Inoculation with endophytic Bacillus megaterium 1Y31 increases Mn accumulation and induces the growth and energy metabolism-related differentially-expressed proteome in Mn hyperaccumulator hybrid pennisetum

2015 ◽  
Vol 300 ◽  
pp. 513-521 ◽  
Author(s):  
Wen-hui Zhang ◽  
Lin-yan He ◽  
Qi Wang ◽  
Xia-fang Sheng
Keyword(s):  
Energy Metabolism ◽  
Bacillus Megaterium ◽  
Differentially Expressed ◽  
Hybrid Pennisetum

scholarly journals Transcriptomic responses of Microcystis aeruginosa under electromagnetic radiation exposure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao Tang ◽  
Ziyan Zhang ◽  
Shen Tian ◽  
Peng Cai
Keyword(s):  
Energy Metabolism ◽  
Electromagnetic Radiation ◽  
Differentially Expressed Genes ◽  
Microcystis Aeruginosa ◽  
Carbon Fixation ◽  
Biological Effects ◽  
Differentially Expressed ◽  
Ecological Environment ◽  
Inhibit Protein Synthesis ◽  
Potential Threat

AbstractElectromagnetic radiation is an important environmental factor. It has a potential threat to public health and ecological environment. However, the mechanism by which electromagnetic radiation exerts these biological effects remains unclear. In this study, the effect of Microcystis aeruginosa under electromagnetic radiation (1.8 GHz, 40 V/m) was studied by using transcriptomics. A total of 306 differentially expressed genes, including 121 upregulated and 185 downregulated genes, were obtained in this study. The differentially expressed genes were significantly enriched in the ribosome, oxidative phosphorylation and carbon fixation pathways, indicating that electromagnetic radiation may inhibit protein synthesis and affect cyanobacterial energy metabolism and photosynthesis. The total ATP synthase activity and ATP content significantly increased, whereas H+K+-ATPase activity showed no significant changes. Our results suggest that the energy metabolism pathway may respond positively to electromagnetic radiation. In the future, systematic studies on the effects of electromagnetic radiation based on different intensities, frequencies, and exposure times are warranted; to deeply understand and reveal the target and mechanism of action of electromagnetic exposure on organisms.

scholarly journals Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Xitong Zhao ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Ting Yang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Energy Metabolism ◽  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Acid Synthesis ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Backfat Thickness ◽  
Lipid Deposition ◽  
Differentially Expressed Mirnas

AbstractFat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.

scholarly journals Transcriptome analysis of genes and pathways associated with metabolism in Scylla paramamosain under different light intensities during indoor overwintering

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Li ◽  
Junming Zhou ◽  
Huan Wang ◽  
Changkao Mu ◽  
Ce Shi ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Light Intensity ◽  
Differentially Expressed Genes ◽  
High Light ◽  
Differentially Expressed ◽  
Scylla Paramamosain ◽  
Strong Impact ◽  
Low Light ◽  
Light Intensities ◽  
Light Group

Abstract Background Scylla paramamosain is one of the commercially crucial marine crustaceans belonging to the genus Scylla, which is commonly distributed along the coasts of China, Vietnam, and Japan. Genomic and transcriptomic data are scarce for the mud crab. Light intensity is one of the ecological factors that affect S. paramamosain during indoor overwintering. To understand the energy metabolism mechanism adapted to light intensity, we analyzed the transcriptome of S. paramamosain hepatopancreas in response to different light intensities (0, 1.43, 40.31 μmol·m− 2·s− 1). Results A total of 5052 differentially expressed genes were identified in low light group (LL group, 3104 genes were up-regulated and 1948 genes were down-regulated). A total of 7403 differentially expressed genes were identified in high light group (HL group, 5262 genes were up-regulated and 2141 genes were down-regulated). S. paramamosain adapts to different light intensity environments through the regulation of amino acids, fatty acids, carbon and energy metabolism. Different light intensities had a strong impact on the energy generation of S. paramamosain by influencing oxygen consumption rate, aerobic respiration, glycolysis/gluconeogenesis pathway, the citrate cycle (TCA cycle) and fatty acid degradation. Conclusion Low light is more conducive to the survival of S. paramamosain, which needs to produce and consume relatively less energy to sustain physiological activities. In contrast, S. paramamosain produced more energy to adapt to the pressure of high light intensities. The findings of the study add to the knowledge of regulatory mechanisms related to S. paramamosain metabolism under different light intensities.

