Microarray analysis of p-anisaldehyde-induced transcriptome of Saccharomyces cerevisiae

Low Toxicological Impact of Commercial Pristine Multi-Walled Carbon Nanotubes on the Yeast Saccharomyces cerevisiae

Carbon nanotubes (CNTs) have attracted the attention of academy and industry due to their potential applications, being currently produced and commercialized at a mass scale, but their possible impact on different biological systems remains unclear. In the present work, an assessment to understand the toxicity of commercial pristine multi-walled carbon nanotubes (MWCNTs) on the unicellular fungal model Saccharomyces cerevisiae is presented. Firstly, the nanomaterial was physico-chemically characterized, to obtain insights concerning its morphological features and elemental composition. Afterwards, a toxicology assessment was carried out, where it could be observed that cell proliferation was negatively affected only in the presence of 800 mg L^-1 for 24 h, while oxidative stress was induced at a lower concentration (160 mg L^-1) after a short exposure period (2 h). Finally, to identify possible toxicity pathways induced by the selected MWCNTs, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L^-1, for two hours, was studied. In contrast to a previous study, reporting massive transcriptional changes when yeast cells were exposed to graphene nanoplatelets in the same exposure conditions, only a small number of genes (130) showed significant transcriptional changes in the presence of MWCNTs, in the higher concentration tested (800 mg L^-1), and most of them were found to be downregulated, indicating a limited biological response of the yeast cells exposed to the selected pristine commercial CNTs.

Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae

Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.

Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials

Graphene oxide has become a very appealing nanomaterial during the last years for many different applications, but its possible impact in different biological systems remains unclear. Here, an assessment to understand the toxicity of different commercial graphene oxide nanomaterials on the unicellular fungal model organism Saccharomyces cerevisiae was performed. For this task, an RNA purification protocol was optimized to avoid the high nucleic acid absorption capacity of graphene oxide. The developed protocol is based on a sorbitol gradient separation process for the isolation of adequate ribonucleic acid levels (in concentration and purity) from yeast cultures exposed to the carbon derived nanomaterial. To pinpoint potential toxicity mechanisms and pathways, the transcriptome of S. cerevisiae exposed to 160 mg L^–1 of monolayer graphene oxide (GO) and graphene oxide nanocolloids (GOC) was studied and compared. Both graphene oxide products induced expression changes in a common group of genes (104), many of them related to iron homeostasis, starvation and stress response, amino acid metabolism and formate catabolism. Also, a high number of genes were only differentially expressed in either GO (236) or GOC (1077) exposures, indicating that different commercial products can induce specific changes in the physiological state of the fungus.

p-Anisaldehyde Exerts Its Antifungal Activity Against Penicillium digitatum and Penicillium italicum by Disrupting the Cell Wall Integrity and Membrane Permeability

Penicillium digitatum and P. italicum are the two important postharvest pathogens in citrus, causing about 90% of the total loss of citrus fruit during storage and transportation. Natural fungicides such as essential oils have been widely used instead of chemical fungicides for preventing and controlling postharvest diseases. In this research, p-anisaldehyde exhibited a strong inhibitory effect on P. digitatum and P. italicum, with the minimum inhibitory concentration and minimum fungicidal concentration values of both being 2.00 μl/ml. Additionally, p-anisaldehyde visibly inhibited both the green mold and blue mold development of citrus fruits inoculated with P. digitatum and P. italicum. The mycelia morphologies of these pathogens were greatly altered, and the membrane permeability and cell wall integrity of mycelia were severely disrupted under p-anisaldehyde treatment. These results suggest that the antifungal activity of p-anisaldehyde against P. digitatum and P. italicum can be attributed to the disruption of the cell wall integrity.

Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets

Graphene nanomaterials have attracted a great interest during the last years for different applications, but their possible impact on different biological systems remains unclear. Here, an assessment to understand the toxicity of commercial polycarboxylate functionalized graphene nanoplatelets (GN) on the unicellular fungal model Saccharomyces cerevisiae was performed. While cell proliferation was not negatively affected even in the presence of 800 mg L-1 of the nanomaterial for 24 hours, oxidative stress was induced at a lower concentration (160 mg L-1), after short exposure periods (2 and 4 hours). No DNA damage was observed under a comet assay analysis under the studied conditions. In addition, to pinpoint the molecular mechanisms behind the early oxidative damage induced by GN and to identify possible toxicity pathways, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L-1 of GN was studied. Both GN concentrations induced expression changes in a common group of genes (337), many of them related to the fungal response to reduce the nanoparticles toxicity and to maintain cell homeostasis. Also, a high number of genes were only differentially expressed in the GN800 condition (3254), indicating that high GN concentrations can induce severe changes in the physiological state of the yeast.

