Immunology & Infection

BIOC 6010. Gene Expression and Omics. 2 Credit Hours.

This course presents 1) the principles of gene expression, including transcription, epigenetic regulation (histone modifications and DNA methylation), mRNA processing and degradation, translation, post-translational modifications, and protein degradation, and 2) the omics approaches for collective characterization and quantification of different aspects of gene expression, including genomics, epigenomics, proteomics, and metabolomics. Two main teaching formats are used in this course: 1) Didactic lectures in which information is delivered to the class, and 2) Paper presentations and discussions, in which students present assigned papers and lead discussions by the entire class. Although one student will present each paper, all students will be expected to read each paper and to be prepared to discuss it in the form of comments and questions. Prerequisites: Permission of the Course Director and IBMS 5000 (or equivalent).

BIOC 6033. Cell Signaling Mechanisms. 2 Credit Hours.

This course covers the molecular mechanisms of action of various extracellular mediators including hormones, neurotransmitters, growth factors, cytokines, etc., and cell signaling events. Several areas will be discussed including: (1) mechanisms of mediator synthesis; (2) interaction of mediators with specific receptors; (3) modulation by mediators of various second messenger systems including cyclic nucleotides, inositol phospholipids, calcium, protein phosphorylation, ion flux, etc.; and (4) intra- and intercellular mechanism for regulating mediator action. Open for Cross Enrollment on Space Available Basis.

BIOC 6036. Macromolecular Structure & Mechanism. 2 Credit Hours.

This course will cover the fundamentals of protein and nucleic acid structure and of enzyme catalysis. The course is required of students in the Molecular Biochemistry and Biophysics Track. Topics to be covered include: DNA and RNA structure, protein structure, protein folding, ligand binding by proteins, and enzyme catalysis. Open for Cross Enrollment on Space Available Basis.

BIOC 6037. Integration Of Metabolic Pathways. 2 Credit Hours.

The course is required of students in the Molecular Biophysics and Metabolic Pathways track. The objective is to provide an understanding of the individual reactions in intermediary metabolism and how the reactions are integrated by regulatory mechanisms. Topics include carbohydrate, lipid, and nitrogen metabolism and mechanisms of regulation of individual enzymes and metabolic pathways. Open for Cross Enrollment on Space Available Basis.

BIOC 6043. Structure & Function Of Membrane Proteins. 2 Credit Hours.

This is a course targeted at students within any of the Graduate Tracks. The objective is to provide a broad view, allowing for in depth consideration in selected areas, of the structure and diverse functions of proteins within a membrane environment. Specific topics covered will include: ion selective channels, large membrane pores, membrane transporters, membrane pumps, and membrane receptors. The format of the course will be didactic lecture followed by student presentations of relevant topics. Open for Cross Enrollment on Space Available Basis.

CSAT 5007. Methods In Cell Biology. 1 Credit Hour.

Through a combination of lectures and demonstrations, the instructors will introduce students to techniques which are currently being used in cellular biology laboratories. The emphasis will be on the applications themselves, their uses, limitations, and the necessary controls. The following topic areas will be covered: imaging and microscopy, immunological techniques, bioinformatics (DNA and protein), rodent anatomy and histology, cytogenetics, and in vitro cell growth and transfection. Course fees: $100.

CSAT 5023. Development. 1 Credit Hour.

The course provides a survey of concepts in developmental biology (induction, cell-cell interactions, morphogen gradients, morphogenetic movements, transcription regulation, organogenesis) using experimental examples from both invertebrate and vertebrate embryos. The first set of lectures will focus on gametogenesis, fertilization, and early developmental events, such as cleavage, midblastula transition, gastrulation, and axis formation. The second set of lectures will explore the fates of germ layers in the contexts of cell type-specific differentiation and cell-cell interactions during organogenesis.

CSAT 5024. RNA Biology and Genomics II. 1 Credit Hour.

