MB - Microbiology
MB 505 Host-Associated Microbiomes: 4 Credits (3 Lec, 1 Lab)
(Sp) This course will introduce students to the microbial ecosystems that colonize human and animal hosts, detailing their essential roles in host nutrition, health and development. Students will also be exposed to modern molecular techniques used to study these systems.
View Course Outcomes:
- Appreciate the importance of the microbial communities (microbiomes) that colonize animals, including humans, with respect to the host’s health, nutrition and development.
- Be able to describe the genetic, functional, phenotypic, and antigenic diversity of microbes and the ecology that underscores host-associated microbiomes
- Have hands-on experience in current molecular research techniques to study microbial communities.
- Have developed skills enabling you to critically evaluate scientific literature.
MB 510 Immunology: 4 Credits (4 Lec)
(F, Sp) Fundamentals of cellular and molecular immunology including consideration of structure, genetics and function of immunoglobulin, T-cell receptors and major histocompatibility antigens; regulation of the immune response; transplantation and immunological diseases.
View Course Outcomes:
- Explain the distinction between innate and adaptive immunity and how these two types of host defenses differ with regard to combating infections.
- Describe organization of the cells and organs of the immune system and how they relate to the processing of foreign substances and the development of the immune system.
- Explain how the cells interact with each other in the formation of an immune response.
- Explain the molecular basis by which the immune system identifies pathogens.\\n
- Comprehend cell and molecular mechanisms mediating antigen-antibody interactions, antigen processing and presentation, and the genetic mechanisms that result in diversity in immunoglobulin structure responsible for antigen recognition.
- Describe cell mediated effector responses, inflammation and the roles that cytokines and complement cascades play in the mediation of these processes.
- Demonstrate the basis of immune response to infectious agents, vaccinations, immunodeficiency, autoimmune reactions, and hypersensitivity reactions.
MB 515 Microbial Ecology: 3 Credits (3 Lec)
(Sp) Offered every other Spring, odd numbered years. Critical review of literature on the distribution and activity of microorganisms in natural microbial communities based on microbial adaption and physical, chemical and biological features of the microenvironment. A critical discussion of literature and approaches. Cross-listed with LRES 515.
View Course Outcomes:
- Explain microbial community organization from individuals to species to functional guilds, and how this organization results in community function.
- Describe critical elements that shape community assembly across temporal and spatial gradients, independent of the microbial community examined.\\n
- Apply community assembly thinking to a microbial community of interest to them.\\n
- Critically read and evaluate microbial ecology and evolution scientific literature.\\n
- Interpret and design microbial ecology experiments.\\n
- Communicate the findings of experiments to their peers in the form of a scientific paper.
MB 519 Programming for Biologists: 3 Credits (2 Lec, 1 Lab)
(F) This course will introduce computer programming languages commonly used in the biological sciences, including Python, R, and command line driven applications. Common commands in each programming language/application will be covered in the context of biological problem-solving using manipulation and analysis of large datasets.
View Course Outcomes:
- Master basic commands in Python by interpreting functions of pre-written code and by generating code to perform simple tasks.
- Use Python to parse files containing different data types (e.g. text and nucleotide sequence) and extract/analyze data sub-sets of interest.
- Master basic commands in R, and understand how to download and run specific R packages.
- Successfully perform an analysis using a pre-built command-line driven pipeline.
MB 520 Microbial Physiology: 3 Credits (3 Lec)
PREREQUISITE: BIOM 360 and BCH 380. (F) Cannot enroll if previously completed BIOM 450. An in-depth examination of microbial cell structure and function, bioenergetics, and intermediary metabolism and control. Students will also be expected to consider biochemical function within the context of genomic sequences, and be able to formulate predictions for carbon and energy flow
MB 525 Advanced Immunology: 3 Credits (3 Lec)
PREREQUISITE: BIOB 410. (Spring, even years.) Offered every other Spring, even numbered years. Recent advances in immunochemistry, immunogenetics, immunopathology, molecular and cellular immunology
MB 527 Toxicology: 3 Credits (3 Lec)
(Sp) This course introduces mechanisms of toxicity; effects of toxicants on major organ systems. major classes of toxicants; absorption, distribution, biotransformation and elimination of toxicants. Human exposure to drugs of abuse and environmental agents, case studies, and risk assessment are discussed. Co-convened with BIOM 425.
MB 528 Advanced Microbial Genetics: 3 Credits (3 Lec)
PREREQUISITE: BIOM 450 or consent of instructor. (Sp) This course is designed to explore recent developments in the molecular biology of prokaryotes, using a literature-based approach. Topics will include: genomics, metagenomics, transcriptomics, phylogeny, regulation of gene expression, DNA recombination, and transfer of mobile genetic elements. Students will also write a literature article or a scientific proposal on a topic in microbial genetics. Students will engage in the written and study panel peer-review process
View Course Outcomes:
- Describe the different methods used to obtain high-throughput DNA sequence information.
- Annotate genomes from the assemble DNA sequence information.
- Use comparative genome approaches to understand molecular mechanisms of genome evolution.
