Expression Levels Of Most Genes Research Articles

Genome-Wide Identification and Expression Analysis of ANS Family in Strawberry Fruits at Different Coloring Stages.

To elucidate the structural characteristics, phylogeny and biological function of anthocyanin synthase (ANS) and its role in anthocyanin synthesis, members of the strawberry ANS gene family were obtained by whole genome retrieval, and their bioinformatic analysis and expression analysis at different developmental stages of fruit were performed. The results showed that the strawberry ANS family consisted of 141 members distributed on 7 chromosomes and could be divided into 4 subfamilies. Secondary structure prediction showed that the members of this family were mainly composed of random curls and α-helices, and were mainly located in chloroplasts, cytoplasm, nuclei and cytoskeletons. The promoter region of the FvANS gene family contains light-responsive elements, abiotic stress responsive elements and hormone responsive elements, etc. Intraspecific collinearity analysis revealed 10 pairs of FvANS genes, and interspecific collinearity analysis revealed more relationships between strawberries and apples, grapes and Arabidopsis, but fewer between strawberries and rice. Chip data analysis showed that FvANS15, FvANS41, FvANS47, FvANS48, FvANS49, FvANS67, FvANS114 and FvANS132 were higher in seed coat tissues and endosperm. FvANS16, FvANS85, FvANS90 and FvANS102 were higher in internal and fleshy tissues. Quantitative real-time PCR (qRT-PCR) showed that the ANS gene was expressed throughout the fruit coloring process. The expression levels of most genes were highest in the 50% coloring stage (S3), such as FvANS16, FvANS19, FvANS31, FvANS43, FvANS73, FvANS78 and FvANS91. The expression levels of FvANS52 were the highest in the green fruit stage (S1), and FvANS39 and FvANS109 were the highest in the 20% coloring stage (S2). These results indicate that different members of the FvANS gene family play a role in different pigmentation stages, with most genes playing a role in the expression level of the rapid accumulation of fruit coloring. This study lays a foundation for further study on the function of ANS gene family.

Identification of unique transcriptomic signatures through integrated multispecies comparative analysis and WGCNA in bovine oocyte development

BackgroundCattle (Bos taurus) are a major large livestock, however, compared with other species, the transcriptional specificity of bovine oocyte development has not been emphasised.ResultsTo reveal the unique transcriptional signatures of bovine oocyte development, we used integrated multispecies comparative analysis and weighted gene co-expression network analysis (WGCNA) to perform bioinformatic analysis of the germinal follicle (GV) and second meiosis (MII) gene expression profile from cattle, sheep, pigs and mice. We found that the expression levels of most genes were down-regulated from GV to MII in all species. Next, the multispecies comparative analysis showed more genes involved in the regulation of cAMP signalling during bovine oocyte development. Moreover, the green module identified by WGCNA was closely related to bovine oocyte development. Finally, integrated multispecies comparative analysis and WGCNA picked up 61 bovine-specific signature genes that participate in metabolic regulation and steroid hormone biosynthesis.ConclusionIn a short, this study provides new insights into the regulation of cattle oocyte development from a cross-species comparison.

Dynamic change of the carotenoid metabolic pathway profile during oolong tea processing with supplementary LED light

Carotenoid-derived volatiles are important contributors to tea aroma quality. However, the profile of the carotenoid pathway and carotenoid-derived volatiles (CDVs) artificial regulation in oolong tea processing has yet to be investigated. In the present work, the content and varieties of carotenoid-derived volatiles, the genome-wide identification of carotenoid cleavage dioxygenase (CsCCD) gene family, the expression level of CsCCD and other key genes in the carotenoid pathway, and the profile of carotenoid substances were analyzed by multi-omics and bioinformatics methods with innovative postharvest supplementary LED light during oolong tea processing. The results showed that during oolong tea processing, a total of 17 CDVs were identified. The content of β-ionone increased up to 26.07 times that of fresh leaves and its formation was significantly promoted with supplementary LED light from 0.54 μg/g to 0.83 μg/g in the third turning over treatment. A total of 11 CsCCD gene family members were identified and 119 light response cis-acting regulatory elements of CsCCD were found. However, the expression level of most genes in the carotenoid pathway including CsCCD were reduced due to mechanical stress. ‘Huangdan’ fresh tea leaves had a total of 1 430.46 μg/g 22 varieties of carotenoids, which mainly composed of lutein(78.10%), β-carotene(8.24%) and zeaxanthin(8.18%). With supplementary LED light, the content of antherxanthin and zeaxanthin in xanthophyll cycle was regulated and CDVs such as α-ionone, β-ionone, pseudoionone, damascenone, 6,10-dimethyl-5,9-undecadien-2-one, citral, geranyl acetate and α-farnesene were promoted significantly in different phases during oolong tea processing. Our results revealed the profile of the carotenoid metabolism pathway in oolong tea processing from the perspective of precursors, gene expression and products, and put forward an innovative way to improve CDVs by postharvest supplementary LED light.

