How to be a Breast Cancer Detective. - Revision history

Susie07 at 15:22, 30 July 2008

2008-07-30T15:22:33Z

←Older revision		Revision as of 15:22, 30 July 2008
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	Part 1- 45 minutes		Part 1- 45 minutes
	Part 1: Predicting the Breast cancer gene through Pedigree charts		Part 1: Predicting the Breast cancer gene through Pedigree charts
		+
	Practice drawing a pedigree chart		Practice drawing a pedigree chart

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	1. Reading and Discussion of Biotechnology and Bioinformatics based on the reading below:		1. Reading and Discussion of Biotechnology and Bioinformatics based on the reading below:
	Biotechnology’s Relation to Cancer Research		Biotechnology’s Relation to Cancer Research
		+
	Biotechnology has applied many of the techniques of cell biology,		Biotechnology has applied many of the techniques of cell biology,
	molecular biology, and protein chemistry to cancer research and treatment over		molecular biology, and protein chemistry to cancer research and treatment over

Susie07 at 15:00, 30 July 2008

2008-07-30T15:00:25Z

←Older revision		Revision as of 15:00, 30 July 2008
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	'''Common Misconceptions'''		'''Common Misconceptions'''

-	Students may not understand the importance and relevance of molecular	+
		+
		+	Students may not understand the importance and relevance of molecular
	genetics to research on today's world. Many students are not aware of the world of Bioinformatics.		genetics to research on today's world. Many students are not aware of the world of Bioinformatics.

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	suppressors, DNA damage sensors, and signal transducers to form a		suppressors, DNA damage sensors, and signal transducers to form a
	large multi-subunit protein complex known as BASC for		large multi-subunit protein complex known as BASC for
-	BRCA1-associated genome surveillance complex~~. This gene product~~	+	BRCA1-associated genome surveillance complex.
-	~~associates with RNA polymerase II, and through the C-terminal~~	+
-	~~domain, also interacts with histone deacetylase complex. This~~	+
-	~~protein thus plays a role in transcription, DNA repair of~~	+
-	~~double-stranded breaks, and recombination. Mutations in this gene~~	+
-	~~are responsible for approximately 40% of inherited breast cancers~~	+
-	~~and more than 80% of inherited breast and ovarian cancers.~~	+
-	~~Alternative splicing plays a role in modulating the subcellular~~	+
-	~~localization and physiological function of this gene. Many~~	+
-	~~alternatively spliced transcript variants have been described for~~	+
-	~~this gene but only some have had their full-length natures~~	+
-	~~identified~~.	+

	CDS of Human Breast cancer gene		CDS of Human Breast cancer gene

Susie07 at 14:57, 30 July 2008

2008-07-30T14:57:24Z

←Older revision		Revision as of 14:57, 30 July 2008
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	1) understand the process by which genes of parents are transferred to their offspring.		1) understand the process by which genes of parents are transferred to their offspring.
-	2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.	+
		+	2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.
		+
	3) read and/or construct a pedigree chart mapping a specific trait in a family.		3) read and/or construct a pedigree chart mapping a specific trait in a family.
		+
	4) determine the probability of a certain phenotype being expressed in a pedigree chart		4) determine the probability of a certain phenotype being expressed in a pedigree chart
		+
	5) Understand the uses of Biotechnology and Bioinformatics in understanding cancer		5) Understand the uses of Biotechnology and Bioinformatics in understanding cancer
		+
	6) Learn to retrieve information from a Bioinformatics source.		6) Learn to retrieve information from a Bioinformatics source.

