scholarly journals Comparative study ofSaccharomyces cerevisiaewine strains to identify potential marker genes correlated to desiccation stress tolerance

2016 ◽  
Vol 16 (3) ◽  
pp. fow015 ◽  
Author(s):  
Angela Capece ◽  
Sonia Votta ◽  
Nicoletta Guaragnella ◽  
Marianna Zambuto ◽  
Rossana Romaniello ◽  
...  
Keyword(s):  
Comparative Study ◽  
Stress Tolerance ◽  
Desiccation Stress ◽  
Marker Genes ◽  
Potential Marker

scholarly journals Exogenous Application of Brassinosteroid 24-Norcholane 22(S)-23-Dihydroxy Type Analogs to Enhance Water Deficit Stress Tolerance in Arabidopsis thaliana

2021 ◽  
Vol 22 (3) ◽  
pp. 1158
Author(s):  
Katy Díaz ◽  
Luis Espinoza ◽  
Rodrigo Carvajal ◽  
Evelyn Silva-Moreno ◽  
Andrés F. Olea ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Water Deficit ◽  
Alternative Pathway ◽  
Recovery Period ◽  
Homogeneous Solution ◽  
Water Deficit Stress ◽  
Marker Genes ◽  
Exogenous Application

Brassinosteroids (BRs) are plant hormones that play an essential role in plant development and have the ability to protect plants against various environmental stresses, such as low and high temperature, drought, heat, salinity, heavy metal toxicity, and pesticides. Mitigation of stress effects are produced through independent mechanisms or by interaction with other important phytohormones. However, there are few studies in which this property has been reported for BRs analogs. Thus, in this work, the enhancement of drought stress tolerance of A. thaliana was assessed for a series of 2-deoxybrassinosteroid analogs. In addition, the growth-promoting activity in the Rice Lamina Inclination Test (RLIT) was also evaluated. The results show that analog 1 exhibits similar growth activity as brassinolide (BL; used as positive control) in the RLIT bioassay. Interestingly, both compounds increase their activities by a factor of 1.2–1.5 when they are incorporated to polymer micelles formed by Pluronic F-127. On the other hand, tolerance to water deficit stress of Arabidopsis thaliana seedlings was evaluated by determining survival rate and dry weight of seedlings after the recovery period. In both cases, the effect of analog 1 is higher than that exhibited by BL. Additionally, the expression of a subset of drought stress marker genes was evaluated in presence and absence of exogenous applied BRs. Results obtained by qRT-PCR analysis, indicate that transcriptional changes of AtDREBD2A and AtNCED3 genes were more significant in A. thaliana treated with analog 1 in homogeneous solution than in that treated with BL. These changes suggest the activation of alternative pathway in response to water stress deficit. Thus, exogenous application of BRs synthetic analogs could be a potential tool for improvement of crop production under stress conditions.

scholarly journals Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 189
Author(s):  
Kinga Kęska ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska ◽  
Małgorzata Czernicka
Keyword(s):  
Stress Tolerance ◽  
De Novo ◽  
Average Length ◽  
Marker Genes ◽  
Long Term Memory ◽  
Low Oxygen ◽  
Waterlogging Tolerance ◽  
Pre Treatment ◽  
Waterlogging Treatment

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.

scholarly journals Overexpression of native Musa-miR397 enhances plant biomass without compromising abiotic stress tolerance in banana

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Prashanti Patel ◽  
Karuna Yadav ◽  
Ashish Kumar Srivastava ◽  
Penna Suprasanna ◽  
Thumballi Ramabhatta Ganapathi
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Copper Deficiency ◽  
Plant Biomass ◽  
Abiotic Stress Tolerance ◽  
Nacl Stress ◽  
Marker Genes ◽  
Wild Type ◽  
Trade Offs ◽  
Micro Rnas

