MSymond1 Week 12 - Revision history

Msymond1: added slides

2024-04-11T07:07:04Z

added slides

Msymond1: /* Meta Data */ finished

2024-04-11T07:05:39Z

‎Meta Data: finished

Msymond1: /* Meta Data */ edited

2024-04-11T07:04:00Z

‎Meta Data: edited

Msymond1: added bibliography

2024-04-11T07:03:23Z

added bibliography

Msymond1: /* Individual Journal Page */ took away links

2024-04-11T04:17:56Z

‎Individual Journal Page: took away links

Msymond1: /* References */ added reference

2024-04-11T04:16:52Z

‎References: added reference

Msymond1: /* Individual Journal Page */ added in text citation

2024-04-11T04:15:57Z

‎Individual Journal Page: added in text citation

Msymond1: /* Individual Journal Page */ fixed link

2024-04-11T01:44:20Z

‎Individual Journal Page: fixed link

Msymond1: /* References */ finished references

2024-04-11T01:43:35Z

‎References: finished references

Msymond1: /* References */ continued references

2024-04-11T01:34:20Z

‎References: continued references

@@ Line 35: / Line 35: @@
 #The authors could take the future direction of testing such transcription factors in higher eukaryotes, for if they are able to predict such binding mechanisms for yeast cells, they can likely do something similar for a higher level organism. Perhaps they will not be able to test as many regulators or have as high of a confidence rate, for I would assume it would be far more difficult to carry out such tests on another higher organism, for there are likely far more regulators and they may have a much larger genome to select from.
 #I believe the authors in this study were able to support their conclusions well with the data acquired, but I do not believe the data was well presented or explained in the article. Much of the materials necessary to understand their methods or to know important details (temperature, time, conditions) of their experiment were not even on the article itself and had to be found in the supplementary section. And even in the supplementary section it was still a very dense topic that is very difficult to understand for anyone who is not a well established expert on the topic. Not to mention the fact there is no defined discussion or conclusion section of the paper. The final section of the article is the methods section which is rather unconventional.
 ==Meta Data==

@@ Line 39: / Line 39: @@
 #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/|The link to the abstract from PubMed]
-#[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/]
+#[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/|The link to the full text of the article in PubMedCentral]
-#[https://www.nature.com/articles/nature02800]
+#[https://www.nature.com/articles/nature02800|The link to the full text of the article (HTML format) from the publisher web site.]
-#[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/]
+#[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/|The link to the full PDF version of the article from the publisher web site.]
 #The copyright is owned by the Author because it is an Author Manuscript
 # Once I open the full text, I do see "Public Access".
@@ Line 50: / Line 50: @@
 #Since 1989
 #Yes, the articles in this journal are peer-reviewed.
-# [https://www.nature.com/nature/editors]
+# [https://www.nature.com/nature/editors|scientific advisory board/editorial board of the journal.]
 # 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

@@ Line 38: / Line 38: @@
 ==Meta Data==
 #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://pubmed.ncbi.nlm.nih.gov/15343339/|The link to the abstract from PubMed]
 #[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/]
 #[https://www.nature.com/articles/nature02800]

@@ Line 35: / Line 35: @@
 #The authors could take the future direction of testing such transcription factors in higher eukaryotes, for if they are able to predict such binding mechanisms for yeast cells, they can likely do something similar for a higher level organism. Perhaps they will not be able to test as many regulators or have as high of a confidence rate, for I would assume it would be far more difficult to carry out such tests on another higher organism, for there are likely far more regulators and they may have a much larger genome to select from.
 #I believe the authors in this study were able to support their conclusions well with the data acquired, but I do not believe the data was well presented or explained in the article. Much of the materials necessary to understand their methods or to know important details (temperature, time, conditions) of their experiment were not even on the article itself and had to be found in the supplementary section. And even in the supplementary section it was still a very dense topic that is very difficult to understand for anyone who is not a well established expert on the topic. Not to mention the fact there is no defined discussion or conclusion section of the paper. The final section of the article is the methods section which is rather unconventional.
 ==Acknowledgements==

