Vpachec3 Week 11 - Revision history

Vpachec3: added genialomics links

2015-11-17T09:30:02Z

added genialomics links

Vpachec3: /* Previous Studies */ syntax fin

2015-11-17T09:29:09Z

‎Previous Studies: syntax fin

Vpachec3: added previous studies section

2015-11-17T09:28:53Z

added previous studies section

Vpachec3: added figures and tables

2015-11-17T09:23:44Z

added figures and tables

Vpachec3: /* Article Outline */ bold fix

2015-11-17T08:56:18Z

‎Article Outline: bold fix

Vpachec3: /* Article Outline */ syntax fix

2015-11-17T08:55:57Z

‎Article Outline: syntax fix

Vpachec3: Added final section for outline

2015-11-17T08:55:29Z

Added final section for outline

Vpachec3: /* Article Outline */ added the outline

2015-11-17T08:41:13Z

‎Article Outline: added the outline

Vpachec3: /* 10 Biological Terms and Definitions */ added the remaining definitions

2015-11-16T10:08:52Z

‎10 Biological Terms and Definitions: added the remaining definitions

Vpachec3: /* 10 Biological Terms and Definitions */ added some definitions

2015-11-16T09:53:13Z

‎10 Biological Terms and Definitions: added some definitions

← Older revision		Revision as of 09:30, 17 November 2015
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	[[Category: Journal Entry]]		[[Category: Journal Entry]]
		+
		+	== GÉNialOMICS Links ==
		+
		+	{{Template:GÉNialOMICS}}
		+
		+	[[Category:Journal Entry]]

@@ Line 97: / Line 97: @@
 ==Previous Studies==
- Most of the studies referenced in the paper were for methodologies of the different experiments run. Toward the conclusion we see that there is an article where they "reawaken" persister cells to counteract the phenotypic changes which allow for antimicrobial resistance. While this study, we see a focus on targeting the cell's mechanisms to deal with ROS. It's more of a proactive approach rather than the reactive approach in the prior literature.
+Most of the studies referenced in the paper were for methodologies of the different experiments run. Toward the conclusion we see that there is an article where they "reawaken" persister cells to counteract the phenotypic changes which allow for antimicrobial resistance. While this study, we see a focus on targeting the cell's mechanisms to deal with ROS. It's more of a proactive approach rather than the reactive approach in the prior literature.
 ==Links==

@@ Line 96: / Line 96: @@
 * Table 5: shows the difference in gene expression as fold changes in the microarray analysis and the qPCR experiment. It shows glyoxylate shunt, Tricarboxylic acid cycle, oxidative phosphorylation, NAD(P)H production and response to oxidative stress.
 [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/User:Vpachec3 Vpachec3 User Page]
 [[Category: Journal Entry]]

← Older revision		Revision as of 09:23, 17 November 2015
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	#**Less persister cells survived when in the presence of ICL and SDH		#**Less persister cells survived when in the presence of ICL and SDH
	#**Overall:mechanism is widespread throughout the various species new approaches to the treatment of persister-related infections		#**Overall:mechanism is widespread throughout the various species new approaches to the treatment of persister-related infections
		+
		+	==Figures and Tables==
		+	* Figure 1: percentage of cells which survived treatment of tobramycin and ciproflaxin. Open circles are biofilms and triangles are planktonic cultures
		+	* Figure 2: fluorescent signal for tobramycin-treated and untreated biofilms. The differences between the two graphs are statistically significant
		+	* Figure 3: percentage of surviving cells in C5424 and two mutants (MDL1 and MDL2) after treated with tobramycin
		+	* Figure 4: percentage of surviving cells in B.cenocepacia J2315 with either only tobramycin (control) or tobramycin and diethlydithiocarbamate
		+	* Figure 5: percentage of surviving cells in J2315 after treated with tobramycin or with ciprofloxacin, both supplemented with itaconate or 3-NP
		+	* Figure 6: percentage of surviving cells after treatment with tobramycin or combo of tobramycin and itaconate
		+	* Figure 7A: percentage of surviving cells for the double mutant, double mutant with 3-NP, the wildtype and the wildtype with 3-NP
		+	* Figure 7B: percentage of surviving cells double mutant strands treated with tobramycin and the double mutant supplemented with 2-thenoyltrifluoroacetone
		+	* Table 5: shows the difference in gene expression as fold changes in the microarray analysis and the qPCR experiment. It shows glyoxylate shunt, Tricarboxylic acid cycle, oxidative phosphorylation, NAD(P)H production and response to oxidative stress.