The challenges of controlling RNA viruses, the promise of RNA vaccines and the recent findings on the roles of ncRNAs and RNA binding proteins in human disease highlight the importance of studying RNA biology. This course, coupled with MMED 6001, covers all aspects of RNA expression and metabolism, such as RNA processing, decay, transport, alternative splicing and translation and, the function of RNA binding proteins and non-coding RNAs. We will also discuss recent discoveries, such as RNA vaccines, RNA granules, RNA modification, the impact of RNA mediated processes in metabolic syndrome, neurodegenerative diseases and cancer and, RNA therapeutics. Another important goal of these courses is to teach students to employ omics methods such as RNA-seq, RIP-Seq, BRIC, CLIP, Ribo-seq, and CRISPR to study these processes and their regulators. This includes hands-on training on biological databases and classes covering examples of the use of genomics. We expect students to acquire skills that will help them visualize how RNA genomics can be used in their own research projects. Open for Cross Enrollment on Space Available Basis.

CSAT 5025. Genetics. 1 Credit Hour.

This course is designed to provide an overview of genetic research. Topics to be covered include: cytogenetics, mitochondrial genetics, cancer genetics, linkage analysis, complex traits, population genetics, animal models, sex determination, and epigenetics.

CSAT 5083. Practical Optical Microscopy. 1 Credit Hour.

This course will be a one-hour elective for graduate students consisting of eight (8) one-hour lectures plus eight (8) one-hour laboratories. The course focuses on the practical aspects of using optical microscopes. The objectives are to teach students the fundamental principles of optical microscopy and to provide them with hands-on experience using the optical instrumentation in the Institutional Imaging Core.

CSAT 5095. Experimental Design And Data Analysis. 3 Credit Hours.

The purpose of the course is to provide an introduction to experimental design and statistical analysis. The emphasis of the course will be on the selection and application of proper tests of statistical significance. Practical experience will be provided in the use of both parametric and nonparametric methods of statistical evaluation. Among the topics to be covered are: data reduction, types of distributions, hypothesis testing, scales of measurement, chi square analysis, the special case of the comparison of two groups; analysis of variance; a posteriori multiple comparisons tests, tests of the assumptions of parametric analyses, advanced forms of the analysis of variance, linear regression, and correlation analysis. This course involves the use of statistical software; therefore, access to a laptop or a computer with web access for classes and examinations is required.

CSAT 6021. Animal Models. 3 Credit Hours.

The relevant biology, applicability, and practical use of a number of animal models to biomedical research is covered. Invertebrate (e.g., C. elegans) and vertebrate (e.g., fish and rodents) model systems are included in the course. Strengths and weaknesses of each organism that render them particularly valuable as animal models are emphasized. Experimental approaches and tools that are utilized in conjunction with each animal model are rigorously examined. The course is taught from primary scientific literature using classic historical publications and recent publications.

CSAT 6048. Biology of Aging. 4 Credit Hours.

Biology of Aging is the core course of the Biology of Aging Track. The course consists of two modules: Aging and Longevity Mechanisms and Molecular and Cellular Mechanisms of Aging. The purpose of this course is to provide students with the most up-to-date information on the current understanding of the aging process. This advanced interdisciplinary graduate course provides experimental understanding of the interrelated areas of aging and age-related diseases. Faculty from several departments will be involved in teaching this course, which will cover the molecular and cell biology of aging, model systems used for aging studies, age-related changes in organs and tissues, and age-related diseases.

CSAT 6049. Cellular and Molecular Mechanisms of Aging. 2 Credit Hours.

This course provides up-to-date information on the current understanding of cellular and molecular mechanisms that contribute to aging. The focus is on investigation of specific mechanisms of aging including oxidative stress, nutrient sensing signaling pathways, stem cells and senescence, and genome stability. Experimental design and analysis, including pros and cons of approaches used to gain knowledge and how to appropriately interpret data, will be discussed throughout the course. The relationship between age-related changes in function and potential contributions age associated diseases will be examined via recently published research.

