Graduate Student Handbook (may take a minute to download)

Course Work

All entering students must complete the core sequence required of all CBMG graduate students, which consists of CBMG 688D Special topics: Cell Biology I and II, CBMG 688F  Special topics:  Genetics I, and CBMG 688I  Special topics:  Genetics II.  In addition, students take the following Virology courses: CBMG 688K  Molecular Virology and MICB 688U Special topics in Virology (two semester sequence, one year apart).  Typical four year course program and descriptions of courses are given below.   All courses are taught on the University of Maryland campus with the exception of the Virology Journal Club, which is offered both at the University of Maryland and at NIH.  After the first year, students will be familiar with modern molecular and cellular biology and how viruses reproduce and interact with their hosts.  Second year students take the Virology Journal Club (CBMG 688V) (first year students should sit in) in the fall, an elective module of their choice, and MICB 688U Special topics in Virology in the Spring.  In the Spring, students will also take CBMG 688_ Ethics in research.  Students in additional years will continue to take the Virology Journal Club.           

 Description of the Core Courses: 

Description of the Core Courses:             

CBMG 688D Cell Biology I, Structure and Function     This course focuses on the basic concepts and recent advances in cell biology and experimental methodologies and current approaches in cell biology research.  Lectures are combined with research literature discussion to teach students how to read research papers, how to define a scientific question, how to find experimental approaches to answer a question, how to interpret experimental data, and how to write a research proposal.

 CBMG 688D  Cell Biology II/Signal Transduction     This course explores the signal transduction networks that coordinate cellular responses controlled by a variety of signaling molecules and second messengers. The course begins with a current overview of the signal transduction pathways and molecular elements to gain an understanding of common and unique signaling networks in plants and animals, based on current review articles and research articles that have become milestones in the field.  Topics of primary focus include cell death signaling, calcium-signaling, signaling through ligand-gated ion channels, and signal transduction in plant-pathogen interactions.  Additional topics include T-cell/B-cell receptor-mediated signaling and insulin signaling.  Current findings from the scientific literature in the field of signal transduction will be discussed in detail.

 CBMG688F Genetics I    This course discusses molecular mechanisms of gene expression.  The class covers the broad topic of gene expression with emphasis on core concepts and current topics.  The first three classes cover core concepts in molecular biology and biochemistry, and how these provide the foundations for the tools used by today’s investigators.  The next section covers prokaryotic transcription, with special emphasis on regulatory networks and DNA/protein interactions.  This sets the stage for more advanced discussion of regulation of eukaryotic transcription.  Regulation of gene expression at the post-transcriptional level is discussed next, including mRNA splicing, capping and polyadenylation, rRNA and tRNA processing, mRNA editing, and RNAi.  This is followed by an in depth discussion of protein translation including strong emphasis on structural biology, quality control and translational recoding.  The final module explores signal transduction in the context of regulatory crosstalk and feedback among the transcriptional, post-transcriptional and translational machinery.

 CBMG 688I Genetics II    Course in advanced genetics emphasizing genetic analyses of model organisms.  Primary species are yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, plant Arabidopsis thaliana, fruit fly Drosophila melanogaster, mouse (Mus musculus), and humans (Homo sapiens). For each model organism both forward genetics (methods for the identification and analysis of informative mutations revealing new genes or new gene functions) and reverse genetics (methods for testing the expression of modified genes) will be considered.  Applicable genomics resources and bioinformatics tools are also covered, as is the application of information from model organisms to important species that lack the tools available in model organisms.  

CBMG 688K  Molecular Virology (2 cr)   This course uses the text “Principles of Virology” by S.J. Flint et al. and concentrates on animal RNA/DNA viruses and host responses to viral infections. In addition to topics on replication and gene expression, students become familiar with the latest research on retroviruses, pathogenesis, virus evolution and establishment of the antiviral state.  Modern methods of purifying viruses and viral components, determining virus structure and assessing virus titers are also covered. Near the end of the semester, small groups of students present a seminar and recent journal paper on topics that focus on the replication and gene expression of RNA viruses and retroviruses. At the completion of the course, students have an advanced understanding of molecular mechanisms of virus replication for several important families of animal viruses.

 CBMG 688U Special Topics in Virology I and II    This course is taken twice for credit by students in their second and third years and students are encouraged to sit in on the class during their remaining years.  The course is team taught by all Virology Program faculty, with each faculty member presenting two weeks of lectures on his/her research area every other year.  This course allows students to become familiar with virus replication and gene expression (and other topics in Virology) in a wide variety of systems including DNA and RNA viruses with human, animal, plant and fungal hosts and such unusual infectious agents as viroids and prions.  Students become familiar with the research process by having prominent virologists describe not only recent results but the history of their project.  In addition, students become familiar with how research is conducted in a number of systems and thus help breakdown barriers that exist between studies on replication and gene expression in plant, animal, and fungal systems.  Since many faculty work on vaccine development, students learn how basic research is applied to real life problems in health and agriculture.

