May 01, 2024

2015-2016 University Catalog

2015-2016 University Catalog [ARCHIVED CATALOG]

Immunology/Microbiology, PhD

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PhD program is closed for entry beginning Fall 2015

Note For the Current Academic Year:

Incoming PhD students should refer to the Integrated Biomedical Sciences section of this catalog. The following information is intended for incoming MS students, current MS and current PhD students. Questions about the future plans should be directed to the program director.

Immunology/Microbiology: Admission Requirements

Students who have received a Baccalaureate degree in biological sciences or a related field may apply for the master’s or the doctoral program. Candidates usually enter the program in the fall semester. Applications should be submitted by February 15 and no later than June 30. Applications will be evaluated by the Departmental Admissions Committee as they are received. It is possible that applications will be closed before June 30 if the class is filled before that date. Considerations for admission will include overall academic record, the recommendations of the sponsors, results of a recent Graduate Record Examination (GRE) and the description of the applicant’s own aspirations and interests. International students are also required to submit a recent result of a TOEFL test. Admission criteria to the program are consistent with the general requirements of The Graduate College. A grade point average of at least 3.0 on a 4.0 scale as well as competitive GRE and TOEFL scores are required. Minimum GRE or TOEFL scores are not assigned. In rare circumstances, students that do not fulfill these requirements may be accepted at the discretion of the Division and the Graduate College Council. Personal interviews will be arranged for potential candidates after the preliminary review. Students will be admitted into the program at levels other than first year only under exceptional circumstances; this will require approval by the Division Director. Students may be accepted directly into a particular laboratory and will have that faculty member serve as their PhD academic/dissertation advisor, or they may be accepted at-large and will have the graduate program director initially serve as faculty advisor. The latter students will be required to fulfill a minimum of two laboratory rotations before selecting a dissertation research advisor. All student-advisor assignments must be approved by the Department Chairperson.

Immunology/Microbiology: Academic Policies

Five-Year-Rule Limit after Matriculation

The Division of Immunology/Microbiology honors the five-year-rule limit after matriculation stated by The Graduate College. The rule states that “Maximum enrollment for degree completion is five calendar years. Any approved leave of absence will be excluded from this time. A student may petition for an extension of the overall time limit to the division director. If such an extension is granted, the student will be expected to enroll full-time for each remaining semester in residence. If a student proposes to maintain active status in The Graduate College while at another location, approval by the Division Director and The Graduate College Council will be necessary. Such a student will enroll each semester with Rush University’s Office of the Registrar for zero hours of credit, and will be charged the enrollment fee rate in effect at that time.”

Vacation

Students are entitled a total of two weeks vacation per year. The advisor must approve the vacation timing.

Parental Leave Policy

Parental leave will first be negotiated between student and advisor, subject to the provision that students may take up to six weeks (total) off during pregnancy and/or following the birth of a baby, with full stipend. If a student elects to take a longer period before returning to full-time graduate status, this additional time will be automatically considered a leave of absence with no stipend provided. A student on paternity/maternity leave of absence is guaranteed reinstatement for up to six months after delivery.

Conditions for Continuation in the Program

If a student leaves residency in the program without completing the requirements of his or her degree, he or she may continue his or her status as a student for an additional two years, provided he or she arranges to meet SDAC every six months. Otherwise, the student will be subject to dismissal at the end of six months after leaving the program.

Ethics

All students are expected to keep a good and careful record of their research. Any student found falsifying, plagiarizing or misrepresenting data will be dismissed from the program. The original of all records must remain in the laboratory in which the student worked.

Problems Between Advisor and Student

Prior to forming the SDAC, if a problem arises between student and advisor, this problem should be discussed with the Division Director, who will then attempt to mediate and provide a reasonable solution to the problem. If a problem arises between a student and the advisor after the student has formed the SDAC, the student and/or the advisor should discuss the problem with the SDAC chair. If the problem is not resolved within one month, the student/advisor should discuss it with the Division Director. It is recommended that difficulties be solved at an early stage. If the informal approaches are unsuccessful, and a student and/or advisor desires to sever their working relationship, those individuals involved shall petition in writing for such change to the program director. From the date of receipt of the written request for a change, two weeks of mutual introspection time is required before any change is considered. The Division Director will make the decision whether or not to honor the student’s request for transfer and will make the necessary arrangements to make the transition smoothly. An advisor change is a serious matter and should only be contemplated after all other avenues have failed. Students must also be aware that an advisor change is not automatically approved, and that the availability of an alternate advisor may be very restricted.

Graduate College/Rush University Academic Policies

Academic policies specific to The Graduate College are located earlier in this catalog. In addition, the Academic Resources and Policies section of this catalog contains Rush University academic policies.

Immunology/Microbiology: Tuition Waivers and Assistantships

Eligibility

As a part of the program’s intention to provide the opportunity to advance academically and develop scholarship in a reasonable period of time, students in the PhD program receive a tuition waiver and a student assistantship to allow vigorous and full-time commitment to their academic endeavors. Students in the MS program do not receive a tuition scholarship or an assistantship.

