Expression Levels Of Certain Genes Research Articles

Study on the inhibitory activity and mechanism of Mentha haplocalyx essential oil nanoemulsion against Fusarium oxysporum growth

Mentha haplocalyx essential oil (MEO) has demonstrated inhibitory effects on Fusarium oxysporum. Despite its environmentally friendly properties as a natural product, the limited water solubility of MEO restricts its practical application in the field. The use of nanoemulsion can improve bioavailability and provide an eco-friendly approach to prevent and control Panax notoginseng root rot. In this study, Tween 80 and anhydrous ethanol (at a mass ratio of 3) were selected as carriers, and the ultrasonic method was utilized to produce a nanoemulsion of MEO (MNEO) with an average particle size of 26.07 nm. Compared to MTEO (MEO dissolved in an aqueous solution of 2% DMSO and 0.1% Tween 80), MNEO exhibited superior inhibition against F. oxysporum in terms of spore germination and hyphal growth. Transcriptomics and metabolomics results revealed that after MNEO treatment, the expression levels of certain genes related to glycolysis/gluconeogenesis, starch and sucrose metabolism were significantly suppressed along with the accumulation of metabolites, leading to energy metabolism disorder and growth stagnation in F. oxysporum. In contrast, the inhibitory effect from MTEO treatment was less pronounced. Furthermore, MNEO also demonstrated inhibition on meiosis, ribosome function, and ribosome biogenesis in F. oxysporum growth process. These findings suggest that MNEO possesses enhanced stability and antifungal activity, which effectively hinders F. oxysporum through inducing energy metabolism disorder, meiotic stagnation, as well as ribosome dysfunction, thus indicating its potential for development as a green pesticide for prevention and control P. notoginseng root rot caused by F.oxyosporum.

Metabolic and Transcriptomic Approaches of Chitosan and Water Stress on Polyphenolic and Terpenoid Components and Gene Expression in Salvia abrotanoides (Karl.) and S. yangii.

In this research, a HPLC analysis, along with transcriptomics tools, was applied to evaluate chitosan and water stress for the prediction of phenolic flavonoids patterns and terpenoid components accumulation in Salvia abrotanoides Karel and S. yangii. The results indicated that the tanshinone contents under drought stress conditions increased 4.2-fold with increasing drought stress intensity in both species. The rosmarinic acid content in the leaves varied from 0.038 to 11.43 mg/g DW. In addition, the flavonoid content was increased (1.8 and 1.4-fold) under mild water deficit conditions with a moderate concentration of chitosan (100 mg L-1). The application of foliar chitosan at 100 and 200 mg L-1 under well-watered and mild stress conditions led to increases in hydroxyl cryptotanshinone (OH-CT) and cryptotanshinone (CT) contents as the major terpenoid components in both species. The expressions of the studied genes (DXS2, HMGR, KSL, 4CL, and TAT) were also noticeably induced by water deficit and variably modulated by the treatment with chitosan. According to our findings, both the drought stress and the application of foliar chitosan altered the expression levels of certain genes. Specifically, we observed changes in the expression levels of DXS and HMGR, which are upstream genes in the MEP and MVA pathways, respectively. Additionally, the expression level of KSL, a downstream gene involved in diterpenoid synthesis, was also affected. Finally, the present investigation confirmed that chitosan treatments and water stress were affected in both the methylerythritol phosphate pathway (MEP) and mevalonate (MVA) pathways, but their commitment to the production of other isoprenoids has to be considered and discussed.

Cloning and Functional Characterization of Cold-Inducible MYB-like 17 Transcription Factor in Rapeseed (Brassica napus L.).

