Course Syllabi

Fall Semester
2013-14

(Missing syllabi will roll in.)

Tosteson Medical Education Center (TMEC) 435

260 Longwood Avenue 
Boston, MA 02115 
 
For Information Call: 617‐432‐0162 
Email: [email protected] 
Table of Contents
1. BBS 230 (formerly Microbiology 230). Analysis of the Biological Literature

2. BCMP 200. Molecular Biology

3. *BCMP 218. Molecular Medicine

4. BCMP 230. Principles and Practice of Drug Development

5. Cell Biology 226. Concepts in Development, Self-Renewal, and Repair

6. Genetics 201. Principles of Genetics

7. Genetics 220. Molecular Biology and Genetics in Modern Medicine (N/A)

8. HBTM 201 (formerly Pathology 209). Tumor Pathophysiology and Transport

Phenomena - A Systems Biology Approach

9. HBTM 235 (formerly BCMP 235.). Principles of Human Disease: Physiology and
Pathology (N/A)

10. *Immunology 201. Principles of Immunology (N/A)

11. *Immunology 301. Immunology Seminar

12. *Medical Sciences 250ab.(HST 010) Human Functional Anatomy

13. *Microbiology 205. Mechanisms of Microbial Pathogenesis (N/A)

14. Neurobiology 200. Neurobiology (N/A)

15. *Neurobiology 220. Cellular Neurophysiology

16. Neurobiology 230. Visual Object Recognition

17. SHBT 200. Acoustics of Speech and Hearing

18. SHBT 201. Biology of the Inner Ear

19. SHBT 206 (formerly Pathology 205). Molecular Biology of the Auditory System

20. *Virology 200. Introduction to Virology

21. Virology 202. Proposal Writing

 Indicates that the course requires faculty signature on study card.

Biological and Biomedical Sciences 230: Analysis of the Biological Literature

Fall 2013

Summary: Students participate in intensive small group discussions focused on critical

analysis of basic research papers from a wide range of fields including biochemistry, cell and
developmental biology, genetics, and microbiology. Papers are discussed in terms of
background, significance, hypothesis, experimental methods, data quality, and interpretation.
Students will be asked to propose future research directions, to generate new hypotheses and
to design experiments aimed at testing them. For the midterm and final exams the students will
be asked to submit written critiques of recent papers from the literature, with an emphasis on
devising new experimental directions to test the models proposed in the papers.

Meeting times: Tuesdays and Thursdays 3:00-6:00pm

Students meet in groups on Tuesdays from 3-6 pm. Students meet in groups with faculty on
Thursdays from 3-6 pm. Exception: first class meets in TMEC250, Thursday September 5,
2013 from 3:00-6:00 pm.

Course directors:
Mike Blower: [email protected]
Adrian Salic: [email protected]

Any questions or concerns please contact the course directors.

Instructors:
Mike Blower: [email protected]
Dipanjan Chowdhury: [email protected]
Nika Danial: [email protected]
Steve Elledge: [email protected]
Jesse Gray: [email protected]
Peter Hammerman: [email protected]
Andreas Herrlich: [email protected]
Joseph Italiano: [email protected]
Laurie Jackson-Grusby: [email protected]
Maria Kontaridis: [email protected]
Cammie Lesser: [email protected]
Sean Megason: [email protected]
Trista North: [email protected]
Carl Novina: [email protected]
Adrian Salic: [email protected]
Mumut Ozcan [email protected]
Jean Zhao: [email protected]
Dates of classes and assigned papers:

Introductory meeting: Thursday 09/05/13, 3:00-6:00 pm, TMEC250. Discussion of course

expectations and paper analysis

In preparation for this meeting, read the following papers:

1. Orth, K, et al. (2000) Disruption of Signaling by Yersinia Effector YopJ, a Ubiquitin-Like

Protein Protease. Science 290,1594-1597.

2. Mukherjee S, et al. (2006) Yersinia YopJ acetylates and inhibits kinase activation by
blocking phosphorylation. Science 312(5777):1211-1214.

CLASS 1 Protein sorting

09/10/13 TUESDAY Student groups
09/12/13 THURSDAY Faculty groups

1. Bankaitis VA, Johnson LM, & Emr SD (1986) Isolation of yeast mutants defective in
protein targeting to the vacuole. Proceedings of the National Academy of Sciences of
the United States of America 83(23):9075-9079.

2. Katzmann DJ, Babst M, & Emr SD (2001) Ubiquitin-dependent sorting into the
multivesicular body pathway requires the function of a conserved endosomal protein
sorting complex, ESCRT-I. Cell 106(2):145-155.

CLASS 2 Polymer dynamics

09/24/13 TUESDAY Student groups
09/26/13 THURSDAY Faculty groups

1. Garner EC, Campbell CS, & Mullins RD (2004) Dynamic instability in a DNA-
segregating prokaryotic actin homolog. Science 306(5698):1021-1025.

2. Garner EC, Campbell CS, Weibel DB, & Mullins RD (2007) Reconstitution of DNA
segregation driven by assembly of a prokaryotic actin homolog. Science
315(5816):1270-1274.

CLASS 3 Bacterial pathogenesis

10/01/13 TUESDAY Student groups
10/03/13 THURSDAY Faculty groups

1. Alto NM, et al. (2006) Identification of a bacterial type III effector family with G protein
mimicry functions. Cell 124(1):133-145.
2. Huang Z, et al. (2009) Structural insights into host GTPase isoform selection by a family
of bacterial GEF mimics. Nature structural & molecular biology 16(8):853-860.

CLASS 4 Prions
10/08/13 TUESDAY Student groups
10/10/13 THURSDAY Faculty groups

1. Prusiner, SB, et al. (1990) Transgenetic studies implicate interactions between

homologous PrP isoforms in scrapie prion replication. Cell 63, 673-686.

2. Tanaka M, Chien P, Naber N, Cooke R, & Weissman JS (2004) Conformational

variations in an infectious protein determine prion strain differences. Nature
428(6980):323-328.

CLASS 5 Signaling
09/17/13 TUESDAY Student groups
09/19/13 THURSDAY Faculty groups

1. Sun L, Wu J, Du F, Chen X, & Chen ZJ (2013) Cyclic GMP-AMP synthase is a cytosolic

DNA sensor that activates the type I interferon pathway. Science 339(6121):786-791.

2. Wu J, et al. (2013) Cyclic GMP-AMP is an endogenous second messenger in innate

immune signaling by cytosolic DNA. Science 339(6121):826-830.

MIDTERM EXAM posted 10/10/2013, due FRIDAY 10/18/2013 no later than 5PM to group
instructors.

10/24/2013 Midterm grades, faculty meet with students by appointment to discuss exam

STUDENTS SHUFFLED INTO NEW GROUPS

CLASS 6 Epigenetics
10/29/2013 TUESDAY Student groups
10/31/2013 THURSDAY Faculty class

1. Jiang J, et al. (2013) Translating dosage compensation to trisomy 21. Nature 2013 Jul
17.
2. Foltz DR, et al. (2009) Centromere-specific assembly of CENP-A nucleosomes is
mediated by HJURP. Cell 137(3):472-484.

CLASS 7 Small RNAs

11/05/2013 TUESDAY Student groups
11/07/2013 THURSDAY Faculty and student groups

1. Lee RC, Feinbaum RL, & Ambros V (1993) The C. elegans heterochronic gene lin-4
encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843-854.

2. Barrangou R, et al. (2007) CRISPR provides acquired resistance against viruses in

prokaryotes. Science 315(5819):1709-1712.

CLASS 8
11/12/2013 TUESDAY Student groups
11/14/2013 THURSDAY Faculty and student groups

1. Ingolia NT, Lareau LF, & Weissman JS (2011) Ribosome profiling of mouse embryonic
stem cells reveals the complexity and dynamics of mammalian proteomes. Cell
147(4):789-802.

2. Kaida D, Berg MG, Younis I, Kasim M, Singh LN, Wan L, Dreyfuss G. (2010) U1 snRNP
protects pre-mRNAs from premature cleavage and polyadenylation. Nature
468(7324):664-8.

CLASS 9 Metabolism
11/19/2013 TUESDAY Student groups
11/21/2013 THURSDAY Faculty and student groups

1. Yang T, et al. (2002) Crucial step in cholesterol homeostasis: sterols promote binding of
SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell
110(4):489-500.

2. Chen XW, et al. (2013) SEC24A deficiency lowers plasma cholesterol through reduced
PCSK9 secretion. eLife 2:e00444.

11/28/13 No Class Thanksgiving vacation

CLASS 10 Complex Genetics

12/03/2013 TUESDAY Student groups
12/05/2013 THURSDAY Faculty and student groups
1. Deutschbauer AM, Davis RW (2005) Quantitative trait loci mapped to single-nucleotide
resolution in yeast. Nat Genet. 37(12):1333-40.

2. Ding L, et al. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by
whole-genome sequencing. Nature 481(7382):506-10.

FINAL EXAM posted 12/05/2013, due by 5 pm on FRIDAY 12/13/13, by email to both

instructors.

12/19/2013 3:00-6:00pm Meet with instructors to go over final exam grades, class
performance.
Harvard  Medical  School  
Biological  and  Biomedical  Sciences  
Fall  2013  
BCMP  200:  Molecular  Biology  
 
Course  Syllabus                        
 
Course  Description:    Molecular  Biology  is  a  course  organized  around  the  Central  Dogma  of  Biology  
with   presentations   covering   fundamental   aspects   of   DNA   and   RNA   structure,   their   function   and  
their  interactions  with  proteins.    The  course  opens  with  a  discussion  of  the  physical  and  chemical  
properties   that   drive   the   interactions   of   proteins   with   nucleic   acids.   This   is   used   as   a   basis   for  
understanding   the   material   presented   in   the   subsequent   five   modules,   which   cover   DNA  
replication,  DNA  repair,  gene  regulation,  transcription  and  translation.      

Course  Website:    http://isites.harvard.edu/k97563    

           Gradebook  available  at  online  at  www.learningboost.com    
 
Course  Details  &  Information                    
Lecture  Days  and  Times:   MWF  10:45  am  –  12:15  pm  
  Wednesday  September  4,  2013  –  Friday  December  6,  2013  
 
Meeting  Space:       Cannon  Room  (for  lectures)  
        Various  break-­‐out  rooms  for  section  
 
Course  Director:     Joe  Loparo,  Ph.D.  
 
Course  Lecturers:     Joe  Loparo,  Ph.D.     [email protected]  
        Johannes  Walter,  Ph.D.     [email protected]    
        Timur  Yusufzai,  Ph.D.     [email protected]    
        Stirling  Churchman,  Ph.D.                    [email protected]  
        Paul  Anderson,  M.D.,  Ph.D.   [email protected]    
 
Faculty  Section  Leaders:   Alan  D’Andrea,  M.D.       [email protected]    
Ralph  Scully,  Ph.D.       [email protected]    
Sun  Hur,  Ph.D.       [email protected]    
        Shobha  Vasudevan,  Ph.D.   [email protected]    
        Wesley  Wong,  Ph.D.     [email protected]    
        Note  that  all  course  lecturers  are  also  section  leaders  
 
Curriculum  Fellow:   Jason  Heustis,  Ph.D.     [email protected]    
 
Teaching  Assistants:   Himanish  Basu       [email protected]    
  Abbe  Clark       [email protected]    
  Mary  Gearing       [email protected]    
  Mitchell  Leibowitz     [email protected]    
  Katie  Richeson       [email protected]    
Recommended  Textbook:   Watson,  JD,  Baker,  TA,  et  al  (2008)    
Molecular  Biology  of  the  Gene,  6th  Edition    
Cold  Spring  Harbor  Laboratory  Press,  New  York    
 
This   is   a   comprehensive   background   textbook   and   it   is   highly  
recommended   that   you   buy   it   and   read   the   associated   pages   before  
each  lecture,  especially  if  your  background  is  rusty.  
 
Grading:       15%   Experimental  Design  Presentation  #1  
        20%   Experimental  Design  Presentation  #2  
        45%   Problem  Sets  –  6  problem  sets,  7.5%  each  
        15%   Quizzes  –  6  quizzes,  one  dropped,  3%  each  
        5%   Participation  
 
Policies  &  Clarifying  Information                  
Course  Objectives  
Through  completion  of  this  course,  students  gain  
1. a   basic   understanding   of   the   structure   and   function   of   DNA   and   RNA   and   the   cellular  
processes   of   DNA   replication,   DNA   repair,   gene   regulation,   transcription   and   translation,  
with  an  appreciation  for  the  big  open  questions  in  the  research  areas  around  these  topics  
2. exposure  to  techniques  used  in  contemporary  molecular  biology  and  biochemistry  research,  
and  an  appreciation  for  advantages  and  disadvantages  of  different  techniques  and  how  they  
have  been  used  to  create  the  current  knowledge  in  the  aforementioned  research  fields  
3. practice   in   experimental   design   and   proposal   presentation,   using   problems   addressing  
contemporary  research  questions  from  molecular  biology    
4. knowledge   of   resources   available   for   viewing   protein   structure,   and   build   skills   in  
visualizing  structures  
5. an  appreciation  for  the  quantitative  aspects  of  data  analysis  and  how  it  may  inform  research  
in  molecular  biology  and  biochemistry  
 
Prerequisites  
We   assume   a   solid   background   in   basic   molecular   biology/biochemistry.     This   is   NOT   an  
introductory   course,   so   if   you   have   no   previous   training   in   this   area,   the   course  may   be   too   difficult  
and   you   should   first   take   Biological   Sciences   52   at   Harvard   University.     We   try   to   cover   basic  
knowledge  quickly  and  then  move  into  current  topics  and  open  questions  in  each  area.    If  you  are  
unsure  of  whether  you  should  take  the  course,  talk  to  the  course  director.  
 