Assistantships for students in the PhD program may be withheld or reduced for those students that fail to provide a full commitment to research and scholarly activities after passing the Pre-Candidacy Examination. This reduction will be submitted to the Graduate Advisory Council (GAC) via a recommendation by the student’s advisor. The GAC may then inquire into this issue and decide on an outcome. Students in good academic/research standing are assured of their assistantship for five years by their sponsoring department or section. Assistantship support beyond five years is at the discretion of the advisor. Students are accepted into the program with the understanding that they will devote their full time to learning and research. Students in the PhD degree track receiving an assistantship and tuition waiver who, for reasons other than departmental and college decisions, transfer to the MS degree track may be required, at the discretion of the GAC, to repay the cost of tuition and assistantship support provided to them.

Immunology/Microbiology: Research Activities

Faculty members are based in an active medical center dedicated to patient care; to the support of clinical, biomedical and basic biological research; and to education in allergy, basic and clinical immunology, and microbiology. The following is a list of current active faculty and their primary research interests, as well as faculty in the Allergy and Immunology clinical program of the Department.

Lena Al-Harthi, PhD, George Washington University (Professor): HIV neuro- and immuno-pathogenesis; Role of Wnt/b-catenin signaling in HIV disease

Edward Barker, PhD, University of Illinois at Chicago (Associate Professor): Mechanisms of HIV immune evasion; Natural killer cells

Linda Baum, PhD, Michigan State University (Professor): Antibody-dependent cellular cytotoxicity in HIV disease

James W. Bremer, PhD, Baylor University (Professor): Clinical virology; Pathogenesis of HIV infection

Christopher Codispoti, MD, PhD, University of Cincinnati (Assistant Professor): Impact of environmental factors on allergic disease

Seema N. Desai, PhD, University of Mumbai (Assistant Professor): Immune activation and senescence in HIV disease

Vineet Gupta, PhD, University of Rochester (Associate Professor): Drug discovery; Integrins and inflammation; Podocyte biology

Nadim James Hallab, PhD, Rush University Medical Center (Associate Professor): Innate and adaptive immune responses to orthopedic implant debris; Implant preservation; Drug testing

Diana D. Huang, PhD, University of Michigan (Assistant Professor): HIV virology; Diagnostic tests for HIV infection

Alan L. Landay, PhD, University of Pittsburgh (Professor and Chair): Immune response to HIV infection; Clinical markers of HIV infection

Nell Lurain, PhD, Loyola University of Chicago (Associate Professor): Cytomegalovirus drug resistance and pathogenesis

Amanda Marzo, PhD, University of Western Australia (Assistant Professor): Mechanisms that govern the induction and maintenance of memory T cells

James N. Moy, MD, University of Illinois at Chicago (Associate Professor): Regulation of atopic disease

Sasha Shafikhani, PhD, University of California, Berkley (Assistant Professor): Pseudomonas aeruginosa pathogenesis; Host response to infection

Gregory T. Spear, PhD, University of Illinois at Chicago (Professor): Factors that affect susceptibility to HIV infection.

David L. Williams, PhD, University of Illinois Urbana- Champaign (Associate Professor and Graduate Program Director): Biochemistry and molecular biology of Schistosoma mansoni; Drug development

Andrew Zloza, MD, PhD, Rush University (Assistant Professor): interplay between infections (HIV and influenza) and cancer; Tumor immunotherapy.

Immunology/Microbiology: Service/Clinical Activities

In addition to offering the graduate program and conducting active research programs, the department teaches immunology and microbiology to medical students, offers an allergy/immunology residency program and maintains a close affiliation with the hospital’s clinical immunology and microbiology laboratory.

Immunology/Microbiology: Curriculum

(Note that the program retains the right to change these requirements in order to keep current with research and education advancements.)

First Year to Completion of the Program

During the first year after matriculation, students will enroll in The Graduate College Core Curriculum classes and other courses required by this Division. The schedule for these classes is:

Year 1

Fall Semester I

GCC - 501 Molecular Biology: Genome to Proteome Credit Hours: (2)
GCC - 502 Cellular Biochemistry: Proteins, Transport and Signaling Credit Hours: (2)
GCC - 511 Readings in Molecular Biology Credit Hours: (1)
GCC - 512 Readings in Cellular Biochemistry Credit Hours: (1)
IMM - 507 Basic Immunology I Credit Hours: (1)
IMM - 520 Advanced Readings in Immunology, Microbiology and Virology Credit Hours: (1)
IMM - 515 Research Seminar Credit Hours: (1)
IMM - 600 Laboratory Rotations in Immunology & Microbiology Credit Hours: (variable)

Spring Semester

GCC - 503 Functional Cell Biology Credit Hours: (1)
GCC - 504 Functional Tissue Biology Credit Hours: (2)
GCC - 506 Research Ethics Credit Hours: (1)
GCC - 513 Readings in Functional Cell Biology Credit Hours: (1)
GCC - 514 Readings in Functional Tissue Biology Credit Hours: (1)
IMM - 508 Basic Immunology II Credit Hours: (1)
IMM - 520 Advanced Readings in Immunology, Microbiology and Virology Credit Hours: (1)
IMM - 515 Research Seminar Credit Hours: (1)
IMM - 600 Laboratory Rotations in Immunology & Microbiology Credit Hours: (variable)

