Virology Graduate Student Handbook (may take a minute to download)

In addition to the information presented below, the handbook contains descriptions of the research of all Virology faculty and contact information

Course Work

All Virology Program Graduate Students must complete the required courses within the Molecular and Cellular Biology concentration within BISI.  These are:

• Cell Biology I: Structure/Function (2 credits, 7 weeks) - Fall Semester
• Nucleic Acids (2 credits, 7 weeks) - Fall Semester
• A choice of one (1) of the following:
  • Genetics I*: Transcription/Translation (2 credits, 7 weeks) - Spring Semester
  • Genetics II: Genomics/Molecular Genetics (2 credits, 7 weeks) - Spring Semester
  • Protein Structure/Function: (2 credits, 7 weeks) - Spring Semester
• Bioethics (2 credits) - Fall or Spring
• Research Experiences (2 credits) - both Fall and Spring
• Teaching Science (1 credit) - Fall Semester (required for all teaching assistants

Genetics I is highly recommended for Virology Program Students and is taught by a Virology Program Faculty Member.  Protein Structure/Function is also highly recommended to take as an additional course

In addition, Virology Program Students are required to take:

• CBMG 688K  Molecular Virology (2 cr)- Fall Semester

• MICB 688U Special Topics in Virology (2 cr)- Spring Semester (must be taken in two consecutive years)

• CBMG 688V  Virology Journal Club (2 cr) or equivalent- Fall Semester  (first year students sit in and students in years 2 on take for credit)

 Description of the Core Courses: 

Description of the Core Courses:             

BCHM 661 and 662  Nucleic Acids I and II.  (Nucleic Acids I is required.  Nucleic Acids II is highly recommended)     These courses concern the structure and function of nucleic acids and the mechanisms of nucleic acid transactions: a biochemical approach to molecular genetics and biological information processing. A background including undergraduate organic chemistry, general chemistry, and molecular biology/genetics is assumed. Both prokaryotic and eukaryotic systems are covered, emphasizing common logic and mechanisms, especially regarding bioenergetics and fidelity. These courses complement CBMG modules on Gene Expression (688F) and Genetics/Genomics (688I).  Module I covers Chemistry and structure of DNA and RNA, from nucleotides to chromatin, chromosomes, and genomes, and methods for studying, synthesizing, sequencing and manipulating nucleic acids. Selected aspects of the biochemistry and regulation of DNA replication, repair, and recombination, and how these processes interact with each other.  Module II covers Interactions between nucleic acids and ligands such as cations, drugs, and especially proteins. Sources of binding affinity and specificity. Selection-amplification methods. Description of protein-nucleic acid complex structures. DNA/RNA engineering. RNA Biology: Basic biochemistry of transcription and translation. Regulation of gene expression by RNA, RNA processing and decay, RNA catalysis, the origin of life, mobile genetic elements

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.

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 and Spring, Year 1.     Laboratory rotations follow the rotations of the MOCB Concentration.  Two rotations lasting 7 weeks each are required in the first semester.  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.  Remember that several students may be vying for a single slot in a lab and the Professor will likely choose the student who is the most dedicated.

Intersession - Year 1.     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 Intersession Rotation has been especially designed for you to rotate with investigators 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.  Students have many flexible choices in Spring semester.  You can choose one of the rotation labs from the Fall or you can chose to rotate in 1-2 labs in the Spring before choosing a permanent place.

Summer - Year 1.     You can elect to remain in one of your rotation labs 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

Monthly group meets are usually held the third Monday of each month at 12:00 noon in 1130 Plant Sciences Building.   Informal interactions 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.   

 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 BRB 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 (2011), the retreat is Saturday,  October 22nd.

   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

The Ph. D. student has two important meetings with the student's research committee in the third year. Specific details regarding the preliminary committee meeting and the requirements for the qualifying exam can be found here

It is expected that the student should be able to complete the research necessary for writing the Ph. D. dissertation within two to three years following the candidacy examination. The student is required to meet with the Research Committee on a yearly annual basis. The research for the Ph. D. degree must establish the student's ability to perform independent and creative scholarly research that makes a substantial contribution to our knowledge about an important question in biology. The ability to do high-quality research must be demonstrated by the submission and the defense of a Ph. D. dissertation.

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 currently composed of Dr. Kim Green and Dr. Jim Culver.  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.  

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.