CSAT 6050. Aging and Longevity Mechanisms. 2 Credit Hours.

This module will focus on and evaluate several approaches used to modulate longevity and how these are used to discover the genetic, physiological and intracellular foundation of aging processes. The course will consist of interactive lectures complemented by guided reading of currently research papers. Students will be taught to hone critical reading skills and develop testable hypotheses to carry research forward. Topics will include: Genetics of Aging, Exceptional Longevity, Pharmacological Interventions, Calorie Restriction, Healthspan and Pathology of Aging.

CSAT 6059. Stem Cells & Regenerative Medicine. 1 Credit Hour.

The fields of stem cells and regenerative medicine are rapidly evolving and have great potential to change the way medicine is practiced. This course will encompass topics from basics of tissue specific stem cell biology to pre-clinical animal models, strategies and progress in regenerative medicine. We will discuss some of the most current research being done in regenerative medicine from stem cell transplantation to biomaterials. Prerequisite: IBMS 5000.

CSAT 6064. Genes & Development. 4 Credit Hours.

Genes and Development is the core course of the Genetics, Genomics, and Development Track. The course consists of four modules: genetics, genomics, developmental biology, and stem cell biology. Basic concepts in genetics such as cytogenetics, mitochondrial genetics, cancer genetics, linkage analysis, complex traits, population genetics, animal models, sex determination, and epigenetics will be presented. The genomics section will include historical aspects of the genome project and high throughput analysis. The students are introduced to new techniques in global analysis as well as have hands-on experience. The developmental biology section provides a survey of concepts in developmental biology (induction, cell-cell interactions, morphogen gradients, morphogenetic movements, transcriptional regulation, organogenesis) using experimental examples from both invertebrate and vertebrate embryos. The stem cell biology section includes the following topics: basic biology of stem cells, including embryonic stem cells, adult stem cells, stem cells in different tissues and model systems; microenvironment-mediated and epigenetic regulators of stem cells; stem cells in medicine, including regenerative medicine, cancer, and aging; and ethics. Required for the Genetics, Genomics & Development Track.

CSAT 6068. Cancer Biology Core 1: An Introductory Course. 1.5 Credit Hour.

This team-taught course will provide an introduction to molecular oncology with a focus on defining cancer and key molecular/cellular changes often associated with the development of cancer. The goal of the course is to provide the student with a solid background in general cancer biology. This course requires a strong background in basic cellular processes, such as those covered in IBMS 5007. These processes will be discussed with regard to how they are altered in cancer and whether such differences from normal biology offer a therapeutic opportunity to target cancer. Tumorigenesis is a multi-step process driven by genetic, epigenetic and metabolic/environmental changes that occur over time. Although cancer is a heterogeneous disease, many human tumors exhibit similar acquired physiological features. This course will cover the underlying molecular and cell biology mechanisms involved in carcinogenesis, tumor growth, and metastasis at a basic level. The implications of these biological findings on cancer prevention, diagnosis, and treatment will also be introduced. Upon completion of the class, students should have a general understanding of the mechanisms by which tumors gain and maintain a growth advantage as well as an initial handle on potential therapeutic targets. This course is meant to be the basic introduction/foundation for CSAT 6069, Cancer Biology Core 2; Advanced Cancer Biology. Open for Cross Enrollment on Space Available Basis.

CSAT 6069. Cancer Biology Core 2; Advanced Cancer Biology. 2.5 Credit Hours.

This course is designed to provide a detailed representation of cancer biology, from progression, standard of care and molecular alterations that drive recent diagnoses and therapeutic strategies. In addition, this course will offer an overview on special populations affected by cancers and models used in the investigation of cancer. Included are basic experimental methods, mouse models, ex vivo systems, molecular profiling and clinical trials. The conceptual notions on clinical trials of cancer drugs and the process of development of novel therapeutic drugs in cancer will be discussed. Required for Cancer Biology Discipline. Prerequisites: INTD 5007 (or INTD 6007 and INTD 6009) and CSAT 6068.

