Difference between revisions of "Anthony J. Wavrin Week 3"

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(Added all of physiological factors)
(Added all of RNA expression)
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*This study tests explores if increasing concentration of ammonia while keeping a constant influx will cause nitrogen related responses.
 
*This study tests explores if increasing concentration of ammonia while keeping a constant influx will cause nitrogen related responses.
 
*The concentrations used resulted in testing from nitrogen limitation to nitrogen excess.
 
*The concentrations used resulted in testing from nitrogen limitation to nitrogen excess.
*Overall, they conduct effects of physiological parameters, RNA expression, and enzyme expression.
+
*Overall, they conduct effects of physiological parameters, RNA expression, and enzyme activites.
  
 
==Physiological parameters==
 
==Physiological parameters==
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**It is interesting to note that at the concentration of 61mM of ammonia, glucose becomes the limiting nutrient.
 
**It is interesting to note that at the concentration of 61mM of ammonia, glucose becomes the limiting nutrient.
 
===Figure 1===
 
===Figure 1===
====A=====
+
====A====
*The X-axis represents the increase in concentration of the ammonia.
+
*The X-axis represents the increase in the concentration of the ammonia.
 
*The Y-axis on the left represents the residual ammonia concentration.
 
*The Y-axis on the left represents the residual ammonia concentration.
 
*The Y-axis on the right represents the biomass (dry weight).
 
*The Y-axis on the right represents the biomass (dry weight).
Line 19: Line 19:
 
*The residual ammonia concentration sky rockets after 61mM which is expected due to nitrogen excess.
 
*The residual ammonia concentration sky rockets after 61mM which is expected due to nitrogen excess.
 
====B====
 
====B====
*The X-axis represents the increase in concentration of the ammonia.
+
*The X-axis represents the increase in the concentration of the ammonia.
 
*The Y-axis on the left represents the CO2 production.
 
*The Y-axis on the left represents the CO2 production.
 
*The Y-axis on the far left represents the O2 usage.
 
*The Y-axis on the far left represents the O2 usage.
 
*The Y-axis on the right represents the respiratory quotient, which is CO2 production/ O2 usage.
 
*The Y-axis on the right represents the respiratory quotient, which is CO2 production/ O2 usage.
*Concentrations above 44mM of ammonia have a relatively flat respiratory quotient.
+
*Concentrations above 44mM of ammonia have a relatively flat respiratory quotient, indicating carbon is the limiting nutrient.
 
====C====
 
====C====
=====Left Figure=====
+
=====Left Panel=====
*The X-axis represents the increase in concentration of the ammonia.
+
*The X-axis represents the increase in the concentration of the ammonia.
 
*The Y-axis on the left represents the concentration of α-ketogluterate present.
 
*The Y-axis on the left represents the concentration of α-ketogluterate present.
*As the ammonia concentration increases, α-ketogluterate concentration decreases until 61mM.
+
*As the ammonia concentration increases, α-ketogluterate concentration decreases until 61mM.  This represents the conversion of α-ketogluterate with nitrogen to form glutamate and eventually glutamine.
=====Middle Figure=====
+
=====Middle Panel=====
*The X-axis represents the increase in concentration of the ammonia.
+
*The X-axis represents the increase in the concentration of the ammonia.
 
*The Y-axis on the left represents the concentration of glutamate present.
 
*The Y-axis on the left represents the concentration of glutamate present.
 
*As the ammonia concentration increases, glutamate concentration increases until 61mM.
 
*As the ammonia concentration increases, glutamate concentration increases until 61mM.
=====Right Figure=====
+
=====Right Panel=====
*The X-axis represents the increase in concentration of the ammonia.
+
*The X-axis represents the increase in the concentration of the ammonia.
 
*The Y-axis on the left represents the concentration of glutamine present.
 
*The Y-axis on the left represents the concentration of glutamine present.
 
*As the ammonia concentration increases, glutamine concentration increases continually.
 
*As the ammonia concentration increases, glutamine concentration increases continually.
  
