Division of Medical Sciences Ph.D. Programs at Harvard Medical School

Course Syllabi Fall Semester 2012-2013 Final versions to be handed out in class (Missing syllabi will roll in.)

For Information Call: 617-432-4134

Table of Contents 1. BBS 230 (formerly Microbiology 230). Analysis of the Biological Literature – (New Course)………………………………………………………………………...……4 2. *BBS 301. Teaching Practicum…………………………………………………………...9 3. BCMP 200. Molecular Biology………………………………………………………….11 4. *BCMP 218. Molecular Medicine ……………………………………..…………..........16 5. BCMP 228. Macromolecular NMR……………………………………………………...21 6. BCMP 230. Principles and Practice of Drug Development ……………………..………24 7. BCMP 235. Principles of Human Disease: Physiology and Pathology………………….27 8. Cell Biology 226. Concepts in Development, Self-Renewal, and Repair………….........30 9. *Developmental & Regenerative Biology 330 (formerly *Cell Biology 330). Experimental Approaches to Developmental Biology JANUARY COURSE…….......N/A 10. Genetics 201. Principles of Genetics ……………………...…………………....…….....31 11. Genetics 219. Inheritance and Weird Stuff……………………………………………...32 12. Genetics 220. Molecular Biology and Genetics in Modern Medicine ……...……….......36 13. *Genetics 390. Experimental Approaches in Genetic Analysis - JANUARY COURSE………………………………………………………...……………………..N/A 14. *Human Biology and Translational Medicine 340. (LHB). Disease-Centered Tutorial Clinics………………………………………………………………………………….N/A 15. *Immunology 201. Principles of Immunology ….............................................................39 16. *Immunology 301. Immunology Seminar……………………………………………….40 17. *Medical Sciences 250ab. Human Functional Anatomy …………………………...…...42 18. Microbiology 202. Molecular Basis of Bacterial Pathogenesis and Host Response ……55 19. *Microbiology 205. Mechanisms of Microbial Pathogenesis …………………..……....58 20. Neurobiology 200. Neurobiology (formerly Introduction to Neurobiology)……………62 21. *Neurobiology 220. Cellular Neurophysiology ………..………………………..……....65 22. Neurobiology 230. Visual Object Recognition…………………………………………..67 23. SHBT 200. Acoustics of Speech and Hearing - (New Course)……………………….…70

24. SHBT 201. Biology of the Inner Ear - (New Course)……………………………………73 25. *SHBT 203. Anatomy of Speech and Hearing - (New Course)- JANUARY COURSE……………………………………………………………………………….N/A 26. *Virology 200. Introduction to Virology ……………………….……….………………74 27. Virology 202. Animal Virology: Seminar ………………………………………….…...76 

Indicates that the course requires faculty signature on study card.

Biological and Biomedical Sciences 230: Analysis of the Biological Literature Fall 2012 Summary: Students participate in intensive small group discussions focused on the 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 their background, significance, hypothesis, experimental methods, data quality, and interpretation of results. 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 proposing 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. First class TMEC250: Thursday September 6, 2012 from 3:00-5:00 pm. Course directors: Mike Blower: Adrian Salic:



Any questions or concerns please contact the course directors. Instructors: Dates of classes and assigned papers:

Introductory meeting: Thursday September 6, 3:00-5:00 pm, TMEC250. Course expectations and brief discussion of paper analysis Posted for all papers in this course: Publishing criteria from several journals.

CLASS 1 Polymer dynamics 9/11/12 TUESDAY Student groups 9/13/12 THURSDAY Faculty groups 1.

Garner EC, Campbell CS, & Mullins RD (2004) Dynamic instability in a DNAsegregating 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 2 Bacterial pathogenesis 9/18/12 TUESDAY Student groups 9/20/12 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):853860.

CLASS 3 Protein aggregation 9/25/12 TUESDAY Student groups 9/27/12 THURSDAY Faculty groups 1.

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.

2.

Kato M, et al. (2012) Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels. Cell 149(4):753-767.

3.

Han TW, et al. (2012) Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies. Cell 149(4):768-779.

CLASS 4 Protein localization and trafficking 10/02/12 TUESDAY Student groups 10/04/12 THURSDAY Faculty groups 1.

Blobel G & Dobberstein B (1975) Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. The Journal of cell biology 67(3):835-851.

2.

Blobel G & Dobberstein B (1975) Transfer of proteins across membranes. II. Reconstitution of functional rough microsomes from heterologous components. The Journal of cell biology 67(3):852-862.

3.

Kaiser CA & Schekman R (1990) Distinct sets of SEC genes govern transport vesicle formation and fusion early in the secretory pathway. Cell 61(4):723-733.

4.

Lee MC, et al. (2005) Sar1p N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle. Cell 122(4):605-617.

CLASS 5 Protein sorting 10/09/12 TUESDAY Student groups 10/11/12 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.

MIDTERM EXAM week of 10/15/2012 Exam due FRIDAY 10/19/2012 at 5PM to group instructors.

MIDTERM GRADING 10/22/2012-10/26/2012 Exams graded and faculty meet with students by appointment

STUDENTS SHUFFLED INTO NEW GROUPS CLASS 6 Epigenetics 10/30/2012 TUESDAY Student groups 11/01/2012 THURSDAY Faculty class 1.

Grewal SI & Klar AJ (1996) Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis. Cell 86(1):95-101.

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 11/06/2012 TUESDAY Student groups 11/08/2012 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 Translation control 11/13/2012 TUESDAY Student groups 11/15/2012 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.

Medenbach J, Seiler M, & Hentze MW (2011) Translational control via proteinregulated upstream open reading frames. Cell 145(6):902-913.

11/20/12 No Class 11/22/12 No Class

Thanksgiving vacation

CLASS 9 Metabolism 11/27/2012 TUESDAY Student groups 11/29/2012 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.

Radhakrishnan A, Goldstein JL, McDonald JG, & Brown MS (2008) Switch-like control of SREBP-2 transport triggered by small changes in ER cholesterol: a delicate balance. Cell metabolism 8(6):512-521.

CLASS 10 Master genes 12/04/2012 TUESDAY Student groups 12/06/2012 THURSDAY Faculty and student groups 1.

Davis RL, Weintraub H, & Lassar AB (1987) Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51(6):987-1000.

2.

Baas AF, et al. (2004) Complete polarization of single intestinal epithelial cells upon activation of LKB1 by STRAD. Cell 116(3):457-466.

FINAL EXAM DUE by 5 pm on FRIDAY Dec 13, by email to both instructors. Instructors will contact you about final exam grades and make appointments to go over class performance. 12/6/2011 3:00-5:00pm TMEC250 General student concerns meeting 12/20/2011 3:00-6:00pm Go over final exams with students in classrooms

Past final exams:

FINAL 2009: de Hoog, C.L., Foster, L.J., and Mann, M. (2004) RNA and RNA Binding Proteins Participate in Early Stages of Cell Spreading through Spreading Initiation Centers. Cell 117, 649–662.

FINAL 2008: Tomas-Loba, A., Flores, I., Fernandez-Marcos, P.J., Cayuela, M.L., Maraver, A., Tejera, A., Borras, C., Matheu, A., Klatt, P., Flores, J.M., Vina, J., Serrano, M., and Blasco, M.A. (2008) Telomerase reverse transcriptase delays aging in cancerresistant mice. Cell 135, 609-622.

BBS 301 Teaching Practicum Course Description: This course is intended for teaching assistants who are currently teaching in one of the BBS Core Courses. The goals of this embedded course are two-fold: 1) to better prepare teaching assistants for the specific course that they are working on and 2) to teach skills for leading discussion sections, grading, formats for delivering educational content, and elements of course design to graduate students and postdocs interested in teaching. This course will help the Core Courses attract the graduate student TAs most committed to teaching. The course will prepare them to be the best possible teaching assistants while also helping them develop skills that will serve them in their further careers as academicians and science communicators. By awarding them credit, we are not only recognizing the extra work that they are doing throughout the semester for the embedded course itself, but we are providing an incentive for students to choose to TA in the Core Courses, which is one of the most rigorous outlets for TA credit at HMS. This opportunity will only be offered in the approved Core Courses, with a Curriculum Fellow directing the TA-embedded course. Learning Goals: At the end of this embedded course students will:  Learn how to develop the skills of an effective small group discussion leader  Learn strategies for developing appropriate assessments (e.g. writing effective problem set and exam questions)  Be able to generate rubrics for grading exams, problem sets, and oral participation  Gain an understanding of course planning and design, including choosing appropriate educational formats for the content and level of the student.  Have written reflective pieces on their own teaching to incorporate into a teaching philosophy. Format and Coursework: Course-related responsibilities: As part of the teaching assistantship, each TA will be required to:  attend all of the lectures, seminars, and workshops associated with the course  attend faculty meetings and TA meetings  teach discussion sections (meet about 10 times per semester)  assign and record grades  be available to students outside of class time for office hours and/or appointments  write problem sets and exam questions  develop rubrics for grading  grade assignments. This course is graded on a satisfactory/ unsatisfactory scale.

Teaching coursework: At the end of each faculty meeting listed above, the TAs and CF will meet to discuss lesson planning for the following section. In addition to this and the other course-specific requirements listed above, there will also be several TA-specific sessions during which readings and discussions will focus on the four objectives outlined above. TAs will read an assigned paper and come to the discussion prepared to discuss it. The topics for these sessions will include:  modes of teaching and learning.  strategies for leading small group discussion sections  how to write effective problem sets and exam questions  developing grading rubrics  how to write a teaching philosophy Assignments and Evaluation: Pedagogy discussions: TAs will be asked to complete at least 5 readings and come prepared to discuss them in the 5 TA meetings throughout the semester. TAs will also be expected to contribute to CF-TA lesson planning discussions at the end of each faculty meeting. Reflective writing: TAs will write a reflective journal entry after each discussion section which addresses questions such as, what parts of my lesson worked, what did not work, what could I try for the future, what were some unexpected outcomes of the lesson. Assessment of TA’s will be based on the following components:  Observation of teaching  Writing of multipart problem set questions  Written teaching reflection journal  Final reflective essay or written teaching philosophy  Participation in pedagogy and lesson planning discussions TAs will receive feedback on all of these components of their evaluation from both the course faculty and Curriculum Fellow. Benefits: Students enrolled in this course will have a structured and rigorous TA experience where they are given assistance in their lesson planning and feedback on their performance. They will:  Learn about teaching by reading, discussing, and practicing the craft.  Learn how to write assessment tools and develop rubric for grading them.  Have the opportunity to formally discuss pedagogy with a cohort of peers, while also reflecting on their own experiences in the classroom.  Be assessed and given feedback by Curriculum Fellows and faculty on their teaching, and will also be offered recommendations based on their participation.  Develop a journal of teaching reflections that can be used in a portfolio or teaching statement.