Mechanism analysis of calcium nitrate application to induce gibberellin biosynthesis and signal transduction promoting stem elongation of Dendrobium officinale

Dendrobium officinale Kimura et Migo is a precious medicinal plant which has high medicinal and commercial value. The length of the stem of D. officinale is an important factor affecting the yield because of its bioactive polysaccharides found in the stem. Nitrate can promote the elongation of young stems, but the mechanisms of calcium nitrate (CN) mediated stem length growth remain largely unknown. In this study, the transcriptome, main organic components, mineral elements and microstructure of D. officinale sprayed with CN were analyzed. 659 differentially expressed genes (DEGs) were detected in the Control and CN treatment. The concentrations of the calcium and nitrate increased significantly, while the concentrations of two kinds of the aldohexoses decreased significantly. Most of the twenty key genes involved in calcium and nitrate signal transduction and carbohydrate metabolism were up-regulated. In the two pathways of gibberellin (GA) biosynthesis and signal transduction, it was found that the expression of four differential genes related to GA biosynthesis was up-regulated, and the contents of nine GAs were also significantly increased, especially the contents of bioactive GA1 and GA4. The expression levels of most genes related to GA signal transduction were also up-regulated after CN treatment. After CN treatment, the expression levels of downstream genes related to stem elongation and tillering were also up-regulated. In addition, the microstructure showed that CN treatment made cells elongate longitudinally, made cell walls and collenchyma thicken, made obvious lignification and the increased the number of vascular bundles, indicating that CN can promote stem elongation by enhancing ductility and mechanical strength. These results provide a theoretical and practical basis for studying how nitrate treatment can improve the stem length and yield of D. officinale.

Genome-wide identification of the ABA receptor PYL gene family and expression analysis in Prunus avium L.

The Pyrabactin resistance 1-like proteins (PYR/PYL/RCAR) are components of the ABA signaling pathway, playing a key role in how plants respond to abiotic stresses. Although PYL genes have been identified in a variety of plants, the evolution and structural characteristics of these genes in sweet cherry (Prunus avium L.) trees are largely unknown. In this study, 11 PaPYL genes were identified at genome-wide level in sweet cherry and were mapped to six chromosomes. According to the phylogenetic analysis, this gene family consisted of four subgroups; genes in the same subgroup had similar conserved motifs and the same number of exons, as revealed by analyzing gene structure. The intra-species collinearity analysis did not find any tandem duplication events in this gene family, and thus fragment duplication may be the primary reason for the generation of some PaPYL genes. Additionally, the inter-species collinearity analysis uncovered a potential evolutionary relationship between them. The expression analysis indicated that some PaPYL genes are specifically expressed in tissues, suggesting they may have unique functions. We also explored the expression of this gene family under different abiotic stress treatments (cold, salinity, drought). The qRT-PCR results showed that the expression levels of most genes were up-regulated under abiotic stress treatments, consistent with the results for their analyzed promoter cis-acting elements. This study provides a basis for further elucidating the function and expression patterning of the PYL gene family in sweet cherry, and helps to further analyze its regulatory mechanism under various abiotic stress factors.

