LMU BioDB 2024 - User contributions [en]

Nstojan1 Week 14&15

2024-05-03T16:21:51Z

Nstojan1-new: /* Acknowledgments */ signature

==Progress Report==
Milestone 3 Complete
*In class, the data from yeastmine was obtained. Dean and I weren’t sure what columns we needed because there were so many so we spoke to Dr. Dalhquist to see what was needed and she made some suggestions.

Milestone 4
*In class, the database was created. After Dean and Andrew worked on it, after I looked at it I noticed that some of the tables only had 0’s and 1’s which is not what excel had. I told this to Dean and Andrew, and we fixed it by importing the text file instead of just copy pasting it. After the relationships were made. I went through it to make sure that we had all of the necessary fields and that each row and column had appropriate headings.

Milestone 5
*Hailey and I both checked the Access database one more time to ensure that everything was indeed correct and that I didn’t miss anything. It was correct and ready to use.

Milestone 6
*The data analyst picked profile 41 to analyze because it had the most genes, there were 23 genes that we needed to get data for. Dean, Andrew and I didn’t know how to do this because there were so many genes and it would have taken forever to do manually. Dr. Dahlquisrt showed us in class how to write the queries. After Dean ran the queries, Hailey and I checked them to make sure we got the same results. During this, we were in communication with Dean to see what was done. The GRNmap was produced and uploaded so that Dr. Dahlquist could run it.

==Presentation==
*We did the presentation as a team and everyone focused on doing the work that they completed. Meaning coders/designers did the slides on what they did during the project and the data analyst and quality assurance did the same. The only problem we had was we didn’t know what other members of the team did. For example, because I worked with Andrew and Dean. I was often confused about what Katie, Charlotte and Hailey were doing. When we were doing the presentation, we talked about the feedback Dr. Dahlquist gave us and we tried to incorporate that into our slides.

==Team Journal Assignment==
# We completed the rest of the project and all of the milestones, we began doing the presentation and talking about what we wanted to do for the paper.
#My reflection on team progress:
#*For the most part everything went well when I checked the database, there were some issues like the ones discussed above but they were a quick fix. At first when Andrew ran the queries, we noticed it was the wrong file and there were a couple of things he did wrong, which Dean was able to fix after. Creating the presentation was smooth and we didn’t have any issues there.
#*Things that didn’t work well was the communication and organization of the files. After the data analyst gave us the file with the genes, there were some duplicates which were fixed. However, there was a misunderstanding about which file should have been used which led to Andrew running queries on the wrong file
#* Dean was able to fix this and do the queries on the right files, in the future, the files need more descriptive names and need to be organized so that it is easier to find.

==Acknowledgments==
All of my groupmates contributed to the project during the last 2 weeks. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Nstojan1-new|Nstojan1-new]] ([[User talk:Nstojan1-new|talk]]) 09:21, 3 May 2024 (PDT)

Nstojan1 Week 14&15

2024-05-03T16:21:18Z

Nstojan1-new: /* Acknowledgments */ added signature

Nstojan1 Week 14&15

2024-05-03T16:19:10Z

Nstojan1-new: /* Acknowledgments */ signature

Nstojan1 Week 14&15

2024-05-03T16:18:46Z

Nstojan1-new: /* Acknowledgments */ added signature

Nstojan1 Week 14&15

2024-05-03T16:18:23Z

Nstojan1-new: /* Progress Report */ edit syntax

Nstojan1 Week 14&15

2024-05-03T16:16:13Z

Nstojan1-new: added work

==Progress Report==
Milestone 3 Complete
*In class, the data from yeastmine was obtained. Dean and I weren’t sure what columns we needed because there were so many so we spoke to Dr. Dalhquist to see what was needed and she made some suggestions.

Milestone 4
*In class, the database was created. After Dean and Andrew worked on it, after I looked at it I noticed that some of the tables only had 0’s and 1’s which is not what excel had. I told this to Dean and Andrew, and we fixed it by importing the text file instead of just copy pasting it. After the relationships were made. I went through it to make sure that we had all of the necessary fields and that each row and column had appropriate headings.

