Difference between revisions of "Ckaplan Week 12"

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[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf]]
 
[[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf]]
  
 +
===Definitons:===
 +
 +
1. thioredoxin- "A ubiquitous protein (104 aa) that participates in various redox reactions through the reversible oxidation of its active centre dithiol to a disulphide and catalyses dithiol–disulphide exchange reactions. The active site (Trp-Cys-Gly-Pro-Cys) is common to bacterial and eukaryotic thioredoxins. Secreted by various cells, despite the lack of a signal sequence. Adult T-cell leukaemia-derived factor is an isoform of thioredoxin and is an autocrine growth factor produced by HTLV-1 or EBV-transformed T-cells that will upregulate interleukin 2 receptor-a (IL-2Ra)" (Oxford, 2008).
 +
 +
2. chromatin immunoprecipitation- "A technique for identifying a specific DNA sequence in the genome (q.v.) to which a particular protein binds in vivo (q.v.). In this procedure, the protein in question is cross-linked to DNA with formaldehyde in vivo. The DNA is then extracted from cells and sheared into small fragments. Antibodies against the bound protein are then used to isolate the protein-DNA complex, the protein is released, and the polymerase chain reaction (PCR) (q.v.) is used to amplify the DNA sequence to which the protein was bound. The amplified DNA can then be identified by sequence analysis" (Oxford, 2008).
 +
 +
3. transcriptome- "The full complement of RNA transcripts of the genes of a cell or organism. The types and relative abundance of different transcripts, i.e. the messenger RNAs (mRNAs), can be obtained by analysing cell contents using oligonucleotide microarrays. Such an analysis provides a ‘snapshot’ of the expression pattern of the cell's genes. See transcriptomics" (Oxford, 2008).
 +
 +
4.lignin- "A complex organic polymer that is deposited within the cellulose of plant cell walls during secondary thickening. Lignification makes the walls woody and therefore rigid. See sclerenchyma" (Oxford, 2008).
 +
 +
5. aeration- "To oxygenate or allow air to penetrate something. This process is used to promote biological degradation of organic matter in water, by exposing it to air. The process may be passive (when waste is simply exposed to air), or active (when a mixing or bubbling device introduces the air into the liquid, generating bubbles and aerosols that lead to the release of the dissolved gases). See also diffused air" (Oxford, 2008).
 +
 +
6. trehalose- "Mushroom sugar, also called mycose, a disaccharide of glucose. Found in some fungi (Amanita spp.), manna, and some insects; hydrolysed by the intestinal enzyme trehalase" (Oxford, 2008).
 +
 +
7. glutaredoxin- "A ubiquitous family of proteins (thiol transferases) which catalyse the reduction of disulphide bonds in their substrate proteins by use of reduced glutathione. Glutaredoxin-like proteins are diverse and their functions are unclear, but various forms have been found in prokaryotes, Plasmodium, and higher plants" (Oxford, 2008).
 +
 +
8. kinetics- The branch of physical chemistry concerned with measuring and studying the rates of chemical reactions. The main aim of chemical kinetics is to determine the mechanism of reactions by studying the rate under different conditions (temperature, pressure, etc.). See also activated-complex theory; Arrhenius equation (Oxford, 2008).
 +
 +
9. reductase- "A donor:acceptor oxidoreductase enzyme (EC class 1) when named after the more oxidized alternative substrate and when O2 is not a substrate. See oxidoreductase" (Oxford, 2008).
 +
 +
10. isoenzymes- "(isozyme) n. a physically distinct form of a given enzyme. Isoenzymes catalyse the same type of reaction but have slight physical and immunological differences. Isoenzymes of dehydrogenases, oxidases, transaminases, phosphatases, and proteolytic enzymes are known to exist" (Oxford, 2008).
 +
 +
https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170
 +
 +
 +
===Questions:===
 
*What is the main result presented in this paper?
 