Effects of Ultraviolet-B Radiation on the Regulation of Ascorbic Acid Accumulation and Metabolism in Lettuce

To understand the effect of ultraviolet (UV)-B irradiation on the antioxidant capacity and growth of lettuce (Lactuca sativa), we subjected lettuce plants to UV-B irradiation (15.55 kJ m−2 d−1) for 7 days and measured yield, photosynthetic performance, hydrogen peroxide (H2O2), reduced glutathione (GSH), and ascorbic acid (AsA) contents, and the enzyme activity and expression of genes involving AsA recycling. UV-B exposure did not significantly decrease the fresh/dry weight of the lettuce shoots. The net photosynthesis rate, internal CO2 concentration, transpiration rate, and stomatal conductance decreased during the first 4 days of irradiation and light but recovered at day 7. In UV-B-treated plants, the levels of AsA, GSH, and H2O2 increased significantly and simultaneously, with a positive correlation found between H2O2 and AsA or GSH levels. UV-B exposure upregulated the expression level of most genes encoding the enzymes involving AsA recycling but downregulated the associated enzymatic activities. The increase of AsA content in UV-B-exposed lettuce might contribute to the AsA–GSH cycle, leading to downregulation of ascorbate oxidase (AO) enzymatic activity and gene expression. UV-B irradiation had a greater impact on metabolite levels than time of UV-B treatment. These results suggest that AsA homeostasis in UV-B-treated lettuce is regulated through a feedback loop between the expression and activity of enzymes associated with AsA recycling. Short-term UV-B supplementation (24 h) could be a promising approach to enhance AsA content in lettuce.

A two-phase gene selection method using anomaly detection and genetic algorithm for microarray data

Cancer diagnosis based on gene analysis is one of the main research areas in bioinformatics and machine learning. Microarray is a technology that can simultaneously study the expression level of thousands of genes in a sample. However, mutation or change in gene expression of only a small number of genes can lead to cancer, and basically, the expression level of most genes is the same between cancerous and healthy samples. On the other hand, the main challenge in microarray data is the high number of genes compared to the very small number of samples. This issue makes gene selection an essential step in microarray analysis. In this paper, we have proposed a new two-phase gene selection method for microarray data. In the first stage of this method, with a different approach, the genes that are the main features of the microarray are considered as training samples instead of cancerous and healthy samples; afterward, we reduce the number of genes to a great extent via anomaly detection. In the second stage, we apply a guided genetic algorithm to the genes obtained from the previous step to reach the final effective genes. Based on the experimental results, our method can reduce the number of genes up to at least 99% on all datasets. Besides, in addition to the very high reduction rate of genes, we managed to significantly increase the classification accuracy using the selected genes.

MicroRNA profiling reveals the role of miR-133b-3p in promoting apoptosis and inhibiting cell proliferation and testosterone synthesis in mouse TM3 cells.

Late-onset hypogonadism (LOH) is an age-related clinical and biological syndrome in which serum testosterone deficiency is an important characteristic and diagnostic indicator. In this study, we firstly analyzed the difference in the expression level of three miR-133s (including miR-133a-3p, miR-133a-5p, and miR-133b-3p) in rat testis samples, blood samples from mice before and 1 wk after testis removal, and mouse TM3 cells. Secondly, the mimics and inhibitors corresponding to the three miR-133s of mouse were transfected into TM3 cells separately to determine the correlation between the three miRNAs. Finally, using mouse TM3 cells to analyze the effect of miR-133b overexpression or inhibition on the proliferation and apoptosis of mouse testicular Leydig cells, the effect on genes related to testosterone synthesis, and the effect on the level of testosterone in the culture medium. We found that, compared with the testis tissue of newborn rats, miR-133a-5p was increased in adult rats, and miR-133a-3p and miR-133b-3p were decreased. In addition, 1 wk after the testis was removed, the expression levels of these three miRNAs in the blood of adult mice decreased. The correlation of the three miRNAs was summarized, and it was found that miR-133b-3p played an important role in it. In TM3 cells, overexpression of miR-133b-3p suppressed the proliferation and promotes apoptosis of cells, suppressed the expression level of most genes related to cell proliferation and testosterone synthesis, and the concentration of testosterone in the culture medium decreased while these phenomena can be reversed by the inhibition of miR-133b-3p expression. It was found that miR-133b-3p can regulate testosterone production in TM3 cells at least by targeting FSCN1. The above results suggest that miR-133b-3p plays an important role in regulating testosterone synthesis. These findings also provide new candidate diagnostic indicators for late-onset hypogonadism in men and provide new clues for the further study of pathogenesis.

Bacteria-mediated RNAi for managing fall webworm, Hyphantria cunea: screening target genes and analyzing lethal effect.