CSAT 6074. Molecular Aspects Of Epigenetics. 2 Credit Hours.

The purpose of this course is to develop an understanding of the molecular aspects of epigenetics. This advanced course will be a unique learning experience that prepares the student to evaluate and design new research in the areas of epigenetic processes including imprinting, gene slicing, X chromosome inactivation, position effect, reprogramming, and the process of tumorigenesis. This module concerns epigenetic mechanisms. Topics include: DNA methylation, histone modifications, epigenetics and stem cells, cancer epigenetics, RNA interference and epigenetics, bioinformatics and epigenetics, and translational epigenetics. This course will include a didactic program and student discussion. For the student discussion module, faculty and students will jointly discuss key publications that serve to bridge the gap between the student's prior understanding of the field and the state of the art in that area.

CSAT 6095. Analysis and Visualization of Genomic Data. 2 Credit Hours.

This course covers the basics of genomic data analysis and visualization. The focus is on general computational methods, their basis in biomedicine, and how to evaluate and visualize analysis results. Students are expected to be able to qualitatively describe the algorithms presented. Prerequisites: CSAT 5095 or Equivalent.

IBMS 6090. Seminar. 1.5 Credit Hour.

This course is required of all students in the IBMS program, except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 seminars per semester and to complete a requirement to demonstrate their attendance and participation. To fulfill the minimum number of seminars, students may include seminars offered by disciplines other than their own in which they are enrolled. However, to enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 6090-1GEN, 6090-2BA, 6090-3CB, 6090-4CGM, 6090-5MIM, 6090-6MBB, 6090-7NS and 6090-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 6090-1GEN. Grading will be Satisfactory or Unsatisfactory. A list of seminars from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS-6090 section, the policy for tracking student's attendance and participation in seminars.

IBMS 7010. Student Journal Club & Research Presentation. 1-2 Credit Hours.

This course is designed to provide graduate students with experience in critical reading of the primary literature, seminar preparation and presentation, data analysis and interpretation, and group-based learning as they relate to the graduate program in Integrated Biomedical Sciences. This course is required of all students in the IBMS program starting in their second year except of those who have signed up for Final Hours. Students are required to attend a minimum of 16 total presentations per semester (journal club or research presentations) and to complete a requirement to demonstrate their attendance and participation. Students are also required to present one journal club presentation per semester until they are Advanced to Candidacy. Once Advanced to Candidacy, the student will present one journal club presentation per academic year and one research presentation per academic year such that the student is giving at least one presentation in each semester. To enroll, students should obtain permission from the course Section Director affiliated with the appropriate discipline. The course numbers of the individual course sections are INTD 7010-1GEN, 7010-2BA, 7010-3CB, 7010-4CGM, 7010-5MIM, 7010-6MBB, 7010-7NS and 7010-8PP for the IBMS Disciplines: Biology of Aging (BA), Cancer Biology (CB), Cell Biology, Genetics & Molecular Medicine (CGM), Molecular Biophysics & Biochemistry (MBB), Molecular Immunology & Microbiology (MIM), Neuroscience (NS), and Physiology & Pharmacology (PP). Some students who have not declared a discipline, and have obtained the approval of their academic advisor and the Senior Associate Dean of the GSBS, may sign up for INTD 7010-1GEN. Grading will be by letter grade (A, B, C, etc). A list of journal clubs from all disciplines will be posted on the Graduate School Web site. Each Section Director will determine, for the relevant IBMS 7010 section, the policy for tracking student's attendance and participation and will be responsible for assigning a final grade.

INTD 6007. Advanced Cell Biology. 2 Credit Hours.

This course provides an in-depth learning experience that instructs students on the fundamentals of cell biology as well as prepares the student to evaluate and design new research in the cutting-edge areas of modern cell biology. The course combines a didactic program of lectures along with a small-group discussion format in which students interact closely with a group of faculty who have active research programs. The course focuses on active areas of research in cell biology: Cell Signaling and Communication, Cell Growth, and Cell Death. Each week, the faculty jointly discuss key publications that serve to bridge the gap between the fundamental underpinnings of the field and the state of the art in that area. Students and faculty will then jointly discuss key publications that serve to bridge the gap between the fundamental underpinnnings of the field and the state of the art in that area.