Lecture  and  Discussion  Section  Format  
Class  is  held  MWF  from  10:45  am  –  12:15  pm.    There  are  6  subject  area  modules  in  the  course  and  
each   module   will   consist   of   a   series   of   lectures,   an   in-­‐depth   research   seminar,   and   a   small   group  
discussion  section.    The  detailed  schedule  is  listed  below.    Lectures  and  seminars  will  take  place  in  
the   Cannon   Room   (HMS,   Building   C).     Discussion   sections   will   meet   in   various   rooms.       Please  
always  arrive  at  10:40  am  so  that  we  can  start  class  promptly  at  10:45  am.  

  2  
Lectures:   In   these   presentations,   basic   information   (that   would   be   covered   in   undergraduate  
courses)  will  be  covered  along  with  more  in-­‐depth  treatment  of  one  or  more  open  questions  in  the  
field.    Relevant  techniques  will  be  covered  in  detail.    Students  are  strongly  encouraged  to  read  the  
recommended  textbook  chapter  before  each  lecture.  

Research  Seminars:  Each  lecturer  will  give  a  research  seminar  based  on  work  performed  in  his/her  
laboratory  on  a  topic  related  to  the  module.    The  purpose  is  to  connect  the  lecture  material  to  real  
research.     Research   seminars   are   held   in   the   Cannon   Room   at   the   usual   time.     After   the   seminar,  
students   will   break   into   small   groups   of   3-­‐4   to   discuss   the   seminar   and   formulate   one   or   more  
questions  for  the  speaker.    Students  will  then  have  time  to  pose  these  questions  to  the  lecturer.  

Discussion   Sections:   For   each   module,   there   will   be   one   problem   set   question   and   three   (3)   open-­‐
ended  experimental  design  questions.    These  materials  will  be  posted  online  in  advance  of  section.    
The  solution  to  the  problem  set  question  is  due  at  the  beginning  of  section.    You  are  free  to  work  
with  your  peers  on  this,  but  you  must  each  submit  your  own  answer.    There  will  also  be  a  short  quiz  
at   the   beginning   of   section   (described   below).     You   should   come   to   section   having   reviewed   the  
lecture   materials,   completed   the   problem   set   questions,   and   having   read   through   and   considered  
the  open-­‐ended  experimental  design  questions.    One  student  will  be  assigned  to  present  a  solution  
to  each  question,  and  this  will  form  the  basis  of  a  discussion.  Sections  will  run  as  follows:  
• Return  of  Graded  Assignments  and  Quiz  (~15  minutes)  
Students  can  direct  questions  about  the  content  of  completed/graded  problem  sets  
to   the   lecturer   of   the   appropriate   module.     A   short   quiz   testing   key   concepts   from  
the  lectures  and  research  seminar  in  the  last  module  will  be  administered.      
• Open-­‐ended  experimental  design  questions  (~1  hour,  15  minutes)  
One   student   will   be   assigned   to   present   on   each   assigned   experimental   design  
question.     All   other   students   should   come  prepared  so  that  they  can  critique  these  
presentations  based  on  content  and  style.  
 
Note:   Videos   of   class   lectures   and   discussion   sections   are   not   made   available   online.     Your  
attendance  at  class  is  important.  
 
Course  Website  Access  
All   students   must   be   officially   registered   in   the   class   or   have   full   access   to   the   course   website.     This  
is   necessary   for   students   to   be   assigned   to   a   discussion   section   and   to   access   all   the   course  
materials.     If   you   are   not   officially   enrolled   in   the   course,   please   e-­‐mail   the   course   Curriculum  
Fellow  for  permission  to  attend  class  and  to  get  access  to  the  site.  
 
Please  note  that  grades  can  be  accessed  through  the  course  website.    You  will  be  redirected  to  an  
externally   hosted   web   gradebook.     If   you   note   any   inaccuracies   in   your   recorded   grades,   please  
contact  the  Curriculum  Fellow  Jason  Heustis.  
 
Additional  Classroom  Technology  
During  lectures,  students’  understanding  of  the  course  material  will  be  periodically  assessed  using  
embedded   Clicker   questions   (multiple   choice   questions   testing   recently   presented   material,  

  3  
assessing   knowledge   and   application).     Clickers   will   be   provided   at   lectures;   you   do   not   have   to  
purchase   a   Clicker   for   use   in   this   class.     Your   responses   are   also   anonymous   and   will   not   be   used   in  
anyway   to   assess   you   as   a   student.     However,   we   ask   that   you   make   an   earnest   attempt   in  
responding,  as  this  provides  feedback  to  the  lecturer    and  helps  guide  the  course  content.  
 
Grades  and  Assessments  
Experimental   Design   Presentations:     Students   will   be   assigned   to   present   twice   throughout   the  
semester   –   once   in   the   first   half   and   once   in   the   second   half   of   the   course.     These   dates   will   be  
posted   online   by   Friday   September   13,   2013   and   these   presentations   will   begin   in   Section   #1   on  
September   20,   2013.     If   you   have   conflicts   with   the   assigned   dates,   please   work   with   another  
student   from   your   section   (based   on   rosters   posted   online)   to   arrange   exchanging   dates.     Once   you  
have   found   someone   with   which   to   switch,   please   contact   the   course   Curriculum   Fellow   Jason  
Heustis  to  have  the  presentation  rosters  posted  online  updated.    Students  will  be  graded  based  on  
the  rubric  posted  online.    Each  student  will  have  25  minutes  for  their  presentation  and  should  be  
prepared  to  deliver  their  presentation  in  12  minutes  with  equal  additional  time  for  questions  from  
the   peers   in   each   section.     Students   should   be   prepared   to   answer   questions   either   during   their  
presentation  or  at  its  end.    This  is  a  strict  25-­‐minute  time  limit  to  ensure  section  ends  on  time.  
 
Problem   Sets:     Students   will   submit   completed   problem   sets   at   the   start   of   each   section.   Problem  
sets  may  consist  of  activities  that  allow  students  to  familiarize  themselves  with  relevant  software  
tools   (e.g.   PYMOL   for   use   in   visualizing   structures),   calculations   that   reinforce   quantitative  
considerations   associated   with   the   related   module,   or   techniques   related   to   the   associated  
experimental  design  questions.    Note:  Each  problem  set  turned  in  late  will  be  penalized  -­‐10%  for  
each   day   (including   weekends)   that   it   is   late.       For   example,   for   an   assignment   worth   40   points   that  
is  submitted  4  days  late,  16  points  will  be  subtracted  from  the  final  grade  irrespective  of  the  grade  
that  would  otherwise  be  awarded.  
 
Quizzes:   The   quiz   will   address   key   points   from   the   module,   including   lectures   and   research  
seminars.  
 
Note:     We   do   not   grade   on   a   curve!!     If   everyone   gets   above   a   certain   grade,   everyone   gets   an   A.     In  
other  words,  don’t  be  competitive  with  your  fellow  students.    Talk  to  each  other  about  the  material,  
study  together,  help  each  other  out.    The  course  will  be  more  fun  this  way,  and  you  will  get  more  
out  of  it.  
 
Academic  Integrity  

Please   be   reminded   that   all   work   submitted   for   credit   in   BCMP   200   should   reflect   individual  
scholarship  and  mastery  of  the  related  course  material.    Violations  of  academic  integrity  in  the  
course  are  considered  to  be  serious  offences  and  will  be  treated  very  seriously.    If  a  student  
submits  an  assignment  that  clearly  or  implicitly  violates  this  code  of  conduct,  a  grade  of  0  will  be  
awarded   for   the   entire   assignment   –   at   a   minimum!     While   we   encourage   teamwork   in   learning  
theory  and  concepts  we  expect  that  all  students  have  individually  mastered  the  material.    To  that  
end,  we  recommended  the  following  actions  when  approaching  assignments:  

  4  
For  experimental  design  questions,  we  encourage  presenters  to  talk  to  other  students  in  the  class  
(including   other   presenters)   when   developing   thoughts   on   the   problem   being   posed   or   the  
approach   to   solving   such   problems.     However,   it   is   not   acceptable   for   two   or   more   presenters   to  
work  together  to  develop  a  single  response  regardless  of  whether  they  are  in  the  same  section  or  
not.      

For   problem   sets,   we   encourage   students   to   work   together   in   developing   strategies   to   answering  
problems  and  in  sharing  ideas.    However,   the  answers  documented  on  your   individually-­‐submitted  
problem   sets,   should   be   in   each   student’s   own   wording   and   each   student   should   be   able   to  
understand   and   explain   the   problem   and   the   proposed   solution.     In   short,   do   not   copy   an   answer  
directly  from  your  peer!  

For   a   complete   description   of   the   Harvard   policy   on   Academic   Integrity,   you   can   visit  
http://www.gsas.harvard.edu/handbook/regulations_and_standards_of_conduct.php.    

 
Special  Support  and  Services  
Students  with  Disabilities:    Be  assured  that  services  for  persons  with  health  conditions  or  disabilities  
are   available   to   all   Harvard   students   who   need   them,   by   way   of   the   Accessible   Education   Office  
(www.aeo.fas.harvard.edu).     With   information   from   you,   along   with   proper   confidential   clinical  
documentation,   they   are   able   to   plan   with   you   to   provide   reasonable   accommodation   of   course  
materials,   classrooms   and   other   aspects   of   student   life,   as   appropriate.     For   more   information,  
please  contact  [email protected]  or  call  617-­‐496-­‐8707.  
 
Additional  Help  &  Tutoring:  Questions  are  always  welcome  during  and  after  the  lectures  (don’t  be  
shy!!).    However,  of  you  need  one-­‐on-­‐one  help,  get  in  touch  with  your  section  TAs  or  the  relevant  
faculty  member.    If  you  need  extensive  help,  there  is  also  a  tutoring  program  run  by  the  BBS  office.    
This  program  is  OPEN  TO  ALL  DMS  students,  even  if  they  are  not  BBS  students.  
 
 
Course  Schedule                            
Classes   will   be   held   on   Friday   October   18,   2013,   during   the   Cell   Biology   Retreat,   which   occurs   from  
Thursday   October   16,   2013   –   Friday   October   18,   2103.     A   video   of   this   lecture   will   be   made  
available  online.  
 
No  classes  will  be  held  on  Wednesday,  October  23rd  since  the  BCMP  Retreat  occurs  from  Tuesday  
October  22,  2013  –  Thursday  October  24,  2013.      
 
MWF   classes   are   also   cancelled   for   Columbus   Day   (Monday   October   14,   2013),   Veterans   Day  
(Monday  November  11,  2013)  and  for  Thanksgiving  Break  (Wednesday  November  27,  2013,  Friday  
November  29,  2013,  and  Monday  December  2,  2013).  
 
A   full   schedule   of   class   meetings,   topics   covered   and   the   associated   reading   are   presented   in   the  
following  table.  
 

  5  
  
Module/Lecturer   Date    &  Day   Topic   Associated  Reading  
(Chapters)  
Module  1   09/04      W   Course  Introduction    
DNA-­‐Protein   Introduction  to  Protein  Structure  
Interactions   09/06      F   Thermodynamics  of  Protein  Folding   2  –  5  
LOPARO   09/09      M   DNA  Structure  and  Topology   6  
09/11      W   Protein-­‐DNA  Interactions  I:  Structural   16  
Considerations  in  the  Lambda  Repressor  
09/13      F   Protein-­‐DNA  Interactions  II:  Kinetic  and    
Thermodynamic  Considerations  in  the  
Lambda  Repressor  
09/16      M   Chromosome  Structure   7  
09/18      W   Research  Seminar    
09/20      F   SECTION  #1    
Module  2   09/23      M   Origins  of  Replication,  DNA  Helicases   8  
DNA  Replication   09/25      W   DNA  Polymerases,  Clamps    
WALTER   09/27      F   Research  Seminar    
09/30      M   SECTION  #2    
Module  3   10/02      W   Ribonucleotide  Excision  Repair  (RER),   9  and  10  
DNA  Repair   Mismatch  Repair  (MMR)  
WALTER   10/04      F   Base  Excision  Repair  (BER)    
Nucleotide  Excision  Repair  (NER)  
10/07      M   Homologous  Recombination  (HR)    
Non-­‐Homologous  End-­‐Joining  (NHEJ)  
10/09      W   Research  Seminar    
10/11      F   SECTION  #3    
10/14      M   NO  CLASS  –  Columbus  Day  
Module  4   10/16      W   Histones  and  Histone  Code   7  
Chromatin   10/18      F   Transcription;  Types  of  RNA;  Sequencing   21  
Structure  and  Gene   N.B.  Class  Videotaped  for  Cell  Biology  
Regulation   Retreat  
YUSUFZAI   10/21      M   Transcription  Factors;  Gene  Regulation   12,  16  and  17  
10/23      W   NO  CLASS  –BCMP  Retreat    
10/25      F   RNA  Polymerase  II    
10/28      M   Transcription  Initiation    
10/30      W   Research  Seminar    
11/01      F   SECTION  #4    
Module  5   11/04      M   Transcription  Elongation    
Transcription   11/06      W   Transcription  Termination    
CHURCHMAN   11/08      F   mRNA  Processing   13  
11/11      M   NO  CLASS  –  Veterans  Day  
11/13      W   mRNA  Transport    
11/15      F   Research  Seminar    
11/18      M   SECTION  #5    
Module  6   11/20      W   Prokaryotic  Translation   14  and  15  
Translation   11/22      F   Eukaryotic  Translation    
ANDERSON   11/25      M   Translation  &  Repression   18  
11/27      W   NO  CLASS  –  Thanksgiving  Break    
11/29      F   NO  CLASS  –  Thanksgiving  Break    
12/02      M   NO  CLASS    
12/04      W   SECTION  #6    
12/06      F   Research  Seminar    

  6  
 HST 140/ BCMP 218 – Molecular Medicine
Fall 2013, Tuesdays 1-3 PM
Location (see schedule): HMS (MEC 227) or MIT (E25-117)

Faculty: Irving London, [email protected]

Assistant: Ken Pierce, 6-7-258-7656, [email protected]

George Q. Daley, [email protected]

Assistant: Kathryn Entner, 617-919-2015, [email protected]

David Cohen, [email protected]

Assistant: James Macdiarmid, 617-525-5092, [email protected]

TA: Daisy Robinton, [email protected]

This course introduces students to a variety of topics in molecular medicine. The course is
conducted as a seminar to study various human diseases and the underlying molecular, genetic
or biochemical basis for the pathogenesis and pathophysiology of the clinical disorders.
Lectures are presented by faculty experts engaged in current research in these fields. Seminars
are conducted by the students, with tutorial and supervision by faculty.

