Blitvak Week 8 - Revision history

Blitvak: added conclusion, uploaded files

2015-10-27T06:03:16Z

added conclusion, uploaded files

Blitvak: added top row comparison between my findings and Anu's (mappfinder)

2015-10-27T05:22:24Z

added top row comparison between my findings and Anu's (mappfinder)

Blitvak: added interpretation of results

2015-10-27T05:09:33Z

added interpretation of results

@@ Line 228: / Line 228: @@
 *'''Group 8 (Bold Black Borders)''': This group is composed of somewhat miscellaneous terms that did not have clear relationships with each other and with other terms (in MAPPfinder). Two of the three terms are involved with monocarboxylic acids (transport and transport activity across membranes). The final term is extracellular region and is related to the space outside of the bacterium in question.
 ===Result Interpretation===
-The work by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776822/ Merrell et al.] indicates that the colonization of ''V. cholerae'' in human hosts results in the creation of a bacterial state that is very infectious/pathogenic; this induced bacterial state, compared to the control lab-derived strains, was found to have increased levels of expression of genes involved with nutrient acquisition and motility (movement). The bacteria derived from human hosts, according to Merrell et al., had a "unique physiological and behavioural state" (Merrell et al. 2002). Using the top 20 GO terms, derived from this investigation, it was found that many genes with increased expression involved the development/maintenance of the flagella (motility) and various processes that assist the bacteria in producing and acquiring certain nutrients/compounds; these observations are in line with what was observed by Merrell et al. At first, it was not clear exactly how the development of a flagella is tied to pathogenicity but it was suspected that the increased motility permitted the bacterium to adapt better to the host environment (which, in turn, led to a higher degree of pathogenicity). A paper by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009794/ Haiko and Westerlund-Wikström] was found, which helped explain how the development of a flagella leads to pathogenic character/behavior in bacteria. According to Haiko and Westerlund-Wikström, the motility associated with flagella assist bacteria in cell invasion, adhesion, and in colonization; it seems apparent that an increased level of movement help bacteria in colonizing and staying within a human host. With respect to the GO terms related to compound production (those related to the metabolic pathways involving branched chain family amino acids and nucleobases), it is possible that the pathogenic state is more demanding and more rapidly dividing than the "normal" state. The increased expression in the genes involving amino acid synthesis could indicate that the pathogenic bacteria exhibit increased levels of translation (possibly of proteins that are related to the bacteria's pathogenicity; virulence proteins that assist the bacteria in colonizing a host, in invading cells, and in adhesion to cell surfaces/environment). The GO terms involving the hydrolysis of carbon-nitrogen bonds in amidine and amide compounds (which indicate increased levels of expression of genes related to those processes) suggest that the bacteria will have to process more compounds with amidine/amide groups, which are likely found in the host environment or in host cells. An enhanced ability to process these kinds of compounds could potentially allow the pathogenic bacteria to better acquire certain nutrients for its own use (like nitrogen). The GO terms related to monocarboxylic acid transport could also be related to the host body environment (increased presence of these types of compounds). A better ability to transport and process monocarboxylic compounds can enhance the nutrient acquisition ability of the pathogenic bacteria. Finally, with respect to the GO terms related to pigment synthesis, it is possible that these produced pigment compounds are toxic or exhibit properties that interfere with the immune system/with host cells.
+The work by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776822/ Merrell et al.] indicates that the colonization of ''V. cholerae'' in human hosts results in the creation of a bacterial state that is very infectious/pathogenic; this induced bacterial state, compared to the control lab-derived strains, was found to have increased levels of expression of genes involved with nutrient acquisition and motility (movement). The bacteria derived from human hosts, according to Merrell et al., had a "unique physiological and behavioural state" (Merrell et al. 2002). Using the top 20 GO terms, derived from this investigation, it was found that many genes with increased expression involved the development/maintenance of the flagella (motility) and various processes that assist the bacteria in producing and acquiring certain nutrients/compounds; these observations are in line with what was observed by Merrell et al. At first, it was not clear exactly how the development of a flagella is tied to pathogenicity but it was suspected that the increased motility permitted the bacterium to adapt better to the host environment (which, in turn, led to a higher degree of pathogenicity). A paper by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009794/ Haiko and Westerlund-Wikström] was found, which helped explain how the development of a flagella leads to pathogenic character/behavior in bacteria. According to Haiko and Westerlund-Wikström, the motility associated with flagella assist bacteria in cell invasion, adhesion, and in colonization; it seems apparent that an increased level of movement help bacteria in colonizing and staying within a human host. With respect to the GO terms related to compound production (those related to the metabolic pathways involving branched chain family amino acids and nucleobases), it is possible that the pathogenic state is more demanding and more rapidly dividing than the "normal" state. The increased expression in the genes involving amino acid synthesis could indicate that the pathogenic bacteria exhibit increased levels of translation (possibly of proteins that are related to the bacteria's pathogenicity; virulence proteins that assist the bacteria in colonizing a host, in invading cells, and in adhesion to cell surfaces/environment). The GO terms involving the hydrolysis of carbon-nitrogen bonds in amidine and amide compounds (which indicate increased levels of expression of genes related to those processes) suggest that the bacteria will have to process more compounds with amidine/amide groups, which are likely found in the host environment or in host cells. An enhanced ability to process these kinds of compounds could potentially allow the pathogenic bacteria to better acquire certain nutrients for its own use (like nitrogen). The GO terms related to monocarboxylic acid transport could also be related to the host body environment (increased presence of these types of compounds). A better ability to transport and process monocarboxylic compounds can enhance the nutrient acquisition ability of the pathogenic bacteria. Finally, with respect to the GO terms related to pigment synthesis, it is possible that these produced pigment compounds are toxic or exhibit properties that interfere with the immune system/with host cells; the GO term extracellular region could also refer to the human host environment that the bacteria interacts with (genes related to it could enhance the pathogenic character of the bacteria by allowing it to interact with the host and its cells in a certain kind of way, such as the secretion of certain compounds, like toxic pigments, into the extracellular space).
+===Conclusion===
 ----
 {{Template:blitvak}}

