Courses

Microbes and society focuses on the impact, good and bad, of microbes on humanity and civilization. The course explores the beneficial effects of microbes on the environment, agriculture, industry, biotechnology, and medicine. In addition, the course describes how microbes and microbial diseases have influenced the history and evolution of humans. The course also explores the negative impact of microbes as pathogens and emerging infectious agents on civilization. Host pathogen interactions including how microbes cause infectious diseases and how the host immune response clears infections and protects the host against re-infection with the same microbe are also covered in the course.

This course will cover topics of critical importance for understanding modern bacterial genetics. The course content will include the study of DNA elements including the chromosome, plasmids and bacteriophage, gene expression at the transcriptional, translational and post-translational levels, methods of genetic analysis, transposition, recombination, and the genetics of antibiotic resistance. Incorporated into these topics will be problem solving exercises, discussions of new directions in bacterial genetics, and selected readings in recent applications of bacterial genetics to pathogenesis, development and spread of antibiotic resistance, disease therapy or the study of the human microbiota. Prereq: BIO 208 or BIO 308 or equivalent or consent of instructor

[3 Credit Hours]

MI 482 will introduce students to the physical, chemical, and biological properties of viruses. The key elements of the viral life cycle will be examined in molecular detail for representative viruses, and critical aspects of host-pathogen interactions will be discussed.

Prereq: BIO 304 and biochemistry or equivalent strongly recommended, or consent of the instructor.

Course Attributes:
Crosslisted with: BIO 482

[3 Credit Hours]

This course provides foundational knowledge on the development and function of immunity. We will discuss the role of the immune system in human health and diseases including but not limited to infectious diseases, hypersensitivities, transplantation, and cancer.

Prereq: BIO 148 and BIO 152; CHE 230 or CHE 236. Recommended or concurrent, but not required: BIO308, BCH401.

Course Attributes:
Crosslisted with: BIO 494G

This course will examine the pathogenic mechanisms used by bacteria to cause human disease. Bacterial virulence factors and host susceptibility factors will be discussed, with an emphasis on understanding the techniques that can be used to identify these traits in newly emerging pathogens. Prerequisites: BIO 308, BIO 315, BCH 401 recommended. Or permission of instructor. (Same as BIO 495G.)

Immunotherapy, the application of immunologic principles to the clinic, often called “Bench to Bedside”, has led to significant objective clinical responses and prolonged time to tumor progression or recurrence in a subset of cancer patients. The current class will discuss basic immunologic principles and show how they apply to the tumor setting. In addition, the class will demonstrate how immunologic mechanisms can be exploited in the treatment of cancer. The semester will be divided into three stages including:

1. A concise review of basic immunology concepts preparing the student for applying those concepts to the tumor setting,
2. A detailed examination of the tumor microenvironment, tumor derived immunosuppression and the effector function of both soluble and cellular mechanisms against tumors of varying stages.
3. A broad overview of immunotherapy including regulatory issues pertaining to reagent development and delivery as well as an in depth review of all of the different approaches utilized to treat cancer since 1980. The course will be lecture based utilizing current and historic literature as well as the Course Directors extensive experience in the field. Prereq: MI 494G or MI 685

[3 Credit Hours]

Physical, chemical and biological properties of viruses. Modes of replication and control of gene product formation displayed by representative plant, animal, and bacterial viruses. Same as MI 582

Prereq: BIO 304 and biochemistry or equivalent strongly recommended, or consent of instructor.

Course Attributes:
Crosslisted with: BIO 582

[3 Credit Hours]

An introduction to the concepts of clinical microbiology through a survey of the microbial diseases of man using an organ system approach.

Prereq: BIO 208 and BIO 209 -OR- BIO 308 and BIO 309.

3 credit hours - Fall

An introductory graduate-level biochemistry course designed to provide a basic knowledge of molecular and biochemical principles necessary for advanced graduate study. Protein structure and function, enzyme catalysis, the generation and storage of metabolic energy, amino acid, nucleotide, and lipid metabolism and biological membranes and transport will be covered.

Prerequisites: CHE 105, 107, 230, and 232; BIO 150 and 152; or equivalents.

