ signaling molecules (i.e.TGFβR1, 2 & 3, SMAD3, SMAD5) and ubiquitous proteins i.e. SMURF1 and SMURF2 genetic expression by potent extracts was determined by RT-PCR using GAPDH (housekeeping gene) as gene of reference. This present study revealed that CME of Fagonia cretica and Argemone mexicana significantly inhibit TGF beta mediated signaling cascade by downregulating the gene expression fold change > 1 of TGFβR 1, 2 & 3 and receptor associated complex protein SMAD3 as compared to control.

Triiodothyronine (T3) Induces Limited Transcriptional and DNA Methylation Reprogramming in Human Monocytes.

Thyroid hormones have immunomodulatory roles, but their effects on the transcriptome and epigenome of innate immune cell types remain unexplored. In this study, we investigate the effects of triiodothyronine (T3) on the transcriptome and methylome of human monocytes in vitro, both in resting and lipopolysaccharide (LPS)-stimulated conditions. In resting monocytes, 5 µM T3 affected the expression of a small number of monocyte-to-macrophage differentiation-associated genes, including TLR4 (p-value < 0.05, expression fold change >1.5). T3 attenuated a small proportion of monocyte-to-macrophage differentiation-associated DNA methylation changes, while specifically inducing DNA methylation changes at several hundred differentially methylated CpG probes (DMPs) (p-value < 0.05, Δβ > 0.05). In LPS-stimulated monocytes, the presence of T3 attenuated the effect of 27% of LPS-induced DMPs (p-value < 0.05, Δβ > 0.05). Interestingly, co-stimulation with T3 + LPS induced a unique DNA methylation signature that was not observed in the LPS-only or T3-only exposure groups. Our results suggest that T3 induces limited transcriptional and DNA methylation remodeling in genes enriched in metabolism and immune processes and alters the normal in vitro LPS response. The overlap between differentially expressed genes and genes associated with DMPs was minimal; thus, other epigenetic mechanisms may underpin the expression changes. This research provides insight into the complex interplay between thyroid hormones, epigenetic remodeling, and transcriptional dynamics in monocytes.

MicroRNA-7 Regulates Insulin Signaling Pathway by Targeting IRS1, IRS2, and RAF1 Genes in Gestational Diabetes Mellitus.

Small non-coding micro RNAs (miRNAs) are indicated in various metabolic processes and play a critical role in disease pathology, including gestational diabetes mellitus (GDM). The purpose of this study was to examine the altered expression of miRNAs and their target genes in placental tissue (PL), cord blood (CB), and maternal blood (MB) of matched non-glucose tolerant (NGT) and GDM mother. In a case-control study, micro-RNA was quantified from forty-five serum (MB n = 15, CB n = 15, and PL n = 15) and matched placental tissue using stem-loop RT-qPCR followed by target prediction, network construction and functional and pathways enrichment analysis. Further, target genes were verified in-vitro through transfection and RT-qPCR. Five miRNAs, namely hsa-let 7a-5P, hsa-miR7-5P, hsa-miR9-5P, hsa-miR18a-5P, and hsamiR23a- 3P were significantly over-expressed (p < 0.05) in all three samples namely PL, CB, and MB of GDM patients. However, the sample-wise comparison reveals higher expression of miRNA 7 in MB while lowest in CB than control. Furthermore, a comparison of fold change expression of target genes discloses a lower expression of IRS1, IRS2, and RAF1 in MB while comparatively higher expression of NRAS in MB and CB. In-vitro validation reveals lower expression of IRS1/2 and RAF1 in response to overexpression of miR-7 and vice-versa. Thus it is evident that increased miRNA7 expression causes down-regulation of its target genes IRS1, IRS2, and RAF1 in GDM mother compared to control. Further, target prediction, pathway enrichment, and hormone analysis (significantly higher FSH & LH in MB of GDM compared to NGT) revealed insulin signaling, inflammatory and GnRH signaling as major pathways regulated by miRNA7. Thus, an elevated level of miRNA7 may be associated with the progression of GDM by altering the multiple pathways like insulin, GnRH, and inflammatory signaling pathways via targeting IRS1, IRS2, and RAF1, implicating a new therapeutic target for GDM.

M6A mRNA Methylation Was Associated With Gene Expression and Lipid Metabolism in Liver of Broilers Under Lipopolysaccharide Stimulation.

Hepatic inflammation is always accompanied with abnormal lipid metabolism. Whether N6-methyladenosine (m6A) mRNA methylation affects irregular inflammatory lipid level is unclear. Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7,815 m6A peaks distributed in 5,066 genes were identified in the normal chicken liver and were mostly located in the CDS, 3′UTR region, and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed and showed 1,200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the latter in the 3′UTR and in the region near the stop codon. The hyper- or hypo-methylated genes were enriched in different GO ontology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, computational prediction of protein–protein interaction (PPI) showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication, and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.

Potential plasma biomarkers: miRNA-29c, miRNA-21, and miRNA-155 in clinical progression of Hepatocellular Carcinoma patients.

This study evaluated differences in the clinical appearance of patients with hepatocellular carcinoma (HCC) based on plasma level and regulation of microRNAs (miRNA-29c, miRNA-21, and miRNA-155). The observational-analytical study with a cross-sectional design was conducted on 36 HCC patients and 36 healthy controls. The blood samples were collected from 2 Province Hospitals (Dr. Sardjito Hospital and Prof. Dr. Margono Soekarjo Hospital) for HCC and the Blood Bank Donor of the Indonesian Red Cross for 36 healthy controls. These blood samples were treated as follows: plasma isolation, RNA isolation, cDNA synthesis, quantification by qRT-PCR using a sequence-specific forward primer, and normalization of miRNA using housekeeping-stably miRNA-16. There were only 27 HCC patients with complete clinical variables (neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), platelet count, albumin, C-reactive protein (CRP), and cholinesterase (ChE)) that were able to analyses for regulation miRNAs based on its fold change expression miRNA target. All 27 HCC subjects were follow-up until 3-years of monitoring for their overall survival. The miRNA plasma expression was analyzed by Bio-Rad CFX 96 Manager software to determine the cycle of quantification, followed by the calculation of expression levels using Livak's methods. Data were analyzed using STATA 11.0, with a significant value of p<0.05. The miRNAs expression of HCC subjects were lower than that healthy control subjects in miRNA-29c (down-regulation 1.83-fold), higher than that healthy control subjects in miRNA 21 and miRNA-155 (up-regulation, 1.74-fold; 1.55-fold) respectively. NLR, CRP, ChE, and platelet count showed a significant difference in miRNA-29c regulation, though neutrophil count showed a significant difference in miRNA-21 and miRNA-155 regulation (p<0.05). Conclusion: Plasma biomarkers: miRNA-21 and miRNA-155 might be potential biomarkers as onco-miR in HCC subjects, while miRNA-29c might act as a tumor suppressor. Significant evidence was identified with clinical progression based on the regulation of miRNAs, which was consistent with miRNA -29c.