Differentially expressed genes in heads and tails of Angelica sinensis diels: Focusing on ferulic acid metabolism

2016 ◽  
Vol 23 (10) ◽  
pp. 779-785 ◽  
Author(s):  
Jie Yang ◽  
Wei-hong Li ◽  
Rong An ◽  
Yi-li Wang ◽  
Yan Xu ◽  
...  
Keyword(s):  
Ferulic Acid ◽  
Differentially Expressed Genes ◽  
Acid Metabolism ◽  
Differentially Expressed ◽  
Angelica Sinensis ◽  
Ferulic Acid Metabolism

scholarly journals Transcriptome Analysis of Differentially Expressed Genes in Wild Jujube Seedlings under Salt Stress

2020 ◽  
Vol 145 (3) ◽  
pp. 174-185 ◽  
Author(s):  
Xinyi Chang ◽  
Junli Sun ◽  
Lianling Liu ◽  
Wang He ◽  
Baolong Zhao
Keyword(s):  
Salt Stress ◽  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Carbon Fixation ◽  
Acid Metabolism ◽  
Chlorophyll Synthesis ◽  
Differentially Expressed ◽  
Gene Encoding ◽  
Chlorophyll Metabolism ◽  
Photosynthetic Antenna

Wild jujube (Ziziphus acidojujuba) and cultivated jujube (Ziziphus jujuba) belong to the family Rhamnaceae. Jujubes have marked drought- and salt-tolerant properties. After salt stress, wild jujube seedling growth was inhibited and photosynthetic efficiency was reduced. A bioinformatics approach was used to analyze the transcriptomics data from wild jujube seedlings grown under salt stress, and the genes differentially expressed under the salt stress were identified to provide a theoretical basis for the development and use of wild jujube plantations in salinized soil. The transcriptome sequencing from leaves of wild jujube seedlings was carried out using second-generation sequencing technology. The effects of salt stress on the differential expression of photosynthesis-related genes in wild jujube seedlings were analyzed. Transcriptome sequencing revealed a total of 5269 differentially expressed genes (DEGs), of which 2729 were up-regulated and 2540 were down-regulated. DEGs were mainly enriched with respect to photosynthesis, photosynthetic antenna proteins, glyoxylic acid and dicarboxylic acid metabolism, linolenic acid metabolism, cysteine and methionine metabolism, and porphyrin and chlorophyll metabolism. Among them, the photosynthesis pathway-related DEGs were most highly enriched. Further analysis of porphyrin and chlorophyll synthesis and photosynthesis-related pathways revealed that they were significantly enriched by 97 photosynthesis-related DEGs. The DEGs in the photosynthesis and photosynthetic antenna protein pathways were down-regulated, whereas the DEGs glutamyl-tRNA reductase (HEMA), ferrochelatase (HEMH), and pheophorbide a oxygenase (PAO) in the porphyrin and chlorophyll synthesis pathways were up-regulated, with the remainder being down-regulated. The nuclear gene encoding Rubisco, the key enzyme in the photosynthetic carbon fixation pathway, was also down-regulated. The results showed that the photosynthetic rate of wild jujube seedlings decreased following exposure to salinity stress, an effect that was related to the increased synthesis of 5-aminolevulinic acid and heme, and the up-regulation of expression of a gene encoding a chlorophyll-degrading enzyme, and was related to the down-regulation of gene expression in photosynthesis-related pathways such as light energy capture and carbon fixation. Selection of nine DEGs related to photosynthesis and chlorophyll biosynthesis by quantitative real-time-PCR confirmed that expression changes of these nine DEGs were consistent with the transcriptome sequencing results.

