Blitvak Week 11 - Revision history

Blitvak: added link to slides

2015-11-17T08:04:58Z

added link to slides

Blitvak: fixed typo

2015-11-16T05:02:42Z

fixed typo

Blitvak: added templates

2015-11-16T04:02:22Z

added templates

Blitvak: finished MOD section

2015-11-16T03:02:46Z

finished MOD section

Blitvak: wrapping up MOD section

2015-11-16T01:39:54Z

wrapping up MOD section

Blitvak: finished results section

2015-11-16T00:28:44Z

finished results section

Blitvak: added some of the results

2015-11-15T23:46:29Z

added some of the results

Blitvak: fixed formatting for the figure section

2015-11-15T08:27:30Z

fixed formatting for the figure section

Blitvak: added figure results

2015-11-15T08:26:27Z

added figure results

Blitvak: added efflux definition

2015-11-15T04:45:19Z

added efflux definition

@@ Line 139: / Line 139: @@
 #*Several different common formats: BCAL####, BCAM####, BCAS####, pBCA### (A's after the numbers were also encountered)
 #*Also noticed: Formats of all types with lower-case r's before the numbers (e.g. BCASr0269A); tags with lower-case r's, with are for tRNA related sequences, often also have letters at the end to signify the type of tRNA (alphabetical order, for related tRNA genes, starting from A)
+====Journal Club Presentation====
 ----

@@ Line 138: / Line 138: @@
 #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_####).
 #*Several different common formats: BCAL####, BCAM####, BCAS####, pBCA### (A's after the numbers were also encountered)
-#*Also countered: Formats of all types with lower-case r's before the numbers (e.g. BCASr0269A); tags with lower-case r's, with are for tRNA related sequences, often also have letters at the end to signify the type of tRNA (alphabetical order, for related tRNA genes, starting from A)
+#*Also noticed: Formats of all types with lower-case r's before the numbers (e.g. BCASr0269A); tags with lower-case r's, with are for tRNA related sequences, often also have letters at the end to signify the type of tRNA (alphabetical order, for related tRNA genes, starting from A)

← Older revision		Revision as of 04:02, 16 November 2015
Line 139:		Line 139:
	#*Several different common formats: BCAL####, BCAM####, BCAS####, pBCA### (A's after the numbers were also encountered)		#*Several different common formats: BCAL####, BCAM####, BCAS####, pBCA### (A's after the numbers were also encountered)
	#*Also countered: Formats of all types with lower-case r's before the numbers (e.g. BCASr0269A); tags with lower-case r's, with are for tRNA related sequences, often also have letters at the end to signify the type of tRNA (alphabetical order, for related tRNA genes, starting from A)		#*Also countered: Formats of all types with lower-case r's before the numbers (e.g. BCASr0269A); tags with lower-case r's, with are for tRNA related sequences, often also have letters at the end to signify the type of tRNA (alphabetical order, for related tRNA genes, starting from A)
		+
		+
		+	----
		+
		+	{{Template:GÉNialOMICS}}
		+	{{Template:blitvak}}

@@ Line 135: / Line 135: @@
 #Run a sample query. Do the results make sense?
 #*A sample query was run via the simple search using the J2315 strain, return was set to similar match, search term utilized was "membrane". The results made sense and were organized in a good manner.
-#*
+#*[[File:Sample_search_results_MOD_BL_11.15.png]]
 #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_####).
-#*Several different formats:
+#*Several different common formats: BCAL####, BCAM####, BCAS####, pBCA### (A's after the numbers were also encountered)