*Milestone 5
Hailey and I both checked the Access database one more time to ensure that everything was indeed correct and that I didn’t miss anything. It was correct and ready to use.

*Milestone 6
The data analyst picked profile 41 to analyze because it had the most genes, there were 23 genes that we needed to get data for. Dean, Andrew and I didn’t know how to do this because there were so many genes and it would have taken forever to do manually. Dr. Dahlquisrt showed us in class how to write the queries. After Dean ran the queries, Hailey and I checked them to make sure we got the same results. During this, we were in communication with Dean to see what was done. The GRNmap was produced and uploaded so that Dr. Dahlquist could run it.

Presentation
*We did the presentation as a team and everyone focused on doing the work that they completed. Meaning coders/designers did the slides on what they did during the project and the data analyst and quality assurance did the same. The only problem we had was we didn’t know what other members of the team did. For example, because I worked with Andrew and Dean. I was often confused about what Katie, Charlotte and Hailey were doing. When we were doing the presentation, we talked about the feedback Dr. Dahlquist gave us and we tried to incorporate that into our slides.

Team Journal Assignment
# We completed the rest of the project and all of the milestones, we began doing the presentation and talking about what we wanted to do for the paper.
#My reflection on team progress:
#*For the most part everything went well when I checked the database, there were some issues like the ones discussed above but they were a quick fix. At first when Andrew ran the queries, we noticed it was the wrong file and there were a couple of things he did wrong, which Dean was able to fix after. Creating the presentation was smooth and we didn’t have any issues there.
#*Things that didn’t work well was the communication and organization of the files. After the data analyst gave us the file with the genes, there were some duplicates which were fixed. However, there was a misunderstanding about which file should have been used which led to Andrew running queries on the wrong file
#* Dean was able to fix this and do the queries on the right files, in the future, the files need more descriptive names and need to be organized so that it is easier to find.

Acknowledgments
All of my groupmates contributed to the project during the last 2 weeks. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Template:Nstojan1

2024-05-03T16:15:28Z

Nstojan1-new: /* Individual Journal Entry */ added 14

== Assignment Page ==
[[Week 1]]

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== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Nstojan1 Week 5]]

[[Nstojan1 Week 6]]

[[Nstojan1 Week 8]]

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[[Nstojan1 Week 10]]

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[[Nstojan1 Week 14&15]]

== Shared Journal Entry ==
[[Journal Entry Week 1]]

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Nstojan1 Week 15

2024-05-02T17:05:01Z

Nstojan1-new: added file

[[Media:Yeast_Beasts_Presentation.zip]]

Nstojan1 Week 15

2024-05-02T17:02:42Z

Nstojan1-new: added file

[[File:

Template:Nstojan1

2024-05-02T17:01:41Z

Nstojan1-new: /* Individual Journal Entry */ added week

== Assignment Page ==
[[Week 1]]

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[[Nstojan Week 1]]

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[[Nstojan1 Week 5]]

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== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

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[[Class Journal Week 8]]

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Nstojan1 Week 14

2024-04-23T21:14:05Z

Nstojan1-new: update on progress

==Week 14 Milestones==

This week, we worked on milestone 3 and entered all of the data tables onto excel. Once the coders and designers input the information into excel, I went through it to make sure the tables from excel matched the tables on access. I noticed that for the production rates and degradation rates, the numbers did not match. It kept showing 0 and 1 instead of the full decimal. I troubleshooted this with Dean and Andrew to see how to fix this.

