scholarly journals Expression Patterns and Gene Analysis of the Cellulose Synthase Gene Superfamily in Eucalyptus grandis

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1254
Author(s):  
Guo Liu ◽  
Yaojian Xie ◽  
Xiuhua Shang ◽  
Zhihua Wu
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Primary Cell Wall ◽  
Regulation Mechanism ◽  
Cellulose Content ◽  
Qrt Pcr ◽  
Different Parts

Cellulose is the world’s most abundant renewable energy resource, and a variety of cellulose synthase genes are involved in the biosynthesis of cellulose. In the process of cellulose synthesis, all cellulose synthases are interrelated and act synergistically. In this study, we analyzed the contents of cellulose, hemicellulose, and lignin in the different parts and tissues of E. grandis. The results showed that the cellulose content had greater differences among three different heights. On this basis, we carried out the transcriptome-wide profiling of gene expression patterns using RNA sequencing. A total of 2066 differentially expressed genes were identified for three pairwise comparisons between three different heights, most of which were related to the programmed photosynthetic membrane and photosystem. A total of 100 transcripts of CSs (58 CesA and 42 Csl) were obtained from transcriptome libraries. The expression pattern of these genes indicated that different CS genes had a wide range of expression profiles. A phylogenetic analysis of 135 reference CS genes showed that the CSs of E. grandis were clustered into six major groups (CesA1-9, CslA, CslB/H, CslD, CslE, and CslG). Based on the weighted gene co-expression network analysis, a dual-directional regulation mechanism between Csl and CesA proteins in the cellulose biosynthesis was identified. The gene expression profile analysis, using qRT-PCR in different tissues of E. grandis, demonstrated that the CSs were highly expressed in xylem, and CesAs had a higher relative expression than Csls. The analysis of sequence similarity combined with the expression pattern indicated that the CesA1, 3, and 6 transcripts were associated with the biosynthesis of the secondary cell wall, and CesA4, 5, and 7 transcripts were more likely to associate with the biosynthesis of the primary cell wall. Finally, the qRT-PCR analysis confirmed the expression of 11 selected CSs in three different parts of E. grandis.

scholarly journals GENECFE-ANFIS: A NEURO-FUZZY INFERENCE SYSTEM TO INFER GENE-GENE INTERACTIONS BASED ON RECOGNITION OF MICROARRAY GENE EXPRESSION PATTERNS

2007 ◽  
Vol 19 (02) ◽  
pp. 71-78 ◽  
Author(s):  
Cheng-Long Chuang ◽  
Chung-Ming Chen ◽  
Grace S. Shieh ◽  
Joe-Air Jiang
Keyword(s):  
Gene Expression ◽  
Fuzzy Inference System ◽  
Fuzzy Inference ◽  
Expression Patterns ◽  
Gene Interactions ◽  
Microarray Gene Expression ◽  
Inference System ◽  
Qrt Pcr ◽  
Neuro Fuzzy ◽  
Microarray Gene

A neuro-fuzzy inference system that recognizes the expression patterns of genes in microarray gene expression (MGE) data, called GeneCFE-ANFIS, is proposed to infer gene interactions. In this study, three primary features are utilized to extract genes' expression patterns and used as inputs to the neuro-fuzzy inference system. The proposed algorithm learns expression patterns from the known genetic interactions, such as the interactions confirmed by qRT-PCR experiments or collected through text-mining technique by surveying previously published literatures, and then predicts other gene interactions according to the learned patterns. The proposed neuro-fuzzy inference system was applied to a public yeast MGE dataset. Two simulations were conducted and checked against 112 pairs of qRT-PCR confirmed gene interactions and 77 TFs (Transcriptional Factors) pairs collected from literature respectively to evaluate the performance of the proposed algorithm.