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	'''The Lesson'''		'''The Lesson'''

-	Preparation Before class~~:''' (materials, handouts etc.)'''~~	+	Preparation Before class
-	Part 1. Introduction to Pedigree charts (handout)Highlighters, pens, pencils, books, chalkboard, and 1 computer with LCD projector and sound system	+
		+	Part 1. PowerPoint to accompany lesson, Introduction to Pedigree charts (handout),Highlighters, pens, pencils, books, chalkboard, and 1 computer with LCD projector and sound system
		+
	Part 2: Computer classroom; one computer per student, LCD projector,sound system		Part 2: Computer classroom; one computer per student, LCD projector,sound system

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	Begin by using PowerPoint presentation which contains links to other resources listed below:		Begin by using PowerPoint presentation which contains links to other resources listed below:
		+
	Mary Claire King: Finding brca1 and 2 by pedigree- http://www.dnai.org/media/a/king296¬04.swf		Mary Claire King: Finding brca1 and 2 by pedigree- http://www.dnai.org/media/a/king296¬04.swf
		+
	Mark Skolnick: Finding the breast cancer gene brca1-http://www.dnai.org/media/a/skolnick298_06.swf		Mark Skolnick: Finding the breast cancer gene brca1-http://www.dnai.org/media/a/skolnick298_06.swf
		+
	Mary Claire king: Can women be tested for breast cancer? http://www.dnaiorg/media/a/king295_08.swf		Mary Claire king: Can women be tested for breast cancer? http://www.dnaiorg/media/a/king295_08.swf

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	Part 2 -2 45 minute periods		Part 2 -2 45 minute periods

-	How do mutations form? View film clip http://www.insidecancer.org/?s=A,1,7	+	How do mutations form?
		+	View film clip http://www.insidecancer.org/?s=A,1,7

	1. Reading and Discussion of Biotechnology and Bioinformatics based on the reading below:		1. Reading and Discussion of Biotechnology and Bioinformatics based on the reading below:
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	Poster of Breast Cancer Pedigree with correct key		Poster of Breast Cancer Pedigree with correct key
		+
	Bioinformatics project using tools and websites found in this lesson.		Bioinformatics project using tools and websites found in this lesson.

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	• Webster K Cavenee and Raymond L. White, “The Genetic Basis		• Webster K Cavenee and Raymond L. White, “The Genetic Basis
	of Cancer,” Scientific American, March 1995.		of Cancer,” Scientific American, March 1995.
		+
	• Matt Ridley, Chapter 17 in Genome: Autobiography of a Species in 23 Chapters		• Matt Ridley, Chapter 17 in Genome: Autobiography of a Species in 23 Chapters
		+
	• Robert Weinberg, One Renegade Cell		• Robert Weinberg, One Renegade Cell
		+
	• Time and Newsweek cover articles on cancer topics		• Time and Newsweek cover articles on cancer topics
		+
	• American Cancer Society: http://www.cancer.org		• American Cancer Society: http://www.cancer.org
		+
	• National Cancer Institute: http://www.nci.nih.gov		• National Cancer Institute: http://www.nci.nih.gov
		+
	• National Childhood Cancer Foundation: http://www.nccf.org		• National Childhood Cancer Foundation: http://www.nccf.org
		+
	• Oncolink: http://www.oncolink.upenn.edu		• Oncolink: http://www.oncolink.upenn.edu
		+
	• NOVA’s program on Judah Folkman, Cancer Warrior: http://pbs.org/wgbh/		• NOVA’s program on Judah Folkman, Cancer Warrior: http://pbs.org/wgbh/
	nova/cancer		nova/cancer
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	'''Glossary'''		'''Glossary'''
		+
	Allele—an alternate form of a gene.		Allele—an alternate form of a gene.
		+
	Chromosome—structure in the cell nucleus that stores and transmits genetic information.		Chromosome—structure in the cell nucleus that stores and transmits genetic information.
		+
	Gene—unit of heredity.		Gene—unit of heredity.
		+
	Genotype—Allelic status of an organism for a genetic trait.		Genotype—Allelic status of an organism for a genetic trait.
		+
	Heterozygous—having different alleles of a gene.		Heterozygous—having different alleles of a gene.
		+
	Homozygous—having indistinguishable alleles of a gene.		Homozygous—having indistinguishable alleles of a gene.
-	Pedigree—diagram showing the expression of a specific characteristic and the biological relationships among members of a family, often of several generations.	+
		+	Pedigree—diagram showing the expression of a specific characteristic and the biological relationships among members of a family, often of several generations.
		+
	Phenotype—the observable organism, the expression of a genetic trait.		Phenotype—the observable organism, the expression of a genetic trait.
		+
	Bioinformatics- the science of using databases to enter or research genetic information on the WWW.		Bioinformatics- the science of using databases to enter or research genetic information on the WWW.
		+
	NCBI-National Center for Biotechnology Information		NCBI-National Center for Biotechnology Information
-	Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products	+
		+	Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products.
		+
	CDS-Coding sequence		CDS-Coding sequence

