scholarly journals Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

PLoS Biology ◽  
2016 ◽  
Vol 14 (6) ◽  
pp. e1002475 ◽  
Author(s):  
Adam J. Book ◽  
Gina R. Lewin ◽  
Bradon R. McDonald ◽  
Taichi E. Takasuka ◽  
Evelyn Wendt-Pienkowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Content ◽  
Cellulolytic Activity ◽  
Selection Of

Selection of reliable reference genes for analysis of gene expression in the rat placenta

2021 ◽  
Author(s):  
Caiyun Ge ◽  
Pengxia Yu ◽  
Man Fang ◽  
Hui Wang ◽  
Yuanzhen Zhang
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Selection Of

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 Memory Based Cuckoo Search Algorithm for Feature Selection of Gene Expression Dataset

2021 ◽  
pp. 100572
Author(s):  
Malek Alzaqebah ◽  
Khaoula Briki ◽  
Nashat Alrefai ◽  
Sami Brini ◽  
Sana Jawarneh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Search Algorithm ◽  
Cuckoo Search ◽  
Cuckoo Search Algorithm ◽  
Gene Expression Dataset ◽  
Selection Of

scholarly journals Use of Heat Stress Responsive Gene Expression Levels for Early Selection of Heat Tolerant Cabbage (Brassica oleracea L.)

2013 ◽  
Vol 14 (6) ◽  
pp. 11871-11894 ◽  
Author(s):  
Hyun Park ◽  
Won Jung ◽  
Sang Lee ◽  
Jun Song ◽  
Suk-Yoon Kwon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Brassica Oleracea ◽  
Early Selection ◽  
Expression Levels ◽  
Heat Tolerant ◽  
Responsive Gene ◽  
Brassica Oleracea L ◽  
Gene Expression Levels ◽  
Selection Of

Gene Expression Profiling of Tumors From Heavily Pretreated Patients With Metastatic Cancer for the Selection of Therapy

2017 ◽  
Vol 40 (2) ◽  
pp. 140-145 ◽  
Author(s):  
Joseba Rebollo ◽  
Manuel Sureda ◽  
Elena M. Martinez ◽  
Francisco J. Fernández-Morejón ◽  
José Farré ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Metastatic Cancer ◽  
Heavily Pretreated ◽  
Pretreated Patients ◽  
Selection Of

O-122 Gene expression signatures for prognosis in NSCLC, coupled with signatures of oncogenic pathway deregulation, provide a novel approach for selection of molecular targets

Lung Cancer ◽  
2005 ◽  
Vol 49 ◽  
pp. S42-S43
Author(s):  
R. Petersen ◽  
A. Bild ◽  
H. Dressman ◽  
M. Joshi ◽  
D. Conlon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Targets ◽  
Oncogenic Pathway ◽  
Novel Approach ◽  
Gene Expression Signatures ◽  
Pathway Deregulation ◽  
Selection Of

Selection of reference genes for gene expression studies in chronically hypoxic heart

2018 ◽  
Vol 120 ◽  
pp. 22-23
Author(s):  
D. Benak ◽  
D. Sotakova ◽  
J. Neckar ◽  
F. Kolar ◽  
M. Hlavackova
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Hypoxic Heart ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Selection Of

scholarly journals Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Dorota M. Krzyżanowska ◽  
Anna Supernat ◽  
Tomasz Maciąg ◽  
Marta Matuszewska ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Reference Genes ◽  
Significance Threshold ◽  
Expression Studies ◽  
Reverse Transcription Quantitative Pcr ◽  
Gene Expression Studies ◽  
The Stability ◽  
Selection Of

Abstract Reverse transcription quantitative PCR (RT-qPCR), a method of choice for quantification of gene expression changes, requires stably expressed reference genes for normalization of data. So far, no reference genes were established for the Alphaproteobacteria of the genus Ochrobactrum. Here, we determined reference genes for gene expression studies in O. quorumnocens A44. Strain A44 was cultured under 10 different conditions and the stability of expression of 11 candidate genes was evaluated using geNorm, NormFinder and BestKeeper. Most stably expressed genes were found to be rho, gyrB and rpoD. Our results can facilitate the choice of reference genes in the related Ochrobactrum strains. O. quorumnocens A44 is able to inactivate a broad spectrum of N-acyl homoserine lactones (AHLs) – the quorum sensing molecules of many Gram-negative bacteria. This activity is attributed to AiiO hydrolase, yet it remains unclear whether AHLs are the primary substrate of this enzyme. Using the established RT-qPCR setup, we found that the expression of the aiiO gene upon exposure to two AHLs, C6-HLS and 3OC12-HSL, does not change above the 1-fold significance threshold. The implications of this finding are discussed in the light of the role of quorum sensing-interfering enzymes in the host strains.

scholarly journals Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

2018 ◽  
Vol 67 (1) ◽  
pp. 57-65
Author(s):  
Alexandre Vaillant ◽  
Astrid Honvault ◽  
Stéphanie Bocs ◽  
Maryline Summo ◽  
Garel Makouanzi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Variance Components ◽  
Genetic Effect ◽  
Field Conditions ◽  
Eucalyptus Urophylla ◽  
Rna Seq ◽  
Intermediate Phenotypes ◽  
False Discovery ◽  
Hybrid Clones ◽  
Selection Of

Abstract To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665±634) than in xylem (23,637±1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were diffe­rentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approa­ches displayed correlated results. A focus on the phenylpro­panoid, cellulose and xylan pathways revealed a large majo­rity of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of geno­type, five of which displaying also clone variance compo­nents. These preliminary results are promising in evaluating whether gene expression can serve as possible ‘intermediate phenotypes’ that could improve the accuracy of selection of grossly observable traits.

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