Rapeseed (Brassica napus L.) is an important crop for edible oil, vegetables, and biofuel. Rapeseed growth and development require a minimum temperature of ~1-3 °C. Notably, frost damage occurs during overwintering, posing a serious threat to the productivity and yield of rapeseed. MYB proteins are important transcription factors (TFs) in plants, and have been proven to be involved in the regulation of stress responses. However, the roles of the MYB TFs in rapeseed under cold stress conditions are yet to be fully elucidated. To better understand the molecular mechanisms of one MYB-like 17 gene, BnaMYBL17, in response to low temperature, the present study found that the transcript level of BnaMYBL17 is induced by cold stress. To characterize the gene's function, the 591 bp coding sequence (CDS) from rapeseed was isolated and stably transformed into rapeseed. The further functional analysis revealed significant sensitivity in BnaMYBL17 overexpression lines (BnaMYBL17-OE) after freezing stress, suggesting its involvement in freezing response. A total of 14,298 differentially expressed genes relative to freezing response were found based on transcriptomic analysis of BnaMYBL17-OE. Overall, 1321 candidate target genes were identified based on differential expression, including Phospholipases C1 (PLC1), FCS-like zinc finger 8 (FLZ8), and Kinase on the inside (KOIN). The qPCR results confirmed that the expression levels of certain genes showed fold changes ranging from two to six when compared between BnaMYBL17-OE and WT lines after exposure to freezing stress. Furthermore, verification indicated that BnaMYBL17 affects the promoter of BnaPLC1, BnaFLZ8, and BnaKOIN genes. In summary, the results suggest that BnaMYBL17 acts as a transcriptional repressor in regulating certain genes related to growth and development during freezing stress. These findings provide valuable genetic and theoretical targets for molecular breeding to enhance freezing tolerance in rapeseed.

The members of the RAS–RAF–MEK–ERK signaling pathway and cancer

Cancer is one of the biggest health problems of contemporary humanity, representing the second cause of death after cardiovascular diseases, caused by many contributing factors, such as population growth, ageing, stress, pollution, unhealthy diet, tumor diversity and heterogenity, difficulties in correct and early diagnosis and inefficiency of current treatments (e.g. cytoreduction, chemotherapy, radiotherapy, etc.). This leads us to look for new ways of dealing with cancer, such as immunotherapy and personalized therapy, which consider the type of tumour, mutations and expression levels of certain genes, making it necessary to detect specific markers. A category of such specific markers is represented by the proteins involved in inter- and intra-cellular signaling which play essential roles in tumor transformation, progression and dissemination. In cancer, some canonical signaling pathways, including RAS-RAF-MEK-ERK, P13K-PKB/AKT, JAK-STAT, HIF1-VEGF, TGFB, NOTCH, RAP1, TP53, B-catenin/WNT, HIPPO, KEAP-NRF2, MYC and CDKN2 (cell cycle), may be dysregulated. In this review, we detail the roles of RAS–RAF–MEK–ERK signaling pathway in tumorigenic processes and the types of abnormalities that affect them in cancer.

Exposure to nitrate induces alterations in blood parameter responses, liver immunity, and lipid metabolism in juvenile turbot (Scophthalmus maximus)

Nitrate (NO3−) pollution of waterbodies has attracted significant global attention as it poses a serious threat to aquatic organisms and human beings. This study aimed to evaluate the role of NO3−, an end product of biological nitrification processes, in immune status and lipid metabolism to have a comprehensive understanding of its toxic effects on fishes. Therefore, in this work, juvenile turbot (Scophthalmus maximus) were subjected to four nominal concentrations of NO3− (i.e., 0, 50, 200, 400 mg/L of NO3−-N) for a 60-day period. The results indicated that increased exposure to NO3– (200 and/or 400 mg/L) enhanced the concentrations of plasma heat shock protein concentrations (HSP70), complement component 3 (C3), complement component 4 (C4), immunoglobulin M (IgM) and lysozyme (LYS), which meant that NO3−caused fluctuations in the plasma immune system. Higher exposure to NO3– (200 and/or 400 mg/L) also caused significant enhancements in plasma glutamic pyruvic transaminase (GPT), as well as glutamic oxaloacetic transaminase (GOT) activity. Furthermore, NO3– exposure resulted in upregulation of liver TNF-α, IL-1β, HSP70, HSP90, and LYS. Additionally, the results suggested that NO3−exposure caused a certain degree of histological damage and inflammation in the liver and activated the immune defense processes of juvenile turbot. Furthermore, the mRNA expression levels of certain genes associated with lipid metabolism (peroxisome proliferator-activated receptor-alpha [PPAR-α], carnitine palmitoyltransferase 1[CPT1], liver X receptor [LXR] together with sterol regulatory element binding protein-1 [SREBP-1]) increased significantly within fish liver exposed to 200/400 mg/L NO3−-N treatments. Finally, the results obtained from the analysis of the integrated biological responses version 2 (IBRv2) also confirmed the toxic effects of NO3− on juvenile turbot. According to these findings, it can be found that NO3− emission in the aquatic environment needs to be strictly controlled, as it may cause immune and lipid metabolism disorders in fish.