The fall webworm, Hyphantria cunea, an invasive forest pest found worldwide, causes serious ecological and economic damage. Currently, the application of chemical pesticides is the most widely used strategy for H. cunea management. However, long-term pesticide use leads to pest resistance, phytotoxicity, human poisoning, and environmental deterioration. RNA interference (RNAi) technology may provide an environmentally friendly and cost-effective option for H. cunea control. However, effective RNAi targets and application methods for H. cunea are lacking. We screened and obtained two highly effective RNAi targets, vATPase A (V-type proton ATPase catalytic subunit A) and Rop (Ras opposite), from 23 candidate genes, using initial and repeat screening tests with the double-stranded RNA (dsRNA) injection method. RNAi against these two genes was effective in suppressing each target messenger RNA level and interfering with larval growth, leading to significant larval mortality and pupal abnormality. For massive production of dsRNA and practical application of RNAi technology in H. cunea, transformed bacteria expressing dsRNAs of these two genes were prepared using the L4440 expression vector and HT115 strain of Escherichia coli. Oral administration of bacterially expressed dsRNA targeting vATPase A and Rop genes showed high mortality and the same malformed phenotype as the injection treatment. To further investigate the lethal effects of targeting these two genes on larval development, transcriptome sequencing (RNA-seq) was performed on RNAi samples. The results demonstrated disorders in multiple metabolic pathways, and the expression levels of most genes related to insect cuticle metabolism were significantly different, which may directly threaten insect survival. In addition, some new findings were obtained via RNA-seq analysis; for example, the progesterone-mediated oocyte maturation and oocyte meiosis processes were significantly different after silencing vATPase A, and the insect olfactory protein-related genes were significantly downregulated after dsHcRop treatment. vATPase A and Rop are two highly effective RNAi-mediated lethal genes in H. cunea that regulate insect growth via multiple metabolic pathways. Oral delivery of bacterially expressed dsRNA specific to vATPase A and Rop can potentially be used for RNAi-based H. cunea management. This is the first study to apply bacteria-mediated RNAi for the control of this invasive pest, which is a major step forward in the application of the RNAi technology in H. cunea. © 2022 Society of Chemical Industry.

Comparing the infection biology and gene expression differences of Plasmodiophora brassicae primary and secondary zoospores.

Plasmodiophora brassicae (Wor.) is an obligate plant pathogen affecting Brassicae worldwide. To date, there is very little information available on the biology and molecular basis of P. brassicae primary and secondary zoospore infections. To examine their roles, we used microscope to systematically investigate the infection differences of P. brassicae between samples inoculated separately with resting spores and secondary zoospores. The obvious development of P. brassicae asynchrony that is characterized by secondary plasmodium, resting sporangial plasmodium, and resting spores was observed at 12 days in Brassica rapa inoculated with resting spores but not when inoculated with secondary zoospores at the same time. Inoculation with resting spores resulted in much more development of zoosporangia clusters than inoculation with secondary zoospores in non-host Spinacia oleracea. The results indicated that primary zoospore infection played an important role in the subsequent development. To improve our understanding of the infection mechanisms, RNA-seq analysis was performed. Among 18 effectors identified in P. brassicae, 13 effectors were induced in B. rapa seedlings inoculated with resting spores, which suggested that the pathogen and host first contacted, and more effectors were needed. Corresponding to those in B. rapa, the expression levels of most genes involved in the calcium-mediated signaling pathway and PTI pathway were higher in plants inoculated with resting spores than in those inoculated with secondary zoospores. The ETI pathway was suppressed after inoculation with secondary zoospores. The genes induced after inoculation with resting spores were suppressed in B. rapa seedlings inoculated with secondary zoospores, which might be important to allow a fully compatible interaction and contribute to a susceptible reaction in the host at the subsequent infection stage. The primary zoospores undertook an more important interaction with plants.

Molecular subtyping of esophageal squamous cell carcinoma by large-scale transcriptional profiling: Characterization, therapeutic targets, and prognostic value