← Older revision		Revision as of 01:39, 16 November 2015
Line 107:		Line 107:
	*Overall, J2315 has a genome that promotes CF lung growth and spread (knowledge of it can help explain its character and infectious nature)		*Overall, J2315 has a genome that promotes CF lung growth and spread (knowledge of it can help explain its character and infectious nature)
	**Many functions were lost through mutations; many functions were gained through horizontal gene transfer (both cases appear to have promoted the growth/persistance within the CF lung environment, success contribution)		**Many functions were lost through mutations; many functions were gained through horizontal gene transfer (both cases appear to have promoted the growth/persistance within the CF lung environment, success contribution)
		+	====Exploring the MOD====
		+	*CITATION: Winsor, G. L., Khaira, B., Van Rossum, T., Lo, R., Whiteside, M. D., & Brinkman, F. S. (2008). The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. Bioinformatics, 24(23), 2803-2804.
		+	#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])?
		+	#*Sequences, annotations, replicon information, sample information (provider, geographic location, host), subcellular localization details, along with a general strain overview are made available for 355 burkholderia strains ( ortholog and subcellular localization predictions are provided). This is a "meta" database that organizes and works with information provided by other databases (NCBI primary databases are utilized). The database is manually curated (in-house) by the The Brinkman Lab at Simon Fraser University; however, annotation updates are based upon other sequence databases, literature review, and research submissions (log of annotation updates is available).
		+	#What individual or organization maintains the database?
		+	#*The Burkholderia Genome Database is managed by The Brinkman Lab at Simon Fraser University
		+	#What is their funding source(s)?
		+	#*Funding is provided by: Cystic Fibrosis Foundation Therapeutics, Inc. (CFFT), "a non-profit drug discovery and development affiliate of the Cystic Fibrosis Foundation".
		+	#Is there a license agreement or any restrictions on access to the database?
		+	#*Publicly available
		+	#How often is the database updated?
		+	#*Functional characterizations (TIGRFAM, COG, PFAM or GO) are updated on an annual basis (updates that utilize other databases occur annually). Updates based on the input in literature/researchers occur much more frequently (all updates are logged, annotation updates occur at variable times, sometimes monthly)
		+	#Are there links to other databases?
		+	#*Links were found to NCBI BioSample, NCBI Taxonomy, NCBI BioProject, NCBI Assembly (as Cross-References on the "Profile" for each strain")
		+	#*On the gene pages, cross-references were found to NCBI Gene, NCBI Protein, UniProt, STRING, and to Ensembl
		+	#Can the information be downloaded?
		+	#*Yes, for sequences (each strain): genomic, ORF DNA, Intergenic, and amino acid data is available. Gene annotations are also downloadable.
		+	#In what file formats?
		+	#*Data related to the sequences are downloadable as text in FASTA format
		+	#*Gene annotations can be downloaded in TAB, CSV, GBK, EMBL, GFF3, and GTF formats
		+	#Evaluate the “user-friendliness” of the database.
		+	#*Database appears very clean and every section is clear and easily found. Searches are simple to conduct and information is available regarding each type of search (with its purpose and result). Site is user-friendly with a clear interface; all searches were easy to conduct and assistance was given in the form of information on several pages.
		+	#Is the Web site well-organized?
		+	#*It is very well-organized with clearly defined sections (no valuable section is relatively hidden, everything is very clear and easy to find
		+	#Does it have a help section or tutorial?
		+	#*No explicit tutorial/help section but there is an FAQ page and several pages that explain the various searches. Many pages/links are accompanied by descriptive text which every section very clear (notes are often provided on pages that explain certain details or clarify others)
		+	#Run a sample query. Do the results make sense?
		+	#*A sample query was run via the simple search using the J2315 strain, return was set to similar match, search term utilized was "membrane". The results made sense and were organized in a good manner.
		+	#*
		+	#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_####).
		+	#*Several different formats:

← Older revision		Revision as of 00:28, 16 November 2015
Line 104:		Line 104:
	**No expression of pyochelin production genes in ET12 strains could support the persistence of the strain within the lung and could facilitate its spread between patients (effects of infection are less pronounced, initially)		**No expression of pyochelin production genes in ET12 strains could support the persistence of the strain within the lung and could facilitate its spread between patients (effects of infection are less pronounced, initially)
	**Chronic infections (J2315) puts pressure against the selection of functions that lead to acute infections (rapid onset of disease) -> J2315 is tied to a long-term infection which facilitates a spread between individuals		**Chronic infections (J2315) puts pressure against the selection of functions that lead to acute infections (rapid onset of disease) -> J2315 is tied to a long-term infection which facilitates a spread between individuals
		+	**Other recent studies have suggested that phenotype switching occurs in ''B. cenocepacia'' strains that reside in the lung environment of CF individuals (study of CF patients in the Vancouver area over a 26-year period); loss of EPS (extracellular polymeric substance) production was tied to increased disease severity (rather than persistence within the lung), ET12 lineage members like J2315 and K56-2 have mutations in the EPS cluster. Recent studies regarding the adaptations/mutations of other bacterial species/strains during infection reflect, in some aspects, what was found with J2315 (some parallels and differences; key difference is the difference between mucoid and nonmucoid character with respect to virulence). Nonmucoid character is tied to lesser virulence in one species but is tied to more virulence with ET12 lineage strains (differences exist in the roles that EPS plays in the pathogenicity and host interactions among CF pathogens)
		+	*Overall, J2315 has a genome that promotes CF lung growth and spread (knowledge of it can help explain its character and infectious nature)
		+	**Many functions were lost through mutations; many functions were gained through horizontal gene transfer (both cases appear to have promoted the growth/persistance within the CF lung environment, success contribution)