BCMP 200 (BP723): Molecular Biology Faculty Dr. Richard Gregory (course director) Dr. Kami Ahmad Dr. Paul Anderson Dr. Stirling Churchman Dr. Joseph Loparo Dr. Johannes Walter Dr. Timur Yusufzai

email address [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

Faculty Section leaders Dr. Steve Buratowski Dr. Sun Hur Dr. Carl Novina Dr. Ralph Scully Dr. Shobha Vasudevan Dr. Wesley Wong

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

Curriculum Fellow Dr. Johanna Gutlerner

[email protected]

Section TAs Kevin Harlen Andrew Giacomelli Stéphane Ricoult Ilana Kelsey Jon Henninger

[email protected] [email protected] [email protected] [email protected] [email protected]

Course Web Page:

http://isites.harvard.edu/k88583 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 of the course materials. If you are not officially enrolled in the course, please email the course Curriculum Fellow for permission to attend class and to get access to the site. Pre-requisites 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 will likely 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.

Format of course Class is held MWF from 10:45 am – 12:15 pm. There are 8 subject area modules in the course and each module will consist of one or more background 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 Canon Room (HMS, Building C). Discussion sections will take place in TMEC (rooms TBA online). Please always arrive at 10:40 AM so that we can start class promptly at 10:45 AM. Lectures: In these presentations, basic information (what students might have learned as undergraduates) will be covered rapidly, followed by a 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: A faculty member (usually the one who gave the background lectures) 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. The speaker will then call on each group to ask their question. Discussion Sections For each module, there will be one problem set question and two 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 question, and read and thought about the open-ended experimental design questions. Two students will be assigned to present solutions to these. Sections will run as follows:  Lecture/Reading review Quiz: (~15 minutes) o A short quiz will be administered at the beginning of section. This quiz may cover any of the material from the module, including lecture and seminar content and readings.  Problem-set question review (~15 minutes) o The group will work through the solution to the problem set question together or discuss a relevant paper.  Open-ended experimental design question (~60 minutes) o For each section, there will be two open-ended experimental design questions assigned. Two students will present at each section with each presenting one of the two assigned questions. All of the other students should come prepared so that they can critique these presentations based on content and style. Students will be graded based on a rubric posted online. 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 Thursday September 13th and these presentations will begin in section #1 on 9/19/12. If you have conflicts with the assigned dates, please contact Johanna Gutlerner.

o

Presentations should be 15 minute chalk talks addressing all of the elements in the posted rubric. There will be 15 minutes for questions and feedback on content and presentation style.

Grading Section attendance and participation Review quizzes 8 solutions to problem set questions – 1 per module section presentation 1 section presentation 2

5% 16% (2% each) 44% (5.5% each) 15% 20%

Readings Review and original research papers relevant to each module will be posted online. If your background in the material is rusty, we have also identified relevant background chapters in the text book (see below). Background text Watson, JD, Baker, TA, et al (2008) Molecular Biology of the Gene, sixth edition. Cold Spring Harbor Laboratory Press, New York. This is a comprehensive background text book and it is highly recommended that you buy it and read the associated chapters before each lecture, especially if your background is rusty. It is available at the Harvard Coop and several copies of this text will also be on reserve at Countway Library. Additional help: You can post any questions or concerns on the general question forum on the course website. Faculty and TAs will monitor this regularly and post answers. Questions are always welcome during and after the lectures (don't be shy!). However, if 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 in BBS. A final 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. Detailed Course Schedule DATE

FACULTY

5-Sep 7-Sep

TOPIC Module 1 -- Guiding principles of protein and DNA interactions W Intro to course/basics of protein structure and function F Protein structure/function and thermodynamics

10-Sep 12-Sep

M DNA structure and topology W Protein-DNA interactions: The lambda repressor

Loparo Loparo

TEXT

Gregory/Loparo Loparo 2,3,4,5 6 16

14-Sep

F

17-Sep 19-Sep

M Research seminar W Discussion on module 1 Module 2 -- DNA packaging, chromatin structure and replication F Chromatin structure

Loparo Section

M Chromatin replication W Research seminar F Discussion on module 2 Module 3 -- DNA replication M DNA replication overview/eukaryotic replication initiation W DNA replisome machines/replication coordination F Research seminar

Ahmad Ahmad Section

21-Sep 24-Sep 26-Sep 28-Sep 1-Oct 3-Oct 5-Oct 8-Oct 10-Oct

Protein-DNA interactions

Loparo

Ahmad

Walter Walter Walter

7

8

12-Oct

M Columbus Day – no class W Discussion on module 3 Module 4 -- DNA repair F DNA repair overview/ mismatch repair (MMR)

15-Oct 17-Oct 19-Oct

M DNA repair -- excision repair pathways BER and NER W DNA double stranded-break repair -- NHEJ and HR** F Research seminar

Walter Walter Walter

22-Oct

M

Section

24-Oct 26-Oct

Discussion on module 4 Module 5 -- Transcription and gene regulation W Transcription I F BCMP retreat -- no class

Yusufzai

21

29-Oct 31-Oct 2-Nov

M Transcription II W Transcription III F Transcription IV

Yusufzai Yusufzai Yusufzai

12,16,17

5-Nov 7-Nov

Yusufzai Section

9-Nov

M Research seminar W Discussion on module 5 Module 6 -- RNA processing and splicing F mRNA capping, termination, and packaging for transport

12-Nov 14-Nov 16-Nov

M Veteran’s Day – no class W mRNA splicing and regulation F Discussion on module 6

Section Walter

Churchman

Churchman Section

9, 10

13

19-Nov 21-Nov 23-Nov

Module 7 -- Post transcriptional regulation M Research Seminar W No Class-Day before Thanksgiving F No Class-Day after Thanksgiving

26-Nov

M

28-Nov 30-Nov 3-Dec 5-Dec 7-Dec 10-Dec 12-Dec 14-Dec

mRNA quality control -- stability and degradation, small regulatory RNAs biogenesis and function W micro RNA gene targeting and silencing F Research seminar Module 8 – Protein translation and the RNA life cycle M Discussion on module 7 W The genetic code, peptide synthesis, and translational fidelity Eukaryotic translation -- initiation, elongation, termination, and F recycling M The RNA life cycle W Research seminar F Discussion on module 8

Churchman

Gregory

18

Gregory Gregory Section Anderson Anderson Anderson Anderson Section

14, 15

HST 140/ BCMP 218 – Molecular Medicine Fall 2012, 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: Judit Totth, 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) 09/11/2012 – Programmed Cell Death in Development and Disease Speaker – Bob Horvitz; Model student presentation—Daisy Robinton Location – E25-117 **Please come prepared having read the following articles for the first class meeting** 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 Inhibitor. Cancer Res 68: 3421-3428 (2008).

 

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09/18/2012 – 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). 09/25/2012 – Sex: Cells, Chromosomes, Development and Disorders Speaker – David Page Location – MIT E25-117 Review (may be changed) : Kimble J, Page DC. The mysteries of sexual identity: the germ cell’s perspective. Science 316: 400-1 (2007). Readings (may be changed): 1. Gill ME, Hu Y-H, Lin Y, Page DC (2011) Licensing of gametogenesis, dependent on RNA binding protein DAZL, as a gateway to sexual differentiation of fetal germ cells. PNAS 108: 7443-7448. 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). 10/02/2012 – Cancer Cell Metabolism Speaker – Lew Cantley Location – MEC 227 Review: Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. Science 324: 1029-1033 (2009). Readings: 1. Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang J-K, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG and Cantley LC. Inhibition of PKM2 by reactive oxygen species contributes to cellular antioxidant responses. Science 334(6060):1278-83 (2011). PMID: 22052977. 2. Ying H, Kimmelman AC, Lyssiotis CA, Hua S, Chu GC, Fletcher-Sananikone E, Locasale JE, Son J, Zhang H, Coloff JL, Yan H, Wang W, Chen S, Viale A, Zheng H, Paik J-H, Lim C, Guimaraes AR, Martin ES, Chang J, Hezel AF, Perry SR, Hu J, Gan B, Xiao Y, Asara JM, Weissleder R, Wang YA, Chin L, Cantley LC & DePinho RA. Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell 149(3):656-70 (2012). PMID: 22541435. 3. Locasale JW, Grassian AR, Melman T, Lyssiotis CA, Mattaini KR, Bass AJ, Heffron G, Metallo CM, Muranen T, Sharfi H, Sasaki AT, Anastasiou D, Mullarky E, Vokes NI, Sasaki M, Beroukhim R, Stephanopoulos G, Ligon AH, Meyerson M, Richardson AL, Chin L, Wagner G,

 

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Asara JM, Brugge JS, Cantley LC, Vander Heiden MG. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet 43(9):869-74 (2011). doi: 10.1038/ng.890. PMID: 21804546. 10/09/2012 – The von Hippel-Lindau Tumor Suppressor Protein: Insights in Oxygen Sensing and Cancer Metabolism Speaker – Bill Kaelin Location – MEC 227 Review: Kaelin WG, Jr., Ratcliffe PJ. Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell 30 (4): 393-402 (2008), and Kaelin WG, Jr. The von Hippel-Lindau tumor suppressor protein: O2 sensing and cancer. Nat Rev Cancer 8 (11): 865-873 (2008). Readings: 1. TBA 2. TBA 10/16/2012 – Induced Pluripotent Stem Cells in Disease and Therapy Speaker – George Q. Daley Location – TBA 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. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LIR, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, Mckinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic Memory in Induced Pluripotent Stem Cells. Nature 467: 285-93 (2010). 2. Moretti A, Bellin M, Welling A, Jung CB, Lam JT, Bott-Flugel L, Dorn T, Goedel A, Hohnke C, Hofmann F, Seyfarth M, Sinnecker D, Schomig A, Laugwitz KL. Patient-specific induced pluripotent stem-cell models for Long-QT syndrome. NEJM 363 (15): 1403-1409 (2010).

10/23/2012 – Using Simple Cells as a Discovery Platform for Neurodegenerative Disease Speaker – Susan Lindquist Location – MIT E25-117 Review (may be changed) : Khurana V and Lindquist S. Modelling neurodegeneration in Saccharomyces cerevisiae: why cook with baker’s yeast? Nat Rev Neurosci 11: 436-49 (2010). Readings (may be changed) : 1. Gitler AD, Chesi A, Geddie ML, Strathearn KE, Hamamichi S, Hill KJ, Caldwell KA, Caldwell GA, Cooper AA, Rochet JC, Lindqust S. α-Synuclein is part of a diverse and highly conserved interaction network that includes PARK9 and manganese toxicity. Nature Genetics 41: 308-315 (2009).

 

3  

2. Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, uluck PK, Geddie ML, Valastyan J, Karger DR, Lindquist S, Fraenkel E. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nature Genetics 4: 316-323 (2009).

10/30/2012 – Checkpoints in Xenobiotic and Pathogen Surveillance and Countermeasures Speaker – Gary Ruvkun Location – MEC 227 Review: Jonathan DG Jones & Jeffery L Dangl. The plant immune system. Nature 444: 323-329 (2006). Readings: 1. Justine A Melo & Gary Ruvkun. Inactivation of Conserved C. elegans Genes Engages Pathogen- and Xenobiotic-Associated Defenses. Cell 149: 452-466 (2012). 2. Shore DE, Carr CE, Ruvkun G. Induction of Cytoprotective Pathways is Central to the Extension of Lifespan Conferred by Multiple Longevity Pathways. PLoS Genetics 8 (7): 1-15 (2012).

