Class Journal Week 10

Class Notes week 10

• To access database pages go through the LMU link
• journal availibility comes through PubMed central if it is funded by the government

Open Access Journals

• Authors submit article to publishers and then pay to have it published
• How well are the quality control standards?
• Copyright rules are in flux
  • most databases are public access

Google Scholar

• serves as a key word search
• date order is all over the place
  • means things can be out of date

Pubmed

• also serves as a keyword search
• Advanced search= use the meSH terms
• For our species we need to find a reference genome = the main reference strain
  • generally the earliest strain by date is the reference genome

Array express

• this is one of the best databases I've seen in reference to finding array data
• The search can be sorted by organism and the arrays can be sorted by kinds

Individual Homework

1. I used pubmed for this part of the assignment
2. The search terms I used for this were Sinorhizobium Meliloti and genome.
3. Most of the results I got were concerned with DNA probes and specific sequences of DNA
4. I got 20 results by using this database

• when I used array express I got 25 results by using the search term for the bacteria species Sinorhizobium Meliloti

Citations

1. Dual RpoH Sigma Factors and Transcriptional Plasticity in a Symbiotic Bacterium. Barnett MJ, Bittner AN, Toman CJ, Oke V, Long SR. , Europe PMC 22773790
2. Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti. Dominguez-Ferreras, Ana; Perez-Arnedo, Rebeca; Becker, Anke; Olivares, Jose; Soto, Maria J.; Sanjuan, Juan. The Journal of Bacteriology 188(21):7617 (2006), Europe PMC 16916894
3. Xavier Bailly, Gilles Béna, Vanina Lenief, Philippe de Lajudie, Jean-Christophe Avarre, Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae, Journal of Microbiological Methods, Volume 67, Issue 1, October 2006, Pages 114-124, ISSN 0167-7012, http://dx.doi.org/10.1016/j.mimet.2006.03.006. (http://www.sciencedirect.com/science/article/pii/S0167701206000662
4. Jan-Philip Schlüter, Jan Reinkensmeier, Svenja Daschkey, Elena Evguenieva-Hackenberg, Stefan Janssen, Sebastian Jänicke, Jörg D Becker, Robert Giegerich, Anke Becker, A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti BMC Genomics. 2010; 11: 245. Published online 2010 April 17. doi: 10.1186/1471-2164-11-245 PMCID: PMC2873474 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873474/

Links

1. http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36186/?keywords=&organism=Sinorhizobium+meliloti&array=&exptype[]=&exptype[]=
2. http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype[0]=&exptype[1]=&sortby=type&sortorder=ascending

Description of the Arrays

1. the first array deals with heat Shock. The control for this experiment was stationary phase growth and the variable was the bacteria under "heat shock"
2. The array deals with the osmotic upshift ellicited by salt or sucrose. The control in this experiment would be a normal osmotic gradient and the variables would be the gradient when subjected to salt and sucrose

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