scholarly journals Comparison of different lipid extraction methods for different tissue types of Arabidopsis thaliana

2020 ◽  
Author(s):  
Cheka Kehelpannala ◽  
Thusitha Wasantha Thilaka Rupasinghe ◽  
Thomas Hennessy ◽  
David Bradley ◽  
Berit Ebert ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Lipid Analysis ◽  
Lipid Extraction ◽  
Extraction Methods ◽  
Single Step ◽  
Lipid Classes ◽  
Model Plant Arabidopsis Thaliana ◽  
Extraction Period ◽  
Different Tissues

Abstract Background: The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken. Results: In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana . Conclusion: While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.

scholarly journals A comparison of different lipid extraction methods for different tissue types of Arabidopsis thaliana

2020 ◽  
Author(s):  
Cheka Kehelpannala ◽  
Thusitha Wasantha Thilaka Rupasinghe ◽  
Thomas Hennessy ◽  
David Bradley ◽  
Berit Ebert ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Lipid Analysis ◽  
Lipid Extraction ◽  
Extraction Methods ◽  
Single Step ◽  
Lipid Classes ◽  
Specific Lipids ◽  
Extraction Period ◽  
Different Tissues

Abstract Background: The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken. Results: In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana. Conclusion: While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.

scholarly journals A comprehensive comparison of four methods for extracting lipids from Arabidopsis tissues

Plant Methods ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Cheka Kehelpannala ◽  
Thusitha W. T. Rupasinghe ◽  
Thomas Hennessy ◽  
David Bradley ◽  
Berit Ebert ◽  
...  
Keyword(s):  
Stress Responses ◽  
Lipid Analysis ◽  
Lipid Extraction ◽  
Single Step ◽  
Lipid Classes ◽  
Plant Tissues ◽  
Specific Lipids ◽  
Comprehensive Comparison ◽  
Extraction Period ◽  
Different Tissues

Abstract Background The plant lipidome is highly complex, and the composition of lipids in different tissues as well as their specific functions in plant development, growth and stress responses have yet to be fully elucidated. To do this, efficient lipid extraction protocols which deliver target compounds in solution at concentrations adequate for subsequent detection, quantitation and analysis through spectroscopic methods are required. To date, numerous methods are used to extract lipids from plant tissues. However, a comprehensive analysis of the efficiency and reproducibility of these methods to extract multiple lipid classes from diverse tissues of a plant has not been undertaken. Results In this study, we report the comparison of four different lipid extraction procedures in order to determine the most effective lipid extraction protocol to extract lipids from different tissues of the model plant Arabidopsis thaliana. Conclusion While particular methods were best suited to extract different lipid classes from diverse Arabidopsis tissues, overall a single-step extraction method with a 24 h extraction period, which uses a mixture of chloroform, isopropanol, methanol and water, was the most efficient, reproducible and the least labor-intensive to extract a broad range of lipids for untargeted lipidomic analysis of Arabidopsis tissues. This method extracted a broad range of lipids from leaves, stems, siliques, roots, seeds, seedlings and flowers of Arabidopsis. In addition, appropriate methods for targeted lipid analysis of specific lipids from particular Arabidopsis tissues were also identified.

scholarly journals Advances in Lipid Extraction Methods—A Review

2021 ◽  
Vol 22 (24) ◽  
pp. 13643
Author(s):  
Ramesh Kumar Saini ◽  
Parchuri Prasad ◽  
Xiaomin Shang ◽  
Young-Soo Keum
Keyword(s):  
Lipid Analysis ◽  
Neutral Lipids ◽  
Lipid Extraction ◽  
Critical Factor ◽  
Biological Tissues ◽  
Extraction Methods ◽  
Single Step ◽  
Green Solvents ◽  
Advantages And Disadvantages ◽  
Environmentally Safe

