CH391L/2013 - Revision history

Ilya J. Finkelstein: Removing all content from page

Ilya J. Finkelstein — Thu, 17 Jan 2013 21:33:40 GMT

Removing all content from page

Ilya J. Finkelstein at 02:16, 16 January 2013

Ilya J. Finkelstein — Wed, 16 Jan 2013 02:16:13 GMT

←Older revision		Revision as of 02:16, 16 January 2013
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	Office: MBB 3.422AA		Office: MBB 3.422AA

-	== Introduction ==	+	= Introduction =

	'''Topics:''' This course will focus on current developments in understanding the molecular mechanisms of genome maintenance and cancerogenesis. A strong emphasis of the course will be to understand the methods and techniques that have enabled modern breakthroughs in understanding genome stability. The course will rely heavily on primary literature and class presentations.		'''Topics:''' This course will focus on current developments in understanding the molecular mechanisms of genome maintenance and cancerogenesis. A strong emphasis of the course will be to understand the methods and techniques that have enabled modern breakthroughs in understanding genome stability. The course will rely heavily on primary literature and class presentations.
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	'''Course web page:''' The [http://openwetware.org/wiki/CH391L/2013 course web site] on the [http://openwetware.org/wiki/Main_Page OpenWetWare] (OWW) Wiki will be used to complete assignments. Participants will be required to register an account on OWW and learn to [http://openwetware.org/wiki/Simple_wiki_editing_examples edit] this Wiki.		'''Course web page:''' The [http://openwetware.org/wiki/CH391L/2013 course web site] on the [http://openwetware.org/wiki/Main_Page OpenWetWare] (OWW) Wiki will be used to complete assignments. Participants will be required to register an account on OWW and learn to [http://openwetware.org/wiki/Simple_wiki_editing_examples edit] this Wiki.

-	== Grading ==	+	= Grading =

	Final grades will be assigned by a straight scale (no curve) based on how many points you accumulate. Grades will be assigned based on the following ruberick:		Final grades will be assigned by a straight scale (no curve) based on how many points you accumulate. Grades will be assigned based on the following ruberick:
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	\|}		\|}

-	== Class Structure ==	+	= Class Structure =

	Each class time will be split into two halves with a 10-15 minute break between them.		Each class time will be split into two halves with a 10-15 minute break between them.

-	=== First Section — New Topics ===	+	== First Section — New Topics ==
-		+
	In the first half of each class, 3-5 participants will have 15 to 20 minutes each to individually present new topics. To prepare for these oral presentations, you are required to complete a written report by creating a new page on the [http://openwetware.org/wiki/CH391L/2013 course web site] that is an in-depth discussion of the topic (aim for ~1000 words, ≥3 citations to scientific reviews and research papers, and explanatory figures.)		In the first half of each class, 3-5 participants will have 15 to 20 minutes each to individually present new topics. To prepare for these oral presentations, you are required to complete a written report by creating a new page on the [http://openwetware.org/wiki/CH391L/2013 course web site] that is an in-depth discussion of the topic (aim for ~1000 words, ≥3 citations to scientific reviews and research papers, and explanatory figures.)

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	'''Be brief and consise.''' The PowerPoint presentation should contain no more than ten slides. You are encouranged to follow the outline of your written Wiki report. Other members of the class are expected to provide feedback by asking questions during your presentation and by editing the Talk pages for your written Wiki report after your presentation. Comments should be constructive, with proper citations were applicable. Your classmates will ask you interesting questions or bring up issues that you may not immediately answer, and that all of us will all learn from the feedback and revision cycle! You are encouraged (but not required) to bring a laptop / tablet / smart-phone to view Wiki pages and related scientific papers during in-class presentations.		'''Be brief and consise.''' The PowerPoint presentation should contain no more than ten slides. You are encouranged to follow the outline of your written Wiki report. Other members of the class are expected to provide feedback by asking questions during your presentation and by editing the Talk pages for your written Wiki report after your presentation. Comments should be constructive, with proper citations were applicable. Your classmates will ask you interesting questions or bring up issues that you may not immediately answer, and that all of us will all learn from the feedback and revision cycle! You are encouraged (but not required) to bring a laptop / tablet / smart-phone to view Wiki pages and related scientific papers during in-class presentations.

