When microspores decide to become embryos — cellular and molecular changesThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology.

2006 ◽  
Vol 84 (4) ◽  
pp. 668-678 ◽  
Author(s):  
K. Peter Pauls ◽  
John Chan ◽  
Grant Woronuk ◽  
Derek Schulze ◽  
Janice Brazolot
Keyword(s):  
Gene Expression ◽  
Cell Biology ◽  
Cell Activation ◽  
Early Stage ◽  
Microspore Culture ◽  
Brassica Napus L ◽  
Embryogenic Cell ◽  
Haploid Embryos ◽  
Microarray Analyses ◽  
Selection Of

Cultured microspores can be induced to develop into fully functional haploid embryos instead of mature pollen. The ability of these cells to change their development in response to environmental stimuli is an exceptional example of totipotency in plants. Discovering the triggers of embryo development in microspore cultures could lead to a greater understanding of the early stages of embryogenesis in plants and might be used to increase the range of crop plants to which microspore culture can be applied for the production of double haploid homozygous lines. The information might also help to define the general characteristics of pluripotent cells in any organism. In this review, the changes that occur in cellular organization and gene expression in early-stage microspore cultures of several species are discussed. Responding cells in these cultures enlarge, their nuclei are repositioned to their cell centres, and their cytoplasms become filled with fragmented vacuoles. We used flow cytometry to track cellular changes in canola ( Brassica napus L.) microspore cultures as well as microarray analyses and real-time PCR to compare gene expression in embryogenic and nonembryogenic cells. A model for embryogenic cell activation in plants that involves alkalinization, Ca2+ signaling, and changes in GTPase activity that lead to significant changes in gene expression is discussed.

scholarly journals Gene Expression Profiling for the Purposes of Biomarker Discovery in Oral Potentially Malignant Lesions: A Systematic Review

2013 ◽  
Vol 7 ◽  
pp. CMO.S12950 ◽  
Author(s):  
Ahmad A. Abdulmajeed ◽  
Camile S. Farah
Keyword(s):  
Gene Expression ◽  
Biomarker Discovery ◽  
Multiple Gene ◽  
Diagnosis And Prognosis ◽  
Potentially Malignant ◽  
Novel Biomarkers ◽  
Malignant Lesions ◽  
Microarray Studies ◽  
Microarray Analyses ◽  
Selection Of

Early and accurate diagnosis of oral potentially malignant lesions (OPML) is of critical importance in preventing malignant transformation. Although histopathological interpretation of the degree of epithelial dysplasia is considered the gold standard for diagnosis, this method is subjective and lacks sensitivity. Therefore, many attempts have been made to identify objective molecular biomarkers to improve diagnosis. Microarray technology has the advantage of screening the expression of the whole genome making it one of the best tools for searching for novel biomarkers. However, microarray studies of OPMLs are limited, and no review has been published to highlight and compare their findings. In this paper, we systematically review all studies that have incorporated microarray analyses in the investigation of gene profile alterations in OPMLs and suggest a set of commonly dysregulated genes across multiple gene expression profile studies. This list of common genes may help focus selection of markers for further analysis regarding their importance in the diagnosis and prognosis of OPMLs.

In vitro selection of herbicide resistance in microspore-derived embryos of oilseed rape (Brassica napus L.)

2006 ◽  
Vol 3 (1) ◽  
pp. 33-38
Author(s):  
Xu Ling ◽  
Zhang Guo-Qing ◽  
Gu Hong-Hui ◽  
He Yun ◽  
Zhou Wei-Jun
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
In Vitro Selection ◽  
Chromosome Doubling ◽  
Microspore Culture ◽  
Brassica Napus L ◽  
Regenerated Plants ◽  
Short Time ◽  
Selection Of

AbstractUsing four oilseed rape (Brassica napus L.) F1 hybrids (7039, 7040, 282 and 5102) as donor plants for microspore culture, the experiment was conducted to select glyphosate- and haloxyfop-resistant embryos through application of these substances to the cultural media with microspore-derived embryos in vitro. Genotypes 7039 and 7040 were used to select glyphosate-resistant regenerated plants, and genotypes 282 and 5102 to select haloxyfop-resistant plants. The embryos at cotyledonary stage were grown on glyphosate- and haloxyfop-containing MS-2 medium for 2 weeks. The non-resistant embryos collapsed after a short time, while the resistant ones turned green and survived for 2 weeks. Transferred into the normal MS-2 medium for further plant regeneration, the regenerated plants from green embryos showed tolerance to 0.25% sprayed glyphosate, indicating the effectiveness and reliability of this in vitro selection method. When the regenerated plants selected from 0.02% haloxyfop were sprayed with 0.05% haloxyfop, most of them grew well; however, the survival rate of the regenerated plants from 0.01% haloxyfop-containing medium was lower. The present experiment indicates that the use of 0.02% haloxyfop in the selection of haloxyfop-resistant plants was more promising than that of 0.01%. The chromosome doubling efficiency of regenerated plants reached 34% and 52% after being treated with 170 mg/l colchicine for 20 and 30 h, respectively.

