Nstojan1 Week 12 - Revision history

Nstojan1-new: answered questions

2024-04-12T05:56:04Z

answered questions

Nstojan1-new: added bibliography

2024-04-12T04:56:56Z

added bibliography

Nstojan1-new: edited questions

2024-04-11T05:44:32Z

edited questions

Nstojan1-new: added answer

2024-04-11T05:19:37Z

added answer

Nstojan1-new: added definition

2024-04-11T05:17:52Z

added definition

Nstojan1-new: /* Evaluating Meta Data */ edited syntax

2024-04-11T05:00:35Z

‎Evaluating Meta Data: edited syntax

Nstojan1-new: added definition

2024-04-11T04:47:14Z

added definition

Nstojan1-new: /* Evaluating Meta Data */ answered questions

2024-04-11T04:37:41Z

‎Evaluating Meta Data: answered questions

Nstojan1-new: /* Evaluating Meta Data */ answered question

2024-04-11T04:33:40Z

‎Evaluating Meta Data: answered question

Nstojan1-new: /* Evaluating Meta Data */ edited syntax

2024-04-11T04:31:34Z

‎Evaluating Meta Data: edited syntax

@@ Line 14: / Line 14: @@
 ##What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? A haploid Saccharomyces cerevisiae W303 strain.
 ##What media did they grow them in? What temperature? What type of incubator? For how long? PCR was used to grow the microarrays. The cells were also grown on YPD media. The temperature is not specified in the paper except for the elevated temperature environmental condition which was 30 degrees and then 37 degrees celsius. The time was different depending on the growth conditions and media. The times ranged from 20 minutes to 14 hours.
-##What controls did they use? Their control was unenriched DNA samples.
+##What controls did they use? Their control was unenriched DNA samples according to the supplementary methods.
 ##How many replicates did they perform per treatment or timepoint? The supplementary methods states that the program was ran 50 times on random sequences on sets of different probes.
-##What method did they use to prepare the RNA, label it and hybridize it to the microarray?
+##What method did they use to prepare the RNA, label it and hybridize it to the microarray? To prepare, they crosslinked the DNA which was then immunoprecipitated. They then reversed the crosslink in order to be able to separate the DNA from protein. Unenriched samples were then amplified and labelled with a ligation-mediated PCR. They hybridized it to the microarray by spotted PCR products.
 ##What mathematical/statistical method did they use to analyze the data? Probability scores were used to determine the significance of the binding interactions.
 ##Are the data publicly available for download? From which web site? The raw data can't be downloaded.
 ##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
-#*Figure 1:
+#*Figure 1: Identifies and maps which specific DNA sequences are bound by yeast transcriptional regulators. The ChIP experiment indicated which DNA sequence is bound to transcriptional factors in yeast cells. The Phylogenetic conservation data shows different sequences in different species of yeast that are important for the binding. The figure also lists different motifs that are binding sites for the transcriptional factors.
-#*Figure 2:
+#*Figure 2: Is a more detailed transcriptional regulatory map. It represents the interactions between different DNA sequences and transcriptional factors they bind to. It also shows the chromosome and how they are distributed among the different sections in yeast.
-#*:Figure 3:
+#*:Figure 3: It shows the arrangement of regulatory sequences in yeast DNA to control gene expression.
-##*What do the X and Y axes represent (if applicable)?
+#*Figure 4: shows the different patterns of DNA binding behavior of transcription regulators in the different environmental conditions.
-##*How were the measurements made?
+#*Figure 5: The main finding is that the binding or regulators to promoters is specific and selective.
-##*What trends are shown by the plots and what conclusions can you draw from the data?
+#* Figure 6: This figure shows the way a large number of motifs are filtered to identify more precise motifs. The key finding was that 65 motifs were assigned to an equal number of regulators. This was reduced from 283 motifs and 82 regulators.
-##How does this work compare with previous studies?
+#*Figure 7: The main findings discovered that in Cin5, the binding site was specific for the newly found DNA motif that was compared to a previous site.
-##What are the important implications of this work?
+#*Figure 8: In a more nutrient rich environment some regulators bind mire to promoter regions compared to when there were little to no amino acids present. Regulatory activity is condition invariant.
-##What future directions should the authors take?
+#*Figure 9:Gcn4 tightly binds to DNA under normal conditions, however, it becomes more relaxed under amino acid starvation. It also indicates that there might be a different gene regulation in response to the stress from the environment.
-##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?
+##*What do the X and Y axes represent (if applicable)? For figure 5, the x-axis is the regulators in the order of the number the promoter regions bind to. The y-axis is the promoter region that's bound to each regulator. In figure 9, the x-axis is the different regulators and the y-axis is the amount of promoter regions that are bind each of these regulators under the 2 conditions.
 ==Bibliography Questions==

