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IU Unit in Virology

IU Unit in Virology


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In a paper recently I saw "Cell are infected with 50,000 IU of virus per 100ul well". I can not seem to find a defintion of this unit? Is it a functional unit or just a count? If someone is familiar with this definition please let me know.

It is a retrovirus. The thesis is here (page 18): https://tspace.library.utoronto.ca/bitstream/1807/98170/3/Mazzanti_Andrew_D_201911_MSc_thesis.pdf


IU Unit in Virology - Biology

Departmental Email:&#[email protected]

Departmental URL: http://www.biology.indiana.edu

(Please note that when conferring University Graduate School degrees, minors, certificates, and sub-plans, The University Graduate School’s staff use those requirements contained only in  The University Graduate School Bulletin. )

Curriculum

Degrees Offered

Master of Science and Doctor of Philosophy in evolution, ecology and behavior Doctor of Philosophy in molecular, cellular, and developmental biology Master of Science and Doctor of Philosophy in microbiology Master of Science and Doctor of Philosophy in plant sciences Master of Science, Doctor of Philosophy, and Master of Arts for Teachers in zoology.

Special Departmental Requirements

(See also general University Graduate School requirements.)

Admission Requirements

Undergraduate major in one of the biological sciences and course work in the program in which a degree is sought. A degree in a related field (e.g., chemistry, physics, or mathemat­ics) may suffice if appropriate biology courses were included in the student’s degree program. Students seeking admission to biology degree programs may apply directly to the Department of Biology or online. Applications must include a complete entrance form, letters of recommendation, undergraduate tran­scripts, and scores on the Graduate Record Examination Gen­eral Test. (While it is not required that applicants also submit scores on the Subject Test in Biology, it is recommended that they do so.) The TOEFL score is required if the native language is other than English.

Special Requirement for the M.S. Degree

It is a requirement of the Department of Biology that the M.S. degrees be completed within five semesters however, the M.A.T. program allows additional time.

For all graduate degrees, students must maintain a minimum GPA of B (3.0) in order to remain in good standing in the Graduate School. Courses to be counted toward the degree must be passed with a grade of B- (2.7) or better. To be eligible for financial support, the Department of Biology requires students to maintain a minimum GPA of 3.2.

Ph.D. Qualifying Examination

Includes written, oral, and research components. See specifics for each program below.

Satisfactory Progress Toward a Degree

After passing the preliminary examination, for a student to remain in “good standing” in the Department of Biology requires that sufficient progress is being made toward completing a thesis. If the research advisory committee judges progress to be unsatisfactory, probation may be recommended. At the end of the probationary period (usually a semester), probation will be lifted if the advisory committee judges the student’s progress to be satisfactory. If the advisory committee judges the student’s progress to remain unsatisfactory, then the student will be required to leave the program.

The final requirement of each Ph.D. program is a Ph.D. thesis, which must be defended in a public research seminar and in a meeting of the research advisory committee. See specifics for each program below for additional requirements and for Master degree requirements.

Other Provisions

All students enrolled in a Ph.D. program in the Department of Biology will be required to serve as associate instructors for at least one semester, regardless of their source of support and they must complete formal instruction in teaching methods in order to enhance their teaching skills. Students whose native language is not English must become sufficiently fluent to pass the university's A.I. exam during the first year to remain in the program. It is the conviction of the department that teaching experience is a vital aspect of graduate education, whether or not the student intends to pursue a teaching career after attainment of the desired degree(s).

Evolution, Ecology and Behavior
Master of Science Degree

Course Requirements

A total of 30 credit hours, of which at least 20 credit hours must be taken in approved ecology and evolutionary biology courses. The courses must have a coherent focus within the general field of ecology and evolutionary biol­ogy and must be approved by the student’s advisory committee.

Final Examination

Includes a public research seminar and an oral de­fense of the thesis before the advisory committee.

Doctor of Philosophy Degree

Course Requirements

A total of 90 credit hours comprised of 29+ formal course credits. Course credits include: (1) a 20 credit ‘major’ (composed mostly of EEB courses, with exceptions approved by the EEB Graduate Program Director [GPD]), including two courses from one concentration area listed below and one course from a sec­ond area (2) a six+ credit ‘minor’ (taken within Biology or through another department: credits vary from 6 to 15 see below) and (3) a three credit statistics ‘toolkit’ class (Z620 Biostatistics or equivalent). Up to six credits in the ‘major’ may come from three sources: (A) Z620 journal clubs, (B) L500 Independent Study/Readings (graded), and/or (C) L501 Rotations (graded). L500/L501 credits require written summaries approved by the students’ graduate advisor(s) and the GPD. Not more than four credits may come from any of sources (A) - (C). Additionally, two credits in the major should come from L570 (Seminar in Ecology and the Environment). Remaining credit hours come from dissertation research. Any changes described here to course requirements can (but do not have to) apply retroactively. A student may apply courses taken for a MS degree if they are approved by the student’s advisory committee and the minor advisor.

Concentration Area Requirements

Ecology/Population Biology

  • E455 (SPEA) Limnology
  • L575 Biodiversity and Ecosystem Functioning
  • L577 Theoretical Ecology
  • L578 Advanced Population Biology
  • L579 Community Ecology
  • L591 Plant Population Biology—An Experimental Approach
  • Z620 Ecological Niches
  • Z620 Ecological Stoichiometry
  • Z620 Ecosystems and Global Change
  • Z620 Quantitative Biodiversity
  • Or other course approved by the EEB Graduate Program

Evolutionary Biology

  • I590 (INFO) SNP Discovery and Population Genetics
  • L505 Molecular Biology of Evolution
  • L533 Evolution of Genes and Genomes
  • L567 Evolution
  • L568 Evolutionary Genetics
  • L563 Evolution of Cells and Proteins
  • Z620 Evolution of Development
  • Z540 Genetics of Structured Populations
  • Z620 Phylogenetics
  • Z620 Systematics
  • G562 (Geo Sci) Geometric Morphometrics
  • Or other course approved by the EEB Graduate Program

Behavior/Physiology

  • A501 Techniques in Reproductive Diversity
  • L560 Physiological Ecology
  • L581 Behavioral Ecology
  • P548 Neuroethology
  • Z460 Animal Behavior
  • Z466 Endocrinology
  • Z563 Comparative Neurobiology of Animal Behavior
  • Z566 Laboratory in Endocrinology
  • Z620 Sensory Ecology
  • Or other course approved by the EEB Graduate Program

Each EEB student must complete coursework for a minor. The minor may obtained from a separate department (e.g., Informatics, Statistics, Environmental Science, Geology, Geography, Education), a relevant interdepart­mental program (e.g., Animal Behavior, Genetics), in a different graduate program in the Depart­ment of Biology (e.g., Genetics, Microbiology), or an ‘Individualized minor’. EEB will waive the three credit ‘toolkit’ requirement in statistics for students minoring in Statistics (15 credit). Requirements are set by the unit administering the minor but will consist of a minimum of 6 credits up to a maximum of 15 credits.

Ph.D. Qualifying Examination

Includes written oral and research components. All full-time Ph.D. students must pass part I of the examination (written and oral breadth of kowledge examination) by the end of the thirteenth week of their fourth semester and must pass part II of the qualifying examination (dissertation proposal defense) by the end of the sixth week of their sixth semester. In the event of failure or postponement of part II, students may retake the examination once, but no later than the end of their sixth semester.

Students write a thesis based on scientific research.

Final Examination

Public research seminar and oral defense of the dissertation before the student’s research committee.

Graduate Minor in Evolution, Ecology, and Behavior

Students in other departments or in other programs in the Department of Biology may concentrate in one of the three areas of specialization (ecology/population biology, evolutionary biology, or behavior/physiology) by selecting two or more courses from the chosen area for a minimum of 6 credits. The minor advisor may also approve of one course from each of two (or three) of the areas described. A course may not simultaneously satisfy both major and minor course requirements. Course offerings outside of the list below can be used to satisfy the EEB minor. However, such substitutions require approval of the minor advisor and the EEB Graduate Program Director. A student may apply courses taken for a MS degree if they are approved by the student’s advisory committee and the minor advisor.

