Graduate Program in Pathobiology

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Course Information

COURSE DESCRIPTION
Ongoing; Year 1 (3 Rotations)
Title:Research in Pathobiology
Course Number:ME: 300.800
Course Director:Lee Martin, PhD
Dates & Time:By arrangement with course directors and individual mentors
AUGUST-MAY (Ongoing)
Long-term research projects will be undertaken with faculty members of the Graduate Program in Pathobiology serving as mentors. Course also covers the three required rotations for 1st Years.

COURSE DESCRIPTION
Year 1, Semester 1
Title:Pathology for Graduate Students: Basic Mechanism of Disease
Course Number:ME: 300.713
Course Directors:Kathy Gabrielson, DVM, PhD
Dates & Time:AUGUST-SEPTEMBER; MWF; 9AM-4:00PM
Location:PCTB 113 Classroom
Pathology for Graduate Students: Basic Mechanisms will concentrate on the basic mechanisms of tissue injury and disease both at the molecular level and as they are manifested in human tissues. Normal tissue histology and function will be discussed in relation to organ systems as a basis for the understanding of disease mechanisms.

Morning lectures and discussion groups will be followed by afternoon laboratory and case studies. This block on basic pathogenic mechanisms will prepare students for more advanced topics on organ specific diseases that can be taken individually or in succession. The advanced blocks will be organized under 3 themes: 1) Neoplasia, 2) Immunopathology, and 3) Neuropathology.

COURSE DESCRIPTION
Year 1, Semester 1
Title:Macromolecular Structure and Analysis
Course Number:ME: 100.709
Course Director:Cynthia Wolberger, PhD
Dates & Time:AUGUST-OCTOBER; T & Th; 9-10:30AM
Location:Wood Basic Science Auditorium/PCTB 115
The structure and properties of biological macromolecules will be presented. Experimental and computational methods used to study macromolecular structure including X-ray crystallography, magnetic resonance, spectroscopy, microscopy, and mass spectrometry will also be covered.

COURSE DESCRIPTION
Year 1, Semester 1
Title:Molecular Biology and Genomics
Course Number:ME: 260.709
Course Director:Rachel Green, PhD
Dates & Time:OCTOBER-NOVEMBER; MWF; 9-10:30AM
Location:Wood Basic Science Auditorium/PCTB 115
This course module covers the Molecular Biology and Genomics of both prokaryotes (using E. coli as the model organism) and eukaryotes, with a focus on "model organisms" including yeast, flies, worms, mice as well as humans. Both the Molecular Biology (reductionist) perspective and the Genomics (systems biology) perspective will be provided on each topic, and there will be heavy emphasis on mechanism and regulation of fundamental processes in biological information transfer DNA->RNA-> protein. This lecture module will cover genes and genomes, transcription and RNA world, replication, chromosome structure and function and genome instability.

COURSE DESCRIPTION
Year 1, Semester 1
Title:Fundamentals of Genetics
Course Number:ME: 260.708
Course Director:Erika Matunis, PhD
Dates & Time:OCTOBER-DECEMBER; T & Th; 9-10:30AM
Location:Wood Basic Science Auditorium/PCTB 115
This short lecture course will cover fundamental principles of genetics, focusing primarily on principles of genetics, focusing primarily on model eukaryotes. Problem sets will be an integral learning tool in this course.

