First Year




THE FIRST YEAR CORE CURRICULUM
The six first year courses are described below.  A list of approved electives can be found on the CMDB webpage at http://cmdb.jhu.edu/.
 
1. 020.601 Current Research in Bioscience (Fall)
This course involves 30 minute sessions with each member of the training faculty.  It is designed to acquaint incoming graduate students with the research topics and research philosophy of each laboratory.  This should help students choose future rotations.  More generally the course provides a range of perspectives on the future of specific fields and strategies for success in science. No grades will be given in this pass/fail course, but
attendance is mandatory.  

2. 020.668  Advanced Molecular Biology (Fall)
Advanced Molecular Biology stresses the basic facts and principles of molecular biology and their application in problem solving and in the design of experiments. Topics covered include nucleic acid structure and synthesis, genetic engineering and important areas of prokaryotic
and eukaryotic genetics.

3. 020.686  Advanced  Cell Biology (Fall)
Advanced Cell Biology covers a wide range of topics, but in general builds from cellular levels of organization, organelles, membrane traffic and cell division, to consider cell interactions with one-another and with their environment. 

4. 020.674 Graduate Biophysical Chemistry (Spring)
Graduate Biophysical Chemistry will provide an overview of protein and nucleic acid structure,fundamentals of thermodynamics and kinetics, ligand binding, folding and stability of macromolecules, and the principles of biophysical methods such as fluorescence spectroscopy, NMR and X-ray crystallography. Students interested in pursuing biophysical research, who have taken undergraduate physical chemistry, may opt to take a two semester series in Molecular Biophysics (250.689-690). Similar topics are covered in the two semester series, but with greater emphasis on mathematical and quantitative analysis.  Students wishing to pursue this option should consult with the CMDB Program Director.  

5. 020.637  Genomics and Development (Spring)
Genomics and Development covers the processes of fertilization, cleavage, gastrulation, organogenesis and gametogenesis with emphasis on the molecules involved and how these processes can be studied using molecular genetics.
 
6.  Responsible Conduct in Research
CMDB program has developed a curriculum for graduate students that encompasses 3 components:
 
a. 360.625  Responsible Conduct in Research Course (Intersession)
Johns Hopkins is committed to promoting the highest ethical standards among our
administration, faculty members, and students. Therefore, all trainees and training faculty are required to attend the discussion series, Responsible Conduct of Research.  The two week series meets for 6 two hour sessions and will be offered every January.  Graduate students must attend the discussion series during their first year of study.  Science has come under increased scrutiny and scientific misconduct has become a public issue regularly addressed in the media. Against this background of public skepticism, each university must make a visible commitment to responsible conduct of research. We believe that this is best accomplished by case-based discussions involving both trainees and faculty
who are active investigators. In addition to general information, such as Honor in Science, participants will be expected to read related handouts sent to them before each session. Copies of the material contained in the suggested reading list will also be available.. 
 
The Dates for the MANDATORY Responsible Conduct in Research Class are in the Calendar section of the Student Handbook Appendix

b.  CMDB RCR Training (Fall Semester)
The Training Faculty of the CMDB Graduate Program are committed to demonstrating to our trainees our serious attitude toward ethical conduct and the responsible practice of scientific research. In addition to the University led class, we developed a specific, CMDB faculty-led Responsible Conduct of Research course for first year students along with an annual discussion session for all graduate students, postdoctoral trainees and CMDB faculty.

This class will be held on Wednesdays from 10-11AM.
 
c. We will hold an annual two hour long session for all CMDB students and faculty (and will also include postdoctoral fellows). These sessions will focus on different aspects of the RCR, including updates on any new RCR issues that have emerged. Reading materials will be provided in advance, and mechanisms such as an on-line ‘pre-quiz’ may be employed as appropriate. A different topic will be discussed at each session, and will include a brief overview of the topic by a faculty member and/or students and postocs, as well as case study discussions in smaller groups. Such sessions are currently held by the CMDB faculty and students of the Carnegie Institution Dept. of Embryology, and we will expand this successful program to include all CMDB faculty and students. This annual session will provide ongoing training in and awareness of scientific ethics.


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ROTATIONS & SELECTION OF RESEARCH ADVISOR          
 
  1. LABORATORY ROTATIONS
 
The laboratory rotation system has been designed so that each graduate student may be exposed to a variety of research projects and techniques and also to the research approach of a variety of professors. Rotations should not be viewed only as an opportunity to preview a potential thesis research laboratory, but also as an opportunity to learn interesting and valuable new information. During the first year, students are required to do rotations in at least four different laboratories. (Students have the option of doing additional rotations during the Summers before or after the first year).  Optional rotations do not count towards the requirement of four rotations during the academic year.  Students should register for each laboratory rotation under a course entitled “Introduction to Research” (020.823-826).  To ensure maximal supervision, only one CMDB student may rotate in a lab during each rotation period.
 
Dates for the four rotation periods are in the Appendix of the Student Handbook.
 
Students may do their rotations in the laboratories of any members of the CMDB Training Faculty. This includes many full-time faculty members of the Biology Department, the Carnegie Institution of Washington’s Department of Embryology, the Biophysics department, and specific
members of the Chemistry Department. Please note that not all faculty of the above departments are CMDB Training Faculty and a complete list of the training faculty can be found on the web at www.jhu.edu/cmdb/ and in the Appendix.   
 