3 credit hours - Fall

An introductory graduate-level course focused on molecular biology and genetics (concepts and techniques) necessary for advanced graduate courses. The course will emphasize basic genetic principles and the molecular mechanisms that underlie the regulated expression of genes, including transcription, mRNA processing and translation, as well as mechanisms of DNA replication/repair and recombination. Genetic engineering and other experimental approaches that are critical to molecular biology research will be covered.

Prerequisites: CHE 105, 107, 230 and 232; BIO 150 and 152; or equivalents.

3 credit hours - Spring

An introduction to cell biology and signaling focused on cell types and architecture, membrane structure, cytoskeleton, mitochondria, cellular mechanisms of development, cell division, cell cycle, apoptosis, necrosis and cancer. Emphasis will also be placed upon the signaling pathways controlling these processes.

Prerequisites: CHE 105, 107, 230 and 232; BIO 150 and 152; or equivalents.

3 credit hours - Spring

This course will consider the function of the mammalian organism from a perspective ranging from cells to organs, with an emphasis on physiological communication between organ systems. It will build upon the Integrated Biomedical Sciences (IBS) series of courses to allow the student to develop a truly integrative appreciation of biologic function.

Prerequisites: IBS 601 and IBS 602.

0 credit hours - Spring

Weekly seminar devoted to the presentation and discussion of classic and new research. May be repeated to a maximum of four times; two semesters are required as part of the IBS curriculum.

Prerequisite: Admission to IBS Curriculum.

2 credit hours - Spring 

IBS 608 emphasizes genomics and bioinformatics approaches that are increasingly important in broad areas of biomedical science. These tools allow us to work with large data sets, analyze the transcriptomes of single cells and whole tissues, visualize data in sophisticated ways, do rigorous experimental design, and perform proper statistical procedures for these types of data. This is a hands-on, experiential course. It includes some lecture material but the emphasis is on computer exercises allowing students to learn tools by using them. In terms of teaching mechanism, this is an in-person course taught in a computer lab. However, be prepared to switch to on-line learning in the event of unusual circumstances, such as university-mandated virtual teaching or personal quarantine.

Prerequisites: Successful completion or concurrent enrollment in IBS 601 and IBS602 is required. A prior course in statistics, such as IBS 611 Practical Statistics, is also required. A strong background in molecular and cell biology is highly recommended.

3 credit hours - Fall

Individualized laboratory and research experience under the supervision of a faculty member. May be repeated to a maximum of six credit hours. Two semesters required as part of IBS curriculum.

Prerequisites: Admission to IBS curriculum and consent of instructor.

2 credit hours - Fall

The major emphasis of this course is to develop within students the ability to critically read, evaluate and critique papers in the areas of biochemistry, molecular biology, and genetics. Students will meet weekly for two hours in a small group setting to discuss papers, with all groups reading the same set of papers. Each group of students (5- 6/group) will meet weekly with one faculty member during the course of the semester. Grading will be based on attendance, participation, mock manuscript reviews, and student-led classes.

Prerequisites: Students are required to have taken IBS 601 and IBS 602 or to take IBS 601 and IBS 602 concurrently with this course.

2 credit hours - Fall

Practical Statistics will introduce students to basic statistical concepts and applications that are used in a majority of biomedical and translational research studies. The emphasis will be on "how" and "why" certain basic statistical applications are used rather than the theory behind various statistical methods. Students will cover materials using didactic lectures, examples of data from the primary literature, and homework problems.

Prerequisites: Some background in molecular biology, cell biology, biochemistry, and/or chemistry (including organic chemistry) at the graduate level is recommended. Courses such as BCH 401G, IBS 601, IBS 602, or IBS 603 would satisfy this recommendation.

1 credit hour - Spring

The course will commence with an overview of good laboratory practices and present them as the basis of good scientific research, along with an overview of quality assurance and appropriate practices in data analysis and data interpretation. The course will then move to the ethics of human and animal experimentation and discuss the concepts of data and intellectual property, their ownership and access to them. The problems of reviewing other workers' intellectual property such as grant applications, research papers and other intellectual property will be addressed.