Ecology/Population Biology

  • E455 (SPEA) Limnology (3 cr)
  • L575 Biodiversity and Ecosystem Functioning (1.5 cr)
  • L577 Theoretical Ecology (3 cr)
  • L578 Advanced Population Biology (3 cr)
  • L579 Community Ecology (3 cr)
  • Z620 Ecological Niches (1.5 cr)
  • Z620 Ecological Stoichiometry (1.5 cr)
  • Z620 Ecosystems and Global Change (1.5 cr)
  • Z620 Quantitative Biodiversity (1.5 cr)

Evolutionary Biology

  • L505 Evolution of Development (1.5 cr)
  • L533 Evolution of Genes and Genomes (3 cr)
  • L534 Evolution of Cells and Proteins (3 cr)
  • L567 Evolution (3 cr)
  • L568 Evolutionary Genetics (3 cr)
  • Z540 Genetics of Structured Populations (3 cr)
  • Z620 Systematics (1.5 cr)
  • I590 (INFO) SNP Discovery and Population Genetics (3 cr)
  • G562 (Geo Sci) Geometric Morphometrics (3 cr)

Behavior/Physiology

  • A501 Techniques in Reproductive Diversity (3 cr)
  • L560 Physiological Ecology (3 cr)
  • L581 Behavioral Ecology (3 cr)
  • Z460 Animal Behavior (3 cr)
  • Z563 Comparative Neurobiology of Animal Behavior (3 cr)
  • Z620 Sensory Ecology (3 cr)
Molecular, Cellular, and Developmental Biology

The MCDB program consists of formal coursework, laboratory research, and professional development. Students in the MCDB program learn how to plan, execute, and critically analyze scientific research. Other professional development includes learning how to give oral presentations and write high-quality research papers and grant proposals. The MCDB program provides students with the training and research experience necessary to pursue a diversity of careers, including academic research, biomedical research, biotech industry, university-level teaching, among others.

Master of Science Degree

Course Requirements

A total of 30 credit hours, of which at least 20 credit hours must be taken in the Department of Biology. The courses must be approved by the student’s advisory committee and the MCDB Graduate Program Director

Thesis defense

The students are required to prepare a research based thesis that must be approved by the student’s advisory committee and must meet the guidelines of the graduate school. The final exam includes a public research seminar and an oral de­fense of the thesis before the advisory committee.

Doctor of Philosophy Degree

Course Requirements

Students must acquire a total of 90 credit hours, which includes formal coursework totaling 22.5 credits for the major plus 6+ credits for the minor (credits vary by minor). MCDB students take a common core program of classes (see below). In addition, students typically do research rotations in three different labs during the first semester, after which they identify a lab in which to do their thesis research and form their advisory committee. Other courses can be substituted for the MCDB requirements pending permission from the students Advisory Committee and the MCDB Program Director. Any changes described here to course requirements can (but do not have to) apply retroactively.

Courses for the MCDB Major

  • B511 Biochemistry (3.0 cr)
  • L585 Genetics (3.0 cr)
  • Z620 Bioinformatics 2 Go (1.5 cr)
  • L523 Critical Analysis Lit. (1.5 cr)
  • L501 Rotations (3.0 cr)
  • L586 Cell Biology (3.0 cr)
  • L587 Dev. Biology (3.0 cr)
  • *Z620 Journal Class (1.5 cr)
  • Z620 Grant Writing (1.5 cr)
  • Z620 Research Ethics and Career Development (1.5 cr)

* Journal Class options: Z620 Chromosome and Genome Biology or Z620 Cell Biology or P550 Physiology of Cancer

Each student must select a minor field distinct from the chosen degree. The student has the option to select any minor in consultation with their advisor and the MCDB Graduate Program Director. The minor may be from within biology or from other units on campus. The requirements for the minor are decided by the minor-granting program.

Ph.D. Qualifying Examination

Includes written, oral and research components. All full-time Ph.D. students must take the qualifying examination by the end of the fourth week of their fifth semester. In the event of failure or postponement, students may retake the examination once, but no later than the end of the twelfth week of their fifth semester.

Students write a thesis based on their scientific research and are expected to publish the findings of their scientific research in peer-reviewed journals.

Final Examination

Public research seminar and oral defense of the dissertation before the student’s research committee.

Graduate Minor in Genetics

The Genetics minor requires 6 credits of course work selected from among the list of courses below. Students may substitute courses for those on this list only upon approval of their Advisory Committees and the MCDB Director. A MCDB student can choose to minor in other fields that match their research and career aspirations with approval of their Advisory Committee and the MCDB Director. Any course requirements described here can (but do not have to) apply retroactively. A student may apply courses taken for a MS degree if the courses are approved by the student’s advisory committee and the minor advisor.

Course Listings for Genetics Minor 1

  • L533 Evolution of Genes and Genomes (3cr)
  • L567 Evolution (3cr)
  • L585 Molecular Genetics (3cr) 2
  • L586 Cell Biology (3cr) 2
  • L587 Developmental Biology (3cr) 2
  • Z620 BioInformatics-2-Go (1.5 cr) 2
  • Z620 Evolution of Proteins and Cells (3cr)
  • Z620 Introduction to Computational Data Processing in Biology (1.5cr)
  • Z620 Introduction to Computational Workflow Design in Biology (1.5cr)
  • Z620 CyberInfrastructure-enabled Computational Genome Science (3cr)
  • Z620 Phylogenetics (3cr)
  • Z620 Evolution (3cr)
  • Z620 Introduction to Genomics and BioInformatics (1.5cr)
  • Z620 Genetics of Behavior (1.5cr)
  • Z620 Microbial Genetics and Techniques (1.5cr)
  • Z620 Chromosome and Genome Biology Journal Class 3
  • Z620 Cell Biology Journal Class 3
  • P550 Physiology of Cancer Journal Class 3
  • Z620 Methods in Epigenomics
  • Z620 The Legacy of Drosophila (3cr)
  • Z620 Digital Imaging and Light Microscopy
  • I590 SNP Discovery and Population Genetics (3cr)
  • P467 Diseases of the Nervous System (3cr)
  • P526 Neurobiology of Learning and Memory (3cr)
  • P566 Molecular and Cellular Neurobiology (3cr)
  • M580 Molecular Biology of Cancer (3cr)
  • M511 Molecular Biology of Prokaryotes (3cr)
  • M541 Bacterial Pathogenesis and Virology (3cr)

1 Or an equivalent course at IU or graduate work transferred from another university with approval of the MCDB Graduate Program Director

2 MCDB students cannot use these courses for the Genetics minor due to overlap with major degree requirements.

3 The same journal class cannot be taken twice to fulfill the major and minor. However, different journal classes can be taken for the major and minor.

Microbiology

Degree programs are available for students with interests in many areas of microbiology. Each student’s curriculum is designed by the student in consultation with the graduate pro­gram director, the student’s mentor, and an appointed advisory committee.

Master of Science Degree

Course Requirements

A total of 30 credit hours. At least 12 credit hours must be courses from the core biology curriculum other than M500 rotation credits or research credits. The courses must be approved by the student’s advisory committee and the Microbiology Graduate Program Director.

Students are expected to rotate (M500) in at least three laboratories dur­ing the fall semester.

The students are required to prepare a research-based thesis that must be approved by the student’s advisory committee.

Final Examination

Normally includes a public research seminar and oral defense of the thesis.

Doctor of Philosophy Degree

Course Requirements

The Microbiology program requires a total of 90 credit hours. Of these, 24 credit hours come from the Core Program course work listed below. Most Advanced Courses are half-semester 1.5-credit hour courses in areas requested by students. Each student must also take Grant Writing and Research Ethics and Career Development courses. Students also typically do research rotations in three different labs during the first semester, after which they identify a lab in which to do their thesis research and form their advisory committee.

The courses that make up the 24 credit hours for the Microbiology major are indicated below. Other appropriate courses may be substituted in their place with permission from the Advisory Committee and the Microbiology Graduate Program Director. Any changes described here to course requirements can (but do not have to) apply retroactively.

Major Course Requirements

  • L585 Genetics (3.0 cr)
  • Z620 Bioinformatics to Go (1.5 cr)
  • L523 Critical Analysis of Scientific Literature (1.5 cr)
  • *B501 Integrated Biochemistry (3.0 cr)
  • *B511 Duplicating and expressing the genome (3.0 cr)
  • *T508 Theory and Application of Biotechnology (3.0 cr)
  • M541 Microbial pathogenesis and Virology (3.0 cr)
  • M511 Molecular Biology of Prokaryotes (3.0 cr)
  • Z620 Grant Writing (1.5 cr)
  • Z620 Ethics and Career Development (1.5 cr)
  • M500 Research rotations (3.0 cr)
  • Elective Advanced Course work - typically Z620 credits (3.0 cr)
  • * Only one these three courses need to be completed for the major

Each student must select a minor field distinct from the chosen degree. The student has the option to select any minor in consultation with their advisor and the MCDB Graduate Program Director. The minor may be from within biology or from other units on campus. The requirements for the minor are decided by the minor-granting program

Ph.D. Qualifying Examination

Includes writtten, oral and research components. All full-time Ph.D. students must take the qualifying examination by the end of the fourth week of their fifth semester. In the event of failure or postponement, students may retake the examination once, but no later than the start of their third year in graduate school.