@@ Line 1: / Line 1: @@
 ==Individual Journal Page==
 #A list of biological terms from the paper I did not know the definitions for when I first read the article
-#*transcription regulator activity: A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons (Gene Ontology, 2024) https://amigo.geneontology.org/amigo/term/GO:0140110.
+#*transcription regulator activity: A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons (Gene Ontology, 2024).
-#*transcription cis-regulatory region binding: Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon (Gene Ontology, 2024). https://amigo.geneontology.org/amigo/term/GO:0000976
+#*transcription cis-regulatory region binding: Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon (Gene Ontology, 2024).
-#*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 (Gene Ontology, 2024). https://amigo.geneontology.org/amigo/term/GO:0022904
+#*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 (Gene Ontology, 2024).
-#*Lysis: The disintegration or rupture of the cell membrane, resulting in the release of cell contents or the subsequent death of the cell (Biology Online, 2024). https://www.biologyonline.com/dictionary/lysis
+#*Lysis: The disintegration or rupture of the cell membrane, resulting in the release of cell contents or the subsequent death of the cell (Biology Online, 2024).
-#*immunoprecipitate: the precipitate formed in an antigen‐antibody reaction (Oxford Reference, 2006). https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-9850?rskey=ZIIfXn&result=1
+#*immunoprecipitate: the precipitate formed in an antigen‐antibody reaction (Oxford Reference, 2006).
-#*DNA ligation: The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase (Gene Ontology, 2024). https://amigo.geneontology.org/amigo/term/GO:0006266
+#*DNA ligation: The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase (Gene Ontology, 2024).
-#*Phylogeny: the scientific study of phylogeny. It studies evolutionary relationships among various groups of organisms based on evolutionary history, similarities, and differences. It makes use of molecular sequencing data (such as homologous sequences, protein sequences, nucleotide sequences, etc.) and morphological data matrices to understand and analyze the protein and gene evolutions of genetically-related groups of organisms (Biology Online, 2024). https://www.biologyonline.com/dictionary/phylogenetics
+#*Phylogeny: the scientific study of phylogeny. It studies evolutionary relationships among various groups of organisms based on evolutionary history, similarities, and differences. It makes use of molecular sequencing data (such as homologous sequences, protein sequences, nucleotide sequences, etc.) and morphological data matrices to understand and analyze the protein and gene evolutions of genetically-related groups of organisms (Biology Online, 2024).
-#*PCR: A laboratory method used to make many copies of a specific piece of DNA from a sample that contains very tiny amounts of that DNA. PCR allows these pieces of DNA to be amplified so they can be detected. PCR may be used to look for certain changes in a gene or chromosome, which may help find and diagnose a genetic condition or a disease, such as cancer. It may also be used to look at pieces of the DNA of certain bacteria, viruses, or other microorganisms to help diagnose an infection. Also called polymerase chain reaction (National Cancer Institute, 2024). https://www.cancer.gov/publications/dictionaries/cancer-terms/def/pcr
+#*PCR: A laboratory method used to make many copies of a specific piece of DNA from a sample that contains very tiny amounts of that DNA. PCR allows these pieces of DNA to be amplified so they can be detected. PCR may be used to look for certain changes in a gene or chromosome, which may help find and diagnose a genetic condition or a disease, such as cancer. It may also be used to look at pieces of the DNA of certain bacteria, viruses, or other microorganisms to help diagnose an infection. Also called polymerase chain reaction (National Cancer Institute, 2024).
-#*Epitope: That part of an antigenic molecule to which the t-cell receptor responds, a site on a large molecule against which an antibody will be produced and to which it will bind (Biology Online, 2024).https://www.biologyonline.com/dictionary/epitope
+#*Epitope: That part of an antigenic molecule to which the t-cell receptor responds, a site on a large molecule against which an antibody will be produced and to which it will bind (Biology Online, 2024).
 #*Microarray: A laboratory tool used to analyze large numbers of genes or proteins at one time (National Cancer Institute, 2024).
 #The main Findings of the paper are that the architecture of the promoter, meaning the arrangements of the DNA binding site, change depending on environmental conditions and can be predicted with confidence what the binding arrangement will be depending on the promoter and the environmental conditions.

← Older revision		Revision as of 04:16, 11 April 2024
Line 50:		Line 50:
	*Cammack, Richard, et al. Oxford Reference. (2006). Immunoprecipitate. Retrieved April 10, 2024, from https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-9850?rskey=ZIIfXn&result=1		*Cammack, Richard, et al. Oxford Reference. (2006). Immunoprecipitate. Retrieved April 10, 2024, from https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-9850?rskey=ZIIfXn&result=1
	*National Cancer Institute. PCR. Retrieved April 10, 2024, from https://www.cancer.gov/publications/dictionaries/cancer-terms/def/pcr		*National Cancer Institute. PCR. Retrieved April 10, 2024, from https://www.cancer.gov/publications/dictionaries/cancer-terms/def/pcr
		+	*National Cancer Institute. Microarray. Retrieved April 10, 2024, from https://www.cancer.gov/search/results?swKeyword=microarray

← Older revision		Revision as of 01:43, 11 April 2024
Line 47:		Line 47:
	*Biology Online. Phylogenetics. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/phylogenetics		*Biology Online. Phylogenetics. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/phylogenetics
	*Biology Online. Epitope. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/epitope		*Biology Online. Epitope. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/epitope
		+	*Cammack, Richard, et al. Oxford Reference. (2006). Immunoprecipitate. Retrieved April 10, 2024, from https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-9850?rskey=ZIIfXn&result=1
		+	*National Cancer Institute. PCR. Retrieved April 10, 2024, from https://www.cancer.gov/publications/dictionaries/cancer-terms/def/pcr

← Older revision		Revision as of 01:34, 11 April 2024
Line 43:		Line 43:
	*Gene Ontology. Transcription cis-regulatory region binding. Retrieved April 10, 2024, from https://amigo.geneontology.org/amigo/term/GO:0000976		*Gene Ontology. Transcription cis-regulatory region binding. Retrieved April 10, 2024, from https://amigo.geneontology.org/amigo/term/GO:0000976
	*Gene Ontology. Respiratory electron transport chain. Retrieved April 10, 2024, from https://amigo.geneontology.org/amigo/term/GO:0022904		*Gene Ontology. Respiratory electron transport chain. Retrieved April 10, 2024, from https://amigo.geneontology.org/amigo/term/GO:0022904
		+	*Gene Ontology. DNA ligation. Retrieved April 10, 2024, from https://amigo.geneontology.org/amigo/term/GO:0006266
		+	*Biology Online. Lysis. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/lysis
		+	*Biology Online. Phylogenetics. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/phylogenetics
		+	*Biology Online. Epitope. Retrieved April 10, 2024, from https://www.biologyonline.com/dictionary/epitope
		+