Prerequisites: Research experiences; consent of instructor.

[3 Credit Hours]

The course will examine the mechanisms by which various biological, chemical and physical agents injure susceptible hosts and the complex biochemical and immunological reactions which occur in response to injury. The host defense mechanisms will be illustrated by an analysis of selected human diseases and animal model systems with particular emphasis on the events at the molecular and cellular level.

Prereq: BCH 502 or concur, BIO 594 or equivalents and consent of instructor.

[3 Credit Hours]

This course will develop the student’s ability to critically read and evaluate the primary literature in selected areas of molecular biology; various experimental systems and techniques are discussed. While there is some lecture, the time will be predominately spent in class discussions of the primary literature.

Prereq: An advanced course in molecular biology and genetics (e.g. IBS602) or consent of instructor.

Course Attributes:
Crosslisted with: BIO 615, BCH 615

[3 Credit Hours]

Biology of cancer will be discussed at the molecular, cellular and organismic level. Emphasis will be placed on cellular signaling, apostosis and cell cycle unique to cancer cells, which affects tumor cell behavior and its interactions with the host immune system. The biology of hematopoitic cells will also be included. Clinicians active in treatment and research of various types of cancer will be invited to participate in the lectures.

Prereq: IBS 601, IBS 602, and/or IBS 603 (or comparable course in biochemistry, molecular biology or cell biology) or otherwise by consent of course director.

Course Attributes:
Crosslisted with: TOX 616, MED 616, PHA 616

[4 Credit Hours]

This course provides knowledge base and analytical skills in the field of molecular neurobiology. An in-depth introduction to current technologies, their rationale and limitations, will be the focus to address normal brain function and neuropathological conditions.

Prereq: BCH 501, 502, NEU 605, or consent of instructor.

Course Attributes:
Crosslisted with: PGY 618

[3 Credit Hours]

An introductory level graduate course surveying current trends in immunology including the organization of the immune system, cells important for immunity, and inflammation; types of immune responses, cellular immunology, molecular immunology, self-nonself discrimination, vaccines, and immune mediated diseases.

Prereq: BCH401G, or IBS 601 or IBS 602 or IBS 603 or equivalent courses.

Course Attributes:
Crosslisted with: BIO 685

[4 Credit Hours]

This is a graduate level course that integrates foundational concepts in microbiology and immunology to illustrate host-pathogen interactions during infection. Topics will include the basic structures of bacteria, viruses, fungi, and parasites and their strategies for growth and metabolism. How the innate immune system recognizes and clears microbes will be discussed, as well as the adaptive immune mechanisms that lead to protective memory against foreign antigens. The course is taught through interactive lectures that incorporate recent and classic literature, modern microbiology and immunology methods, data analysis, and experimental design.

Prereq: MI 308 and MI 494G are recommended, or status as a Ph.D. student in the Microbiology, Immunology, and Molecular Genetics department, or permission of instructor.

[2 Credit Hours]

This is a graduate level course that focuses on modern techniques used in microbiology and immunology research. Students will evaluate experimental design, analyze data, perform statistical analysis, and generate graphic representations of conclusions. In person attendance in class is required. A significant portion of the assignments will be graded for mastery with the option to redo the assignments once and a comprehensive final exam will assess the students ability to apply what they have learned during the semester to analysis of microbiology and immunology datasets.

Prereq: MI 308 and MI 494G are recommended, or status as a Ph.D. student in the Microbiology, Immunology, and Molecular Genetics department, or permission of instructor.

[4 Credit Hours]

This graduate level course will examine the pathogenic mechanisms used by microbes (bacteria, protozoan parasites, fungi and viruses) to persist in a human host and discuss important factors for designing vaccines to prevent infection. Human diseases that result from aberrant immune responses such as autoimmunity, allergy, asthma, cancer, and chronic inflammation will be discussed. An emphasis will be placed on understanding current techniques used to study infection and immunity and designing experimental approaches that can be used to address specific hypotheses.

Prereq: MI 701 Infection and Immunity I or permission of instructor.