Students write a thesis based on scientific research.

Final Examination

Public research seminar and oral defense of the dissertation before the student’s research committee.

Graduate Minor in Microbiology

Students in other departments or in other programs in the Department of Biology may minor in Microbiology by completing a minimum of 6 graduate credits from the courses listed below.  A minor advisor must join the student's Advisory Committee and participate in designating required course work. This minor advisor will approve courses that meet the minor requirement. A course may not simultaneously satisfy both major and minor course requirements. Course offerings outside the list below can be used to satisfy the Microbiology minor, but such substitutions require approval of the minor advisor and the Microbiology Graduate Program Director. An overall average of B (3.0) or better is required in the Microbiology minor coursework.

  • M430 Virology Lecture (3 cr.)
  • M440 Medical Microbiology: Lecture (3 cr.)
  • M460 Microbial Evolution (3 cr.)
  • M480 Microbial and Molecular Genetics (3 cr.)
  • Z620 Medical Microbiology and Medical Immunology (3 cr.)
  • M511 Molecular Biology of Prokaryotes (3 cr.)
  • M525 Microbial Physiology and Biochemistry (3 cr.)
  • M541 Microbial Pathogenesis and Virology (3 cr.)
  • M550 Microbiology (3 cr.)
Plant Sciences

(Department is not currently admitting students to this program)

Master of Science Degree

(Department is not currently admitting students to this program)

Course Requirements

A total of 30 credit hours, stressing suitable advanced courses in plant sciences and cognate areas. At least 20 of the credit hours must be in the major area.

Normally required an alternative project may, however, be approved by the student's advisory committee.

Final Examination

A public research seminar and an oral de­fense of the thesis or defense of an approved alternative project before the student's advisory committee.

Doctor of Philosophy Degree

(Department is not currently admitting students to this program)

Ph.D. students choosing a molecular approach will follow the procedures of the genetics and molecular, cellular, and developmental biology graduate programs. Likewise, students choosing an organismal approach will follow the procedures of the evolution, ecology and behavior program.

Zoology

(Department is not currently admitting students to this program)

Master of Science Degree

(Department is not currently admitting students to this program)

Course Requirements

A total of 30 credit hours, of which at least 20 credit hours must be taken in the Department of Biology.

Normally required an alternative project may, however, be approved by the student's advisory committee.

Final Examination

Normally includes a public research seminar and an oral de­fense of the thesis or defense of an approved alternative project before the student's advisory committee.

Doctor of Philosophy Degree

(Department is not currently admitting students to this program)

Ph.D. students choosing a molecular approach will follow the procedures of the genetics and molecular, cellular, and developmental biology graduate programs. Likewise, students choosing an organismal approach will follow the procedures of the evolution, ecology and behavior program.

Course Requirements

A total of 90 credit hours of advanced course work, including dissertation.

Selected in consultation with research advisor and zoology program director.

Master of Arts for Teachers Degree

The Master of Arts for Teachers in biology is offered by the University Graduate School (not the School of Education) to provide training beyond the bachelor’s degree for those who intend to teach in junior or senior high school and who wish additional training in biology. Each student in the program must possess a teacher’s certificate by the time the degree is con­ferred, with the exception of international students who intend to return to their native country.

Admission Requirements

Bachelor’s degree from a regionally accredited institution with sufficient hours in biology to enable the student to take courses carrying graduate credit.

Course Requirements

A total of 36 credit hours, of which a minimum of 25 credit hours must be in courses in the biological sciences that carry graduate credit the remaining 11 credit hours may be in edu­cation. All programs of study must be approved by the Master of Arts for Teachers program advisor.

Certification Requirements

For a complete list of courses in education and other areas that are required for provisional certification, consult the School of Education Undergraduate Program Bulletin.


QCB News

Kristen Alanis (Baker lab) was author on Imaging with Ion Channels, a paper published in Analytical Chemistry.

Walsh Publication

Selivanovitch Publication

Kate Selivanovitch (Douglas lab) was first author on Molecular exclusion limits for diffusion across a porous capsid, a paper published in Nature Communications.

Ramos Publication

Spring QCB Evening, April 5, 2021

Join us for the Spring QCB Evening on Monday, April 5th from 5:00-6:00pm on Zoom.

Allison Adkins, career coach from the Walter Center will be giving a workshop on how to create resumés and CVs. We will then use these insights to evaluate resumes and CVs from our department.

Please find more details, including the Zoom ID, here.

Fadler Publication

Brown Publication

Schlicksup Publications

Christopher Schlicksup (Zlotnick lab) was first author on Viral structural proteins as targets for antivirals, a paper published in Current Opinion in Virology and Local Stabilization of Subunit–Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids, a paper published in ACS Chemical Biology.

He was also second author on Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly, a paper published in Journal of the American Chemical Society.

Visit With Dr. Eranthie Weerapana

Please join us for Dr. Eranthie Weerapana’s virtual visit and seminar, hosted by Professor Giedroc, on Friday, February 12.
She is an associate professor of chemistry at Boston College, and her talk is titled “Chemical-proteomic strategies to investigate reactive cysteines.”

The seminar is set to take place at 2:30 p.m. Following her seminar, at 3:30 p.m., all QCB trainees and any others who may be interested are invited to visit with Dr. Weerapana.

Please find the Zoom link for both the seminar and afterwards here.

Trainee Spotlight

Matthew Jordan

My research focuses on investigating metallochaperones in s. aureus.

Fun Fact: I am a nephew of both Michael Jordan and J. Cole.

Degree Program: Biochemistry

Lab: Giedroc

Undergrad Institution: Manchester University

Ekaterina Selivanovitch

My research focuses on the development of nanotechnology using virus-like particles.

Fun Fact: I do not like ice cream.

Degree Program: Chemistry

Lab: Douglas

Undergrad Institution: St. Francis College, St. John's University


Titles & Appointments

  • Associate Professor of Clinical Pathology & Laboratory Medicine
  • Adjunct Associate Professor of Clinical Microbiology & Immunology
  • Medical Director, IU Health Division of Clinical Microbiology
  • Medical Director, Eskenazi Health Clinical Microbiology and Serology
  • Medical Director, IU Health Special Pathogens Unit Laboratory
  • Associate Medical Director, IU Health Division of Molecular Pathology
  • Director, IU School of Medicine CPEP-Accredited Medical and Public Health Laboratory Microbiology Fellowship Program

Research in my laboratory is currently focused on four specific areas concerning emerging viruses:

1. Surveillance for emerging pathogenic viruses in arthropods collected in Indiana and abroad. By using a combination of classical and modern methods, including viral culture, real-time polymerase chain reaction (PCR), and next-generation sequencing, we seek to determine the prevalence of several emerging pathogenic viruses in possible vector and reservoir species endemic to Indiana and abroad. Work is performed at both biosafety level (BSL)-2 and BSL-3, if cultivation of risk group-3 viruses is required for further analysis. To do so, we have partnered with Project Vector Shield, an Indiana University Movement Ecology working group, to capture, identify, and analyze ticks and mosquitoes from Indiana for viruses such as Bourbon virus, Heartland virus, Lone Star virus, Powassan virus, and others. In addition, we will soon begin collaborations with scientists at the National Institutes of Health (NIH) Rocky Mountain Laboratories (RML) and the Mayo Clinic to assess the neurovirulence of clinical and field isolates of California encephalitis serogroup viruses, a large group of mosquito-borne orthobunyaviruses that include Jamestown Canyon virus, Inkoo virus, and La Crosse virus, among others. Another collaboration with the New England College of Osteopathic Medicine will focus on the prevalence of tick-borne viruses in tick populations gathered from Maine.


