Learning Outcomes: 1. Understand, analyze, and evaluate information effectively.
Audience: Undergraduate

2. Describe what makes up a microorganism. How is the make up different between a microorganism and a human being?
Audience: Undergraduate

3. Define a disease. Describe how your body, your doctor, and the government fight disease.
Audience: Undergraduate

4. Understand where we came from. Analyze the various theories of how life originated and express an opinion on which is most plausible.
Audience: Undergraduate

5. Articulate the positive impacts microbes have on your health, the well-being of their host organisms, the cycling of important elements, and the environment.
Audience: Undergraduate

Learning Outcomes: 1. Identify the three Domains of the phylogenetic tree of life and draw inferences about evolutionary processes based on phylogenetic trees.
Audience: Undergraduate

2. Describe the basic cell structure of cells (bacteria, archaea, eukarya) and the structure of viruses and explain how this affects microbial function.
Audience: Undergraduate

3. Understand the impact of environmental conditions on microbial growth and how this impacts the abundance and distribution of microbes on Earth.
Audience: Undergraduate

4. Describe how microbes obtain nutrients and energy from the environment and how this is important to food production, waste treatment, sustainability and global ecosystems.
Audience: Undergraduate

5. Describe the flow and exchange of information in microbial cells and populations and understand how this affects microbial diversity and evolution.
Audience: Undergraduate

6. Compare different methods of microbial growth control and their impact on microbes.
Audience: Undergraduate

7. Compare and contrast the different ways in which microbes interact with their human hosts and the impacts on global health and disease.
Audience: Undergraduate

8. Describe the human immune response to microbes.
Audience: Undergraduate

Learning Outcomes: 1. Demonstrate competencies in microbiological laboratory techniques.
Audience: Undergraduate

2. Isolate and identify bacteria.
Audience: Undergraduate

3. Keep careful records of observations.
Audience: Undergraduate

4. Develop hypotheses, and think critically and make valid conclusions about them.
Audience: Undergraduate

5. Assess the credibility of scientific sources.
Audience: Undergraduate

6. Communicate scientific findings and ideas effectively through writing.
Audience: Undergraduate

Learning Outcomes: 1. Describe the academic skills and practical steps required to succeed as a microbiology major
Audience: Undergraduate

2. Discuss the research and teaching interests of department faculty
Audience: Undergraduate

3. Describe the variety of career opportunities available to individuals with microbiology and life science backgrounds
Audience: Undergraduate

4. Identify university, college, and department resources that support success at UW-Madison
Audience: Undergraduate

5. Identify credible sources of information related to microbiome research
Audience: Undergraduate

6. Discuss the major research questions in the study of the microbiome
Audience: Undergraduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

Learning Outcomes: 1. Explain the historical context of microbiology from a human and evolutionary perspective.
Audience: Undergraduate

2. Compare different microbial cell structures and predict behaviors based upon those structures.
Audience: Undergraduate

3. Explain how mutations occur in cells, the mechanisms organisms have to combat these changes, and how these changes relate to the evolution of species.
Audience: Undergraduate

4. Predict the modes of growth of microbes based upon the enzymes they contain and the metabolic breakdown of substrates.
Audience: Undergraduate

5. Describe the regulatory paradigms in microbes and predict the changes in behavior that occur when these pathways are disrupted.
Audience: Undergraduate

6. Explain the symbiotic and dysbiotic state in a host-microbe interaction and list factors that can affect this relationship.
Audience: Undergraduate

7. Compare common virulence factors and explain their effect on symbiotic relationships and how these virulence factors contribute to disease.
Audience: Undergraduate

Learning Outcomes: 1. Demonstrate proficiency in microscopy, media preparation, aseptic technique, and microbiological measurements.
Audience: Undergraduate

2. Identify representative groups of microorganisms. Those that are important in: antibiotic production, sewage treatment, disease, food manufacturing, and the local environment.
Audience: Undergraduate