The CMDB Program Director is responsible for rotation assignments. These assignments are based primarily on preferences expressed by the students.  Preferences for laboratory rotations should be given to the CMDB Program Director at least four weeks prior to the start of the next rotation.  Except for the first rotation, students are REQUIRED to contact prospective rotation advisors before submitting their requests to the CMDB Program Director.

One purpose of rotations is to give students an opportunity to sample various labs in which they might want to do their thesis research.  Students should pay attention both to the nature of the research in the lab and to the philosophy and organization of the lab.  For example, a person who craves a great deal of independence may not be happy in a lab with a great deal of structure and vice versa.  Rotations also provide research training and experience.  For example, a rotation is good way to learn specific techniques or to become familiar with a particular model system.  Students should plan their rotations to their advantage. 
 
Rotation faculty advisors are asked to orally review a student’s performance at the end of the rotation, and to submit a written evaluation and grade.  Rotations grades count similarly to course grades for calculating a student’s GPA and evaluating academic standing. Students are also required to present their rotation project as a short talk at the end of each rotation.  All first year students are expected to attend these rotation talks, which are also attended by faculty and other members of the program. 
 
Summer rotations are available to CMDB students in advance of the matriculation year.  If you conduct one of your rotations during the summer. you will present results of your rotation during the orientation week.  This rotation will not count as one of the 4 rotations required by the program.

  2. SELECTION OF RESEARCH ADVISOR
 
A research advisor is usually chosen at the end of the fourth rotation.  To prevent decisions being made prematurely, no agreements between a faculty member and a student regarding joining a lab for thesis work may be made prior to the end of the last rotation
period.  During the final week, students may approach prospective thesis mentors to express interest in thesis work and to discuss potential projects.  To formally join a laboratory, written permission from the proposed research advisor is required (see below). This form can be obtained from the Academic Affairs Administrator and a copy will be placed in student mailboxes after the last rotation talks are completed. Only training faculty affiliated with the CMDB program are eligible to be mentors for CMDB students, without exception. If a student fails to find a mentor by August 31st, they will be asked to leave the program.
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D.  PARTICIPATION IN CMDB AND DEPARTMENTAL EVENTS
 
A number of academic activities occur on a regular basis that constitute a large portion of the training experience in the CMDB Graduate Program.  Progress Reports, departmental seminars and Colloquia present opportunities for one’s horizons to be broadened and to be exposed to a wide array of subjects and experimental approaches.  As a significant adjunct to individual thesis training, student attendance at these activities is mandatory. In addition, individual
labs or groups of investigators with shared interests also have group meetings, journal clubs and other intellectual activities in which a student is expected to participate.
 
Progress Reports are held in Mudd 100 each Tuesday at noon and involve research talks from students in the CMDB program and postdoctoral fellows in the Biology Department. All CMDB students are required to present a Progress Report each year after their second year (see below).  Students are expected to regularly attend the Progress Report talks. 
 
Seminars. The Biology Department (Thursdays at 4PM), Biophysics Department (Mondays at 12PM), Chemistry Department (Wednesdays at 4PM) and Carnegie Institution (Mondays at 12:15PM) each sponsor seminar series which include talks by visitors from other universities.
Attendance at seminars is strongly encouraged, and attending at least one seminar per week is required. Notices concerning seminars in other departments are located on the bulletin board across from Mudd 100 and on each department’s web pages.  The schedule can be found on the Biology Department website at http://www.bio.jhu.edu/ or a Hopkins-wide seminar listing can be found at http://www.hopkinsmedicine.org/scical/.
 
Biology Colloquia are held once a month during the academic year. This series involves members of the CMDB Training Faculty. These talks commence at 4:30PM on the first Wednesday of each month (with a few exceptions) and attendance by CMDB students is required. 
 
CMDB Program Retreat. During the Fall semester, there is a retreat for all CMDB students along with faculty, postdoctoral fellows, and research associates from the Biology Department, and training faculty from Carnegie, Chemistry, and Biophysics. During the retreat, members of the Training Faculty will present short talks about the research that is currently being conducted in their laboratories.  Graduate students and postdoctoral fellows also present their work at a poster session. In addition to the stimulating science, the retreat offers a chance for CMDB students to become acquainted with training faculty and other members of our scientific community in a relaxed and enjoyable atmosphere. CMDB students are expected to attend and participate in the retreat during each of their years in the program.


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EVALUATION OF THE PERFORMANCE OF GRADUATE STUDENTS
At the end of each academic year, the Program Director of the training program will convene the entire Training Faculty to discuss the progress of all graduate students. For first year students, performance in laboratory rotations and the students' coursework record will be evaluated after the first semester by the Program Director, and at the end of the first year by the Training Faculty. As discussed above, any student who receives two grades of C+ or worse during the first year, who has a combined GPA less than 3.0, or who fails to otherwise meet the conditions of a probation, may be subject to dismissal from the program. The performance of students in the second year and beyond will also be reviewed by the CMDB Program Director and the training faculty. Close attention will be paid to the outcome of the annual thesis reviews, as well as to the completion of other degree requirements (above).  Students failing to make adequate progress toward the Ph.D. degree will be placed on probation and may be subject to dismissal from the program.  Students entering the sixth year or greater of
graduate study must present a plan for completion of study, and obtain permission to continue in the program signed by the Program Director, in order to register.