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	Questions		Questions
		+
	1.What is a locus? A position in the genome where a particular gene is found		1.What is a locus? A position in the genome where a particular gene is found
		+
	2.How many “bp” base pairs are found in this locus? 3759 base pairs		2.How many “bp” base pairs are found in this locus? 3759 base pairs
		+
	3.Where is the gene found? mRNA Homo Sapiens		3.Where is the gene found? mRNA Homo Sapiens
		+
	4.What does the gene encode for?		4.What does the gene encode for?
		+
	This gene encodes a nuclear phosphoprotein that plays a		This gene encodes a nuclear phosphoprotein that plays a
	role in maintaining genomic stability and acts as a tumor		role in maintaining genomic stability and acts as a tumor
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	this gene but only some have had their full-length natures		this gene but only some have had their full-length natures
	identified.		identified.
		+
	CDS of Human Breast cancer gene		CDS of Human Breast cancer gene
	tggatttat ctgctcttcg cgttgaagaa gtacaaaatg		tggatttat ctgctcttcg cgttgaagaa gtacaaaatg

Susie07 at 14:51, 30 July 2008

2008-07-30T14:51:35Z

←Older revision		Revision as of 14:51, 30 July 2008
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	--------------------------------------------------------------------------------		--------------------------------------------------------------------------------

-	'''Goals and Objectives'''	+	'''Goals and Objectives'''
		+
	1) understand the process by which genes of parents are transferred to their offspring.		1) understand the process by which genes of parents are transferred to their offspring.
	2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.		2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.
	3) read and/or construct a pedigree chart mapping a specific trait in a family.		3) read and/or construct a pedigree chart mapping a specific trait in a family.
-	•4) determine the probability of a certain phenotype being expressed in ~~an •~~	+	4) determine the probability of a certain phenotype being expressed in a pedigree chart
-	'''Common Misconceptions'''	+	5) Understand the uses of Biotechnology and Bioinformatics in understanding cancer
		+	6) Learn to retrieve information from a Bioinformatics source.
		+
		+	'''Common Misconceptions'''
		+
	Students may not understand the importance and relevance of molecular		Students may not understand the importance and relevance of molecular
	genetics to research on today's world. Many students are not aware of the world of Bioinformatics.		genetics to research on today's world. Many students are not aware of the world of Bioinformatics.

Susie07 at 14:48, 30 July 2008

2008-07-30T14:48:21Z

←Older revision		Revision as of 14:48, 30 July 2008
Line 14:		Line 14:
	•4) determine the probability of a certain phenotype being expressed in an •		•4) determine the probability of a certain phenotype being expressed in an •
	'''Common Misconceptions'''		'''Common Misconceptions'''
-	Students may not understand the importance and relevance of molecular genetics to research on today's world. Many students are not aware of the world of Bioinformatics.	+	Students may not understand the importance and relevance of molecular
		+	genetics to research on today's world. Many students are not aware of the world of Bioinformatics.