Sourdough yeast-bacteria interactions can change ferulic acid metabolism during fermentation

2021 ◽  
pp. 103790
Author(s):  
Sonia Boudaoud ◽  
Chahinez Aouf ◽  
Hugo Devillers ◽  
Delphine Sicard ◽  
Diego Segond
Keyword(s):  
Ferulic Acid ◽  
Acid Metabolism ◽  
Ferulic Acid Metabolism ◽  
Sourdough Yeast

A proteomic analysis of ferulic acid metabolism in Amycolatopsis sp. ATCC 39116

2018 ◽  
Vol 102 (14) ◽  
pp. 6119-6142 ◽  
Author(s):  
Florian Meyer ◽  
Julius Netzer ◽  
Christina Meinert ◽  
Birgit Voigt ◽  
Katharina Riedel ◽  
...  
Keyword(s):  
Ferulic Acid ◽  
Proteomic Analysis ◽  
Acid Metabolism ◽  
Ferulic Acid Metabolism

scholarly journals POS0421 COMBINED ANALYSIS OF METABOLIC AND TRANSCRIPTOMIC KIDNEY PROFILES OF NZW/B-F1 MURINE LUPUS UNCOVERS BIOLOGICAL MECHANISMS PRECEDING THE ONSET OF NEPHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 439.2-440
Author(s):  
T. Manolakou ◽  
I. Tsiara ◽  
D. Nikolopoulos ◽  
P. Garantziotis ◽  
D. Benaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Univariate Analysis ◽  
Differentially Expressed ◽  
Disease Stage ◽  
Cellular Respiration ◽  
H Nmr

Background:Metabolic pathways are important regulators of immune differentiation and activation in kidneys. Kidneys directly impact systemic metabolism, circulating metabolite levels, and express intrinsic metabolic activity. The integration of renal metabolomic and transcriptomic profiles may unravel unique gene-metabolite pairs of biological significance in lupus nephritis (LN).Objectives:To decipher gene-metabolite signatures at both pre-nephritic and nephritic stages of lupus.Methods:Kidneys were isolated and snap-frozen after perfusion from female NZB/NZW-F1 lupus mice at the pre-nephritic (3-month-old) and nephritic (6-month-old exhibiting ≥100 ng/dL of urine protein) stage of lupus (n=6/group). Age-matched female C57BL/6 mice were used as healthy controls. Sample extracts were used for RNA sequencing and 1H-NMR spectroscopy metabolic profiling. DESeq2 was used to identify differentially expressed genes. Univariate analysis was used to reveal metabolic differences characteristic for nephritis.Results:Comparative transcriptomic analyses uncovered multiple transcripts related to metabolic pathways: In pre-nephritic kidneys, lipid metabolism, cellular respiration, TCA cycle, amino acid metabolism processes were overrepresented in the upregulated genes while in nephritic kidneys, amino acid metabolism processes were overrepresented among the downregulated genes (Figure 1). 1H-NMR analysis revealed a total of 49 metabolites. Comparison of the metabolic levels of nephritic and pre-nephritic animals revealed that ADP, ATP, NAD+, Taurine and Myo-inositol decreased, while Thr increased significantly. The comparison to corresponding control animals, demonstrated that only myo-inositol increased significantly. Integration of kidney metabolomics and transcriptomics indicated the involvement of processes related to glutathione metabolism, leukocyte trans-endothelial migration and antigen presentation during the established renal disease stage.Conclusion:The combined transcriptomics and metabolomics analysis revealed metabolic derangements in lupus-affected kidneys both during subclinical and overt LN. Deregulated tissue-levels of taurine and myo-inositol at the subclinical stage of the disease suggest aberrant renal biochemistry preceding the development of overt LN that may directly impact systemic metabolism and circulating metabolite levels.Figure 1.Pathways linked to cell metabolism were overrepresented among 3-month upregulated and 6-month lupus mice (F1) downregulated DEGS (differentially expressed genes) compared to controls (C57BL/6).Acknowledgements:This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742390).Disclosure of Interests:None declared

scholarly journals 557. Impact of Heavy Metal Exposure in the Transcriptional Response of Methicillin--Resistant Staphylococcus aureus (MRSA)-USA300 Latin-American Variant (USA300-LV)

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S264-S265
Author(s):  
Aura M Echeverri ◽  
Sandra Rincon ◽  
Sebastian Solano ◽  
Rafael Rios ◽  
Lina P Carvajal ◽  
...  
Keyword(s):  
Immune System ◽  
Amino Acid ◽  
Functional Groups ◽  
Differentially Expressed Genes ◽  
Unknown Function ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Differentially Expressed ◽  
Host Immune System ◽  
Qrt Pcr