Optional header 2

Professors
Peter Cherbas, Keith Clay, Sears Crowell (Emeritus), Thomas F. Donahue, Patricia Foster, Gerald Gastony, George Hegeman (Emeritus), Ellen Ketterson, Arthur Koch (Emeritus), Curtis Lively, Mike Lynch, Paul Mahlberg (Emeritus), George Malacinski, Carlos Miller (Emeritus), Craig Nelson, Val Nolan (Emeritus, Law), David Parkhurst (Public and Environmental Affairs), Elizabeth Raff, Rudolf Raff, J. C. Randolph (Public and Environmental Affairs), Loren Rieseberg, William Rowland, Albert Ruesink, Drew Schwartz (Emeritus), Susan Strome, Milton Taylor, Robert Togasaki (Emeritus), Michael Wade, Maxine Watson, Eugene Weinberg (Emeritus), Meredith West (Psychology), David White (Emeritus), Donald Whitehead (Emeritus), Frank Zeller (Emeritus)

Associate Professors
Alan D. Bender, José Bonner, Edmund Brodie III, Yves Brun, Yean Chooi-Odle, Lynda Delph, Roger Hangarter, George Hudock (Emeritus), Roger Innes, Cheng Kao, Emilia Martins, William Saxton, Stefan Surzycki, Michael Tansey, Miriam Zolan

Assistant Professors
James Bever, Lingling Chen*, Greg Demas, James Drummond, Joseph Duffy, Wayne Forrester, Clay Fuqua, David Kehoe, Anne Prieto*, Heather Reynolds*, Troy Smith*, Kelly Williams, Joel Alcasid Ybe*

Senior Scientist
Lucy Cherbas*

Assistant Scientist
Kevin R. Cook*

Adjunct Professors
David Dilcher (Geological Sciences), Elisabeth Lloyd (History and Philosophy of Science), John Richardson (Chemistry), Roderick Suthers (Medical Sciences), Nicholas Toth (Anthropology), Daniel Willard (Emeritus, Public and Environmental Affairs), William Timberlake (Psychology)

Adjunct Associate Professors
David Daleke (Medical Sciences), Anton Neff (Medical Sciences), Flynn Picardal (Public and Environmental Affairs), Henry Prange (Medical Sciences), Ted Widlanski (Chemistry)

Adjunct Assistant Professors
Donald Burke* (Chemsitry), Andrew Feig* (Chemistry), Evelyn Jabri* (Chemistry), Vicki Meretsky*, Martha Oakley*, Martin Stone* (Chemistry)

Director of Graduate Studies
Professor Elizabeth Raff, Jordan Hall 325, (812) 855-1861

Degrees Offered

Master of Arts and Doctor of Philosophy in ecology and evolutionary biology Doctor of Philosophy in genetics Master of Arts and Doctor of Philosophy in microbiology Doctor of Philosophy in molecular, cellular, and developmental biology Master of Arts and Doctor of Philosophy in plant sciences Master of Arts and Doctor of Philosophy in zoology and Master of Arts for Teachers.

(See also general University Graduate School requirements.)

Admission Requirements
Undergraduate major in one of the biological sciences and course work in the program in which a degree is sought. A degree in a related field (e.g., chemistry, physics, or mathematics) may suffice if appropriate biology courses were included in the student's degree program. Students seeking admission to biology degree programs should apply directly to the Department of Biology. Applications must include a complete entrance form, letters of recommendation, undergraduate transcripts, and scores on the Graduate Record Examination General Test. (While it is not required that applicants also submit scores on the Subject Test in biology, it is recommended that they do so.)

Special Requirement for the M.A. Degree
It is a requirement of the Department of Biology that the M.A. degree be completed within five semesters, although some programs such as the M.A.T. and joint SPEA/Biology programs allow additional time.

Ph.D. Qualifying Examination
Includes written, oral, and research components. All full-time Ph.D. students must take the qualifying examination by the end of the fourth week of their fifth semester. In the event of failure or postponement, students may retake the examination once, but no later than the end of the twelfth week of their fifth semester.

Final Examination
Oral defense of the dissertation before the research committee. For additional requirements in certain programs, see below.

Other Provisions
All students enrolled in a Ph.D. program in the Department of Biology will be expected to serve as associate instructors for at least two semesters, regardless of their source of support and they must complete formal instruction in teaching methods in order to enhance their teaching skills. It is the conviction of the department that teaching experience is a vital aspect of graduate education, whether or not the student intends to pursue a teaching career after attainment of the desired degree(s).

Ecology and Evolutionary Biology

Master of Arts Degree

Course Requirements
A total of 30 credit hours, of which at least 20 credit hours must be taken in approved ecology and evolutionary biology courses. The courses that each student takes must have a coherent focus within the general field of ecology and evolutionary biology. At least one seminar should be taken each year.

Thesis
Normally required an alternative project may, however, be approved by the student's advisory committee.

Final Examination
Normally includes a public research seminar and an oral defense of the thesis or alternative project before the advisory committee.

Doctor of Philosophy Degree

Course Requirements
A total of 90 credit hours, including two courses from one concentration area listed below and one course from a second area, Z620 Biostatistics (or equivalent), and dissertation. Students must enroll in a seminar at least one semester during each of the first three years in the program.

Concentration Area Requirements

Ecology/Population Biology
E455 (SPEA) Limnology
L575 Biodiversity and Ecosystem Functioning
L578 Advanced Population Biology
L579 Community Ecology
L591 Plant Population Biology&mdashAn Experimental Approach

Evolutionary Biology
B555 Special Topics in Plant Systematics
L505 Molecular Biology of Evolution
Z540 Genetics of Populations
L567 Evolution
Z620 Molecular Evolutionary Genetics

Behavior/Physiology
Z460 Ethology
P548 Neuroethology
L560 Physiological Ecology
Z566 Laboratory in Endocrinology
Z581 Behavioral Ecology

Minor
The minor may be in a separate department, an interdepartmental program, a different graduate program in the Department of Biology, or in biometrics. Requirements are as set by the unit administering the minor.

Foreign Language/Research Skill Requirements
Determined by the student's advisory committee.

Final Examination
In addition to the oral defense of the dissertation before the student's research committee, a public research seminar is required.

Genetics

Molecular, Cellular, and Developmental Biology

Doctor of Philosophy Degree

Programs leading to the Ph.D. degrees in genetics, and in molecular, cellular, and developmental biology are administered by the Faculty Committee on Molecular Biology and Genetics (MBG), in collaboration with members of the Department of Chemistry. The Ph.D. in plant sciences can be pursued under the supervision of MBG or that of Ecology and Evolutionary Biology, depending upon the nature of a student's research interests.

The degrees administered by MBG are intended to serve the needs of students who wish to employ molecular and genetic approaches to problems in cell biology, developmental biology, genetics, microbiology, molecular biology, molecular evolution, and plant sciences. Students enter these two degree programs through a common portal: the Core Program of first-year study administered by the MBG. After the first year, students' advanced work is monitored by the individual degree committees.

Common Requirements
During the first year, each student takes a common Core Program. Fall: L501, L523, L585, and C581 and C584 or another graduate-level biochemistry course spring: L501, L586, L587. Biology L501 is a rotation course in which each student participates in research projects in at least three different laboratories prior to selecting a permanent research advisor and laboratory at the end of the first year. In addition, students whose native language is not English are expected to become sufficiently fluent to pass the university's Examination in English for Associate Instructors during the course of the first year.

At the end of the first year, each student selects a research advisor and laboratory. Together with the advisor, the student also selects the other members of an advisory committee of three or four faculty members appropriate to the student's intended degree and one from the prospective minor field (see below). This advisory committee guides and monitors the student's subsequent independent work and guides the student's selection of advanced courses. MBG requires that each student meet with the advisory committee at least once per year.

The MBG-administered degree programs require a total of 90 credit hours including the Core Program and at least six advanced courses (see below). They also require that each student register for Journal Club (Z620) during the second year and make two oral presentations in Journal Club during the course of his/her career. Each student must also take a Z620 course in Scientific Practices (Ethics) during the third year, and each student must teach for at least two semesters.

Grades
Every student must maintain a minimum GPA of B (3.0) in order to remain in good standing. Courses to be counted toward the Ph.D. degree must be passed with a grade of B- (2.7) or better.

Preliminary Examination
Students in all programs take a preliminary examination at the end of the fourth semester. Students who pass this examination and complete the required course work are admitted to formal candidacy for the Ph.D.

Satisfactory Progress Toward a Degree
After passing the preliminary examination, for a student to remain in "good standing" in MBG requires that sufficient progress be made toward completing a thesis. If the research advisory committee judges progress to be unsatisfactory, probation may be recommended. At the end of the probationary period (usually a semester), if the advisory committee judges the student's progress to be satisfactory, then probation will be lifted. If the advisory committee judges the student's progress to remain unsatisfactory, then the student will be required to leave the program.

