Difference between revisions of "YBR138C"

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{|{{Prettytable}} align = 'right' width = '200px'
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YBR138C YBR138C]  
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000000342 YBR138C]  
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name'''        ||'' ''
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
 
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
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|nowrap| Chr II:515330..513756
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|nowrap| Chr II:515336..513762
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID'''          || S000000342
 
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'''Description of {{PAGENAME}}:''' Cytoplasmic protein of unknown function, potentially phosphorylated by Cdc28p; YBR138C is not an essential gene<ref name='S000074306'>Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64 {{SGDpaper|S000074306}} PMID 14574415</ref><ref name='S000074185'>Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 {{SGDpaper|S000074185}} PMID 14562095</ref><ref name='S000039796'>Kucharczyk R, et al. (1999) Disruption of six novel yeast genes located on chromosome II reveals one gene essential for vegetative growth and two required for sporulation and conferring hypersensitivity to various chemicals. Yeast 15(10B):987-1000
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'''Description of YBR138C:''' Cytoplasmic protein of unknown function, potentially phosphorylated by Cdc28p; YBR138C is not an essential gene<ref name='S000074185'>Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 {{SGDpaper|S000074185}} PMID 14562095</ref><ref name='S000039796'>Kucharczyk R, et al. (1999) Disruption of six novel yeast genes located on chromosome II reveals one gene essential for vegetative growth and two required for sporulation and conferring hypersensitivity to various chemicals. Yeast 15(10B):987-1000 {{SGDpaper|S000039796}} PMID 10407278</ref><ref name='S000074306'>Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64
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  {{SGDpaper|S000039796}} PMID 10407278</ref>
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  {{SGDpaper|S000074306}} PMID 14574415</ref>
 
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{{ShortCenteredHR}}
 
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{{UW-Stout}}
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===[[UW-Stout/Growth_Curve|Growth Curve]]===
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[[Image:YBR138C_YPD.png]]
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In a BY4735 background, knocking out YBR138C seems to have no effect on growth rate in log-phase.  In this assay, the BY4735 strain's doubling time was 414 minutes, while the YBR138C knock-out strain's doubling time was 432minutes.  (These doubling times are the means of three experiments.)
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Caffeine and Yeast Cells
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[[Image:megan24.png]]
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This graph shows the growth curve with and without caffeine. It has the knockout strain and wild type yeast cells. The caffeine enhanced the growth in both wild type and knockout strain. The average doubling time between the three experiments for the knockout strand was 689.46 minutes. The caffeine also had a positive effect on the growth curve for the wild type with the average doubling time being 1245.02 minutes. The results were concluded from the wild type and knockout strand was with this amount of caffeine it leads to an increase in growth. 
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The protocol can be found at
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===[[UW-Stout/Caffeine_FA19|Caffeine]]===
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[[File:yBR138cUV_Exposure.png]]
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This bar graph shows that compared to a BY4735 background, yBR138c makes yeast less sensitive to UV light exposure.
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The protocol can be found at
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===[[UW_Stout/UV_Light_FA19|UV Light Exposure]]===
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===Cycloheximide effecting YBR138C===
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[[File:Cycloheximide 5.png]]
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In this image we see that tests 2&3 are surviving and tests 1&4 are not doing as well under this stress. 1 is very low compared to 3 and this is kind of weird. The three Growth models are YBR138C not be stressed.
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===Effect of 3% [[UW Stout/DMSO FA19|DMSO]] on YBR138C===
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[[Image:Effect_of_3%_DMSO_on_YBR138C.png|600px]]
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The graph above shows the effect of 3% DMSO on YBR138C. From the data represented the average doubling rate for the YBR138C knockout strain without DMSO was 570 minutes. When DMSO is added the average doubling time increased to 835 minutes. This shows that 3% DMSO did add stress to this knockout strain. The average doubling time of WT:BY4735 without DMSO was 514 minutes. The average doubling rate for WT:BY4735 with DMSO was 1529 minutes. If we compare the average doubling rate of WT:BY4735 with DMSO to YBR138C with DMSO we can see that without the YBR138C gene the yeast was able to grow more quickly under DMSO induced stress, so much so that it almost halves the doubling time. Given both controls it also appears that the YBR138C gene has very little effect on the growth of the yeast in optimal conditions.
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===[[UW Stout/Proline FA19|Growth in Proline and Ammonium Sulfate]]===
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[[File:KO5.png|650 px]]
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This strand had an average doubling rate of 41.43 minutes in proline media and 42.23 minutes in ammonium sulfate media. There is not much of a difference, but it grew faster in proline media. For the wild types, the fastest average doubling rate was in ammonium sulfate media at 47.3 minutes. The average doubling time in proline was 50.63 minutes.
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==Ethanol Tolerance in YBR138C==
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[[Image:YBR138C_ethonal.png]]
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This graph shows the growth between YBR138C treated and untreated with ethanol. The rate of growth of the treated yeast is 1324.94 minutes. The rate of growth of the untreated yeast is 166.2485 minutes. This shows that the strands of YBR138C treated with ethanol had a decrease rate of growth compared to the strands that weren't.
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===[[UW-Stout/Prednisone_FA19|Prednisone Effects on YBR138C]]===
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[[File:YBR138C.png|750 px]]
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The graph above shows how dilutions P2 (30 µg/ml) and E2 (10% ethanol solution) impacted the growth rate of the knockout yeast strain YBR138C over 24 hours. The concentration did not double for test 3 of P2 for this experiment, so by taking only the first two test results, the doubling rate averages to around 962.5 minutes for only ethanol. As for the Prednisone with ethanol, the doubling rate averages to around 880 minutes. Overall, the Prednisone increased the rate of growth by about 82.5 minutes. The ethanol typically inhibits the growth of YBR138C more than the Prednisone with ethanol. These results conclude that Prednisone promotes the growth of yeast cells without the gene YBR138C.
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===1% Formamide Yeast Torture[[https://wiki.yeastgenome.org/index.php/UW_Stout/Formamide_FA19]]===
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[[Image:image_5.png]]
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This graph shows the growth curve of the knockout yeast strain YBR138C and wild type BY4735 in 1% formamide in 3 trials. The average calculated doubling time for YBR138C with 1% formamide was 2,710.55 minutes, while the unstressed strain was 3,131.33 minutes. This concluded that the unstressed strain is slightly sensitive to 1% formamide, and grows at a slower pace in this environment. Our stressed wild types doubling time was 3,459.91 minutes, and the unstressed was 2,468.04 minutes. This shows that the addition of 1% formamide constrains growth for the stressed wild type.
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[[File:Nitrogen_Starvation_YBR138C.jpg|463 x 599|Caption]]
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The Wild Type BY4735 has data located at the Nitrogen Starvation Protocol.
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==[[UW-Stout/Nitrogen_starvation_FA19|Nitrogen starvation]]==
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== [https://wiki.yeastgenome.org/index.php?title=UW-Stout/Hydroxyurea_FA19&oldid=401696 Hydroxyurea] ==
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[[File:AvaYBR138C.png]]
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The averaging doubling time for YBR138C is 532.72 minutes. The averaging doubling time for the unstressed YBR138C is 376.44 minutes
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<!-- PLEASE ADD Community Commentary ABOVE THIS MESSAGE. See below for an example of community annotation -->
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<!--
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Specifically higher expression in carbon limited chemostat cultures versus carbon excess.
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<ref>Boer VM, et al. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur.
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J Biol Chem 278(5):3265-74</ref>
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-->
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===Zone of Inhibition of 30% [https://wiki.yeastgenome.org/index.php/UW-Stout/Hydrogen_peroxide_FA19 Hydrogen Peroxide] on YBR138C===
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[[File:JJ6.PNG]]
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[[File:JaredJ6.PNG]]
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The bar graph represents the zone of inhibition of the knockout strain versus the wild type. Our data collected shows that the knockout strain saw a larger zone of inhibition (cells were not able to grow there). The error bar on the knockout strain represents the standard deviation of the experiment and how recreatable our results were with these results. Using these observations it is evident that the yeast strain YBR138C undergoes more stress from the oxidative properties of 30 percent hydrogen peroxide. The zone of inhibition is larger because the yeast cells are not able to grow as well as the wild type can in these conditions. For the strain YBR138C our plate values were as follows (in cm) 2.4, 2.4 and 2.35 compared to our wild type plate which stayed constant 2.1, 2.1 and 2.2 cm
 
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==References==
 
==References==
 
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Latest revision as of 09:14, 18 December 2019

Share your knowledge...Edit this entry! <protect>

Systematic name YBR138C
Gene name
Aliases HDR1
Feature type ORF, Uncharacterized
Coordinates Chr II:515336..513762
Primary SGDID S000000342


Description of YBR138C: Cytoplasmic protein of unknown function, potentially phosphorylated by Cdc28p; YBR138C is not an essential gene[1][2][3]




</protect>

Community Commentary

About Community Commentary. Please share your knowledge!

Protein Details

Protein Modification

Modification(s): Phosphorylation

Identified as an efficient substrate of Clb2-Cdk1-as1 in a screen of a proteomic GST-fusion library. [3] [4]

This gene is part of the UW-Stout Orphan Gene Project. Learn more here.

Growth Curve

YBR138C YPD.png

In a BY4735 background, knocking out YBR138C seems to have no effect on growth rate in log-phase. In this assay, the BY4735 strain's doubling time was 414 minutes, while the YBR138C knock-out strain's doubling time was 432minutes. (These doubling times are the means of three experiments.)

Caffeine and Yeast Cells

megan24.png

This graph shows the growth curve with and without caffeine. It has the knockout strain and wild type yeast cells. The caffeine enhanced the growth in both wild type and knockout strain. The average doubling time between the three experiments for the knockout strand was 689.46 minutes. The caffeine also had a positive effect on the growth curve for the wild type with the average doubling time being 1245.02 minutes. The results were concluded from the wild type and knockout strand was with this amount of caffeine it leads to an increase in growth.

The protocol can be found at

Caffeine

yBR138cUV Exposure.png

This bar graph shows that compared to a BY4735 background, yBR138c makes yeast less sensitive to UV light exposure.

The protocol can be found at

UV Light Exposure

Cycloheximide effecting YBR138C

Cycloheximide 5.png

In this image we see that tests 2&3 are surviving and tests 1&4 are not doing as well under this stress. 1 is very low compared to 3 and this is kind of weird. The three Growth models are YBR138C not be stressed.


Effect of 3% DMSO on YBR138C

Effect of 3% DMSO on YBR138C.png

The graph above shows the effect of 3% DMSO on YBR138C. From the data represented the average doubling rate for the YBR138C knockout strain without DMSO was 570 minutes. When DMSO is added the average doubling time increased to 835 minutes. This shows that 3% DMSO did add stress to this knockout strain. The average doubling time of WT:BY4735 without DMSO was 514 minutes. The average doubling rate for WT:BY4735 with DMSO was 1529 minutes. If we compare the average doubling rate of WT:BY4735 with DMSO to YBR138C with DMSO we can see that without the YBR138C gene the yeast was able to grow more quickly under DMSO induced stress, so much so that it almost halves the doubling time. Given both controls it also appears that the YBR138C gene has very little effect on the growth of the yeast in optimal conditions.


Growth in Proline and Ammonium Sulfate

KO5.png

This strand had an average doubling rate of 41.43 minutes in proline media and 42.23 minutes in ammonium sulfate media. There is not much of a difference, but it grew faster in proline media. For the wild types, the fastest average doubling rate was in ammonium sulfate media at 47.3 minutes. The average doubling time in proline was 50.63 minutes.

Ethanol Tolerance in YBR138C

YBR138C ethonal.png

This graph shows the growth between YBR138C treated and untreated with ethanol. The rate of growth of the treated yeast is 1324.94 minutes. The rate of growth of the untreated yeast is 166.2485 minutes. This shows that the strands of YBR138C treated with ethanol had a decrease rate of growth compared to the strands that weren't.

Prednisone Effects on YBR138C

YBR138C.png

The graph above shows how dilutions P2 (30 µg/ml) and E2 (10% ethanol solution) impacted the growth rate of the knockout yeast strain YBR138C over 24 hours. The concentration did not double for test 3 of P2 for this experiment, so by taking only the first two test results, the doubling rate averages to around 962.5 minutes for only ethanol. As for the Prednisone with ethanol, the doubling rate averages to around 880 minutes. Overall, the Prednisone increased the rate of growth by about 82.5 minutes. The ethanol typically inhibits the growth of YBR138C more than the Prednisone with ethanol. These results conclude that Prednisone promotes the growth of yeast cells without the gene YBR138C.


1% Formamide Yeast Torture[[1]]

image 5.png

This graph shows the growth curve of the knockout yeast strain YBR138C and wild type BY4735 in 1% formamide in 3 trials. The average calculated doubling time for YBR138C with 1% formamide was 2,710.55 minutes, while the unstressed strain was 3,131.33 minutes. This concluded that the unstressed strain is slightly sensitive to 1% formamide, and grows at a slower pace in this environment. Our stressed wild types doubling time was 3,459.91 minutes, and the unstressed was 2,468.04 minutes. This shows that the addition of 1% formamide constrains growth for the stressed wild type. Caption

The Wild Type BY4735 has data located at the Nitrogen Starvation Protocol.

Nitrogen starvation

Hydroxyurea

AvaYBR138C.png The averaging doubling time for YBR138C is 532.72 minutes. The averaging doubling time for the unstressed YBR138C is 376.44 minutes


Zone of Inhibition of 30% Hydrogen Peroxide on YBR138C

JJ6.PNG JaredJ6.PNG

The bar graph represents the zone of inhibition of the knockout strain versus the wild type. Our data collected shows that the knockout strain saw a larger zone of inhibition (cells were not able to grow there). The error bar on the knockout strain represents the standard deviation of the experiment and how recreatable our results were with these results. Using these observations it is evident that the yeast strain YBR138C undergoes more stress from the oxidative properties of 30 percent hydrogen peroxide. The zone of inhibition is larger because the yeast cells are not able to grow as well as the wild type can in these conditions. For the strain YBR138C our plate values were as follows (in cm) 2.4, 2.4 and 2.35 compared to our wild type plate which stayed constant 2.1, 2.1 and 2.2 cm <protect>

References

See Help:References on how to add references

  1. ↑ Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 SGD PMID 14562095
  2. ↑ Kucharczyk R, et al. (1999) Disruption of six novel yeast genes located on chromosome II reveals one gene essential for vegetative growth and two required for sporulation and conferring hypersensitivity to various chemicals. Yeast 15(10B):987-1000 SGD PMID 10407278
  3. ↑ 3.0 3.1 Ubersax JA, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425(6960):859-64 SGD PMID 14574415 Cite error: Invalid <ref> tag; name "S000074306" defined multiple times with different content
  4. ↑ submitted by Jeff Ubersax on 2004-01-21

See Help:Categories on how to add the wiki page for this gene to a Category </protect>

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