← Older revision		Revision as of 23:46, 15 November 2015
Line 88:		Line 88:
	*'''TABLE 5''': Many virulence determinants found in other '''B. cenocepacia''' strains were found to be pseudogenes in J2315		*'''TABLE 5''': Many virulence determinants found in other '''B. cenocepacia''' strains were found to be pseudogenes in J2315
	*'''TABLE 6''': All tested ET12 strains possess pseudogenes which disrupt cepacian capsule functions and pyochelin biosynthesis. Only J2315 has a pseudogene at BCAL3517 (T2SS) with a 110 bp deletion. O antigen is also interrupted in J2315 and similarly in BCC0016 (which is an ET12 strain), all others are uninterrupted or with no product. BCAL3223 is also interrupted (differently from the K56-2 strain).		*'''TABLE 6''': All tested ET12 strains possess pseudogenes which disrupt cepacian capsule functions and pyochelin biosynthesis. Only J2315 has a pseudogene at BCAL3517 (T2SS) with a 110 bp deletion. O antigen is also interrupted in J2315 and similarly in BCC0016 (which is an ET12 strain), all others are uninterrupted or with no product. BCAL3223 is also interrupted (differently from the K56-2 strain).
		+	====How the results relate to other work====
		+	*Exchange of mobile genetic elements/genomic island movement supports the spread of genetic information between diverse bacteria (a benefit to a bacterium in its current environment, or something that can allow the bacterium to adapt to new niches like that of the CF lung via a host-associated pathogen lifestyle)
		+	*J2315 genome has 14 genomic islands that are absent from the other ''B. cenocepacia'' strains; acquirement of genomic island genes are suggested to have introduced adaptations and functions that promote survival/pathogenic character within the lung environment)
		+	**CCI (BcenGI11) island is involved with infection, is found throughout the members of the ET12 lineage, and is more frequently occuring in IIIA strains than IIIB; this island is important with respect to the virulence and survival of the strain within the lung environment and the importance/contribution of the other genomic islands is yet unclear (many islands involved with metabolic functions or have still unknown functions)
		+	*Other RODs do not have mobile genetic element properties and are a more stable part of the genome of J2315; cable pilus locus and AdHA adhesion protein are located within these unique genes. Cable pilus/AdhA complex has been tied to the binding of mucin (abundant in the CF lung environment as a result of poor clearance) and cytokeratin 13 (cytoplasmic protein that is known to become surface exposed during chronic infection in individuals with CF). The complex is also related with the ability of the species to bind/invade epithelial lung cells (is known to bind to explant culture lung tissue from CF patients). Each piece of the complex is suggested to have been acquired independently but it exhibits synergy (orthologs abasent from other BCC strains)
		+	**Many other virulence related genes have been found in the RODs specific to J2315
		+	*''B. cenocepacia'' strains have been shown to be very hardy and resistant to a variety of antibiotics in recent studies; strains derived from the ET12 lineage have different antibiotic sensitivities compared to other lineages/strains.
		+	**Among other members of the ET12 lineage, J2315 has shown to have an enhanced level of antibiotic resistance to several antimicrobial agents
		+	**It was found that the J2315 genome has drug resistance related genes within the islands and RODs (conclusions: horizontal gene transfer plays a role in the acquirement/evolution of drug resistance in already resistant organisms).
		+	*Enhanced drug resistance is suggested to have been the result of point mutation (a mutation affecting only one or few nucleotides in a sequence)
		+	**gene loss via mutation played an important role, in conjunction with the acquirement of new functions, played essential roles in the success and development of J2315
		+	*Other work has found that BCC have many characteristic virulence determinants that hold important roles in the survival within the "natural" environment (soil); this study found that many of these determinants are pseudogenes or are nonfunctional within the J2315 strain
		+	**The work suggests that many of these functions are not essential or are even superfluous for the lung environment (lack of these genes could have actually boosted the survival and success of J2315 as a host-associated pathogen)
		+	*All screen ET12 strains were found to have the exact same frameshift mutation (insertions or deletions of a number of nucleotides) in the ''pchF'' gene (pyochelin siderophore biosynthesis); other studies have found that pyochelin-negative strains occur more frequently in patients with moderate/mild CF related infections whereas pyochelin-positive strains were more frequently found in patients with serious pulmonary disease (high possible mortality, cases). Pyochelin production was linked in previous studies to a more severe disease progression (towards mortality) and the lack of pyochelin production in J2315 sheds some light on its infectious nature.
		+	**No expression of pyochelin production genes in ET12 strains could support the persistence of the strain within the lung and could facilitate its spread between patients (effects of infection are less pronounced, initially)
		+	**Chronic infections (J2315) puts pressure against the selection of functions that lead to acute infections (rapid onset of disease) -> J2315 is tied to a long-term infection which facilitates a spread between individuals