A bio-based pro-antimicrobial polymer network via degradable acetal linkages

The synthesis of a fully degradable, bio-based, sustained release, pro-antimicrobial polymer network comprised of degradable acetals (PANDA) is reported. The active antimicrobial agent - p-anisaldehyde (pA) (an extract from star anise) - was converted into a UV curable acetal containing pro-antimicrobial monomer and subsequently photopolymerized into a homogenous thiol-ene network. Under neutral to acidic conditions (pH < 8), the PANDAs undergo surface erosion and exhibit sustained release of pA over 38 days. The release of pA from PANDAs was shown to be effective against both bacterial and fungal pathogens. From a combination of confocal microscopy and transmission electron microscopy, we observed that the released pA disrupts the cell membrane. Additionally, we demonstrated that PANDAs have minimal cytotoxicity towards both epithelial cells and macrophages. Although a model platform, these results point to promising pathways for the design of fully degradable sustained-release antimicrobial systems with potential applications in agriculture, pharmaceuticals, cosmetics, household/personal care, and food industries.

STATEMENT OF SIGNIFICANCE

With the increasing number of patients prescribed immunosuppressants coupled with the rise in antibiotic resistance - life-threatening microbial infections are a looming global threat. With limited success within the antibiotic pipeline, nature-based essential oils (EOs) are being investigated for their multimodal effectiveness against microbes. Despite the promising potential of EOs, difficulties in their encapsulation, limited water solubility, and high volatility limit their use. Various studies have shown that covalent attachment of these EO derivatives to polymers can mitigate these limitations. The current study presents the synthesis of a fully-degradable, sustained release, cytocompatible, pro-antimicrobial acetal network derived from p-anisaldehyde. This polymer network design provides a pathway toward application-specific EO releasing materials with quantitative encapsulation efficiencies, sustained release, and broad-spectrum antimicrobial activity.

Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure

Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a nonionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/l; <15% cell number reduction) and high (5 mg/l; >65% cell number reduction) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/l NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed. Similarly, 678 (168 repressed, 510 induced) and 688 genes (215 repressed, 473 induced) were differentially expressed in cells exposed to 5 mg/l NP for 120 and 180 min, respectively. Only 15 downregulated and 63 upregulated genes were common between low and high NP inhibitory concentration exposure for 120 min, whereas 16 downregulated and 31 upregulated genes were common after the 180-min exposure. Several processes/pathways were prominently affected by either low or high inhibitory concentration exposure, while certain processes were affected by both inhibitory concentrations, including ion transport, response to chemicals, transmembrane transport, cellular amino acids, and carbohydrate metabolism. While minimal expression changes were observed with low inhibitory concentration exposure, 5 mg/l NP treatment induced substantial expression changes in genes involved in oxidative phosphorylation, cell wall biogenesis, ribosomal biogenesis, and RNA processing, and encoding heat shock proteins and ubiquitin-conjugating enzymes. Collectively, these results provide considerable information on effects of NP at the molecular level.

RNA Sequencing Reveals that Endoplasmic Reticulum Stress and Disruption of Membrane Integrity Underlie Dimethyl Trisulfide Toxicity against Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium wilt of banana, a destructive disease that affects banana production, is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). In a previous study, we confirmed the strong inhibitory effects of Chinese leek (Allium tuberosum) on the incidence of this disease. Sulfur compounds are the primary antifungal constituents of Chinese leek. Among these, dimethyl trisulfide (DT) was the most abundant and exhibited the strongest inhibition of Foc TR4 growth and development. In the present study, the global gene expression profiles of Foc TR4 isolates treated with DT at 4,000-folds dilution (concentration of 1/4,000, v/v) for 1.5, 6, and 12 h were investigated by using RNA sequencing. The expression patterns of 15 DEGs were validated based on quantitative real-time PCR (qRT-PCR) assay. Untreated sample presented 2,556, 1,691, and 1,150 differentially expressed genes (DEGs) at 1.5, 6, and 12 h after the onset of the experiment, respectively, whereas DT-treated isolates presented 2,823, 3,546, and 6,197 DEGs. Based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, DEGs involved in endoplasmic reticulum (ER), glycosylation, and steroid biosynthesis were significantly inhibited by DT exposure. The similar expressional patterns of 15 DEGs between RNA-seq and qRT-PCR assays indicated the reliability of the RNA-seq data. In conclusion, ER stress related to glycosylation inhibition and damage to cell membrane integrity might contribute to the toxicity of DT against Foc TR4. As the results presented here evidenced changes in gene expression associated with DT exposure, which might be used to develop new approaches for controlling FWB.

Transcriptional profiling analysis of Penicillium digitatum, the causal agent of citrus green mold, unravels an inhibited ergosterol biosynthesis pathway in response to citral

Background

Green mold caused by Penicillium digitatum is the most damaging postharvest diseases of citrus fruit. Previously, we have observed that citral dose-dependently inhibited the mycelial growth of P. digitatum, with the minimum inhibitory concentration (MIC) of 1.78 mg/mL, but the underlying molecular mechanism is barely understood.