scholarly journals Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jorge A. Ramírez-Tejero ◽  
Jaime Jiménez-Ruiz ◽  
Alicia Serrano ◽  
Angjelina Belaj ◽  
Lorenzo León ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Expression Level ◽  
Resistant Cultivars ◽  
Pathogen Invasion ◽  
Wide Range ◽  
Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

Biological Image Analysis via Matrix Approximation

2011 ◽  
pp. 166-170
Author(s):  
Jieping Ye ◽  
Ravi Janardan ◽  
Sudhir Kumar
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Controlled Vocabulary ◽  
Gene Expression Patterns ◽  
Image Content ◽  
Gene Expressions ◽  
Microarray Gene Expression ◽  
Individual Gene

Understanding the roles of genes and their interactions is one of the central challenges in genome research. One popular approach is based on the analysis of microarray gene expression data (Golub et al., 1999; White, et al., 1999; Oshlack et al., 2007). By their very nature, these data often do not capture spatial patterns of individual gene expressions, which is accomplished by direct visualization of the presence or absence of gene products (mRNA or protein) (e.g., Tomancak et al., 2002; Christiansen et al., 2006). For instance, the gene expression pattern images of a Drosophila melanogaster embryo capture the spatial and temporal distribution of gene expression patterns at a given developmental stage (Bownes, 1975; Tsai et al., 1998; Myasnikova et al., 2002; Harmon et al., 2007). The identification of genes showing spatial overlaps in their expression patterns is fundamentally important to formulating and testing gene interaction hypotheses (Kumar et al., 2002; Tomancak et al., 2002; Gurunathan et al., 2004; Peng & Myers, 2004; Pan et al., 2006). Recent high-throughput experiments of Drosophila have produced over fifty thousand images (http://www. fruitfly.org/cgi-bin/ex/insitu.pl). It is thus desirable to design efficient computational approaches that can automatically retrieve images with overlapping expression patterns. There are two primary ways of accomplishing this task. In one approach, gene expression patterns are described using a controlled vocabulary, and images containing overlapping patterns are found based on the similarity of textual annotations. In the second approach, the most similar expression patterns are identified by a direct comparison of image content, emulating the visual inspection carried out by biologists [(Kumar et al., 2002); see also www.flyexpress.net]. The direct comparison of image content is expected to be complementary to, and more powerful than, the controlled vocabulary approach, because it is unlikely that all attributes of an expression pattern can be completely captured via textual descriptions. Hence, to facilitate the efficient and widespread use of such datasets, there is a significant need for sophisticated, high-performance, informatics-based solutions for the analysis of large collections of biological images.

scholarly journals Yy1 regulates Senp1 contributing to AMPA receptor GluR1 expression following neuronal depolarization

2019 ◽  
Vol 26 (1) ◽  
Author(s):  
Tao Wu ◽  
Mary E. Donohoe
Keyword(s):  
Gene Expression ◽  
Ampa Receptor ◽  
Neuronal Activity ◽  
Cortical Neurons ◽  
Expression Patterns ◽  
Luciferase Assay ◽  
Regulation Mechanism ◽  
Phosphatase Inhibitors ◽  
Ampa Receptor Subunit