Thesis
The final requirement of each program is a Ph.D. thesis, which must be defended in a public research seminar and in a meeting of the research advisory committee.

Advanced Courses and Minor
The MBG, in conjunction with the degree program committees, offers a program of half-semester advanced courses (Z620). The selection of courses changes each year. Courses are offered in all the degree subjects. Each program requires that its students take at least six of these courses, at least four of which should be certified by the student's committee as appropriate to the chosen degree.

Each student must select a minor field distinct from the chosen degree. Ordinarily a student will select as a minor one of the MBG degree programs not selected for the major. In those cases, the Core Program courses meet minor requirements. In some cases a student may select another minor and must meet any additional requirements set by that minor.

For students from other programs who wish to minor in one of the MBG degree areas, the requirement is 6 credit hours of work in that field. The course selection should be approved by the director of MBG.

Microbiology

Degree programs are available for students with interests in many areas of microbiology. Each student's curriculum is designed by the student in consultation with the graduate program director, the student's mentor, and an appointed advisory committee.

Master of Arts Degree with a Research Thesis

Course Requirements
A total of 30 credit hours, 12 of these must be course work not including M500, M800, or M850. Course options include Z620 Advanced Biological Mechanisms (4.5 cr.), L585, C483, C484, M440, M460, M480, M416, M430, M525, L586, Z620 (Special topics, 1.5-3 cr.). Students are expected to rotate (M500) in at least two laboratories during the fall semester and to participate in M850 Microbiology Journal Club each time it is offered in the fall and spring.

Grades
A minimum of B- (2.7) in each required course.

Thesis
Required.

Final Examination
Oral defense of thesis.

Master of Arts Degree with a Library Thesis

The department also offers a program in microbiology leading to a terminal master's degree that does not require a laboratory research project. A student enrolled in this program will write a thesis critically evaluating and reviewing some aspect of microbiology reported in the literature. All other requirements for the degree are identical to those stated above for the research-thesis Master of Arts. The degree is designed to give individuals an opportunity to pursue graduate study at the master's level without acquiring expertise in laboratory research.

Doctor of Philosophy Degree

Course Requirements
A total of 90 credit hours, including the following core courses: L585 and Z620 (Advanced Biological Mechanisms, 4.5 cr.). C483 and C484 can be substituted for the core Z620. Three or four elective courses also required. Electives include L523, M480, M440, M460, and Z620 (Host Pathogen Interactions), M430, M572, M525, L586, Z620 (Special Topics). Additional courses from this or other departments with written permission of the Microbiology Program Director may be substituted for the electives. Also required are M850 (Microbiology Journal Club) taken each fall and spring (except for the first semester), six advanced courses Z620 Half-Semester Seminars), and Scientific Practices (Ethics) in the third year. During the first year, students are required to complete three rotations (M500).

Grades
A minimum of B- (2.7) or better in each required course.

Advisory Committee
The committee will consist of the research advisor, one member of the microbiology faculty, a faculty representative of the student's minor field, and one or two additional members of the faculty.

Thesis
Required.

Final Examination
In addition to the oral defense of the dissertation before the research committee, a public seminar is required.

Plant Sciences

Master of Arts Degree

Course Requirements
A total of 30 credit hours, stressing suitable advanced courses in plant sciences and cognate areas. At least 20 of the credit hours must be in the major area.

Grades
B average (3.0) required.

Thesis
Required. An equivalent creative project may be accepted in lieu of the thesis.

Doctor of Philosophy Degree

Ph.D. students choosing a molecular approach will follow the procedures in all respects (courses, seminars, research rotations, preliminary examination, etc., of the Genetics and MCDB (Molecular, Cellular, and Developmental Biology) graduate programs. Likewise, students choosing an organismal approach will follow the exact procedures of the Ecology and Evolutionary Biology program.

Zoology

Each degree program is tailored to the specific interests and needs of the student.

Master of Arts Degree

Course Requirements
A total of 30 credit hours, of which at least 20 credit hours must be taken in the Department of Biology.

Grades
B average (3.0) required.

Thesis
Required. An alternative project may be accepted in lieu of the thesis.

Doctor of Philosophy Degree

Course Requirements
A total of 90 credit hours of advanced course work, including dissertation.

Minor
Selected in consultation with research advisor and zoology program director.

Master of Arts for Teachers Degree

The Master of Arts for Teachers in biology is offered by the University Graduate School (not the School of Education) to provide training beyond the bachelor's degree for those who intend to teach in junior or senior high school and who wish additional training in biology. Each student in the program must possess a teacher's certificate by the time the degree is conferred, with the exception of international students who intend to return to their native country.

Admission Requirement
Bachelor's degree from a regionally accredited institution with sufficient hours in biology to enable the student to take courses carrying graduate credit.

Course Requirements
A total of 36 credit hours, of which a minimum of 25 credit hours must be in courses in the biological sciences that carry graduate credit the remaining 11 credit hours may be in education. All programs of study must be approved by the Master of Arts for Teachers program advisor.

Certification Requirements
For a complete list of courses in education and other areas that are required for provisional certification, consult the School of Education Bulletin, Undergraduate Program.

Courses

M300 Biomedical Sciences Documentation (1 cr.)

M310 Microbiology (3 cr.)

L313 Cell Biology Laboratory (3 cr.) P: BIOL L113 and L211, or CHEM C342, or consent of instructor. R: BIOL L312, CHEM C484.

M315 Microbiology Laboratory (2 cr.)

B351 Fungi (3 cr.)

B352 Fungi: Laboratory (2 cr.)

B364 Summer Flowering Plants (5 cr.)

B368 Ethnobotany (3 cr.) P: BIOL L111. Plants in relation to man with primary emphasis on food plants. Credit given for only one of L370 or B368.

B371 Ecological Plant Physiology (3 cr.)

B372 Ecological Plant Physiology Laboratory (2 cr.)

B373 Mechanisms of Plant Development (3 cr.)

Z373 Entomology (3 cr.)

Z374 Invertebrate Zoology (3 cr.)

Z383 Laboratory in Entomology (2 cr.)

Z406 Vertebrate Zoology (5 cr.)

B415 Phytogeography (2 cr.)

L417 Molecular Aspects of Development (3 cr.)

Z420 Cytology (3 cr.)

B423 Introduction to Paleobotany (3 cr.)

M430 Virology: Lecture (3 cr.)

M435 Viral-Tissue-Culture Laboratory (3 cr.) P or C: M430, or consent of instructor.

M440 Medical Microbiology (3 cr.)

B445 Experimental Molecular and Cellular Biology of Eukaryotes (4 cr.)

M460 Biology of the Prokaryotes (3 cr.)

Z460 Ethology (3 cr.)

L465 Advanced Field Biology (3 cr.)

M465 Biology of the Prokaryotes: Laboratory (3 cr.)

Z466 Endocrinology (3 cr.)

L473 Ecology (3 cr.)

L474 Field and Laboratory Ecology (2 cr.)

Z476 Biology of Fishes (3 cr.)

L479 Evolution and Ecology (4 cr.)

M480 Microbial and Molecular Genetics (3 cr.)

M485 Microbial and Molecular Genetics Laboratory (3 cr.)

Z486 Standards and Techniques of Animal Experimentation (2 cr.)

L500 Independent Study (cr. arr.) P: written consent of faculty member supervising research.

M500 Introduction to Research (Microbiology) (1-6 cr.) P: graduate standing. Objectives and techniques of microbiological research. Assignment to a research problem with a faculty member to be completed in two semesters.

L501 Independent Study (1-6 cr.) P: written consent of faculty member supervising work. Supervised work. S/F grading.

L505 Evolution of Development (3 cr.) P: senior or graduate standing and consent of instructor. An integrative approach to the link between development and the evolution of morphology. Topics: evolution of developmental mechanisms and of developmental regulatory genes, production of evolutionary changes through changes in developmental processes, developmental constraints, and origins of major body plans.

Z508 Advanced Ornithology (4 cr.) P: Z406. Emphasis on avian ecology, distribution, and behavior discussion and evaluation of recent literature. Field work includes investigation of populations of a wintering species and a breeding species.

L510 Introduction to the Research Laboratory (3 cr.) P: graduate standing. Objectives and techniques of biological research. Completion of a one-semester research problem with a faculty member.