@@ Line 19: / Line 19: @@
 ==Article Outline==
-#Introduction
+#'''Introduction'''
 #**Bcc are opportunistic pathogens
 #**found in cystic fibrosis patients
 #**Infections are species dependent
 #**Hard to eradicate because they are good at resisting antibiotics and are good at creating biofilms
-#Materials and Methods
+#'''Materials and Methods'''
 #*'''Strains and Culture Conditions'''
 #** 18 strains in the ''Burkholderia cepacia'' group

@@ Line 76: / Line 76: @@
 #**Antisense overexpression mutant involved amplifying BCAM0967 and BCAM0968
 #**Needed to confirm the significance of SDH
-#Results and Discussion
+#'''Results and Discussion'''
 #**TCA cycle was downregulated
 #**Gene expression in the electron transport chain was downregulated
@@ Line 83: / Line 83: @@
 #**Glyoxylate shunt and ICL encoding genes were upregulated
 #**Less persister cells survived when in the presence of ICL and SDH
-#**Overall:mechanism is widespread throughout the various species
+#**Overall:mechanism is widespread throughout the various species new approaches to the treatment of persister-related infections
 new approaches to the treatment of persister-related infections

@@ Line 46: / Line 46: @@
 #** Chose 11 selected genes to use RT-qPCR on
 #**RNA was extracted from biofilms
-#**
+#**cDNA was synthesized
 #*'''Flow Cytometry'''
 #**Aim: to see induction of reactive oxygen species by tobramycin
@@ Line 55: / Line 58: @@
 #**Cells were measured using flow cytometer
 #**50,000 cells per sample
 ==Links==

@@ Line 2: / Line 2: @@
 #'''Aminoglycoside antibiotic'''- group of antibiotics active against many acrobic Gram-negative and some Gram-positive bacteria. Composed of two or more amino sugars attached by a glycosidic linkage to a hexose nucleus; polycationic and highly polar compounds. Inhibit bacterial protein synthesis by binding to a site on the 30S ribosomal subunit thereby altering codon-anticodon recognition.
 #'''Fluoroquinolone'''- bactericidal and inhibit the activity of DNA gyrase. Newer fluoroquinolones (e.g. ciprofloxacin) had a broader spectrum of activity
-#Sessile cells
+#'''Sessile cells'''- (1)of, pertaining to, or relating to the state of sessility or the inability to move actively or spontaneously.(2) being permanently attached to the substrate or to the base, hence, not freely moving[http://www.biology-online.org/dictionary/Sessile]
 #'''cDNA'''-Complementary DNA Viral reverse transcriptase can be used to synthesize DNA that is complementary to RNA. The cDNA can be used, for example, as a probe to locate the gene or can be cloned in the double-stranded form.
 #'''Flow cytometry'''-Slightly imprecise but common term for the use of the fluorescence activated cell sorter (FACS). Cells are labelled with fluorescent dye and then passed, in suspending medium, through a narrow dropping nozzle so that each cell is in a small droplet. A laser-based detector system is used  to excite fluorescence and droplets with positively fluorescent cells are given an electric charge. Charged and uncharged droplets are separated as they fall between changed plates and so collect in different tubes. the machine can be used either as an analytical tool, counting the number of labelled cells in a population, or to separate the cells for subsequent growth of the selected population. further sophistication can be built into the system by using a second laser system at right angles to the first look at a sec on fluorescent label or to gauge cell size on the basis of light scatter. The great strength of the system is that it looks at larger numbers of individual cells and makes possible the separation of populations with, for example, particular surface properties.
 #'''Isocitrate'''- an intermediate in the tricarboxylic acid cycle (citric acid cycle)
-#Persister
+#'''Persister cells'''- bacterial cells that survive killing by antibiotics that block synthesis of peptidoglycan or DNA, but remain sensitive to that antibiotic upon being regrown and give rise to the same small fraction of persisters. [http://ecoliwiki.net/colipedia/index.php/Persister_Cells]
-#Exconjugants
+#'''Exconjugants'''- a member of a conjugating pair of protozoan ciliates after separation and prior to the subsequent mitotic division of each of the exconjugant's.[http://www.biology-online.org/dictionary/Exconjugant]
-#Mutagenesis
+#'''Mutagenesis'''- act of mutation by deleting or changing the nucleotide sequence[http://www.biology-online.org/dictionary/Mutagenesis]
 #'''Glyoxylate shunt'''- (See glyoxalate cycle) Glyoxylate cycle: metabolic pathway present in bacteria and in the glyoxisome of plants, in which two acetyl-CoA molecules are converted to a 4-carbon dicarboxylic acid, initially succinate. Includes two enzymes not found elsewhere, isocitrate lyase and malate synthase. Permits nest synthesis of carbohydrates from lipid, and hence is prominent in those seeds in which lipid is the principle food reserve.
@@ Line 14: / Line 14: @@
 Definitions for numbers 1, 2, 4, 5,6 and 10 were found in ''Dictionary of Cell and Molecular Biology'' (Citation below).
 Lackie, J. M. (2007). Dictionary of Cell and Molecular Biology. Kidlington, GBR: Academic Press. Retrieved from http://www.ebrary.com