Project description:Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression. These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance. Ten days old seedlings of two Arabidopsis ecotypes, Sha and Ler, were treated with 100 mM NaCl on MS plate. Plant materials were collected for RNA extraction at 4th days after treatments.

Project description:In this study, RNA-Seq was used to reveal the differences of molecular pathways in hepatopancreas of O. niloticus adapated to water with salinity of 8 or 16 practical salinity (psu), respectively, with fish at freshwater as the control,. Significantly changed pathways were mainly related to lipid metabolism, glucose utilization, protein consumption, osmotic regulation, signal transduction and immunology. Based on the tendencies from freshwater to 8 or 16 psu, the differentially expressed gene unions were categorized into eight unique models, which were further classified into three categories which were constant-change (either keep increasing or decreasing), change-then-stable and stable-then-change. In constant-change category, steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were extremely significantly affected by ambient salinity (P < 0.01), indicating that these pathways play pivotal roles in molecular response to salinity acclimation from freshwater to saline water in O. niloticus, and should be the main research focus in the future. In change-then-stable category, ribosome, oxidative phosphorylation, peroxisome proliferator-activated receptors (PPAR) signaling pathway, fat digestion and absorption changed significantly with ambient increasing salinity (P < 0.01), showing these pathways were sensitive to environmental salinity variation, but had a response threshold, and would stop changing once salinity exceeds the threshold. In stable-then-change category, protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis - keratan sulfate were the top changed pathways (P < 0.01), suggesting that these pathways were not sensitive to salinity variation, but these pathways will respond significantly under salinity exceeding a certain level. The pathways and genes reported in this study laid on a solid foundation for future studies in understanding the underlying mechanism for salinity adaptation of freshwater fish. Examination of 3 different salinities treated hepatopancreas in Nile tilapia

Project description:In this study, RNA-Seq was used to reveal the differences of molecular pathways in hepatopancreas of O. niloticus adapated to water with salinity of 8 or 16 practical salinity (psu), respectively, with fish at freshwater as the control,. Significantly changed pathways were mainly related to lipid metabolism, glucose utilization, protein consumption, osmotic regulation, signal transduction and immunology. Based on the tendencies from freshwater to 8 or 16 psu, the differentially expressed gene unions were categorized into eight unique models, which were further classified into three categories which were constant-change (either keep increasing or decreasing), change-then-stable and stable-then-change. In constant-change category, steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were extremely significantly affected by ambient salinity (P < 0.01), indicating that these pathways play pivotal roles in molecular response to salinity acclimation from freshwater to saline water in O. niloticus, and should be the main research focus in the future. In change-then-stable category, ribosome, oxidative phosphorylation, peroxisome proliferator-activated receptors (PPAR) signaling pathway, fat digestion and absorption changed significantly with ambient increasing salinity (P < 0.01), showing these pathways were sensitive to environmental salinity variation, but had a response threshold, and would stop changing once salinity exceeds the threshold. In stable-then-change category, protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis - keratan sulfate were the top changed pathways (P < 0.01), suggesting that these pathways were not sensitive to salinity variation, but these pathways will respond significantly under salinity exceeding a certain level. The pathways and genes reported in this study laid on a solid foundation for future studies in understanding the underlying mechanism for salinity adaptation of freshwater fish.

Project description:Background: Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, use a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of C. semilaevis to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity change. Results: The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of C. semilaevis. One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, cytoskeleton remodeling, and apoptosis were affected during acclimation to low salinity. Genes acat2, fdps, hmgcr, hmgcs1, mvk, pmvk, ebp, lss, dhcr7, and dhcr24 were up-regulated and abat, ddc, acy1 were down-regulated in metabolic pathways. Genes aqp10 and slc6a6 were down-regulated in osmoregulation and ion transport. Genes abat, fdps, hmgcs1, mvk, pmvk and dhcr7 were first reported to be associated with salinity adaptation in teleosts. Conclusions: Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish.

Project description:Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression. These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance.

			Action	DRS
	F1RS20171012_AK_DDA_AllSamples.msf	Msf
	F1RS20171012_AK_DDA_AllSamples.pep.xml	Pepxml
	F1RS20171012_AK_DDA_Sample04.raw	Raw
	F1RS20171012_AK_DDA_Sample06.raw	Raw
	F1RS20171012_AK_DDA_Sample15.raw	Raw

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A Data-Independent-Acquisition-based proteomic approach towards understanding the acclimation strategy of Microchloropsis gaditana CCMP526 in hypersaline conditions

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Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga <i>Microchloropsis gaditana</i> CCMP526 in Hypersaline Conditions.

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