COURSE DESCRIPTION
Year 1, Semesters 1 & 2
Title:Computational Biology and Bioinformatics
Course Number:ME: 800.707
Course Director:Sarah Wheelan, MD, PhD
Dates & Time:NOVEMBER-JANUARY; Mon; 9-10:30AM
Location:PCTB 115 STILE Classroom
This course is a survey of quantitative methods in modern biology and the computational concepts that are developing to analyze large data sets. Topics range from a review of statistics to problems in sequence analysis to the modeling of complex systems. The goal of the course is to familiarize students with the concepts of computational biology rather than to achieve a deep understanding of any one topic.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Cell Structure and Dynamics
Course Number:ME: 110.728
Course Director:Hiromi Sesaki, PhD
Dates & Time:JANUARY-MARCH; MWF; 9-10:30AM
Location:Wood Basic Science Auditorium/PCTB 115
The objective of this course is to provide the basics of cell biology, including the structure, function and biogenesis of cellular organelles. Also covered are essential concepts on the cytoskeleton, cell-cell and cell-extracellular matrix interactions, cell motility, chaperones, and protein turnover.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Pathways and Regulation
Course Number:ME: 360.728
Course Director:Guang William Wong, PhD
Dates & Time:JANUARY-FEBRUARY; T & Th; 9-10:30AM
Location:Wood Basic Science Auditorium/PCTB 115
This course will cover the principles of membrane transport, bioenergetics, metabolic pathways, cell cycle and cell death with particular emphasis on regulatory mechanisms including receptor-mediated signaling, small GTPases, lipid molecules, kinases and phosphatases.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Graduate Immunology
Course Number:ME: 250.703
Course Director:Mark Soloski, PhD
Dates & Time:FEBRUARY-MAY; T & Th; 10:30AM-12:30PM
Location:Wood Basic Science Auditorium/PCTB 115
This is an introductory course designed to provide graduate students with a comprehensive survey of modern cellular and molecular immunology. The course consists predominately of lectures but also includes discussion sessions focusing on important recent research papers. This course is open to all graduate students and postdoctoral fellows.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Pathology for Graduate Students: Cancer
Course Number:ME: 300.714
Course Director:Angelo DeMarzo, MD, PhD
Dates & Time:MARCH-APRIL; MWF; 9AM-12:00PM
Location:Carnegie 489
Pathology for Graduate Students: Cancer will concentrate on the biology of cancer at the molecular, cellular, and tissue levels. While the course is largely organized to study cancer in the context of specific organs, general principles of neoplasia will be continuously discussed as a basis for understanding the disease process. The format will include lectures, discussion of research papers, and review of histological slides.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Pathobiology and Disease Mechanisms
Course Number:ME: 300.710
Course Director:Richard Roden, PhD
Dates & Time:MARCH-JUNE; W & F; 1-2:30PM
Location:TBA
Pathobiology and Disease Mechanisms provides an intensive study of human disease through traditional lectures, and the discussion of the primary scientific literature including classic and current cutting edge papers. The course combines lectures with small group discussions, and will cover topics relevant to infectious, degenerative, neoplastic, and inflammatory disease of the major organ systems. The primary objective of the course is to understand how research findings elucidate the underlying mechanisms leading to clinical manifestations of disease (seen grossly and microscopically in the traditional Pathology component of the course). Active student participation is required in the form of presenting and discussing papers. The course is open to all PhD and MD/PhD students.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Pathology for Graduate Students: Immunology & Infectious Disease
Course Number:ME: 300.716
Course Director:Petros Karakousis, PhD
Dates & Time:APRIL-MAY; MWF; 9AM-12:00PM
Location:Carnegie 489
Pathology for Graduate Students: Immunology and Infectious Disease will concentrate on the basic mechanisms of Immunology and Infection in human diseases. The format will include lectures, discussion of research papers, and review of histological slides.

COURSE DESCRIPTION
Year 1, Semester 2
Title:Pathology for Graduate Students: Neuropathology
Course Number:ME: 300.715
Course Director:Philip Wong, PhD
Dates & Time:MAY; MWF; 9AM-12:00PM
Location:Carnegie 489
Pathology for Graduate Students: Neuropathology will concentrate on the basic mechanisms of Neuropathology both at the molecular level and in human diseases. Normal tissue histology and function will be discussed as a basis for the understanding of Neuropathology. Animal models of neuropathological diseases will be critically considered.