M511 Molecular Biology of Prokaryotes (3 cr.) P: CHEM C584. The course will first develop an understanding of nucleic acid structure and function to a professional level, then use these principles to explore molecular aspects of gene expression and evolution. Emphasis will be on prokaryotes.

M512 Molecular Biology of AIDS Virus (3 cr.) P: CHEM C341 and BIOL L311. A detailed consideration of the human immunodeficiency virus (HIV, causative agent of AIDS). The functions of the HIV genes and how those functions affect pathology and normal cellular mechanisms.

L519 Bioinformatics: Theory and Application (3 cr.) Overview of theory and applications in bioinformatics, based on fundamentals of molecular biology and information sciences. Common problems, data and tools in the field are outlined. These include biosequence analysis, alignment and assembly, genomics, proteomics and phylogenetics, biological databases and data mining, and internet bio-information services.

L520 Seminar in Genetics (cr. arr.) P: L364 or Z420 or equivalents.

L521 Problems in Genetics-Higher Organisms (3 cr.) P: L364 or equivalent. Selected topics in the genetics of higher organisms emphasizing studies at the molecular level.

L522 Advanced Eukaryotic Molecular Genetics (3 cr.) P: consent of instructor beginning course in genetics. Correlation of genetic data with changes in chromosome structure and number. Mechanics of chromosome behavior in crossing over and disjunction.

L523 Critical Analysis of the Scientific Literature (1-6 cr.) Detailed analysis of current research papers in biology. Emphasis on experimental design, research methods, interpretation of results, and suitability of controls. Generally taken in the first semester of graduate residence. Topics may vary to suit specific fields (e.g., molecular, cellular, and developmental biology and genetics, or ecological and evolutionary biology).

M525 Topics in Microbial Biochemistry and Physiology (3 cr.) P: graduate standing and C483 or M350 or equivalent. The course will consider topics in physiology and biochemistry of eukaryotic and prokaryotic microorganisms. Subjects include membrane physiology and regulatory networks in metabolism and gene expression.

L529 Bioinformatics in Molecular Biology and Genetics: Practical Applications (4 cr.) P: I501, I502, L519, or consent of instructor. Practical experience in a range of data analysis and software engineering methods applied to molecular biology data.

B530 Anatomy and Morphology Seminar (cr. arr.) P: consent of instructor. Seminars will include current research studies in plant anatomy and morphology.

M540 Medical Microbiology and Medical Immunology (2-5 cr.) Basic concepts of immunology microorganisms as agents of disease host-parasite relationships epidemiology chemotherapy.

Z540 Genetics of Populations (3 cr.) P: consent of instructor: R: Z465, MATH M216 or equivalent. Survey of the theoretical basis of population genetics and a review of current problems and experimental findings. Content varies from year to year.

M545 Medical Microbiology Laboratory (1 cr.) P: M540. Laboratory experiments to illustrate material discussed in M540.

M550 Microbiology (3 cr.) P: two semesters of college chemistry L211 recommended prior or concurrently. Application of fundamental principles to the study of microorganisms. Significance of microorganisms to humans and their environment. Critical evaluation of current microbiological literature.

B555 Special Topics in Plant Systematics (3 cr.) Topics vary from year to year. Examples of subjects to be treated: phylogeny and families of flowering plants, biology of ferns, biosystematics, molecular markers in populational biology and systematics. Enrollment of advanced undergraduates encouraged.

L555 Alternative Approaches to Teaching College Biology (2 cr.) Frameworks for teaching college biology. Addresses different teaching objectives (knowledge, applications, scientific thinking, ethical and policy considerations) different teaching methods (lectures, readings, recitations, discussions, exercises, experiments, projects) student heterogeneity (expectations, abilities, development, learning styles) evaluation and grading course and curriculum design and evaluation and improvement of teaching.

B560 Seminar in Systematics (cr. arr.) P: consent of instructor. Topics vary each semester.

L560 Physiological Ecology (3 cr.) Influence of the abiotic environment on energy and material transfers in individual organisms, with emphasis on terrestrial animals.

Z566 Laboratory in Endocrinology (2 cr.) P: Z466. Development and structure of major endocrine glands their role in maintaining constancy of internal environment. Limited to 12 students.

L567 Evolution (3 cr.) P: graduate standing in Psychology or Biology or consent of the instructor. Topics include quantitative genetics, population genetics and strategic models of natural selection. Special topics include: life history theory, sex and sexual selection, kin selection, shifting-balance theory, speciation, macroevolution, and comparative methods.

B570 Seminar in Physiology and Molecular Biology of Plants (cr. arr.) P: consent of instructor.

L570 Seminar in Ecology and Environmental Biology (1 cr.) P: consent of instructor. Presentations and discussions of current research in evolution, ecology, and behavior. May be repeated for credit.

B572 Photobiology (3 cr.) P: S305 or L367 or CHEM C483 or equivalent. Biochemical and biophysical relationship between light and biological systems. Topics will include photosynthesis, visual processes, photorespiration, phototaxis, bioluminescence, and photomorphogenesis, with emphasis on photosynthesis.

L572 Microbial Ecology (3 cr.) Principles of microbial ecology with emphasis on the population, community, and ecosystem ecology of bacteria and fungi.

B573 Special Topics in Plant Physiology (2-5 cr.) P: consent of instructor. Advanced topics in plant physiology. With consent of instructor, may be taken more than once for credit.

L575 Ecosystem Structure and Function (3 cr.) P: L473 and L474 (or equivalent) or instructor's consent. Does biodiversity matter? Analysis of relationships between biodiversity and ecosystem functioning. Emphasis on current literature, including theoretical and empirical work. Lectures will alternate with class discussion and debate.

M575 Human Parasitology (3 cr.) P: BIOL M310 and M315. Biology of human parasites focusing on their etiology, epidemiology, immunology, diagnosis, and treatment. Major groups of protozoa, helminths, and medically important arthropods covered. Independent research assigned on a special topic. Lab presents both live and fixed materials complementing lecture.

B576 Developmental Plant Physiology (3 cr.) P: consent of instructor. Chemically oriented examination of substances uniquely involved in growth and development in higher plants. Application of information to lower plants only briefly discussed.

Z576 Invertebrate Zoology Laboratory (2 cr.) P or C: Z374. Laboratory and field studies of invertebrates, with an emphasis on experiments with living specimens.

B577 Plant Biochemistry (2 cr.) A comparative treatment of selected biochemical topics, emphasizing unique or important processes in plant metabolism and development.

L578 Advanced Population Biology (3 cr.) P: courses in ecology, genetics, and basic calculus, and permission of instructor. A detailed assessment of population-ecological and population-genetic theory, and the factors determining the size and composition of animal populations in nature.

L579 Community Ecology (3 cr.) P: ecology and genetics. Survey of ecological and evolutionary topics between population and ecosystem levels. Review of scientific levels of selection and speciation. Major emphasis on interactions among populations (consumer-producer, competition, symbiosis, etc.) and community analysis (island biogeography, niche, diversity, and community structure).

L580 Introduction to Research (1 cr.) Individual faculty from the various graduate programs in biology present seminars on their research programs. Discussion between students and faculty about possible thesis research projects is encouraged.

L581 Behavioral Ecology (3 cr.) Integrated elements of ethology, physiology, ecology, and evolutionary biology providing a synthetic approach to animal behavior. Emphasis on integrated studies providing new insights into both evolutionary and mechanistic questions. Students are asked to analyze the literature critically and debate controversial issues actively.

L585 Molecular Genetics (3 cr.) The molecular basis of genetic interactions, with emphasis on microbial systems. The course covers the molecular mechanisms of mutation, suppression, recombination, complementation, etc., as well as mechanisms for gene transfer in bacteria and bacteriophage. The application of genetic analysis to variety of molecular biological topics is emphasized.

L586 Cell Biology (4.5 cr.) Critical analysis of recent advances in our understanding of molecular organization and function of cellular structures. The emphasis of this course will be on eukaryotic cells. Topics include membrane organization, cytoskeleton assembly and functions, signal transduction, cell-cycle regulation, protein sorting, and vesicle trafficking.

L587 Developmental Biology (4.5 cr.) Evaluation of classical and current molecular and genetic approaches to studying development of eukaryotic organisms. A significant portion of the course is devoted to discussing recent findings from molecular genetic studies in Drosophila and C. elegans.