Requirements: Attendance is mandatory and any absences must be excused in advance by

one of the course directors. Participation is required in all scheduled sessions, given the
interactive nature of the course. All students will give two 20-minute presentations on a research
paper selected by the lecturers.

Credits: Harvard units: 2 (P) / MIT units: 2-0-4 [P/D/F] (H-level credit). Grading is pass/fail
unless your program requires a letter grade.

Website: http://mycourses.med.harvard.edu (please contact TA if you do not have access)

09/10/2013 – Gleevec and the Triumph of Target-Directed Chemotherapy

Speaker – George Daley; Model student presentation: Daisy Robinton
Location – MEC 227
**Please come prepared having read the following articles for the first class meeting**

Review: Brian J. Druker, Translation of the Philadelphia chromosome into therapy for CML.
Blood 112: 4808 – 4817 (2008).

Commentary: Dolgin E, As leukemia options grow, drugs jockey to be first-line therapeutics.

Nature Medicine 19(1):7 (2013).

Readings:
1. Cortes JE et al. Ponatinib in refractory Philadelphia chromosome-positive leukemias.
N Engl J Med, 29;367(22):2075-88 (2012).
2. Notta F, Mullighan CG, Wang J, Poeppl A, Doulatov S, Philips LA, Ma J, Minden, MD,
Downing JR, Dick JE. Evolution of BCR-ABL1 lymphoblastic leukaemia-initiating cells.
Nature, 469: 362-367 (2011).

09/17/2013 – Sex: Cells, Chromosomes, Development and Disorders

  1  
Speaker – David Page
Location – MIT E25-117

Review: Bluma J Lesch and David C Page. Genetics of germ cell development. Nature
Reviews Genetics 13: 781-94 (2012).

Readings:
1. Dokshin GA, Baltus AE, Eppig JJ, Page DC. Oocyte differentiation is genetically
dissociable from meiosis in mice. Nature Genetics (2013). doi:10.1038/ng.2672
2. Lange J, Skaletsky H, van Daalen S KM, Embry, SL, Korver CM, Brown LG, Oates
RD, Silber S, Repping S, Page DC. Isodicentric Y chromosomes and sex disorders as
byproducts of homologous recombination that maintains palindromes. Cell 138: 855-
69 (2009).

09/24/2013 – Protein Homeostasis in Health and Disease

Speaker – Susan Lindquist
Location – MIT E25-117

Review: Lindquist SL and Kelly JW. Chemical and biological approaches for adapting
proteostasis to ameliorate protein misfolding and aggregation diseases: progress and
prognosis. Cold Spring Harb Perspect Biol (2011).

Readings:
1. Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B,
Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist
S. Tight coordination of protein translation and HSF1 activation supports the anabolic
malignant state. Science 341(6143):1238303 (2013).
2. Taipale M, Krykbaeva I, Koeva M, Kayatekin C, Westover KD, Karras GI, Lindquist S.
Quantitative analysis of Hsp90::client interactions reveals principles of substrate
recognition. Cell 150(5):987-1001. PMID: 22939624 (2012).

10/01/2013 – Drug Delivery and Targeting

Speaker – Robert Langer
Location – E25-117

Review: Robert Langer. Drug Delivery and Targeting. Nature 392: 5-10 (1998).

Readings:
1. R Langer & J Folkman. Polymers for the Sustained Release of Proteins and Other
Macromolecules. Nature 263: 797-800 (1976).
2. Rosen HB, Chang J, Wnek GE, Linhardt RJ, Langer R. Bioerodible Polyanhydrides for
Controlled Drug Delivery. Biomaterials 4: 131-133 (1983).

10/08/2013 – Defining Pathways that Regulate Stem Cell Self-Renewal and Migration
Speaker – Len Zon
Location – MEC 227

Review: Orkin SH and Zon LI. SnapShot: hematopoiesis. Cell. 132(4):712 (2008).

  2  
Readings:
1. North TE, Goessling W, Walkley CR, Lengerke C, Kopani KR, Lord AM, Weber GJ,
Bowman TV, Jang IH, Grosser T, Fitzgerald GA, Daley GQ, Orkin SH, Zon LI.
Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature
447(7147):1007-11 (2007).
2. Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, DiBiase A, Martin CS, Cech
JN, Sessa AK, Leblanc JL, Li P, Durand EM, Mosimann C, Heffner GC, Daley GQ,
Paulson RF, Young RA, Zon LI. Lineage regulators direct BMP and Wnt pathways to
cell-specific programs during differentiation and regeneration. Cell 147 (3):577-89
(2011).

10/15/2013 – Title TBA

Speaker – Barbara Kahn
Location –MEC 227

Review: TBA

Readings:
1. TBA
2. TBA

10/22/2013 – Personal Genomes and Guide RNA Genome Therapeutics

Speaker – George Church
Location – MEC 227

Review: Mali P, Esvelt KM, Church GM. A versatile tool for engineering biology: Cas9 as the
Unifactor. Nature Methods (submitted).

Readings:
1. Guye P, Busskamp V, Lewis NE, Sanjana NE, Li Y, Zhang F, Ron Weiss R, Church
GM. Early transcriptional changes in Neurogenin-induced human stem cell derived
neurons. Neuron (submitted)
2. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM.
RNA-guided human genome engineering via Cas9. Science 339:823-6 (2013).

10/29/2013 – Defining the mutational vulnerabilities of HIV for rational design of vaccines
Speaker – Arup K. Chakraborty
Location – MIT E25-117

Review: Virgin, H, Walker, B.D. Immunology and the elusive AIDS vaccine, Nature 464, 224-
231 (11 March 2010).

Readings:
1. V. Dahirel et al. Coordinate linkage of HIV evolution reveals regions of immunological
vulnerability. Proc Nat Acad Sci 108, 11530-11535 (2011)
2. Ferguson et al., Translating HIV Sequences into Quantitative Fitness Landscapes
Predicts Viral Vulnerabilities for Rational Immunogen Design. Immunity Volume 38,

  3  
 Issue 3, 606-617 (2013).

11/05/2013 – The Biology of Non-Coding RNAs

Speaker – Phil Sharp
Location – MIT E25-117

Review: Gurtan AM, Sharp PA. The role of miRNAs in regulating gene expression networks. J
Mol Biol doi: 10.1016/j.jmn.2013.03.007 (2013).

Readings:
1. Heravi-Moussavi A, Anglesio MS, Cheng SW, Senz J, Yang W, Prentice L, Fejes AP,
Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan AN, Maines-Bandiera S,
Salamanca C, Pasini B, Clarke BA, Lee AF, Lee CH, Zhao C, Young RH, Aparicio SA,
Sorensen PH, Woo MM, Boyd N, Jones SJ, Hirst M, Marra MA, Gilks B, Shah SP,
Foulkes WD, Morin GB, Huntsman DG. Recurrent somatic DICER1 mutations in
nonepithelial ovarian cancers. N Engl J Med 366(3): 234-42 (2011).
2. Gurtan AM et al. Let-7 represses Nr6a1 and a mid-gestation developmental program
in adult fibroblasts. Genes Dev 15;27(8): 941-54 (2013).

11/12/2013 – Induced Pluripotent Stem Cells in Disease and Therapy

Speaker – George Q. Daley
Location –MEC 227

Review: Daisy A. Robinton & George Q. Daley. The promise of induced pluripotent stem cells in
research and therapy. Nature 481: 295-305 (2012).

Readings:
1. Hanna J et al. Treatment of Sickle Cell Anemia Mouse Model with iPS Cells
Generated from Autologous Skin. Science 318: 1920-23 (2007).
2. Tulpule A et al. Pluripotent Stem Cell Models of Shwachman-Diamond Syndrome
Reveal a Common Mechanism for Pancreatic and Hematopoietic Dysfunction. Cell
Stem Cell 12, 1-10 (2013).

11/19/2013 – Programmed Cell Death in Development and Disease

Speaker – Bob Horvitz
Location – E25-117

Reviews: H. Robert Horvitz. Worms, Life and Death (Nobel Lecture). Chem Bio Chem 4: 697-
711 (2003).

Readings:
1. MO Hengartner & HR Horvitz. C. elegans Cell Survival Gene ced-9 Encodes a
Functional Homolog of the Mammalian Proto-Oncogene bcl-2. Cell 76: 665-676
(1994).
2. Tse C, Shoemaker AR, Adickes J, Anderson MG, Chen J, Jin S, Johnson EF, Marsh
KC, Mitten JM, Nimmer P, Roberts L, Tahir SK, Xiao Y, Yang X, Zhang H, Fesik S,
Rosenberg SH, Elmore SW. ABT-263: A Potent and Orally Bioavailable Bcl-2 Family

  4  
 Inhibitor. Cancer Res 68: 3421-3428 (2008).

11/26/2013 – von Hippel-Lindau Disease as a Model for Studying Oxygen Sensing and
Cancer Metabolism
Speaker – Bill Kaelin
Location – MEC 227

Review: Kaelin WG, Jr. & Ratcliffe PJ (2008) Oxygen sensing by metazoans: the central role of
the HIF hydroxylase pathway. Mol Cell 30(4):393-402.

Readings:
1. Ivan M, Kondo K, Yang H, Kim W, Valiando J, Ohh M, Salic A, Asara J, Lane W, &
Kaelin WG, Jr. (2001) HIFalpha targeted for VHL-mediated destruction by proline
hydroxylation: implications for O2 sensing. Science 292:464-468.
2. Losman JA, Looper RE, Koivunen P, Lee S, Schneider RK, McMahon C, Cowley GS,
Root DE, Ebert BL, & Kaelin WG, Jr. (2013) (R)-2-hydroxyglutarate is sufficient to
promote leukemogenesis and its effects are reversible. Science 339(6127):1621-
1625.

12/3/2013 – Congenital Heart Disease: Many Genes Lead to a Broken Heart

Speaker – Christine Seidman
Location – MEC 227

Review: Fahed AC, Gelb BD, Seidman JG, Seidman CE. Genetics of congenital heart disease:
the glass half empty. Circulation Research 112(4):707-20 (2013).

Readings:
1. Zaidi S et al. De novo mutations in histone-modifying genes in congenital heart
disease. Nature 498(7453):220-3 (2013).
2. Cordell et al. Genome-wide association study of multiple congenital heart disease
phenotypes identifies a susceptibility locus for atrial septal defect at chromosome
4p16. Nature Genetics 45(7):822-4 (2013).

12/10/2013 – Human Genetic Variation and Disease

Speaker – David Altshuler
Location – MIT E25-117

**Readings may change**

**Review: Altshuler D, Daly MJ, Lander E. Genetic Mapping in Human Disease. Science
322(5903): 881-888 (2008).

**Readings:
1. Voight et al. Plasma HDL cholesterol and risk of myocardial infarction: a mendelian
randomization study. The Lancet 380(9841): 572-80 (2012).
2. Jonsson T et al. A mutation in APP protects against Alzheimer’s disease and age-related
cognitive decline. Nature 488: 96-99 (2012).

  5  
 MIT Principles and Practice of Drug Development 
Fall 2013 
7.547J, 10.547J, 15.136J, ESD.691J, HST.920J, BCMP 230 
 

Building 4, Room 163 
 

Thursdays, 3:00 – 6:00 pm 
 
Instructors: 
Thomas J. Allen, Ph.D.  NE25‐758  617‐253‐6651  [email protected] 
Charles L. Cooney, Ph.D.  56‐469B  617‐253‐3108  [email protected] 
Stan N. Finkelstein, M.D.  E40‐251  617‐253‐8014  [email protected] 
G.K. Raju, Ph.D.  E19‐611  617‐258‐8583  [email protected] 
Anthony J. Sinskey, Sc.D.  68‐370A  617‐253‐6721  [email protected] 
 
Teaching Assistant: 
Abby Horn      [email protected] 
 
 
This course serves as a description and critical assessment of the major issues and stages of 
developing a pharmaceutical or biopharmaceutical. Topics covered include drug discovery, 
preclinical development, clinical investigation, manufacturing and regulatory issues considered 
for small and large molecules, and economic and financial considerations of the drug 
development process. A multidisciplinary perspective is provided by the faculty, who represent 
clinical, life, and management sciences. Various industry guests also participate. 
 
CLASS SCHEDULE
 
 
September 5    Introduction (Faculty) 
        From Discovery to Market: An Integrated View 
      Charles L. Cooney, Ph.D. 
 
 
September 12   Introduction: The Pharmaceutical Industry and the Drug Development 
Process; Brief economic history of the pharmaceutical industry 
      Anthony J. Sinskey, Sc.D. 
      Stan N. Finkelstein, M.D     
 
September 19   Basic Science  
      Anthony J. Sinskey, Sc.D. 