Alternative splicing: An efficient regulatory approach towards plant developmental plasticity.

Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.

Loss of CREB Coactivator CRTC1 in SF1 Cells Leads to Hyperphagia and Obesity by High-fat Diet But Not Normal Chow Diet.

Cyclic adenosine monophosphate responsive element-binding protein-1-regulated transcription coactivator-1 (CRTC1) is a cytoplasmic coactivator that translocates to the nucleus in response to cyclic adenosine monophosphate. Whole-body knockdown of Crtc1 causes obesity, resulting in increased food intake and reduced energy expenditure. CRTC1 is highly expressed in the brain; therefore, it might play an important role in energy metabolism via the neuronal pathway. However, the precise mechanism by which CRTC1 regulates energy metabolism remains unknown. Here, we showed that mice lacking CRTC1, specifically in steroidogenic factor-1 expressing cells (SF1 cells), were sensitive to high-fat diet (HFD)-induced obesity, exhibiting hyperphagia and increased body weight gain. The loss of CRTC1 in SF1 cells impaired glucose metabolism. Unlike whole-body CRTC1 knockout mice, SF1 cell-specific CRTC1 deletion did not affect body weight gain or food intake in normal chow feeding. Thus, CRTC1 in SF1 cells is required for normal appetite regulation in HFD-fed mice. CRTC1 is primarily expressed in the brain. Within the hypothalamus, which plays an important role for appetite regulation, SF1 cells are only found in ventromedial hypothalamus. RNA sequencing analysis of microdissected ventromedial hypothalamus samples revealed that the loss of CRTC1 significantly changed the expression levels of certain genes. Our results revealed the important protective role of CRTC1 in SF1 cells against dietary metabolic imbalance.

LncRNA HOTAIR enhances breast cancer radioresistance through facilitating HSPA1A expression via sequestering miR-449b-5p.

BackgroundBreast cancer (BRCA) is the leading cause of cancer‐related death in women worldwide. Pre‐ and postoperative radiotherapy play a pivotal role in BRCA treatment but its efficacy remains limited and plagued by the emergence of radiation resistance, which aggravates patient prognosis. The long noncoding RNA (lncRNA)‐implicated mechanisms underlying radiation resistance are rarely reported. The aim of this study was to determine whether lncRNA HOX transcript antisense RNA (HOTAIR) modulated the radiosensitivity of breast cancer through HSPA1A.MethodsA Gammacell 40 Exactor was used for irradiation treatment. Bioinformatic tools and luciferase reporter assay were adopted to explore gene expression profile and demonstrate the interactions between lncRNA, miRNA and target mRNA 3′‐untranslated region (3′‐UTR). The expression levels of certain genes were determined by real‐time PCR and western‐blot analyses. in vitro and in vivo functional assays were conducted by cell viability and tumorigenicity assays.ResultsThe levels of oncogenic lncRNA HOTAIR were positively correlated with the malignancy of BRCA but reversely correlated with the radiosensitivity of breast cancer cells. Moreover, the expression levels of HOTAIR were positively associated with those of heat shock protein family A (Hsp70) member 1A (HSPA1A) in clinical BRCA tissues and HOTAIR upregulated HSPA1A at the mRNA and protein levels in irradiated BRCA cells. Mechanistically, miR‐449b‐5p restrained HSPA1A expression through targeting the 3′‐UTR of HSPA1A mRNA, whereas HOTAIR acted as a competing sponge to sequester miR‐449b‐5p and thereby relieved the miR‐449b‐5p‐mediated HSPA1A repression. Functionally, HOTAIR conferred decreased radiosensitivity on BRCA cells, while miR‐449b‐5p overexpression or HSPA1A knockdown abrogated the HOTAIR‐enhanced BRCA growth under the irradiation exposure both in vitro and in vivo.ConclusionsLncRNA HOTAIR facilitates the expression of HSPA1A by sequestering miR‐449b‐5p post‐transcriptionally and thereby endows BRCA with radiation resistance.Key pointsTherapeutically, HOTAIR and HSPA1A may be employed as potential targets for BRCA radiotherapy. Our findings shed new light into the mechanism by which lncRNAs modulate the radiosensitivity of tumors.