Susie07 at 14:47, 30 July 2008

2008-07-30T14:47:22Z

←Older revision		Revision as of 14:47, 30 July 2008
Line 12:		Line 12:
	2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.		2) understand the difference between a dominant and recessive trait and understand how the presence of a trait may effect the physical characteristics of an individual.
	3) read and/or construct a pedigree chart mapping a specific trait in a family.		3) read and/or construct a pedigree chart mapping a specific trait in a family.
-	4) determine the probability of a certain phenotype being expressed in an ~~individual.~~	+	•4) determine the probability of a certain phenotype being expressed in an •
-	~~5) learn bioinformatics techniques of searching for specific genes in databases.~~	+
-	~~6) learning how to read a bioinformatics gene page~~	+
-	~~7) finding similar coding sequence regions in other organisms~~	+
-		+
	'''Common Misconceptions'''		'''Common Misconceptions'''
	Students may not understand the importance and relevance of molecular genetics to research on today's world. Many students are not aware of the world of Bioinformatics.		Students may not understand the importance and relevance of molecular genetics to research on today's world. Many students are not aware of the world of Bioinformatics.
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	Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products		Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products
	CDS-Coding sequence		CDS-Coding sequence
-
-
-


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	• In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes (as a string of molecular "letters") and replicated (by a templating mechanism). Each DNA molecule in a cell forms a single chromosome.		• In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes (as a string of molecular "letters") and replicated (by a templating mechanism). Each DNA molecule in a cell forms a single chromosome.
		+
		+	• Recognize and analyze alternative explanations and models, reviewing current scientific understanding.

	'''Teacher Answer Key'''		'''Teacher Answer Key'''
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	this gene but only some have had their full-length natures		this gene but only some have had their full-length natures
	identified.		identified.
-	CDS	+	CDS of Human Breast cancer gene
	tggatttat ctgctcttcg cgttgaagaa gtacaaaatg		tggatttat ctgctcttcg cgttgaagaa gtacaaaatg
	241 tcattaatgc tatgcagaaa atcttagagt gtcccatctg tctggagttg atcaaggaac		241 tcattaatgc tatgcagaaa atcttagagt gtcccatctg tctggagttg atcaaggaac

Susie07 at 14:39, 30 July 2008

2008-07-30T14:39:19Z

←Older revision		Revision as of 14:39, 30 July 2008
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	'''Education Standards'''		'''Education Standards'''

-		+	• Living systems also have different levels of organization--for example, cells, tissues, organs, organisms, populations, and communities. Within these systems, interactions between components occur. Further, systems at different levels of organization can manifest different properties and functions.
		+
		+	• Models are tentative schemes or structures that correspond to real objects, events, or classes of events, and that have explanatory power. Models help scientists and engineers understand how things work. Models take many forms, including physical objects, plans, mental constructs, mathematical equations, and computer simulations.
		+
		+	• Cells have particular structures that underlie their functions. Every cell is surrounded by a membrane that separates it from the outside world. Inside the cell is a concentrated mixture of thousands of different molecules which form a variety of specialized structures that carry out such cell functions as energy production, transport of molecules, waste disposal, synthesis of new molecules, and the storage of genetic material.
		+
		+	• Cells store and use information to guide their functions. The genetic information stored in DNA is used to direct the synthesis of the thousands of proteins that each cell requires.
		+
		+	• In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes (as a string of molecular "letters") and replicated (by a templating mechanism). Each DNA molecule in a cell forms a single chromosome.

	'''Teacher Answer Key'''		'''Teacher Answer Key'''

Susie07 at 14:35, 30 July 2008

2008-07-30T14:35:49Z

←Older revision		Revision as of 14:35, 30 July 2008
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	'''Student Handouts for the Lesson Plan'''		'''Student Handouts for the Lesson Plan'''

-	~~Describe any handouts~~ and ~~provide links to documents that include~~ the ~~handouts. Remember to upload the handouts to the wiki before linking to them.~~	+	Instruction sheet on steps in finding genes and using the NCBI website