MIT Principles and Practice of Drug Development – Fall 2010 1

 MIT Principles and Practice of Drug Development 
(continued) 
 
 
September 26   Business of Biopharmaceuticals 
      Guest:  Robert Mulroy, M.P.P.M., Director, President & CEO,  
        Merrimack Pharmaceuticals 
 
      Guest:  Sumit Khedekar, Director, Global Healthcare Group,  
        Bank of America, Merrill Lynch 
 
October 3    Accelerating Cancer Cures:  A Global Frontier 
      Guest:  Jason Sager, M.D., Head of Early Development Oncology Portfolio 
        Sanofi 
 
October 10    Clinical Drug Development  
      Guest:  Clet Niyikiza, Ph.D., Executive Vice President 
        Merrimack Pharmaceuticals 
 
October 17    Drug Delivery Systems 
      Guest:  Portuguese faculty (Luís Almeida, Ph.D., João Nuno Moreira, Ph.D., Sérgio 
Simões, Ph.D.  University of Coimbra, Portugal) 
 
 
October 24    Regulation, Reimbursement 
      Stan N. Finkelstein, M.D. 
 
 
October 31    Manufacturing I 
      Charles L. Cooney, Ph.D.  
         G.K. Raju, Ph.D. 
 
 
November 7    Emerging Pharmaceutical Science and Technology 
Guest:  Lee L. Rubin, Ph.D., Professor 
        Regenerative  Medicine, Harvard 
 
      Guest:  Brock Reeve, MPhil, MBA, Executive Director 
Harvard Stem Cell Institute 
 
 
November 14    Manufacturing II 
Charles L. Cooney, Ph.D.  
         G.K. Raju, Ph.D. 
 
      Guest:  Ajaz Hussain, Ph.D., Principal 
Insight, Advice & Solutions, LLC 
 
 
MIT Principles and Practice of Drug Development – Fall 2010 2
 MIT Principles and Practice of Drug Development 
(continued) 
 
November 21    Manufacturing III 
Charles L. Cooney, Ph.D. 
G.K. Raju, Ph.D. 
 
 
November 28    Thanksgiving Day – No Class 
 
 
December 5  Student Presentations  

MIT Principles and Practice of Drug Development – Fall 2010 3

Cell Biology 226. Concepts in Development, Self-Renewal, and Repair

Catalog Number: 8747

Enrollment: Limited to 12.

Half course (fall term). Fridays, 2–5pm.

Course directors: Iain Drummond and Andrew Brack; Lecturers: David Langenau,
Hanno Hock, Nabeel Bardeesy, Jay Rajagopal, Amar Sahay.

Overview: This course explores developmental mechanisms that persist throughout the
life cycle, examining pluripotency and cell fate restriction in embryos and adult tissues.
The course is divided into 3 Units. Unit 1 (4 Fridays) will examine general developmental
mechanisms that are essential for both tissue formation and self-renewal. Special
emphasis will be given to lineage restriction and cell fate determination in embryos. Unit
2 (4 Fridays) will analyze the renewal and repair of specific adult tissues. We will
emphasize in vivo approaches to understanding how tissues renew or repair themselves
following normal wear or wounding. Unit 3 (4 Fridays) will explore new frontiers of
regenerative biology. We will cover regenerative medicine, tissue engineering, and
regeneration in emerging model organisms. In the final class, we will discuss general
themes from the course content.

Structure of the course: The first class will include an organizational meeting. Each
subsequent class has two parts, a lecture and a discussion of an original research
paper. The lectures are designed to introduce significant topics in development, tissue
repair and self-renewal. For each class, all students are required to read a review article
and original research paper. A student will introduce the paper and lead the discussion
to build upon the previous week’s lecture. Papers will highlight major questions and key
methodologies. At the end of the discussion, the class will generate a list of potential
research directions and questions. Leaders in the fields of developmental genetics and
stem cell biology will lecture and facilitate the discussions. There are no exams.
Students will be evaluated by their preparation and participation in each class (40%),
presentation of discussion paper (30%), and one written assignment (30%). The written
assignment is a five-page mini-proposal that addresses an outstanding question from
the class topics. The proposal must include the basic elements of any research
proposal: introduce the question, justify its significance, develop a hypothesis to answer
the question, and then propose two experiments to test that hypothesis, using
appropriate methodologies.

Prerequisite: Upper division Cell Biology, Genetics, or Developmental Biology.

First Class and Organizational Meeting: Thursday 9/5, 2-3:30 PM, TMEC L-007.
Students present at this class will have priority for enrollment. If needed, we will hold a
lottery to select the 12 students enrolled in the course. If a student cannot attend, she/he
must email Iain Drummond by 5PM Tues. 9/3/2013. ([email protected]). All
Subsequent classes will be at MGH.

MGH course shuttle bus leaves Vanderbilt Hall at 1:30 PM

 DATE START FINISH Lecture Lecturer Room
04-Sep-13 W 9:00 AM 10:20 AM Lecture 1 Winston Cannon
06-Sep-13 F 9:00 AM 10:20 AM Lecture 2 Winston Cannon
09-Sep-13 M 9:00 AM 10:20 AM Lecture 3 Winston Cannon
13-Sep-13 F 9:00 AM 10:20 AM Lecture 4 Winston Cannon
16-Sep-13 M 9:00 AM 10:20 AM Lecture 5 Winston Cannon
18-Sep-13 W 9:00 AM 10:20 AM Lecture 6 Winston Cannon
23-Sep-13 M 9:00 AM 10:20 AM Lecture 7 Winston Cannon
25-Sep-13 W 9:00 AM 10:20 AM Computational Workshop Cannon
27-Sep-13 F 9:00 AM 10:20 AM Lecture 8 Bernhardt Cannon
30-Sep-13 M 9:00 AM 10:20 AM Lecture 9 Bernhardt Cannon
02-Oct-13 W 9:00 AM 10:20 AM Lecture 10 Bernhardt Cannon
07-Oct-13 M 9:00 AM 10:20 AM Lecture 11 Bernhardt Cannon
10-Oct-13 Th 9:00 AM 10:20 AM Midterm Exam Cannon/TMEC
11-Oct-13 F 9:00 AM 10:20 AM Midterm Exam due Cannon/TMEC
16-Oct-13 W 9:00 AM 10:20 AM Lecture 12 Kuroda Cannon
18-Oct-13 F 9:00 AM 10:20 AM Lecture 13 Kuroda Cannon
21-Oct-13 M 9:00 AM 10:20 AM Lecture 14 Kuroda Cannon
25-Oct-13 F 9:00 AM 10:20 AM Lecture 15 Kuroda Cannon
30-Oct-13 W 9:00 AM 10:20 AM Lecture 16 Heiman Cannon
01-Nov-13 F 9:00 AM 10:20 AM Lecture 17 Heiman Cannon
04-Nov-13 M 9:00 AM 10:20 AM Lecture 18 Heiman Cannon
06-Nov-13 W 9:00 AM 10:20 AM Lecture 19 Heiman Cannon
13-Nov-13 W 9:00 AM 10:20 AM Lecture 20 McCarroll Cannon
15-Nov-13 F 9:00 AM 10:20 AM Lecture 21 McCarroll Cannon
18-Nov-13 M 9:00 AM 10:20 AM Lecture 22 McCarroll Cannon
20-Nov-13 W 9:00 AM 10:20 AM Lecture 23 McCarroll Cannon
25-Nov-13 M 9:00 AM 10:20 AM Lecture 24 McCarroll Cannon
02-Dec-13 M 9:00 AM 10:20 AM Lecture 25 McCarroll Cannon
04-Dec-13 W 9:00 AM 10:20 AM Lecture 26 Winston Cannon
06-Dec-13 F 9:00 AM 10:20 AM Lecture 27 Winston Cannon
11-Dec-13 W 9:00 AM 10:20 AM Final exam Cannon/TMEC
12-Dec-13 Th 9:00 AM 10:20 AM Final exam due Cannon/TMEC

Supplemental Lectures
18-Sep-13 W 12:30 PM 1:30 PM Supplemental Lecture 1 Brault Cannon/TMEC
04-Oct-13 F 12:30 PM 1:30 PM Supplemental Lecture 2 Brault Cannon/TMEC
28-Oct-13 M 12:30 PM 1:30 PM Supplemental Lecture 3 Brault Cannon/TMEC

11 Discussion rooms (7-9 people each)

11-Sep-13 W 9:00 AM 10:20 AM Discussion Section 1 TAs Break Out Rooms
20-Sep-13 F 9:00 AM 10:20 AM Discussion Section 2 TAs Break Out Rooms
04-Oct-13 F 9:00 AM 10:20 AM Discussion Section 3 TAs Break Out Rooms
09-Oct-13 W 9:00 AM 10:20 AM Discussion Section 4 TAs Break Out Rooms
28-Oct-13 M 9:00 AM 10:20 AM Discussion Section 5 TAs Break Out Rooms
08-Nov-13 F 9:00 AM 10:20 AM Discussion Section 6 TAs Break Out Rooms
22-Nov-13 F 9:00 AM 10:20 AM Discussion Section 7 TAs Break Out Rooms
09-Dec-13 M 9:00 AM 10:20 AM Discussion Section 8 TAs Break Out Rooms
NO ROOMS NEEDED:
02-Sep-13 M Labor Day: No Classes
14-Oct-13 M Columbus Day: No Classes
23-Oct-13 W BCMP Retreat: No Classes
11-Nov-13 M Veterans Day: No Class
27-Nov-13 W Thanksgiving Break: No Class
29-Nov-13 F Thanksgiving Break: No Class
TIMES AND LOCATIONS:
Lectures: Cannon Room in Building C on the indicated days from 9:00 AM to 10:20 AM
Discussion Sections: Sections are from 9:00 AM to 10:20 AM.
Go to Section Assignments for your assigned TA and room location.
Supplementary Lectures: September 18 (TBA), October 4 (TBA) and October 23 (TBA) from 12:30-1:30 PM.

GENETICS 201: 2013 SCHEDULE

DATE START FINISH LECTURE

09/02/13 M Labor Day: No Classes
09/04/13 W 9:00 AM 10:20 AM Lecture 1: What we learned from Mendel – Winston
09/06/13 F 9:00 AM 10:20 AM Lecture 2: Introduction to yeast genetics; complementation
analysis – Winston
Problem Set 1 Distributed
09/09/13 M 9:00 AM 10:20 AM Lecture 3: Linkage and tetrad analysis in yeast – Winston
09/11/13 W 9:00 AM 10:20 AM Discussion Section 1
09/13/13 F 9:00 AM 10:20 AM Lecture 4: Molecular and genomic studies in yeast – Winston
09/16/13 M 9:00 AM 10:20 AM Lecture 5: Suppressor analysis in yeast – Winston
09/18/13 W 9:00 AM 10:20 AM Lecture 6: Non-Mendelian inheritance in yeast – Winston
09/18/13 W 12:30 PM 1:30 PM Supplemental Lecture 1 – Brault
09/20/13 F 9:00 AM 10:20 AM Discussion Session 2
09/23/13 M 9:00 AM 10:20 AM Lecture 7: Molecular mechanisms of homologous recombination:
genetic analysis – Winston
Problem Set 1 Due
Problem Set 2 Distributed
09/25/13 W 9:00 AM 10:20 AM Computational Workshop
09/27/13 F 9:00 AM 10:20 AM Lecture 8: Introduction to Bacterial genetics I – Bernhardt
09/30/13 M 9:00 AM 10:20 AM Lecture 9: Genetic selections and screens for gene discovery –
Bernhardt
10/02/13 W 9:00 AM 10:20 AM Lecture 10: Chemical genetics and antibiotics – Bernhardt
10/04/13 F 9:00 AM 10:20 AM Discussion Section 3
10/04/13 F 12:30 PM 1:30 PM Supplemental Lecture 2 – Brault
10/07/13 M 9:00 AM 10:20 AM Lecture 11: Genetics of bacterial pathogenesis – Bernhardt
Problem Set 2 Due
10/09/13 W 9:00 AM 10:20 AM Section 4
10/10/13 Th 9:00 AM Midterm handed out
10/11/13 F 9:00 AM Midterm handed in
10/14/13 M Columbus Day: No Classes
10/16/13 W 9:00 AM 10:20 AM Lecture 12: Introduction to Drosophila: genotypes, maps, and
balancer chromosomes – Kuroda
Problem Set 3A Distributed
10/18/13 F 9:00 AM 10:20 AM Lecture 13: Mapping mutants in Drosophila: meiotic and physical
mapping, gene isolation and transformation – Kuroda
10/21/13 M 9:00 AM 10:20 AM Lecture 14: Classical genetic screens and pathway analysis in flies
– Kuroda
10/23/13 W BCMP Retreat: No Classes
10/25/13 F 9:00 AM 10:20 AM Lecture 15: Modifier screens: enhancers, suppressors, and mosaic
analysis in flies – Kuroda
10/28/13 M 9:00 AM 10:20 AM Discussion Section 5
10/28/13 M 12:30 PM 1:30 PM Supplemental Lecture 3– Brault
10/30/13 W 9:00 AM 10:20 AM Lecture 16: How to do a C. elegans screen – Heiman
Problem Set 3A Due
Problem Set 3B Distributed
11/01/13 F 9:00 AM 10:20 AM Lecture 17: How to study developmental mechanisms using C.
elegans – Heiman
11/04/13 M 9:00 AM 10:20 AM Lecture 18: C. elegans methods workshop – Heiman
11/06/13 W 9:00 AM 10:20 AM Lecture 19: How to study the neural basis of behavior using C.
elegans – Heiman
11/08/13 F 9:00 AM 10:20 AM Discussion Section 6
11/11/13 M Veterans Day: No Class
11/13/13 W 9:00 AM 10:20 AM Lecture 20: Of mice and men – mammals and mammalian
genomes – McCarroll
Problem Set 3B Due
Problem Set 4 Distributed
11/15/13 F 9:00 AM 10:20 AM Lecture 21: Experimental manipulation of mammalian genomes –
McCarroll
11/18/13 M 9:00 AM 10:20 AM Lecture 22: Analysis of Mendelian phenotypes and high-
penetrance genome variation – McCarroll
11/20/13 W 9:00 AM 10:20 AM Lecture 23: The reservoir of segregating polymorphism in freely
living populations – McCarroll
11/22/13 F 9:00 AM 10:20 AM Discussion Section 7
11/25/13 M 9:00 AM 10:20 AM Lecture 24: Analysis of complex traits and heritability – McCarroll
11/27/13 W Thanksgiving Break: No Class
11/29/13 F Thanksgiving Break: No Class
12/02/13 M 9:00 AM 10:20 AM Lecture 25: Mapping complex genetic traits in humans –
McCarroll
12/04/13 W 9:00 AM 10:20 AM Lecture 26: Epigenetics – Winston
12/06/13 F 9:00 AM 10:20 AM Lecture 27: Epigenetics – Winston
Problem Set 4 Due
12/09/13 M 9:00 AM 10:20 AM Discussion Section 8
12/11/13 W 9:00 AM Final exam handed out
12/12/13 Th 9:00 AM Final exam due
TUMOR PATHOPHYSIOLOGY AND TRANSPORT PHENOMENA:
A SYSTEMS BIOLOGY APPROACH
LECTURE SCHEDULE
Human Biology and Translational Medicine – HBTM (Cat. # 5934)
(HST 525J / HBTM 201 / HMS PA 712.0)
September 9 – December 9, 2013
5-7 PM (MONDAYS)
Room: MIT : To be determined

DATE LECTURE TOPIC LECTURER

(2012) (2013)

September Tumor Microenvironment

9 I: R.K. Jain
Vascular Transport and (HMS/MGH)
the
Normalization Hypothesis

September Tumor Microenvironment

16 II: R.K. Jain
Interstitial and Lymphatic (HMS/MGH)
Transport

September -OK- R. Langer

23

September Cancer drug development T. Batchelor

30 from mice to humans – (HMS/MGH)
case studies of
bevacizumab and cediranib

October Quantitative Measures of

7 Tumor Vascular James W. Baish,
Architecture: Implications PhD
for Diagnosis, Treatment (Bucknell/Steele
and Prognosis Lab)

Oct. 14 HOLIDAY (Columbus No class

Day)

Invasion, Metastasis and

October Cancer Cells R. Weinberg
21 (Cancer Cell Biology and (MIT)
Tumorigenesis)

October Proteomics, Proteases, and M. Moses

28 Metastasis (HMS/CH)
 November Role of Bone Marrow-
4 derived Cells in Cancer G. Dan Duda
Progression and Treatment (HMS/MGH)
& &
Mathematical Modeling of Lance Munn
Tumor Blood Vessel (HMS/MGH)
Dynamics

November 11 HOLIDAY (Veterans No Class

Day)

November Targeted Therapies J. Engelman

18 (HMS/MGH)

November25 ~To be determined ~

December 2 Class Presentations

December 9
Class Presentations

TA = Pichet Adstamongkonkul : Email address: [email protected]

 IMMUNOLOGY 301
2013-2014
Course Directors: Michael Carroll; [email protected]
Nick Haining; [email protected]

Course Manager: Susan Perkins; [email protected]

Immunology 301 is a required course, to be taken in the Fall and Spring semester of the
G1 year.

To fulfill the requirements of this course and receive a satisfactory grade, students must
attend each Discussion class and turn in a 1-2 page paper on the assigned reference paper.
You are also required to attend each Lunch and Seminar.

Lunch: 12:15 - 1:15pm in Rosen Classroom, Rm. 100A, Jeffrey Modell Center
Each Wednesday, students registered for IMM301 meet with the seminar speaker over a
casual lunch and may discuss anything that is considered relevant.

Discussion Class: Wednesdays, 3:30 - 5:00pm in Rosen Classroom, Rm. 100A,

Jeffrey Modell Center
The IMM 301 discussion class meets from 3:30 pm-5: 00pm, throughout the year, and is
led by an Immunology faculty member whose expertise is in the topic of the seminar.
The 1-2 page write-ups are due via email to the faculty member leading the session by
2pm the day before the class (Tuesday).

The course will be divided into two halves (Fall and Spring). The overall course
objectives are the same in both halves, but the emphasis in Spring broadens to include
consideration of scientific significance.

Fall Semester: Prior to each Wednesday afternoon seminar, the speaker provides a set of
2-3 references. Students are expected to read all the references and the faculty leading the
discussion class will select one of the articles to be written up and reviewed by the
students and discussed in detail in class.

Points for students to address in their 1-2 page review of the article:
 Do the experiments described in this paper test a hypothesis (if so, how would this
hypothesis be phrased), or could this work be classified as descriptive?
 What is the state of this particular field at the moment of publication (i.e. what is the
background of the work more generally?)
 What is the methodology employed to address the questions asked, and is this
methodology appropriate? Are there alternative methods that would be equally
useful?
 Do the data presented warrant the conclusions made by the authors?
 Are there additional experiments/controls that would have strengthened the authors'
conclusions?
 What would you consider a logical extension of the work presented?
 On the whole, would you consider this paper a significant contribution to the field?
Spring Semester: The goal of the discussion class in the second half of the year is to
focus on the scientific significance of references in addition to their technical merits.
Prior to each Wednesday afternoon seminar, the speaker provides their CV with a
complete or selected bibliography. Students are expected to:

a) review the body of work completed by the speaker

b) select 1 – 3 papers from the list based on their significance to read in detail
c) demonstrate an understanding of how these papers advance existing thought on the
subject.

Points for students to address in their 1-2 page review of the article:
 What are the main findings of the paper(s)? Summarize in 1 – 3 sentences.
 What is (or was) the state of the particular field at the moment of publication, and
does the paper advance the field? How?
 Do the experiments lead to novel lines of inquiry?
 Do the experiments described in the paper change existing scientific models? Are the
results surprising or controversial?
 Does the paper introduce new concepts or new understanding of existing concepts?
 Do the experiments apply new scientific techniques or approaches to an existing
problem? Have these techniques/approaches subsequently become widespread?

Seminar: 5:00 - 6:00pm in the Armenise Amphitheater

Post Seminar Reception: 6:00 – 6:45pm in Modell Center Atrium

Post Seminar Dinners take place at various local restaurants for out-of town speakers.
The dinners are attended by the seminar speaker, faculty host, and two students, and will
begin on September 11.
Directors: IMM301  Seminar  Discussion  Course  2013-­‐2014
Nick  Haining; 3:30-­‐5PM
[email protected] Modell  100A
Mike  Carroll;  [email protected]
Last First Institution Seminar  Date MGH  Seminar  Date Title Discussion  Leader
Staudt Louis Center  for  Cancer  Research,  National  Cancer  Institute 09/11/2013 Self  ligand  oncogenic  signaling  in  human  
lymphomas Nir  Hacohen
Fitzgerald Kate University  of  Massachusetts  Medical  School 09/18/2013 Long  non-­‐coding  RNA  and  regulation  of  
Innate  Immunity Edda  Fiebiger
Förster Reinhold Hannover  Medical  School 09/25/2013 9/26/13 Lymph  node  homing  of  immune  cells  via  
afferent  lymphatics Andy  Luster
Kuchroo Vijay Brigham  and  Women's  Hospital 10/02/2013 Transcriptional  network  controlling  
development  of  Tregs  and  Th17  cells Nick  Haining
Golenbock Douglas University  of  Massachusetts  Medical  School 10/09/2013 Innate  Immune  Response  in  Malaria Hao  Wu
Kanneganti Thirmula St.  Jude  Children's  Hospital 10/16/2013 10/17/2013 Regulators  of  inflammatory  responses Andy  Lichtman
Cheroutre Hilde La  Jolla  Institute  for  Allergy  &  Immunology 10/23/2013 10/24/2013 New  players  in  T  cell  activation  and  
differentiation Vijay  Kuchroo
Topalian* Suzanne John  Hopkins  Medicine 10/30/2013 Immune  checkpoint  blockade:  A  new  
paradigm  for  cancer  therapy Arlene  Sharpe
Gilboa Eli University  of  Miami 11/06/2013 Aptamer-­‐targeted  RNA  therapeutics:  a  
novel  platform  for  cancer  immunotherapy Judy  Lieberman
Chervonsky Alexander The  University  of  Chicago 11/13/2013 Commensal  bacteria  and  host's  fitness James  Moon
Frenette Paul Albert  Einstein  College  of  Medicine 11/20/2013 Dissecting  the  hematopoietic  stem  cell  
niche Chris  Carman
Jacks Tyler Koch  Institute  for  Integrative  Cancer  Research  at  MIT 12/04/2013 Nick  Haining
Neuberger** Michael Trinity  College  at  Cambridge                                                   12/11/2013 DNA  Deamination  by  AID/APOBEC  enzymes  
in  Antibody  diversification  and  Cancer
Roberto  Chiarle
Chawla Ajay UCSF 01/29/2014 1/30/2014 Innate  control  of  metabolism  and  tissue  
regeneration Diane  Mathis
Nolan Garry Stanford  University  School  of  Medicine 02/05/2014 2/6/2014 Mass  Cytometry:  Next  generation  flow  
cytometry Kai  Wucherpfennig
Hooper Lora UT  Southwestern  Medical  Center 02/12/2014 2/13/2014 Circadian  regulation  of  intestinal  immunity Wendy  Garrett
June Carl University  of  Pennsylvania 02/19/2014 2/20/2014 Engineering  T  cells  to  overcome  tolerance Galit  Alter
Medzhitov** Ruslan Yale  University  School  of  Medicine 02/26/2014 2/27/2014 Jon  Kagan
Artis David University  of  Pennsylvania 03/05/2014 3/6/2014 Immune  regulation  at  barrier  surfaces Rick  Blumberg
Bendelac Albert University  of  Chicago 03/12/2014 3/13/2014 Regulation  of  Innate  Effector  Lymphocytes   Dale  Umetsu
Lemaitre Bruno Swiss  Federal  Institute  of  Technology,  Lausanne,  Switzerland 03/26/2014 The  Drosophila  gut:  innate  immunity  in  
epithelia Robert  Luo
Engleman Edgar Stanford  University 04/02/2014 Shiv  Pillai
Yokoyama Wayne HHMI;  Washington  University  Medical  Center 04/09/2014 Tissue-­‐resident  Natural  Killer  Cells Michael  Brenner
Shastri Nilabh University  of  California,  Berkeley 04/16/2014 All  the  peptides  that  fit:  Producing  a  
peptide-­‐MHC  repertoire  for  immunity Christophe  Benoist
Ghosh Sankar Columbia  University 04/23/2014 4/24/2014 Novel  regulatory  mechanisms  of  the  NF-­‐kB  
pathway  in  inflammation Jon  Kagan
Chen James UT  Southwestern  Medical  Center 04/30/2014 Innate  Immune  Sensing  and  Signaling  of  
Cytosolic  DNA  and  RNA Nir  Hacohen
Ramakrishnan Lalita University  of  Washington 05/07/2014 5/8/2014 Insights  into  the  immunity  to  tuberculosis  
from  the  zebrafish Branch  Moody

*Benacerraf  Lecturer
**Rosen  Lecturer
HST-010 Human Functional Anatomy

Wed Sep 4, 2013

1:30pm - 2pm Course Introduction (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Course Introduction

2:15pm - 3:15pm Organogenesis (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Embryology: Organogenesis Room sched

3:30pm - 4:30pm Intro to Peripheral nn (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

4:30pm - 5pm Dissection Table Selection (Gehrke)

W h e r e : TMEC 419, 420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Dissection Table Slection

Fri Sep 6, 2013

1:30pm - 2:30pm Anatomy of Thorax (Zimkus)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:30pm - 3pm Intro to Laboratory (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Introduction to Dissection room sched.

3pm - 6pm Chest wall

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
Tank, 14th edition : LAB 1-4 (read in advance); 54,55 (at skeleton); 19-20; 24
(pectoral region)-28 (axilla); 55 (intercostal space)-57 (removal of thoracic wall) Tank, 15th
edition: LAB 1-4 (read in advance); 63,64 (at skeleton); 21-22 (Dissection instructions 1-11); 26
(pectoral region)-30 (axilla); 65 (intercostal space)-66 (removal of thoracic wall)

3:30pm - 6pm Thorax Prosection (half class; Zimkus)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Thorax and Lungs
HST-010 Human Functional Anatomy

Mon Sep 9, 2013

1:30pm - 2:45pm Thoracic Surgery (Sugarbaker)

W h e r e : Cannon Room
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Invited; email 5/27/13 confirmed 5/27/13

3pm - 6pm LAB: Removal of anterior chest wall; Lungs

W h e r e : TMEC 419, 420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 58-63 15th: 66 (removal of anterior thoracic wall) - 72 (mediastinum)

3pm - 6pm PRO: Thorax (2nd half class; Zimkus)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Wed Sep 11, 2013

1:30pm - 2:45pm Embryology Heart (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Embryology: Heart

3pm - 6pm LAB: Anterior Mediastinum and Middle Mediastinum

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 64-73 15th: 72-82 (to superior mediastinum)

3pm - 6pm PRO Fresh Bovine Heart (self directed; supplemental instructions)
W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Fresh Bovine Heart

3pm - 5:30pm PRO: Lungs, Posterior Mediastinum (Hildebrandt?)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Sep 13, 2013

1:30pm - 2:15pm Radiology: Breast & Breast Imaging (Slanetz)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Breast and Breast Imaging confirmed 5/22/13

2:15pm - 3pm Radiology: Chest Imaging (Dr. Spirn, BIDMC)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13
HST-010 Human Functional Anatomy

3pm - 3:15pm Radiology: Intro to top 25 Cases (Slanetz)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

3:30pm - 6:30pm LAB:Superior Mediastinum and Posterior Mediastinum

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th:73-77 15th: 82-87

Mon Sep 16, 2013

1:30pm - 2:30pm Heart Imaging: Echocardiography (Stultz)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/13 confirmed 5/27/13

2:45pm - 5:15pm LAB: Superficial Back

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 5-9 (stop at superficial muscles) 15th: 5-9 (stop at superficial muscles)