-	=== Second Section — Topic Updates. ===	+	== Second Section — Topic Updates. ==

	In the second half of the class period, students who presented new topics the previous time will present their answers to questions that were raised during the in-class discussion of their topic or on the Wiki talk pages since they presented. You may need to add additional citations to research papers to expand on the background.		In the second half of the class period, students who presented new topics the previous time will present their answers to questions that were raised during the in-class discussion of their topic or on the Wiki talk pages since they presented. You may need to add additional citations to research papers to expand on the background.
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	To keep a record of your changes, you should keep track of your point-by-point responses and the Wiki edits that you made to your written report on your topic's Talk page as if you were responding to reviewers of a scientific paper.		To keep a record of your changes, you should keep track of your point-by-point responses and the Wiki edits that you made to your written report on your topic's Talk page as if you were responding to reviewers of a scientific paper.

-	=== Topic Choice ===	+	== Topic Choice ==

	Topic choices should be discussed with the instructor and class at least '''one week''' prior to the scheduled presentation. A list of topics can be found below, but there is significant leeway to tailor the papers and topics toward your specific interests.		Topic choices should be discussed with the instructor and class at least '''one week''' prior to the scheduled presentation. A list of topics can be found below, but there is significant leeway to tailor the papers and topics toward your specific interests.
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	The goal of the topic component of the class is to create a reference work that you can come back to after completing the class to remember key details.		The goal of the topic component of the class is to create a reference work that you can come back to after completing the class to remember key details.

-	=== Scholastic Dishonesty ===	+	== Scholastic Dishonesty ==

	If you are caught in some form of [http://deanofstudents.utexas.edu/sjs/scholdis_whatis.php scholastic dishonesty] you will '''receive an F in the course''', and you will be reported to Student Judicial Services (Office of the Dean of Students). You will receive no warning before these actions are taken. Be particularly careful when editing OWW Wiki pages— include references to all copyrighted material (such as figures from papers) that are not in the public domain.		If you are caught in some form of [http://deanofstudents.utexas.edu/sjs/scholdis_whatis.php scholastic dishonesty] you will '''receive an F in the course''', and you will be reported to Student Judicial Services (Office of the Dean of Students). You will receive no warning before these actions are taken. Be particularly careful when editing OWW Wiki pages— include references to all copyrighted material (such as figures from papers) that are not in the public domain.

-	=== Special Accomodations ===	+	== Special Accomodations ==

	The University of Austin provides appropriate academic accommodations for qualified students with disabilities upon request. For more information, contact the Office of the Dean of Students at 471-6259, 471-6441 TTY.		The University of Austin provides appropriate academic accommodations for qualified students with disabilities upon request. For more information, contact the Office of the Dean of Students at 471-6259, 471-6441 TTY.

Ilya J. Finkelstein: /* Week 9 (Mar 20: Nucleotide Excision Repair */

Ilya J. Finkelstein — Wed, 16 Jan 2013 02:05:41 GMT

Week 9 (Mar 20: Nucleotide Excision Repair

←Older revision		Revision as of 02:05, 16 January 2013
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	=== Week 8 (Mar 6): Special Topics Lecture ===		=== Week 8 (Mar 6): Special Topics Lecture ===
-	=== Week 9 (Mar 20: Nucleotide Excision Repair ===	+	=== Week 9 (Mar 20): Nucleotide Excision Repair ===
		+
	=== Week 10 (Mar 27): Base Excision Repair ===		=== Week 10 (Mar 27): Base Excision Repair ===
	=== Week 11 (Apr 3): Damage Tolerance and Mutagenesis — Prokaryotes ===		=== Week 11 (Apr 3): Damage Tolerance and Mutagenesis — Prokaryotes ===

Ilya J. Finkelstein: /* Topics */

Ilya J. Finkelstein — Wed, 16 Jan 2013 02:04:46 GMT

Topics

←Older revision		Revision as of 02:04, 16 January 2013
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	=== Week 3 (Jan 30): Double Strand Break (DSB) & Associated Diseases ===		=== Week 3 (Jan 30): Double Strand Break (DSB) & Associated Diseases ===
		+	==== Suggested Topics ====
	* DSB Repair: Pathway Choice		* DSB Repair: Pathway Choice

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	=== Week 6 (Feb 20): Mismatch Repair, Adaptation & Diseases===		=== Week 6 (Feb 20): Mismatch Repair, Adaptation & Diseases===
		+	==== Suggested Topics ====
	*Mismatch repair and adaptation		*Mismatch repair and adaptation
		+	** Mutagenesis in Bacteria
		+	** Mutagenesis in Eukaryotes
		+
		+	* Meiotic-specific Roles of Mismatch Repair Proteins