The tumor heterogeneity of the transcriptional profiles is independent of genetic variation. Several studies have successfully identified esophageal squamous cell carcinoma (ESCC) subtypes based on the somatic mutation profile and copy number variations on the genome. However, transcriptome-based classification is limited. In this study, we classified 141 patients with ESCC into three subtypes (Subtype 1, Subtype 2, and Subtype 3) via tumor sample gene expression profiling. Differential gene expression (DGE) analysis of paired tumor and normal samples for each subtype revealed significant difference among subtypes. Moreover, the degree of change in the expression levels of most genes gradually increased from Subtype 1 to Subtype 3. Gene set enrichment analysis (GSEA) identified the representative pathways in each subtype: Subtype 1, abnormal Wnt signaling pathway activation; Subtype 2, inhibition of glycogen metabolism; and Subtype 3, downregulation of neutrophil degranulation process. Weighted gene co-expression network analysis (WGCNA) was used to elucidate the finer regulation of biological pathways and discover hub genes. Subsequently, nine hub genes (CORO1A, CD180, SASH3, CD52, CD300A, CD14, DUSP1, KIF14, and MCM2) were validated to be associated with survival in ESCC based on the RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) database. The clustering analysis of ESCC granted better understanding of the molecular characteristics of ESCC and led to the discover of new potential therapeutic targets that may contribute to the clinical treatment of ESCC.

Down-regulating a fiber-specific KCR like gene GhKCRL1 suppressed fiber elongation through blocking the synthesis of sphingolipids in fiber cell

Cotton is an important natural fiber crop in the world. Cotton fiber cell is an extremely elongated single-cell trichome of seeds. Therefore, the fiber cell is an ideal model for studying plant cell elongation (polar expansion) and secondary wall deposition. Moreover, the two processes determine the quality (length, strength and fineness) of mature cotton fiber. However, the regulatory mechanism of fiber elongation remains unclear. Ligon lintless-1 ( Li-1 ) mutant is a fiber elongation mutant and a good material to study fiber elongation. In the present study, through analyzing the different expression genes in 10-DPA (day post anthesis) fiber cell of Li-1 mutant and its wild type (TM-1), we found a KCR (3-Ketoacyl-Coenzyme A Reductase) like gene, GhKCRL1 , was strikingly down-regulated in Li-1 mutant. GhKCRL1 shared low sequence identity with the 17 beta-hydroxysteroid dehydrogenase 12 of animal and the reported GhKCR1, GhKCR2, and GhKCR3 of upland cotton. GhKCRL1 was specifically expressed in fiber cells and its expression level peaked in 10-DPA fiber cells. GhKCRL1 is located in the endoplasmic reticulum . Down-regulating the expression of GhKCRL1 suppressed fiber elongation and significantly shortened mature fiber length. The sphingolipids contained VLCFA and LCFA strikingly declined in RNAi fiber cells. Consistently, the expression levels of most genes involved in sphingolipid biosynthesis and very long chain fatty acid (VLCFA) biosynthesis decreased in GhKCRL1 down-regulated cotton fibers. And the exogenous application of VLCFA (C24 FA) could rescue the elongation of GhKCRL1 down-regulated fiber cells. Taken together, the results revealed that the fiber-specific GhKCRL1 play some roles in cotton fiber elongation by regulating sphingolipid biosynthesis. Pattern diagram of the GhKCRL regulating fiber elongation. • GhKCRL1 is a novel KCR gene in upland cotton. • GhKCRL1 specifically expressed in fibers cells. • Down-regulating GhKCRL1 expression suppressed fiber cell elongation. • Down-regulating GhKCRL1 blocking the synthesis of sphingolipids in fiber cell.

Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans).

High-elevation adaptation provides an excellent system for examining adaptive evolution, and adaptive variations may manifest at gene expression or any other phenotypic levels. We examined gene expression profiles of Asiatic toads (Bufo gargarizans) along an elevational gradient from both wild and common-garden acclimated populations. Asiatic toads originated from high altitudes have distinctive gene expression patterns. We identified 18 fixed differentially expressed genes (DEGs), which are different in both wild and acclimated samples, and 1217 plastic DEGs, which are different among wild samples. The expression levels of most genes were linearly correlated with altitude gradient and down-regulated in high-altitude populations. Expression variations of several genes associated with metabolic process are fixed, and we also identified a co-expression module that is significantly different between acclimated populations and has functions related to DNA repair. The differential expression of the vast majority genes, however, are due to phenotypic plasticity, revealing the highly plastic nature of gene expression variations. Expression modification of some specific genes related to metabolism and response to UV radiation play crucial role in adaptation to high altitude for Asiatic toads. Common-garden experiments are essential for evaluating adaptive evolution of natural populations.