@@ Line 79: / Line 79: @@
 *Complete genomic sequence of ''B. cenocepacia'' strain J2315 was placed in the EMBL database (accession numbers: AM747720, AM747721, AM747722, and AM747723)
 ====Figure/Table Results====
-'''FIG. 1''': Complete genome of J2315 is comprised of three circular chromosomes and a plasmid. Chromosomes are of sizes 3,870,082, 3,217,062, and 875,977 bp; plasmid is 92,661 bp. There exist several relatively large RODs and genomic islands (many other ''B. cenocepacia'' strains lack orthologues with respect to the genomic islands). Chromosome 1 seems to have a moderate number of genomic islands and too many RODs, Chromosome 2 appears to have the smallest number and size with respect to the genomic islands, Chromosome 3 seems to have the largest number of genomic islands and RODs (and, consequently, the smallest percent of orthologous genes compared to the other strains and to ''Ralstonia solanacearum'').
+*'''FIG. 1''': Complete genome of J2315 is comprised of three circular chromosomes and a plasmid. Chromosomes are of sizes 3,870,082, 3,217,062, and 875,977 bp; plasmid is 92,661 bp. There exist several relatively large RODs and genomic islands (many other ''B. cenocepacia'' strains lack orthologues with respect to the genomic islands). Chromosome 1 seems to have a moderate number of genomic islands and too many RODs, Chromosome 2 appears to have the smallest number and size with respect to the genomic islands, Chromosome 3 seems to have the largest number of genomic islands and RODs (and, consequently, the smallest percent of orthologous genes compared to the other strains and to ''Ralstonia solanacearum'').
-'''FIG. 2''': Chromosomes 2 and 3 contain a greater number (proportion) of coding sequences that have an accessory role (involved with functions like horizontal gene transfer and protective response) or with an unknown function. Chromosome 1 has a greater proportion of coding sequences that are related to core cell functions, such as cell division/chromosome replication, macromolecule/amino acid/nucleotide biosynthesis (genes related to metabolism and division).
+*'''FIG. 2''': Chromosomes 2 and 3 contain a greater number (proportion) of coding sequences that have an accessory role (involved with functions like horizontal gene transfer and protective response) or with an unknown function. Chromosome 1 has a greater proportion of coding sequences that are related to core cell functions, such as cell division/chromosome replication, macromolecule/amino acid/nucleotide biosynthesis (genes related to metabolism and division).
-'''FIG. 3''': Number/percent of orthologous coding sequences in the J2315 was greatest in groups that were more taxonomically related to J2315. 78 to 63% of total coding sequences in BCC members,  56 to 50% in other ''Burkholderia'' species, and 37% of all coding sequences in ''Ralstonia solanacearum''. Chromosome 1 has the highest degree of conservation, chromosome 2 a little less, and chromosome 3 has the lowest degree of conservation.
+*'''FIG. 3''': Number/percent of orthologous coding sequences in the J2315 was greatest in groups that were more taxonomically related to J2315. 78 to 63% of total coding sequences in BCC members,  56 to 50% in other ''Burkholderia'' species, and 37% of all coding sequences in ''Ralstonia solanacearum''. Chromosome 1 has the highest degree of conservation, chromosome 2 a little less, and chromosome 3 has the lowest degree of conservation.
-'''TABLE 1''':8,055,782 total bp; chromosome 1 largest, chromosome 2 is similar to size but is smaller, chromosome 3 is the smallest (also exists a small plasmid). G+C content % is similar between all four replicons (smallest in plasmid, followed by chromosome 1). There are 7,261 total coding sequences (85.9% of DNA involved with coding). Plasmid has the smallest average gene length. Chromosome 1 possess the vast majority of tRNA related genes (66, compared to the 6 and 2 of chromosome 2 and 3, respectively). Chromosome 1 also holds the majority of IS elements (vast), pseudogenes/partial genes (moderate majority), and of miscellaneous RNA (vast majority).