	*Diseases		*Diseases
	** Lynch Syndrome		** Lynch Syndrome
-

	=== Week 7 (Feb 27): Mitochondrial DNA Damage ===		=== Week 7 (Feb 27): Mitochondrial DNA Damage ===
		+	==== Suggested Topics ====
		+	* Structure of Mitochondrial DNA
		+	* Mechanisms of DNA Repair
		+	* Mitochondrial DNA repair and aging
		+	* Diseases Associated with Mitochondrial DNA Damage
		+
	=== Week 8 (Mar 6): Special Topics Lecture ===		=== Week 8 (Mar 6): Special Topics Lecture ===
	=== Week 9 (Mar 20: Nucleotide Excision Repair ===		=== Week 9 (Mar 20: Nucleotide Excision Repair ===

Ilya J. Finkelstein: /* Topics */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:55:30 GMT

Topics

←Older revision		Revision as of 01:55, 16 January 2013
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	** Alternative End-Joining		** Alternative End-Joining

-	=== Week 3 (Jan 30): ~~Diseases Associated with~~ DSB ~~Repair~~ ===	+	=== Week 3 (Jan 30): Double Strand Break (DSB) & Associated Diseases ===
-	* Seckel & Jawad Syndromes	+	* DSB Repair: Pathway Choice
-	* Nijmegen Breakage Syndrome	+
-	* Ataxia - telangiectasia	+	* DSB-related diseases:
-	* Werner & Bloom Syndromes	+	** Seckel & Jawad Syndromes
		+	** Nijmegen Breakage Syndrome
		+	** Ataxia - telangiectasia
		+	** Werner & Bloom Syndromes

	=== Week 4 (Feb 6): DNA Replication as a Source of Genomic Instability ===		=== Week 4 (Feb 6): DNA Replication as a Source of Genomic Instability ===
	==== Suggested Topics ====		==== Suggested Topics ====
-	* ~~DSB repair mechanisms in prokaryotes~~	+	* Replicating Aberrant Structures
-	** ~~Homologous Recombination~~	+	** DNA Hairpins
-	** ~~SOS Response~~	+	** Z-DNA
		+	** G-Quadruplex DNA
		+	** Chromosome Fragile Sites

-	* ~~DSB repair in eukaryotes~~	+	* Replication-Transcription Conflicts
-	** Homologous Recombination	+
-	** Non-Homologous End Joining	+	* Replication-Collapse at Interstrand Cross Links
-	** Alternative End-~~Joining~~	+

	=== Week 5 (Feb 13): Mechanisms of DNA Mismatch Repair===		=== Week 5 (Feb 13): Mechanisms of DNA Mismatch Repair===
		+	==== Suggested Topics ====
		+	* Mismatch Repair in Prokaryotes
		+
		+	* Very short patch repair
		+
		+	* Mismatch Repair in Eukaryotes
		+	** How is a Mismatch Recognized?
		+	** How is a Mismatch Removed?
		+
		+	=== Week 6 (Feb 20): Mismatch Repair, Adaptation & Diseases===
		+	*Mismatch repair and adaptation
		+
		+	*Diseases
		+	** Lynch Syndrome

-	~~=== Week 6 (Feb 20): Diseases Associated with Mismatch Repair ===~~

	=== Week 7 (Feb 27): Mitochondrial DNA Damage ===		=== Week 7 (Feb 27): Mitochondrial DNA Damage ===

Ilya J. Finkelstein: /* Topics */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:41:00 GMT

Topics

←Older revision		Revision as of 01:41, 16 January 2013
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	=== Week 2 (Jan 23): Double Strand Break (DSB) Repair ===		=== Week 2 (Jan 23): Double Strand Break (DSB) Repair ===
-
	==== Suggested Topics ====		==== Suggested Topics ====
-
	* DSB repair mechanisms in prokaryotes		* DSB repair mechanisms in prokaryotes
	** Homologous Recombination		** Homologous Recombination
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	* Werner & Bloom Syndromes		* Werner & Bloom Syndromes

		+	=== Week 4 (Feb 6): DNA Replication as a Source of Genomic Instability ===
		+	==== Suggested Topics ====
		+	* DSB repair mechanisms in prokaryotes
		+	** Homologous Recombination
		+	** SOS Response

-	~~=== Week 4 (Feb 6): Mechanisms of Mismatch Repair ===~~	+	* DSB repair in eukaryotes
		+	** Homologous Recombination
		+	** Non-Homologous End Joining
		+	** Alternative End-Joining

-	=== Week 5 (Feb 13): ~~Diseases Associated with Mismach~~ Repair===	+	=== Week 5 (Feb 13): Mechanisms of DNA Mismatch Repair===

-	=== Week 6 (Feb 20): ~~Double-Strand Break (DSB)~~ Repair ===	+	=== Week 6 (Feb 20): Diseases Associated with Mismatch Repair ===