487 Gene Expression Profiles for Prognosis Provide a Novel Approach for Selection of Individualized Therapies in Early Stage Colon Carcinoma

2008 ◽  
Vol 134 (4) ◽  
pp. A-66
Author(s):  
Katherine S. Garman ◽  
Marian Grade ◽  
Chaitanya Acharya ◽  
Kelli S. Walters ◽  
Shivani Sud ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Carcinoma ◽  
Early Stage ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Novel Approach ◽  
Selection Of

An Integrated Feature Selection Algorithm for Cancer Classification using Gene Expression Data

2019 ◽  
Vol 21 (9) ◽  
pp. 631-645 ◽  
Author(s):  
Saeed Ahmed ◽  
Muhammad Kabir ◽  
Zakir Ali ◽  
Muhammad Arif ◽  
Farman Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Accuracy ◽  
Early Stage ◽  
Small Sample Size ◽  
Feature Selection Method ◽  
Small Sample ◽  
Expression Data ◽  
Base Function

Aim and Objective: Cancer is a dangerous disease worldwide, caused by somatic mutations in the genome. Diagnosis of this deadly disease at an early stage is exceptionally new clinical application of microarray data. In DNA microarray technology, gene expression data have a high dimension with small sample size. Therefore, the development of efficient and robust feature selection methods is indispensable that identify a small set of genes to achieve better classification performance. Materials and Methods: In this study, we developed a hybrid feature selection method that integrates correlation-based feature selection (CFS) and Multi-Objective Evolutionary Algorithm (MOEA) approaches which select the highly informative genes. The hybrid model with Redial base function neural network (RBFNN) classifier has been evaluated on 11 benchmark gene expression datasets by employing a 10-fold cross-validation test. Results: The experimental results are compared with seven conventional-based feature selection and other methods in the literature, which shows that our approach owned the obvious merits in the aspect of classification accuracy ratio and some genes selected by extensive comparing with other methods. Conclusion: Our proposed CFS-MOEA algorithm attained up to 100% classification accuracy for six out of eleven datasets with a minimal sized predictive gene subset.

scholarly journals Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L.

2021 ◽  
Vol 22 (3) ◽  
pp. 1033
Author(s):  
Abirami Rajavel ◽  
Selina Klees ◽  
Johanna-Sophie Schlüter ◽  
Hendrik Bertram ◽  
Kun Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Brassica Napus ◽  
Oil Content ◽  
Seed Oil ◽  
Seed Oil Content ◽  
Complex Interplay ◽  
Brassica Napus L ◽  
Data Set ◽  
Developmental Switches

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals The Potential of 2-aza-8-Oxohypoxanthine as a Cosmetic Ingredient

Cosmetics ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 60
Author(s):  
Hisae Aoshima ◽  
Masayuki Ito ◽  
Rinta Ibuki ◽  
Hirokazu Kawagishi
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Microarray Analysis ◽  
Dna Microarray ◽  
Cell Activation ◽  
Skin Barrier ◽  
Efficacy Evaluation ◽  
Activation Effect ◽  
Expression Levels ◽  
Dna Microarray Analysis

In this study, we verified the effects of 2-aza-8-oxohypoxanthine (AOH) on human epidermal cell proliferation by performing DNA microarray analysis. Cell proliferation was assessed using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, which measures mitochondrial respiration in normal human epidermal keratinocyte (NHEK) cells. Gene expression levels were determined by DNA microarray analysis of 177 genes involved in skin aging and disease. AOH showed a significant increase in cell viability at concentrations between 7.8 and 31.3 μg/mL and a significant decrease at concentrations above 250 μg/mL. DNA microarray analysis showed that AOH significantly increased the gene expression of CLDN1, DSC1, DSG1, and CDH1 (E-cadherin), which are involved in intercellular adhesion and skin barrier functioning. AOH also up-regulated the expression of KLK5, KLK7, and SPIMK5, which are proteases involved in stratum corneum detachment. Furthermore, AOH significantly stimulated the expression of KRT1, KRT10, TGM1, and IVL, which are considered general differentiation indicators, and that of SPRR1B, a cornified envelope component protein. AOH exerted a cell activation effect on human epidermal cells. Since AOH did not cause cytotoxicity, it was considered that the compound had no adverse effects on the skin. In addition, it was found that AOH stimulated the expression levels of genes involved in skin barrier functioning by DNA microarray analysis. Therefore, AOH has the potential for practical use as a cosmetic ingredient. This is the first report of efficacy evaluation tests performed for AOH.

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