*What is the main result presented in this paper?
 
The paper shows how Saccharomyces cerevisiae responds in the first 20 minutes to oxidative stress caused by cumene hydroperoxide (CHP). Using experiments with time controls and duplicate samples, the study finds new genes involved in this stress response and highlights differences in how cells react to CHP compared to hydrogen peroxide. The study used the data only up to t 20, highlighting how after 20 minutes, the yeast exhibited a stress response.
 
The paper shows how Saccharomyces cerevisiae responds in the first 20 minutes to oxidative stress caused by cumene hydroperoxide (CHP). Using experiments with time controls and duplicate samples, the study finds new genes involved in this stress response and highlights differences in how cells react to CHP compared to hydrogen peroxide. The study used the data only up to t 20, highlighting how after 20 minutes, the yeast exhibited a stress response.
Line 55: Line 81:
 
*What do the X and Y axes represent (if applicable)?
 
*What do the X and Y axes represent (if applicable)?
  
 +
Figure 1: Y concentration, X is time
 +
Figure 2: Y number of genes, X time
 +
Figure 3: Y standard deviation, X is time
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Figure 4: Y z-score, X is time
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Figure 5: Y z-score, X is time
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Figure 6: none
 +
Figure 7: Y standard deviation, X is time
 +
Figure 8: Y fold change, X is time
 +
Figure 9: Y is z-score, X is time
  
 
*How were the measurements made?
 
*How were the measurements made?
−
 
+
Microarray technology
  
 
*What trends are shown by the plots and what conclusions can you draw from the data?
 
*What trends are shown by the plots and what conclusions can you draw from the data?
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*Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
 
*Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
 +
Concerns arise regarding figure caption inconsistencies and poor proofreading, particularly evident in y-axis labeling inconsistencies. The y-axis labeling in multiple figures claim to display Z-scores, while the figure legends suggest a scale of unit standard deviation. Despite a time frame extending up to 120 minutes, only the data up to 20 minutes was utilized for analysis.With this selective use of data, the reliability of recorded trends is thereby brought into question, impacting the quality of this research.
 +
 +
 +
===Bibliography===
 +
*The complete bibliographic reference in the APA style (see this link), with DOI.
 +
 +
 +
*The link to the abstract from PubMed (LMU-specific link)
 +
 +
 +
*The link to the full text of the article in PubMedCentral (if not available, write N/A).
 +
 +
 +
*The link to the full text of the article (HTML format) from the publisher web site.
 +
 +
 +
*The link to the full PDF version of the article from the publisher web site.
 +
 +
 +
*Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
 +
 +
 +
*Additionally, is the article available under a Creative Commons license?
 +
 +
 +
*How is the article available to you?
 +
 +
 +
*Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
 +
 +
 +
*If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
 +
 +
 +
*Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
 +
 +
 +
*Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
 +
 +
 +
*Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
 +
 +
 +
*What organization is the publisher of the journal?
 +
 +
 +
*What type of organization is it?
 +
 +
 +
*Is the publisher for-profit or non-profit?
 +
 +
 +
*Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
 +
 +
 +
*Does the publisher belong to the Open Access Publishers Association?
 +
 +
 +
*What country is the journal published in?
 +
 +
 +
*How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
 +
 +
 +
*Are the articles in this journal peer-reviewed?
 +
 +
 +
*Provide a link to the scientific advisory board/editorial board of the journal.
 +
 +
 +
*What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
 +
 +
 +
*On what date was the article submitted?
 +
 +
 +
*On what date was the article accepted?
 +
 +
 +
*Did the article undergo any revisions before acceptance?
 +
 +
 +
*When was the article published?
 +
 +
 +
*What is the approximate elapsed time between submission and publication?
 +
 +
*What are the institutions with which the authors are affiliated?
 +
 +
 +
*Have the authors published other articles on this subject? (How will you find this out?) Hint:
 +
Google Scholar
 +
PubMed (LMU-specific link)
 +
Web of Science (LMU pays subscription fee for access)
 +
 +
 +
*Is there a conflict of interest for any of the authors?
 +
 +
 +
*Are the data associated with this article available? If so, provide a link to the dataset.
 +
 +
 +
*Perform a prospective search on your article in the Web of Science and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
 +
How many articles does this article cite?
 +
How many articles cite this article?
  
