BISC220/S10: Lecture Syllabus

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'''Lab Instructor:''' Melissa Beers<br>
'''Lab Instructor:''' Melissa Beers<br>
'''Lab Prep :''' Padma Kannabiran<br>
'''Lab Prep :''' Padma Kannabiran<br>
-
'''Study Group Leader/ Course Peer Mentor:''' <br><br>
+
'''Study Group Leader/ Course Peer Mentor:''' Christie Sze<br><br>
-
'''Contact Info:''' Jennifer Hood-DeGrenier:  Office  SC376A ; office phone  x3313; email: @wellesley.edu<br>
+
'''Contact Info:'''<br>
-
Office Hours: TBA<br><br>
+
Jennifer Hood-DeGrenier:  Office  SC376A ; office phone  x3313; email: @wellesley.edu<br>
 +
Office Hours: Tues. 1:00-2:30 pm or by appointment (SC376A)<br><br>
Melissa Beers: Office  SC175; office phone X3521; email: mbeers@wellesley.edu<br>
Melissa Beers: Office  SC175; office phone X3521; email: mbeers@wellesley.edu<br>
-
Office Hours: by arrangement<br><br>
+
Office Hours: by arrangement (SC175) <br><br>
-
'''Lectures:''' Tuesdays & Fridays 11:10-12:20, SCI377<br>
+
'''Lectures:''' Tuesdays & Fridays 11:10-12:20 (SC396)<br>
-
'''Labs:''' : Tues. 12:30-4; Wed. 2:15-5:45; Thurs. 1-4:30;<br><br>
+
'''Labs:''' : Tues. 12:30-4; Wed. 2:15-5:45; Thurs. 1-4:30 (SC304)<br>
 +
<br>
 +
'''Text:'''  Alberts, B. et al. (2008) ''Molecular Biology of the Cell'', 5th ed., Garland Science<br>
 +
<br>
 +
'''Reserve texts and Problem Books:'''<br>
 +
Lodish,  H. et al. (2008) ''Molecular Cell Biology'', 6th ed. <br>
 +
Alberts, B. et al. (2008) ''Molecular Biology of the Cell'', 5th ed.<br>
 +
Wilson, J. and Hunt T. (2002) ''Molecular Biology of the Cell:  A Problems Approach'', 4th ed.<br>
 +
<br>
 +
<br>
 +
'''Reference material for labs:''' The lab manual is published electronically at: http://openwetware.org/wiki/BISC220/S10<br>
 +
'''In the interest of conservation, please do not print out the entire lab manual. Copies will be available for your use in the lab. Notes about the procedures prior to or during the labs should be made in your lab notebook.''' <br>
 +
Additional lab resource material is posted to the First Class lab conferences for BISC220<br>
 +
<br>
 +
'''EXPECTED OUTCOMES:'''<br>
 +
By the end of this course, you should be familiar with many of the essential physiological processes of the cell and have a strong understanding of how proteins collaborate to carry out those processes. You will also have acquired a “methods tool-kit” and an understanding of how to apply various experimental techniques to answer cell biological questions. Finally, you should have gained confidence in reading and interpreting primary-source scientific articles enhanced your scientific writing abilities.<br>
 +
<br>
 +
'''GRADING:'''<br>
 +
{| border="1"
 +
|+
 +
! Assessment    !! Points   
 +
|-
 +
! Hour Exams
 +
| 200 points
 +
|-
 +
! Final Exam
 +
| 140 points
 +
|-
 +
! Homework/Quizzes
 +
| 60 points
 +
|-
 +
! Laboratory
 +
| 200 points
 +
|-
 +
! Total !! 600 points
 +
|-
 +
|}
 +
<br>
 +
'''POLICY ON LATE ASSIGNMENTS AND MAKE-UP EXAMS:'''<br>
 +
Make-up exams and quizzes will only be given in the case of a serious personal illness or family emergency that '''has been documented by your class dean'''. Similarly, excused extensions for lab reports or homework will not be granted except in the cases described. In such situations, if at all possible, the instructor should be notified '''prior''' to the class period in which the exam or quiz is to be administered or when the assignment is due. '''Unexcused late work will be penalized 5% per day and will not receive credit more than one week after the due date'''. Students who have a legitimate conflict with a scheduled exam are requested to speak with the instructor as soon as possible about taking the exam '''early''', but no more than 48 hours in advanced of the scheduled exam.
 +
<br><br>
 +
 
