BIOL200 2013 - Revision history

imported>Cmartin: moved User talk:Cmartin to BIOL200 2013: rename

2013-03-04T20:38:25Z

moved User talk:Cmartin to BIOL200 2013: rename

← Older revision	Revision as of 20:38, 4 March 2013
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imported>Cmartin: /* LAB REPORT GRADING GUIDE */

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LAB REPORT GRADING GUIDE

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	(not to be copied from the Lab Manual)</pre>		(not to be copied from the Lab Manual)</pre>
	*'''MATERIALS AND METHODS'''<span style="font-weight:bold;color:OrangeRed;"> 0 points</span> ''':'''		*'''MATERIALS AND METHODS'''<span style="font-weight:bold;color:OrangeRed;"> 0 points</span> ''':'''
	<pre>This should be a brief synopsis and must include any changes or deviations		<pre>This should be a brief synopsis and must include any changes or deviations from the procedures
	from the procedures outlined in the Lab Manual. Specify which organisms were		outlined in the Lab Manual. Specify which organisms were used to create the phylogram.</pre>
	used to create the phylogram.</pre>
	*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''		*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''
	<pre>A print out of the phylogram will suffice.</pre>		<pre>A print out of the phylogram will suffice.</pre>

imported>Cmartin: /* LAB REPORT GRADING GUIDE */

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LAB REPORT GRADING GUIDE

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	used to create the phylogram.</pre>		used to create the phylogram.</pre>
	*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''		*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''
	<pre>A print out of the phylogram will suffice.		<pre>A print out of the phylogram will suffice.</pre>
	*'''DISCUSSION'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''		*'''DISCUSSION'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''
	Responses to discussion questions.</pre>		<pre>Responses to discussion questions.</pre>
	*'''SUMMARY \|CONCLUSION'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''		*'''SUMMARY \|CONCLUSION'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''
	<pre>Two sentence summary of your findings.</pre>		<pre>Two sentence summary of your findings.</pre>

imported>Cmartin: /* LAB REPORT GRADING GUIDE */

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LAB REPORT GRADING GUIDE

imported>Cmartin: /* INTRODUCTION */

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INTRODUCTION

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	\| Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.<br /> The evolutionary history of a group is called a phylogeny, and can be represented by a phylogram (Figure 1). A major goal of evolutionary analysis is to understand this history. We do not have direct knowledge of the path of evolution, as by definition, extinct organisms no longer exist. Therefore, phylogeny must be inferred indirectly. Originally, evolutionary analysis was based upon the organisms’ morphology and metabolism. This is the basis for the Linnaean classification scheme (the “Five Kingdoms” scheme). However, this method can lead to mistaken relationships. Different species living in the same environment may have similar morphologies in order to deal with specific environmental factors. Thus these similarities have nothing to do with how related the organisms are, but are a direct result of shared surroundings. However, with the advent of genomics, organisms can be grouped based upon their sequence relatedness. Since evolution is a process of inherited nucleotide change, analyzing DNA sequence differences allows for the reconstruction of a better phylogenetic history.<br/>		\| Evolution can be defined as descent with modification. In other words, changes in the nucleotide sequence of an organsim’s genomic DNA is inherited by the next generation. According to this, all organisms are related through descent from an ancestor that lived in the distant past. Since that time, about 4 billion years ago, life has undergone an extensive process of change as new kinds of organisms arose from other kinds existing in the past.<br /> The evolutionary history of a group is called a phylogeny, and can be represented by a phylogram (Figure 1). A major goal of evolutionary analysis is to understand this history. We do not have direct knowledge of the path of evolution, as by definition, extinct organisms no longer exist. Therefore, phylogeny must be inferred indirectly. Originally, evolutionary analysis was based upon the organisms’ morphology and metabolism. This is the basis for the Linnaean classification scheme (the “Five Kingdoms” scheme). However, this method can lead to mistaken relationships. Different species living in the same environment may have similar morphologies in order to deal with specific environmental factors. Thus these similarities have nothing to do with how related the organisms are, but are a direct result of shared surroundings. However, with the advent of genomics, organisms can be grouped based upon their sequence relatedness. Since evolution is a process of inherited nucleotide change, analyzing DNA sequence differences allows for the reconstruction of a better phylogenetic history.<br/>
	\|-		\|-
	\|[[File:TreeLife.~~png\|thumb~~\|center\|alt=The Tree of Life.\|Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]		\|[[File:TreeLife.PNG\|center\|alt=The Tree of Life.\|Tree of life based on 16S ribosomal RNA (image credit: NR Pace, Science 1997)]]
	\|-style="background-color:powderblue;"		\|-style="background-color:powderblue;"
	\|Of course, when comparing DNA sequences, the question of which genes to use arises. The most widely used genes are those coding for the 16S rRNA gene in prokaryotes and the 18S rRNA gene in eukaryotes. These genes code for small subunit ribosomal RNA and are used for evolutionary analysis because they 1) are found in all organisms, 2) are functionally conserved, 3) vary only slightly between organisms (their nucleotide sequence changed slowly throughout evolution), and 4) have adequate length. In this lab, you will be performing evolutionary analysis by constructing a phylogram of 15 microbes spanning bacteria, archaea and eukarya. You will find and download rRNA sequences, align them and use that alignment to create a phylogram.		\|Of course, when comparing DNA sequences, the question of which genes to use arises. The most widely used genes are those coding for the 16S rRNA gene in prokaryotes and the 18S rRNA gene in eukaryotes. These genes code for small subunit ribosomal RNA and are used for evolutionary analysis because they 1) are found in all organisms, 2) are functionally conserved, 3) vary only slightly between organisms (their nucleotide sequence changed slowly throughout evolution), and 4) have adequate length. In this lab, you will be performing evolutionary analysis by constructing a phylogram of 15 microbes spanning bacteria, archaea and eukarya. You will find and download rRNA sequences, align them and use that alignment to create a phylogram.