 
==RNA Expression==
 
==RNA Expression==
 +
*To measure the levels of RNA of nitrogen related genes, northern analysis was performed.
 +
*RNA was detected using labeled phosphate oligonucleotides or 2.5kB <i>Xho</i>1-<i>Bam</i>1 DNA fragments.
 +
*X-ray films were utilized to quantify the RNA Detected.
 +
===Figure 2===
 +
=====Left Panel=====
 +
*The X-axis represents the increase in the concentration of ammonia.
 +
*The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
 +
*As the ammonia concentration increases past 61mM, GDH1 decreases while GDH2 increases, indicating that GDH1 is repressed by excess nitrogen while GDH2 is induced by excess nitrogen.
 +
=====Middle Panel=====
 +
*The X-axis represents the increase in the concentration of ammonia.
 +
*The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
 +
*Both GAP1 and PUT4 "peak" and 44mM and decrease til 78mM then become relatively stable, indicating that they are repressed by excess nitrogen.
 +
=====Right Panel=====
 +
*The X-axis represents the increase in the concentration of ammonia.
 +
*The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
 +
*GLN1, HIS4, and ILV5 all peak around 66mM and 78mM and stay at a high expression until the highest concentration (118mM), in which the expression decreases drastically.
 +
 +
==Enzyme Activities==

Revision as of 20:25, 30 January 2013

Introduction

  • This article is exploring one of the possible explanations of how nitrogen, used in the form of ammonia in this study, can effect Saccharomyces cerevisiae.
  • It is well known that nitrogen is an essential nutrient that can increase growth, as utilized in fertilizer.
  • It is hypothesized that the actual influx of nitrogen may cause growth instead of the concentration.
  • This study tests explores if increasing concentration of ammonia while keeping a constant influx will cause nitrogen related responses.
  • The concentrations used resulted in testing from nitrogen limitation to nitrogen excess.
  • Overall, they conduct effects of physiological parameters, RNA expression, and enzyme activites.

Physiological parameters

  • The concentrations of ammonia used were 29, 44, 61, 66, 78, 90, 96, 114, and 118mM.
    • It is interesting to note that at the concentration of 61mM of ammonia, glucose becomes the limiting nutrient.

Figure 1

A

  • The X-axis represents the increase in the concentration of the ammonia.
  • The Y-axis on the left represents the residual ammonia concentration.
  • The Y-axis on the right represents the biomass (dry weight).
  • The Y-axis on the far right represents the ammonia flux, which is calculated using ammonia concentration, residual ammonia concentration, and biomass.
  • As ammonia increased to ammonia saturation, there was an increase in biomass, but stayed relatively constant after ammonia excess (>61mM).
  • The residual ammonia concentration sky rockets after 61mM which is expected due to nitrogen excess.

B

  • The X-axis represents the increase in the concentration of the ammonia.
  • The Y-axis on the left represents the CO2 production.
  • The Y-axis on the far left represents the O2 usage.
  • The Y-axis on the right represents the respiratory quotient, which is CO2 production/ O2 usage.
  • Concentrations above 44mM of ammonia have a relatively flat respiratory quotient, indicating carbon is the limiting nutrient.

C

Left Panel
  • The X-axis represents the increase in the concentration of the ammonia.
  • The Y-axis on the left represents the concentration of α-ketogluterate present.
  • As the ammonia concentration increases, α-ketogluterate concentration decreases until 61mM. This represents the conversion of α-ketogluterate with nitrogen to form glutamate and eventually glutamine.
Middle Panel
  • The X-axis represents the increase in the concentration of the ammonia.
  • The Y-axis on the left represents the concentration of glutamate present.
  • As the ammonia concentration increases, glutamate concentration increases until 61mM.
Right Panel
  • The X-axis represents the increase in the concentration of the ammonia.
  • The Y-axis on the left represents the concentration of glutamine present.
  • As the ammonia concentration increases, glutamine concentration increases continually.

RNA Expression

  • To measure the levels of RNA of nitrogen related genes, northern analysis was performed.
  • RNA was detected using labeled phosphate oligonucleotides or 2.5kB Xho1-Bam1 DNA fragments.
  • X-ray films were utilized to quantify the RNA Detected.

Figure 2

Left Panel
  • The X-axis represents the increase in the concentration of ammonia.
  • The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
  • As the ammonia concentration increases past 61mM, GDH1 decreases while GDH2 increases, indicating that GDH1 is repressed by excess nitrogen while GDH2 is induced by excess nitrogen.
Middle Panel
  • The X-axis represents the increase in the concentration of ammonia.
  • The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
  • Both GAP1 and PUT4 "peak" and 44mM and decrease til 78mM then become relatively stable, indicating that they are repressed by excess nitrogen.
Right Panel
  • The X-axis represents the increase in the concentration of ammonia.
  • The Y-axis represents the % expression of a given RNA, using ACT1 and H2A-H2B as internal controls.
  • GLN1, HIS4, and ILV5 all peak around 66mM and 78mM and stay at a high expression until the highest concentration (118mM), in which the expression decreases drastically.

Enzyme Activities