 +
'''STUDENTS WITH SPECIAL NEEDS: ''' <br>
 +
Students entitled to disability-related accommodations are requested to speak with the instructor about their needs well in advance of scheduled quizzes, exams, and assignment due dates.<br><br>
 +
 
 +
'''POLICY ON COLLABORATION: ''' <br>
 +
Working in groups with your classmates is encouraged as a valuable way to enhance your understanding of the course material; however, the actual writing of all assignments, including homework and lab reports, must be completed individually.<br><br>
 +
 
 +
'''POTENTIAL CHANGES TO THE SYLLABUS: ''' <br>
 +
The instructor reserves the right to modify the syllabus during the semester as she deems necessary to meet the course goals in a reasonable manner.<br><br>
 +
 
 +
 
 +
'''Please let your instructors know if you are having trouble during the semester. The sooner you bring a problem to our attention, the sooner we can help you address it.'''
 +
 
 +
== BISC220 Lecture Schedule ==
 +
{| border="1"
 +
|+
 +
! Lec. #  !! Date !! Topics !! Reading   
 +
|-
 +
! 1
 +
| T 1/26
 +
| Intro:  The AMAZING World of the Cell <br><br> Protein Structure
 +
| Review Ch. 1 & Ch. 2 (general background, review from BISC 110) <br> Ch. 3, p. 125-148 <br>
 +
Ch. 8, p. 527-530 (protein structure determination)<br>
 +
http://www.youtube.com/watch?v=BtZEqQ1cpmk (Harvard BioVisions)<br><br>
 +
View Cell Biology Interactive (CBI) videos 3.1-3.6, 3.9 (DVD that came with your textbook—see conference for access notes)
 +
|-
 +
! 2
 +
| F 1/29
 +
| Protein Regulation & Social Context <br><br> Enzymes I:  Mechanism of Catalysis
 +
| Ch. 2, p. 72-81 <br> Ch. 3, p. 152-161, 164-167 & 175-190<br>
 +
CBI videos 3.7, 3.8 & 3.11 <br> <br>Ringe D, Petsko G A (2008) How enzymes work. Science 320:1428-1429.*
 +
|-
 +
! 3
 +
| T 2/2
 +
| Enzymes II:  Kinetics & Regulation <br><br> '''Quiz:  Amino Acids (10 pts)'''
 +
| Ch. 3 p. 162-163 & 166-174 <br> CBI video 3.10 <br>
 +
Biology Hypertextbook Enzyme Biochemistry http://www.sciencegateway.org/resources/biologytext/index.html sections 3 & 4 (also try practice problems #1-3)
 +
|-
 +
! 4
 +
| F 2/5
 +
| Protein Methods I: Protein Separation & Antibody Detection
 +
| Ch. 8, p. 508-509 & 517-522  <br> Ch. 25, p. 1551-1561 (on the textbook DVD) <br> CBI video 25.2
 +
|-
 +
! 5
 +
| T 2/9
 +
| Protein Methods II:  Protein Purification & Functional Analysis
 +
| Ch. 8, p. 510-516, 522-531 & 564-576 <br><br>
 +
Snyder M and Gallagher JEG (2009) Systems biology from a yeast omics perspective. FEBS Letters 583:3895-3899.*
 +
|-
 +
! 6
 +
| F 2/12
 +
| The Life Cycle of a Protein:  Folding to Destruction
 +
| Ch. 6 p. 387-399<br><br>
 +
Kolata G (1986) New Rule Proposed for Protein Degradation. Science 234:151-152.*<br><br>
 +
Bachmir A, Finley D, Varshavsky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Nature 234:179-186.*<br><br>
 +
Wolf DH, Sommer T, Hilt W (2004) Death gives birth to life: the essential role of the ubiquitin-proteasome system in biology. Biochim Biophys Acta 1695:1-2.*
 +
|-
 +
!
 +
| T 2/16
 +
|''' No Class—Monday Schedule'''
 +
|
 +
|-
 +
! 7
 +
| F 2/19
 +
| Imaging Cells & Molecules <br><br> '''BLAST Homework (#1) Due (10 pts)'''
 +
| Ch. 9 <br><br>
 +
http://bioeducate.ascb.org/ — check out 2008 ASCB “Celldance” Contest winning videos
 +
|-
 +
! 8
 +
| T 2/23
 +
| Membranes & Membrane Proteins
 +
| Ch. 10 <br><br> CBI videos 10.1-10.6
 +
|-
 +
!
 +
| F 2/26
 +
| '''EXAM I (100 pts)'''
 +
|
 +
|-
 +
! 9
 +
| T 3/2
 +
| Membrane Transport & Electrical Properties of Membranes
 +
| Ch. 11 p. 651-683 <br> CBI videos 11.1-11.6 & 15.1<br><br>
 +
Doyle DA et al. (1998) The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity. Science 280:69-77.*
 +
|-