Inhibition of monogalactosyldiacylglycerol synthesis by down-regulation of MGD1 leads to membrane lipid remodeling and enhanced triacylglycerol biosynthesis in Chlamydomonas reinhardtii

BackgroundMembrane lipid remodeling involves regulating the physiochemical modification of cellular membranes against abiotic stress or senescence, and it could be a trigger to increase neutral lipid content. In algae and higher plants, monogalactosyldiacylglycerol (MGDG) constitutes the highest proportion of total membrane lipids and is highly reduced as part of the membrane lipid remodeling response under several abiotic stresses. However, genetic regulation of MGDG synthesis and its influence on lipid synthesis has not been studied in microalgae. For development of an industrial microalgae strain showing high accumulation of triacylglycerol (TAG) by promoting membrane lipid remodeling, MGDG synthase 1 (MGD1) down-regulated mutant of Chlamydomonas reinhardtii (Cr-mgd1) was generated and evaluated for its suitability for biodiesel feedstock.ResultsThe Cr-mgd1 showed a 65% decrease in CrMGD1 gene expression level, 22% reduction in MGDG content, and 1.39 and 5.40 times increase in diacylglyceryltrimethylhomoserines (DGTS) and TAG, respectively. The expression levels of most genes related to the decomposition of MGDG (plastid galactoglycerolipid degradation1) and TAG metabolism (diacylglycerol O-acyltransferase1, phospholipid:diacylglycerol acyltransferase, and major lipid droplet protein) were increased. The imbalance of DGDG/MGDG ratio in Cr-mgd1 caused reduced photosynthetic electron transport, resulting in less light energy utilization and increased reactive oxygen species levels. In addition, endoplasmic reticulum stress was induced by increased DGTS levels. Thus, accelerated TAG accumulation in Cr-mgd1 was stimulated by increased cellular stress as well as lipid remodeling. Under high light (HL) intensity (400 µmol photons/m2/s), TAG productivity in Cr-mgd1–HL (1.99 mg/L/d) was 2.71 times higher than that in wild type (WT–HL). Moreover, under both nitrogen starvation and high light intensity, the lipid (124.55 mg/L/d), TAG (20.03 mg/L/d), and maximum neutral lipid (56.13 mg/L/d) productivity were the highest.ConclusionsBy inducing lipid remodeling through the mgd1 gene expression regulation, the mutant not only showed high neutral lipid content but also reached the maximum neutral lipid productivity through cultivation under high light and nitrogen starvation conditions, thereby possessing improved biomass properties that are the most suitable for high quality biodiesel production. Thus, this mutant may help understand the role of MGD1 in lipid synthesis in Chlamydomonas and may be used to produce high amounts of TAG.

Silver nanoparticles reduce the tolerance of Cronobacter sakazakii to environmental stress by inhibiting expression of related genes

Cronobacter sakazakii is a food-borne pathogen that is resistant to a variety of environmental stress conditions. It can survive in harsh environments. We studied the effects of silver nanoparticles (AgNP) on the environmental tolerance and biofilm formation of C. sakazakii. First, we determined the minimum inhibitory concentration (MIC) of AgNP to C. sakazakii and determined the growth curve of C. sakazakii treated with different concentrations of AgNP by using the plate counting method. After determining the sub-inhibition concentrations (SIC) of AgNP on C. sakazakii, we studied the effects of AgNP on the resistance of C. sakazakii to heat, desiccation, osmotic pressure, and acid. The antibiofilm activity of AgNP was also studied. Finally, real-time quantitative PCR was used to analyze the transcription levels of 16 genes related to the environmental tolerance of C. sakazakii. The SIC of AgNP significantly reduced the survival rate of C. sakazakii under various environmental stress conditions. The results showed that AgNP at 0.625 and 1.25 μg/mL significantly inhibited the formation of C. sakazakii biofilms. The expression levels of most genes were significantly downregulated in C. sakazakii cells treated with 0.625 and 1.25 μg/mL AgNP. Therefore, AgNP may reduce the environmental tolerance of C. sakazakii by inhibiting the expression of genes related to stress tolerance. Moreover, AgNP inhibited the production of ATP in C. sakazakii cells and the formation of C. sakazakii biofilms. Our research provides a theoretical basis for the application of AgNP in food packaging, bactericidal coatings, and other fields.

Identification of Serum Exosome-Derived circRNA-miRNA-TF-mRNA Regulatory Network in Postmenopausal Osteoporosis Using Bioinformatics Analysis and Validation in Peripheral Blood-Derived Mononuclear Cells.