Particulate matter (PM10) induces cardiovascular developmental toxicity in zebrafish embryos and larvae via the ERS, Nrf2 and Wnt pathways

Particulate matter (PM10) is one of the most important indicators of the pollution that characterizes air quality. Epidemiological studies have shown that PM10 can cause cardiovascular-related diseases in the population. And, we studied the developmental toxicity of PM10 and the underlying mechanism of its effects on the cardiovascular system of zebrafish embryo/larva. Changes in cardiac morphology, sinus venosus and bulbus arteriosus (SV-BA) distance, heart rate, vascular subintestinalis, blood flow, returned blood volume, and reactive oxygen species (ROS) level were measured, and changes in the expression levels of certain genes were assessed via RT-PCR. The results showed that PM10 caused a significant increase in pericardial sac area and SV-BA distance, a decrease in heart rate, inhibition of vascular subintestinalis growth, blood flow obstruction, reduced venous return, and other cardiovascular toxicities. PM10 induced an increase in the ROS level and significant increases in the expression levels of ERS signalling pathway factors and Nrf2 signalling pathway factors. The expression levels of the Wnt pathway-related genes also showed significant changes. Furthermore, ROS inhibitor N-Acetyl-l-cysteine (NAC) could ameliorate the cardiovascular toxicity of PM10 in zebrafish larvae. It is speculated that PM10 may result in cardiovascular toxicity by inducing higher ROS levels in the body, which could then induce ERS and lead to defects in the expression of genes related to the Wnt signalling pathway. The Nrf2 signalling pathway was activated as a stress compensatory mechanism during the early stage of PM10-induced cardiovascular injury. However, it was insufficient to counteract the PM10-induced cardiovascular toxicity.

Branched chain fatty acid composition of yak milk and manure during full-lactation and half-lactation

BackgroundBranched chain fatty acids (BCFA) are bioactive food compounds and are well known to be essential components of human, cow and caprine milk. In Qinghai-Tibet plateau, yaks are domesticated in large numbers and their milk in addition to meat are commercially important to millions of Tibetans and Chinese. ObjectiveWe tested the hypotheses that concentrations of BCFA in yak milk and manure differ between lactation periods and evaluated gene expression levels of certain genes involved in the biosynthesis and elongation of fatty acids. DesignFresh milk and manure were collected from each yak and their fatty acid compositions compared with emphasis on BCFA. Participants/settingYak milk and manure samples from the full lactation (October, 2015) and half lactation periods (March, 2016) were collected and BCFA levels were analyzed in detail by GC-FID and structures verified by GC-EI-MS/MS. Gene expression studies were carried out by semi-quantitative real time PCR method. Statistical analyses performedThe difference between full lactation and half lactation was tested using student's t-test. Linear regression model was modelled in Excel and its significance was tested by ANOVA. Statistical significance was determined by performing student's t-test for gene expression studies. ResultsBCFA ranged from 3–6% of total fatty acids in yak milk samples. The half-lactation yak milk contained higher levels of BCFA (5.29 ± 0.53) than the full-lactation milk (4.00 ± 0.46). The total BCFA in yak manure was found to be 14.67 ± 1.21, high in anteiso-15:0 and anteiso-17:0. ELOVL1 enzyme involved in the elongation of saturated C18 to C26 acyl-CoA substrates and MCAT enzyme involved in the transfer of a malonyl group to the mitochondrial acyl carrier protein are significantly upregulated in full-lactation milk. ConclusionsBCFA in yak manure especially anteiso BCFA are positively correlated with yak milk from the same animal, indicating that these BCFA come from dietary sources. Yak milk delivers 777 mg BCFA compared to 158 mg per cup of whole U.S. dairy milk. QTP herders known to consume up to 2 kg of yak yogurt take in an estimated 3,500–5,000 mg BCFA per day. We conclude that BCFA intake for yak milk consumers is among the highest known in the world, higher when drawn from half lactating yaks.

Effect of sub-MIC values of metronidazole, ciprofloxacin, and imipenem on the growth and toxin production in Clostridioides difficile.