  
 
{{ckaplan}}
 
{{ckaplan}}

Latest revision as of 18:00, 17 April 2024

Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf

Definitons:

1. thioredoxin- "A ubiquitous protein (104 aa) that participates in various redox reactions through the reversible oxidation of its active centre dithiol to a disulphide and catalyses dithiol–disulphide exchange reactions. The active site (Trp-Cys-Gly-Pro-Cys) is common to bacterial and eukaryotic thioredoxins. Secreted by various cells, despite the lack of a signal sequence. Adult T-cell leukaemia-derived factor is an isoform of thioredoxin and is an autocrine growth factor produced by HTLV-1 or EBV-transformed T-cells that will upregulate interleukin 2 receptor-a (IL-2Ra)" (Oxford, 2008).

2. chromatin immunoprecipitation- "A technique for identifying a specific DNA sequence in the genome (q.v.) to which a particular protein binds in vivo (q.v.). In this procedure, the protein in question is cross-linked to DNA with formaldehyde in vivo. The DNA is then extracted from cells and sheared into small fragments. Antibodies against the bound protein are then used to isolate the protein-DNA complex, the protein is released, and the polymerase chain reaction (PCR) (q.v.) is used to amplify the DNA sequence to which the protein was bound. The amplified DNA can then be identified by sequence analysis" (Oxford, 2008).

3. transcriptome- "The full complement of RNA transcripts of the genes of a cell or organism. The types and relative abundance of different transcripts, i.e. the messenger RNAs (mRNAs), can be obtained by analysing cell contents using oligonucleotide microarrays. Such an analysis provides a ‘snapshot’ of the expression pattern of the cell's genes. See transcriptomics" (Oxford, 2008).

4.lignin- "A complex organic polymer that is deposited within the cellulose of plant cell walls during secondary thickening. Lignification makes the walls woody and therefore rigid. See sclerenchyma" (Oxford, 2008).

5. aeration- "To oxygenate or allow air to penetrate something. This process is used to promote biological degradation of organic matter in water, by exposing it to air. The process may be passive (when waste is simply exposed to air), or active (when a mixing or bubbling device introduces the air into the liquid, generating bubbles and aerosols that lead to the release of the dissolved gases). See also diffused air" (Oxford, 2008).

6. trehalose- "Mushroom sugar, also called mycose, a disaccharide of glucose. Found in some fungi (Amanita spp.), manna, and some insects; hydrolysed by the intestinal enzyme trehalase" (Oxford, 2008).

7. glutaredoxin- "A ubiquitous family of proteins (thiol transferases) which catalyse the reduction of disulphide bonds in their substrate proteins by use of reduced glutathione. Glutaredoxin-like proteins are diverse and their functions are unclear, but various forms have been found in prokaryotes, Plasmodium, and higher plants" (Oxford, 2008).

8. kinetics- The branch of physical chemistry concerned with measuring and studying the rates of chemical reactions. The main aim of chemical kinetics is to determine the mechanism of reactions by studying the rate under different conditions (temperature, pressure, etc.). See also activated-complex theory; Arrhenius equation (Oxford, 2008).

9. reductase- "A donor:acceptor oxidoreductase enzyme (EC class 1) when named after the more oxidized alternative substrate and when O2 is not a substrate. See oxidoreductase" (Oxford, 2008).