Wed Sep 18, 2013

1:30pm - 2:30pm Development of the Extremities (Gehrke: Zimkus?)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 6pm LAB: Back Musculature

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 9-15 (vertebral canal) 15th: 9-15 (vertebral canal)

2:45pm - 6pm PRO (Lutchman) Vertebral column, back, sub-occipital region

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Vertebral column, back, sub-occipital region

Fri Sep 20, 2013

1:30pm - 2:30pm Back lecture (Keel)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Invited 5/27/2013 confirmed 6/1/2013

2:45pm - 6pm LAB: Vertebral Canal, Spinal Cord, Scapular Region

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
14th: 15-18; 22-24 (pectoral region) 15th: 15-19; 24 (scapular region) - 26
(pectoral region)
HST-010 Human Functional Anatomy

Mon Sep 23, 2013

1:30pm - 2:30pm Organization of Upper Extremity (van Houten)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 6pm LAB: Upper Extremity and Brachial Plexus

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
14th: 19-21; 28 (axilla)-32 (arm and cubital fossa) 15th: 21-24; 30 (axilla) - 34
(arm and cubital fossa)

2:45pm - 6pm PRO Shoulder & Brachial Plexus (Hildebrandt)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Shoulder, brachial plexus

Wed Sep 25, 2013

1:30pm - 2:30pm Organizat i o n o f L o w e r E x tr e m i ty (v a n Ho u te n )

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 6pm LAB: Arm and Forearm flexors (Hildebrandt)

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 32-40 (palm of the hand) 15th: 34-46 (palm of the hand)

2:45pm - 6pm PRO (Arm, forearm flexors) (Lutchman)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Arm, forearm flexor regions

Fri Sep 27, 2013

1:30pm - 2:30pm Func. Anatomy Hand (Van Houten)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Functional Anatomy of Hand

2:45pm - 6pm LAB: Palm of the Hand

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 40-46 (extensor region) 15th: 46-53 (extensor region)

2:45pm - 6pm P RO:P alm of Ha n d (V a n Ho u te n )

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Palm of the hand
HST-010 Human Functional Anatomy

Mon Sep 30, 2013

All day distribute problem set

Mon Sep 30, 2013 - Tue Oct 1, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

1:30pm - 2:30pm Limb Biomechanics (Herr)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: wrote to Hugh about these dates on 5/5/2013 confirmed 5/22/13

2:45pm - 6pm LAB: Extensor surfaces; joints of upper extremity

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 47-53 15th: 53-62

2:45pm - 6pm
PRO: Arm, forearm extensors; joints of upper extremity (Van
Houten)
W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Arm, forearm extensors; Joints of upper extremity

Wed Oct 2, 2013

1:30pm - 2:30pm Hip, Knee, Ankle (Herr)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
Hip, Knee, and Ankle wrote to Hugh about these dates on 5/5/2013 confirmed
5/22/13

2:30pm - 3pm Practice Identifications (Gehrke)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Lee Gehrke

3:15pm - 6:30pm
LAB: Lower extremity; superficial & anterior thigh
(Hildebrandt)
W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 148-159 15th: 165-176 Sabine Hildebrandt in laboratory

3:15pm - 6:30pm PRO: Anterior & Medial Thigh (Lutchman)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Ant. & medial thigh
HST-010 Human Functional Anatomy

Fri Oct 4, 2013

All day problem sets due

Fri Oct 4, 2013 - Sat Oct 5, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

1:30pm - 2:30pm Human Gait (Herr)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Human gait wrote to Hugh about these dates on 5/5/2013 confirmed 5/22/13

2:30pm - 3pm Practice Identifications (Gehrke)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Lee Gehrke

3:15pm - 6:30pm LAB: Gluteal region; Posterior thigh

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th:159-167 (leg and dorsum of foot) 15th: 176-184 (leg and dorsum of foot)

3:15pm - 6:30pm
PRO: Gluteal region; hamstrings; popliteal fossa
(Hildebrandt)
W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Gluteal region, hamstrings, popliteal fossa

Mon Oct 7, 2013

1:30pm - 2:15pm Radiology: Reading MSK images (Wu)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

2:15pm - 2:45pm Radiology: Review top 25 chest/MSK images (Slanetz)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

2:45pm - 6pm LAB: Leg

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th:167-175 15th: 184-193

2:45pm - 6pm Radiology: Small Group MSK radiology (Hochman, Wu, Slanetz)
W h e r e : TMEC 218
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Radiology of extremities Confirmed 5/27/13
HST-010 Human Functional Anatomy

Wed Oct 9, 2013

1:30pm - 2:30pm Physical Exam of Extremities (Rodriguez)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Invited 5/27/2013 confirmed 5/27/13

2:45pm - 6pm LAB: Sole of Foot; Joints of Lower extremity (Hildebrandt)

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th:175-185 15th: 193-203

2:45pm - 6pm PRO: Knee Joint (self-directed)

W h e r e : TME 419, 420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 5:45pm
PRO: Leg (all compartments); dorsum of foot; dorsum and
sole of foot (Lutchman)
W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Posterior and lateral crural compartments; foot perhaps should do this on Friday?

Fri Oct 11, 2013

1:30pm - 2:30pm Review Statics Homework + Biomechanics (Herr)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: wrote to Hugh about these dates on 5/5/2013 confirmed 5/22/13

2:40pm - 3:15pm Review of organogenesis & heart development (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: review session

3:30pm - 4pm Review Thorax and limb development (Zimkus)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Review: Limbs, brachial plexus

4pm - 4:45pm
Review upper and lower extremities; brachial plexus (van
Houten)
W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Review: Thorax & Limbs
HST-010 Human Functional Anatomy

Mon Oct 14, 2013

All day Columbus Day - No Class

Mon Oct 14, 2013 - Tue Oct 15, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Wed Oct 16, 2013

1:30pm - 3pm Mid-term examination

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Room sched.

3pm - 6:30pm Midterm examination grading (Faculty Only)

W h e r e : TMEC 204
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Oct 18, 2013

1:30pm - 2:30pm Devel of GI system (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Embryology: Gut

2:45pm - 6pm LAB: Abdominal wall; inguinal region

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
14th: 78-87 (reflection of the abdominal wall) 15th: 89-98 (reflection of the
abdominal wall)

Mon Oct 21, 2013

1:30pm - 2:15pm Radiology: Abdominal Imaging (Dr. Alex Guimaraes)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Anatomical spaces confirmed 5/22/13

2:15pm - 2:45pm Radiology: Top 25 Abdo/pelvis imaging cases (Slanetz)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

2:45pm - 6pm LAB: Peritoneum; Peritoneal cavity

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 87-96 (SMA) 15th: 98-107 (SMA)
HST-010 Human Functional Anatomy

Wed Oct 23, 2013

1:30pm - 2:30pm Dev. UG System (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Surgery: Congenital Defects

2:45pm - 6pm LAB: Mesenteric Vessels; Abdominal viscera

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
14th: 96-105 (posterior abdominal viscera) 15th: 107-116 (posterior abdominal
viscera)

2:45pm - 6pm
PRO: Abdominal viscera, celiac axis, mesenteric vessels, portal
vein; post. abdom. wall (Zimkus)
W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: prior years Doug split this in two

Fri Oct 25, 2013

1:30pm - 2:30pm GI Endoscopy (Ketwaroo)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: wrote to Avi about this lecture 5/5/2013 Confirmed 5/5/2013

2:45pm - 6pm LAB: Posterior abdominal visceral; inferior diaphragm

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 105-112 15th: 116-124

Mon Oct 28, 2013

1:30pm - 2:30pm Organization of Pelvis and Perineum (van Houten)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 5:30pm LAB: Pelvis & Perineum Part 1

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 105-112 15th: 125-129; 129-137 (M) or 147- 152 (F)

Wed Oct 30, 2013

1:30pm - 2:30pm Obstetrical Anatomy (Carusi)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Invited 5/27/2013 Confirmed 5/28/13
HST-010 Human Functional Anatomy

2:30pm - 3pm
Radiology: Abdo/Pelvis case review; intro to Head/Neck imaging
(Slanetz)
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

3:15pm - 6:30pm LAB: Pelvis and Perineum Part 2

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 113-117; 117-129 (M) or 133-143 (F) 15th: 137-142 (M) or 152- 159 (F)

3:15pm - 6pm Pathology Correlation (Drs. Mitchell and Padera)

W h e r e : TMEC 419.420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: email invitation 6/16/2013

3:15pm - 6:30pm PRO: Pelvis & Perineum (van Houten)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Nov 1, 2013

10:10am - 11:10am
Abdomen and Pelvis through a laparoscopic view
(Awtrey)
W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 6/1/2012 confirmed 6/4/2012

1:30pm - 2:30pm Devel. Enteric Nervous System (Goldstein)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 Confirmed 5/29/13

2:30pm - 5:30pm LAB: Internal Iliac vessels; Pelvic diaphragm

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 129-133 (M); 143-147(F) 15th: 143-147 (M); 159-163 (F)

2:30pm - 5pm
Radiology: Small Group Radiology (Guimaraes, Bennett, Slanetz,
van Houten)
W h e r e : TMEC 218
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
abdomen and pelvis NB This should be held a day earlier, to coincide with
Priscilla's lecture on abdo cases.
HST-010 Human Functional Anatomy

Mon Nov 4, 2013

1:30pm - 2:30pm Development of Head & Neck (Stankovic)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Invited 5/27/2013 confirmed 6/21/2013

2:45pm - 6pm LAB: Face, Scalp

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
14th:199-206; 208 (scalp)-210 (temporal region) 15th: 218 (head)-226 (parotid
region); 228 (scalp)-229

2:45pm - 6pm Prosection: Face (van Houten)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Wed Nov 6, 2013

1pm - 1:30pm Distribute Skulls

W h e r e : D Amph
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

1:30pm - 2:15pm Cranial Cavity (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Cranial Cavity

2:20pm - 3pm Intro to Cran i a l Ne r v e s (v a n Ho u te n )

W h e r e : D Amph
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

3:15pm - 6:30pm LAB: Interior of skull; meninges; cranial nerves

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 215-227 (orbit) 15th: 235-245 (orbit)

Fri Nov 8, 2013

1:30pm - 2:30pm Eye & Orbit (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Eye and Orbit

2:45pm - 6pm LAB: Eye and Orbit

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 227-234 15th: 245- 252
HST-010 Human Functional Anatomy

2:45pm - 6pm PRO:Fresh Bovine Eye (self- directed)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Fresh Bovine Eye explain that this cannot be done on a Monday

Mon Nov 11, 2013

All day Veteran's Day - No Class

Mon Nov 11, 2013 - Tue Nov 12, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Wed Nov 13, 2013

1:30pm - 2:30pm Organization of the Neck (van Houten)

W h e r e : D Amph
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:45pm - 6pm LAB: Triangles of the neck

W h e r e : TMEC 419, 420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 186-194 15th: 205-215 (end at "thyroid and parathyroids")

2:45pm - 6pm PRO: Neck Triangles; Cerv. Viscera (Zimkus)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Nov 15, 2013

1:30pm - 2:30pm Facial Nerve Regeneration (Lindsay)

W h e r e : TMEC 109
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: email invitation 5/27/2013 confirmed 5/28/13

2:45pm - 6pm LAB: Thyroid region; parotid region

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 195-199; 206-208 15th: 215-218 (end at "Head"); 226-228 (end at "Scalp")

Mon Nov 18, 2013

1:30pm - 2:30pm Jaws, Mastication, Swallowing (Bhatt)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
invited 5/27/2013 response on 5/29/13. "Should be ok but I may be in India doing
charity work"
HST-010 Human Functional Anatomy

2:45pm - 6pm LAB: Temporal Region; infratemporal fossa (Hildebrandt)

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 210-214 15th: 230-235

2:45pm - 6pm PRO: Infratemporal region; PT Fossa (Lutchman)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Infratemporal region; pterygopalatine fossa

Wed Nov 20, 2013

1:30pm - 2:15pm Review: Pelvic Floor (van Houten)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:15pm - 2:45pm Review Gut & UG system Development (Gehrke)

C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: room confirmed 8/1/2010

3pm - 5:45pm Disarticulation of Head

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 234-240 15th 252-259

Fri Nov 22, 2013

1:30pm - 2:30pm Clinical anatomy of the oral cavity (Abdul-Aziz)

W h e r e : D Amph
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
invited 5/27/2013 confirmed 5/28/13 (she had some reservation about confirming
the date re her clinical schedule.

2:45pm - 6pm LAB: Nasal cavities and palate

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 240-249 15th: 259-268

2:45pm - 6pm PRO: Bisected head, palate, pharynx (Hildebrandt)

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Bisected head, palate, pharynx

Mon Nov 25, 2013

1:30pm - 2:30pm Larynx (Kobler)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 confirmed 5/28/13
HST-010 Human Functional Anatomy

2:30pm - 6pm LAB: Oral region and larynx

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 249-255 15th: 268-274

2:45pm - 6pm PRO: Fresh Bovine Larynx (Supplementary Instructions)

W h e r e : TMEC 419, 420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

3pm - 6pm Temporal Bone Prosection; Dr. Vernick

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
invited: 5/27/2013 get TA to work on getting 3-D projection for him; plus a room
for prosection confirmed 6/6/13

Wed Nov 27, 2013

All day Thanksgiving Holiday - No Class

Wed Nov 27, 2013 - Sat Nov 30, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Thu Nov 28, 2013

All day Thanksgiving Holiday - No Class

Wed Nov 27, 2013 - Sat Nov 30, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Nov 29, 2013

All day Thanksgiving Holiday - No Class

Wed Nov 27, 2013 - Sat Nov 30, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Mon Dec 2, 2013

1:30pm - 2pm
Middle/Inner Ear: Cranial VII and Parasympathetic Ganglia
(Gehrke)
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

2:15pm - 3:15pm Inner Ear and Balance (Oman)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 confirmed June 11, 2013

3:15pm - 6:30pm LAB: Middle and inner ear

W h e r e : TMEC 419,420
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: 14th: 255-259 15th: 274-278
HST-010 Human Functional Anatomy

3:15pm - 6:15pm Temporal Bone Prosection; Dr. Vernick

W h e r e : TMEC 414
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 confirmed 6/6/13

Wed Dec 4, 2013

1:30pm - 2:30pm Dr. Pomahac; Face Transplantation

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 May be in China; 12/9 is not good for him.