- Describe how high-throughput approaches are used to obtain transcriptomics and metatranscriptomics information on microbial adaptation to their environments.
- Describe molecular mechanisms involved in gene regulation at the transcriptional level.
- Describe the role of mRNA secondary structure and other post-transcriptional regulatory mechanisms are involved in gene expression.
- Write a proposal or a manuscript based on original work in microbial genetics.
- Learn to participate in the peer-review process, as they conduct written reviews of other student’s proposals or manuscripts.
MB 530 Virology: 3 Credits (3 Lec)
PREREQUISITE: BIOB 160 or BIOB 260 or BIOB 375 or BIOH 320 or BCH 380 or BCH 442 or BCH 444R. (F) Offered every other Fall, odd numbered years. Fundamentals of virology with emphasis on animal viruses of medical importance. Molecular aspects of structure, replication transmission and host response to viral infection will be covered
MB 533 Current Topics in Microbiology for Teachers: 3 Credits (1 Lec, 1 Lab, 1 Other)
(F) This course will provide an inquiry based examination of current microbiology related topics. Topics may vary from semester to semester and will be selected by the assessment of what is considered “newsworthy.” Topics could include but not be limited to hospital acquired and community acquired infections, antibiotic resistance, immunizations, food safety and drinking water. Emphasis will be placed on the ramifications of issues with respect to industry, medicine, and personal health. A review of literature will provide background information for the topics in order to provide teachers sufficient and correct information to hold discussions regarding these topics in their classrooms.
View Course Outcomes:
- summarize the current topics presented during the semester
- analyze peer reviewed papers covering the selected current topics
- evaluate current literature as well as news articles in order to discuss the issues surrounding the current topic
- critique potential solutions to the issue/topic
- create a final project which will consist of a presentation geared to the student grade level. Students will select a topic that was not covered in the class.
MB 536 Exploring Microbiology: 3 Credits (3 Other)
() Explore microscopy, prokaryotes, microbial eukaryotes, viruses, acellular agents, microbial evolution, diversity, by focusing on an experimental microcosm. Ideal for middle/high school/lower level college teachers and others in education and outreach roles, e.g. museums, zoos, National Parks, nature preserves, environmental health. Offered Spring.
MB 538 Cell & Molecular Biol: 2 Credits (2 Lab)
() An inquiry-based laboratory in prokaryotic and eukaryotic CMB provides training in microbiological techniques: recombinant DNA, phylogenetic analyses, growth, cell cycle regulation, gene expression, protein purification, and immunoassays. Current literature and laboratory discussions cover molecular approaches for investigating complex cellular mechanisms. Offered Summer.
MB 539 Infection and Immunity: 3 Credits (3 Other)
(Sp) An inquiry-based study of recent advances in understanding the etiology, pathogenesis, chemotherapy and prevention of infectious disease which includes analysis of current literature, case histories, and online sources of information. This course is intended for practicing teachers and those in the MSSE program. Offered Fall.
View Course Outcomes:
- identify and define basic aspects of microbiology as they relate to infectious disease.
- describe how antimicrobial agents kill or inhibit microbes without seriously harming humans
- identify and describe important infectious diseases of humans: their causes, pathogenesis, epidemiology, diagnosis, treatment and prevention
- synthesize and analyze scientific journal articles and solve case histories involving infectious disease and immunology
- summarize and submit a personal reflection of weekly discussion posts specific to course content\\n
MB 540 Environmental Microbiology: 3 Credits (3 Other)
(Summer, odd years.) Offered every other Summer, odd years. Biotechnology, industrial microbiology, antimicrobial chemotherapy, public health, epidemiology, climate change, food water, wastewater, extreme environments, space travel, biodegradation, bioremediation and bioaugmentation. Ideal for middle/high school/college teachers, and others in education/outreach, e.g., museums, zoos, National Parks, nature preserves, environmental health. Offered Summer.
View Course Outcomes:
- compare key structural differences between bacteria, archaea and eukaryotes
- describe metabolism and catabolism
- identify key microbial species within each environment studied
- create biogeochemical cycling diagrams
- develop lesson plans specific to their teaching situation that cover aspects of this course content\\n
MB 541 Microbial Genomics: 3 Credits (3 Lec)
(Spring, even years.) This course provides an inquiry-based study of prokaryotic genomics. Emphasis will be placed on the advances in microbial genomics and effects on technological and medical advances. The goal of this course is to rigorously examine these and related topics.
View Course Outcomes:
- define and describe fundamentals of genetic processes in bacteria (prokaryotes)
- define and describe the basic concepts of transcription, translation, mutation and recombination are similar if not identical in all organisms.
- define and describe the fundamental processes of genetics particularly as they apply to microorganisms
- synthesize and analyze scientific journal articles and solve case histories involving infectious disease and immunology
- summarize and submit a personal reflection of weekly discussion posts specific to course content\\n
MB 542 Microbial Ecology: 3 Credits (3 Lec)
() Ecology of microorganisms, their nutrition, growth, control, metabolism, biogeochemical cycling, natural environments, habitats and interactions. Centered on an experiment, this discovery-based course is ideal for middle/high school/lower level college teachers, and others in education/outreach roles, e.g., nature facilities, environmental health. Offered Fall.