BackgroundOsteoporosis is one of the most common systemic metabolic bone diseases, especially in postmenopausal women. Circular RNA (circRNA) has been implicated in various human diseases. However, the potential role of circRNAs in postmenopausal osteoporosis (PMOP) remains largely unknown. The study aims to identify potential biomarkers and further understand the mechanism of PMOP by constructing a circRNA-associated ceRNA network.MethodsThe PMOP-related datasets GSE161361, GSE64433, and GSE56116 were downloaded from the Gene Expression Omnibus (GEO) database and were used to obtain differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to determine possible relevant functions of differentially expressed messenger RNAs (mRNAs). The TRRUST database was used to predict differential transcription factor (TF)-mRNA regulatory pairs. Afterwards, combined CircBank and miRTarBase, circRNA-miRNA as well as miRNA-TF pairs were constructed. Then, a circRNA-miRNA-TF-mRNA network was established. Next, the correlation of mRNAs, TFs, and PMOP was verified by the Comparative Toxicogenomics Database. And expression levels of key genes, including circRNAs, miRNAs, TFs, and mRNAs in the ceRNA network were further validated by quantitative real-time PCR (qRT-PCR). Furthermore, to screen out signaling pathways related to key mRNAs of the ceRNA network, Gene Set Enrichment Analysis (GSEA) was performed.ResultsA total of 1201 DE mRNAs, 44 DE miRNAs, and 1613 DE circRNAs associated with PMOP were obtained. GO function annotation showed DE mRNAs were mainly related to inflammatory responses. KEGG analysis revealed DE mRNAs were mainly enriched in osteoclast differentiation, rheumatoid arthritis, hematopoietic cell lineage, and cytokine-cytokine receptor interaction pathways. We first identified 26 TFs and their target mRNAs. Combining DE miRNAs, miRNA-TF/mRNA pairs were obtained. Combining DE circRNAs, we constructed the ceRNA network contained 6 circRNAs, 4 miRNAs, 4 TFs, and 12 mRNAs. The expression levels of most genes detected by qRT-PCR were generally consistent with the microarray results. Combined with the qRT-PCR validation results, we eventually identified the ceRNA network that contained 4 circRNAs, 3 miRNAs, 3 TFs, and 9 mRNAs. The GSEA revealed that 9 mRNAs participate in many important signaling pathways, such as “olfactory transduction”, “T cell receptor signaling pathway”, and “neuroactive ligand-receptor interaction”. These pathways have been reported to the occurrence and development of PMOP. To sum up, key mRNAs in the ceRNA network may participate in the development of osteoporosis by regulating related signal pathways.ConclusionsA circRNA-associated ceRNA network containing TFs was established for PMOP. The study may help further explore the molecular mechanisms and may serve as potential biomarkers or therapeutic targets for PMOP.

Biofilm genes expression of Listeria monocytogenes exposed to Latilactobacillus curvatus bacteriocins at 10 °C

Listeria monocytogenes is a foodborne pathogen able to survive in a wide range of conditions, including low temperatures, being highly persistent in the food-processing environments. Anti-listerial bacteriocins produced by Latilactobacillus curvatus CRL705 and CRL1579 were used to prevent/control biofilm formation of L. monocytogenes FBUNT, Scott A and CECT 4031T strains at 10 °C and genes transcription was evaluated. Sub-inhibitory concentrations of bacteriocins were able to reduce biofilm after six days at 10 °C, which was confirmed by crystal violet staining, motility assay and confocal laser scanning microscopy. When a set of thirty genes related to adhesion, virulence and stress response were investigated by using RT-qPCR, adaptation of L. monocytogenes to the concurrence of cold and bacteriocin stresses induced the expression of luxS, agrA, agrB, cspB and cell surface proteins related to biofilm formation genes for the three Listeria strains, whereas actA gene decreased and sigB gene increased its transcription, showing changes in the relative expression (log2) between −2 and 4-fold for Scott A and CECT 4031T strains in presence of lactocin AL705. Results showed that bacteriocin treatment affected the expression levels of most genes, while a lack of transcription of the virulence regulatory prfA was observed in the assayed strains. In addition, some genes related to energy production and sugar transport were up-regulated, exhibiting up to 1.8-fold changes in the presence of the bacteriocins. A better understanding of bacteriocins, particularly of lactocin AL705, to control biofilm formation of L. monocytogenes strains on abiotic surfaces at 10 °C, was achieved. Bacteriocins represent a successful intervention strategy to mitigate post-processing contamination.