Template:Nstojan1

2024-04-23T21:08:38Z

Nstojan1-new: /* Individual Journal Entry */

== Assignment Page ==
[[Week 1]]

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[[Week 10]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Nstojan1 Week 5]]

[[Nstojan1 Week 6]]

[[Nstojan1 Week 8]]

[[Nstojan1 Week 9]]

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== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

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[[Class Journal Week 8]]

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[[Category:Journal Entry]]

Template:Nstojan1

2024-04-23T21:08:30Z

Nstojan1-new: /* Individual Journal Entry */ added week

== Assignment Page ==
[[Week 1]]

[[Week 2]]

[[Week 3]]

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[[Week 5]]

[[Week 6]]

[[Week 8]]

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[[Week 10]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Nstojan1 Week 5]]

[[Nstojan1 Week 6]]

[[Nstojan1 Week 8]]

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== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

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[[Class Journal Week 8]]

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Nstojan1 Week 13

2024-04-18T22:00:58Z

Nstojan1-new: /* Mile Stone 2 was Completed and Milestone 3 was started */ added acknowledgments

==Mile Stone 2 was Completed and Milestone 3 was started==
*I downloaded the the different tables and worked with the coders/designers and was helping them with cleaning and inputting the information during class. We had an issue with filtering the data from the network table. Once they input the data in excel, I looked at the different workbooks and tables and went through them carefully making sure that everything was the same. The "network" table was the most difficult to go through because I wasn't with them when they were filtering it.

*One thing that we need to be better is with communicating with each other. At times, the coders and designers were working on the same table and I think that we could have completed everything faster if we talked about which table should be created by who. However, towards the end it got easier. It was also nice to have 2 excel sheets to compare the tables to.

*I have to better communicate with coders and designers and I think that in the future, whatever they have I should ask for them to upload, that way they can stat creating the database in access sooner because I will be able to check the data as soon as they complete it even if its a portion of it.

==Acknowledgement==
I worked with [[User:msymonds1]] and [[User:asandle1]] in class to check the tables they input
[[User:Nstojan1]]
{{Template:Nstojan1}}

Nstojan1 Week 13

2024-04-18T21:53:51Z

Nstojan1-new: added template

Nstojan1 Week 13

2024-04-18T21:49:43Z

Nstojan1-new: /* Mile Stone 2 was Completed and Milestone 3 was started */ edit syntax

Nstojan1 Week 13

2024-04-18T21:49:09Z

Nstojan1-new: /* Mile Stone 2 was Completed and Milestone 3 was started */ added template

Nstojan1 Week 13

2024-04-18T21:48:32Z

Nstojan1-new: added milestones

Template:Nstojan1

2024-04-18T21:13:30Z

Nstojan1-new: /* Individual Journal Entry */ added week

== Assignment Page ==
[[Week 1]]

[[Week 2]]

[[Week 3]]

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[[Week 5]]

[[Week 6]]

[[Week 8]]

[[Week 9]]

[[Week 10]]

== Individual Journal Entry ==
[[Nstojan Week 1]]

[[Nstojan Week 2]]

[[Week 3]]

[[AgeAnnoMO Week 4]]

[[Nstojan1 Week 5]]

[[Nstojan1 Week 6]]

[[Nstojan1 Week 8]]

[[Nstojan1 Week 9]]

[[Nstojan1 Week 10]]

[[Nstojan1 Week 12]]

[[Nstojan1 Week 13]]

== Shared Journal Entry ==
[[Journal Entry Week 1]]

[[Week 2]]

[[Week 3]]

[[Week 4]]

[[Week 5]]

[[Week 6]]

[[Class Journal Week 8]]

[[Week 9]]

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[[Category:Journal Entry]]

Nstojan1 Week 12

2024-04-12T05:56:04Z

Nstojan1-new: answered questions

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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)
##Reading frame: One of the three possible ways of reading a nucleotide sequence. As the genetic code is read in nonoverlapping triplets (codons) there are three possible ways of translating a sequence of nucleotides into a protein, each with a different starting point. For example: given the nucleotide sequence: AGCAGCAGC, the three reading frames are: AGC AGC AGC, GCA GCA, CAG CAG (Biology Online, 2022).