INTD 6008. Mitochondria & Apoptosis. 1 Credit Hour.

This course will focus in depth on Mitochondria and Apoptosis. Topics will include: Mitochondria and Respiration; Mitochondria and Reactive Oxygen Species; Mitochondria and Apoptosis. It will provide an opportunity for a unique learning experience where the student can prepare to evaluate and design new research in the cutting-edge areas of modern cell biology and molecular biology. Instead of a didactic program of lectures, the entire course comprises a small-group format in which students interact closely with a group of faculty who have active research programs. Each week, faculty will provide students with a brief overview of the research area. Students and faculty will then jointly discuss key publications that serve to bridge the gap between the student's prior understanding of the field and the state of the art in that area.

INTD 6009. Advanced Molecular Biology. 2 Credit Hours.

This course will provide an in-depth learning experience on the fundamentals of molecular biology as well as prepare the student to evaluate and design new research in the cutting-edge areas of modern molecular biology. The course combines a didactic program of lectures along with a small- group discussion format in which students interact closely with a group of faculty who have active research programs. The course focuses on active areas of research in molecular biology: Chromatin structure, Transcription, DNA Replication and Repair, Recombination, RNA processing and regulation, Protein processing, targeting and degradation. Each week, the faculty provide students with didactic lectures on a current research area. Students and faculty then jointly discuss Key publications that serve to bridge the gap between the fundamental underpinnings of the field and the state of the art in that area.

INTD 6062. Next-Generation Sequencing Data Analysis. 2 Credit Hours.

Next-generation sequencing (NGS) is becoming increasingly commonplace in biomedical research. For many labs, the main bottleneck to implementing NGS applications is data analysis. This course is designed to introduce students to bioinformatics analysis of NGS data. The course consists of two modules: the first module covers working in the Unix/Linux environment, mapping NGS data to a genome of interest, and performing downstream analysis of RNA-seq, ChIP-seq, and ATAC-seq data. The second module will be an introduction to the programming language Perl, which will enable students to perform custom bioinformatics analysis. This course will be taught in the form of interactive hands-on computer classes. No prior knowledge of programming or coding is required.

MICR 5025. Eukaryotic Pathogens. 1 Credit Hour.

The course will provide students with the opportunity to gain a basic comprehensive understanding of parasitology and mycology. The first part of this course will focus on virulence mechanisms and the host immune response with respect to a variety of parasites that cause major human diseases. The second part of this course will cover several important areas of medical mycology including molecular biology, diagnostic/epidemiology, mating/phenotypic switching, morphology, pathogenesis, and antifungal therapies.

MICR 5026. Bacterial Pathogenesis. 1 Credit Hour.

This is an introductory course in microbial pathogenesis focusing on bacterial pathogens that are important in human disease. Students will receive a foundation in the basic concepts and experimental approaches that are crucial for understanding the discipline through directed readings and didactic instruction. Specific concepts, strategies, and mechanisms used by human bacterial pathogens to cause disease will be illustrated.

MICR 5027. Immunology. 1 Credit Hour.

MICR 5027 is designed to build on the immunological concepts covered in MICR 5051 given in the Fall semester and to put those concepts to use as we focus on understanding the world of the mammalian host response to infection and on applying fundamental immunological concepts to the understanding of current immunological research questions in a student-presentation and in-class discussion format. Prerequisite: MICR 5051.

MICR 5028. Virology. 1 Credit Hour.

This course focuses on the molecular and cellular biology of animal viruses, and their interactions with host cells. Many of the viruses to be covered in this course are medically significant or have provided critical information that has expanded our understanding of cell biology, immunology, development, and differentiation.