10. isoenzymes- "(isozyme) n. a physically distinct form of a given enzyme. Isoenzymes catalyse the same type of reaction but have slight physical and immunological differences. Isoenzymes of dehydrogenases, oxidases, transaminases, phosphatases, and proteolytic enzymes are known to exist" (Oxford, 2008).

https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170


Questions:

  • What is the main result presented in this paper?

The paper shows how Saccharomyces cerevisiae responds in the first 20 minutes to oxidative stress caused by cumene hydroperoxide (CHP). Using experiments with time controls and duplicate samples, the study finds new genes involved in this stress response and highlights differences in how cells react to CHP compared to hydrogen peroxide. The study used the data only up to t 20, highlighting how after 20 minutes, the yeast exhibited a stress response.

  • What is the importance or significance of this work?

This research is important because it's the first to show how yeast quickly responds (within 0-6 minutes) to CHP-induced stress. It also uncovers the roles of Yap3, Yap5, and Yap7 in yeast's response to oxidative stress, which weren't known before. Understanding these processes better could help us grasp how cells deal with stress and how it relates to diseases.

  • What were the limitations in previous studies that led them to perform this work?

Previous studies didn't use control groups and incubated the CHP. Because of these issues, it was hard to understand the data well. This study tried to fix these problems by keeping track of time, using enough samples, and controlling environmental factors tightly to get a better understanding of how cells respond early to CHP-induced stress.

  • How did they treat the yeast cells (what experiment were they doing?)

CHP- cumene hydroperoxide.

  • What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?

Diploid- BY4743.

  • What media did they grow them in? What temperature? What type of incubator? For how long?

2% (w/v) sucrose with uracil L-leucine, and L-histidine at 30ºC using BioFlo fermentors.

  • What controls did they use?

Yeast strain BY4743 was used but was not exposed to CHP.

  • How many replicates did they perform per treatment or timepoint?

3

  • What method did they use to prepare the RNA, label it and hybridize it to the microarray?

The researchers used GeneChip® One-Cycle cDNA synthesis kit to amplify the RNA samples, as recommended by the manufacturer. After amplification, labeled targets were hybridized to Affymetrix GeneChip® Yeast Genome S98 arrays.

  • What mathematical/statistical method did they use to analyze the data?

A 2 way ANOVA gene model was used to assess the significance of differences between transcripts across two time points.

  • Are the data publicly available for download? From which web site?

Yes, the data is publicly available on Gene Expression Omnibus (GEO)database.

  • Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.

Figure 1- the data illustrate how yeast efficiently converts cumene hydroperoxide (CHP) into cumyl alcohol (COH) within the initial 20 minutes of exposure. This transformation indicates the effectiveness of yeast in processing CHP, with the majority of this conversion occurring due to yeast activity rather than spontaneous chemical reactions in the medium itself.

Figure 2 shows the researchers' exploration of yeast's response to CHP-induced oxidative stress over time. Control cultures without CHP were included. Significant alterations are observed in the control cultures at the 40-minute mark, prompting the researchers to focus their analysis on the first 20 minutes.

In Figure 3- the researchers identify each of the clusters: Cluster A exhibits a rapid surge in activity at 6 minutes, indicating an immediate defensive response to oxidative stress. In contrast, Cluster B shows a slower but sustained increase in activity starting at 12 minutes, suggesting a secondary wave of defense mechanisms kicking in. Cluster C displays a temporary decrease in activity, suggesting a redistribution of yeast resources to respond to oxidative stress defenses. Cluster D demonstrates a gradual and steady increase in activity commencing at the 20-minute mark, potentially reflecting long-term adjustments aimed at enhancing survival strategies against oxidative stress

Figure 4 illustrates the identification of gene induction or repression within 3 to 6 minutes of exposure. In Graph A, genes rapidly induced return to their normal mRNA levels by 12 minutes but continue to decrease afterward. In Graph B, genes rapidly repressed return to their normal mRNA levels by 12 minutes but continue to increase thereafter.

