Ckaplan Week 12 - Revision history

Ckapla12: citation

2024-04-18T02:00:28Z

citation

Ckapla12: answering concerns

2024-04-18T01:59:54Z

answering concerns

Ckapla12: format

2024-04-18T01:57:21Z

format

Ckapla12 at 01:47, 18 April 2024

2024-04-18T01:47:37Z

Ckapla12: format

2024-04-18T01:47:03Z

format

Ckapla12: adding definitions

2024-04-18T01:45:58Z

adding definitions

Ckapla12: format

2024-04-18T01:28:45Z

format

Ckapla12: answering gene questions

2024-04-18T01:27:09Z

answering gene questions

Ckapla12: answering question about figures

2024-04-18T01:15:47Z

answering question about figures

Ckapla12: format

2024-04-18T01:01:16Z

format

← Older revision		Revision as of 02:00, 18 April 2024
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	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).		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

← Older revision		Revision as of 01:59, 18 April 2024
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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===		===Bibliography===

← Older revision		Revision as of 01:57, 18 April 2024
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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?
		+
		+	===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}}

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 . 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).
-.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).
+. 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).
 . 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).

@@ Line 4: / Line 4: @@
 . 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).
 .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).
 . 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).
 .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).
 . 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).
 . 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).
 . 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).
 . 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).
 . 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).
 . 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).

← Older revision		Revision as of 01:45, 18 April 2024
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	===Definitons:===		===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).

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 [[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf]]
 *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.

@@ Line 55: / Line 55: @@
 *What do the X and Y axes represent (if applicable)?
 *How were the measurements made?
+Microarray technology
 *What trends are shown by the plots and what conclusions can you draw from the data?

@@ Line 26: / Line 26: @@
 *What method did they use to prepare the RNA, label it and hybridize it to the microarray?
-*What mathematical/statistical method did they use to analyze the data?
+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
-*Are the data publicly available for download? From which web site?
+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.
-*Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
+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.
 *What do the X and Y axes represent (if applicable)?

@@ Line 3: / Line 3: @@
 *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?
@@ Line 14: / Line 12: @@
 *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?