 +
! 10
 +
| F 3/5
 +
| Protein Sorting:  Principles & Experimental Approaches <br><br> Protein Insertion into the Endoplasmic Reticulum
 +
| Ch. 12 p. 695-704 & 723-738 <br> CBI videos 12.1, 12.4, & 12.6
 +
|-
 +
! 11
 +
| T 3/9
 +
| ER Quality Control & Principles of Vesicle Trafficking
 +
| Ch. 12, p. 738-742 <br> Ch. 13, p. 749-766 <br> CBI videos 13.1 & 13.4 <br><br>
 +
Pucadyil TJ, Schmid S (2009) Conserved Functions of Membrane Active GTPases in Coated Vesicle Formation. Science 325:1217-1220.*
 +
|-
 +
! 12
 +
| F 3/12
 +
| Intra- and Trans-Cellular Vesicle Trafficking  <br><br> I'''on Channel Homework (#2) Due (10 pts)'''
 +
| Ch. 13, p.  766-809 <br> CBI videos 13.2, 13.3, 13.5 & 13.6
 +
|-
 +
! 13
 +
| T 3/16
 +
| Nucleocytoplasmic Transport
 +
| Ch. 12, p. 704-710 <br> CBI videos 12.2 & 12.5 <br><br>
 +
Weis K (2007) The Nuclear Pore Complex: Oily Spaghetti or Gummy Bear? Cell 130:405-407.*
 +
|-
 +
! 14
 +
| F 3/19
 +
| '''Workshop:'''  Nuclear Transport in STAT1 Transcription Factor Function
 +
| McBride KM, Banninger G, McDonald C, Reich, NC (2002) Regulated nuclear import of the STAT1 transcription factor by direct binding of importin-α. EMBO J. 21:1754-1763.* <br><br>
 +
McBride KM, Reich NC (2003) The ins and outs of STAT1 nuclear transport. Sci STKE 195:RE13*
 +
|-
 +
!
 +
| 3/23 & 3/26
 +
| '''SPRING BREAK'''
 +
|
 +
|-
 +
! 15
 +
| T 3/30
 +
| Cell Signaling I:  Overview/ RTKs & Ras-MAPK Pathway
 +
| Ch. 15, p. 879-903 & 921-930 <br> CBI videos 15.4 & 15.5
 +
|-
 +
! 16
 +
| F 4/2
 +
| Cell Signaling II:  GPCRs & Second Messengers <br><br> '''Workshop HW (#3) Due (10 pts)'''
 +
| Ch. 15, p. 904-921; Ch. 8, p. 540-542 <br> CBI videos 15.3 & 15.6
 +
|-
 +
! 17
 +
| T 4/6
 +
| Cytoskeleton I:  Filament Structure, Dynamics & Regulation
 +
| Ch. 16, p. 965-983, 987-988 & 992-1004 <br> CBI videos 16.1 & 16.3-16.5 <br><br>
 +
Rohn JL, Baum B (2010) Actin and cellular architecture at a glance. J Cell Science 123:155-158.*
 +
|-
 +
!
 +
| F 4/9
 +
| '''EXAM II (100 pts)'''
 +
|
 +
|-
 +
! 18
 +
| T 4/13
 +
| Cytoskeleton II:  Motor Proteins & Cell Movement
 +
| Ch. 16, 1010-1022 & 1036-1046 <br> CBI videos 16.2 & 16.6-16.10
 +
|-
 +
! 19
 +
| F 4/16
 +
| Cellular Reproduction I:  The Cell Cycle & Cyclin Dependent Kinases
 +
| Ch. 17, p. 1053-1066 <br> CBI video 17.1 <br> Lodish Ch. 20, p. 851-862 (on reserve)
 +
|-
 +
! 20
 +
| T 4/20
 +
| Cellular Reproduction II:  Mechanics of S Phase & Mitosis <br><br> '''Cytoskeleton Homework (#4) Due (10 points)'''
 +
| Ch. 14, p. 1067—1090 <br> CBI videos 17.3-17.7
 +
|-
 +
! 21
 +
| F 4/23
 +
| Cellular Reproduction III:  Checkpoints & Control of Cell Division
 +
| Ch. 17, p. 1061, 1088 & 1101-1110 <br> CBI video 17.2 <br><br>
 +
May KM, Hardwick KG (2006) The spindle checkpoint. J Cell Science 119:4139-4142.*
 +
|-
 +
! 22
 +
| T 4/27
 +
| Apoptosis:  Programmed Cell Death
 +
| Ch. 18 <br> CBI video 18.1 <br><br>
 +
http://www.nature.com/milestones/development/milestones/full/milestone15.html
 +
|-
 +
! 23
 +
| F 4/30
 +
| Cancer I:  Features of Cancer Cells/Oncogenes & Tumor Suppressors <br><br> '''Cell Cycle Homework (#5) Due (10 points)'''
 +
| Ch. 20, p. 1205-1240 <br> CBI videos 20.1, 20.2
 +
|-
 +
! 24
 +
| T 5/4
 +
| Cancer II:  Molecular Basis of Cancer & Novel Therapies
 +
| Ch. 20, p. 1241-1265
 +
|-
 +
|}
 +
<br>
 +
‡ All readings are in the Alberts text unless otherwise noted. The starred (*) articles are available as electronic links or PDF documents on the E-Reserve sub-conference of the course FirstClass conference. The electronic version of this syllabus that is posted to the “Lecture Material” sub-conference of the course conference contains hyperlinks to the web resources listed as Readings.

Current revision

Wellesley College     BISC 220     Cellular Physiology

Home        Lecture Syllabus        Lab Calendars/Point Distribution        Assignments        Resources        Glossary       
Enzymes        Secretory Pathway        Cytoskeleton        OWW Basics              

BISC220 Cell Physiology

Lecturer: Jennifer Hood-DeGrenier
Lab Instructor: Melissa Beers
Lab Prep : Padma Kannabiran
Study Group Leader/ Course Peer Mentor: Christie Sze

Contact Info:
Jennifer Hood-DeGrenier: Office SC376A ; office phone x3313; email: @wellesley.edu
Office Hours: Tues. 1:00-2:30 pm or by appointment (SC376A)

Melissa Beers: Office SC175; office phone X3521; email: mbeers@wellesley.edu
Office Hours: by arrangement (SC175)

Lectures: Tuesdays & Fridays 11:10-12:20 (SC396)
Labs: : Tues. 12:30-4; Wed. 2:15-5:45; Thurs. 1-4:30 (SC304)

Text: Alberts, B. et al. (2008) Molecular Biology of the Cell, 5th ed., Garland Science

Reserve texts and Problem Books:
Lodish, H. et al. (2008) Molecular Cell Biology, 6th ed.
Alberts, B. et al. (2008) Molecular Biology of the Cell, 5th ed.
Wilson, J. and Hunt T. (2002) Molecular Biology of the Cell: A Problems Approach, 4th ed.


Reference material for labs: The lab manual is published electronically at: http://openwetware.org/wiki/BISC220/S10
In the interest of conservation, please do not print out the entire lab manual. Copies will be available for your use in the lab. Notes about the procedures prior to or during the labs should be made in your lab notebook.
Additional lab resource material is posted to the First Class lab conferences for BISC220

EXPECTED OUTCOMES:
By the end of this course, you should be familiar with many of the essential physiological processes of the cell and have a strong understanding of how proteins collaborate to carry out those processes. You will also have acquired a “methods tool-kit” and an understanding of how to apply various experimental techniques to answer cell biological questions. Finally, you should have gained confidence in reading and interpreting primary-source scientific articles enhanced your scientific writing abilities.

GRADING:

Assessment Points
Hour Exams 200 points
Final Exam 140 points
Homework/Quizzes 60 points
Laboratory 200 points
Total 600 points


POLICY ON LATE ASSIGNMENTS AND MAKE-UP EXAMS:
Make-up exams and quizzes will only be given in the case of a serious personal illness or family emergency that has been documented by your class dean. Similarly, excused extensions for lab reports or homework will not be granted except in the cases described. In such situations, if at all possible, the instructor should be notified prior to the class period in which the exam or quiz is to be administered or when the assignment is due. Unexcused late work will be penalized 5% per day and will not receive credit more than one week after the due date. Students who have a legitimate conflict with a scheduled exam are requested to speak with the instructor as soon as possible about taking the exam early, but no more than 48 hours in advanced of the scheduled exam.

STUDENTS WITH SPECIAL NEEDS:
Students entitled to disability-related accommodations are requested to speak with the instructor about their needs well in advance of scheduled quizzes, exams, and assignment due dates.

POLICY ON COLLABORATION:
Working in groups with your classmates is encouraged as a valuable way to enhance your understanding of the course material; however, the actual writing of all assignments, including homework and lab reports, must be completed individually.

POTENTIAL CHANGES TO THE SYLLABUS:
The instructor reserves the right to modify the syllabus during the semester as she deems necessary to meet the course goals in a reasonable manner.


Please let your instructors know if you are having trouble during the semester. The sooner you bring a problem to our attention, the sooner we can help you address it.

BISC220 Lecture Schedule

Lec. # Date Topics Reading
1 T 1/26 Intro: The AMAZING World of the Cell

Protein Structure
Review Ch. 1 & Ch. 2 (general background, review from BISC 110)
Ch. 3, p. 125-148

Ch. 8, p. 527-530 (protein structure determination)
http://www.youtube.com/watch?v=BtZEqQ1cpmk (Harvard BioVisions)

View Cell Biology Interactive (CBI) videos 3.1-3.6, 3.9 (DVD that came with your textbook—see conference for access notes)

2 F 1/29 Protein Regulation & Social Context

Enzymes I: Mechanism of Catalysis
Ch. 2, p. 72-81
Ch. 3, p. 152-161, 164-167 & 175-190

CBI videos 3.7, 3.8 & 3.11

Ringe D, Petsko G A (2008) How enzymes work. Science 320:1428-1429.*

3 T 2/2 Enzymes II: Kinetics & Regulation

Quiz: Amino Acids (10 pts)
Ch. 3 p. 162-163 & 166-174
CBI video 3.10

Biology Hypertextbook Enzyme Biochemistry http://www.sciencegateway.org/resources/biologytext/index.html sections 3 & 4 (also try practice problems #1-3)

4 F 2/5 Protein Methods I: Protein Separation & Antibody Detection Ch. 8, p. 508-509 & 517-522
Ch. 25, p. 1551-1561 (on the textbook DVD)
CBI video 25.2
5 T 2/9 Protein Methods II: Protein Purification & Functional Analysis Ch. 8, p. 510-516, 522-531 & 564-576

Snyder M and Gallagher JEG (2009) Systems biology from a yeast omics perspective. FEBS Letters 583:3895-3899.*

6 F 2/12 The Life Cycle of a Protein: Folding to Destruction Ch. 6 p. 387-399

Kolata G (1986) New Rule Proposed for Protein Degradation. Science 234:151-152.*

Bachmir A, Finley D, Varshavsky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Nature 234:179-186.*

Wolf DH, Sommer T, Hilt W (2004) Death gives birth to life: the essential role of the ubiquitin-proteasome system in biology. Biochim Biophys Acta 1695:1-2.*

T 2/16 No Class—Monday Schedule
7 F 2/19 Imaging Cells & Molecules

BLAST Homework (#1) Due (10 pts)
Ch. 9

http://bioeducate.ascb.org/ — check out 2008 ASCB “Celldance” Contest winning videos

8 T 2/23 Membranes & Membrane Proteins Ch. 10

CBI videos 10.1-10.6
F 2/26 EXAM I (100 pts)
9 T 3/2 Membrane Transport & Electrical Properties of Membranes Ch. 11 p. 651-683
CBI videos 11.1-11.6 & 15.1