 CBMG 688V Virology Journal Club.           In the semester that the Special Topics in Virology course does not meet (i.e., Fall semester), students are required to participate in the Virology Journal Club, either at University of Maryland or at NIH (The NIH journal club is organized by advanced Virology Program students).   Journal Clubs are also attended by post-doctoral researchers and faculty.  Pre-doctoral students present papers on a variety of topics and systems in Virology with an emphasis on virus replication and translation.  Students learn to become comfortable with the literature on a number of different systems and learn how to critically analyze experiments and results.  In addition, students learn how to review papers by reviewing anonymous manuscripts submitted to the journal Virology, and comparing their reviews with those of professional science reviewers. 

CMBG 688B Bioethics         This course provides an introduction to ethics, the social foundations of science, responsibilities of student and advisor, treatment of data, collaborations, conflicts of interest, use of animals and humans in research and other topics that you will routinely encounter as a scientist

Additional elective module and full semester courses:   

Students are required to take one additional module course and may elect to take additional module courses or full semester courses in consultation with their research director and their dissertation committee.   

Description of the module courses available for students

 CBMG688J Special Topics in Cell Biology and Molecular Genetics: Genetics: Immunology and Host Defense     This class uses the text "Cellular and Molecular Immunology" by Lichtman and Abbas.  A comprehensive series of lectures on innate and adaptive immunology, including cellular and humoral immunity,  is complemented by original research articles and a review of technical approaches to immunological problems.  There are two examinations and each student presents a research article to the class on a selected topic.  At the completion of the class students are expected to have a thorough understanding of  immunological concepts, a broad-based understanding of immunological techniques, and an introduction to signal transduction events during immune cell activation.

 CBMG688M Special Topics in Cell Biology and Molecular Genetics: Genetics: Microbial Genetics  This course focuses on the review and discussion of research literature to examine experimental design, methodology, and interpretation of both historical and contemporary relevance to microbial genetics. The fundamental concepts of bacterial and bacteriophage genetics including mutagenesis, mechanisms of both vertical and horizontal genetic transfer, gene regulation, and genetic approaches to study complex cellular processes will be covered.  Special emphasis is placed on the requirements for gene expression in bacteria.

 CBMG 688H Bioinformatics: Genome Analysis.  The course provides a graduate-level introduction to the concepts and principles that form the basis  for bioinformatic techniques, particularly similarity search and  pairwise alignment algorithms (e.g., BLAST, FASTA, Needleman-Wunch,  Smith-Waterman), and techniques for homology assessment and  functional inference.  No prior experience with programming is required, but students should be comfortable working with computers.  

laboratory rotations

Fall, Year 1.     Laboratory rotations differ from the rotations of other CBMG students.  The multi-institutional nature of the Virology Training Program is a great strength and we want all Virology students to experience the breadth of the training opportunities available.  The rotations have been designed to allow you to experience what training is like at a number of labs in different settings, and then give you the opportunity to conduct extended research in one or two labs before having to decide on a thesis advisor. During your first semester, all students, in consultation with the First Year Student Committee, will choose three laboratories to rotate through for three weeks each. Since you will also have teaching assignments, for logistical reasons these three labs must be chosen from faculty at the University of Maryland or USDA.  During these three weeks, you will have the opportunity to participate in some aspect of research within the lab.  It is also your opportunity to interact with principal investigators (PIs), postdoctoral researchers and graduate students, learn about the systems being studied, the techniques being used and the questions being addressed (see Appendix B for sample schedule and ideas on questions to ask the professor and students in each lab).  You are expected to spend at least 10 hours a week in the rotation lab.

 Intersession - Year 1.     You will choose a laboratory to conduct an intersession rotation from one of the labs at the NIH or NCI.  This choice will be made in consultation with the First Year Student Committee.  This NIH/NCI rotation will be conducted during intersession (in January- can start right after classes end in December as well) since you will have no teaching or course work, allowing for ease in commuting to the NIH/NCI campuses.  (See Appendix C for information you need to provide to Teresa Thompson (teresa@umd.edu; 5-8990), the Virology Program Assistant, before you can begin the rotation at NIH/NCI.  It is very important that you provide the information by the times indicated).

 Spring - Year 1.     By the end of January, you will need to select a laboratory to conduct a one-semester rotation, extending through the end of June.  It is highly advised that this rotation be conducted in one of the labs that you visited during the Fall, since teaching and course work will make traveling to NIH/NCI difficult during this rotation, you will learn how to conduct research, usually under the guidance of a graduate student or postdoc in the lab.