11/06/2012 – Mutation-Directed Therapy for Lung Cancer Speaker – Matthew Meyerson Location – MEC 227 Review (may be changed) : Zhang Z, Stiegler AL, Boggon TJ, Kobayashi S, Halmos B. EGFR-mutated lung cancer: a paradigm of molecular oncology. Oncotarget. 1(7): 497-514 (2010). PMID: 21165163. Readings (may be changed) : 1. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, Naoki K, Sasaki H, Fujii Y, Eck MJ, Sellers WR, Johnson BE, Meyerson M. EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefatinib Therapy. Science 304: 1497-1500 (2004). 2. Mok TS, Wu YL, Thongprasert S, Yang CH, Chu DT, Saijo N, Sunpaweravong P, Han B, Margono B, Ichinose Y, Nishiwaki Y, Ohe Y, Yang J, Chewaskulyong B, Jiang H, Duffield EL, Watkins CL, Armour AA, Fukuoka M. Gefitinib or Carboplatin-Paclitaxel in Pulmonary Adenocarcinoma. NEJM 361: 947-57 (2009).

11/13/2012 – Title Speaker – Sangeeta Bhatia Location – MIT E25-117 Review: TBA Readings: 1. TBA 2. TBA

 

4  

11/20/2012 – The Roles of miRNAs in Normal and Disease Processes Speaker – Phil Sharp Location – MIT E25-117 Review (may be changed) : Bartel DP. MicroRNAs: Target Recognition and Regulatory Functions. Cell 136: 215-33 (2009). Readings (may be changed): 1. Anokye-Danso F, Trivedi CM, Juhr D, Gupta M, Cui Z, Tian Y, Zhang Y, Yang W, Gruber PJ, Epstein JA, Morrisey EE. Highly Efficient miRNA-Mediated Reprogramming of Mouse and Human Somatic Cells to Pluirpotency. Cell Stem Cell 8: 376-388 (2011). 2. Boldin MP, Taganov KD, Rao DS, Yang L, Zhao JL, Kalwani M, Garcia-Flores Y, Luong M, Devrekanli A, Xu J, Sun G, Tay J, Linsley PS, Baltimore D. miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice. JEM 1189-1201 (2011).

11/27/2012 – Title Speaker – Li-Huei Tsai Location – MIT E25-117 Review: Gräff J, Kim D, Dobbin MM, Tsai L. Epigenetic regulation of gene expression in physiological and pathological brain processes. Physiol Rev 91: 603-649 (2011). Readings: 1. Guan J, Haggarty SJ, Giacometti E, Dannenberg J, Joseph N, Gao J, Nieland TJ, Zhou Y, Wang X, Mazitschek R, Bradner JE, DePinho RA, Jaenisch R, Tsai L. HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459: 55-63 (2009). 2. Gräff J, Rei D, Guan J, Wang W, Seo J, Hennig KM, Nieland TJF, Fass DM, Kao PF, Kahn M, Su SC, Samiei A, Joseph N, Haggarty SJ, Delalle I, Tsai L. An epigenetic blockade of cognitive functions in the neurodegenerating brain. Nature 483: 222-228 (2012). 12/4/2012 – Human Genetic Variation and Disease Speaker – David Altshuler Location – MIT E25-117 Review: Readings: TBA

 

5  

BCMP 228

Wagner/Chou - NMR course 2012

Macromolecular NMR (BCMP 228) Fall 2012 Instructors: G. Wagner, J. Chou, K. Oxenoid. J. Sun, G. Heffron, H. Arthanari, S. Hyberts This course will teach basic principles and skills of macromolecular NMR, in particular on proteins. The goal is to teach basic principles of pulsed NMR, to understand the mechanisms of the most common NMR experiments and to provide the opportunity to write pulse sequences that can be executed on NMR spectrometers. The course will offer NMR theory and workshop sessions. The workshops will focus on writing executable pulse programs in the Bruker and Agilent environments, performing assignments and calculating structures. We will include sessions on advanced sampling and spectra reconstruction methods. Lectures will be Mondays and Fridays 2:00 - 3:30 First lecture 9/10/12 Room TMEC 227 Web Page: bcmp228.med.harvard.edu __________________________________________________________________ 1. Introduction to biomolecular NMR Wagner

M 9-10-12

2. Classical approach to spin F 9-14-12 Classical understanding of NMR with 1H 1D experiments as examples Chou __________________________________________________________________ 3. 1H 1D experiments (water suppressed, diffusion) M 9-17-12 Chou 4. Quantum approach to spin F 9-21-12 Quantum mechanical understanding of NMR, spin states Wagner __________________________________________________________________ 5. Operator Formalism Theory and Workshop M 9-24-12 Wagner 6. INEPT and HSQC F 9-28-12 JCout Oxenoid __________________________________________________________________ 7. Workshop: HSQC and variants M 10-1-12 Chou 8. Triple resonance F 10-5-12 Chou __________________________________________________________________ Columbus day M 10-8-12 9. Workshop: triple resonance Chou

M 10-12-12 GWout

10. NMR pulse programming language

F 10-15-12 GWout 1

1

BCMP 228

Wagner/Chou - NMR course 2012

Heffron __________________________________________________________________ 11. NMR pulse programming workshop M 10-19-12 GWout Arthanari 12. Setting up NMR experiments F 10-22-12 Arthanari ________________________________________________________________ Retreat

F 10-26-12

13. Nuclear Overhauser Enhancement Theory M 10-29-12 JCout Wagner ________________________________________________________________ 14. Workshop: NOESY and variants Oxenoid

M 11-2-12 JCout

15. Relaxation : concepts F 11-5-12 Oxenoid ________________________________________________________________ 18. Relaxation: protein dynamics M 11-9-12 Wagner 19. TROSY F 11-12-12 JCout Oxenoid __________________________________________________________________ 20. TROSY workshop M 11-16-12 JCout Oxenoid 21. Residual dipolar coupling F 11-19-12 Chou __________________________________________________________________ Thanksgiving no lecture

F 11-23-12

________________________________________________________________ 22. Workshop: RDCs Chou

M 11-26-12 GWout

23. NMR structure determination Cyana M 11-30-12 Sun ___________________________________________________________________ 24. NMR structure determination XPLOR F 12-3-12 Chou ___________________________________________________________________ 2

2

BCMP 228

Wagner/Chou - NMR course 2012

25. Non-uniform sampling and processing Hyberts

M-12-7-12

26. Implementation of NUS and Data Reconstruction Arthanari, Hyberts

M-12-10-12

End of course

3

3

MIT Principles and Practice of Drug Development Fall 2012 7.547J, 10.547J, 15.136J, ESD.691J, HST.920J, BCMP 230

Building 4 (Whitaker Building), Room 163 Thursdays, 3:00 – 6:00 pm Instructors: Thomas J. Allen, Ph.D. Charles L. Cooney, Ph.D. Stan N. Finkelstein, M.D. G.K. Raju, Ph.D. Anthony J. Sinskey, Sc.D.

NE25-758 56-469B E40-251 E19-611 68-370A

617-253-6651 617-253-3108 617-253-8014 617-258-8583 617-253-6721

[email protected] [email protected] [email protected] [email protected] [email protected]

Teaching Assistant: Abby Horn

[email protected]

CLASS SCHEDULE (update lectures) September 6

Introduction. (Faculty) From Discovery to Market: An Integrated View Charles L. Cooney, Ph.D.

September 13

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 20

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 27

Special session (symposium): FDA Regulation of Drug Manufacturing GK Raju and roundtable

October 4

October 11

Business of Biopharmaceuticals Guest:

Robert Mulroy, MBA, Director, President & CEO, Merrimack Pharmaceuticals

Guest:

Sumit Khedekar, Director, Global Healthcare Group, Bank of America, Merrill Lynch

Clinical Drug Development Guest:

October 18

Drug Delivery Systems Guest:

October 25

Clet Niyikiza, Ph.D., Executive Vice President Merrimack Pharmaceuticals

Portuguese faculty (Luís Almeida, Ph.D., João Nuno Moreira, Ph.D., Sérgio Simões, Ph.D. University of Coimbra, Portugal)

Regulation, Reimbursement Stan N. Finkelstein, M.D.

November 1

Manufacturing I G. K. Raju, Ph.D. Charles L. Cooney, Ph.D.

MIT Principles and Practice of Drug Development – Fall 2010

2

MIT Principles and Practice of Drug Development (continued)

November 8

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 15

Manufacturing II Charles L. Cooney, Ph.D. G. K. Raju, Ph.D.

November 22

Thanksgiving Day – No Class

November 29

Open (previously: Organizing for Drug Development, Thomas J. Allen, Ph.D.)

December 6

Student Presentations

MIT Principles and Practice of Drug Development – Fall 2010

3



BCMP 235: Syllabus and Schedule Fall 2012  Date 

 

 

 

Lecturer 

Problem set or case 

M‐ Sept. 3 

Labor Day Holiday 

W‐ Sept. 5 

Introduction to Pharmacology I   

 

Carl Rosow 

 

      Problem set (PS) 1  No 

F‐ Sept. 7 

Introduction to Pharmacology II          

  

Carl Rosow 

 

       PS 1 

 

Yes 

  

 

Case preparation lunch: case 1 presentation: DCM 

        Case 1 

 

 No 

 

        Case 1 

 

 No 

 

Topic   

 

 

      Evaluation 

 

M‐ Sept. 10 

Normal Cardiac Physiology I 

W‐ Sept. 12 

Tutorial 1‐1…  Dilated Cardiomyopathy   

F‐ Sept. 14 

Atherothrombosis            

M‐ Sept. 17 

Heart Failure                                                     

W‐ Sept. 19 

Tutorial 1‐2…Dilated Cardiomyopathy 

F‐ Sept. 21 

Introduction to Respiratory Physiology            

Robert Padera             

         PS 2 

 

No 

M‐ Sept. 24 

Lung Transplantation Biology 

Robert Padera   

         PS 2 

 

Yes 

W‐ Sept. 26 

Tutorial 1‐3…Dilated Cardiomyopathy 

 

Case preparation lunch: case 2 presentation: IBD 

 

                             Tony Rosenzweig 

 

 

              Tony Rosenzweig 

  

Tony Rosenzweig                     Case 1                        Yes 

 

F‐ Sept. 28 

Introduction to GI Physiology 

 

  

Daniel Kamin   

         Case 2 

 

Yes 

M‐ Oct. 1 

Liver Disease/Hepatitis   

 

  

Raymond Chung 

          PS  3 

 

Yes 

 

Patient presentation 

M‐ Oct. 1 

Immunology lecture (optional)   

 

 

 

 

PS 

W‐ Oct. 3 

Tutorial 2‐1…IBD: Crohn’s Disease 

F‐ Oct. 5 

 Stem Cells and Developmental Biology                 Paola Arlotta   

 

 

 

Yes 

M‐ Oct. 8 

Columbus Day Holiday 

W‐ Oct. 10 

Tutorial 2‐2… IBD: Crohn’s Disease 

F‐ Oct. 12 

Renal physiology 

 

 

 

Dennis Brown   

         PS  3 

 

No 

M‐ Oct. 15 

Acidosis and  

 

 

 

Dennis Brown   

         PS 3 

 

Yes 

 

 

 

 

W‐ Oct. 17 

Tutorial 2‐3… IBD: Crohn’s Disease 

 

Case preparation lunch: case 3 presentation: Parkinson’s Disease 

 

F‐ Oct. 19 

Neuroanatomy/disease  

 

 

 David Cardozo   

Case 3   

No 

M‐ Oct. 22 

Neurophysiology/disease 

 

 

David Cardozo   

 Case 3   

No 

W‐ Oct. 24 

Tutorial 3‐1…Parkinson’s Disease 

F‐ Oct. 26 

Neuropathology I 

 

 

 

David Cardozo   

  Case 3  

No 

M‐ Oct. 29 

Neuropathology II 

 

 

 

David Cardozo   

  Case 3  

Yes 

W‐ Oct. 31 

Tutorial 3‐2… Parkinson’s Disease 

F‐ Nov. 2 

Reproductive Endocrinology 

 

 

Hope Ricciotti   

            PS 4 

 

Yes 

M‐ Nov. 5 

Intro to endocrinology   

 

 

Evan Rosen 

 

            PS 4 

    

No 

W‐ Nov. 7 

Tutorial 3‐3… Parkinson’s Disease 

 

             PS 4 

 

Yes 

Feedback lunch 

Case preparation lunch case 4 presentation: Breast cancer  F‐ Nov. 9 

Pituitary 

 

M‐ Nov. 12 

Veterans Day Holiday 

 

 

 

Evan Rosen 

W‐ Nov. 14 

Tutorial 4‐1…Breast Cancer 

F‐ Nov. 16 

Introduction to Cancer Biology:   

 

Sandy Mcallister 

 

Case 4   

Yes 

M‐ Nov. 19 

Tumor Immunology 

 

 

Glenn Dranoff   

 

Case 4   

Yes 

 

 

Rachel Meyers   

 

 

 

Yes 

 

W‐F Nov. 21 – 23:  Thanksgiving Holiday  M‐ Nov. 26 

RNA Therapeutics 

 

W‐ Nov. 28 

Tutorial 4‐2…Breast Cancer 

F‐ Nov. 30 

Viruses as therapeutic agents   

 

Connie Cepko   

 

 

 

Yes 

M‐ Dec. 3 

Personalized Cancer Medicine   

 

David Livingston 

 

 

 

Yes 

W‐ Dec 5th  

Tutorial 4‐3…Breast Cancer 

 

 

 

Due Dec X. Take home final exam  Legend:  Location: NRB 360 seminar room from 9am to 10:30 AM;   In yellow: No class: holidays 

 

In Green: tutorials  In Blue: Lunches for tutors (optional) and day 1 presenters (required)  Tutorials rooms: TMEC X, TMEC X, TMEC X, TMEC X.  

Cell Biology 226. Concepts in Development, Self-Renewal, and Repair Catalog Number: 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, Kellee Siegried-Harris, 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: Friday 9/6, 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. 9/5/2010. ([email protected]). All Subsequent classes will be at MGH. MGH course shuttle bus leaves Vanderbilt Hall at 1:30 PM

DATE 05-Sep-12 W 07-Sep-12 F

START FINISH LECTURE LECTURER ROOM 9:00 AM ####### Lecture 1: What we learned from Mendel – Winston Winston Canon 9:00 AM ####### Lecture 2: Introduction to yeast genetics; complementation analysis – Winston Winston Canon Problem Set 1 Distributed 10-Sep-12 M 9:00 AM ####### Lecture 3: Linkage and tetrad analysis in yeast – Winston Winston Canon 12-Sep-12 W 9:00 AM ####### Section 14-Sep-12 F 9:00 AM ####### Lecture 4: Molecular and genomic studies in yeast – Winston Winston Canon 17-Sep-12 M 9:00 AM ####### Lecture 5: Suppressor analysis in yeast – Winston Winston Canon 19-Sep-12 W 9:00 AM ####### Lecture 6: Non-Mendelian inheritance in yeast – Winston Winston Canon 19-Sep-12 W ####### 1:30 PM Supplemental Lecture – Brault Brault MEC 250/canon 21-Sep-12 F 9:00 AM ####### Section 24-Sep-12 M 9:00 AM ####### Lecture 7: Molecular mechanisms of homologous recombination: genetic analysis – WinWinston Canon Problem Set 1 Due Problem Set 2 Distributed 26-Sep-12 W 9:00 AM ####### Lecture 8: Bacaterial genetics I – Bernhardt Bernhardt Canon 28-Sep-12 F 9:00 AM ####### Lecture 9: Bacterial genetics 2 – Bernhardt Bernhardt Canon 01-Oct-12 M 9:00 AM ####### Lecture 10: Bacterial genetics 3 – Bernhardt Bernhardt Canon 03-Oct-12 W 9:00 AM ####### Section 05-Oct-12 F 9:00 AM ####### Lecture 11: Bacterial genetics 4 – Bernhardt Bernhardt Canon 05-Oct-12 F ####### 1:30 PM Supplemental Lecture – Brault Brault MEC 250/canon 08-Oct-12 M Columbus Day - No Class 10-Oct-12 W 9:00 AM ####### Section Problem Set 2 Due 11-Oct-12 Th Midterm handed out 12-Oct-12 F Midterm handed in 15-Oct-12 M 9:00 AM ####### Lecture 12: Introduction to Drosophila: genotypes, maps, and balancer chromosomes –Kuroda Canon Problem Set 3A Distributed 17-Oct-12 W 9:00 AM ####### Lecture 13: Mapping mutants in Drosophila: meiotic and physical mapping, gene Kuroda Canon isolation and transformation – Kuroda (Cell Bio retreat) 19-Oct-12 F 9:00 AM ####### Lecture 14: Classical genetic screens and pathway analysis in flies – Kuroda Kuroda Canon 22-Oct-12 M 9:00 AM ####### Lecture 15: Modifier screens: enhancers, suppressors, and mosaic analysis in flies – KuKuroda Canon 22-Oct-12 M ####### 1:30 PM Supplemental Lecture – Brault Brault MEC 250/canon 24-Oct-12 W 9:00 AM ####### Section 26-Oct-12 F BCMP retreat - No Lecture 29-Oct-12 M 9:00 AM ####### Lecture 16: Introduction to C. elegans as a genetic system – Heiman Heiman Canon Problem Set 3A Due Problem Set 3B Distributed 31-Oct-12 W 9:00 AM ####### Lecture 17: Genetic screens in C. elegans – Heiman Heiman Canon 02-Nov-12 F 9:00 AM ####### Lecture 18: Genetic mapping in C. elegans – Heiman Heiman Canon 05-Nov-12 M 9:00 AM ####### Lecture 19: Mosaic and epistasis analysis in C. elegans -Heiman Heiman Canon 07-Nov-12 W 9:00 AM ####### Section 09-Nov-12 F 9:00 AM ####### Lecture 20: Mendelian traits and pedigree analysis in mammals – McCarroll McCarroll Canon Problem Set 3B Due Problem Set 5 Distributed 12-Nov-12 M Veterans Day - No Class 14-Nov-12 W 9:00 AM ####### Lecture 21: Basics of linkage analysis: phase, informativeness, and the LOD score – M McCarroll Canon 16-Nov-12 F 9:00 AM ####### Lecture 22: Haplotype analysis; Genetic screens in the mouse – McCarroll McCarroll Canon 19-Nov-12 M 9:00 AM ####### Lecture 23: Transgenic and knockout mice: techniques and applications – McCarroll McCarroll Canon 21-Nov-12 W pre-Thanksgiving vacation; no class 23-Nov-12 F post-Thanksgiving vacation; no class 26-Nov-12 M 9:00 AM ####### Section 28-Nov-12 W 9:00 AM ####### Lecture 24: Strategies for mapping complex genetic traits in humans – McCarroll McCarroll Canon 30-Nov-12 F 9:00 AM ####### Lecture 25: Overview of association studies in humans – McCarroll McCarroll Canon 03-Dec-12 M 9:00 AM ####### Lecture 26: Epigenetics – Winston Winston Canon 05-Dec-12 W 9:00 AM ####### Lecture 27: Epigenetics – Winston Winston Canon Problem Set 5 Due 07-Dec-12 F 9:00 AM ####### Section 10-Dec-12 M 9:00 AM ####### Final exam given out 11-Dec-12 T 9:00 AM ####### Final exam due Canon

Genetics 219

Fall 2011

Genetics 219: Inheritance and Weird Stuff Catalogue Number: 14189 Fall 2012 Note: This syllabus may change before the start of classes.

Time & location:

Tuesday, 10-1 pm September 11 - November 27 To be announced

Prerequisites:

Primarily for first-year graduate students but, space permitting, is open to other graduate students, medical students, and advanced undergraduates. A basic understanding of genetics is recommended but not essential.

Instructors:

Kami Ahmad

Dept. of BCMP Building C, Room 204 [email protected] 617-432-0588 Telephone

Steve McCarroll

Dept. of Genetics NRB 260 [email protected] 617-432-7794 Telephone

David Reich

Dept. of Genetics NRB 260 [email protected] 617-432-6548 Telephone

Ting Wu (Course director)

Dept. of Genetics NRB 264 [email protected] 617-432-4431 Telephone

What does 'inheritance' mean? How do we recognize inheritance and, when we do recognize it, what is the entity that is being inherited and by what mechanism does the inheritance occur? Given the surprising forms of inheritance that have been discovered in recent years, these questions are gaining import even as their answers are growing more complex. In this course, we will explore inheritance, keeping in mind the many ramifications for medical research and human health. We will begin with a quick review of the better known principles of genetics and then delve into observations and phenomena of a variety of organisms, including humans, mice, nematodes, fungi, and plants. The format of the course will be a mix of lectures, discussion, and in class group problem-solving. Grading will rest entirely on class participation (i.e., no tests, problem sets, or papers). Page 1 of 4

Genetics 219

Fall 2011 Schedule of classes

September 11 (Ting)

Segregation, complementation, recombination .... and rearrangements: This class will start our foray into the lesser known forms of inheritance. We will begin in 1915 with William Bateson, who was one of the strongest proponents of Mendel, even as he urged geneticists to be aware of other forms of inheritance. We will consider the chromosome and the gene as well as debate the pros and cons of assuming 'principles' of inheritance. We will further consider the concepts of complementation, segregation, and recombination and then address the impact of chromosome rearrangements, including deletions, duplications, inversions, and translocations.

September 18 (Ting)

From mating-type switching in yeast to handedness, hair whorls, and schizophrenia in humans: We have all heard about random assortment. What do we mean by random, and how do we recognize it? How prevalent is it in nature? In this class, we will follow the work of Amar Klar, as he takes us from mating-type switching in the fission yeast to handedness, hair whorls, and schizophrenia in humans. Our discussion will take straight down to the individual DNA strands.

September 25 (Ting)

Repeat-induced point mutation: We will extend our familiarity with chromosome rearrangements by tackling genetic problems during class. We will then continue on the theme of unusual patterns of inheritance by considering repeat-induced point mutation (RIP) in Neurospora, which is a predominantly haploid organism that has little tolerance for duplications. Discussion will include a description of the sexual cycle, which produces ordered octads.

October 2 (Ting)

Chromosomes – from the double helix to Watson and Crick: After beginning class with additional problem solving exercises, we will continue our consideration of RIP. This discussion will focus on the consequences of replication on inheritance at the level of sister chromatids and address the potential of methylation and mutation to render Watson and Crick asymmetrically marked. Our discussion will also touch on the implications of the genetic code.

