Tag Archives: PlantGDB

Happy Memorial Day (and gardening) to you this weekend!

Summer is rapidly approaching and I’m so looking forward to a nice long Memorial Day weekend with outdoor cookouts and plenty of time for gardening. Those of us New Englanders that have endured a long, hard winter really appreciate ending our hibernation and spending time outside in the spring and summer. Gardening is one of my favorite activities, and in this region we are strongly advised to wait until Memorial Day to do the majority of our planting. But after hearing that one of my colleagues had just come down with poison ivy, I began to wonder why these plants so often get in the way of enjoying our short season of outdoor life. Poison ivy, oak and sumac have always been a very annoying part of growing up in New England. They are plants that I never had too many fond thoughts of. Yet, I never really knew much at all about them – other than the itchy, irritating red rash they cause – that is. I decided to do a little digging, reasoning that they must have some redeeming, or at least interesting, biological qualities. After all, it seems that they are only protecting themselves against all of us herbivores. They can’t exactly run away from us, so they have to keep us at bay some how. Their defense mechanism seems quite clever actually.

A quick check in Wikipedia revealed that poison ivy is a member of the Anacardiaceae family of flowering plants. To my surprise cashew and pistachio plants are also members of this same family. Apparently not all members of this plant family are skin irritants at least! The reaction you get from poison ivy is due to contact with urushiol, a very potent oil found in the sap. In fact, only about 1 nanogram is needed to cause a rash (as little as ¼ of an ounce is said to be necessary to cause a rash on every person on earth). The rash, or Toxicodendron dermatitis, is a result of the immune system’s delayed hypersensitivity response – i.e., the reaction may take hours or days to develop. Interestingly, about 20% of the population is not allergic to urushiol. They can wander through poison ivy indefinitely and have no problems (the genetic variations responsible for this trait are certain to be an interesting topic for future work in the genomics and immunology fields). Another surprising fact was that many animals don’t have any type of allergic reaction to urushiol. Deer, goats, horses and cattle are fine with these poisonous plants. In fact, one of the suggested ways to get rid of poison ivy is to get a goat. This seems to be another very interesting genetics of immunity issue – how and why do some animals manage to not only evade these plants, but thrive on them. As more complete genomes are resolved the genes, SNPs, or genetic variations in general, will be uncovered and we should all be enlightened.

Continue reading

New Online Tutorials on ZFIN, SGD, PlantGDB and GBrowse Resources

Comprehensive tutorials on the model organism databases ZFIN, SGD and PlantGDB and GBrowse, a model organism genome browser, enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA September 15, 2008 — OpenHelix today announced the availability of new tutorial suites on several model organism resources including Zebrafish Information Network (ZFIN), Saccharomyces Genome Database (SGD) and the Plant Genome Database (PlantGDB) and also a tutorial using genome browsers with GBrowse. These four tutorials expand OpenHelix’s model organism database training which now also includes tutorials on MGI (mouse), FlyBase (drosophila), Gramene (grasses), RGD (rat), WormBase and more to come soon. Model organisms are integral to our understanding of basic biology and modern biomedical research. ZFIN is a collection of data, tools, and resources on the zebrafish (Danio rerio), a popular model organism for developmental biology and genetics research and SGD is a collection of data, tools and analyses centered around Saccharomyces cerevisiae, commonly known as bakers’ or budding yeast. PlantGDB is the primary resource for plant comparative genomics.

Additionally, OpenHelix has added a tutorial on GBrowse, a web application that allows you to explore genomic sequences together with annotated data. GBrowse is rapidly becoming the genomic browser of choice amongst model organism databases, because the browser is both universal and yet customizable.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ZFIN

  • to perform effective searches and understand the displays
  • to access advanced searches enabling multifaceted queries
  • to use the various databases of genes and markers, expression data, mutant genotype/phenotype details, ontologies, and more
  • to investigate many related resources associated with ZFIN

SGD

  • to navigate the SGD site, locate Basic and Advanced Search options, and use the site map to access additional search tools
  • perform the two Basic SGD Quick and Text Search types and understand the displays
  • to navigate the SGD Locus Page and access data from a variety of tools, tabs, and links
  • to investigate many related resources associated with SGD

PlantGDB

  • to perform quick searches and navigate sequence pages
  • to conduct BLAST searches across several plant species of your choice
  • to create exon/intron gene predictions and sequence alignments
  • to construct tables displaying highly varied information from many datasets
  • GBrowse

  • the basic layout and search methods at GBrowse
  • how to access detailed annotation data tied to genomic sequences
  • how to select and customize annotations using Tracks
  • how to upload and incorporate your own data or other external data sources
  • take a tour of different GBrowse installations at model organism databases

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics.