CMR2/YOR093C Week 3 - Revision history

Dmadere: /* What was different about the information provided about your gene in each of the parent databases? */ revised paragraph

2019-09-19T05:54:12Z

‎What was different about the information provided about your gene in each of the parent databases?: revised paragraph

Dmadere: /* What was different about the information provided about your gene in each of the parent databases? */ added an s to referencecs

2019-09-19T05:50:56Z

‎What was different about the information provided about your gene in each of the parent databases?: added an s to referencecs

Dmadere: /* Why did you choose your particular gene? i.e., why is it interesting to you and your partner? */ added italics

2019-09-19T05:49:39Z

‎Why did you choose your particular gene? i.e., why is it interesting to you and your partner?: added italics

Dmadere: /* Why did you choose your particular gene? i.e., why is it interesting to you and your partner? */ added reference to question and changed citation

2019-09-19T05:49:15Z

‎Why did you choose your particular gene? i.e., why is it interesting to you and your partner?: added reference to question and changed citation

Jnimmers at 05:48, 19 September 2019

2019-09-19T05:48:42Z

Jnimmers: Summary Update

2019-09-19T05:48:09Z

Summary Update

Dmadere: /* What was different about the information provided about your gene in each of the parent databases? */ added reference at end of question

2019-09-19T05:47:43Z

‎What was different about the information provided about your gene in each of the parent databases?: added reference at end of question

Dmadere: /* Why did you choose your particular gene? i.e., why is it interesting to you and your partner? */

2019-09-19T05:44:06Z

‎Why did you choose your particular gene? i.e., why is it interesting to you and your partner?

Dmadere: /* What was different about the information provided about your gene in each of the parent databases? */ answered question of how each parent database was different

2019-09-19T05:43:03Z

‎What was different about the information provided about your gene in each of the parent databases?: answered question of how each parent database was different

Dmadere: /* Acknowledgements */ added acknowledgement statement

2019-09-19T05:25:09Z

‎Acknowledgements: added acknowledgement statement

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 *CMR2 functions include: Extending the lifespan of yeast bacteria, increase chemical resistance, and increase catalytic activity. ''Question answered with SGD''
 === What was different about the information provided about your gene in each of the parent databases? ===
-* Each database consisted of similar information relating to CMR2. In regards to content, each database had similar information about the functions of the gene and the molecular aspects of it, but the difference that each database had was the gene identifier. Each database had its own unique identifier. In addition, Ensembl also references Uniprot with the identifier name and provided a link to more information on the Uniprot page. Each database also had different research articles that tested the gene. The literature had similar concepts, but the experiments were performed by completely different scientists that may have referenced each other when completing it. In regards to the presentation of the database, NCBI and Ensembl were the more complex to navigate in comparison to SGD and Uniprot. NCBI and Ensembl had more of the molecular level type information including interactions that the gene had with other genes, and had more navigation links that connected the interactions with the genes. SGD and Uniprot provided more information on the performance of the gene in a yeast cell as well as the phenotype data from it including its resistance to chemicals. The information in SGD and Uniprot were more organized and had different categories and subsections that made it easier to navigate. ''Question answered with SGD, Ensembl, Uniprot, and NCBI''
+* Each database consists of similar information relating to CMR2. In regards to content, each database has similar information about the functions of the gene and the molecular aspects of it, but the gene identifiers are different. Each database has their own unique identifier. In addition, Ensembl also references Uniprot with the identifier name and provides a link to more information on the Uniprot page. Each database also has different research articles that tested the gene. The literature had similar concepts, but the experiments were performed by completely different scientists that may have referenced each other when completing it. In regards to the presentation of the database, NCBI and Ensembl were more complex to navigate in comparison to SGD and Uniprot. NCBI and Ensembl had more of the molecular level type information including interactions that the gene had with other genes, and had more navigation links that connected the interactions with the genes. SGD and Uniprot provided more information on the performance of the gene in a yeast cell as well as the phenotype data from it including its resistance to chemicals. The information in SGD and Uniprot were more organized and had different categories and subsections that made it easier to navigate. ''Question answered with SGD, Ensembl, Uniprot, and NCBI''
 === Why did you choose your particular gene? i.e., why is it interesting to you and your partner? ===

@@ Line 138: / Line 138: @@
 *CMR2 functions include: Extending the lifespan of yeast bacteria, increase chemical resistance, and increase catalytic activity. ''Question answered with SGD''
 === What was different about the information provided about your gene in each of the parent databases? ===
-* Each database consisted of similar information relating to CMR2. In regards to content, each database had similar information about the functions of the gene and the molecular aspects of it, but the difference that each database had was the gene identifier. Each database had its own unique identifier. In addition, Ensembl also reference Uniprot with the identifier name and provided a link to more information on the Uniprot page. Each database also had different research articles that tested the gene. The literature had similar concepts, but the experiments were performed by completely different scientists that may have referenced each other when completing it. In regards to the presentation of the database, NCBI and Ensembl were the more complex to navigate in comparison to SGD and Uniprot. NCBI and Ensembl had more of the molecular level type information including interactions that the gene had with other genes, and had more navigation links that connected the interactions with the genes. SGD and Uniprot provided more information on the performance of the gene in a yeast cell as well as the phenotype data from it including its resistance to chemicals. The information in SGD and Uniprot were more organized and had different categories and subsections that made it easier to navigate. ''Question answered with SGD, Ensembl, Uniprot, and NCBI''
+* Each database consisted of similar information relating to CMR2. In regards to content, each database had similar information about the functions of the gene and the molecular aspects of it, but the difference that each database had was the gene identifier. Each database had its own unique identifier. In addition, Ensembl also references Uniprot with the identifier name and provided a link to more information on the Uniprot page. Each database also had different research articles that tested the gene. The literature had similar concepts, but the experiments were performed by completely different scientists that may have referenced each other when completing it. In regards to the presentation of the database, NCBI and Ensembl were the more complex to navigate in comparison to SGD and Uniprot. NCBI and Ensembl had more of the molecular level type information including interactions that the gene had with other genes, and had more navigation links that connected the interactions with the genes. SGD and Uniprot provided more information on the performance of the gene in a yeast cell as well as the phenotype data from it including its resistance to chemicals. The information in SGD and Uniprot were more organized and had different categories and subsections that made it easier to navigate. ''Question answered with SGD, Ensembl, Uniprot, and NCBI''
 === Why did you choose your particular gene? i.e., why is it interesting to you and your partner? ===

@@ Line 141: / Line 141: @@
 === Why did you choose your particular gene? i.e., why is it interesting to you and your partner? ===
-*We chose the CMR2 gene because we were interested in learning about a gene that had a longer lifespan than others. In a study done on the CMR2 gene in ''Saccharomyces cerevisiae'', Postma and other scientists found out that cells containing this gene along with a few other genes, were able to survive for about 5 years on YPD plates due to their ability to undergo long periods of low metabolic rates (Postma et al., 2009). From this paper, we were curious to research the different ways that scientists would stress this gene enough to cause an apoptotic cell death. The literature has been consistent with their research indicating that the presence of this gene in Saccharomyces cerevisiae will decrease cell death. ''Question answered with SGD''
+*We chose the CMR2 gene because we were interested in learning about a gene that had a longer lifespan than others. In a study done on the CMR2 gene in ''Saccharomyces cerevisiae'', Postma and other scientists found out that cells containing this gene along with a few other genes, were able to survive for about 5 years on YPD plates due to their ability to undergo long periods of low metabolic rates (Postma et al., 2009). From this paper, we were curious to research the different ways that scientists would stress this gene enough to cause an apoptotic cell death. The literature has been consistent with their research indicating that the presence of this gene in ''Saccharomyces cerevisiae'' will decrease cell death. ''Question answered with SGD''
 [[File:CMR2.PNG | thumb | Location of gene within a yeast cell. The locations include presence in the cytosol, cellular bud neck, and the integral component of the membrane]]

@@ Line 141: / Line 141: @@
 === Why did you choose your particular gene? i.e., why is it interesting to you and your partner? ===
-*We chose the CMR2 gene because we were interested in learning about a gene that had a longer lifespan than others. In a study done on the CMR2 gene in ''Saccharomyces cerevisiae'', Postma and other scientists found out that cells containing this gene along with a few other genes, were able to survive for about 5 years on YPD plates due to their ability to undergo long periods of low metabolic rates (Postma, et al.). From this paper, we were curious to research the different ways that scientists would stress this gene enough to cause an apoptotic cell death. The literature has been consistent with their research indicating that the presence of this gene in Saccharomyces cerevisiae will decrease cell death.
+*We chose the CMR2 gene because we were interested in learning about a gene that had a longer lifespan than others. In a study done on the CMR2 gene in ''Saccharomyces cerevisiae'', Postma and other scientists found out that cells containing this gene along with a few other genes, were able to survive for about 5 years on YPD plates due to their ability to undergo long periods of low metabolic rates (Postma et al., 2009). From this paper, we were curious to research the different ways that scientists would stress this gene enough to cause an apoptotic cell death. The literature has been consistent with their research indicating that the presence of this gene in Saccharomyces cerevisiae will decrease cell death. ''Question answered with SGD''
 [[File:CMR2.PNG | thumb | Location of gene within a yeast cell. The locations include presence in the cytosol, cellular bud neck, and the integral component of the membrane]]

@@ Line 3: / Line 3: @@
 === Summary ===
-The CMR2 gene found in ''Saccharomyces cerevisiae'' is a unique gene having a longer lifespan. Not much is studied on the gene itself, but it is known from literature that this gene can live for as long as five years. Found within the cytoplasm of Saccharomyces cerevisiae cells, this gene is able to withstand certain harmful chemicals and low temperatures to keep itself alive. As said previously, this gene is relatively new in its discovery, leading to its lack of highly informational literature on it's full functions, however, the studies that have been carried out have shown that, while still being relatively viable, yeast cells with the CMR2 a.k.a. YORO93 gene are in some way less competitively fit than those without the activated gene, however, when the gene is deleted from the genome, the mutant becomes sensitive  to factors that create responses for unfolded protein. This gene is full of many secrets, but hopefully as time goes on, more studies on the gene will allow for great discoveries on its functions and capabilities [https://www.yeastgenome.org/locus/S000005619#reference  As show by the SGD database].
+The CMR2 gene found in ''Saccharomyces cerevisiae'' is a unique gene having a longer lifespan. Not much is studied on the gene itself, but it is known from literature that this gene can live for as long as five years. Found within the cytosol of Saccharomyces cerevisiae cells, this gene is able to withstand certain harmful chemicals and low temperatures to keep itself alive. As said previously, this gene is relatively new in its discovery, leading to its lack of highly informational literature on it's full functions, however, the studies that have been carried out have shown that, while still being relatively viable, yeast cells with the CMR2 a.k.a. YORO93 gene are in some way less competitively fit than those without the activated gene, however, when the gene is deleted from the genome, the mutant becomes sensitive  to factors that create responses for unfolded protein. This gene is full of many secrets, but hopefully as time goes on, more studies on the gene will allow for great discoveries on its functions and capabilities [https://www.yeastgenome.org/locus/S000005619#reference  As show by the SGD database].
 *'''Standard Name:''' CMR2

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 === Acknowledgements ===
-* I would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the databases utilized during this research assignment.
+* We would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the databases utilized during this research assignment.
 * Thank you to my homework partner [[User:Dmadere| Delisa Madere]] for her partnership in this assignment. We met in person and spoke over the phone in order to discuss the sharing of responsibility, contents of the page, and understanding of the assignment. All work was shared between the two of us.
 *Except for what is noted above, this journal entry was done by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 17:29, 18 September 2019 (PDT)
 === References ===