 Summer - Year 1.     By the end of Spring semester, you can elect to remain in your rotation lab as your thesis lab (providing that the PI agrees), or conduct a summer rotation at NIH/NCI or in another Virology lab.  You are required to choose a dissertation laboratory by Fall of your second year, at the latest.  When you have made a decision, the information needs to be conveyed to Ms. Thompson

Monthly group meetings

 Informal interaction between faculty and students is an integral part of our training program.  At each monthly group meetings, all faculty and students in the program gather to hear the latest results from two faculty labs.  Talks are given by faculty, postdocs, and senior predoctoral trainees and include guest talks from other Virology researchers at nearby institutions, including other investigators at NIH and Fredrick Cancer Research Center .  These talks lead to many lively discussions and a much better appreciation and understanding of different systems by both faculty and students.  Some of the labs break into groups after the meeting to discuss specific research topics in more detail.  This informal setting is ideal for establishing relationships and formation of a coherent group.  

 Yearly retreat   

With the large number of labs in the Virology Program, you may not have the opportunity to present your research more than once at the monthly group meetings.  For that reason, and to foster increased interactions by members of the Virology Training Program, the Virology Program holds an annual retreat in October in the Plant Sciences Building at the University of Maryland .  In addition to guest speakers, there are talks from faculty, predoctoral and postdoctoral trainees in the program, and a  poster session where all students not presenting talks present their research, starting in their third year.  This will allow you the opportunity to become familiar with describing your research to a diverse virology audience in preparation for similar presentations at national and international virology meetings.   This year (2008), the retreat is Saturday,  October 25^th.

   Seminars

 All Units with faculty involved in the Virology Training Program sponsor weekly seminar speakers.  All first year students are required to attend the CBMG seminar series.  After the first semester, you can continue to attend the CBMG seminars or attend the weekly seminars presented in the program units of your laboratory director. 

Advancement to candidacy

By the end of their fourth semester, trainees, in conjunction with their research advisor, will choose a Research Committee whose first assignment will be to conduct the Admission to Candidacy Examination. The Examination is held in two parts. Students will be required to write and submit a research proposal by the end of their 5th semester that summarizes the relevant literature, objectives, experimental methods, and significance of a research project that the student and the advisor believe is appropriate for a PhD dissertation. A meeting based upon the written proposal will be held at which time the committee will either approve the proposal or suggest changes. By the end of the 6th semester, the official Admission to Candidacy Oral Examination will be held. In particular, the student is expected: 1) to exhibit a sophisticated understanding of the advanced knowledge necessary to conceptualize and to perform the critical experiments in the research proposal; 2) to defend the project outlined in the research proposal as having the potential to become appropriate and worthy of a high-quality PhD dissertation; and 3) to demonstrate considerable ability for independent and creative thinking as it relates to the identification of important questions, the design of experimental hypotheses, and the testing of those hypotheses in other relevant research areas not addressed in the proposal. In addition, the faculty reserve the option to ask general knowledge questions in other areas of Virology. After passing the Advancement to Candidacy Exam, students will be required to hold yearly meetings with their Research Committee (although more can be scheduled, if desired).

Monitoring and guidance of students

The Virology Training Program places great emphasis on the monitoring and guidance of trainees.  When students first arrive, they have meetings with both Dr. Simon and the First Year Student Committee, which is composed of one member from NIH and a second member from either CBMG, CBR, VetMed or USDA.  The First Year Student Committee helps students choose laboratories for their three rotations (based on the interests of the students) and help them navigate the logistics of the fourth rotation at the NIH/NCI and USDA (e.g., transportation, security and parking).  Students contact the committee members as needed during their first year to help with any classroom, TA, or research situations that arise.  When students choose a dissertation laboratory, the guidance duties switch to the laboratory’s Virology faculty member and the Program Director.  In addition, students who have chosen laboratories at NIH/NCI/USDA have a Virology faculty member from CBMG as their associate research advisor (if possible, someone with whom the student did a rotation).  The associate research advisor usually talks with their students monthly at the group meetings.  In addition, the Program Director meets with at least once each semester following the monthly group meetings, with pre-doctoral trainees to discuss any concerns that they are having about their training experience, and ways of improving the Virology Training Program.  This has led to rescheduling of classes (to avoid conflicts) and reformulating the rotations to provide additional time and research experience (originally there were 5 two-week rotations).   In addition, trainees are encouraged to stay in contact with, and approach Committee members for advice any time during the training period.

            Trainee progress is monitored at the end of the first year with regards to coursework, teaching and research by the CBMG Program Director.  Such monitoring is the first line of evaluation of each pre-doctoral trainee.  In addition, since pre-doctoral traineeship awards are made on a yearly basis, the Selection Committee evaluates all trainees who request renewal of their support for a additional year to determine research progress as well as if they are fulfilling the requirements of the program, participating in seminars, monthly meetings and journal clubs.  Trainees, and their mentors, will be asked to provide input to the evaluation process and the trainees are given feedback as to the findings of the Selection Committee.  The previous records of Virology Program Members indicate great success at placing students in quality post-doctoral positions and many of our previous students are now heading their own laboratories in Academia or Industry.