Anuvarsh Week 11 - Revision history

Anuvarsh: /* Burkholderia cenocepacia Genome Paper and Presentation */ updated presentation link

2015-11-17T22:32:44Z

‎Burkholderia cenocepacia Genome Paper and Presentation: updated presentation link

Anuvarsh: added genome presentation

2015-11-17T04:17:41Z

added genome presentation

Anuvarsh: /* Questions */ finished this off

2015-11-17T04:16:10Z

‎Questions: finished this off

Anuvarsh: /* Outline of Paper */ fixed a typo

2015-11-17T03:11:05Z

‎Outline of Paper: fixed a typo

Anuvarsh: /* Questions */ answered some more questions

2015-11-17T02:00:01Z

‎Questions: answered some more questions

Anuvarsh: /* Model Organism Database Analysis */ started answering questions

2015-11-16T06:27:04Z

‎Model Organism Database Analysis: started answering questions

Anuvarsh: created section for MOD analysis

2015-11-16T05:39:03Z

created section for MOD analysis

Anuvarsh: /* Biological Terms and Definitions */ added terms and definitions

2015-11-16T05:37:56Z

‎Biological Terms and Definitions: added terms and definitions

Anuvarsh: /* Outline of Paper */ finished discussion

2015-11-16T05:22:01Z

‎Outline of Paper: finished discussion

Anuvarsh: /* Outline of Paper */ finished results

2015-11-16T05:19:40Z

‎Outline of Paper: finished results

@@ Line 1: / Line 1: @@
 =''Burkholderia cenocepacia'' Genome Paper and Presentation=
 *'''Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.'''
-*[[Media:GenomePresentation-AnuBrandon-Genialomics.pdf|Genome Presentation]]
+*[[Media:Genome_Presentation_-_Anu_and_Brandon_-_Genialomics(FIXED).pdf|Genome Presentation]]
 =Biological Terms and Definitions=
 #Pseudogenes

@@ Line 1: / Line 1: @@
-=''Burkholderia cenocepacia'' Genome Paper=
+=''Burkholderia cenocepacia'' Genome Paper and Presentation=
-'''Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.'''
+*'''Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.'''
+*[[Media:GenomePresentation-AnuBrandon-Genialomics.pdf|Genome Presentation]]
 =Biological Terms and Definitions=
 #Pseudogenes

@@ Line 126: / Line 126: @@
 **I find the website to be generally very well organized. All important links are easily accessible from the home page. Search results are easily understood.
 *Does it have a help section or tutorial?
-**[[Image:genialomics-Membrane-search.png]]
+**Though it does not have a special help section or tutorial, each page has great explanations regarding how to use the database as well as "search hints" to help researchers find what they are looking for. There is also an FAQ page that answers some questions regarding searching and submitting to the database.
 *Run a sample query. Do the results make sense?
-**
+**As presented in the image above, the results of a search query make sense in regards to the search term "membrane". Each of the results came equipped with several gene annotations that made it easier to understand what I was looking at.
 *What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
-**
+**In general, we found 4 regular expressions of gene ID's for the species including:  BCAL####, BCAM####, BCAS####, pBCA###. We suspect that there are 4 types of gene names because each gene name is related to one of the 3 chromosomes or 1 plasmid.
 {{Template:Anuvarsh}}
 {{Template:GÉNialOMICS}}

@@ Line 62: / Line 62: @@
 ***B. cenocepecia strain J2315 was compared to several other burkholderia species
 **PCR screening
-***CRP amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.
+***PCR amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.
 *Results
 **Fig. 1: Genome contained 3 circular chromosomes and a plasmid. The figure features diagrams of each of the chromosome and plasmid that are color coded according to CDSs.
@@ Line 95: / Line 95: @@
 **In Toronto and Cleveland, a study was performed that indicated that pyochelin-positive strains of CF existed in patients with severe pulmonary disease. Lack of expression of pyochelin in ET12 and its related strains may result in resistance in the CF lungs, thereby helping the bacteria spread from patient to patient.
 **Another study in Vancouver found that 50% of the 506 B. cenocepacia strains collected from CF patients were nonmucoid. The loss of a specific cluster of genes (EPS) may have resulted in increased virulence in a CF lung.
 **A recent study by Smith et al. found that virulence factors are the most mutated class of genes throughout the infection time frame. This study found that the O antigen in P. aeruginosa received mutations, and the same antigen was found to have mutations in J2315.
 =Model Organism Database (MOD) Analysis=