October 9 (Steve)

Heritability: How do we establish that a complex trait is genetically heritable in humans and other organisms? How is heritability measured, and why are measurements of heritability potentially confounded? How do new kinds of genetic data offer novel ways to measure the heritability of quantitative traits and disease risk? Centromere inheritance: Centromeres are essential sites of eukaryotic chromosomes, but the mechanisms that specify their location are diverse. We will consider evidence that centromeres are epigenetically defined by distinctive nucleosomes.

October 16 (Kami)

October 23

Meiotic drive: The mechanics of chromosome segregation Page 2 of 4

Genetics 219

Fall 2011

(Kami)

provide opportunities for competition between genetic elements. We will discuss evidence that such elements contribute to evolutionary innovation and the separation of species.

October 30 (Kami)

Heterochromatin and chromatin elimination: Some organisms specialize their genomes in somatic cells by eliminating repetitive sequences around centromeres and telomeres. Are these elements simply junk DNA? We will examine potential functions in systems where portions of the genome are destroyed.

November 6 (David)

Genetic differences among human populations: What is the nature of genetic differences among human populations? Do self-defined ethnic groups correspond to objectively real clusters as determined by genetic data? What is the historical origin of human population differences? What can we learn from human differences about history, the process of natural selection, and about disease?

November 13 (Ting)

Ultraconservation: Much to the surprise of bioinformaticists, geneticists, and evolutionary biologists, it appears that some sequences of mammalian genomes have remained essentially unchanged for hundreds of millions of years. Do these sequences form a special class or are they simply the tail end of a normal distribution of conserved sequences? If the former, what mechanism(s) could explain their ultraconservation?

November 20

To be announced:

November 27

To be announced:

Page 3 of 4

Genetics 219

Fall 2011

Genetics 219 Sign-up sheet for registration in course (Due at end of the first class) Name Email address Status: ( ) Graduate student:

Program

Year

( ) Other: Department (if appropriate): Laboratory (if appropriate): How certain are you that you will take this course if you are offered a spot? Are you taking Genetics 201 this semester? Why are you interested in taking this course?

What areas of biology interest you in general?

So that we can more easily match your name to our memory of you in class, please feel free to note down distinguishing comments or questions that you may have brought up during this first class.

Page 4 of 4

Harvard-MIT Division of Health Sciences and Technology HST.160

Fall 2012

Tuesdays, 2-5 PM, MIT Building 1, room 190; Fridays 9:30 AM – 12:30 PM Discussion Sections, 9:30 – 10:20 TMEC 443, TMEC 445, TMEC 446, TMEC 448 Lecture/clinic TMEC 209, 10:30 – 12:30 209

Molecular Biology and Genetics in Modern Medicine

Course Directors: David Housman MIT E18-521 [email protected] (617) 253-3013

Anne Giersch HMS, NRB 160 [email protected] (617) 525-4541

Teaching Assistants:

Vineeta Agarwala [email protected]

Jesse Engreitz [email protected]

Elena Helman [email protected]

Dan Day [email protected]

Day

Date

Time

Topic

Lecturer

Friday

Sept. 7

9:30-12:30

Introduction/ Preliminary assessment/ Genome architecture

Tuesday

Sept. 11

2:00 - 5:00

Retinoblastoma

Housman

Friday

Sept. 14

9:30-12:30

Hypertrophic cardiomyopathy

Seidman

Tuesday

Sept. 18

2:00 - 5:00

Breast cancer

TBA

Friday Friday

Sept. 21 Sept. 21

9:30-10:20 10:30-12:30

Discussion sections Deafness

Anne Giersch

Tuesday

Sept. 25

2:00 - 5:00

Thalassemia

David Nathan

Friday

Sept. 28

9:30-10:20 10:30 – 12:30

Discussion sections Newborn Screening

Harvey Levy

Giersch/Housman

Tuesday

Oct. 2

2:00 - 5:00

Chromosomes and CNVs

Anne Giersch

Friday

Oct. 5 Oct. 5

9:30-10:20 10:30 – 12:30

Discussion sections Mitochondria

David Simon

Tuesday

Oct.9

2:00 - 5:00

Williams syndrome

Barbara Pober

Friday Friday

Oct. 12 Oct. 12

9:30 - 10:30 10:30-12:30

Discussion sections Hemophilia

Ellis Neufeld

Lewis Holmes

Omar Khwaja

Tuesday

Oct. 16

2:00 - 5:00

Genetic counseling and prenatal diagnosis

Friday

Oct. 19

9:30-10:30 10:30-12:30

Discussion sections Rett syndrome

Tuesday

Oct. 23

2:00 - 5:00

Midterm exam

Friday Friday

Oct. 26 Oct. 26

9:30-10:20 10:30-12:30

Discussion sections Fanconi Anemia

Alan D’Andrea

2

Tuesday

Oct.30

2:00 - 5:00

Colon Cancer

Dan Chung

Friday Friday

Nov. 2 Nov. 2

9:30-10:20 10:30-12:30

Discussion sections Huntingtons disease

David Housman

Tuesday

Nov. 6

2:00 - 5:00

RNAi

Carl Novina

Friday Friday

Nov. 9 Nov. 9

9:30-10:20 10:30-12:30

Discussion sections Myotonic dystrophy

Eric Wang

Nov. 13 Tuesday

(path midterm)

2:00 - 5:00

Whole Genome sequencing

Rehm/Funke/Murray

Friday Friday

Nov. 16 Nov. 16

9:30-10:20 10:30-12:30

Discussion sections Forensic DNA

Frederick Bieber

Tuesday

Nov. 20

2:00 - 5:00

Gene patents

David Resnick

Friday

Nov. 22

Tuesday

Nov. 27

Friday

Nov. 30

Thanksgiving – No Class 2:00 - 5:00

Review Session Final exam

Final papers are due Sunday Nov. 25th Presentation of your papers in small group sessions will be the first week of December dates/times/places TBA. Presentation is mandatory.

Grading: Homework assignments/problem sets Discussion section participation, presentation and written assignments Midterm quiz Final exam (cumulative) Clinical project paper and presentation

15% 20% 15% 25% 25%

3

IMM201 PRINCIPLES OF IMMUNOLOGY   Fall 2012 Syllabus    Lectures: Tuesdays and Thursdays, 1:30‐4:00pm  Workshops: See schedule below  First Meeting: September 4th  Location: Rosen Classroom, Modell Center, Room 100A  Course Directors: Shannon Turley & Uli von Andrian    Teaching Assistants:   Jon Chang ‐ [email protected]  Ezana Demissie ‐ [email protected]  Cat Tan ‐ [email protected]  David Puyraimond‐Zemmour ‐ [email protected]    LECTURES  Date    Lecturer      Topic__________________        Sept 4th            von Andrian & Turley    Course Introduction  von Andrian      Overview of the Immune System  Sept. 6th  Sept 11th  Rossi        Hematopoiesis & Stem Cells  Sept. 13th  Stuart        Innate Immunity  Sept. 18th  Carroll        Link between Innate and Adaptive Immunity  Turley        Development of Lymphoid Tissues  Sept. 20th  Sept. 25th  Pillai        B Cell Development and Selection      Early Lymphoid Development**  **Sept. 26th  Melchers  Pillai        B Cell Activation and Differentiation  Sept. 27th  Oct 2nd  Alt        VDJ Recombination in B Cell Development        Class Switch Recombination  Oct. 4th    Alt  Carroll        B cell Acquisition of Antigen  Oct. 9th   Oct. 11th  Serwold      T Cell Development and Selection  Oct. 16th  ‐‐‐‐‐‐‐‐‐‐‐      Review  Oct. 18th  ‐‐‐‐‐‐‐‐‐‐‐      Midterm Exam  rd Oct. 23   Wucherpfennig    MHC Class I and II Antigen Presentation  Oct 25th  Wucherpfennig    T Cell Recognition of Antigen  Moody        CD1 Antigen Presentation  Oct. 30th  Nov. 1st   Turley        Dendritic Cells  Nov 6th   Sharpe       T Cell Regulation I  th Sharpe       T Cell Regulation II   Nov. 8   Nov 13th  von Andrian      Homing and Lymphocyte Trafficking    Nov 15th            Mathis        Immunometabolism  Nov. 20th  Lieberman      Programmed Cell Death and Cytotoxic Lymphocytes  Nov 22nd  No Class      Thanksgiving Holiday   Nov. 27th   Ploegh        Viral Escape of Host Immunity      ‐‐‐‐‐‐‐‐‐‐‐  Review  Nov. 29th  Dec. 4th   ‐‐‐‐‐‐‐‐‐‐‐       Final Exam            WORKSHOPS (4:30­6:00pm)    Date    Lecturer      Topic__________________      Rossi        Flow Cytometry and Cell Sorting  Sept. 17th   von Andrian      Tissue Anatomy  Oct. 1st    th Wucherpfennig    How Do I Study Proteins?   Nov. 5    Hacohen      Systems Immunology  Nov 19th   

IMMUNOLOGY 301 2012-2013 Immunology 301 is a required course, to be taken in the Fall and Spring semester of your G1 year. To fulfill the requirements of this course and receive a satisfactory grade, you 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: 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 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 5.

HT-010 Human Functional Anatomy Wed Sep 5, 2012 All day

HST 010 Begins

Wed Sep 5, 2012 - Thu Sep 6, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 2pm

Course Introduction (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2pm - 2:30pm

Dissection Table Seletion (Gehrke)

W h e r e : TMEC 419, 420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 3:45pm

Organogenesis (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

4pm - 5pm

Intro to Peripheral nn (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Sep 7, 2012 1:30pm - 2:30pm

Anatomy of Thorax (Cotanche)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:30pm - 3pm

Intro to Laboratory (Cotanche)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

Chest wall

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3:30pm - 6pm

Thorax Prosection (half class) (Cotanche)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Sep 10, 2012 1:30pm - 2:45pm

Thoracic Surgery (Sugarbaker)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

PRO: Thorax (2nd half class) (Cotanche)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Sep 12, 2012 1:30pm - 2:45pm

Embryology Heart (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

LAB: Anterior Mediastinum and Middle Mediastinum

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Sep 14, 2012 1:30pm - 2:15pm

Breast & Breast Imaging (Slanetz)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:15pm - 3pm

Chest Imaging (Dr. Spirn, BIDMC)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 3:15pm

Intro to top 25 Cases (Slanetz)

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3:30pm - 6:30pm PRO Fresh Bovine Heart (self directed; supplemental instructions) W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Sep 17, 2012 1:30pm - 2:30pm

Heart Imaging: Echocardiography (Stultz)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 2:45pm - 5:15pm

LAB: Superficial Back

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Sep 19, 2012 1:30pm - 2:30pm

Development of the Extremities (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Back Musculature

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Sep 21, 2012 1:30pm - 2:30pm

Clinical Biomechanics of Spine; Back Pain (?)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Sep 24, 2012 1:30pm - 2:30pm

Organization of Upper Extremity (van Houten)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO Shoulder & Brachial Plexus (Cotanche)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Sep 26, 2012 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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 2:45pm - 6pm

LAB: Arm and Forearm flexors

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO (Arm, forearm flexors) (Izamis)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Sep 28, 2012 1:30pm - 2:30pm

Func. Anatomy Hand (Van Houten)

W h e r e : MEC 227 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Palm of the Hand