← Older revision		Revision as of 04:56, 12 April 2024
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	##What future directions should the authors take?		##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?		##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 Questions==
		+
		+	#Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., & Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99–104. https://doi.org/10.1038/nature02800
		+	#[https://pubmed.ncbi.nlm.nih.gov/15343339/]
		+	#https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/
		+	# [https://www.nature.com/articles/nature02800]
		+	#[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/]
		+	#The copyright is owned by the Author because it is an Author Manuscript
		+	# Once I open the full text, I do see "Public Access".
		+	#* The article is open access.
		+	#*Accessing it from NIH was free, however to access it from "nature" it says that it is a subscription content and must be accessed via the institution
		+	#The journal Nature is available for print, since it is available to subscribe to print.
		+	#The publisher of the Journal is Nature Portfolio, which is part of Springer Nature, they are for profit. They are not a member of OAPA.
		+	#Since 1989
		+	#Yes, the articles in this journal are peer-reviewed.
		+	# [https://www.nature.com/nature/editors]
		+	# 64.8 was the 2 year impact factor and 60.9 was the 5 year impact factor (2022).
		+	#The article was submitted on March 11 2004
		+	#The article was accepted on July 1st 2004
		+	#No/unknown, all it says is that it was published in final edited form 2004, Sept 2.
		+	#The article was published on September 2 2004
		+	#7 months
		+	# Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology, MIT Computer Science and Artificial Intelligence Laboratory
		+	#One of the authors, Christopher T Harbison, had published a paper in 2002 on Transcriptional Regulatory Networks in Saccharomyces cerevisiae. He also published a paper on Genome-wide map of nucleosome acetylation and methylation in yeast in 2005. Another author, D Benjamin Gordon, also published a paper relating to transcription factors in 2004, as well as An improved map of conserved regulatory sites for Saccharomyces cerevisiae in 2006.
		+	#Yes, “Some authors have filed a patent application covering aspects of this work and are pursuing commercialization.”
		+	#There isn't data associated with the dataset.
		+	#This article has cites 30 articles, and has been cited by 1671 articles.

@@ Line 12: / Line 12: @@
 ##What were the limitations in previous studies that led them to perform this work? Previously, they weren't;t able to map the transcriptional regulatory code because there was limited understanding if the specific DNA sequenced that were bound by transcriptional regulators. They also didn't understand how the different growth conditions affected transcriptional regulators which was important in order to understand the regulatory mechanism. There was also little understanding about regulatory elements and how they were used by regulators in different environments in yeast promoters.
 ##How did they treat the yeast cells (what experiment were they doing?) The yeast cells were treated in a couple of ways: with the Myc-epitope coding which allowed for all of the 203 regulators to be tagged for further analysis. Crosslinkng and Immunoprecipitation, cross linking stabilized interactions between the target DNA sequence and transcriptional regulators, using immunoprecipitation, they were able to isolate specific DNA fragments that were tagged with the myc-tagged regulators. Then the ligation-medicated PCR was used to augment the DNA for further analysis. Using microarray hybridization, they were able to detect the DNA sequence that was bound by transcriptional regulators in the yeast.
-##What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? They don't specify if the strain was haploid or diploid but it was the W303 strain.
+##What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? A haploid Saccharomyces cerevisiae W303 strain.
-##What media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
+##What media did they grow them in? What temperature? What type of incubator? For how long? PCR was used to grow the microarrays. The cells were also grown on YPD media. The temperature is not specified in the paper except for the elevated temperature environmental condition which was 30 degrees and then 37 degrees celsius. The time was different depending on the growth conditions and media. The times ranged from 20 minutes to 14 hours.
-##What controls did they use? They do not specify this
+##What controls did they use? Their control was unenriched DNA samples.
-##How many replicates did they perform per treatment or timepoint? They do not specify this
+##How many replicates did they perform per treatment or timepoint? The supplementary methods states that the program was ran 50 times on random sequences on sets of different probes.
 ##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? Probability scores were used to determine the significance of the binding interactions
+##What mathematical/statistical method did they use to analyze the data? Probability scores were used to determine the significance of the binding interactions.
-##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
+##Are the data publicly available for download? From which web site? The raw data can't be downloaded.
 ##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
 ##*What do the X and Y axes represent (if applicable)?
 ##*How were the measurements made?
@@ Line 27: / Line 30: @@
 ##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?

@@ Line 67: / Line 67: @@
 #Are the data associated with this article available? If so, provide a link to the dataset. There isn't data associated with 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 does this article cite? 30
 #*How many articles cite this article?

@@ Line 4: / Line 4: @@
 ##In  vitro: (Of a biological process) made to occur outside the living organism, i.e. in an artificial environment such as within a glassware, a test tube, etc. (Biology Online, 2021)
 ## Respiratory electron transport chain: A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. (AmiGO 2)
 #Answer the following questions about your article. Your answers need to be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's answers either. Even if you work together to understand the article, your individual entries need to be in your own words.
 ##What is the main result presented in this paper?

@@ Line 36: / Line 36: @@
 #*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. I don't see "open access" or "unlocked" icon. Once I open the  full text, I do see "Public Access".
+#*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. I don't see "open access" or "unlocked" icon. Once I open the full text, I do see "Public Access".
 #*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. I could not find "open access" or "unlocked" icon, however I could see "free full text" and was able to access the article.
 #*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. Accessing it from NIH was free, however to access it from "nature" it says that it is a subscription content and must be accessed via the institution

@@ Line 57: / Line 57: @@
 #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? Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA 2Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
+#What are the institutions with which the authors are affiliated? Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology, MIT Computer Science and Artificial Intelligence Laboratory
 #Have the authors published other articles on this subject? (How will you find this out?) Hint:
 #*Google Scholar