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 *The results file, in the format "XXX-CriterionX-GO.txt" was copied and pasted in the folder housing all of the files related to this investigation (XXX = name given to file, CriterionX refers to the Criterion #; Criterion0 refers to the Increased criterion, Criterion1 refers to the Decreased criterion, if the Increased criterion was done first)
 *The "CriterionGO" file was opened via Excel in order to show the results in a tabular format
-*The top rows of the opened file (in Excel) were examined; these are rows of information that give background information as to how MAPPFinder made the calculations
+*The top rows of the opened file (in Excel) were examined; these are rows of information that give background information as to how MAPPFinder made the calculations:
 **[[File:MAPPFINDER INFO BL.png]]
 *The list in the file was filtered in order to show the top GO terms represented in the data for the "Increased" criterion
 *A cell was clicked in the row of headers and the autofilter was turned on (Data menu -> Filter > Autofilter)
@@ Line 228: / Line 230: @@
 The work by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776822/ Merrell et al.] indicates that the colonization of ''V. cholerae'' in human hosts results in the creation of a bacterial state that is very infectious/pathogenic; this induced bacterial state, compared to the control lab-derived strains, was found to have increased levels of expression of genes involved with nutrient acquisition and motility (movement). The bacteria derived from human hosts, according to Merrell et al., had a "unique physiological and behavioural state" (Merrell et al. 2002). Using the top 20 GO terms, derived from this investigation, it was found that many genes with increased expression involved the development/maintenance of the flagella (motility) and various processes that assist the bacteria in producing and acquiring certain nutrients/compounds; these observations are in line with what was observed by Merrell et al. At first, it was not clear exactly how the development of a flagella is tied to pathogenicity but it was suspected that the increased motility permitted the bacterium to adapt better to the host environment (which, in turn, led to a higher degree of pathogenicity). A paper by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009794/ Haiko and Westerlund-Wikström] was found, which helped explain how the development of a flagella leads to pathogenic character/behavior in bacteria. According to Haiko and Westerlund-Wikström, the motility associated with flagella assist bacteria in cell invasion, adhesion, and in colonization; it seems apparent that an increased level of movement help bacteria in colonizing and staying within a human host. With respect to the GO terms related to compound production (those related to the metabolic pathways involving branched chain family amino acids and nucleobases), it is possible that the pathogenic state is more demanding and more rapidly dividing than the "normal" state. The increased expression in the genes involving amino acid synthesis could indicate that the pathogenic bacteria exhibit increased levels of translation (possibly of proteins that are related to the bacteria's pathogenicity; virulence proteins that assist the bacteria in colonizing a host, in invading cells, and in adhesion to cell surfaces/environment). The GO terms involving the hydrolysis of carbon-nitrogen bonds in amidine and amide compounds (which indicate increased levels of expression of genes related to those processes) suggest that the bacteria will have to process more compounds with amidine/amide groups, which are likely found in the host environment or in host cells. An enhanced ability to process these kinds of compounds could potentially allow the pathogenic bacteria to better acquire certain nutrients for its own use (like nitrogen). The GO terms related to monocarboxylic acid transport could also be related to the host body environment (increased presence of these types of compounds). A better ability to transport and process monocarboxylic compounds can enhance the nutrient acquisition ability of the pathogenic bacteria. Finally, with respect to the GO terms related to pigment synthesis, it is possible that these produced pigment compounds are toxic or exhibit properties that interfere with the immune system/with host cells.
 ----
 {{Template:blitvak}}