Abstract Background Neuronal activity-induced changes in gene expression patterns are important mediators of neuronal plasticity. Many neuronal genes can be activated or inactivated in response to neuronal depolarization. Mechanisms that activate gene transcription are well established, but activity-dependent mechanisms that silence transcription are less understood. It is also not clear what is the significance of inhibiting these genes during neuronal activity. Methods Quantitative Real Time-PCR, western blot and immunofluorescence staining were performed to examine the expression of Senp1 and GluR1 in mouse cortical neurons. The alterations of Yy1 phosphorylation upon neuronal depolarization and the interaction of Yy1 with Brd4 were studied by protein co-immunoprecipitation. The regulators of Yy1 phosphorylation were identified by phosphatase inhibitors. Chromatin immunoprecipitation, in vitro DNA binding assay, luciferase assay and gene knockdown experiments were used to validate the roles of Yy1 and its phosphorylation as well as Brd4 in regulating Senp1 expression. Results We report that neuronal depolarization deactivates the transcription of the SUMO protease Senp1, an important component regulating synaptic transmission, scaling, and plasticity, through Yy1. In un-stimulated neurons, Senp1 transcription is activated by a Yy1-Brd4 transcription factor protein complex assembled on the Senp1 promoter. Upon membrane depolarization, however, Yy1 is dephosphorylated and the Yy1-Brd4 complex is evicted from the Senp1 promoter, reducing Senp1 transcription levels. Both Yy1 and Senp1 promote the expression of AMPA receptor subunit GluR1, a pivotal component in learning and memory. Conclusions These results reveal an axis of Yy1/Brd4-Senp1 which regulates the expression of GluR1 during neuronal depolarization. This implicates a regulation mechanism in silencing gene expression upon neuronal activity.

scholarly journals The Spatio-Temporal Distribution of Cell Wall-Associated Glycoproteins During Wood Formation in Populus

2020 ◽  
Vol 11 ◽  
Author(s):  
Tayebeh Abedi ◽  
Romain Castilleux ◽  
Pieter Nibbering ◽  
Totte Niittylä
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Wood Formation ◽  
Cell Type Specificity ◽  
Spatio Temporal ◽  
Ray Cell

Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.

Follistatin alters myostatin gene expression in C2C12 muscle cells

2004 ◽  
Vol 52 (2) ◽  
pp. 135-141 ◽  
Author(s):  
H. Kocams¸ ◽  
N. Gulmez ◽  
S. Aslan ◽  
M. Nazlı
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Time Course ◽  
Expression Patterns ◽  
Mrna Level ◽  
Gene Expression Pattern ◽  
Muscle Cells ◽  
Treated Group ◽  
Myostatin Gene ◽  
Significant Difference

The objective of the present study was to determine the effects of follistatin addition on myostatin and follistatin gene expression patterns in C2C12 muscle cells. C2C12 cells were administered with 100 ng/ml recombinant human (rh) follistatin in Dulbecco's modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS), 4 mM glutamine and antibiotics daily for three days. Rh follistatin was not added in the control wells. Follistatin and myostatin gene cDNAs were synthesised by reverse transcriptase polymerase chain reaction (RT-PCR).The time course of follistatin gene expression pattern was similar in both the control and the follistatin-treated group. Myostatin mRNA level significantly increased in the follistatin-treated group after 24 h of culture (Fig. 3, P < 0.01). Amounts then sharply decreased (Fig. 3, P < 0.01) at 48 h of culture, whereas there was no significant difference between the control and the follistatin-treated group at 72 h of culture. Our results demonstrated that myostatin and follistatin mRNA were expressed in C2C12 cells and rh follistatin changed the myostatin expression pattern.

scholarly journals Differential Gene Expression of Brachypodium distachyon Roots Colonized by Gluconacetobacter diazotrophicus and the Role of BdCESA8 in the Colonization

2021 ◽  
Author(s):  
Xuan Yang ◽  
Kathleen A. Hill ◽  
Ryan S. Austin ◽  
Lining Tian
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Rna Sequencing ◽  
Crop Production ◽  
Brachypodium Distachyon ◽  
Cellulose Synthesis ◽  
Gibberellin Biosynthesis ◽  
Cellulose Content ◽  
Gluconacetobacter Diazotrophicus ◽  
Nitrogen Fixing