This study intends to investigate the effect of sub-minimum inhibitory concentration (sub-MIC) of metronidazole, ciprofloxacin, and imipenem on the growth and toxin production in Clostridioides difficile. C. difficile is the most common causative agent of hospital-acquired diarrhea. Toxin production in C. difficile appears to be a critical process for induction of the disease. Several factors such as antibiotics can facilitate growth and toxin production in C. difficile. Five C. difficile strains were grown with and without sub-MIC concentrations of metronidazole, ciprofloxacin, and imipenem (0.5x MIC). The bacterial growth was measured by density at OD620 nm in 0, 4, 8, 12 and 24 h post inoculation. Toxin production was detected using ELISA in culture supernatants as well as in cell pellet. The five strains showed minor growth variations in the presence and absence of antibiotic sub-MIC values, except for metronidazole, in which the sub-MIC concentration reduced the growth rate of the resistant isolate in comparison with the control without antibiotic. There were no significant variations in the levels of toxin production with the sub-MIC values of antibiotics examined in comparison with antibiotic-free controls. However, the amount of toxin production in the culture supernatant was greater than in the cell pellet. The findings of this study suggested that sub-MIC concentrations of antibiotics may have minor effects on bacterial growth and toxin production of C. difficile. Taken together, these findings suggest that presence of antimicrobial agents increased expression levels of certain genes, particularly virulence genes, which may help C. difficile to survive.

Immune Condition of Colorectal Cancer Patients Featured by Serum Chemokines and Gene Expressions of CD4+ Cells in Blood.

Background Colorectal cancer (CRC), the most common malignancy worldwide, causes inflammation. We explored the inflammatory pathophysiology of CRC by assessing the peripheral blood parameters. Methods The differences in gene expression profiles of whole blood cells and cell subpopulations between CRC patients and healthy controls were analyzed using DNA microarray. Serum cytokine/chemokine concentrations in CRC patients and healthy controls were measured via multiplex detection immunoassays. In addition, we explored correlations between the expression levels of certain genes of peripheral CD4+ cells and serum chemokine concentrations. Results The gene expression profiles of peripheral CD4+ cells of CRC patients differed from those of healthy controls, but this was not true of CD8+ cells, CD14+ cells, CD15+ cells, or CD19+ cells. Serum IL-8 and eotaxin-1 levels were significantly elevated in CRC patients, and the levels substantially correlated with the expression levels of certain genes of CD4+ cells. Interestingly, the relationships between gene expression levels in peripheral CD4+ cells and serum IL-8 and eotaxin-1 levels resembled those of monocytes/macrophages, not T cells. Conclusions Serum IL-8 and eotaxin-1 concentrations increased and were associated with changes in the gene expression of peripheral CD4+ cells in CRC patients.

A stitch in time: Replicate early and escape dosage compensation to express more.

The biological significance of conserved replication timing patterns in eukaryotic genomes remains a mystery. In this issue, Müller and Nieduszynski (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201701061) find that early replication is a requirement for the highest expression levels of certain genes.

Novel insights into the effect of nitrogen on storage protein biosynthesis and protein body development in wheat caryopsis

Molecular and cytological mechanisms concerning the effects of nitrogen on wheat (Triticum aestivum L.) storage protein biosynthesis and protein body development remain largely elusive. We used transcriptome sequencing, proteomics techniques, and light microscopy to investigate these issues. In total, 2585 differentially expressed genes (DEGs) and 57 differentially expressed proteins (DEPs) were found 7 days after anthesis (DAA), and 2456 DEGs and 64 DEPs were detected 18 DAA after nitrogen treatment. Gene ontology terms related to protein biosynthesis processes enriched these numbers by 678 and 582 DEGs at 7 and 18 DAA, respectively. Further, 25 Kyoto Encyclopedia of Genes and Genomes pathways were involved in protein biosynthesis at both 7 and 18 DAA. DEPs related to storage protein biosynthesis contained gliadin and glutenin subunits, most of which were up-regulated after nitrogen treatment. Quantitative real-time PCR analysis indicated that some gliadin and glutenin subunit encoding genes were differentially expressed at 18 DAA. Structural observation revealed that wheat endosperm accumulated more and larger protein bodies after nitrogen treatment. Collectively, our findings suggest that nitrogen treatment enhances storage protein content, endosperm protein body quantity, and partial processing quality by altering the expression levels of certain genes involved in protein biosynthesis pathways and storage protein expression at the proteomics level.