	'''Alternative Assessments'''		'''Alternative Assessments'''
		+
	Poster of Breast Cancer Pedigree with correct key		Poster of Breast Cancer Pedigree with correct key
	Bioinformatics project using tools and websites found in this lesson.		Bioinformatics project using tools and websites found in this lesson.
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	NCBI-National Center for Biotechnology Information		NCBI-National Center for Biotechnology Information
	Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products		Biotechnology-the scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products
		+	CDS-Coding sequence


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	'''Education Standards'''		'''Education Standards'''

-	~~Please align your lesson plan with any education standards that apply.~~	+

	'''Teacher Answer Key'''		'''Teacher Answer Key'''
		+
	Part 2: Bioinformatics Brca 1 gene:		Part 2: Bioinformatics Brca 1 gene:

Susie07 at 14:30, 30 July 2008

2008-07-30T14:30:22Z

←Older revision		Revision as of 14:30, 30 July 2008
Line 46:		Line 46:

	Part 2 -2 45 minute periods		Part 2 -2 45 minute periods
-
-	~~Part 2:~~

	How do mutations form? View film clip http://www.insidecancer.org/?s=A,1,7		How do mutations form? View film clip http://www.insidecancer.org/?s=A,1,7

Susie07 at 13:47, 30 July 2008

2008-07-30T13:47:15Z

←Older revision		Revision as of 13:47, 30 July 2008
Line 30:		Line 30:

	'''During class'''		'''During class'''
		+
		+	'''Time required'''
		+
		+	Part 1- 45 minutes
	Part 1: Predicting the Breast cancer gene through Pedigree charts		Part 1: Predicting the Breast cancer gene through Pedigree charts
	Practice drawing a pedigree chart		Practice drawing a pedigree chart
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	Mark Skolnick: Finding the breast cancer gene brca1-http://www.dnai.org/media/a/skolnick298_06.swf		Mark Skolnick: Finding the breast cancer gene brca1-http://www.dnai.org/media/a/skolnick298_06.swf
	Mary Claire king: Can women be tested for breast cancer? http://www.dnaiorg/media/a/king295_08.swf		Mary Claire king: Can women be tested for breast cancer? http://www.dnaiorg/media/a/king295_08.swf
		+
		+
		+	'''Time required'''
		+
		+	Part 2 -2 45 minute periods

	Part 2:		Part 2:

-	1. Discussion of Biotechnology and ~~bioinformatics~~ based on reading ~~[[Image~~:~~biotechnology.doc]]~~	+	How do mutations form? View film clip http://www.insidecancer.org/?s=A,1,7
		+
		+	1. Reading and Discussion of Biotechnology and Bioinformatics based on the reading below:
	Biotechnology’s Relation to Cancer Research		Biotechnology’s Relation to Cancer Research
	Biotechnology has applied many of the techniques of cell biology,		Biotechnology has applied many of the techniques of cell biology,
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	cascade of cancer events. Computer modeling allows proteins to be considered		cascade of cancer events. Computer modeling allows proteins to be considered
	in a variety of new lights, including indentifying potential docking clefts for		in a variety of new lights, including indentifying potential docking clefts for
-	the introduction of small molecules or proteins that might interfere with cancer causing	+	the introduction of small molecules or proteins that might interfere with cancer causing protein functions. Bioinformatics and combinatorial chemistry allow
-	protein functions. Bioinformatics and combinatorial chemistry allow	+
	scientists to sort through molecules (both natural and synthetic) that		scientists to sort through molecules (both natural and synthetic) that
	interfere with cancer’s progress in a variety of ways. In addition, the ability		interfere with cancer’s progress in a variety of ways. In addition, the ability
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	2. Finding the Brca 1 gene using bioinformatics		2. Finding the Brca 1 gene using bioinformatics

-
-
-	~~'''Time required'''~~
-
-	~~Part 1- 45 minutes~~
-	~~Part 2 -2 45 minute periods~~

	'''Student Handouts for the Lesson Plan'''		'''Student Handouts for the Lesson Plan'''