imported>Cmartin: /* ANALYSIS */

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ANALYSIS

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	\|-		\|-
	\|		\|
	[[ File:Phylo.PNG\|center~~\|thumb~~\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]		[[ File:Phylo.PNG\|center\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]
	\|-style="background-color:powderblue;"		\|-style="background-color:powderblue;"
	\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.		\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.

imported>Cmartin: /* ANALYSIS */

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ANALYSIS

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	\|-		\|-
	\|		\|
	[[ File:Phylo.~~png~~\|center\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]		[[ File:Phylo.PNG\|center\|thumb\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]
	\|-style="background-color:powderblue;"		\|-style="background-color:powderblue;"
	\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.		\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.

imported>Cmartin: /* ANALYSIS */

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ANALYSIS

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	The branches define the order of descent and the ancestry of the nodes. The branch length represents the number of changes that have occurred along that branch. Thus, the more recently two organisms share a common ancestor, the more closely related they are. Trees can be either “unrooted” or “rooted”. Unrooted trees show the relationships among the microorganisms under study, but not the evolutionary path leading from an ancestor to a strain.<br/>		The branches define the order of descent and the ancestry of the nodes. The branch length represents the number of changes that have occurred along that branch. Thus, the more recently two organisms share a common ancestor, the more closely related they are. Trees can be either “unrooted” or “rooted”. Unrooted trees show the relationships among the microorganisms under study, but not the evolutionary path leading from an ancestor to a strain.<br/>
	\|-		\|-
	\|[[File:~~phylo~~.png\|center~~\|alt= The Tree of Life.~~\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]		\|
			[[ File:Phylo.png\|center\|Phylogram with internal nodes (a, b, c, d) and tips (1, 2, 3, 4, 5). Nodes at the tips are species that exist today, and internal nodes are extinct ancestors.]]
	\|-style="background-color:powderblue;"		\|-style="background-color:powderblue;"
	\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.		\|A rooted tree shows the unique path from an ancestor (internal node) to each strain. Trees are rooted by inclusion of an outgroup in the analysis. An outgroup is an organism that is less closely related to the other organisms under study than the organisms are to each other.

imported>Cmartin at 19:01, 4 March 2013

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Show changes

imported>Cmartin: /* March 5 */

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March 5

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 |}
-===March 5===
+===References===
 {| class="collapsible collapsed wikitable"
 |- style="background-color:lightsteelblue;"
-! Assignment #5
+! Reference & Resource
 |-style="background-color:powderblue;"
-| '''BioPerl Assignment'''
+#Jungck, J. R.; Fass, M.F.; Stanley, E. D. (ed.). 2003 (2006 Revision). Microbes Count! Problem Posing, Problem Solving, and Peer Persuasion in Microbiology. BioQUEST Curriculum Consortium. (Chapter 6, pg 191)
-For this assignment, you will use the .predict file you made with glimmer in [[#February_19 | assignment 3]].
+#Holt. J. G. Editor-in-Chief (1984). Bergey’s Manual of Systematic Bacteriology, Volume 1-4. Williams & Wilkins: Baltimore. http://www.cme.msu.edu/bergeys/pubinfo.html
 |}

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	CELL BIO II Experiment #4:		CELL BIO II Experiment #4:
	*'''Introduction'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''		*'''Introduction'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''
	Statement of objectives or aims of the experiment in the student’s own words.		<pre>Statement of objectives or aims of the experiment in the student’s own words.
	(not to be copied from the Lab Manual)		(not to be copied from the Lab Manual)</pre>
	*'''MATERIALS AND METHODS'''<span style="font-weight:bold;color:OrangeRed;"> 0 points</span> ''':'''		*'''MATERIALS AND METHODS'''<span style="font-weight:bold;color:OrangeRed;"> 0 points</span> ''':'''
	This should be a brief synopsis and must include any changes or deviations		<pre>This should be a brief synopsis and must include any changes or deviations
	from the procedures outlined in the Lab Manual. Specify which organisms were		from the procedures outlined in the Lab Manual. Specify which organisms were
	used to create the phylogram.		used to create the phylogram.</pre>
	*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''		*'''RESULTS'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''
	A print out of the phylogram will suffice.		<pre>A print out of the phylogram will suffice.
	*'''DISCUSSION'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''		*'''DISCUSSION'''<span style="font-weight:bold;color:OrangeRed;"> 4 points</span> ''':'''
	Responses to discussion questions.		Responses to discussion questions.</pre>
	*'''SUMMARY \|CONCLUSION'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''		*'''SUMMARY \|CONCLUSION'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''
	Two sentence summary of your findings.		<pre>Two sentence summary of your findings.</pre>
	*'''REFERENCES'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''		*'''REFERENCES'''<span style="font-weight:bold;color:OrangeRed;"> 1 point</span> ''':'''
	Credit is given for pertinent references obtained from sources other than the Lab Manual.		<pre>Credit is given for pertinent references obtained from sources other than the Lab Manual.
	This point is in addition to the 10 for the lab report..		This point is in addition to the 10 for the lab report..</pre>

	===INTRODUCTION===		===INTRODUCTION===