MB 544 Advanced Bioinformatics: 4 Credits (3 Lec, 1 Lab)
(Sp) This course will cover advanced topics in Bioinformatics, including genome assemblies and functional annotations of proteins. The course is meant to support experimental work by training students to make confident predictions from biological sequences and to develop testable hypotheses that will guide their experimental work. Students will learn about using local and worldwide prediction servers.
MB 547 Thermal Biology of YNP: 2 Credits (1 Lec, 1 Lab)
Thermal Biology, an interdisciplinary science that incorporates biology, geology, and chemistry to discover where and under what conditions life can exist in the thermal features of Yellowstone National Park. As such, it lends itself easily to incorporation to most science curricula. The two goals of this are to: 1)provide a basic understanding of the ecology of a variety of life forms and their thermal habitats, and 2) provide a survey of observational techniques and hands-on activities appropriate for science educators. -.
MB 552 Adv Soil & Env Microbiology: 3 Credits (3 Lab)
PREREQUISITE: BIOM 452 or consent of instructor. (Sp) Offered every other Spring, even numbered years. Advanced laboratory course. Microorganisms are targeted for isolation and characterization, emphasizing those not normally encountered in general microbiology laboratory. Biochemical cycling, contaminant biodegradation, extremophiles, and plant-microbe interactions are typical topics is investigated. Students employ classic and novel cultivation approaches, identifying microbes based morphology, physiology, and phylogeny. Cross-listed with LRES 552
MB 558 Human Pathophysiology: 3 Credits (3 Lec)
PREREQUISITE: graduate level standing, prior completion of college-level immunology course. (Sp) Students will research up to three diseases of their own choosing and give a class presentation of their findings. Students will participate in discussions on disease mechanism and pathophysiology based on the primary research articles presented in class. Graduate students will additionally research, write a paper and in-class present on a specific mechanism of pathology in a chosen disease category for which there are opposing experimental or clinical evidence
View Course Outcomes:
- Interpret and categorize concepts within molecular and cellular basis of disease pathophysiology. \\n
- Defend the contribution of both host immune system and pathogens to disease pathophysiology and symptoms.
- Categorize physiological consequences of disease pathology.
- Integrate and interpret the concepts of disease symptoms and disease pathophysiology.\\n
- Evaluate the impact of disease treatment on pathophysiology.\\n
- Develop and defend hypotheses for molecular and cellular basis of disease pathophysiology.\\n
MB 563 Scientific Writing: 3 Credits (3 Lec)
(Sp) In today’s highly competitive funding climate, research scientists and engineers must be skilled grant writers. The goal of this course is to provide doctoral students with strategies, practical skills, and experience in seeking funding for their research as well as writing and evaluating scientific proposals. The student should leave this course with a research proposal that is ready or near ready for submission to an identified funding agency.
MB 575 Professional Paper: 1-4 Credits (1-4 Other)
PREREQUISITE: Graduate standing and committee approval. (F, Sp, Su) A research or professional paper or project dealing with a topic in the field. The topic must have been mutually agreed upon by the student and his or her major adviser and graduate committee
Repeatable up to 6 credits.
MB 589 Graduate Consultation: 1-3 Credits (1-3 Other)
PREREQUISITE: Master's standing and approval of the Dean of Graduate Studies. (F, Sp, Su) This course may be used only by students who have completed all of their coursework (and thesis, if on a thesis plan) but who need additional faculty or staff time or help
MB 590 Master's Thesis: 1-10 Credits (1-10 Other)
PREREQUISITE: Master's standing
Repeatable up to 20 credits.
View Course Outcomes:
- Master's Thesis
MB 591 Special Topics: 1-4 Credits (1-4 Other)
PREREQUISITE: Upper division courses and others as determined for each offering. Courses not required in any curriculum for which there is a particular one time need, or given on a trial basis to determine acceptability and demand before requesting a regular course number
MB 592 Independent Study: 1-3 Credits (1-3 Lec)
(F, Sp, Su) Independent study.
Repeatable up to 6 credits.
View Course Outcomes:
- Varies based on independent study
MB 594 Seminar: 1 Credits (1 Other)
PREREQUISITE: Graduate standing or seniors by petition. (F, Sp) Course prerequisites as determined for each offering. Topics offered at the graduate level which are not covered in regular courses. Students participate in preparing and presenting discussion material. There are separate sections for departmental seminar, general/environmental and biomedical microbiology journal clubs and graduate reading; consult the Department of Microbiology Graduate Student Handbook for specific requirements
Repeatable up to 4 credits.
MB 598 Internship: 2-12 Credits (2-12 Other)
PREREQUISITE: Graduate standing, consent of instructor and approval of department head. (F, Sp, Su) An individualized assignment arranged with an agency, business or other organization to provide guided experience in the field
Repeatable up to 99 credits.