2:45pm - 3:30pm Review Abdominal and Pelvic Vasculature (van Houten)

W h e r e : MEC 250
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: room confirmed 8/1/2010

Fri Dec 6, 2013

1:30pm - 2:15pm Anatomical Review of Cranial Nerves (van Houten)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: Review: Cranial Nerve Anatomy

2:30pm - 4pm Clinical Cranial Nerve Review (Khoshbin)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: invited 5/27/2013 Confirmed 5/29/13

Mon Dec 9, 2013

1:30pm - 2:30pm Tabin: The Development of Symmetry

W h e r e : Armenisi Amph
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description:
invited 5/27/13 confirmed 5/27/13, although Cliff has to catch a flight for a talk at
CalTech. He will try to make the flight for 5 pm after the lecture.

2:45pm - 3:30pm Radiology: Head & Neck Imaging (Moonis)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Lee Gehrke
Description:
This was several days earlier (11/26) in the original syllabus, but was moved this
year for PS schedule. confirmed 5/22/13

3:30pm - 4:30pm Top 25 Radiology Jeopardy (Guimaraes and Slanetz)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13
HST-010 Human Functional Anatomy

Wed Dec 11, 2013

1:30pm - 2:30pm Bionics (Herr)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Description: confirmed 5/22/13

2:30pm - 3:30pm Practice Identifications (Gehrke)

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

Fri Dec 13, 2013

All day HST 010 Final Exam

Fri Dec 13, 2013 - Sat Dec 14, 2013
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

1:30pm - 4:30pm HST-010 Final

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy

5pm - 6:30pm HST-010 Celebration

W h e r e : AA
C a l e n d a r : HST-010 Human Functional Anatomy
C r e a t e d b y : Elizabeth Hoy
Fall Semester 2013

Neurobiology 220. Cellular Neurophysiology

Bruce Bean, Michael Do, Wade Regehr, Bernardo Sabatini, Gary Yellen
Meets 9:00 am – 12:00 noon, Tuesdays and Thursdays. Goldenson 122.
Introduction to the physiology of neurons. Topics include structure and function of ion
channels, generation and propagation of action potentials, and physiology of synaptic
transmission, with a focus on mammalian central neurons. Includes problem sets and reading
of original papers.

9/3/2013 Tue Intro // Passive electrical properties gy

9/5/2013 Thu Resting potential & ionic conductances gy
9/10/2013 Tue Action potential basics; Intro to voltage clamp bb
9/12/2013 Thu Cable theory bb
9/17/2013 Tue Propagated action potentials bb
9/19/2013 Thu Voltage clamp methods & strategies gy
9/24/2013 Tue Channel structure: basis of permeation & gating gy
9/26/2013 Thu Channel pharmacology: v- & state-depend't blockade gy
10/01/2013 Tue Channel variety and modular organization gy
10/03/2013 Thu Na+ channels bb
10/08/2013 Tue Ca channels and K channels bb
10/10/2013 Thu Review
10/15/2013 Tue Midterm exam
10/17/2013 Thu Ca as a signaling molecule (*) wr
10/22/2013 Tue Ligand gated ion channels (*) bb
10/24/2013 Thu Presynaptic mechanisms I (*) wr
10/29/2013 Tue Presynaptic mechanisms II (*) wr
10/31/2013 Thu Postsynaptic mechanisms (*) bb
11/05/2013 Tue Transmitters & G-protein modulation (*) bb
11/07/2013 Thu Sensory transduction (md)
11/12/2013 Tue Synaptic plasticity I: NMDA-LTP extracellular recording (*) wr
11/14/2013 Thu Synaptic Plasticity II: LTP-LTD (*) bs
11/19/2013 Tue Dendritic properties (*) bs
11/21/2013 Thu Firing patterns and intrinsic membrane properties (*) bb
11/26/2013 Tue Optical control of neuronal circuits (*) bs
11/28/2013 Thu Thanksgiving
12/03/2013 Tue Paper presentations (*)
12/05/2013 Thu Paper presentations (*)
12/10/2013 Tue Paper presentations (*)
12/17/2013 Thu Review
12/19/2013 Tue Final
Neurobiology HMS230
Harvard / GSAS 78454
Visual object recognition:
From computational and biophysical algorithms to cognition

FALL 2013

Overview
Visual recognition is essential for most everyday tasks including navigation, reading and
socialization. Visual pattern recognition is also important for many engineering
applications such as automatic analysis of clinical images, face recognition by
computers, security tasks and automatic navigation. In spite of the enormous increase in
computational power over the last decade, humans still outperform the most
sophisticated engineering algorithms in visual recognition tasks. In this course, we will
examine how circuits of neurons in visual cortex represent and transform visual
information. The course will cover the following topics: functional architecture of visual
cortex, lesion studies, physiological experiments in humans and animals, visual
consciousness, computational models of visual object recognition, computer vision
algorithms.

Class web site

http://klab.tch.harvard.edu/academia/classes/hms_neuro300_vision/index.html  
(can be accessed through: http://tinyurl.com/vision-class  )  
Lecture notes, slides, reading assignments and other information will be posted
in the class web site.

Location: Biolabs 1075

Course Meeting Times and Schedule

Mondays 3:30 pm to 5:30 pm
Lectures: 60 minutes / week.
Reading assignment discussion: 60 minutes/week

Faculty: Gabriel Kreiman

Contact information:
617-919-2530
[email protected]

Prerequisites:
Life Sciences 1a (or Life and Physical Sciences A) and Life Sciences 1b. [or
equivalent]
Recommended: Math (Maa/Mab, Math1A,1B, Math19a or equivalent). Physical
Sciences 1. MCB80.

Topics:
 • Introduction to pattern recognition. Why is vision difficult? Overview of key
questions in the field.
• Characterization of the visual input. Natural image statistics.
• The retina, LGN and primary visual cortex. Neurophysiology and
neuroanatomy.
• Lesion studies in humans and animals.
• Adventures into terra incognita: Neurophysiology beyond primary visual
cortex.
• Electrical stimulation in visual cortex and causality.
• Biophysically inspired computational models of visual object recognition.
• Computer vision. Engineering algorithms and their applications. Machine
learning applications to vision.
• Human perception. Psychophysics. Visual Illusions.
• Engineering and prosthetic devices for visual recognition
• Towards understanding subjective visual perception.

Suggested Books

Ullman S (1996) High-level vision. MIT Press.

Wandell BA (1995) Foundations of vision. Sunderland Sinauer Associates.
Chalupa LM and Werner JS (editors) (2003). The Visual Neurosciences. MIT Press.
Ripley. Pattern recognition and neural networks (1996). Cambridge University Press.
Rao, Olshausen and Lewicki (eds) (2002). Probabilistic models of the brain. MIT Press.
Koch C (2005) The quest for consciousness. Roberts & Company Publishers.
Deco, G. and E.T. Rolls, Computational Neuroscience of Vision, Oxford Oxford
University Press.
Dayan and Abbott (2002). Theoretical Neuroscience. MIT Press.
Horn BKP. Robot Vision. MIT Press.
Kriegeskorte N and Kreiman G. (2011) Understanding visual population codes. MIT
Press.
Davies ER. (2005). Machine Vision, Third Edition: Theory, Algorithms, Practicalities
(Signal Processing and its Applications). Elsevier.

Homework, Reading assignments and writing requirements

Each week, students have to read, understand and discuss a scientific paper. The paper
relates to the topics covered in the previous class and illustrates state-of-the-art
research efforts in the field.
Students are required to hand in a discussion of the reading assignment including one of
the following (typically half a page to one page):
1) A critic of the paper including missing controls or alternative interpretation of the
findings or a critical discussion of the findings
2) Two follow up questions (computational modeling or experiments or computer
vision applications)
Do not copy and paste from the paper (the instructor has already read the papers…).
Homework is due (electronic format) before the beginning of each class.

Final paper. A final paper is due at the end of the class (details to be provided in
class)

Grading

Final grades are computed as follows:

Homework – 60%
Class discussion – 20%
Final paper – 20%

Schedule

CLASS Date Title Comment

1 09/09/13 [Mon] Introduction to visual pattern
recognition.
2 09/16/13 [Mon] Why is vision difficult? Natural Discussion
image statistics and the retina. Reading 1
3 09/23/13 [Mon] Primary visual cortex HW1 due.
Discussion
Reading 2.
4 09/30/13 [Mon] Psychophysical studies of visual HW2 due.
object recognition Discussion
Reading 3.
Lecture by invited
guest.
5 10/07/13 [Mon] Lesions and neurological HW3 due.
examination of extrastriate Discussion
visual cortex Reading 4.
Lecture by invited
guest.
6 10/14/13 [Mon] NO CLASS: Columbus Day Note: HW 4 due
via e-mail on
10/15
7 10/21/13 [Mon] Adventures into terra incognita: Discussion
probing the neurophysiological Reading 5.
responses along the ventral
visual stream
8 10/28/13 [Mon] First steps into inferior temporal HW5 due.
cortex Discussion
Reading 6.
11/04/13 [Mon] From the highest echelons of HW6 due.
visual processing to cognition Discussion
Reading 7.
9 11/11/13 [Mon] From correlation to causation: HW7 due.
electrical stimulation of visual Discussion
cortex Reading 8.
10 11/18/13 [Mon] First steps towards in silico HW8 due.
vision Discussion
 Reading 9.
Lecture by invited
guest
11 11/25/13 [Mon] Computational models of the HW9 due.
ventral visual stream Discussion reading
10.
12 12/02/13 [Mon] Computer vision HW10 due.
Discussion.
Reading 11.
13 12/09/13 [Mon] Neural correlates of visual HW 11 due
consciousness 12/04/12
12/19/13 [Th] Final paper due
 
 General Information: Acoustics of Speech & Hearing A Joint Course at HMS and MIT

Acoustics of Speech & Hearing

HMS: SHBT 200
MIT: 6.551J / HST.714J
(This information is also available at http://web.mit.edu/6.551j/www/)
Description
The Acoustics of Speech and Hearing is a graduate level course at HMS and MIT H-Level graduate course (4-
1-7) that reviews the physical processes involved in the production, propagation and reception of human
speech. Particular attention is paid to how the acoustics and mechanics of the speech and auditory system
define what sounds we are capable of producing and what sounds we can sense. Areas of discussion include
(1) the acoustic cues used in determining the direction of a sound source, (2) the acoustic and mechanical
mechanisms involved in speech production and (3) the acoustic and mechanical mechanism used to transduce
and analyze sounds in the ear.
General Information
The class meets for two 1.5 hour lectures and one 1-hour recitation session each week with two take home
laboratory sessions scheduled during the semester. There are 15 written assignments during the year
consisting of problem sets (11 throughout the term), lab reports (2 throughout the term) and two take-home
exams (a mid-term and a final). There are also 5 paper discussion sessions in which everyone is expected to
participate.
Grading: 15% of the final grade is based on homework, 15% is based on participation in class and in
discussions of relevant literature, 10% is based on the two lab reports, 60% is based on the mid-term and final
exam. Students are encouraged to seek the help of the faculty and teaching assistants in performing the
homeworks.
Who Should Take This Course
The Acoustics of Speech and Hearing course is open to beginning graduate students and upper level
undergraduates who have had two semesters of college-level physics (or equivalent) and differential and
integral calculus. Past students have included Physics, EE and ME juniors, seniors and graduate students as
well as graduate students from the Media Lab.
Where & When
Classes are held at MIT
Lectures are held Tuesdays (T) and Thursdays (R) from 1PM - 2:30PM in 26-302.
Recitations are on Wednesdays (W) from 12:00 to 1:00 PM in 36-156
Text Books & Library Resources
The recommended (but not required) textbook for the course is: The Speech Chain: The physics and biology
of spoken speech by P.B. Denes & E.N. Pinson, WH Freeman 2nd ed. 1993, ISBN 0716722569.
This text is written for non-engineers but it contains a clear basic description of the physiologic and physical
processes involved in speech production, transmission, reception and recognition. This book may be
purchased for $27 from Amazon.com or Barnes & Noble.com.
A text/workbook that covers some of the course material in more detail is; "The Fundamentals of Sounds with
Applications to Speech and Hearing" by WJ Mullin, WJ Gerace.JP Mestre and SL Velleman, Published by
Allyn and Bacon, Boston, 2003, ISBN 0-205-37087-X . This book is available from Barnes and Noble
(www.bn.com) for $67 new or $20 to $35 used.

18-July-2013 page 1
 General Information: Acoustics of Speech & Hearing A Joint Course at HMS and MIT
Other more engineering oriented texts will be useful from time to time and that can be found in the
Engineering Library, include:
Fundamentals of Acoustics by Kinsler, Frey, Coppens and Saunders, Academic Press 1982.
Acoustics by Leo Beranek, American Institute of Physics 1986.
Acoustic Phonetics by Ken Stevens, MIT Press 1998.
Signals and System for Speech and Hearing by Stuart Rosen & Peter Howell , Academic Press 1991.
A book that gives a more balanced view point of acoustics and speech and hearing is Acoustic Systems in
Biology by Neville Fletcher, Oxford University Press 1992.
A more thorough treatment of the hearing process is Fundamentals of Hearing Science by William Yost, 3rd
edition, Academic Press, 1994.