Extraction of lipids from biological tissues is a crucial step in lipid analysis. The selection of appropriate solvent is the most critical factor in the efficient extraction of lipids. A mixture of polar (to disrupt the protein-lipid complexes) and nonpolar (to dissolve the neutral lipids) solvents are precisely selected to extract lipids efficiently. In addition, the disintegration of complex and rigid cell-wall of plants, fungi, and microalgal cells by various mechanical, chemical, and enzymatic treatments facilitate the solvent penetration and extraction of lipids. This review discusses the chloroform/methanol-based classical lipid extraction methods and modern modifications of these methods in terms of using healthy and environmentally safe solvents and rapid single-step extraction. At the same time, some adaptations were made to recover the specific lipids. In addition, the high throughput lipid extraction methodologies used for liquid chromatography-mass spectrometry (LC-MS)-based plant and animal lipidomics were discussed. The advantages and disadvantages of various pretreatments and extraction methods were also illustrated. Moreover, the emerging green solvents-based lipid extraction method, including supercritical CO2 extraction (SCE), is also discussed.

scholarly journals Differential expression analysis of boron transporters and some stress-related genes in response to 24-epibrassinolide and boron by semi-quantitative RT-PCR in Arabidopsis thaliana (L.) Heynh

Genetika ◽  
2016 ◽  
Vol 48 (2) ◽  
pp. 547-563 ◽  
Author(s):  
Yonca Surgun ◽  
Bekir Çöl ◽  
Betül Bürün
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Differential Expression Analysis ◽  
Transcriptional Level ◽  
Rt Pcr ◽  
Model Plant Arabidopsis Thaliana ◽  
Induced Genes ◽  
High Concentrations ◽  
Stress Related Genes ◽  
Root Tissues

Plant steroidal hormones, brassinosteroids (BRs), promote plant developmental processes and enhance tolerance to several abiotic stresses including high boron (B) stress. To examine the possible role of BR in high B-induced stress at the transcriptional level, we investigated the response of B transporter genes (BOR1-4), high B-induced genes (MATE, Hsp-like), BR-induced genes (Hsp70-4, Hsp90-1) and other stress-related genes (LTI/COR78, LEA4-5) upon exogenous treatments of 24-epibrassinolide (EBL) on Arabidopsis thaliana (L.) Heynh exposed to high concentrations of boric acid (BA) using semi-quantitative RT-PCR. BA treatments led to down regulation of BOR1 and BOR3 genes in leaf and root tissues and higher concentration of EBL further decreased expression of these genes in roots. The expression of high B-induced genes was observed to be upregulated by 1 ?M EBL treatment under high B stress in both tissues of the seedlings. The upregulation of BR-induced genes were clearly evident in root tissues co-treated with 1 ?M EBL and BA as compared to BA alone. Higher concentration of EBL was found to be more effective in increasing expression of LTI/COR78 gene in root and LEA4-5 gene in shoot tissues. To our knowledge, this is the first report how exogenous application of EBL modulates high B stress responses at molecular level in model plant Arabidopsis thaliana.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Fused Graphical Lasso Recovers Flowering Time Mutation Genes in Arabidopsis Thaliana

Inventions ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 52
Author(s):  
Rajan Kapoor ◽  
Aniruddha Datta ◽  
Michael Thomson
Keyword(s):  
Arabidopsis Thaliana ◽  
Crop Improvement ◽  
Phenotypic Traits ◽  
The Novel ◽  
Model Plant ◽  
Graphical Lasso ◽  
Analysis Strategy ◽  
Model Plant Arabidopsis Thaliana ◽  
Beneficial Traits ◽  
Delayed Flowering

Conventional breeding approaches that focus on yield under highly favorable nutrient conditions have resulted in reduced genetic and trait diversity in crops. Under the growing threat from climate change, the mining of novel genes in more resilient varieties can help dramatically improve trait improvement efforts. In this work, we propose the use of the joint graphical lasso for discovering genes responsible for desired phenotypic traits. We prove its efficiency by using gene expression data for wild type and delayed flowering mutants for the model plant. Arabidopsis thaliana shows that it recovers the mutation causing genes LNK1 and LNK2. Some novel interactions of these genes were also predicted. Observing the network level changes between two phenotypes can also help develop meaningful biological hypotheses regarding the novel functions of these genes. Now that this data analysis strategy has been validated in a model plant, it can be extended to crop plants to help identify the key genes for beneficial traits for crop improvement.