Doyle DA et al. (1998) The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity. Science 280:69-77.*

10 F 3/5 Protein Sorting: Principles & Experimental Approaches

Protein Insertion into the Endoplasmic Reticulum
Ch. 12 p. 695-704 & 723-738
CBI videos 12.1, 12.4, & 12.6
11 T 3/9 ER Quality Control & Principles of Vesicle Trafficking Ch. 12, p. 738-742
Ch. 13, p. 749-766
CBI videos 13.1 & 13.4

Pucadyil TJ, Schmid S (2009) Conserved Functions of Membrane Active GTPases in Coated Vesicle Formation. Science 325:1217-1220.*

12 F 3/12 Intra- and Trans-Cellular Vesicle Trafficking

Ion Channel Homework (#2) Due (10 pts)
Ch. 13, p. 766-809
CBI videos 13.2, 13.3, 13.5 & 13.6
13 T 3/16 Nucleocytoplasmic Transport Ch. 12, p. 704-710
CBI videos 12.2 & 12.5

Weis K (2007) The Nuclear Pore Complex: Oily Spaghetti or Gummy Bear? Cell 130:405-407.*

14 F 3/19 Workshop: Nuclear Transport in STAT1 Transcription Factor Function McBride KM, Banninger G, McDonald C, Reich, NC (2002) Regulated nuclear import of the STAT1 transcription factor by direct binding of importin-α. EMBO J. 21:1754-1763.*

McBride KM, Reich NC (2003) The ins and outs of STAT1 nuclear transport. Sci STKE 195:RE13*

3/23 & 3/26 SPRING BREAK
15 T 3/30 Cell Signaling I: Overview/ RTKs & Ras-MAPK Pathway Ch. 15, p. 879-903 & 921-930
CBI videos 15.4 & 15.5
16 F 4/2 Cell Signaling II: GPCRs & Second Messengers

Workshop HW (#3) Due (10 pts)
Ch. 15, p. 904-921; Ch. 8, p. 540-542
CBI videos 15.3 & 15.6
17 T 4/6 Cytoskeleton I: Filament Structure, Dynamics & Regulation Ch. 16, p. 965-983, 987-988 & 992-1004
CBI videos 16.1 & 16.3-16.5

Rohn JL, Baum B (2010) Actin and cellular architecture at a glance. J Cell Science 123:155-158.*

F 4/9 EXAM II (100 pts)
18 T 4/13 Cytoskeleton II: Motor Proteins & Cell Movement Ch. 16, 1010-1022 & 1036-1046
CBI videos 16.2 & 16.6-16.10
19 F 4/16 Cellular Reproduction I: The Cell Cycle & Cyclin Dependent Kinases Ch. 17, p. 1053-1066
CBI video 17.1
Lodish Ch. 20, p. 851-862 (on reserve)
20 T 4/20 Cellular Reproduction II: Mechanics of S Phase & Mitosis

Cytoskeleton Homework (#4) Due (10 points)
Ch. 14, p. 1067—1090
CBI videos 17.3-17.7
21 F 4/23 Cellular Reproduction III: Checkpoints & Control of Cell Division Ch. 17, p. 1061, 1088 & 1101-1110
CBI video 17.2

May KM, Hardwick KG (2006) The spindle checkpoint. J Cell Science 119:4139-4142.*

22 T 4/27 Apoptosis: Programmed Cell Death Ch. 18
CBI video 18.1

http://www.nature.com/milestones/development/milestones/full/milestone15.html

23 F 4/30 Cancer I: Features of Cancer Cells/Oncogenes & Tumor Suppressors

Cell Cycle Homework (#5) Due (10 points)
Ch. 20, p. 1205-1240
CBI videos 20.1, 20.2
24 T 5/4 Cancer II: Molecular Basis of Cancer & Novel Therapies Ch. 20, p. 1241-1265


‡ All readings are in the Alberts text unless otherwise noted. The starred (*) articles are available as electronic links or PDF documents on the E-Reserve sub-conference of the course FirstClass conference. The electronic version of this syllabus that is posted to the “Lecture Material” sub-conference of the course conference contains hyperlinks to the web resources listed as Readings.
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