Abstract Background USA 300-LV is the predominant MRSA clone in Colombia and contains a genomic island designated “COMER” with genes for copper (Cu) and mercury (Hg) resistance. HM environmental contamination is a serious threat to public health in Colombia and could also influence the selection and evolution of HM resistance genes in MRSA. Here, we investigate the global transcriptomic responses of USA300-LV after exposure to HM under the hypothesis that USA300-LV strains are highly capable of sustaining higher HM concentrations Methods We performed comparative RNAseq experiments in USA300-LV clinical strain (CA-MRSA12). Total RNA was isolated in exponential phase in the absence and presence of sub-inhibitory concentrations of Cu and Hg (3 replicates). cDNA libraries were prepared and sequenced on an Illumina platform. Differentially expressed genes (DEG) were calculated by DeSeq2 (p-adjusted value ˂ 0.01) and results on 19 selected genes were confirmed by qRT-PCR. Results US300-LV exhibited a larger number of differentially expressed genes when exposed to Hg (n = 114) compared with Cu treatment (n = 16). The most common functional groups of genes upregulated after Hg exposure included those involved in amino acid metabolism (n = 18). In contrast, 45 genes were downregulated after Hg exposure, mostly associated to host immune system defense (n = 11). qRT-PCR confirmed that the most upregulated genes were those involved in murein hydrolase activity, Hg resistance and the transcriptional regulator Cro/CI. Of 9 genes that were downregulated, functional groups included ype VII secretion system, immune modulators and leucocidins. Copper treatment resulted in only 12 genes that were upregulated including those in the COMER element (n = 6), aminoacid metabolism (n = 3), ROS response (n = 1), host immune system defense (n = 1) and unknown function (n = 1). Downregulated genes were those associated to host immune system defense (n = 2), energy generation (n = 1) and unknown function (n = 1). Conclusion Differential adaptive responses after exposure to HM in USA300-LV suggest a role in the evolution of antimicrobial resistance and successful spread in the region. Metabolic adaptations involving amino acid metabolism seem to play a role in the evolution of HM resistance in MRSA. Disclosures All authors: No reported disclosures.

scholarly journals Interleukin 20 receptor A expression in colorectal cancer and its clinical significance

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12467
Author(s):  
Rui Liu ◽  
Honghao Yin ◽  
Xin Sun ◽  
Songyi Liu ◽  
Ang Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fatty Acid ◽  
Differentially Expressed Genes ◽  
Fatty Acid Metabolism ◽  
Acid Metabolism ◽  
Differentially Expressed ◽  
Clinicopathological Parameters ◽  
Oxygen Binding ◽  
Hormone Activity ◽  
Normal Tissues

Background Interleukin 20 receptor A (IL20RA) has been shown to play a role in the establishment and progression of multiple tumors. However, the expression of this protein in colorectal cancer (CRC) and its correlation with the clinicopathological parameters of CRC have remained unclear. Methods A total of 323 paraffin sections including CRC tissues and adjacent normal tissues after surgery were collected. IL20RA protein expression was detected by immunohistochemical staining. The difference expression of IL20RA mRNA between CRC and normal tissues was also explored in the Oncomine and GEO databases. In addition, the IL20RA-related differentially expressed genes were analyzed in TCGA database and enrichment analysis was conducted to explore the cell functions and pathways related to IL20RA expression. Results There was increased IL20RA expression in CRC compared with that in normal tissues. High IL20RA expression was associated with greater tumor diameter, lymph node metastasis, and poor TNM stage in CRC, while also being suggestive of poor prognosis. The main pathways of IL20RA-related differentially expressed genes in TCGA were protein heterodimerization activity, oxygen binding, oxygen transporter activity, hormone activity, and lipid transporter activity. Meanwhile, IL20RA-related differentially expressed genes were mainly enriched in peroxidase, nucleotide stimulant repair, fatty acid metabolism, basal transcription factor, and RNA degradation. Conclusions IL20RA might have a role as a biomarker for CRC. Its upregulation might contribute to an aggressive phenotype in CRC. IL20RA’s involvement in the development and progression of CRC might occur through it affecting fatty acid metabolism, oxygen binding, oxygen transport, and hormone activity.

Sign in / Sign up

Export Citation Format

Share Document