DWARF WITH SLENDER LEAF1 encoding a histone deacetylase plays diverse roles in rice development
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ABSTRACT:
PROVIDER: PRJNA577663 | ENA |
REPOSITORIES: ENA
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Project description:To detect the genes that differentially expressed between dsl1 and wild type at the vegetative stage, we performed microarray analysis using Rice (US) gene 1.0 ST array. We analyzed gene expression profiles of the shoot apices of WT and dsl1.
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Project description:Comparison of Snell Dwarf and Wild Type mouse liver RNA levels in response to 3-NPA (3-nitropropionic acid). Keywords: time-course
2004-06-07 | GSE1381 | GEO
Project description:Despite the progress achieved in elucidating the ecological mechanisms of adaptive radiation, there has been little focus on documenting the extent of adaptive differentiation in physiological functions during this process. Moreover, a thorough understanding of the genomic basis underlying phenotypic adaptive divergence is still in its infancy. One important evolutionary process for which causal genetic mechanisms are largely unknown pertains to life-history trade-offs. We analysed patterns of gene transcription in liver tissue of sympatric dwarf and normal whitefish from two natural lakes, as well as from populations reared in controlled environments, using a 16 006-gene cDNA microarray in order to: (i) document the extent of physiological adaptive divergence between sympatric dwarf and normal species pairs, and (ii) explore the molecular mechanisms of differential life history trade-offs between growth and survival potentially involved in their adaptive divergence. In the two natural lakes, 6.45% of significantly transcribed genes showed regulation either in parallel fashion (2.39%) or in different directions (4.06%). Among genes showing parallelism in regulation patterns, we observed a higher proportion of over-expressed genes in dwarf relative to normal whitefish (70.6%). Patterns observed in controlled conditions were also generally congruent with those observed in natural populations. Dwarf whitefish consistently showed significant over-expression of genes potentially associated with survival through enhanced activity (energy metabolism, iron homeostasis, lipid metabolism, detoxification), whereas more genes associated with growth (protein synthesis, cell cycle, cell growth) were generally down-regulated in dwarf relative to normal whitefish. Overall, parallelism in patterns of gene transcription, as well as patterns of interindividual variation across controlled and natural environments, provide strong indirect evidence for the role of selection in the evolution of differential regulation of genes involving a vast array of potentially adaptive physiological processes between dwarf and normal whitefish. Our results also provide a first mechanistic, genomic basis for the observed trade-off in life-history traits distinguishing dwarf and normal whitefish species pairs, wherein enhanced survival via more active swimming, necessary for increased foraging and predator avoidance, engages energetic costs that translate into slower growth rate and reduced fecundity in dwarf relative to normal whitefish.
2010-03-31 | GSE21130 | GEO
Project description:Rice gall dwarf virus (RGDV) is the causal agent of rice gall dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection.
2012-12-01 | GSE34264 | GEO
Project description:Kinase activity of cGMP-dependant, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic growth transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. We compared growth plate cartilage gene expression profiles of PRKG2R678X/R678X, dwarf and PRKG2R678X/+, unaffected Angus cattle using microarray technology to discover pathways regulated by PRKG2. Calves used in this analysis were produced by the mating between a dwarf carrier sire and two dams- a mother (carrier) and daughter (dwarf) pair. Each dam produced three calves by embryo transfer, which were born in two calving groups. Growth plate cartilage was harvested from the tibia of each animal at approximately 215 days of age. Total RNA was extracted by a modified Trizol protocol. The bovine cDNA microarray (GEO Accession: GPL8813) was used for this analysis. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group. Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis. Dwarf PRKG2 R678X homozygous cattle were compared to unaffected, age matched samples. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group (i.e. unaffected samples had 2 technical replicates). Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.
2011-08-24 | E-GEOD-31627 | biostudies-arrayexpress
Project description:Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection.
2012-12-01 | GSE34263 | GEO
Project description:Kinase activity of cGMP-dependant, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic growth transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. We compared growth plate cartilage gene expression profiles of PRKG2R678X/R678X, dwarf and PRKG2R678X/+, unaffected Angus cattle using microarray technology to discover pathways regulated by PRKG2. Calves used in this analysis were produced by the mating between a dwarf carrier sire and two dams- a mother (carrier) and daughter (dwarf) pair. Each dam produced three calves by embryo transfer, which were born in two calving groups. Growth plate cartilage was harvested from the tibia of each animal at approximately 215 days of age. Total RNA was extracted by a modified Trizol protocol. The bovine cDNA microarray (GEO Accession: GPL8813) was used for this analysis. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group. Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.
2011-08-25 | GSE31627 | GEO
Project description:Female Ames dwarf mouse (df/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
2005-01-10 | GSE1086 | GEO
Project description:Abstract Objective: This study was designed to reveal the potential molecular mechanisms of long-term overgrazing-induced dwarf of sheepgrass (Leymus chinensis). Methods: The electrospray ionization-mass spectrometry (ESI-MS) system was used to generate the proteomic data in dwarf sheepgrass from long-term overgrazed rangeland and normal sheepgrass from long-term enclosed rangeland. The differentially expressed proteins (DEPs) between dwarf and normal sheepgrass were identified, following the analyses of potential functions and interactions of DEPs. Additionally, the expressions of DEPs were confirmed by high performance liquid chromatography-mass spectrum (HPLC-MS) system with multiple reaction monitoring (MRM) method. Results: A total of 51 up-regulated proteins and 53 down-regulated proteins were identified in the dwarf sheepgrass, compared with the normal controls. Some proteins like SAT5_ARATH and DAPA_MAIZE were enriched in the pathway of amino acid biosynthesis. In the protein-protein interaction network, RPOB2_LEPTE, A0A023H9M8_9STRA, ATPB_DIOEL, RBL_AMOTI and DNAK_GRATL interacted with each other. Furthermore, 4 modules were extracted from the PPI network. In addition, the HPLC-MS analysis confirmed the up-regulation of ATPB_DIOEL and the down-regulation of DNAK_GRATL in dwarf samples compared with the controls. Conclusion: The up-regulated ATPB_DIOEL and down-regulated DNAK_GRATL, as well as the proteins that interacted with them, such as RPOB2_LEPTE, A0A023H9M8_9STRA and RBL_AMOTI, may be associated with the long-term overgrazing-induced sheepgrass dwarf.
2017-05-26 | PXD006548 | Pride
Project description:Female Ames dwarf mouse (df/df) with ad libitum access to water and fed 30% less of the standard pelleted diet with respect to the amount consumed by female ad libitum fed df/df mice (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
2005-01-10 | GSE1087 | GEO