scholarly journals Identification of the Differentially Expressed Genes of Muscle Growth and Intramuscular Fat Metabolism in the Development Stage of Yellow Broilers

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Dongfeng Li ◽  
Zaixu Pan ◽  
Kun Zhang ◽  
Minli Yu ◽  
Debing Yu ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Developmental Stage ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Intramuscular Fat ◽  
Regulatory Genes ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
The Common

High-quality chicken meat is an important source of animal protein for humans. Gene expression profiles in breast muscle tissue were determined, aiming to explore the common regulatory genes relevant to muscle and intramuscular fat (IMF) during the developmental stage in chickens. Results show that breast muscle weight (BMW), breast meat percentage (BMP, %), and IMF (%) continuously increased with development. A total of 256 common differentially expressed genes (DEGs) during the developmental stage were screened. Among them, some genes related to muscle fiber hypertrophy were upregulated (e.g., CSRP3, LMOD2, MUSTN1, MYBPC1), but others (e.g., ACTC1, MYL1, MYL4) were downregulated from Week 3 to Week 18. During this period, expression of some DEGs related to the cells cycle (e.g., CCNB3, CCNE2, CDC20, MCM2) changed in a way that genetically suggests possible inhibitory regulation on cells number. In addition, DEGs associated with energy metabolism (e.g., ACOT9, CETP, LPIN1, DGAT2, RBP7, FBP1, PHKA1) were found to regulate IMF deposition. Our data identified and provide new insights into the common regulatory genes related to muscle growth, cell proliferation, and energy metabolism at the developmental stage in chickens.

scholarly journals Endophytic Bacillus megaterium BM18-2 mutated for cadmium accumulation and improving plant growth in Hybrid Pennisetum

2019 ◽  
Vol 24 ◽  
pp. e00374 ◽  
Author(s):  
Juanzi Wu ◽  
Nehal Kamal ◽  
Huanhuan Hao ◽  
Chen Qian ◽  
Zhiwei Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacillus Megaterium ◽  
Cadmium Accumulation ◽  
Hybrid Pennisetum

scholarly journals PSXIII-30 Analysis of gene expression profiles in liver and muscle tissue of pigs divergent in feed efficiency

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Energy Metabolism ◽  
Immune Function ◽  
Feed Efficiency ◽  
Molecular Mechanisms ◽  
Protein Targeting ◽  
Expression Profiles ◽  
Cell Signalling ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Joint Analysis

Abstract The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle in pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated in two populations of pigs from two different farms of origin. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals in each population were selected for further analysis of Longissimus Dorsi muscle and liver. Three different analysis were performed: 1) Identification of differentially expressed genes (DE) in liver, 2) Identification of DE genes in muscle and 3) Identification of genes commonly DE in both tissues. Hierarchical clustering revealed that transcriptomic data segregated based on the RFI value of the pig rather than farm of origin. A total of 6464 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. In the muscle-only analysis, genes associated with RNA, protein synthesis and energy metabolism were downregulated in the LRFI animals while in the liver-only analysis, genes associated with cell signalling and lipid homeostasis were upregulated in the LRFI animals. Genes that were commonly DE between muscle and liver (n = 526) were used for the joint analysis. These 526 genes were associated with protein targeting to membrane, extracellular matrix organization and immune function. There are pathways common to both muscle and liver in particular genes associated with immune function. In contrast, tissue-specific pathways contributing to differences in feed efficiency were also identified with genes associated with energy metabolism identified in muscle and lipid metabolism in liver. This study identifies key mechanisms driving changes in feed efficiency in pigs.

scholarly journals The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiome across development and adult life

2019 ◽  
Author(s):  
W Yang ◽  
C Petersen ◽  
B Pees ◽  
J Zimmermann ◽  
S Waschina ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Metabolic Network ◽  
Differentially Expressed Genes ◽  
Adult Life ◽  
Differentially Expressed ◽  
Promoter Regions ◽  
Data Set ◽  
C Elegans ◽  
Folate Biosynthesis ◽  
Transcriptome Response