@@ Line 110: / Line 110: @@
 **The only mentioned funding source for the development of this database is the Cystic Fibrosis Foundation Therapeutics (Cystic Fibrosis Foundation).
 *Is there a license agreement or any restrictions on access to the database?
-**
+**Data is easily accessed with no restrictions (publicly available).
 *How often is the database updated?
-**
+**Updates depending on researchers and published literature happen as they come in and are reviewed, but updates regarding the databases associated with the Burkholderia database happen annually.
 *Are there links to other databases?
-**
+**This database does link other databases. Some of these databases include:  NCBI BioSample, NCBI Taxonomy, NCBI BioProject, NCBI Assembly. On the gene pages, there were links to databases such as: NCBI Gene, NCBI Protein, UniProt, STRING, and to Ensembl.
 *Can the information be downloaded?
-**
+**The information can be downloaded.
 *In what file formats?
 ** Files are available in CSV, TAB, GBK, and EMBL formats.
 *Evaluate the “user-friendliness” of the database.
-**
+**I find the database to be incredibly user-friendly. All important sections (for information or for search engines) are easily accessed either directly from the home page or via links within the navigation bar. Titles on the links in the navigation bar are descriptive and relevant to the information provided. I found in incredibly easy to find all necessary information regarding how to search and submit genetic data on their website, as well as other information regarding documentation of functionalities and updates.
 *Is the Web site well-organized?
-**
+**[[Image:Genialomics-MOD-Homepage.png]]
 *Does it have a help section or tutorial?
-**
+**[[Image:genialomics-Membrane-search.png]]
 *Run a sample query. Do the results make sense?
 **

← Older revision		Revision as of 05:37, 16 November 2015
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	=Biological Terms and Definitions=		=Biological Terms and Definitions=
		+	#Pseudogenes
		+	#*Pseudogenes are genomic DNA sequences similar to normal genes but non-functional; they are regarded as defunct relatives of functional genes.
		+	#*Citation: [http://pseudogene.org/background.php]
		+	#Melioidosis
		+	#*Melioidosis, also called Whitmore's disease, is an infectious disease that can infect humans or animals. The disease is caused by the bacterium Burkholderia pseudomallei.
		+	#*Citation: [http://www.cdc.gov/melioidosis/]
		+	#Glanders
		+	#*Glanders is an infectious disease that is caused by the bacterium Burkholderia mallei.
		+	#*Citation: [http://www.cdc.gov/glanders/]
		+	#Orthologous
		+	#*Orthologs are genes in different species that evolved from a common ancestral gene by speciation.
		+	#*Citation: [http://homepage.usask.ca/~ctl271/857/def_homolog.shtml]
		+	#Genomic islands
		+	#*Genomic islands (GIs) are commonly defined as clusters of genes of probable horizontal origin >8 kb in size in bacterial and archaeal genomes (Langille et al., 2010).
		+	#*Citation: [http://omictools.com/genomic-islands-c1568-p1.html]
		+	#Mobile genetic elements
		+	#*Mobile genetic elements (MGEs) are segments of DNA that encode enzymes and other proteins that mediate the movement of DNA within genomes (intracellular mobility) or between bacterial cells (intercellular mobility).
		+	#*Citation: [http://www.nature.com/nrmicro/journal/v3/n9/full/nrmicro1235.html]
		+	#Horizontal transfer of genes
		+	#*Horizontal gene transfer is defined to be the movement of genetic material between bacteria other than by descent in which information travels through the generations as the cell divides. It is most often thought of as a sexual process that requires a mechanism for the mobilization of chromosomal DNA among bacterial cells.
		+	#*Citation: [https://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html]
		+	#Exoenzymes
		+	#*An enzyme that acts outside the cell that secretes it.
		+	#*Citation: http://medical-dictionary.thefreedictionary.com/exoenzyme
		+	#Metalloproteases
		+	#*Metalloproteases are a group of enzymes comprising a section of the protease family that contain a catalytic metal ion at their active site which aids in the hydrolysis of peptide bonds leading to protein degradation.
		+	#*Citation: [http://chemwiki.ucdavis.edu/Biological_Chemistry/Catalysts/Metalloproteases]
		+	#Actinobacterium
		+	#*The Actinobacteria are a group of Gram-positive bacteria. Most are found in the soil, and they include some of the most common soil life, playing important roles in decomposition and humus formation.
		+	#*Citation: [http://eol.org/pages/7861/overview]
		+	#Nonmucoid
		+	#*(noun)Any of various glycoproteins, especially a mucoprotein, similar to the mucins. (adj) Of, relating to, or resembling mucus.
		+	#*Citation: [http://www.thefreedictionary.com/mucoid]

	=Outline of Paper=		=Outline of Paper=

@@ Line 49: / Line 49: @@
 ***Chromosome 2 has the largest number of products that result in drug resistance.
 Some drugs J2315 is known to be resistant to include: Fosmidomycin, aminoglycosides, trimethoprim, tetracycline, and others.
+*Discussion