Alternatives to synthetic nitrogen fertilizer are needed to reduce the costs of crop production and offset environmental damage. Nitrogen-fixing bacterium Gluconacetobacter diazotrophicus has been proposed as a possible biofertilizer for monocot crop production. However, the colonization of G. diazotrophicus in most monocot crops is limited and deep understanding of the response of host plants to G. diazotrophicus colonization is still lacking. In this study, the molecular response of the monocot plant model Brachypodium distachyon was studied during G. diazotrophicus root colonization. The gene expression profiles of B. distachyon root tissues colonized by G. diazotrophicus were generated via next-generation RNA sequencing, and investigated through gene ontology and metabolic pathway analysis. The RNA sequencing results indicated that Brachypodium is actively involved in G. diazotrophicus colonization via cell wall synthesis. Jasmonic acid, ethylene, gibberellin biosynthesis. nitrogen assimilation, and primary and secondary metabolite pathways are also modulated to accommodate and control the extent of G. diazotrophicus colonization. Cellulose synthesis is significantly downregulated during colonization. The loss of function mutant for Brachypodium cellulose synthase 8 (BdCESA8) showed decreased cellulose content in xylem and increased resistance to G. diazotrophicus colonization. This result suggested that the cellulose synthesis of the secondary cell wall is involved in G. diazotrophicus colonization. The results of this study provide insights for future research in regard to gene manipulation for efficient colonization of nitrogen-fixing bacteria in Brachypodium and monocot crops. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Selection and validation of reference genes for normalization of qRT-PCR data to study secondary metabolite related genes in industrial hemp

2021 ◽  
Author(s):  
Michihito Deguchi ◽  
Shobha Potlakayala ◽  
Zachary Spuhler ◽  
Hannah George ◽  
Vijay Sheri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heavy Metal ◽  
Expression Analysis ◽  
Reference Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Differential Gene ◽  
Industrial Hemp

Abstract Industrial hemp (Cannabis sativa L.) is a dioecious crop widely known for its production of phytocannabinoids, flavonoids, and terpenes. In the past two years since its legalization, there has been significant interest in researching this important crop for pharmaceutical applications. Although many scientific reports have demonstrated gene expression analysis of hemp through OMICs approaches, accurate validation of omics data cannot be performed because of lack of reliable reference genes for normalization of qRT-PCR data. The differential gene expression patterns of 13 candidate reference genes under osmotic, heavy metal, hormonal, and UV stress were evaluated through four software packages: geNorm, NormFinder, BestKeeper, and RefFinder. The EF-1a ranked as the most stable reference gene across all stresses, TUB was the most stable under osmotic stress, and TATA was the most stable under both heavy metal and hormonal stress. The expression profiles of two cannabinoid pathway genes, AAE1 and THCAS, using the two most stable and single least stable reference genes confirmed that two most stables genes were apt for normalization of gene expression data. This work will contribute to the future studies on the expression analysis of hemp genes regulating the synthesis, transport and accumulation of secondary metabolites.

scholarly journals Transvection regulates the sex-biased expression of a fly X-linked gene

Science ◽  
2021 ◽  
Vol 371 (6527) ◽  
pp. 396-400 ◽  
Author(s):  
Charalampos Chrysovalantis Galouzis ◽  
Benjamin Prud’homme
Keyword(s):  
Gene Expression ◽  
Sexual Dimorphism ◽  
Sex Determination ◽  
Expression Pattern ◽  
X Chromosome ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Regulatory Interaction ◽  
Linked Gene ◽  
Homologous Chromosomes

Sexual dimorphism in animals results from sex-biased gene expression patterns. These patterns are controlled by genetic sex determination hierarchies that establish the sex of an individual. Here we show that the male-biased wing expression pattern of the Drosophila biarmipes gene yellow, located on the X chromosome, is independent of the fly sex determination hierarchy. Instead, we find that a regulatory interaction between yellow alleles on homologous chromosomes (a process known as transvection) silences the activity of a yellow enhancer functioning in the wing. Therefore, this enhancer can be active in males (XY) but not in females (XX). This transvection-dependent enhancer silencing requires the yellow intron and the chromatin architecture protein Mod(mdg4). Our results suggest that transvection can contribute more generally to the sex-biased expression of X-linked genes.

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