MICR 5031. Pathogenic Microbiology. 3 Credit Hours.

This lecture-only course integrates different disciplines (immunology, cell biology, genetics, biochemistry, molecular biology, physiology, and medical microbiology) with a central theme focused on molecular mechanisms of microbial pathogenesis in humans. Recommended prerequisites for this course are Biochemistry and Molecular Biology.

MICR 5035. Emerging Trends in Immunology and Infection. 2 Credit Hours.

An intense and advanced exploration of the primary literature focusing on the latest emerging trends in immunological research. The format will allow students to develop skills of in depth critical analysis and will involve a combination of student presentations of current data and discussions of the historical development and evolution of new directions in immunological research.

MICR 5051. Intro To Immunology. 2 Credit Hours.

This course is a study of immune responses with emphasis on experimental strategies for elucidating cellular and molecular mechanisms. Three phases of study: (1) immunochemistry and molecular biology of antibodies, lymphocyte receptors, and products of the major histocompatibility complex; (2) cellular interactions and immuno-regulation; and (3) immunopathologies (hypersensitivity, autoimmunity, immunodeficiency, transplantation rejection, and tumor immunology). Prerequisites: consent of instructor, courses in General Biology and Genetics recommended.

MICR 5091. Current Topics In Microbiology And Immunology. 0.5-3 Credit Hours.

Students will be given an opportunity to gain in-depth understanding of selected topics in microbiology and immunology through a combination of library research and discussion with faculty. Prerequisites: consent of instructor.

MICR 5095. Current Topics in Immunobiology and Host-microbe Interactions. 1 Credit Hour.

This course is designed to enhance and expand on the existing Research Progress Report (RPR) course (MICR 5090) that is required of all graduate students in the Molecular Immunology & Microbiology discipline of the IBMS Graduate Program. Although the RPR course allows students to gain experience with regard to making formal lecture presentations of their research, it is limited in that students present their work only once a year, the opportunity for full discussion is limited by the time available after presentations, and being a course in which participants are exclusively students, there are no opportunities to observe examples of how skilled seasoned investigators (i.e., faculty and postdoctoral fellows) present their work. In the currently proposed course, graduate students will not only have more frequent opportunities to present their own research and receive vital feedback and critiques, but will also hear and critique presentations by more senior investigators regarding projects performed in labs throughout the Department of Microbiology, Immunology & Molecular Genetics. Prerequisites: MICR 5090.

MICR 6030. The Microbiome & The Associated Metabolites in Health and Diseases. 2.5 Credit Hours.

This course provides an overview on the role of the microbiome and the associated metabolites in human health and diseases. It will focus on clarifying the conceptual framework for understanding how microbiome and the associated metabolites, particularly gut microbiome, impact human health and well- being. The course will also introduce students to the technologies and approaches used to study the microbiome and the associated metabolites in human and murine models. Prerequisites: MICR 5051 Open for Cross Enrollment on Space Available Basis.

MICR 6097. Research. 1-12 Credit Hours.

This course consists of independent, original research under the direction of faculty advisor. May be conducted in bacteriology, virology, mycology, parasitology, and immunology.

MICR 6098. Thesis. 1-12 Credit Hours.

Registration for at least one term is required of M.S. candidates. Admission to candidacy for the Master of Science degree is required.

TSCI 5070. Responsible Conduct of Research. 2 Credit Hours.

This foundational course introduces students to core ethical content necessary for responsible research conduct. Through interactive seminars, students will learn about (1) scientists as responsible members of society (contemporary ethical issues in biomedical research and environmental/social impacts of research), (2) policies for research with human subjects and vertebrate animals, (3) collaborative research, (4) conflicts of interest (personal, professional, financial), (5) data acquisition and laboratory tools (management, sharing, ownership), (6) responsible authorship and publication, (7) mentor/trainee responsibilities and relationships, (8) peer review (9) research misconduct (forms of misconduct and management policies) (10) informed consent, privacy regulations, good clinical practice, and special populations in clinical investigations.