Msaeedi23 Week 11 - Revision history

Msaeedi23: /* DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL. */

2015-12-21T06:41:02Z

‎DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.

Msaeedi23: /* DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL. */

2015-11-17T07:42:48Z

‎DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.

Msaeedi23 at 07:41, 17 November 2015

2015-11-17T07:41:03Z

Msaeedi23 at 07:35, 17 November 2015

2015-11-17T07:35:48Z

Msaeedi23: /* How do the results of this study compare to the results of previous studies? */

2015-11-17T07:29:26Z

‎How do the results of this study compare to the results of previous studies?

Msaeedi23 at 06:57, 17 November 2015

2015-11-17T06:57:23Z

Msaeedi23 at 06:55, 17 November 2015

2015-11-17T06:55:01Z

Msaeedi23 at 06:52, 17 November 2015

2015-11-17T06:52:29Z

Msaeedi23 at 06:48, 17 November 2015

2015-11-17T06:48:59Z

Msaeedi23 at 06:47, 17 November 2015

2015-11-17T06:47:03Z

@@ Line 154: / Line 154: @@
 * Biological vs technical replicants- for vibrio control was the untreated strain, technical replicates = splitting a sample, different from biological replicates. Biological replicates are derived from the original strain. *note how many replicates of each. # of chips(microarrays) (for vibrio it was 9, total number of samples)
 #** Dye swaps, cy3 green dye and cy5 red. note how many swaps. Swaps done to avoid dye playing an effect in replication.
-#***Draw a diagram to help of how chips were obtained.
+#***Draw a diagram to help of how chips were obtained. [[File: Microarray_flow_chart.docx]]
 . Sample + data relationship. In raw data there should be one file to each chip. Match file name to sample. raw.zip on arrayexpress has one file for each chip. Sdrf.txt open in excel to show whats in the samples-should tell you all of the samples, their matches, and dye swaps.

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 . Deliverables-describing methods, production of tables including the sanity check, etc.
 *In discussion compare what we found vs to what they found.
 {{Template: msaeedi23}}

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 Genome Paper:
 <http://www.nature.com/ng/journal/v35/n1/full/ng1227.html>
 ===Week 11===

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 <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243#pone-0115243-g006>
-* For the microarray paper (GenMAPP Users only), include the following:
+==For the microarray paper (GenMAPP Users only)==
 **Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
 This paper identified polysaccharide (PS) capsules as important virulence determinants for bacterial pathogens and and KpsT as a membrane protein involved in the transport of PS polymers across the cellular envelope in ''Bordetella pertussis''. To determine the impact of PS capsules on the virulence of ''B. pertussis'', a microarray experiment was run testing a ∆KpsT mutant against the wild-type.

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 * Construct a flow chart that illustrates the above.
+[[Media: Flow_chart_db_project.docx]]
 ==DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.==

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 Write an outline of the article.  The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length).  Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it.  The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it.  However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
 What is the importance or significance of this work (i.e., your species)?
-*'''Introduction/Significance:'''
+===Introduction/Significance===
 (Used in accordance with GenMAPP user lolufson)
 **The Gram-negative bacterium Bordetella pertussis is the causative agent of pertussis or whooping cough.
@@ Line 50: / Line 50: @@
 What were the methods used in the study?
 (Used in accordance with GenMAPP user lolufson)
-*'''Methods:'''
+===Methods===
 **''Bacterial Strains and growth conditions''
 ***All B. pertussis strains were grown at 37°C on Bordet-Gengou (BG) agar (Difco) supplemented with 10% defibrinated sheep blood with 1% glycerol or in modified Stainer-Scholte (SS) medium containing 2,6-O-dimethyl-β-cyclodextrin (Sigma Chemical) at 1 g/liter supplemented with either 10 μg/ml gentamicin, 100 μg/ml streptomycin or 30 μg/ml chloramphenicol.
@@ Line 104: / Line 104: @@
 ***Each experiment was performed at least twice independently.
-Briefly state the result shown in each of the figures and tables.
+===Briefly state the result shown in each of the figures and tables===
 *Table 1: Lists all of the B. Pertussis strains used in the study along with their genotypes/relevant features, and the source where the strain was obtained.
 *Table 2: A complete list of all of the forward and reverse primers used in cloning are provided with their sequences, 5'-3', and their indicated mode of amplification (forward or reverse).
@@ Line 117: / Line 117: @@
 *Figure 8: The results portrayed in this figure support that neither KpsT alone nor the KpsMT complex is enough to restore fully a parental colonization profile in KOcaps. "Therefore, instead of KpsT alone, the entire capsule transport machinery may play a role in the BvgS-mediated signal transduction and indirectly in the overall bacterial virulence."
-How do the results of this study compare to the results of previous studies?
+===How do the results of this study compare to the results of previous studies?===
 * Previous research showed that B. pertussis PS capsule is not involved in the classical capsule-defense mechanisms including phagocytosis, complement-mediated killing and antimicrobial peptides attack. This new study provides evidence that the PS capsule transport proteins, in particular the membrane associated KpsT protein, are necessary for B. pertussis virulence in an indirect mode-of-action. The data suggest a structural role for the entire PS capsule transport machinery in the cell envelope and a consequential impact on the BvgA/S-mediated signal transduction and virulence gene expression. The work presented in this paper demonstrates for the first time that a vrg locus (the PS capsule locus) plays a role in pertussis pathogenesis. Therefore, it is demonstrated for the first time that a vrg locus (specifically the capsule locus) i) is expressed and modulated during in vivo infection, and ii) plays an indirect role in B. pertussis in vivo virulence. This finding apparently contradicts a previous study which claimed that the Bvg- phase is dispensable for bacterial in vivo virulence based on a Bvg+ phase locked mutant. This new observation thus suggests that in vivo, dynamic gene regulation occurs thereby implying that over time the micro-environmental conditions encountered by the bacteria vary. The PS capsule locus in B. pertussis is physically distinct from the bps locus which encodes proteins involved in biofilm formation. The data indicates that absence of the membrane-associated protein KpsT (and to a lesser extent KpsE) affects significantly pertussis pathogenesis. "In conclusion, this research portrays that the B. pertussis PS capsule transporter-export machinery and in particular KpsT are necessary for optimal expression of virulence genes and therefore play an important role in pertussis pathogenesis."
 <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243#pone-0115243-g006>
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-DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.
+==DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.==
 . Experimental design-what is the treatment and what is the control

@@ Line 140: / Line 140: @@
 *[[Media: GSM1519511_3-B3_vs_dB5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2.
 *[[Media: GSM1519514_4-B5_vs_dB3.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2 by dye-swap color.
-*[[Media
+*[[Media: GSM1519516_5-C3_vs_dC5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 3.
 * Construct a flow chart that illustrates the above.

@@ Line 138: / Line 138: @@
 *[[Media: GSM1519507_1-A3_vs_dA5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1.
 *[[Media: GSM1519509_2-A5_vs_dA3.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1 by dye-swap color.
+*[[Media: GSM1519511_3-B3_vs_dB5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2.
 * Construct a flow chart that illustrates the above.

← Older revision		Revision as of 06:47, 17 November 2015
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	* Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.		* Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
		+	*[[Media: GSM1519507_1-A3_vs_dA5.dav.txt.gz]]-Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1
		+	*
		+
	* Construct a flow chart that illustrates the above.		* Construct a flow chart that illustrates the above.