Dimorphic placental stress: A repercussion of interaction between endocrine disrupting chemicals (EDCs) and fetal sex

Placental homeostasis is critical for fetal development as it determines the health of mother and fetus during pregnancy and in later life. Interestingly even the fetus, in a sexually dimorphic manner, influences the pedantic growth and development of placenta. Although placenta is thought to act as a protective barrier against chemical exposures, certain endocrine disrupting chemicals (EDCs) that are circulating in mother’s blood tend to cross placenta. These EDCs have been reported to cause changes in expression levels of certain genes, immunogenic factors and non-coding RNAs such as micro RNA (miRNA) and long non-coding RNA (lncRNA) leading to placental stress. We hypothesize that these changes in placenta occur in a sexually dimorphic manner as a result of interaction between EDC exposure and fetal sex. Therefore, we propose that the ability of placenta to respond and buffer EDC exposure depends on fetal sex and, hence the EDC associated disease susceptibility of one sex differs from the other.

Constraint based temporal event sequence mining for Glioblastoma survival prediction

ObjectiveA significant challenge in treating rare forms of cancer such as Glioblastoma (GBM) is to find optimal personalized treatment plans for patients. The goals of our study is to predict which patients survive longer than the median survival time for GBM based on clinical and genomic factors, and to assess the predictive power of treatment patterns. MethodWe developed a predictive model based on the clinical and genomic data from approximately 300 newly diagnosed GBM patients for a period of 2years. We proposed sequential mining algorithms with novel clinical constraints, namely, ‘exact-order’ and ‘temporal overlap’ constraints, to extract treatment patterns as features used in predictive modeling. With diverse features from clinical, genomic information and treatment patterns, we applied both logistic regression model and Cox regression to model patient survival outcome. ResultsThe most predictive features influencing the survival period of GBM patients included mRNA expression levels of certain genes, some clinical characteristics such as age, Karnofsky performance score, and therapeutic agents prescribed in treatment patterns. Our models achieved c-statistic of 0.85 for logistic regression and 0.84 for Cox regression. ConclusionsWe demonstrated the importance of diverse sources of features in predicting GBM patient survival outcome. The predictive model presented in this study is a preliminary step in a long-term plan of developing personalized treatment plans for GBM patients that can later be extended to other types of cancers.

Activation of Toll-like receptor 7 regulates the expression of IFN-λ1, p53, PTEN, VEGF, TIMP-1 and MMP-9 in pancreatic cancer cells.

Toll-like receptors (TLRs) are critical in the induction of the immune response in tumor development. TLR7 has previously been demonstrated to be associated with the development of pancreatic cancer, and the release of cytokines and chemokines from other types of cancer cell; however, the specific expression induced by TLR7 agonists in pancreatic cancer cells remains to be elucidated. The present study aimed to investigate the effects of the TLR7 agonist, gardiquimod, on ERK1/2 signaling pathway, and on the expression of genes involved in the pathogenesis of cancer, including phosphatase and tensin homolog deleted on chromosome 10 (PTEN), p53, type Ⅲ interferon (IFN-λ1), vascular endothelial growth factor (VEGF), matrix metalloproteinase 9 (MMP-9) and tissue inhibitor of metalloproteinase 1 (TIMP-1). The results demonstrated that activation of TLR7 upregulated the expression levels of certain genes to varying degrees; the expression levels of IFN-λ1 and MMP-9 were increased by ~3 fold, whereas other genes (p53, PTEN, TIMP-1) were upregulated by ~2 fold, and VEGF was marginally upregulated after 10 min. Furthermore, gardiquimod increased the expression levels of phosphorylated-extracellular signal-regulated kinase (ERK)1/2. In addition, PD98059, a specific inhibitor of ERK phosphorylation, inhibited the ability of gardiquimod to activate ERK1/2; consequently weakening the effect of gardiquimod on gene regulation. These findings indicated that the effect of TLR7 agonists, including gardiquimod, on gene expression in BxPC-3 pancreatic cancer cells was partly associated with the mitogen-activated protein kinase-ERK1/2 signaling pathway.

Bayesian Partition Models for Identifying Expression Quantitative Trait Loci

Expression quantitative trait loci (eQTLs) are genomic locations associated with changes of expression levels of certain genes. By assaying gene expressions and genetic variations simultaneously on a genome-wide scale, scientists wish to discover genomic loci responsible for expression variations of a set of genes. The task can be viewed as a multivariate regression problem with variable selection on both responses (gene expression) and covariates (genetic variations), including also multi-way interactions among covariates. Instead of learning a predictive model of quantitative trait given combinations of genetic markers, we adopt an inverse modeling perspective to model the distribution of genetic markers conditional on gene expression traits. A particular strength of our method is its ability to detect interactive effects of genetic variations with high power even when their marginal effects are weak, addressing a key weakness of many existing eQTL mapping methods. Furthermore, we introduce a hierarchical model to capture the dependence structure among correlated genes. Through simulation studies and a real data example in yeast, we demonstrate how our Bayesian hierarchical partition model achieves a significantly improved power in detecting eQTLs compared to existing methods. Supplementary materials for this article are available online.