Staff
Louis D. Braida, Ph.D., Henry Ellis Warren Professor of Electrical Engineering, Office 36-791, phone: 3-
2575, email: [email protected]
Satrajit S. Ghosh, Ph.D. Research Scientist, Research Laboratory of Electronics, Office 36-547, phone: 3-
5957, email: [email protected]
John J. Rosowski, Ph.D., Professor of Otology and Laryngology and Health Sciences and Technology,
Harvard Medical School, Office 36-597 & Mass Eye & Ear, phone 3-5896 or 573-4237,
email: [email protected]
Christopher A. Shera, Ph.D., Associate Professor of Otology and Laryngology and Health Sciences and
Technology, Harvard Medical School, Office 36-847 & Mass Eye & Ear, phone 573-4235,
email: [email protected]
Shirin Farrahi, Part-Time TA, Office 36-873, phone: 8-5943, email: [email protected]

Lectures include:
3 Lectures on sound propagation in space
1 Lecture on Sound Diffraction Sound Localization
2 Lectures on Sound Localization
1 paper discussion on sound localization
4 Lectures on electro-acoustic circuits
3 Lectures on acoustic transducers including the middle ear
1 Lecture on middle-ear disease and reconstruction
1 Paper discussion on middle ear models
3 lectures on sound in tubes
2 Lectures on the inner ear
2 Lectures on the perception of sound and hearing loss
2 Lectures on speech sound production
2 Paper discussions on frequency selectivity in the auditory system
1 Lecture on the processing of speech by the auditory system

Laboratory sessions include:

1 Lab on the acoustic analysis of speech
1 Lab on quantifying the perception of sound

see http://web.mit.edu/6.551j/www/ for an up-to-date class schedule

18-July-2013 page 2
 General Information: Acoustics of Speech & Hearing A Joint Course at HMS and MIT
Lecture handouts, homeworks and other material is (or will be) available for registered class participants at
http://stellar.mit.edu/S/course/HST/fa12/HST.714/ and on HMS ecommons.

18-July-2013 page 3
 SHBT 201 Biology of the Inner Ear (aka HST 721)
Instructors: Liberman, Maison
Lecture 1: Introduction

Lecture 2: Inner Ear Anatomy

Laboratory 1: Inner Ear Anatomy Laboratory

Lecture 3: Inner Ear Development & Regeneration

Literature Discussion 1: Inner Ear Development & Regeneration

Lecture 4: Stria Vascularis and the Endolymphatic Potential

Literature Discussion 2: Stria Vascularis and the Endolymphatic Potential

Lecture 5: Hair Cells and Mechanoelectric Transduction

Literature Discussion 3: Hair Cells and Mechanoelectric Transduction

Lecture 6: Outer Hair Cell Electromotility & Cochlear Micromechanics

Literature Discussion 4: Outer Hair Cell Electromotility & Cochlear Mechanics

Lecture 7: Introduction to the In Vitro Hair Cell Biophysics Laboratory

Laboratory 2: In Vitro Hair Cell Biophysics

Lecture 8: Afferent Synaptic Transmission in the Inner Ear

Literature Discussion 5: Afferent Synaptic Transmission in the Inner Ear

Lecture 9: Stimulus Coding in the Auditory Periphery - Auditory Nerve Response

Literature Discussion 6: Stimulus Coding in the Auditory Periphery - Auditory
Nerve Response

Lecture 10: Feedback Control in the Auditory Periphery – the Olivocochlear

Efferent Syetem
Literature Discussion 7: Feedback Control of the Auditory Periphery – the
Olivocochlear Efferent System

Lecture 11: Introduction to the In Vivo Cochlear Physiology Laboratory

Laboratory 3: In Vivo Cochlear Physiology

Lecture 12: Mechanisms of Cochlear Damage and Protection

Literature Discussion 8: Mechanisms of Cochlear Damage and Protection

Lecture 13: Pathophysiology of Sensorineural Hearing Loss

Literature Discussion 9: Pathophysiology of Sensorineural Hearing Loss
SHBT 206
Molecular Biology of the Auditory System
Course director: Albert Edge
Instructors: Zheng-Yi Chen, Ruth Anne Eatock, Albert Edge, Cynthia Morton, Tina Stankovich

Date Lecturer Topic

17-Sep AE Molecular biology: bacteria

24-Sep AE Molecular biology: eukaryotic cells
1-Oct ZYC Genetics of model organisms: chick, zebrafish
8-Oct AE Mouse models: knock in and out
15-Oct AE Development of the ear: embryo to placode
22-Oct RAE Genes and hair cell function
29-Oct CM Human deafness: how mutations are found
5-Nov CM Human deafness: what mutations tell us about gene function
12-Nov ZYC Development of the ear: placode to hair cells
19-Nov KS Proteomics and genomics
26-Nov KS Expression arrays
3-Dec ZYC Inner ear regeneration: chick to man
10-Dec AE Inner ear regeneration: embryonic stem cells, cochlear stem cells
17-Dec AE Therapeutic approaches to inner ear regeneration
 Virology 200: Introduction to Virology
Fall 2013
Course Overview and Schedule

One objective of this course is for students to gain knowledge of the principal groups of human viruses and
current research themes concerning them. Another objective is for students to gain experience in writing and
speaking about this subject.

The course is open to Virology, Immunology, and BBS Program students. Other graduate or undergraduate
students should contact Prof. Max Nibert ([email protected]) prior to registration.

Course components and schedule

A detailed schedule is found on the following page. In most cases, Mondays will be for Lectures and
questions, and Wednesdays will be for written critiques and Discussions of research articles. Because of
scheduling necessities, three Lectures will be on Wednesdays this year (Sept 4, Nov 13, and Nov 20), and
two Discussions will be on Mondays this year (Nov 18 and Nov 25). Each participant will also prepare and
present an initial and a final research proposal based on his/her rotation research. The initial Student
Presentations will be on Wed. Oct. 16 and the final ones will be on Mon. Dec. 9 and Wed. Dec. 11. Additional
details about these course components can be found in the syllabus.

Location and times

All sessions will be held in TMEC 333. Regardless of day (Monday or Wednesday), the twelve Lecture
sessions will run from 1:30 to 3:00 PM, the eleven Discussion sessions will run from 1:30 to 3:30 PM, and the
three Student Presentations sessions will also run from 1:30 to 3:30 PM.

Grading

Final grade for the course will be determined as a composite of class participation/written critiques of papers
(50%) and proposals/presentations (50%). The final proposal will serve as the final exam for this course.

Contact information

Course organizers:
Prof. Elliott Kieff: [email protected]
Prof. David Knipe: [email protected]
Prof. Karl Münger: [email protected]
Prof. Max Nibert: [email protected] (course director)
Prof. Priscilla Yang: [email protected]
Graduate teaching assistant:
To Be Named
 Schedule for Virology 200 Fall 2013

Wed. Sept. 4 Lecture—Virology Basics Münger

Mon. Sept. 9 Lecture—Structural Virology Harrison
Wed. Sept. 11 Discussion—Structural Virology Nibert/Yang
Mon. Sept. 16 Lecture—Plus-strand RNA Viruses: Picorna- & Caliciviruses Nibert
Wed. Sept. 18 Discussion—Plus-strand RNA Viruses: Picorna- & Caliciviruses Nibert/Yang
Mon. Sept. 23 Lecture—Plus-strand RNA Viruses: Flavi- & Togaviruses Yang
Wed. Sept. 25 Discussion—Plus-strand RNA Viruses: Flavi- & Togaviruses Nibert/Yang
Mon. Sept. 30 Lecture—Minus-strand RNA Viruses: Rhabdo- & Paramyxoviruses Whelan
Wed. Oct. 2 Discussion—Minus-strand RNA Viruses: Rhabdo- & Paramyxoviruses Nibert/Yang
Mon. Oct. 7 Lecture—Minus-strand RNA Viruses: Orthomyxoviruses Gack
Wed. Oct. 9 Discussion—Minus-strand RNA Viruses: Orthomyxoviruses Nibert/Yang
Mon. Oct. 14 Holiday—Columbus Day
Wed. Oct. 16 Student Presentations—Initial Proposals Münger/Nibert/Yang

Mon. Oct. 21 Lecture—Double-strand RNA Viruses Nibert

Wed. Oct. 23 Discussion—Double-strand RNA Viruses Münger/Nibert
Mon. Oct. 28 Lecture—Reverse-transcribing Viruses: Retro- & Hepadnaviruses Cunningham
Wed. Oct. 30 Discussion—Reverse-transcribing Viruses: Retro- & Hepadnaviruses Münger/Nibert
Mon. Nov. 4 Lecture—DNA Viruses: Polyoma- & Papillomaviruses Münger
Wed. Nov. 6 Discussion—DNA Viruses: Polyoma- & Papillomaviruses Münger/Yang
Mon. Nov. 11 Holiday—Veterans Day
Wed. Nov. 13 Lecture—DNA Viruses: Adenoviruses Chodosh
Mon. Nov. 18 Discussion—DNA Viruses: Adenoviruses Münger/Yang
Wed. Nov. 20 Lecture—DNA Viruses: Herpesviruses Knipe
Mon. Nov. 25 Discussion—DNA Viruses: Herpesviruses Gack/Münger
Wed. Nov. 27 Holiday—Thanksgiving
Mon. Dec. 2 Lecture—DNA Viruses: Poxviruses Kieff
Wed. Dec. 4 Discussion—DNA Viruses: Poxviruses Münger/Yang
Mon. Dec 9 Student Presentations—Final Proposals (1st half) Münger/Nibert/Yang

Wed. Dec 11 Student Presentations—Final Proposals (2nd half) Münger/Nibert/Yang

All sessions will be held in TMEC 334: Lecture sessions, 1:30 to 3:00 PM; Discussion sessions, 1:30 to 3:30
PM; and Student Presentations sessions, also 1:30 to 3:30 PM.
Virology 202 Wednesdays, 1:30 - 4:45 pm First meeting: Sep 4, TMEC (room TBD)
Faculty: Michaela Gack, Todd Allen, Samuel Rabkin, Fred Wang

Teaching assistant: Jessica Chiang ([email protected]; phone: 617-432-

2379)
Course purposes: to develop students’ skills in research proposal writing and presentation,
and in critically evaluating research proposals of others.
Grading. Individual proposal 50%, Critique 30%, General participation 20%
NOTE: This schedule below is significantly compressed from that in previous years to
accommodate students’ expressed desire to have more time for PQE preparation. To keep to
this schedule, we will need to be very efficient in and out of class.
Course Syllabus 2013
September
Full class 4 Introduction, course organization (20 minutes), preliminary
topic presentations. Students present hypothesis/topic ~5 minutes
each, with 5-10 minute discussion. Prepare 1-2 slides describing the
hypothesis(es) or question(s) you want to develop for your
proposal, and be familiar with the background material relevant to
your proposal. Slides should be emailed to Jessica
([email protected]) by 9 pm the day before the first
class.
Small groups 11 Small group development of hypothesis and specific aims.
Prepare revised hypothesis and specific aims on 2-3 slides, with
relevant background information. Print key background papers for
other small class members (no more than two). In class, hypothesis
and aims are presented and discussed. Preliminary discussion of
weaknesses and possible experimental approaches.
Deadline 16 First draft of written proposal. Prepare a 5-page draft (not
including references) of the proposal including hypothesis/key
question, specific aims, background and significance. Email this
proposal by 7 pm to other small group members.
Small groups 18 Small group critique of draft 1 and development of
experimental approaches. Students should have prepared revised
specific aims and have developed experimental approaches for each
aim, with possible outcomes, pitfalls, and alternatives considered.
Students should also have read and be able to critique 5-page
proposals within group. Only if absolutely necessary, students may
change topic or hypothesis at this point. A first set of primary intra-
group reviewers will be assigned.
Deadline 23 Second draft of written proposal. Prepare a ~10-page draft of
proposal now including details of experimental approach, to be
distributed by email by 9 pm to other small group members.
Small groups 25 Small group commentary on written proposals. Primary intra-
group reviewer leads discussion of draft proposals. Weaknesses are
identified, and modifications suggested. A second, different set of
intragroup reviewers are assigned.
Deadline 30 Third draft of written proposal. Incorporating discussion from
previous classes, a third ~10 page draft of proposal is prepared,
and distributed by email by 9 pm to other small group members.
October
Small groups 2 Small group commentary on written proposals. Primary intra-
group reviewer leads discussion of draft proposals. Primary external
reviewers for proposals of other groups are assigned.
Deadline 3 Final Draft of research proposal. A final 10-page draft
incorporating in class discussion should be emailed by 9 pm to all
faculty and to students in the review group. Students should
continue to improve their proposals until final deadline.
Small groups 9 Pre-site-visit meeting. Primary external reviewers should have
prepared 1-page draft critiques of assigned proposal from other
group, and have read and be able to discuss all of the proposals
from that group. In class, primary reviewers introduce the proposal
and discuss its significance, innovation, and especially experimental
approach.
Deadline 9 Final critiques due. Primary reviewer finalizes critique, and emails
review summary that incorporates pre-site-visit discussion to
students of his/her group and all faculty.
Small groups 16 Final small group meeting. 10 min-presentations summarizing the
modifications made to the proposal based on final critiques.
Full Class 23 Final “site visit” presentations and reviews. 20 min- presentation
and 15 min-discussions for each of three proposals. Presenting
students receive final critiques.
Full Class 30 Final “site visit” presentations and reviews. (three proposals)
November
Full Class 6 Final “site visit” presentations and reviews. (two proposals)
Deadline 8 Last day to submit final proposal revisions.

Faculty contact:
Todd Allen (617-726-7846; [email protected]). CD8 T cells, HIV, HCV
Michaela Gack (617-432-2378; [email protected]). Innate immunity
Samuel Rabkin (617-726-6817; [email protected]). HSV vectors
Fred Wang (617-525-4258; [email protected]). EBV

Small group rooms: TMEC 425 (Michaela, Samuel), TMEC 428 (Fred, Todd)

Compiled emails: [email protected]; [email protected];

[email protected]; [email protected];