-	=== Week 7 (Feb 27): ~~DSBs and Genomic Rearrangements~~ ===	+	=== Week 7 (Feb 27): Mitochondrial DNA Damage ===
	=== Week 8 (Mar 6): Special Topics Lecture ===		=== Week 8 (Mar 6): Special Topics Lecture ===
	=== Week 9 (Mar 20: Nucleotide Excision Repair ===		=== Week 9 (Mar 20: Nucleotide Excision Repair ===

Ilya J. Finkelstein: /* Week 2 (Jan 23): Double Strand Break (DSB) Repair */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:38:55 GMT

Week 2 (Jan 23): Double Strand Break (DSB) Repair

←Older revision		Revision as of 01:38, 16 January 2013
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	* DSB repair mechanisms in prokaryotes		* DSB repair mechanisms in prokaryotes
-	* Homologous Recombination	+	** Homologous Recombination
-	* ~~Non-homologous end joining~~	+	** SOS Response
-	* SOS Response	+

	* DSB repair in eukaryotes		* DSB repair in eukaryotes
-	* Homologous Recombination	+	** Homologous Recombination
-	* Non-Homologous End Joining	+	** Non-Homologous End Joining
		+	** Alternative End-Joining

	=== Week 3 (Jan 30): Diseases Associated with DSB Repair ===		=== Week 3 (Jan 30): Diseases Associated with DSB Repair ===

Ilya J. Finkelstein: /* Topics */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:37:59 GMT

Topics

←Older revision		Revision as of 01:37, 16 January 2013
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	* Overview of course structure and topics.		* Overview of course structure and topics.

-	=== Week 2 (Jan 23): ~~Sources of DNA Damage~~ ===	+	=== Week 2 (Jan 23): Double Strand Break (DSB) Repair ===

	==== Suggested Topics ====		==== Suggested Topics ====

-	~~Exogenous Damage:~~	+	* DSB repair mechanisms in prokaryotes
-	* ~~Ionizing Radiation~~	+	* Homologous Recombination
-	* UV-~~induced Damage~~	+	* Non-homologous end joining
-	* ~~Viruses~~	+	* SOS Response

-	~~Endogenous Damage~~:	+	* DSB repair in eukaryotes
-	* Z-~~DNA~~	+	* Homologous Recombination
-	* ~~Aberra~~	+	* Non-Homologous End Joining
		+
		+	=== Week 3 (Jan 30): Diseases Associated with DSB Repair ===
		+	* Seckel & Jawad Syndromes
		+	* Nijmegen Breakage Syndrome
		+	* Ataxia - telangiectasia
		+	* Werner & Bloom Syndromes

-	~~=== Week 3 (Jan 30): DNA Replication & Damage ===~~

	=== Week 4 (Feb 6): Mechanisms of Mismatch Repair ===		=== Week 4 (Feb 6): Mechanisms of Mismatch Repair ===

Ilya J. Finkelstein: /* Week 2 (Jan 23): Sources of DNA Damage */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:28:32 GMT

Week 2 (Jan 23): Sources of DNA Damage

←Older revision		Revision as of 01:28, 16 January 2013
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	=== Week 2 (Jan 23): Sources of DNA Damage ===		=== Week 2 (Jan 23): Sources of DNA Damage ===
-	~~'' Suggested Topics ''~~	+
-	==== ~~External Damage~~ ====	+	==== Suggested Topics ====
		+
		+	Exogenous Damage:
	* Ionizing Radiation		* Ionizing Radiation
	* UV-induced Damage		* UV-induced Damage
		+	* Viruses

-	~~==== Endongenous~~	+	Endogenous Damage:
		+	* Z-DNA
		+	* Aberra

	=== Week 3 (Jan 30): DNA Replication & Damage ===		=== Week 3 (Jan 30): DNA Replication & Damage ===

Ilya J. Finkelstein: /* Week 2 (Jan 23): Sources of DNA Damage */

Ilya J. Finkelstein — Wed, 16 Jan 2013 01:24:13 GMT

Week 2 (Jan 23): Sources of DNA Damage

←Older revision		Revision as of 01:24, 16 January 2013
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	=== Week 2 (Jan 23): Sources of DNA Damage ===		=== Week 2 (Jan 23): Sources of DNA Damage ===
		+	'' Suggested Topics ''
		+	==== External Damage ====
		+	* Ionizing Radiation
		+	* UV-induced Damage
		+
		+	==== Endongenous
		+
	=== Week 3 (Jan 30): DNA Replication & Damage ===		=== Week 3 (Jan 30): DNA Replication & Damage ===