Analysis of Glucosinolate Content and Metabolism Related Genes in Different Parts of Chinese Flowering Cabbage.

Glucosinolates (GSLs) are important secondary metabolites that play important defensive roles in cruciferous plants. Chinese flowering cabbage, one of the most common vegetable crops, is rich in GSLs and thus has the potential to reduce the risk of cancer in humans. Many genes that are involved in GSL biosynthesis and metabolism have been identified in the model plant Arabidopsis thaliana; however, few studies investigated the genes related to GSL biosynthesis and metabolism in Chinese flowering cabbage. In the present study, the GSL composition and content in three different organs of Chinese flowering cabbage (leaf, stalk, and flower bud) were determined. Our results showed that the total GSL content in flower buds was significantly higher than in stalks and leaves, and aliphatic GSLs were the most abundant GSL type. To understand the molecular mechanisms underlying the variations of GSL content, we analyzed the expression of genes encoding enzymes involved in GSL biosynthesis and transport in different tissues of Chinese flowering cabbage using RNA sequencing; the expression levels of most genes were found to be consistent with the pattern of total GSL content. Correlation and consistency analysis of differentially expressed genes from different organs with the GSL content revealed that seven genes (Bra029966, Bra012640, Bra016787, Bra011761, Bra006830, Bra011759, and Bra029248) were positively correlated with GSL content. These findings provide a molecular basis for further elucidating GSL biosynthesis and transport in Chinese flowering cabbage.

Sodium Selenite Enhances Antibiotics Sensitivity of Pseudomonas aeruginosa and Deceases Its Pathogenicity by Inducing Oxidative Stress and Inhibiting Quorum Sensing System.

Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is commonly found in clinical settings and immuno-compromised patients. It is difficult to be eradicated due to its strong antibiotic resistance, and novel inactivation strategies have yet to be developed. Selenium is an essential microelement for humans and has been widely used in dietary supplement and chemoprevention therapy. In this study, the physiological and biochemical effects of sodium selenite on P. aeruginosa PAO1 were investigated. The results showed that 0~5 mM sodium selenite did not impact the growth of PAO1, but increased the lethality rate of PAO1 with antibiotics or H2O2 treatment and the antibiotics susceptibility both in planktonic and biofilm states. In addition, sodium selenite significantly reduced the expression of quorum sensing genes and inhibited various virulence factors of this bacterium, including pyocyanin production, bacterial motilities, and the type III secretion system. Further investigation found that the content of ROS in cells was significantly increased and the expression levels of most genes involved in oxidative stress were up-regulated, which indicated that sodium selenite induced oxidative stress. The RNA-seq result confirmed the phenotypes of virulence attenuation and the expression of quorum sensing and antioxidant-related genes. The assays of Chinese cabbage and Drosophila melanogaster infection models showed that the combination of sodium selenite and antibiotics significantly alleviated the infection of PAO1. In summary, the results revealed that sodium selenite induced oxidative stress and inhibited the quorum sensing system of P. aeruginosa, which in turn enhanced the antibiotic susceptibility and decreased the pathogenicity of this bacterium. These findings suggest that sodium selenite may be used as an effective strategy for adjunct treatment of the infections caused by P. aeruginosa.

Transcriptome profiling reveals differential gene expression in the rumen of Hu lambs at different developmental stages

The development of the rumen is a critical physiological challenge in newborn ruminants. However, the molecular mechanism underlying different stages of rumen development in sheep remains poorly understood. Here, RNA sequencing and bioinformatics analysis were performed to compare the transcription profiles of rumen development at 7, 28 and 56 days of birth (D7, D28 and D56). We identified 1246, 2257 and 627 differentially expressed genes (DEGs) between D7 and D28, between D7 and D56, between D28 and D56, respectively. Also, 70 DGEs were co-expressed at these three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated most DEGs mainly related to transporter activity, channel activity and metabolism pathways. Noteworthy, the expression levels of most genes (CA4, CA9, CA12 and CA14) in nitrogen metabolic pathways were negatively correlated with the papilla length and width, but the papilla length and width were positively correlated with the expression of genes (PLA2G3, SLC26A9, SLC34A3) in ion transport pathway, suggesting that these genes may be involved in nitrogen metabolic and ion transport pathway and thus affect rumen development. These results provide new insight into the changes in RNA expression at different time points of rumen development in Hu sheep.