+*'''TABLE 1''':8,055,782 total bp; chromosome 1 largest, chromosome 2 is similar to size but is smaller, chromosome 3 is the smallest (also exists a small plasmid). G+C content % is similar between all four replicons (smallest in plasmid, followed by chromosome 1). There are 7,261 total coding sequences (85.9% of DNA involved with coding). Plasmid has the smallest average gene length. Chromosome 1 possess the vast majority of tRNA related genes (66, compared to the 6 and 2 of chromosome 2 and 3, respectively). Chromosome 1 also holds the majority of IS elements (vast), pseudogenes/partial genes (moderate majority), and of miscellaneous RNA (vast majority).
-'''TABLE 2''': 15 genomic islands (most and largest appear on chromosome 1); many genomic islands also have IS elements which are integrated into various sites in the bacterial genome (all islands, except one, contain one putative integrase). Many islands are prophages/have phage origins and most are miscellaneous islands. Many resistances are linked to the cenocepacia island (antibiotic/arsenic resistance, along with stress response coding sequences).
+*'''TABLE 2''': 15 genomic islands (most and largest appear on chromosome 1); many genomic islands also have IS elements which are integrated into various sites in the bacterial genome (all islands, except one, contain one putative integrase). Many islands are prophages/have phage origins and most are miscellaneous islands. Many resistances are linked to the cenocepacia island (antibiotic/arsenic resistance, along with stress response coding sequences).
-'''TABLE 3''': Variety of virulence functions are encoded in the J2315 genome; several genes related to the virulence functions are absent from other strains of ''B. cenocepacia''. Cable pilus coding sequences are unique to J2315 compared to other strains; five BuHA family proteins are also unique to J2315
+*'''TABLE 3''': Variety of virulence functions are encoded in the J2315 genome; several genes related to the virulence functions are absent from other strains of ''B. cenocepacia''. Cable pilus coding sequences are unique to J2315 compared to other strains; five BuHA family proteins are also unique to J2315
-'''TABLE 4''': Many drug resistance determinants target unknown antibiotics/antimicrobial compounds. Some coding sequences are strain-specific (J2315 has elevated drug resistance, compared to other strains). Six families of transport systems were identified (ABC, MFS, MATE, RND, SMR, and fusaric acid resistance family proteins)
+*'''TABLE 4''': Many drug resistance determinants target unknown antibiotics/antimicrobial compounds. Some coding sequences are strain-specific (J2315 has elevated drug resistance, compared to other strains). Six families of transport systems were identified (ABC, MFS, MATE, RND, SMR, and fusaric acid resistance family proteins)
-'''TABLE 5''': Many virulence determinants found in  other '''B. cenocepacia''' strains were found to be pseudogenes in J2315
+*'''TABLE 5''': Many virulence determinants found in  other '''B. cenocepacia''' strains were found to be pseudogenes in J2315
-'''TABLE 6''': All tested ET12 strains possess pseudogenes which disrupt cepacian capsule functions and pyochelin biosynthesis. Only J2315 has a pseudogene at BCAL3517 (T2SS) with a 110 bp deletion. O antigen is also interrupted in J2315 and similarly in BCC0016 (which is an ET12 strain), all others are uninterrupted or with no product. BCAL3223 is also interrupted (differently from the K56-2 strain).
+*'''TABLE 6''': All tested ET12 strains possess pseudogenes which disrupt cepacian capsule functions and pyochelin biosynthesis. Only J2315 has a pseudogene at BCAL3517 (T2SS) with a 110 bp deletion. O antigen is also interrupted in J2315 and similarly in BCC0016 (which is an ET12 strain), all others are uninterrupted or with no product. BCAL3223 is also interrupted (differently from the K56-2 strain).