L590 Seminar in Molecular, Cellular, and Developmental Biology (2 cr.) P: consent of instructor. Presentation and discussion of topics in molecular and cellular biology as seminar by students. Topics from current literature. Concentration on a particular area each semester to be announced before registration. S/F grading.

L591 Plant Population Biology&mdashAn Experimental Approach (3 cr.) P: ecology course and evolution course. The mechanisms by which plants, as individuals, contribute to development of population structure. Experimental studies of intra- and inter-specific mechanisms of population regulation, reproduction, and vegetative growth. Emphasis on development and physiological characteristics which determine mode of interaction. Greenhouse projects designed and conducted by students.

L600 Special Topics in Genetics (cr. arr.) P: L364 or equivalent. Topics not extensively treated in other courses, e.g., population genetics, human genetics, immunogenetics, biochemical genetics of clones of mammalian cells. Topic presented will not be duplicated within three to five years. L600 carries credit in Plant Sciences, Microbiology, and Zoology programs.

M610 Recent Advances in Microbiology (1-3 cr.) P: graduate standing in microbiology or related area. Course content changes each semester so that over a cycle of several years, major research areas are covered. May be repeated for credit.

M612 Microbial Development (3 cr.) P: graduate standing or consent of instructor. An analysis of recent publications concerned with the biochemistry of development in viral, prokaryotic, and simple eukaryotic systems. The topics vary and emphasize the regulatory aspects of development. Cell differentiation and cell-cell interactions are discussed.

Z620 Special Topics in Zoology (cr. arr.) P: advanced undergraduate or graduate standing. Topics not extensively treated in other courses, e.g., theoretical zoology, oceanography, reservoir limnology, human ecology, biochemistry, viruses and disease, critical analysis of the scientific literature, and other fields. Topics presented will be treated every three to five years.

L800 Research (1-15 cr.)

M800 Research (1-12 cr.)

M850 Seminar (1 cr. ) P: graduate standing in microbiology or consent of instructor. Reports on assigned topics of current interest. May be repeated for credit. S/F grading.


Could rotavirus genome be key to COVID-19 vaccine for kids? IU researchers say yes.

BLOOMINGTON, Ind. -- Since the pandemic struck the United States more than a year ago, Indiana University Bloomington virologist John Patton, graduate student Asha Philip and others have been working on a COVID-19 vaccine for young children, based on a well-established childhood vaccine for the common illness rotavirus.

Currently, no available COVID-19 vaccines have been authorized for use in children younger than 16.

View print quality image John Patton. Photo by Eric Rudd, Indiana University

By reverse-engineering the rotavirus genome to serve as a vector for the now-familiar SARS-CoV-2 spike protein, the research team succeeded in generating genetically stable recombinant rotaviruses that contain portions of the spike protein, which could lead to a combined rotavirus-COVID-19 vaccine to replace current widely used rotavirus vaccines.

"Our findings raise the possibility of constructing rotavirus vaccine strains that are capable of protecting against not only rotavirus but also COVID-19," Philip said.

Patton is a professor of biology and Blatt Chair of Virology in the College of Arts and Sciences at IU Bloomington. Philip is a Ph.D. student in Patton's lab and lead author on the study.

Preliminary findings from their research have been posted in the preprint "Rotavirus as an Expression Platform of the SARS-CoV-2 Spike Protein" on the open-access platform bioRxiv and as part of the National Institutes of Health Preprint Pilot. Preprints are working papers awaiting peer review.

Rotavirus is common among young children, causing nausea and diarrhea, but vaccination has long reduced its spread in many countries. A combined rotavirus-COVID-19 targeted vaccine would be a huge step forward, Philip said.

By leveraging rotavirus immunization programs already in place, a combined vaccine could be distributed and administered to infants and young children around the world. Although children make up a tiny fraction of COVID-19 infections and deaths, they may be asymptomatic carriers of the disease, compromising our ability to reach herd immunity.

A vaccine for young children would also allow schools to open up more freely, enabling activities that involve close contact. And the process used to create rotavirus-based combination vaccines may also prove useful for vaccines against other intestinal viruses such as norovirus.

The IU team is now working to determine how successful the combined rotavirus-SARS-CoV-2 vaccine is at producing the desired antibody response. Meanwhile, their current results emphasize the potential of a combined vaccine becoming a routine immunization for children in the not-too-distant future.


Key Publications

Chang HC, Sehra S, Goswami R, Yao W, Yu Q, Stritesky GL, Jabeen R, Han L, Nguyen ET, McKinley CD, Tepper RS, Robertson MJ, Perumal NB, Nutt SL and Kaplan MH. (2010) The transcription factor PU.1 is required for the development of IL-9-secreting T cells and allergic inflammation. Nature Immunology. 11:527-534. PMC3136246.

Jabeen R, Goswami R, Awe O, Kulkarni A, Nguyen ET, Attenasio A, Walsh D, Olson MR, Kim MH, Tepper RS, Sun J, Kim CH, Taparowsky EJ, Zhou B and Kaplan MH. (2013). Th9 cell development requires a BATF-regulated transcriptional network. Journal of Clinical Investigation. 123(11):4641–4653. PMC3809790.

Sehra S, Yao W, Nguyen ET, Glosson-Byers NL, Akhtar N, Zhou B, and Kaplan MH. (2015). Th9 cells are required for tissue mast cell accumulation during allergic inflammation. J Allergy Clin Immunol. 136(2):433-440.e1. PMC4530056

Serezani APM, Bozdogan G, Sehra S, Walsh D, Krishnamurthy P, Potchanant EAS, Nalepa G, Goenka S, Turner MJ, Spandau DF, Kaplan MH. (2017) IL-4 impairs wound healing potential in the skin by repressing fibronectin expression. J. Allergy Clin Immunol. 139(1):142-151.e5. PMC5222746

Koh B, Abdul Qayum A, Srivastava R, Fu Y, Ulrich BJ, Janga SC, Kaplan MH. 2018. A conserved enhancer regulates Il9 expression in multiple lineages. Nat. Commun. 9:4803. PMC6237898

Deak PE, Kim B, Abdul Qayum A, Shin J, Vitalpur G, Kloepfer KM, Turner MJ, Smith N, Shreffler WG, Kiziltepe T, Kaplan MH and Bilgicer B. (2019). Designer Covalent Heterobivalent Inhibitors Prevent IgE-Dependent Responses to Peanut Allergen. Proc. Natl. Acad. Sci.-USA. 116:8966-8974. PMC6500160

Koh B, Ulrich BJ, Nelson AS, Panangipalli G, Kharwadkar R, Wu W, Xie MM, Fu Y, Turner MJ, Paczesny S, Janga SC, Dent AL, and Kaplan MH (2020) Bcl6 and Blimp1 reciprocally regulate ST2+ Treg cell development in the context of allergic airway inflammation. J All Clin Immunol. 146(5):1121-1136.e9. PMCID: PMC7487006

Park S, Griesenauer B, Jiang H, Adom J, Mehrpouya-Bahrami P, Chakravorty S, Kazemian M, Srivastava R, Hayes TA, Pardo J, Janga SC, Paczesny S, Kaplan MH and Olson MR. (2020) Granzyme A producing T helper cells are critical for acute grant-versus-host disease. JCI Insight. 5(18):124465. (Co-corresponding/senior author) PMCID: PMC7526544


Fu Y, Wang J, Panangipalli G, Ulrich BJ, Koh B, Xu C, Kharwadkar R, Chu X, Wang Y, Gao H, Wu W, Sun J, Tepper RS, Zhou B, Janga SC, Yang K, Kaplan MH. (2020) STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus. Nat. Comm. 11(1):4882. PMC7523001

Mehrpouya-Bahrami P, Moriarty A, de Melo P, Keeter WC, Alakhras N, Nelson AS, Hoover M, Barrios M, Nadler JL, Serezani H, Kaplan MH, Galkina EV. (2021) STAT4 is expressed in neutrophils and promotes antimicrobial immunity. JCI Insight. In press. (Co-corresponding/senior author)


Vesicle-Cloaked Virus Clusters Are Optimal Units for Inter-organismal Viral Transmission

In enteric viral infections, such as those with rotavirus and norovirus, individual viral particles shed in stool are considered the optimal units of fecal-oral transmission. We reveal that rotaviruses and noroviruses are also shed in stool as viral clusters enclosed within vesicles that deliver a high inoculum to the receiving host. Cultured cells non-lytically release rotaviruses and noroviruses inside extracellular vesicles. In addition, stools of infected hosts contain norovirus and rotavirus within vesicles of exosomal or plasma membrane origin. These vesicles remain intact during fecal-oral transmission and thereby transport multiple viral particles collectively to the next host, enhancing both the MOI and disease severity. Vesicle-cloaked viruses are non-negligible populations in stool and have a disproportionately larger contribution to infectivity than free viruses. Our findings indicate that vesicle-cloaked viruses are highly virulent units of fecal-oral transmission and highlight a need for antivirals targeting vesicles and virus clustering.

