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Nitrogen-ion-beam implantation effect on rice dry seeds

ABSTRACT: Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE36152 | GEO | 2012/03/01

SECONDARY ACCESSION(S): PRJNA152893

REPOSITORIES: GEO

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Nitrogen-ion-beam implantation effect on rice dry seeds

Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam. Three sample groups—the controls, the ion-beam implanted samples and vacuum-treated samples. Three replicates were included in each sample group. Radiation induced gene expression rice seedlings was measured at 96 hours after germination of the seeds.

2012-03-01 | E-GEOD-36152 | biostudies-arrayexpress

LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [time]

Project description:Linear energy transfer (LET) is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET-dependently regulated genes, whose expression level increased with the rise of LET value, were also identified.

2016-07-01 | GSE78997 | GEO

LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [LET]

2016-07-01 | GSE78994 | GEO

LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [LET]

2016-07-01 | E-GEOD-78994 | biostudies-arrayexpress

LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [time]

2016-07-01 | E-GEOD-78997 | biostudies-arrayexpress

Transcription profiling of rat keratinocytes exposed to a 56Fe ion beam

Project description:The purpose of the present work was to examine gene expression patterns in a rat keratinocyte line exposed to a 56Fe ion beam Experiment Overall Design: The cells were exposed to 1.01 geV/nucleon 56Fe ions generated by the NASA Space Radiation Laboratory facility. Data from Affymetrix rat microarrays (RAT 230_2) were processed by BRB ArrayTools 3.3.0 software, and the Gene Ontogeny (GO) database was utilized to categorize significantly responding genes.

2007-11-29 | E-GEOD-6299 | biostudies-arrayexpress

Multiplexed protein and drug imaging by super-resolution ion beam imaging

Project description:Multiplexed protein and drug imaging by super-resolution ion beam imaging

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A phase I/II clinical study of Carbon Ion Radiotherapy using 1 fraction for Liver Metastasis from Colorectal Cancer

Project description:Interventions: Prescribed heavy-ion beam (carbon-ion beam) dose. Initial dose 36Gy(RBE). Dose escalated until dose limiting toxicity is met. Primary outcome(s): Acute toxicity and initial tumor response Study Design: expanded access Non-randomized

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Gene expression profiles in growth-inhibition rice seedling implanted by the low-energy N+ beam

Project description:Knowledge of genes expression related to the growth-inhibition biological effects induced by low-energy N+ in plant. This study investigated the differentially expressed genes (DEGs) related to the growth-inhibition biological effects induced by low-energy N+ in plant by RNA-seq. Ion fluences (40Kev, curren intensity=3mA) of 1×1017N+/cm2，2×1017N+/cm2，4×1017N+/cm2，6×1017N+/cm2，8×1017N+/cm2 were used in the ion-implanted experiments. Biological effects with growht-inhibition were arised from the samples implanted by the ion fluences of 6×1017N+/cm2，8×1017N+/cm2 because of the inhibition of seedling height and root length. We sequenced mRNA from these damaged rice seedlings and others. We identified 776 transcripts as reliable DEGs at the growth inhibition sample campared with the control.The pathway enrichment analysis of these 776 DEGs showed that pathway of photosynthesis - antenna proteins was down-regulated. Meanwhile transcription factor analysis showed that genes related to AUX/IAA were also down-regulated. This study were contributed to a better understanding of molecular events responsible for adaption to the implantation of low-energy ion beam in plant.

2016-04-09 | GSE45908 | GEO

Multiplexed protein and drug imaging by super-resolution ion beam imaging

Project description:Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses.

2021-05-25 | GSE141138 | GEO

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