Difference between revisions of "Laurmagee: Week 11"
From LMU BioDB 2013
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#* All of the definitions were found: In Merriam Webster Online, Retrieved November 11, 2013, from http://www.merriam-webster.com/dictionary. | #* All of the definitions were found: In Merriam Webster Online, Retrieved November 11, 2013, from http://www.merriam-webster.com/dictionary. | ||
# Write an outline of the article. | # Write an outline of the article. | ||
| + | #* Nitrogen is often found in soil and fertilizer and it is essential for proper plant growth. | ||
| + | #* When a plant is deprived of necessary nitogen, rhizobia infect the roots of the plant to create nodules. The bacteria then begin nitrogen-fixation in the cell cytoplasm. This establishes a symbiotic relationship between the rhizobia and the plant, where the plant is provided with nitrogen and the rhizobia receive plant carbon compounds. | ||
| + | #* The genome of Sinorhizobium meliloti is being studied, because it serves as a rhizobia symbiont to alfalfa and can offer incite on how other endosymbionts function. | ||
| + | #* Sinorhizobium meliloti is classified as a a-probacterium that is also closely related to bacterial plant and animal pathogens. Sprain 1021 of Sinorhizobium meliloti has been completely sequenced. | ||
| + | #* The genome of interest consists of three replicons: one large replicon of 3.65 Mb, a smaller replicon (pSymA) of 1.35 Mb, and another small replicon (pSymB) of 1.68 Mb. | ||
| + | #* The genes of Sinorhizobium meliloti are not highly repeated, but almost half of them are related to different family classification ranging from 2-134 genes per family. | ||
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| + | #* | ||
| + | #* | ||
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# What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])? | # What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])? | ||
# What individual or organization maintains the database? | # What individual or organization maintains the database? | ||
Revision as of 07:36, 12 November 2013
- Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms.
- symbiont: an organism living in symbiosis; especially the smaller member of a symbiotic pair.
- a-proteobacterium: a class of the group proteobacteria.
- tripartite: made between or involving three parties.
- endosymbionts: symbiosis in which a symbiont dwells within the body of its symbiotic partner.
- organogenesis: the origin and development of bodily organs.
- rhizosphere: soil that surrounds and is influenced by the roots of a plant
- plasmid: extrachromosomal ring of DNA especially of bacteria that replicates autonomously.
- putative: commonly accepted or supposed.
- asparagine: a nonesstential amino acid that is an amide of aspartic acid.
- cyclases: an enzyme that catalyzes.
- All of the definitions were found: In Merriam Webster Online, Retrieved November 11, 2013, from http://www.merriam-webster.com/dictionary.
- Write an outline of the article.
- Nitrogen is often found in soil and fertilizer and it is essential for proper plant growth.
- When a plant is deprived of necessary nitogen, rhizobia infect the roots of the plant to create nodules. The bacteria then begin nitrogen-fixation in the cell cytoplasm. This establishes a symbiotic relationship between the rhizobia and the plant, where the plant is provided with nitrogen and the rhizobia receive plant carbon compounds.
- The genome of Sinorhizobium meliloti is being studied, because it serves as a rhizobia symbiont to alfalfa and can offer incite on how other endosymbionts function.
- Sinorhizobium meliloti is classified as a a-probacterium that is also closely related to bacterial plant and animal pathogens. Sprain 1021 of Sinorhizobium meliloti has been completely sequenced.
- The genome of interest consists of three replicons: one large replicon of 3.65 Mb, a smaller replicon (pSymA) of 1.35 Mb, and another small replicon (pSymB) of 1.68 Mb.
- The genes of Sinorhizobium meliloti are not highly repeated, but almost half of them are related to different family classification ranging from 2-134 genes per family.
- What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
- What individual or organization maintains the database?
- What is their funding source(s)?
- Is there a license agreement or any restrictions on access to the database?
- How often is the database updated?
- Are there links to other databases?
- Can the information be downloaded? In what file formats?
- Evaluate the “user-friendliness” of the database. Is the Web site well-organized? Does it have a help section or tutorial? Run a sample query. Do the results make sense?
- What is the format (regular expression) of the main type of gene ID for this species? (for example, for Vibrio cholerae it was VC#### or VC_####).