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Oct 1, 2012 1:30pm - 2:30pm

Limb Biomechanics (Herr)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Oct 3, 2012 1:30pm - 2:30pm

Hip, Knee, Ankle (Herr)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Lower extremity; superficial & anterior thigh

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 2:45pm - 6pm

PRO: Anterior & Medial Thigh (Lutchman)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Oct 5, 2012 1:30pm - 2:30pm

Human Gait (Herr)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Gluteal region; Posterior thigh

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Gluteal region; hamstrings; popliteal fossa (?)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Tue Oct 9, 2012 All day

P athology E xam

Tue Oct 9, 2012 - Wed Oct 10, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Oct 10, 2012 12:30pm - 1:30pm

Review upper and lower extremities (van Houten)

W h e r e : MEC 309 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 2:15pm

Radiology: Reading MSK images (Wu)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:15pm - 2:45pm

Review to p 2 5 c h e s t/ MS K i m a g e s (S l a n e tz )

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Leg

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Small Group MSK radiology (Yablon, Wu, Slanetz)

W h e r e : TMEC 218 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy Fri Oct 12, 2012 12:30pm - 1:30pm

Review Thorax & Brachial Plexus (Cotanche)

W h e r e : MEC 324 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 2:30pm

Physical Exam of Extremities (Rodriguez)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Sole of Foot; Joints of Lower extremity

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Knee Joint (self-directed)

W h e r e : TME 419, 420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Oct 15, 2012 1:30pm - 2:30pm

Review of development (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 4pm

Review Statics Homework + Biomechanics (Herr)

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

4:15pm - 4:45pm

show practice ID's (Cotanche)

W h e r e : TMEC 209 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Oct 17, 2012 1:30pm - 3pm

Mid-term examination

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6:30pm

Midterm examination grading (Faculty Only)

W h e r e : TMEC 204 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy Fri Oct 19, 2012 1:30pm - 2:30pm

Devel of GI system (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Abdominal wall; inguinal region

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Anterior Abdo. Wall (Lutchman)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Oct 22, 2012 1:30pm - 2:15pm

Abdominal Imaging (Dr. Alex Guimaraes)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:15pm - 2:45pm

Top 25 Abdo/pelvis imaging cases (Slanetz)

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Peritoneum; Peritoneal cavity

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Oct 24, 2012 1:30pm - 2:30pm

Dev. UG System (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Mesenteric Vessels; Abdominal viscera

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm PRO: Abdominal viscera, celiac axis, mesenteric vessels, portal vein; post. abdom. wall (Cotanche) W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Oct 26, 2012 All day

Immunology exam (tentative)

Fri Oct 26, 2012 - Sat Oct 27, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 1:30pm - 2:30pm

Devel. Enteric Nervous System (Goldstein)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Oct 29, 2012 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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Pelvis and Perineum

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

Pathology Correlation (Drs. Mtchell and Padera)

W h e r e : TMEC 419.420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Pelvis & Perineum (van Houten)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Oct 31, 2012 1:30pm - 2:30pm

Obstetrical Anatomy (Carusi)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:30pm - 3pm

Abdo/Pelvis case review; intro to Head/Neck imaging

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

LAB: Internal Iliac vessels; Pelvic diaphragm

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Nov 2, 2012 1:30pm - 2:30pm

Abdomen and Pelvis through a laparoscopic view (Awtrey)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:30pm - 3:30pm

GI Endoscopy (Kelsey)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 3:30pm - 6pm Small Group Radiology (Guimaraes, Bennett, Slanetz, van Houten) W h e r e : TMEC 218 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Nov 5, 2012 1:30pm - 2:30pm

Development of Head & Neck (Stankovic)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Face, Scalp

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

Prosection: Face (Cotanche)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Nov 7, 2012 1pm - 1:30pm

Distribute Skulls

W h e r e : D Amph C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 2:15pm

Cranial Cavity (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:20pm - 3pm

Intro to Cranial Nerves (Cotanche)

W h e r e : D Amph C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Nov 9, 2012 All day

P athology E xam

Fri Nov 9, 2012 - Sat Nov 10, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 2:30pm

Eye & Orbit (Gehrke)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 2:45pm - 6pm

LAB: Eye and Orbit

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO:Fresh Bovine Eye (self- directed)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Nov 12, 2012 All day

HST Holiday - NO CLASS

Mon Nov 12, 2012 - Tue Nov 13, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Nov 14, 2012 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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Triangles of the neck

W h e r e : TMEC 419, 420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Neck Triangles; Cerv. Viscera (van Houten)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Nov 16, 2012 1:30pm - 2:30pm

Facial Nerve Regeneration (Lindsay)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Thyroid region; parotid region

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Nov 19, 2012 1:30pm - 2:30pm

Jaws, Mastication, Swallowing (Bhatt)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Temporal Region; infratemporal fossa

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy 2:45pm - 6pm

PRO: Infratemporal region; PT Fossa (Cotanche)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Nov 21, 2012 All day

No Class

Wed Nov 21, 2012 - Sat Nov 24, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Thu Nov 22, 2012 All day

No Class

Wed Nov 21, 2012 - Sat Nov 24, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Nov 23, 2012 All day

No Class

Wed Nov 21, 2012 - Sat Nov 24, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Nov 26, 2012 1:30pm - 2:15pm

Review: Pelvic Floor (van Houten)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:15pm - 2:45pm

Review Gut & UG system Development (Gehrke)

C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 5:45pm

Disarticulation of Head

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Nov 28, 2012 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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Nasal cavities and palate

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

PRO: Bisected head, palate, pharynx (Van Houten)

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy Fri Nov 30, 2012 1:30pm - 2:30pm

Larynx (Kobler)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:30pm - 6pm

LAB: Oral region and larynx

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

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 : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

Temporal Bone Prosection; Dr. Vernick

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Dec 3, 2012 1:30pm - 2:30pm

Inner Ear and Balance (Oman)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 6pm

LAB: Middle and inner ear

W h e r e : TMEC 419,420 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 6pm

Temporal Bone Prosection; Dr. Vernick

W h e r e : TMEC 414 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Dec 5, 2012 1:30pm - 2:30pm

Dr. Pomahac; Face Transplantation

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 3:30pm

Head & Neck Imaging (Moonis)

W h e r e : TMEC 227 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3:30pm - 4:30pm

Top 25 Radiology Jeopardy (Guimaraes and Slanetz)

W h e r e : TMEC 227 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

HT-010 Human Functional Anatomy Fri Dec 7, 2012 1:30pm - 2:15pm

Review of Cranial Nerve Anatomy (Cotanche)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:30pm - 4pm

Clinical Cranial Nerve Review (Khoshbin)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Mon Dec 10, 2012 1:30pm - 2:30pm

Tabin: The Development of Symmetry

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

2:45pm - 3:30pm

Review Abdominal and Pelvic Vasculature (Cotanche)

W h e r e : D Amph C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Wed Dec 12, 2012 1:30pm - 2:30pm

Bionics (Herr)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

3pm - 4pm

Practice Identifications (Cotanche)

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Fri Dec 21, 2012 All day

HST 010 Final Exam

Fri Dec 21, 2012 - Sat Dec 22, 2012 C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

1:30pm - 4:30pm

HST-010 Final

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

5pm - 6:30pm

HST-010 Celebration

W h e r e : AA C a l e n d a r : HT-010 Human Functional Anatomy C r e a t e d b y : [email protected]

Microbiology 202: Molecular basis of bacterial pathogenesis and host response Fall Semester 2012 Tuesday and Thursdays 10 am – 11:30 am Location: to be determined in the NRB or HIM10 Description This course will provide an overview of classic concepts in bacterial-host interactions. A 30-45 minute formal lecture will be followed by a 45-60 minute group discussion of 2-3 selected papers from the literature. Lectures and paper discussion will focus on pathogenic strategies and mechanisms used by representative bacterial pathogens (paradigms) as well as experimental approaches in the field. How bacteria escape the innate and adaptive host immune defenses will also be emphasized in the course as well as concepts in chemotherapy and prevention of bacterial infections. Grading will be based on participation in paper discussions as well as two short take home exams and a written proposal. Extra credit may come from presentation of the proposal to the class on November 22nd and 29th. This plan may change! The course will follow to some degree the text "Bacterial Pathogenesis" (Wilson, Salyers, Whitt, and Winkler, 3rd edition ASM Press 2011), which will be provided to registered students. Sample questions can be found at the end of this book’s chapters. Instructors: John Mekalanos, Stephen Lory, Lee Wetzler, Gerald Pier, Darren Higgins, Marcia Goldberg, Michael Gilmore, Suzanne Walker, Michael Starnbach, Eric Rubin

Lecturer

Title

Date

Wilson Chapters

Mekalanos

Bacterial Pathogenesis: General concepts Genomics and evolution of virulence Paradigms / Uropathogenic E. coli

September 4

1, 2, 6

September 6

7, 8, 14

September 11

11

Lory Lory

Lory Lory Mekalanos Mekalanos Wetzler Pier Higgins

Higgins

Starnbach Rubin ? Gilmore

Secretion Systems Paradigms / Pseudomonas Bacterial strategies for evading the host defenses Paradigms / Cholera and Pertussis Host innate immune system Antibodies and their effector mechanisms Mechanisms of Intracellular Bacterial Pathogenesis Cellular Immune responses and approaches to immunization Chronic infections Paradigm/ Chlamydia TB and drug discovery

September 13 September 18

13 19

September 20

11

September 25

14

September 27

3, 5

October 2

4

October 4

10, 11, 14

October 9

4,17

October 11

17

October 16

15, 16

October 18 October 23

18

October 25

18

October 30

15, 16 15, 16

Walker

Extracellular Gram+ virulence strategies Paradigms / Enterococci, Staph, Strep or Pneumococci Antibiotics 1

Walker

Antibiotics 2

November 1

Goldberg

Paradigms / Pathogens and Rho and ARF GTPases CD8 Effector mechanisms and resistance Paradigms / Manipulation of host protein degradation machinery

November 6

Gilmore

Starnbach Goldberg

November 8 November 13

3, 4

?

?

November 15

http://micro.med.harvard.edu Click on Micro 202 in course list You will find links to PDFs Name: micro202 Password: bugsrus (please keep access confidential for copyright reasons)

Updated 5/14/12 Draft

Microbiology 205 (HST 040) Mechanisms of Microbial Pathogenesis * Fall 2012 Draft Clyde S. Crumpacker 617-632-9957 Harvey Simon 617-763-7666 Dusten Griesemer (TA) Wilfredo Garcia-Beltran (TA) Mimi Gunning (Course Coordinator) 617-632-0760 Padrig Deighan (Lab Coordinator) 617-432-1922 Laura Williams 617-355-8737 Date

Lecture Topics

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] Lecturer

Chapter in Schaechter*

Lab Exercises/ CPMs

BACTERIOLOGY/MYCOLOGY 9/4 8:30 AM Tues

Bacterial Structure and Physiology: Relationships to Microbial Pathogenicity

Lory

2, 3, 4, 10

9/4 9:40 AM Tues 9/6 9:40 AM Thurs

Host Response to Infectious Agents Acute extracellular pyogenic pathogens: Streptococcus and Staphylococcus Antiphagocytic Mechanisms: Pneumococcus, Hemophilus and Meningococcus

Simon Simon

6-7 10-12

Simon

13,14

9/13 9:40 AM Thurs

Gonococcus and Spirochetes

Simon

14,24

9/18 8:30 AM Tues

Antimicrobial Agents: Mechanisms of Action

Jacoby

5

9/18 9:40 AM Tues 9/20 8:30 AM Thurs

Selected Topics of Antibiotic Resistance Mechanisms of Pathogenesis of Gram Negative Organisms Hemoflagellates

Jacoby Goldberg

5,8,30 16,17, 66

Ryan

29,21

9/11 9:40 AM Tues

9/25 8:30am Tues

***PLEASE REMEMBER TO PICK UP YOUR MICROSCOPES Exercise 1: Meet the Microbes Exercise 1: Meet the Microbes Completed Exercise 2: GI Flora, Enteric Unknowns and Antibiotics

*Schaechter’s – “Mech. Of Microbial Disease” by Engleberg, DiRita & Dermody, 2007 4 th (eds) Lectures will begin promptly at 8:30 A.M. in room 250 of the MEC. Lectures, laboratory sessions and CPMs are mandatory.

