IHUB
Collaborative International Network For Ionomics
A new tool for identifying interesting papers based on the actions of researchers browsing RSS feeds of scientific literature. The power of LitCloud's concept is that it aggregates the actions of many users, as they look for papers of interest, to rank papers based on their importance for a given subject as they are published.
Improving our understanding of how plants take up, transport and store their nutrient and toxic elements, collectively known as the ionome, will benefit human health and the natural environment. Here you will find curated ionomic data on many thousands of plant samples freely available to the public.
Arabidopsis Thaliana
commonly referred to as Arabidopsis, is a small flowering plant widely used as a model organism in plant biology and genetics. Native to Europe, Asia, and northern Africa, it is now a cornerstone of modern biological research due to its simplicity and genetic tractability.
Particularities
Genomic Simplicity
- Arabidopsis thaliana was the first plant to have its genome completely sequenced (2000), comprising about 125 million base pairs and around 27,000 genes.
- Its compact genome makes it ideal for studying gene functions and regulatory
Fast Life Cycle
- Life cycle of approximately 6-8 weeks, from germination to seed production.
- Facilitates rapid experimentation and observation across generations.
Ease of Cultivation
- Thrives in small spaces with minimal requirements.
- Can be grown in soil or on agar plates in controlled conditions.
Why Arabidopsis is a Model Organism:
2. Molecular Studies
- Ideal for studying processes such as signal transduction, gene regulation, and epigenetics.
- Serves as a model for other plant species, particularly crops.
4. Environmental and Stress Responses
Well-suited for studying abiotic (drought, salinity) and biotic (pathogen) stress responses, which are critical for agricultural research.
3. Omics Integration
Facilitates multi-omics studies (genomics, transcriptomics, proteomics, metabolomics) due to abundant resources and databases (e.g., TAIR - The Arabidopsis Information Resource).
1. Genetic Research
- Extensive mutant libraries and transgenic lines are available for studying gene function.
- Widely used in forward and reverse genetics experiments.
Arabidopsis Database
Rice Database
Rice databases are specialized platforms that provide comprehensive information about the genomics, genetics, transcriptomics, and functional biology of rice (Oryza sativa). They are crucial resources for researchers aiming to understand rice biology, improve crop yield, or develop resilient varieties to meet global food demands.
1. The Rice Genome Annotation Project (RGAP)
- Focus: High-quality annotation of the rice genome.
- Features:
- Genome sequence and gene structure information.
- Tools for gene and sequence search, expression analysis, and comparative genomics.
- Applications: Functional genomics and breeding programs.
2. Rice Annotation Project Database (RAP-DB)
- Focus: Comprehensive annotation of the Oryza sativa japonica genome.
- Features:
Genome browser for visualizing gene models.
Cross-references to orthologous genes in other species.
Integration with transcriptomics and proteomics data.
- Applications: Studying gene evolution and functional annotation.
3.Applications of Rice Databases:
- Crop Improvement: Identifying genes related to yield, disease resistance, or stress tolerance for breeding.
- Functional Genomics: Annotating genes and their roles in growth, development, or metabolism.
- Comparative Genomics: Exploring evolutionary relationships between rice and other cereals like wheat and maize.
- Climate Resilience Research: Developing varieties that adapt to drought, salinity, and temperature extremes.
Rice Database
100 completed ICP-MS runs
28799 unique lines
26268 total samples
- 6872 total samples
- 946 unique lines
- 24 completed ICP-MS runs
- 11924 unique lines
- 6408 unique genes
- 228 completed ICP-MS runs