← Older revision		Revision as of 08:26, 15 November 2015
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	=====Sequence and Annotation Deposit=====		=====Sequence and Annotation Deposit=====
	*Complete genomic sequence of ''B. cenocepacia'' strain J2315 was placed in the EMBL database (accession numbers: AM747720, AM747721, AM747722, and AM747723)		*Complete genomic sequence of ''B. cenocepacia'' strain J2315 was placed in the EMBL database (accession numbers: AM747720, AM747721, AM747722, and AM747723)
		+	====Figure/Table Results====
		+	'''FIG. 1''': Complete genome of J2315 is comprised of three circular chromosomes and a plasmid. Chromosomes are of sizes 3,870,082, 3,217,062, and 875,977 bp; plasmid is 92,661 bp. There exist several relatively large RODs and genomic islands (many other ''B. cenocepacia'' strains lack orthologues with respect to the genomic islands). Chromosome 1 seems to have a moderate number of genomic islands and too many RODs, Chromosome 2 appears to have the smallest number and size with respect to the genomic islands, Chromosome 3 seems to have the largest number of genomic islands and RODs (and, consequently, the smallest percent of orthologous genes compared to the other strains and to ''Ralstonia solanacearum'').
		+	'''FIG. 2''': Chromosomes 2 and 3 contain a greater number (proportion) of coding sequences that have an accessory role (involved with functions like horizontal gene transfer and protective response) or with an unknown function. Chromosome 1 has a greater proportion of coding sequences that are related to core cell functions, such as cell division/chromosome replication, macromolecule/amino acid/nucleotide biosynthesis (genes related to metabolism and division).
		+	'''FIG. 3''': Number/percent of orthologous coding sequences in the J2315 was greatest in groups that were more taxonomically related to J2315. 78 to 63% of total coding sequences in BCC members, 56 to 50% in other ''Burkholderia'' species, and 37% of all coding sequences in ''Ralstonia solanacearum''. Chromosome 1 has the highest degree of conservation, chromosome 2 a little less, and chromosome 3 has the lowest degree of conservation.
		+	'''TABLE 1''':8,055,782 total bp; chromosome 1 largest, chromosome 2 is similar to size but is smaller, chromosome 3 is the smallest (also exists a small plasmid). G+C content % is similar between all four replicons (smallest in plasmid, followed by chromosome 1). There are 7,261 total coding sequences (85.9% of DNA involved with coding). Plasmid has the smallest average gene length. Chromosome 1 possess the vast majority of tRNA related genes (66, compared to the 6 and 2 of chromosome 2 and 3, respectively). Chromosome 1 also holds the majority of IS elements (vast), pseudogenes/partial genes (moderate majority), and of miscellaneous RNA (vast majority).
		+	'''TABLE 2''': 15 genomic islands (most and largest appear on chromosome 1); many genomic islands also have IS elements which are integrated into various sites in the bacterial genome (all islands, except one, contain one putative integrase). Many islands are prophages/have phage origins and most are miscellaneous islands. Many resistances are linked to the cenocepacia island (antibiotic/arsenic resistance, along with stress response coding sequences).
		+	'''TABLE 3''': Variety of virulence functions are encoded in the J2315 genome; several genes related to the virulence functions are absent from other strains of ''B. cenocepacia''. Cable pilus coding sequences are unique to J2315 compared to other strains; five BuHA family proteins are also unique to J2315
		+	'''TABLE 4''': Many drug resistance determinants target unknown antibiotics/antimicrobial compounds. Some coding sequences are strain-specific (J2315 has elevated drug resistance, compared to other strains). Six families of transport systems were identified (ABC, MFS, MATE, RND, SMR, and fusaric acid resistance family proteins)
		+	'''TABLE 5''': Many virulence determinants found in other '''B. cenocepacia''' strains were found to be pseudogenes in J2315
		+	'''TABLE 6''': All tested ET12 strains possess pseudogenes which disrupt cepacian capsule functions and pyochelin biosynthesis. Only J2315 has a pseudogene at BCAL3517 (T2SS) with a 110 bp deletion. O antigen is also interrupted in J2315 and similarly in BCC0016 (which is an ET12 strain), all others are uninterrupted or with no product. BCAL3223 is also interrupted (differently from the K56-2 strain).

@@ Line 47: / Line 47: @@
 **Citation: [http://www.biology-online.org/dictionary/Prophage]
 *'''Efflux system''': An active transport system (localized in the cytoplasmic membrane) with the purpose of moving substrate in and out of a bacterial cell (e.g. antibiotics)
 *'''Peritrichous''': Related to cilia/appendage organs projecting from around the cell; uniform distribution of flagella over a cell
 **Citation: [http://www.biology-online.org/dictionary/Peritrichous]