scholarly journals Identification and Quantification of Coumarins by UHPLC-MS in Arabidopsis Thaliana Natural Populations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1804
Author(s):  
Izabela Perkowska ◽  
Joanna Siwinska ◽  
Alexandre Olry ◽  
Jérémy Grosjean ◽  
Alain Hehn ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
High Performance ◽  
Biological Activities ◽  
Natural Populations ◽  
Biologically Active ◽  
Stress Factors ◽  
Mass Spectrometry Analysis ◽  
Engineering Research ◽  
Spectrometry Analysis ◽  
Model Plant Arabidopsis Thaliana

Coumarins are phytochemicals occurring in the plant kingdom, which biosynthesis is induced under various stress factors. They belong to the wide class of specialized metabolites well known for their beneficial properties. Due to their high and wide biological activities, coumarins are important not only for the survival of plants in changing environmental conditions, but are of great importance in the pharmaceutical industry and are an active source for drug development. The identification of coumarins from natural sources has been reported for different plant species including a model plant Arabidopsis thaliana. In our previous work, we demonstrated a presence of naturally occurring intraspecies variation in the concentrations of scopoletin and its glycoside, scopolin, the major coumarins accumulating in Arabidopsis roots. Here, we expanded this work by examining a larger group of 28 Arabidopsis natural populations (called accessions) and by extracting and analysing coumarins from two different types of tissues–roots and leaves. In the current work, by quantifying the coumarin content in plant extracts with ultra-high-performance liquid chromatography coupled with a mass spectrometry analysis (UHPLC-MS), we detected a significant natural variation in the content of simple coumarins like scopoletin, umbelliferone and esculetin together with their glycosides: scopolin, skimmin and esculin, respectively. Increasing our knowledge of coumarin accumulation in Arabidopsis natural populations, might be beneficial for the future discovery of physiological mechanisms of action of various alleles involved in their biosynthesis. A better understanding of biosynthetic pathways of biologically active compounds is the prerequisite step in undertaking a metabolic engineering research.

scholarly journals Long-Term Exposure to Nanosized TiO2 Triggers Stress Responses and Cell Death Pathways in Pulmonary Epithelial Cells

2021 ◽  
Vol 22 (10) ◽  
pp. 5349
Author(s):  
Mayes Alswady-Hoff ◽  
Johanna Samulin Erdem ◽  
Santosh Phuyal ◽  
Oskar Knittelfelder ◽  
Animesh Sharma ◽  
...  
Keyword(s):  
Cell Death ◽  
Epithelial Cells ◽  
Health Effects ◽  
Stress Responses ◽  
Cell Stress ◽  
Lipid Classes ◽  
Long Term Effects ◽  
Cell Death Pathways ◽  
Pulmonary Epithelial Cells

There is little in vitro data available on long-term effects of TiO2 exposure. Such data are important for improving the understanding of underlying mechanisms of adverse health effects of TiO2. Here, we exposed pulmonary epithelial cells to two doses (0.96 and 1.92 µg/cm2) of TiO2 for 13 weeks and effects on cell cycle and cell death mechanisms, i.e., apoptosis and autophagy were determined after 4, 8 and 13 weeks of exposure. Changes in telomere length, cellular protein levels and lipid classes were also analyzed at 13 weeks of exposure. We observed that the TiO2 exposure increased the fraction of cells in G1-phase and reduced the fraction of cells in G2-phase, which was accompanied by an increase in the fraction of late apoptotic/necrotic cells. This corresponded with an induced expression of key apoptotic proteins i.e., BAD and BAX, and an accumulation of several lipid classes involved in cellular stress and apoptosis. These findings were further supported by quantitative proteome profiling data showing an increase in proteins involved in cell stress and genomic maintenance pathways following TiO2 exposure. Altogether, we suggest that cell stress response and cell death pathways may be important molecular events in long-term health effects of TiO2.

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