Figure 5 presents the expression of six YAP family genes (YAP1, 2, 3, 4, 5, and 7), which encode bZIP proteins acting as transcription factors. It indicates the time point at which each YAP gene's expression is induced. Remarkably, the study notes the first observation of YAP3, YAP5, and YAP7 being induced by oxidative stress, with their functions previously unknown.

Figure 6 displays the gene expression response of the genes belonging to three overlapping regulons: YAP1, SKN7, and MSN2/4. It demonstrates that there are more overlapping genes between MSN2/4 and YAP1 compared to any other category. In the visualization, red indicates induction, and green indicates repression. The logarithm of the ratio of median values divided by the median value at time zero quantifies the intensity.

In Figure 7, the data reveal the induction of redox protein-encoding genes upon exposure to CHP. These genes are crucial for maintaining the reduced state of the cytosol and are associated with the glutathione and thioredoxin systems.

Figure 8 is organized into four different "functions," with the lag time of transcriptional response of genes increasing from left to right. The squares represent CHP-treated cultures, while triangles represent control cultures.

Figure 9 shows proteasome proteolysis, which targets partially-oxidized proteins prone to aggregation. This process occurs later in the oxidative stress response, around the 20-minute mark. The transcription of genes encoding proteasome subunits is regulated by Rpn4, a transcription factor.

  • What do the X and Y axes represent (if applicable)?

Figure 1: Y concentration, X is time Figure 2: Y number of genes, X time Figure 3: Y standard deviation, X is time Figure 4: Y z-score, X is time Figure 5: Y z-score, X is time Figure 6: none Figure 7: Y standard deviation, X is time Figure 8: Y fold change, X is time Figure 9: Y is z-score, X is time

  • How were the measurements made?

Microarray technology

  • What trends are shown by the plots and what conclusions can you draw from the data?


  • How does this work compare with previous studies?


  • What are the important implications of this work?


  • What future directions should the authors take?


  • Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

Concerns arise regarding figure caption inconsistencies and poor proofreading, particularly evident in y-axis labeling inconsistencies. The y-axis labeling in multiple figures claim to display Z-scores, while the figure legends suggest a scale of unit standard deviation. Despite a time frame extending up to 120 minutes, only the data up to 20 minutes was utilized for analysis.With this selective use of data, the reliability of recorded trends is thereby brought into question, impacting the quality of this research.


Bibliography

  • The complete bibliographic reference in the APA style (see this link), with DOI.


  • The link to the abstract from PubMed (LMU-specific link)


  • The link to the full text of the article in PubMedCentral (if not available, write N/A).


  • The link to the full text of the article (HTML format) from the publisher web site.


  • The link to the full PDF version of the article from the publisher web site.


  • Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.


  • Additionally, is the article available under a Creative Commons license?


  • How is the article available to you?


  • Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.


  • If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.


  • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.


  • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.


  • Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.


  • What organization is the publisher of the journal?


  • What type of organization is it?


  • Is the publisher for-profit or non-profit?


  • Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)


  • Does the publisher belong to the Open Access Publishers Association?


  • What country is the journal published in?


  • How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)


  • Are the articles in this journal peer-reviewed?


  • Provide a link to the scientific advisory board/editorial board of the journal.


  • What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)


  • On what date was the article submitted?


  • On what date was the article accepted?


  • Did the article undergo any revisions before acceptance?


  • When was the article published?


  • What is the approximate elapsed time between submission and publication?
  • What are the institutions with which the authors are affiliated?


  • Have the authors published other articles on this subject? (How will you find this out?) Hint:

Google Scholar PubMed (LMU-specific link) Web of Science (LMU pays subscription fee for access)


  • Is there a conflict of interest for any of the authors?


  • Are the data associated with this article available? If so, provide a link to the dataset.


  • Perform a prospective search on your article in the Web of Science and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):

How many articles does this article cite? How many articles cite this article?


Assignment Pages

Individual Journal Entry Pages

Shared Journal Entry Pages

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