[2 Credit Hours]

MI 704 is targeted to pre-qualifying second-year graduate students pursuing a PhD, but may also be of value for post-qualifying graduate students and postdoctoral trainees. The primary objective is to help students improve their writing and critical thinking skills, structured around the development of an NIH National Research Service Award (NRSA) F31 Individual Fellowship. Students will become familiar with the NIH structure and resources, the different sections of an NRSA grant application, and the process of grant submission at UK. This will be done through in-class lectures and the writing/editing of NRSA fellowship components, including in-class time for writing and editing.

Prereq: Students must have completed all required first year coursework and be in their second year (or later) of a PhD program. Upper-level students and postdocs can take the course for credit or audit with permission of the Course Director.

[0 - 3 Credit Hours] - Repeatable to a maximum of 3

This course will deal with controversial and evolving areas of immunology. Lectures in a given topic will be accompanied by student discussion of contemporary literature.

Prereq: MI 685 or equivalent or consent of instructor.

Course Attributes:
Crosslisted with: BIO 707

[0 - 3 Credit Hours] - Repeatable to a maximum of 6

This course will explore contemporary microbiology topics relating to the structure, function, or pathogenesis of bacteria, viruses, fungi or parasites.  Classroom sessions will focus on discussion of recently published primary research papers.

Prereq: MI 701 or permission of instructor.

[3 Credit Hours]

Molecular basis of structure and function in unicellular microbes. Molecular genetic and structural approaches to the analysis of bacterial architecture growth, division, and differentiation.

Prereq: (to reflect appropriate IBS course).

Course Attributes:
Crosslisted with: BIO 720, OBI 720

[3 Credit Hours]

Mechanisms of Microbial Pathogenesis is designed to cover major pathogenic mechanisms of bacteria, protozoa, fungi and viruses. Since it is impossible to include every possible pathogen, we instead focus on selected pathogens that illustrate particular lifestyles and pathogenic strategies. Emphasis is given to covering host mechanisms that combat the different weapons and lifestyles of the disease causing microbes. Students will gain an understanding of the interplay between pathogen and host and appreciate the myriad ways in which microbes have learned to subvert host pathways and evade the immune system. The course starts with an introduction to pathogenic concepts and immune responses, and then proceeds to the selected pathogens, including Listeria, Chlamydia, Mycobacterium, Toxoplasma, Ebola, Influenza, and HIV. The course is a mixture of lecture and discussion. Students will read current literature, assigned by their instructors, and participate in classroom discussions of the papers.

Prereq: MI 720 or MI 495G.

[0 Credit Hours]

Half-time to full-time work on thesis. May be repeated to a maximum of six semesters.

Prereq: All course work toward the degree must be completed. Note: Registration for this course is not available via telephone (UK-VIP) or webUK. For enrollment information contact the Graduate School at 257-4905.

May be repeated to a maximum of six semesters.

Prereq: Registration for two full-time semesters of 769 residence credit following the successful completion of the qualifying exams. Note: Registration for this course is not available via telephone (UK-VIP) or webUK. For enrollment information contact the Graduate School at 257-4905.

Course Attributes:
Crosslisted with: MB 749

Residency credit for dissertation research after the qualifying examination. Students may register for this course in the semester of the qualifying examination. A minimum of two semesters are required as well as continuous enrollment (Fall and Spring) until the dissertation is completed and defended.

May be repeated to a maximum of 12 hours. (Same as MB 768.)

May be repeated indefinitely. (Same as MB 769.)

Review of current literature in microbiology; presentation of papers on work in progress in the department or on assigned topics; reports on meetings of national and international scientific and professional societies and symposia. Required of all graduate students. Two hours per week. May be repeated nine times for a maximum of 10 credits. (Same as BIO 772.)

May be repeated to a maximum of 24 credits. Prerequisites: Consent of instructor. (Same as BIO 798.)

The course provides basic concepts of immunology and bacterial, viral, fungal and protozoal biology. It focuses on mechanisms of human immunity, immunologically mediated disease, and pathogenesis in infectious disease. The material covered includes relevant pathology associated with both immunologic and infectious diseases, and a summary of infectious diseases from a clinical perspective. Prereq: Enrolled in the DMD curriculum. (Same as OBI 828.)