Summer Semester

IMM - 615 Pre-Dissertation Research in Immunology & Microbiology Credit Hours: (variable)
(A pre-candidacy examination for doctoral candidates-described below)

Note:

Students in the PhD track must complete the requirement for a Pre-Candidacy Examination (PCE) by the end of the summer semester. The PCE consists of both a written and oral portion. The written portion is based on a research proposal submitted to an examination committee appointed by the Graduate Advisory Committee (GAC). The topic of research must be preapproved by the GAC and must be different from the proposed research for PhD dissertation. The proposal should be based on the NIH R21 grant application format and should be no more than 7 pages in length (single-spaced) excluding bibliography. The oral portion of the PCE will consist of a presentation and defense of the grant proposal and may also include basic questions in their area of interest (immunology/microbiology). Students who fail the PCE will be asked to take a comprehensive written examination in immunology and microbiology. Failing this comprehensive written examination will result in recommendation for dismissal by the GAC to the Dean of The Graduate College.

Students are also expected to devote substantial time to research during the summer semester. After all core courses are completed, a student will be evaluated by the GAC for her or his performance in courses, laboratory work, motivation, etc., to determine continuation of the student in the program. This evaluation will take place before the beginning of the fall semester of the second year.

Second Year to Completion of the Program:

Year 2

Fall Semester I

IMM - 510 Advanced Immunology I Credit Hours: (3)
IMM - 515 Research Seminar Credit Hours: (1)
IMM - 520 Advanced Readings in Immunology, Microbiology and Virology Credit Hours: (1)
IMM - 615 Pre-Dissertation Research in Immunology & Microbiology Credit Hours: (variable)

Spring Semester

IMM - 610 Special Topics in Immunology & Microbiology Credit Hours: (variable)
IMM - 515 Research Seminar Credit Hours: (1)
IMM - 520 Advanced Readings in Immunology, Microbiology and Virology Credit Hours: (1)
IMM - 615 Pre-Dissertation Research in Immunology & Microbiology Credit Hours: (variable)

Summer Semester

IMM - 615 Pre-Dissertation Research in Immunology & Microbiology Credit Hours: (variable)
PhD students should defend a dissertation proposal to move to candidacy.

Note:

Before the start of the fall semester, the student will select a laboratory and advisor for their dissertation research. The student and advisor will submit a list of faculty for their Student Dissertation Advisory Committee (SDAC) for approval by the GAC. The members of the SDAC will be allowed to change with GAC approval if the project changes substantially or if the faculty is no longer appointed at Rush. The composition of the SDAC must be consistent with guidelines of the Graduate College Council. At this time, the SDAC must consist of at least five members:

The advisor
Two faculty members from the Division of Immunology/ Microbiology. This may include a co-advisor.
One faculty member from another division in The Graduate College
An additional faculty member from within or from outside of Rush University

The student will prepare a dissertation proposal describing her or his plan for dissertation research and submit the proposal to his or her SDAC during the spring or summer semester of the second year. The SDAC must approve both the written document and oral defense of the document before the end of the summer semester. Preliminary data should be included, if available, but it is not necessary and the presentation/defense should not be deferred to collect such data. While it is mandatory that students complete this requirement by the end of the summer semester, students are strongly urged to complete this requirement before this deadline so that they may begin their doctoral dissertation research in earnest as soon as possible. After successful defense of the research proposal and the dissertation proposal, the student will be admitted to candidacy. If the proposal defense is failed, the SDAC may require that the proposal be rewritten and defended prior to the end of the fall semester of the third year. A failure at the second defense will result in a recommendation for dismissal from the program.

Three to Five Years to Completion of the Program

Students should continue to register for Special Topic (IMM 610 ) courses from years 2 through 4 until they have completed two special topic courses prior to graduation. In special circumstances, students may substitute special topic courses with an elective, contingent upon permission of the Graduate Program Director. Doctoral students are expected to register for IMM 520 Advanced Readings in Immunology and Microbiology, IMM 515 Research Seminar and IMM 620 Dissertation Research each fall and spring semester. Examples of previous special topics courses include: Current Topics in Cellular Immunology-From Bedside to Bench; HIV Gene Structure and Function; Viral Mimicry; Tolllike Receptors; Signal Transduction in Lymphocytes; Vaccines; and Th2, Parasites, and Allergy. Students must also devote maximum time to research during these years.

When the student and the advisor have determined that sufficient data have been obtained and that the project has reached an acceptable degree of completion, a data defense meeting with SDAC is held in which the student summarizes the data that will be included in the dissertation. If the SDAC approves, the student will commence writing the dissertation. A requirement for graduation is an accepted first author publication in a peer-reviewed journal based on the student’s dissertation research.