Keywords: exosomes extracellular vesicles fecal-oral mucosal immunology multiplicity of infection norovirus phosphatidylserine rotavirus viral transmission virus.


Additional Information

Transferring from Another Major or School

The program is designed to allow students to move between the major and the general Biological Sciences major without penalty. Providing for such movement is necessary because a student will NOT be allowed to major both in Microbiology and Immunology and in Biological Sciences. A student may move into the Microbiology and Immunology major at any time during their third or even fourth years simply by taking Bio 116L as the prerequisite to the other laboratory courses M122L and M127L. These courses will not carry majors only restrictions, leaving the path to the Microbiology and Immunology major open to Biological Sciences majors even as late as the fourth year. However, the requirement to take M121, M122 and M124A means that students should begin taking these courses in the 3rd year if they are considering entering the major. Such late transfer might provide a path into the major for a student who does not meet the eligibility requirement based on their second year Bio and Chem GPA. Such a student could petition for entry based on their performance in the appropriate Bio courses during their third and/or fourth years.

Conversely, since the existing Bio Core beyond Bio 99 requires no set order in which the courses must be taken, and since M116L, M121, M122, M124A and the associated labs should be acceptable satellites for the Bio major, a student can move out of the major and into the Biological Sciences major at any time without penalty.

We encourage Community College and other transfer students to apply for entrance into the Microbiology and Immunology major. Transfer students may not be admitted directly into the Microbiology and Immunology major, but instead will enter UCI as a Biological Sciences major and then change to the Microbiology and Immunology major once they have completed at least six of the required four-unit courses in Biological Sciences (minimum of two required in BioSci), Chemistry, Math and/or Physics (including labs and eligible electives) and earned a GPA of 3.0 or above in those courses. The basic principle is that to be eligible to transfer into this high level major, a student must demonstrate the ability to do B or better work in the field over an extended period of time.

In accordance with this principle, a UCI student transferring from outside of Biological Sciences is also required to transfer initially into the Biological Sciences major. Subsequent eligibility to transfer into the Microbiology and Immunology major will be as described for other Biological Science majors.

Specific Courses


Contents

The WIV was founded in 1956 as the Wuhan Microbiology Laboratory under the Chinese Academy of Sciences (CAS). In 1961, it became the South China Institute of Microbiology, and in 1962 was renamed Wuhan Microbiology Institute. In 1970, it became the Microbiology Institute of Hubei Province when the Hubei Commission of Science and Technology took over the administration. In June 1978, it was returned to the CAS and renamed Wuhan Institute of Virology. [4]

In 2003, the Chinese academy of Sciences approved the construction of China's first biosafety level 4 (BSL-4) laboratory at the WIV. The construction of the WIV's National Bio-safety Laboratory was completed at a cost of 300 million yuan ($44 million) in collaboration with the French government's CIRI lab at the end of 2014. [3] [5] The new laboratory building has 3000 m 2 of BSL-4 space, and also 20 BSL-2 and two BSL-3 laboratories. [6] The BSL-4 facilities were accredited by the China National Accreditation Service for Conformity Assessment (CNAS) in January 2017, [3] with the BSL-4 level lab put into operation in January 2018. [7] The highest level biosafety installation is necessary because the Institute investigated highly dangerous viruses, such as SARS, influenza H5N1, Japanese encephalitis, and dengue, along with germ causing anthrax. [8]

The National Bio-safety Laboratory has strong ties to the Galveston National Laboratory in the University of Texas. [9] It also had ties with Canada's National Microbiology Laboratory until WIV staff scientists Xiangguo Qiu and her husband Keding Cheng, who were also remunerated by the Canadian government, were escorted from the Canadian lab for undisclosed reasons in July 2019. [10] Researchers from the WIV have also collaborated in gain of function research on coronaviruses with American colleagues. [11]

A number of safety precautions were taken into consideration when building the Wuhan lab. The lab was built far away from any flood plain. It was also built to withstand a magnitude-7 earthquake, even though the region has no history of earthquakes. The scientific community was also reassured that many Wuhan lab scientists were trained in safety procedures at a BSL-4 lab in Lyon, France. [3] Scientists such as U.S. molecular biologist Richard H. Ebright, who had expressed concern of previous escapes of the SARS virus at Chinese laboratories in Beijing and had been troubled by the pace and scale of China's plans for expansion into BSL-4 laboratories, [3] called the institute a "world-class research institution that does world-class research in virology and immunology" while he noted that the WIV is a world leader in the study of bat coronaviruses. [9]

SARS-related coronaviruses

In 2005, a group including researchers from the Wuhan Institute of Virology published research into the origin of the SARS coronavirus, finding that China's horseshoe bats are natural reservoirs of SARS-like coronaviruses. [12] Continuing this work over a period of years, researchers from the institute sampled thousands of horseshoe bats in locations across China, isolating over 300 bat coronavirus sequences. [13]

In 2015, an international team including two scientists from the institute published successful research on whether a bat coronavirus could be made to infect HeLa. The team engineered a hybrid virus, combining a bat coronavirus with a SARS virus that had been adapted to grow in mice and mimic human disease. The hybrid virus was able to infect human cells. [11] [14]

In 2017, a team from the institute announced that coronaviruses found in horseshoe bats at a cave in Yunnan contain all the genetic pieces of the SARS virus, and hypothesized that the direct progenitor of the human virus originated in this cave. The team, who spent five years sampling the bats in the cave, noted the presence of a village only a kilometer away, and warned of "the risk of spillover into people and emergence of a disease similar to SARS". [13] [15]

In 2018, another paper by a team from the institute reported the results of a serological study of a sample of villagers residing near these bat caves (near Xiyang Township 夕阳乡 in Jinning District of Yunnan). According to this report, 6 out of the 218 local residents in the sample carried antibodies to the bat coronaviruses in their blood, indicating the possibility of transmission of the infections from bats to people. [16]

Prior to and throughout the COVID-19 pandemic, coronavirus research at the WIV has been conducted in BSL-2 and BSL-3 laboratories. [17]

COVID-19 pandemic

In December 2019, cases of pneumonia associated with an unknown coronavirus were reported to health authorities in Wuhan. The institute checked its coronavirus collection and found the new virus had 96% genetic similarity to RaTG13, a virus its researchers had discovered in horseshoe bats in southwest China. [18] [19]

As the virus spread worldwide, the institute continued its investigation. In February 2020, a team led by Shi Zhengli at the institute were the first to identify, analyze and name the genetic sequence of the novel coronavirus (2019-nCoV), upload it to public databases for scientists around the world to understand, [20] [21] [22] and publish papers in Nature. [23] On 19 February 2020, the lab released a letter on its website describing how they successfully obtained the whole virus genome. [24] In February 2020, in a move that raised concerns regarding intellectual property rights, [25] the institute applied for a patent in China for the use of remdesivir, an experimental drug owned by Gilead Sciences, which the institute found inhibited the virus in vitro. [26] The WIV said it would not exercise its new Chinese patent rights "if relevant foreign companies intend to contribute to the prevention and control of China's epidemic". [27]

The laboratory has been the focus of conspiracy theories and unsubstantiated speculation about the origin of the virus, [28] [29] [30] which has been a source of political tension between the United States and China. [31] Shi Zhengli, a leading researcher at the WIV, has vehemently denied any connection between the WIV and the emergence of Covid-19. [32] In April 2020, the Trump administration terminated an NIH grant to research how coronaviruses spread from bats to humans. [33] [34] On 9 February 2021, after investigations in Wuhan, the WHO team said a laboratory leak origin for COVID-19 was "extremely unlikely", [35] [36] confirming what experts already expected about the likely origins and early transmission. [37] In response to the report, scientists, politicians, and members of the media, as well as WHO director-general Tedros Adhanom Ghebreyesus, have called for further investigations into the matter. [38] [39] [40] [41]


Watch the video: Vincent Racaniello: Viruses and Vaccines. Lex Fridman Podcast #216 (January 2023).