Results

In this study, the transcriptional profiling of the control and 1/2MIC-citral treated P. digitatum mycelia after 30 min of exposure were analyzed by RNA-Seq. A total of 6355 genes, including 2322 up-regulated and 4033 down-regulated genes, were found to be responsive to citral. These genes were mapped to 155 KEGG pathways, mainly concerning mRNA surveillance, RNA polymerase, RNA transport, aminoacyl-tRNA biosynthesis, ABC transporter, glycolysis/gluconeogenesis, citrate cycle, oxidative phosphorylation, sulfur metabolism, nitrogen metabolism, inositol phosphate metabolism, fatty acid biosynthesis, unsaturated fatty acids biosynthesis, fatty acid metabolism, and steroid biosynthesis. Particularly, citral exposure affected the expression levels of five ergosterol biosynthetic genes (e.g. ERG7, ERG11, ERG6, ERG3 and ERG5), which corresponds well with the GC-MS results, the reduction in ergosterol content, and accumulation of massive lanosterol. In addition, ERG11, the gene responsible for lanosterol 14α-demethylase, was observed to be the key down-regulated gene in response to citral.

Conclusion

Our present finding suggests that citral could exhibit its antifungal activity against P. digitatum by the down-regulation of ergosterol biosynthesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2943-4) contains supplementary material, which is available to authorized users.

Use of a bovine genome chip to identify new biological pathways for beef quality in cattle

The accumulation of muscle is largely influenced by the genetic background of cattle. Muscle tissue was collected from the longissimus muscle of Lilu beef cattle at 12, 18, 24 and 30 months old. Using meat quality analysis, we found that the Lilu beef cattle have good production and slaughter performance, the performance meets the criterion of beef cattle. Microarray analysis was able to identify a total of 4,219 genes that are differentially expressed (P ≤ 0.01) between the two groups of cattle (12 vs 18; 18 vs 24; 24 vs 30). Bioinformatics analysis results suggested that most of the differentially expressed genes are involved in the metabolic pathways and neuroactive ligand-receptor interaction pathways. In the future study that aims to look for genes relating to growth and meat quality, we will focus on the genes that have been shown to have a significant variation between groups and are involved in the two pathways.

Exposure of Candida to p-anisaldehyde inhibits its growth and ergosterol biosynthesis

p-Anisaldehyde (4-methoxybenzaldehyde), an extract from Pimpinella anisum seeds, is a very common digestive herb of north India. Antifungal activity of p-anisaldehyde was investigated on 10 fluconazole-resistant and 5 fluconazole-sensitive Candida strains. Minimum inhibitory concentrations (MIC(90)) ranged from 250 µg/ml to 600 µg/ml for both sensitive and resistant strains. Ergosterol content was drastically reduced by p-anisaldehyde-62% in sensitive and 66% in resistant strains-but did not corelate well with MIC(90) values. It appears that p-anisaldehyde exerts its antifungal effect by decreasing NADPH routed through up-regulation of putative aryl-alcohol dehydrogenases. Cellular toxicity of p-anisaldehyde against H9c2 rat cardiac myoblasts was less than 20% at the highest MIC value. These findings encourage further development of p-anisaldehyde.

Metabolic and transcriptomic responses of weaned pigs induced by different dietary amylose and amylopectin ratio

Starch is one of the major dietary energy sources for mammals. However, the nutritional value of starch largely depends on its amylose and amylopectin ratio. In this study, the overall metabolic and transcriptomic responses of weaned pigs fed with different dietary starches were assessed. Sixteen weaned pigs were randomly allotted to two experimental diets containing either of pure cassava starch (CS) or maize starch (MS) as the sole energy source (the amylose-amylopectin ratio were 0.25 and 0.43, respectively). Results indicated that the body weight gain was not affected by different dietary starches. However, a moderate fatty liver was observed in CS-fed group. Long-term ingestion of CS not only increased the total liver fat content, but significantly elevated the liver triglyceride and cholesterol content (P<0.05). In addition, the serum insulin and cholesterol concentrations were both elevated in CS-fed group (P<0.05). Microarray analysis led to the identification of 648 genes differentially expressed in liver (P<0.05), and a lot of them were involved in lipid and carbohydrate metabolism. Additionally, pathway analysis indicated that both the insulin and PPAR signaling pathways were acutely affected by dietary amylose-amylopectin ratio. Long-term ingestion of CS activated the transcription of lipogenic genes such as hmgr and fasn, but decreased the expression of lipolytic genes such as aox1, ppara and fbp. The microarray results correlated well with the measurements of several key enzymes involved in hepatic lipid metabolism. Our results suggested that both the metabolic and transcriptomic responses of weaned pigs were tightly regulated by dietary starch composition, and a high amylose ratio starch (i.e MS) may be more healthful for mammals as the long-term energy source by down-regulation of hepatic lipogenesis and steroidogenesis.