#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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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? 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 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? 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: 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: 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: It shows the arrangement of regulatory sequences in yeast DNA to control gene expression.
#*Figure 4: shows the different patterns of DNA binding behavior of transcription regulators in the different environmental conditions.
#*Figure 5: The main finding is that the binding or regulators to promoters is specific and selective.
#* 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.
#*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.
#*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.
#*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.
##*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.
##What future directions should the authors take? Perhaps they could expand the genomic analyses and use different types of yeast species to see the evolution of regulatory and transcriptional elements. It could help discover other regulatory motifs across different species of yeast.
##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? I think that they supported their conclusions well with the data, however a major flaw in the paper is that the data was not explained well. It would be almost impossible for someone to replicate the experiment without looking at the supplementary methods and for a paper like this, the materials and methods section was too short. While the order of the tables does make sense and you can draw connections, the fact that they combined several data types, they could have done a better job at explaining. At first, the paper was extremely hard to understand unless you are in the biology field. The figures were also hard to understand and they never really state their most important findings, there isn't a result or conclusion, after every "topic" they throw in the main findings which makes it confusing for the reader.

==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.

Nstojan1 Week 12

2024-04-12T04:56:56Z

Nstojan1-new: added bibliography

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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)
##Reading frame: One of the three possible ways of reading a nucleotide sequence. As the genetic code is read in nonoverlapping triplets (codons) there are three possible ways of translating a sequence of nucleotides into a protein, each with a different starting point. For example: given the nucleotide sequence: AGCAGCAGC, the three reading frames are: AGC AGC AGC, GCA GCA, CAG CAG (Biology Online, 2022).

#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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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? 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.
##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.
##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 2:
#*:Figure 3:
##*What do the X and Y axes represent (if applicable)?
##*How were the measurements made?
##*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?

==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.

Nstojan1 Week 12

2024-04-11T05:44:32Z

Nstojan1-new: edited questions

Nstojan1 Week 12

2024-04-11T05:19:37Z

Nstojan1-new: added answer

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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)
##Reading frame: One of the three possible ways of reading a nucleotide sequence. As the genetic code is read in nonoverlapping triplets (codons) there are three possible ways of translating a sequence of nucleotides into a protein, each with a different starting point. For example: given the nucleotide sequence: AGCAGCAGC, the three reading frames are: AGC AGC AGC, GCA GCA, CAG CAG (Biology Online, 2022).

#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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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. 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? 30
#*How many articles cite this article?

Nstojan1 Week 12

2024-04-11T05:17:52Z

Nstojan1-new: added definition

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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)
##Reading frame: One of the three possible ways of reading a nucleotide sequence. As the genetic code is read in nonoverlapping triplets (codons) there are three possible ways of translating a sequence of nucleotides into a protein, each with a different starting point. For example: given the nucleotide sequence: AGCAGCAGC, the three reading frames are: AGC AGC AGC, GCA GCA, CAG CAG (Biology Online, 2022).

#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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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. 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 cite this article?

Nstojan1 Week 12

2024-04-11T05:00:35Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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. 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 cite this article?

Nstojan1 Week 12

2024-04-11T04:47:14Z

Nstojan1-new: added definition

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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. 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 cite this article?

Nstojan1 Week 12

2024-04-11T04:37:41Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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. 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 cite this article?

Nstojan1 Week 12

2024-04-11T04:33:40Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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 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
#*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?

Nstojan1 Week 12

2024-04-11T04:31:34Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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
3MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA
4Broad Institute, One Kendall Square, Building 300, Cambridge, Massachusetts 02139, USA
#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?

Nstojan1 Week 12

2024-04-11T04:30:32Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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)
#* Since 1989
#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.) 60.9 was the 5 year impact factor (2022)
#On what date was the article submitted?
#On what date was the article accepted?
#Did the article undergo any revisions before acceptance? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
#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
3MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA
4Broad Institute, One Kendall Square, Building 300, Cambridge, Massachusetts 02139, USA
#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?

Nstojan1 Week 12

2024-04-11T04:21:17Z

Nstojan1-new: /* Evaluating Meta Data */ added answer

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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)
#* Since 1989
#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?

Nstojan1 Week 12

2024-04-11T04:12:35Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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?

Nstojan1 Week 12

2024-04-11T04:09:52Z

Nstojan1-new: /* Evaluating Meta Data */ added answer

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. https://www.nature.com/articles/nature02800
#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. 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.
#*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?

Nstojan1 Week 12

2024-04-10T16:20:05Z

Nstojan1-new: /* Evaluating Meta Data */ added answer

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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. 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.
#*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?