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 *monocarboxylic acid transmembrane transporter activity: "Enables the transfer of monocarboxylic acids from one side of the membrane to the other. A monocarboxylic acid is an organic acid with one COOH group."
 ====Group Summaries====
-*Group 1 (Yellow): Related to the processes behind the assembly/formation of cell projections (like flagella)
+*'''Group 1 (Yellow)''': Related to the processes behind the assembly/formation of cell projections (like flagella)
-*Group 2 (Light Brown): Related to the biosynthetic and metabolic processes that involve branched chain family amino acids
+*'''Group 2 (Light Brown)''': Related to the biosynthetic and metabolic processes that involve branched chain family amino acids
-*Group 3 (Light Blue): Involves the synthesis of nitrogenous bases (purines), and related metabolic processes
+*'''Group 3 (Light Blue)''': Involves the synthesis of nitrogenous bases (purines), and related metabolic processes
-*Group 4 (Dark Blue): Involves processes/reactions that incorporate ligand binding. One term involves interactions with thiamine pyrophosphate, which is a derivative of thiamine (an essential vitamin); thiamine pyrophosphate is a catalyst of many important biochemical reactions. The other term involves the synthesis of acetolactate from 2 pyruvates via an enzyme (acetolactate is involved in the biosynthesis of several branched chain amino acids).
+*'''Group 4 (Dark Blue)''': Involves processes/reactions that incorporate ligand binding. One term involves interactions with thiamine pyrophosphate, which is a derivative of thiamine (an essential vitamin); thiamine pyrophosphate is a catalyst of many important biochemical reactions. The other term involves the synthesis of acetolactate from 2 pyruvates via an enzyme (acetolactate is involved in the biosynthesis of several branched chain amino acids).
-*Group 5 (Salmon): Involves the development of certain structures in the flagellum (distal rod of the "flagellar basal body"); the distal rod is an important flagellar structure that is transmembrane and it is connected to the other parts of the flagellum (like the filament/cap)
+*'''Group 5 (Salmon)''': Involves the development of certain structures in the flagellum (distal rod of the "flagellar basal body"); the distal rod is an important flagellar structure that is transmembrane and it is connected to the other parts of the flagellum (like the filament/cap)
-*Group 6 (Green): Involves the biosynthetic/metabolic processes related to pigments (pigment production)
+*'''Group 6 (Green)''': Involves the biosynthetic/metabolic processes related to pigments (pigment production)
-*Group 7 (Grey): Involved with the hydrolysis (catalysis of the process) of the carbon-nitrogen bonds (non-peptide) in linear amidine and amide compounds
+*'''Group 7 (Grey)''': Involved with the hydrolysis (catalysis of the process) of the carbon-nitrogen bonds (non-peptide) in linear amidine and amide compounds
-*Group 8 (Bold Black Borders): This group is composed of somewhat miscellaneous terms that did not have clear relationships with each other and with other terms (in MAPPfinder). Two of the three terms are involved with monocarboxylic acids (transport and transport activity across membranes). The final term is extracellular region and is related to the space outside of the bacterium in question.
+*'''Group 8 (Bold Black Borders)''': This group is composed of somewhat miscellaneous terms that did not have clear relationships with each other and with other terms (in MAPPfinder). Two of the three terms are involved with monocarboxylic acids (transport and transport activity across membranes). The final term is extracellular region and is related to the space outside of the bacterium in question.
 ===Result Interpretation===