Abstract Plant micro RNAs (miRNAs) control growth, development and stress tolerance but are comparatively unexplored in banana, whose cultivation is threatened by abiotic stress and nutrient deficiencies. In this study, a native Musa-miR397 precursor harboring 11 copper-responsive GTAC motifs in its promoter element was identified from banana genome. Musa-miR397 was significantly upregulated (8–10) fold in banana roots and leaves under copper deficiency, correlating with expression of root copper deficiency marker genes such as Musa-COPT and Musa-FRO2. Correspondingly, target laccases were significantly downregulated (>−2 fold), indicating miRNA-mediated silencing for Cu salvaging. No significant expression changes in the miR397-laccase module were observed under iron stress. Musa-miR397 was also significantly upregulated (>2 fold) under ABA, MV and heat treatments but downregulated under NaCl stress, indicating universal stress-responsiveness. Further, Musa-miR397 overexpression in banana significantly increased plant growth by 2–3 fold compared with wild-type but did not compromise tolerance towards Cu deficiency and NaCl stress. RNA-seq of transgenic and wild type plants revealed modulation in expression of 71 genes related to diverse aspects of growth and development, collectively promoting enhanced biomass. Summing up, our results not only portray Musa-miR397 as a candidate for enhancing plant biomass but also highlight it at the crossroads of growth-defense trade-offs.

scholarly journals Aquatic Plant Genomics: Advances, Applications, and Prospects

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Shiqi Hu ◽  
Gaojie Li ◽  
Jingjing Yang ◽  
Hongwei Hou
Keyword(s):  
Molecular Markers ◽  
Comparative Study ◽  
Stress Tolerance ◽  
Transcriptome Sequencing ◽  
Aquatic Plant ◽  
Plant Genomics ◽  
Sequencing Technology ◽  
Genome Composition ◽  
Genomics Research ◽  
Biological Methods

Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.

scholarly journals A comparative study of metagenomics analysis pipelines at the species level

2016 ◽  
Author(s):  
Yee Voan Teo ◽  
Nicola Neretti
Keyword(s):  
Comparative Study ◽  
Species Level ◽  
Marker Genes ◽  
Closely Related Species ◽  
Full Reference ◽  
Quantification Accuracy ◽  
Reference Genomes ◽  
Metagenomics Analysis ◽  
Higher Sensitivity

AbstractMany metagenomics classification tools have been developed with the rapid growth of the metagenomics field. However, the classification of closely related species remains a challenge for this field. Here, we compared MetaPhlAn2, kallisto and Kraken for their performances in two metagenomics settings, human metagenomics and environmental metagenomics. Our comparative study showed that kallisto demonstrated higher sensitivity than MetaPhlAn2 and Kraken and better quantification accuracy than Kraken at the species level. We also showed that classification tools that run on full reference genomes misidentified many species that were not truly present. In order to reduce false positives, we introduced marker genes from MetaPhlAn2 into our pipeline, which uses kallisto for the classification step, as an additional filtering step for species detection.

scholarly journals The association between fecal enterotoxigenic B. fragilis with colorectal cancer

2019 ◽  
Author(s):  
Fakhri Haghi ◽  
Elshan Goli ◽  
Bahman Mirzaei ◽  
Habib Zeighami
Keyword(s):  
Colorectal Cancer ◽  
Direct Detection ◽  
Mucosal Immune Response ◽  
Colorectal Disease ◽  
Marker Genes ◽  
Tissue Samples ◽  
Potential Marker ◽  
Paired Normal Tissue ◽  
Stool Samples ◽  
Pcr Targeting

Abstract Background Enterotoxigenic Bacteroides fragilis (ETBF) is an enterotoxin-producing bacterium that possibily has a role in the occurrence and progression of colorectal cancer (CRC) by modulating the mucosal immune response and inducing epithelial cell changes. The aim of this study was to investigate the frequency of ETBF in stool samples of CRC patients and healthy volunteers.Methods A total of 60 stool samples from confirmed CRC patients and 60 stool samples from healthy volunteers with no personal or familial history or diagnosis of colorectal disease were collected. Stool samples were screened for direct detection of B. fragilis using PCR targeting the marker genes of neu and bft. Enterotoxin isotypes bft-1, bft-2 and bft-3 were also detected in B. fragilis positive samples.Results The frequency of B. fragilis among CRC and control cases was 58.3% and 26.6%, respectively (P<0.05). The rate of bft gene in CRC cases was significantly higher than in controls (P<0.05). Also, the presence of bf t gene in CRC patients stage III was significantly higher than stages I and II (P< 0.05). Enterotoxin isotype bft-2 was detected with higher frequency among CRC patients than healthy control (P<0.05).Conclusion Our results show the association between fecal ETBF and CRC, and we suggest that detection of ETBF may be a potential marker for colorectal cancer diagnosis. However, additional investigations on tumor and paired normal tissue samples are required to substantiate this possible correlation.

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