Nstojan1 Week 12

2024-04-10T16:14:17Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#* 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
#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?

Nstojan1 Week 12

2024-04-10T16:13:39Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#The complete bibliographic reference in the APA style (see this link), with DOI.
#The link to the abstract from PubMed (LMU-specific link.
#* 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
#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?

Nstojan1 Week 12

2024-04-10T16:07:52Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#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?

Nstojan1 Week 12

2024-04-10T16:06:48Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#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?

Nstojan1 Week 12

2024-04-10T16:06:02Z

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

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#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?

Nstojan1 Week 12

2024-04-10T16:05:20Z

Nstojan1-new: added questions

#Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
##Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
##Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
##
## 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?
#*The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
##What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
##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 media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
##What controls did they use? They do not specify this
##How many replicates did they perform per treatment or timepoint? They do not specify this
##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
##Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
##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?
##*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?

==Evaluating Meta Data==
#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?

Nstojan1 Week 12

2024-04-10T16:00:30Z

Nstojan1-new: answered questions

Nstojan1 Week 12

2024-04-09T21:57:17Z

Nstojan1-new: added definition

Nstojan1 Week 12

2024-04-09T21:49:47Z

Nstojan1-new: edited syntax

Nstojan1 Week 12

2024-04-09T21:47:46Z

Nstojan1-new: add definition

Nstojan1 Week 12

2024-04-09T21:29:01Z

Nstojan1-new: edit bullet point

Nstojan1 Week 12

2024-04-09T21:28:27Z

Nstojan1-new: added definition

Nstojan1 Week 10

2024-04-05T15:44:52Z

Nstojan1-new: added step 2

Rows: 4727 filter greater than 0.05
[[Media:Screenshots.pptx]]
[[Media:Natalija_Stojanovic_File_New.xlsx]]

Rows: 4727 filter greater than 0.05
[[Media:Screenshots.pptx]]
[[Media:Natalija_Stojanovic_File_New.xlsx]]

*Purpose: The purpose of this assignment is to analyze a DNA microarray dataset that involves clustering and analysis of gene regulation networks using the GRNsight software.

*Procedure:
#*Preparing the microarray data file for loading into STEM:
#**Insert a new worksheet into Excel workbook, and make it dCIN5_stem
#**Select all the data from "dCIN5_ANOVA" worksheet and Paste Special > paste the values into "dCIN5_stem" worksheet.
#**The leftmost column should have a column header "Master Index". Rename it to "Spot". Rename Column B ("ID") to "Gene Symbol" and delete the column named "Standard_Name".
#**Filter the data on the B-H corrected value to be > 0.05
#**Once it has been filtered, select all of the rows (not header row) and delete the row by right clicking and choosing "Delete Row" from the context menu. Undo the filter, this will cluster only the genes with "significant" change in expression and not the noise.
#**Delete all of the columns EXCEPT for the Average Log Fold change columns for each timepoint.
#**Rename the columns with just the time and unites, for example 15m,30m,etc.
#**If you had #DIV/0! errors, to remove them, open Find/Replace dialog. Search #DIV/0!, but don't put anything in the replace field. Click "Replace all" to remove the errors
#**Save the work. Use Save As to saver the spreadsheet as Text. Click OK to warnings and close the file.

#*Now download and extract the STEM software. Click here to go to the STEM web site.
#**Click on the download link and download the stem.zip file to your Desktop.
Extract the file by right-clicking on it and selecting "Extract all" from the menu.
This will create a folder called stem.
You now need to download the Gene Ontology and yeast GO annotations and place them in this folder.
Click here to download the file "gene_ontology.obo".
Click here to download the file "gene_association.sgd.gz".
Inside the folder, double-click on the stem.jar to launch the STEM program.

Nstojan1 Week 10

2024-04-05T15:43:03Z

Nstojan1-new: added to procedure

Nstojan1 Week 10

2024-04-05T15:38:31Z

Nstojan1-new: added purpose and procedure

Nstojan1 Week 12

2024-04-04T21:29:14Z

Nstojan1-new: edit syntax