1

Updated 5/14/12 Draft

HST 040 Mechanisms of Microbial Pathogenesis * Fall 2010 Date

Lecture Topics

Lecturer

Coordinate regulation, signal transduction and the control of bacteria virulence; Cholera and Pertussis as paradigms Bacterial Toxins: Structure and Function

Mekalanos

Chapter in Schaechter* 17,19

Collier

15,20

10/2 8:30 AM Tues

Facultative intracellular parasites: Salmonella, Listeria and Legionella

Higgins

17,21

10/2 9:40 AM Tues

Obligate anaerobic bacteria Clostridia and Bacteroides

Simon

51,52

10/4 8:30 AM Thurs

Malaria, Toxoplasmosis and Babesiosis

Ryan

29, 21

10/4 9:40 AM Thurs

Fastidious organisms: Mycoplasma and Legionella

Simon

27,28

10/9 8:30 AM Tues

Molecular Aspects of Malaria

Wirth

10/9 9:40 AM Tues

Mycobacteria

Simon

10/11 8:30 AM Thurs

Obligate intracellular parasites: Rickettsia and Chlamydia

Simon

10/11 9:40 AM Thurs 10/16 Tues

Fungi MIDTERM EXAM 9 A.M. – 12 Noon MEC 250

Simon

9/27 8:30 AM Thurs

9/27 9:40 AM Thurs

9

55 51,52

Lab Exercises/ CPMs Exercise 2: GI flora, Enteric Unknowns and Antibiotics Completed

Exercise 3: Some medically important bacteria

Exercise 3: Some medically important bacteria Completed Exercise 4: Advanced Unknowns Exercise 4: Advanced Unknowns Continued

Exercise 4: Advanced Unknowns Completed REVIEW SESSION

*Schaechter’s – “Mech. Of Microbial Disease” by Engleberg, DiRita & Dermody, 2007 4 th (eds) Lectures will begin promptly at 8:30 A.M. in room 250 of the MEC. Lectures, laboratory sessions and CPMs are mandatory.

2

Updated 5/14/12 Draft

Date

10/18 8:30 AM Thurs

Lecture Topics

Lecturer

VIROLOGY Animal viruses: Structure, classification, Zhang replication and diagnosis

Chapter in Schaechter*

31

10/18 9:15 AM Thurs

Respiratory viruses – Influenza

Crumpacker

36

10/23 8:30 AM Tues

Human retroviruses and transformation: HTLV-1 and HTLV-11

Sodroski

38

10/23 9:30 AM Tues 10/25 8:30 AM Thurs

HIV and AIDS Epidemiology of Antibiotic Resistance

Sodroski D’Agata

38,71 5,8,30

10/25 9:40 AM Thurs

Journal Club “Mechanisms of pathogenesis: Virulence and emergenes of NDM-1 (New Delhi metallo-Beta Lactamase -1)

Snyder

10/25 11:00 AM Thurs

Hepatitis

Dienstag

43

10/30 8:30 AM Tues

HIV and SIV vaccines

Desrosies

45,71

10/30 9:40 AM Tues

Generalized viruses affecting immune function - EBV and CMV

Kieff

42

11/1 8:30 AM Thurs

DNA Tumor Viruses-Human Pappilloma Viruses Molecular Diagnosis AIDS Clinical aspects and treatment

Munger

39,40

Kim Crumpacker

71

11/1 9:45 AM Thurs 11/6-1 8:30 AM Tues

Lab Exercises/ CPMs

*Schaechter’s – “Mech. Of Microbial Disease” by Engleberg, DiRita & Dermody, 2007 4 th (eds) Lectures will begin promptly at 8:30 A.M. in room 250 of the MEC. Lectures, laboratory sessions and CPMs are mandatory.

3

Updated 5/14/12 Draft

Date

Lecture Topics

Lecturer

11/8 8:30 AM Thurs

HSV&VZV - Basic Sciences

Knipe

Chapter in Schaechter* 33,35

11/8 10:00 AM Thurs 11/13 8:30AM Tues

HSV &VZV - Clinic aspects PicoRNAviruses

Crumpacker Whelan

41,44 32

11/13 9:40 AM Tues

Antibiotics

Simon

30

11/15 8:30 AM Thurs 11/15 9:45 AM Thurs 11/20 8:300 AM Tues

CLINICAL CORRELATIONS Upper Respiratory Infections Simon

Lab Exercises/ CPMs

62

CPM I: Pulmonary

Pulmonary Infections Bacterial meningitis

Simon Malley

62 67

CPM II: CNS

Zinner

64

CPM IV: Endocarditis

11/27 9:30 AM Tues

Urinary Tract Infections HAPPY THANKSGIVING – NO CLASSES Endocarditis

Crumpacker

67

CPM III: Bone and Joint

11/27 9:40 AM Tues 11/29 9:30 AM Thurs 12/4 9:40 AM Tues

Bone and Joint Infections Skin Infections Intraabdominal Infections

Simon Simon Simon

63 62 61

CPM V: UTI

12/6 9:30 AM Thurs

No Lecture, Lab starts at 9:30 am

Simon

12/11 9:40 AM Tues 12/13 9:40 AM Thurs

Bacteremia and septic shock Fever

Simon Simon

11/20 9:40AM Tues 11/22 Thurs

12/13 10:30 AM Thurs 12/13 LAST CLASS DAY 12/19 Wednesday

CPM VI: Altered Hosts *Special Time: 9:30am-12:30p 66 74

PARTY FINAL EXAM 9:00 AM – 12 Noon, Room 250, HST SKILLS AREA

*Schaechter’s – “Mech. Of Microbial Disease” by Engleberg, DiRita & Dermody, 2007 4 th (eds) Lectures will begin promptly at 8:30 A.M. in room 250 of the MEC. Lectures, laboratory sessions and CPMs are mandatory.

4

Block I – Molecular and Cellular Properties of Neurons 9:00-10:15

10:30-11:45

1. Monday 8/29

LECTURE: Ion Channel Permeation D. Corey

LECTURE: Neurocytology: Neurons & Myelin E. Raviola

2. Wednesday 8/31

LECTURE: Ion Channel Gating D. Corey

LECTURE: Neurocytology: Synapses E. Raviola

3. Friday 9/2

LECTURE: Action Potentials & Axonal Conduction D. Corey

LECTURE: Ion Channel Diseases R. Brown

Monday 9/5

No class – Labor Day

4. Wednesday 9/7

LECTURE: Synapses: Neuromuscular Junction T. Schwarz

LECTURE: Synapses: Transmitter Release T. Schwarz

5. Friday 9/9

LECTURE: Synapses: CNS Receptors T. Schwarz

PROBLEM SET: Permeation & Gating

6. Monday 9/12

PATIENT PRESENTATION: Diseases of Nerve Conduction A. Sandrock

PROBLEM SET: Action Potentials

7. Wednesday 9/14

LECTURE: GPCRs & Second Messengers S. Liberles

LECTURE: Synaptic Integration C. Chen

8. Friday 9/16

LECTURE: Synaptic Plasticity & LTP C. Chen

PROBLEM SET: Synaptic Physiology

9. Monday 9/19

LECTURE: Epilepsy E. Thiele

LECTURE: Psychopharmacology S. Hyman

10. Wednesday 9/21

EXAM I (9:00-10:30)

P

Block II – Neuroanatomy and Neuropathology 11. Friday 9/23

8:30 – 9:15 Part I 9:30 – 10:15 Part II LECTURE: Meninges, Ventricular System, Spinal Cord M. Frosch

10:30-12:00 LAB: Spinal Cord Homework assignment due in lab

12. Monday 9/26

LECTURE: Cranial Nerves & Brainstem I M. Frosch

LAB: Brainstem I Homework assignment due in lab

13. Wednesday 9/28

LECTURE: Cranial Nerves & Brainstem II M. Frosch

LAB: Brainstem II Homework assignment due in lab

14. Friday 9/30

LECTURE: Cranial Nerves & Brainstem III M. Frosch

LAB: Brainstem III Homework assignment due in lab

15. Monday 10/3

LECTURE: Cerebellum M. Frosch

LAB: Cerebellum Homework assignment due in lab

16. Wednesday 10/5

LECTURE: Thalamus & Hypothalamus M. Frosch

LAB: Brain cutting in the horizontal plane Homework assignment due in lab

17. Friday 10/7

LECTURE: Basal Ganglia M. Frosch

LAB: Brain cutting in the coronal plane Homework assignment due in lab

Monday 10/10

No Class – Columbus Day

18. Wednesday 10/12

LECTURE: Cerebral Cortex M. Frosch

LAB: Cerebral Cortex Homework assignment due in lab

19. Friday 10/14

LECTURE: Limbic System M. Frosch

LAB: Limbic System Homework assignment due in lab

20. Monday 10/17

LECTURE: Diffuse Systems & Review M. Frosch

LAB: Diffuse Systems & Review Homework assignment due in lab

21. Wednesday 10/19

LECTURE: Vasculature M. Frosch

LAB: Vasculature Homework assignment due in lab

22. Friday 10/21

EXAM II (9:00-11:00)

Yom Kippur

Block III – Sensory and Motor Systems 9:00-10:15

10:30-11:45

23. Monday 10/24

LECTURE: Hair Cells of the Inner Ear D. Corey

LECTURE: Auditory Coding & Deafness D. Corey

24. Wednesday 10/26

LECTURE: Somatic Sensation & Nociception D. Corey

LECTURE: Pain, Arousal Circuitry & General Anesthesia E. Brown

25. Friday 10/28

LECTURE: The Eye E. Raviola

LECTURE: Neural Processing in the Retina R. Masland

26. Monday 10/31

LECTURE: Primary Visual Coding R. Masland

LECTURE: Olfaction R. Datta

27. Wednesday 11/2

LECTURE: Visual Processing in the Cortex J. Assad

LECTURE: Higher Visual Processing J. Assad

28. Friday 11/4

LECTURE: Eye Movements R. Born

LECTURE: Muscles, Nerves, Spinal Cord E. Eskandar

29. Monday 11/7

LECTURE: Brainstem & Cortex J. Assad

LECTURE: Neurological Exam J. Martin

30. Wednesday 11/9

LECTURE: Basal Ganglia E. Eskandar

PATIENT PRESENTATION: Amyotrophic Lateral Sclerosis M. Cudkowicz

Friday 11/11 SfN begins 31. Monday 11/14 32. Wednesday 11/16 SfN ends

No Class – Veteran’s Day LECTURE: Cerebellum J. Assad

EXAM III (9:00-10:30)

