scholarly journals Comparative transcriptome analysis revealed the conversions of stamens into pistil-like structures in Aegilops crassa cytoplasmic male sterile wheat (Triticum aestivum)

2019 ◽  
Author(s):  
Qi Liu ◽  
Zi han Liu ◽  
Wei Li ◽  
Xi Yue Song
Keyword(s):  
Energy Metabolism ◽  
Mechanical Response ◽  
Paraffin Section ◽  
Oxygen Metabolism ◽  
Differentially Expressed ◽  
Morphological Observation ◽  
Male Sterile ◽  
Class B ◽  
High Degree ◽  
Aegilops Crassa

Abstract Background: Aegilops crassa cytoplasm is an essential material for investigating the cytoplasm of cytoplasmic male sterility (CMS). Moreover, the stamens of C303A exhibit a high degree of pistillody, turning almost white. However, the underlying molecular mechanism of C303A pistillody remains unclear. Therefore, to gain a better understanding of C303A, the phenotypic and cytological features of C303A were observed to identify the key stage that the homeotic transformation of stamens into pistil-like structures, transcriptome profiles were determined by Illumina RNA sequencing technology (RNA-Seq) of stamen. Results: Through morphological observation, for CMS wheat with Aegilops crassa cytoplasm (CMS-C) line C303A, the pistil of which developed normally, but stamens were ultimately aborted and the stamens released no pollen when mature. According to the results of the paraffin section, stamens began to transform into pistils or pistil-like structures at binucleate stage (BNS). Therefore, the stamens of line C303A and its maintainer 303B at BNS were collected for transcriptome sequencing. A total of 20,444 wheat genes were detected as being differentially expressed between C303A and 303B stamens, included 10,283 up-regulated and 10,161 down-regulated genes. Gene Ontology Enrichment Analyses showed that most differentially expressed genes (DEGs) distributed on the metabolic process, cell, cellular process, catalytic activity and cell part. From KEGG, we knew that DEGs were mainly enriched to energy metabolism. We also found several essential genes that may contribute to pistillody in C303A. Based on the above analysis, we believe that due to the confusion of energy metabolism and reactive oxygen metabolism, thereby inducing the pistillody and eventually lead to the abortion of C303A. Conclusion:This study unravels the complex transcriptome profiles in C303A stamen, highlighting the energy metabolism and class B MADS-box genes related to pistillody. This work should lay the foundations of future studies in the mechanical response to wheat stamen and pollen development in CMS.

scholarly journals Comparative transcriptome analysis revealed the conversions of stamens into pistil-like structures in Aegilops crassa cytoplasmic male sterile wheat (Triticum aestivum)

2019 ◽  
Author(s):  
Qi Liu ◽  
Zi han Liu ◽  
Wei Li ◽  
Xi Yue Song
Keyword(s):  
Energy Metabolism ◽  
Mechanical Response ◽  
Paraffin Section ◽  
Oxygen Metabolism ◽  
Differentially Expressed ◽  
Morphological Observation ◽  
Male Sterile ◽  
Class B ◽  
High Degree ◽  
Aegilops Crassa

Abstract Background: Aegilops crassa cytoplasm is an essential material for investigating the cytoplasm of cytoplasmic male sterility (CMS). Moreover, the stamens of C303A exhibit a high degree of pistillody, turning almost white. However, the underlying molecular mechanism of C303A pistillody remains unclear. Therefore, to gain a better understanding of C303A, the phenotypic and cytological features of C303A were observed to identify the key stage that the homeotic transformation of stamens into pistil-like structures, transcriptome profiles were determined by Illumina RNA sequencing technology (RNA-Seq) of stamen. Results: Through morphological observation, for CMS wheat with Aegilops crassa cytoplasm (CMS-C) line C303A, the pistil of which developed normally, but stamens were ultimately aborted and the stamens released no pollen when mature. According to the results of the paraffin section, stamens began to transform into pistils or pistil-like structures at binucleate stage (BNS). Therefore, the stamens of line C303A and its maintainer 303B at BNS were collected for transcriptome sequencing. A total of 20,444 wheat genes were detected as being differentially expressed between C303A and 303B stamens, included 10,283 up-regulated and 10,161 down-regulated genes. Gene Ontology Enrichment Analyses showed that most differentially expressed genes (DEGs) distributed on the metabolic process, cell, cellular process, catalytic activity and cell part. From KEGG, we knew that DEGs were mainly enriched to energy metabolism. We also found several essential genes that may contribute to pistillody in C303A. Based on the above analysis, we believe that due to the confusion of energy metabolism and reactive oxygen metabolism, thereby inducing the pistillody and eventually lead to the abortion of C303A. Conclusion:This study unravels the complex transcriptome profiles in C303A stamen, highlighting the energy metabolism and class B MADS-box genes related to pistillody. This work should lay the foundations of future studies in the mechanical response to wheat stamen and pollen development in CMS.

scholarly journals Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum

2021 ◽  
Vol 31 (1) ◽  
pp. 36-56
Author(s):  
Vanessa Schnaars ◽  
Lars Wöhlbrand ◽  
Sabine Scheve ◽  
Christina Hinrichs ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Gene Clusters ◽  
Transport Systems ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Type Iv ◽  
Aromatic Compound Degradation ◽  
High Degree ◽  
Reducing Bacteria ◽  
Gliding Movement

The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69–96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

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.

Een Onderzoek Naar De Effecten Van Luister- En Leesvaardigheids-Training

1986 ◽  
Vol 26 ◽  
pp. 7-17 ◽  
Author(s):  
Heiko Anceaux
Keyword(s):  
Control Group ◽  
Light Weight ◽  
Research Project ◽  
Ability Test ◽  
School Year ◽  
Class B ◽  
Ability Tests ◽  
Listening Ability ◽  
Grammar Tests ◽  
High Degree

This article discusses the final written results of a research project carried out in a number of first-year forms in three Dutch schools for secondary education. In each of the three schools the research project offered a light-weight extra listening programme in class A, and a light-weight extra reading programme in class B, while the regular programme for French was carried out in class C, which served as a control group. At the end of the school year the pupils' reading and listening ability, grammatical knowledge and vocabulary (receptive as well as productive) were evaluated in classes, and C. The general conclusion is that at the elementary level a light-weight extra listening programme does indeed lead to a high degree of listening ability when compared with the other groups. This holds good to an even slightly greater extent for the light-weight extra reading programme. Moreover, it appears that the extra reading programme also leads to a high degree of listening ability. The control groups who had the greatest amount of grammatical training, do indeed score highest in grammar tests, but this knowledge does not become apparent at all in the ability tests /reading and listening). The results of the vocabulary tests are hardly clear. It is probable that at this level reading promotes the acquisition of a productive vocabulary. In the ability test girls generally score higher than boys.

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.

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