Antioxidant-mediated preventative effect of Dragon-pearl tea crude polyphenol extract on reserpine-induced gastric ulcers.

Dragon-pearl tea is a type of green tea commonly consumed in Southwest China. In the present study, the antioxidative and anti-gastric ulcer effects of Dragon-pearl tea crude polyphenols (DTCP) were determined in vitro and in vivo. Treatment with 25, 50 or 100 µg/ml DTCP resulted in notable antioxidant effects in vitro, which manifested as 2,2-diphenyl-1-picrylhydrazyl and OH radical-scavenging activity. Furthermore, using an in vivo mouse model, DTCP was shown to reduce the gastric ulcer area in the stomach, in which the 200 mg/kg DTCP dose exhibited the most marked effect, with a gastric ulcer index inhibitory rate of 72.63%. In addition, DTCP was demonstrated to improve stomach acidity conditions in vivo by increasing the pH and reducing the level of gastric juice, as compared with the reserpine-induced gastric ulcer control mice. Furthermore, DTCP altered the serum levels of a number of oxidation-related biomolecules, including superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), malondialdehyde (MDA), lipid peroxidation (LPO) and catalase (CAT), to subsequently exert an anti-gastric ulcer effect. Treatment with 50, 100 and 200 mg/kg DTCP increased the SOD, GSH-Px and CAT levels and reduced the MDA and LPO levels in the mouse model of gastric ulcers. These serum level alterations resulted in the modified serum levels of prostaglandin E2 (PGE2) and nitric oxide (NO), which are associated with gastric mucosal protection. A reverse transcription-quantitative polymerase chain reaction (RT-PCR) assay is a molecular biology experiment which could determine the changes of mRNA in tissues. Using the RT-PCR assay, DTCP was observed to increase the mRNA expression levels of certain genes associated with gastric ulcers: Epidermal growth factor, epidermal growth factor receptor, vascular endothelial growth factor and vascular endothelial growth factor receptor 1, while reducing gastrin expression levels. Therefore, the results indicated that DTCP induced a marked preventative effect on reserpine-induced gastric ulcers in vivo, as a result of its antioxidative capacity.

Assessment of cellular and mucosal immune responses in chicks to Newcastle disease oral pellet vaccine (D58 strain) using qPCR.

To assess the cell mediated and mucosal immune responses in chicks to Newcastle disease vaccine, expression levels of certain genes encoding cytokines and chemokines were quantified by q-PCR. The utility of cytokine and chemokine gene expression profile in estimating the cell mediated and humoral immune response has been established. The cell mediated immune response was assessed by quantifying the IFN-γ gene expression in splenocytes and compared with colorimetric blastogenesis assay. The mucosal immune response was assessed by quantifying the expression of IL-8, IL1-β, MIP1-β, K60 and K203 in the intestinal cells and compared with IgA ELISA. On 14th day post vaccination, the expression of IFN-γ was upregulated by 12-folds in the Group I, which have received oral pellet vaccine and fourfolds in the Group II where birds have received live thermostable vaccine as occulonasal instillation. 3 and 7days after receiving booster, the same cytokine gene was upregulated by 12-folds and 27-folds respectively in the Group III, where birds have received live thermostable ND vaccine as priming vaccine and oral pellet vaccine as booster. On 21st day post vaccination the expression of IL-8 was upregulated by 42.8-folds in Group I and 3.3-folds in the Group II. The expression of IL-1β was upregulated by eightfolds on 3rd day post vaccination and 23-folds on 21st day post vaccination in Group I. The expression of macrophage inflammatory protein-1β (MIP-1β) was upregulated by 16-folds in Group I and 70-folds in Group II on 14th day post vaccination. No significant change in expression of chemokine genes K60 and K203 in vaccinated birds. The results were comparable with the results of conventional tests and proved the utility of qPCR in estimating the cellular and mucosal immune responses.