COURSE DESCRIPTION
Year 1 and Beyond
Title:Pathobiology Journal Club
Course Number:ME: 300.803
Course Director:Saraswati Sukumar, PhD & H. (Ben) Larman, PhD
Dates & Time:SEPT - MAY; TUES; 12:15-1:15PM
Location:CRB II, Rm. 111
The objective of this course is to train graduate students in the fundamentals and art of understanding and determining the quality and structure of scientific publications. Students will select publications for presentation. The paper selection process will be a joint effort with a faculty member. Papers will be carefully read and scrutinized for detail of experimen tal background and logic, experimental approach and methods, results, figure composition and present ation, and interpretation. Students, with advice from a faculty mentor, will prepare and present to an audience a PowerPoint presentation (approximately 45 minutes) on the selected paper. Th e student will anticipate and prepare for questions about the paper as part of the presentation . The course is open to all graduate students and postdoctoral fellows.

COURSE DESCRIPTION
Year 2 required
Title:*Research Ethics Course - Section I and Section II
Course Director:Office of Graduate Student Affairs
Time:2 Half Day Sessions - Fall and Spring
Location:TBA
Recognize the key concepts in the responsible conduct of research, including data acquisition and management, mentor/trainee responsibilities, publication practices and authorship standards, conflicts of interest and commitment, and scientific misconduct.

*NOTE: Completion of this course is a SOM requirement for graduation. This course is offered in two parts, Section I in the fall and Section II in the spring.

COURSE DESCRIPTION
Year 2 and Beyond
Title:Scientific Presentations
Course Number:ME: 300.718
Course Director:Lee Martin, MD, PhD
Dates & Time:TBA
Location:TBA
The objective of this course is to train graduate studen ts in the fundamentals and art of making clear scientific presentations given through PowerPoint an d lecturing. Basic organization and layout skills and PowerPoint tools will be discussed and illustrated. Students will select topics for presentation. Presentation outlines will be discussed and then form al presentations will be prepared and given to the class for peer-review. Presentations will be critiqued i n their clarity and detail of experimental background and logic, experimental approach and methods, results, figure composition, and interpretation. The student will anticipate and prepare for peer questions about their presentation. The course is open to all graduate students and postdoctoral fellows.

COURSE DESCRIPTION
Year 2, Semester 4
Title:Grant Writing 101
Course Number:ME: 300.717
Course Director:James Eshleman, MD, PhD
Dates & Time:MARCH-MAY; MWF; 10:00-11:00AM
Location:TBA
The course will explore how to pick a scientific area. Students will write mini-grants in the format of an NIH F31 pre-doctoral award.

COURSE DESCRIPTION
Year 2, Semester 4; Summer 2
Title:Introduction to Translational Research
Course Number:ME: 300.711 & ME: 300.712
Course Director:Kathy Burns, MD, PhD
Dates & Time:Two Sections: One-half quarter each approximately 16 hours, each.
Location:Assigned by Course Director
Introduction to Translational Research is designed to acquaint pre-doctoral students with the language of anatomic pathology and clinical pathology through practical experiences. Students will rotate through surgical pathology and various laboratory services including chemistry, hematology, the blood bank, medical microbiology, and diagnostic immunology. Students will become acquainted with the resources that can be made available to research, and will appreciate the translational relevance of their research to clinical medicine. Open to students in the Graduate Program in Pathobiology and others with permission of the Program Directors.

COURSE DESCRIPTION
Year 2 and Beyond
Title:Teaching in Pathobiology
Course Number:ME: 300.802
Course Director:Staff
Dates & Time:all quarters
Location:Assigned by Course Director
Teaching in Pathobiology is designed to prepare students for teaching through participation as a teaching assistant for Pathobiology required courses. When registering for the course, please indicate the course number for which you will serve as a teaching assistant.

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ELECTIVES
All students in their second year and beyond are required to take a one-semester elective course for credit in each academic year. Courses may be taken for a grade or pass/fail. Students may choose a course offered in the Johns Hopkins Medical Institutions, or on the Homewood Campus subject to approval by the Program Director. Please note that Grant Writing 101 is a required second year course and does not count as an elective.

ELECTIVE COURSE SEARCH LINK: https://isis.jhu.edu/classes/

COURSE REGISTRATION FORM