AbstractThe biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiome affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode C. elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiome. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiome and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiome members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes and the affected functions. Our analysis further identified a core set of 86 genes that consistently responded to the microbiome members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiome isolates on C. elegans life history and thereby provide a framework for further analysis of microbiome-mediated host functions.

scholarly journals Genes Involved in Energy Metabolism Are Differentially Expressed During the Day–Night Cycle in Murine Retinal Pigment Epithelium

2020 ◽  
Vol 61 (5) ◽  
pp. 49 ◽  
Author(s):  
Elja M. M. Louer ◽  
Guoqiang Yi ◽  
Claudia Carmone ◽  
Joris Robben ◽  
Henk G. Stunnenberg ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Retinal Pigment Epithelium ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Differentially Expressed

P1889Quantitative global proteomics and lysine acetylome analysis of changes in left atrial appendage tissue from valvular heart disease patients with atrial fibrillation

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
T Tu ◽  
F Qin ◽  
F Bai ◽  
Y Xiao ◽  
X Liao ◽  
...  
Keyword(s):  
Heart Disease ◽  
Energy Metabolism ◽  
Valvular Heart Disease ◽  
Left Atrial ◽  
Left Atrial Appendage ◽  
Interaction Network ◽  
Bioinformatic Analysis ◽  
Cardiac Contraction ◽  
Differentially Expressed ◽  
Related Proteins

Abstract Background Previous studies have shown that acetylation plays a critical role in regulating the progress of cardiovascular diseases by acetylated histone and non-histones protein. However, the global lysine acetylome during atrial fibrillation (AF) were not fully understood. Purpose The aim of the present study was to identify the underlying mechanisms of AF via profiling of the quantitative changes of global proteomics and lysine acetylome in the left atrial appendage (LAA) tissues from valvular heart disease patients with AF. Methods This study obtained LAA specimens from patients undergoing cardiac surgery for severe valvular heart disease. The LAA specimens were obtained from both 9 patients with AF and with sinus rhythm (SR). The changes of proteome and acetylome in the AF-LAA vs SR-LAA tissues were studied using dimethyl-labeling, HPLC fractionation, affinity enrichment, LC-MS/MS analysis, database Search and bioinformatic analysis. The acetylated levels of each lysine acetylated site were normalized on the basis of the corresponding protein abundance. Results The bioinformatic analysis indicates 294 up-regulated (AF/SR ratio >1.3) proteins and 169 down-regulated (AF/SR ratio <1/1.3) proteins in the AF-LAA vs SR-LAA were detected. Moreover, 3,880 sites in 1,044 proteins were quantified. Motif analysis of the identified acetylated peptides indicated that a total of 14 significantly enriched amino acid sequence motifs from −10 to +10 surrounding the acetylated lysine (Kac) were defined according to 3412 peptides from 1115 proteins. Among the quantified acetylated sites and proteins, 231 up-regulated acetylated sites in 130 proteins and 121 down-regulated acetylated sites in 74 proteins were detected. The enrichment-based clustering analysis showed that energy metabolism and cardiac contraction-related proteins were highly differentially expressed in the AF-LAA vs SR-LAA. Meanwhile, the protein-protein interaction network of the differentially expressed acetylated proteins demonstrated that there were 146 nodes and 569 interactions in the network and quite a lot of interactions in energy metabolism-related proteins and in cardiac contraction-related proteins. Furthermore, the acetylated levels of most differentially expressed energy metabolism-related proteins involving in oxidative phosphorylation, TCA cycle, respiratory ETC, fatty acid metabolism were up-regulated. On the contrary, the acetylated levels of most acetylated sites in differentially expressed cardiac contraction-related proteins including the key contraction proteins were down-regulated. Interaction network of Ac-proteins Conclusions This study details and expands our understanding of the changes of proteome and lysine acetylome in the LAA tissues from valvular heart disease patients with AF. The data suggest important expression differences of acetylated proteins related to energy metabolism and cardiac contraction which may be involved in the matrix of AF formation and maintainence. Acknowledgement/Funding This work was supported by the grants from the National Natural Science Foundation of China (no. 81600273, no. 81570310, no.81770337 and no.81870258)

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