PATIENT PRESENTATION: Cerebellar Ataxia T. Herrington

P

Block IV – Development 9:00-10:15

10:30-11:45

33. Friday 11/18

LECTURE: Neural Induction & Cell Fate L. Goodrich

LECTURE: Axon Guidance L. Goodrich

34. Monday 11/21

LECTURE: Survival & Apoptosis R. Segal

LECTURE: Synapse Formation R. Segal

35. Wednesday 11/23

LECTURE: Glia & Myelination L. Goodrich

LECTURE: Developmental & Adult Plasticity T. Hensch

Friday 11/25

No Class – Thanksgiving Holiday

Block V – Disease

36. Monday 11/28

9:00-10:15 LECTURE: Spinal Disorders – Brains Without Brawn Z. Williams

10:30-11:45 LECTURE: Addiction & Reward S. Hyman

37. Wednesday 11/30

LECTURE: Developmental Disorders C. Walsh

LECTURE: Multiple Forms of Memory Impairment B. Dickerson

38. Friday 12/2

LECTURE: Vascular Disorders C. Ogilvy

LECTURE: Neural Progenitors, Stem Cells & Regenerative Biology J. Macklis

39. Monday 12/5

LECTURE: Neurodegenerative Disorders D. Selkoe

LECTURE: Brain Tumors M. Frosch

40. Wednesday 12/7

LECTURE: Neuroradiology G. Gonzalez

LECTURE: Neuroimmunology H. Weiner

41. Friday 12/9

LECTURE: The Frontal Lobes: Don’t leave home without them K. Daffner

LECTURE: Neurotrauma E. Rosenthal

42. Friday 12/16

FINAL EXAM (9:00-12:00)

Neurobiology 220. Cellular Neurophysiology Bruce Bean, 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. 7/16/1012. The schedule below is a draft and subject to change 9/4/2012 9/6/2012 9/11/2012 9/13/2012 9/18/2012 9/20/2012 9/25/2012 9/27/2012 10/02/2012 10/04/2012 10/09/2012 10/11/2012 10/16/2012 10/18/2012

Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu

Intro // Passive electrical properties gy Resting potential & ionic conductances gy Action potential basics; Intro to voltage clamp bb Cable theory bb Propagated action potentials bb Voltage clamp methods & strategies BB Channel structure: basis of permeation & gating gy Channel variety and modular organization gy Channel pharmacology: v- & state-depend't blockade gy Na+ channels bb Ca channels and K channels bb

10/23/2012 10/25/2012 10/30/2012 11/01/2012 11/06/2012 11/08/2012

Tue Thu Tue Thu Tue Thu

Ligand gated ion channels (*) bb Presynaptic mechanisms I (*) wr Presynaptic mechanisms II (*) wr

11/13/2012 11/15/2012 11/20/2012 11/22/2012 11/24/2012 11/29/2012 12/04/2012 12/06/2012 12/11/2012 12/13/2012 12/18/2012

Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue

Synaptic plasticity I: NMDA-LTP extracellular recording (*) wr Synaptic Plasticity II: LTP-LTD (*) bs Dendritic properties (*) bs Thanksgiving Firing patterns and intrinsic membrane properties (*) bb Optical control of neuronal circuits (*) wr Paper presentations (*) Paper presentations (*) Paper presentations (*) Review Final

Demo Day I: Channels and action potentials Midterm exam Ca as a signaling molecule (*) wr)

Demo Day II: Synaptic transmission Postsynaptic mechanisms (*) bb Transmitters & G-protein modulation (*) bb

Neurobiology HMS230 Harvard / GSAS 78454 Visual object recognition: From computational and biophysical algorithms to cognition FALL 2012 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 1

Date 09/05/12

2

09/10/12

3 4

09/17/12 09/24/12

5

10/01/12

6

10/08/12 10/15/12

7

10/22/12

8

10/29/12

9

11/05/12

10

11/12/12

11

11/19/12

12 13

11/26/12 12/03/12 12/14/2012

 

Title Introduction to visual pattern recognition. Why is vision difficult? Natural image statistics and the retina. Primary visual cortex Lesions and neurological examination of extrastriate visual cortex Adventures into terra incognita: probing the neurophysiological responses along the ventral visual stream NO CLASS: Columbus Day Psychophysical studies of visual object recognition

Comment

First steps into inferior temporal cortex From the highest echelons of visual processing to cognition From correlation to causation: electrical stimulation of visual cortex First steps towards in silico vision Computational models of the ventral visual stream Computer vision Neural correlates of visual consciousness

HW4 due

Final paper due

Note: Special Wednesday Class

HW1 due HW2 due

HW3 due 10/10 Note: HW due vi a e-m ai l o n 10/ 10

HW5 due HW6 due HW7 due HW8 due HW9 due HW10 due 12/10 Note: HW due vi a e-m ai l o n 12/ 10

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 (41-7) 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.

22-July-2012

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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: 32575, email: [email protected] Satrajit S. Ghosh, Ph.D. Research Scientist, Research Laboratory of Electronics, Office 36-547, phone: 35957, 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 22-July-2012

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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.

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SHBT 201 Biology of the Inner Ear (aka HST 721) Instructors: Eatock, 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

Virology 200: Introduction to Virology The objective of this course is to gain knowledge of the principal groups of Animal Viruses and current research themes. Mondays are for lectures and questions, and Wednesdays are for written critiques and detailed discussions of research articles. Each participant will also prepare and present an initial and a final research proposal based on his/her rotation research. 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.

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

The Monday and occasional Wednesday lectures will be from 1:30 to 3:00 PM in Armenise Building Room 330. Wednesday discussion sessions will be from 1:00 to 3:00 PM in the same room, Armenise Building Room 330. Contact information: Prof. Karl Munger: Prof. Max Nibert: Prof. Elliott Kieff: Prof. David Knipe: TA Lindsey Robinson:

[email protected] [email protected] (Course Director) [email protected] [email protected] [email protected]

Schedule for Virology 200 – Fall 2011 ---------------------------------------------------------------------------------------------------------------------------------------Date Event Lecturer/Faculty ---------------------------------------------------------------------------------------------------------------------------------------Wed. Sep. 5 Lecture: Virology Basics Münger Mon. Sept. 10 Lecture: Structural Virology Harrison Wed. Sept. 12 Discussion: Structural Virology Münger/Nibert Mon. Sept. 17 Lecture: Picorna- & Caliciviruses Nibert Wed. Sept. 19 Discussion: Picorna- & Caliciviruses Münger/Nibert Mon. Sept. 24 Lecture: Flavi- & Togaviruses Farzan Wed. Sept. 26 Discussion: Flavi- & Togaviruses Münger/Nibert Mon. Oct. 1 Lecture: Reoviruses Nibert Wed. Oct. 3 Discussion: Reoviruses Nibert Mon. Oct. 8 Holiday: Columbus Day Wed. Oct. 10 Student Presentations: Initial Proposals Münger/Nibert Mon. Oct. 15 Lecture: Orthomyxoviruses Gack Wed. Oct. 17 Discussion: Orthomyxoviruses Yang/Nibert Mon. Oct. 22 Lecture: Rhabdo- & Paramyxoviruses Whelan Wed. Oct. 24 Discussion: Rhabdo- & Paramyxoviruses Yang/Nibert Mon. Oct. 29 Lecture: Retro- & Hepadnaviruses Cunningham Wed. Oct. 31 Discussion: Retro- & Hepadnaviruses Yang/Nibert Mon. Nov. 5 Lecture: Polyoma- & Papillomaviruses Münger Wed. Nov. 7 Discussion: Polyoma- & Papillomaviruses Münger/Nibert Mon. Nov. 12 Holiday: Veterans Day Wed. Nov. 14 Lecture: Herpesviruses Kieff Mon. Nov. 19 Lecture: Poxviruses Kieff Wed. Nov. 21 Holiday: Thanksgiving Mon. Nov. 26 Lecture: Adenoviruses Chodosh Wed. Nov. 28 Discussion: Adenoviruses Yang/Nibert Mon. Dec. 3 Student Presentations: Final Proposals (1st half) Yang/Nibert Wed. Dec 5 Student Presentations: Final Proposals (2nd half) Yang/Nibert ----------------------------------------------------------------------------------------------------------------------------------------

Virology 202 Wednesdays, 1:30 - 4:30 pm

First meeting: Sep 5, TMEC TBD

Faculty: David Evans, Galit Alter, Mike Farzan, Michaela Gack, Samuel Rabkin, Fred Wang, Teaching assistant: Matthew Gardner ([email protected], 508-786-3315) 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. Because this is relatively a large class, and to keep to this schedule, we will need to be very efficient in and out of class. Course Syllabus 2012 September Full class

5

Small groups

12

Galit at AIDS Vaccine 2012 Deadline

18

Small groups

19

Deadline

23

Introduction, course organization (20 minutes), preliminary. topic presentations. Students present hypothesis/topic ~5 minutes each, with 5-10 minute discussion. Prepare a slide 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. Slide should be emailed to Matt ([email protected]) by 9 pm day before first class. Small group development of hypothesis and specific aims. Prepare revised hypothesis and specific aims on one or two 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. First draft of written proposal. Prepare a ~five-page (not including references) draft of the proposal including abstract with hypothesis/key question, specific aims, background and significance. Email this proposal by 7 pm to other small group members. 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 proposal within group. Some students may change topic or hypothesis at this point. A first set of primary intra-group reviewers assigned. Second draft of written proposal. Prepare a ~10-page draft of proposal now including details of experimental approach, to be

Small groups

26

Yom Kippur

distributed by email by 9 pm to other small group members. Students who have changed topic may present a somewhat less detailed proposal. Small group commentary on written proposals. Primary intragroup reviewer leads discussion of draft proposals. Weaknesses are identified, and modifications suggested. A second, different set of intragroup reviewers are assigned.

October Deadline

1

Small groups

3

Deadline

3

Small groups

10

Deadline

10

Full Class

17

Full Class Full Class Full Class November Deadline

24 31 7

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. Small group commentary on written proposals. Primary intragroup reviewer leads discussion of draft proposals. Primary external reviewers for proposals of other groups are assigned. Final Draft of research proposal. A final draft, 10 pages or less, 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 Oct 27. Pre-site-visit meeting. Primary external reviewers should have prepared one 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. 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. Final “site visit” presentations and reviews (or final small group meeting). 20 minutes presentation and 15 minute discussion for each of four proposals. Presenting students receive final critiques. Final “site visit” presentations and reviews. Final “site visit” presentations and reviews. Final “site visit” presentations and reviews.

4

Last day to submit final proposal revisions.

Faculty contact: David Evans (508-624-8025; [email protected]). Tetherin, NK cells, ADCC Todd Allen (617-726-7846; [email protected]). CD8 T cells, HIV, HCV Galit Alter (617.724.0546; [email protected]). NK cells, HIV, HCV, Ab glycans. Michaela Gack (508-786-3304; [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 TBD (Dave, Michaela), TMEC TBD (Fred, Galit), and TMEC TBD (Todd, Sam). Compiled emails:

[email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]