3. Characterize microbial isolates from nature and describe their taxonomy.
Audience: Undergraduate

4. Create detailed lab notes that describe accurately the experiments performed.
Audience: Undergraduate

5. Develop hypotheses, design experiments, perform experiments, collect data, analyse data critically, report data to others clearly and accurately, and communicate about scientific topics in a precise manner.
Audience: Undergraduate

Learning Outcomes: 1. Recognize the breadth of the field of microbiology and nature of the science.
Audience: Undergraduate

2. Describe the scientific method used in presented material.
Audience: Undergraduate

3. Demonstrate critical thinking and problem solving skills through an exploration of seminal papers and cutting-edge research in the field of microbiology.
Audience: Undergraduate

4. Critique primary scientific papers by identifying the hypothesis, analyzing the data being presented, and proposing future experiments or directions for a particular study.
Audience: Undergraduate

5. Communicate analysis of primary literature to others.
Audience: Undergraduate

Learning Outcomes: 1. Utilize laboratory techniques to identify microorganisms in food.
Audience: Undergraduate

2. Describe the principles involving food preservation via fermentation processes.
Audience: Undergraduate

3. Demonstrate understanding of the role and significance of microbial inactivation, adaptation, and environmental factors (i.e., water activity, pH, temperature) on growth and response of microorganisms in various environments.
Audience: Undergraduate

4. Identify the conditions, including sanitation practices, under which important pathogens and spoilage microorganisms are commonly inactivated, killed, or made harmless in foods.
Audience: Undergraduate

Learning Outcomes: 1. Identify and summarize the impacts of intrinsic and extrinsic factors on microorganisms.
Audience: Undergraduate

2. Calculate and apply thermal processing parameters to reductions in microbial numbers.
Audience: Undergraduate

3. Apply Hazard Analysis Critical Control Point (HACCP) concepts and principles to food production processes.
Audience: Undergraduate

4. Demonstrate knowledge of foodborne microbial pathogens.
Audience: Undergraduate

5. Describe methods and principles of sampling and testing food for microorganisms.
Audience: Undergraduate

6. Compare and contrast the principles, practices, and pathways of food fermentations.
Audience: Undergraduate

7. Analyze and use microbiological data sets.
Audience: Undergraduate

8. Evaluate the benefits and hazards of modern food production, organic foods, and genetically-engineered foods.
Audience: Undergraduate

Learning Outcomes: 1. Describe the potential outcomes of host-microbe interactions and basic mechanisms of pathogenesis.
Audience: Undergraduate

2. Identify major mechanisms of host defense, including barrier/chemical defenses, the innate immune response and the adaptive immune response and how microbes circumvent these defenses.
Audience: Undergraduate

3. Demonstrate the general mechanisms used by microbes to establish disease within their hosts and within populations.
Audience: Undergraduate

4. Outline conditions that lead to dysbiosis in each of the organ/tissue systems studied: skin, urogenital tract, respiratory tract, circulatory and nervous systems, and gastrointestinal tract.
Audience: Undergraduate

5. Compare the basic microbiological characteristics, mechanisms of transmission, and molecular basis of pathogenesis and virulence of major pathogens discussed in class.
Audience: Undergraduate

6. Identify mechanisms that have been developed to control infectious disease at the population level as well as within specific human hosts.
Audience: Undergraduate

7. Demonstrate the ability to read primary literature focused on a microbial pathogen and make valid conclusions from the research presented.
Audience: Undergraduate

Learning Outcomes: 1. Describe how microorganisms interact with plant and animal (including human) hosts in beneficial, neutral or detrimental ways.
Audience: Undergraduate

2. Express how the environment affects these host-microbe interactions.
Audience: Undergraduate

3. Summarize new molecular and bioinformatic methods that allow for the study of microbial communities.
Audience: Undergraduate

4. Describe how microbial communities are essential for life as we know it, and the processes that support life.
Audience: Undergraduate

5. Articulate several ways in which microbial communities are essential to plant and animal (including human) health.
Audience: Undergraduate

6. Explain our current knowledge about the diversity of microbial life and why its effects and potential benefits have not been fully explored.
Audience: Undergraduate

Learning Outcomes: 1. Describe different types of parasites/pathogens and their modes of transmission
Audience: Undergraduate

2. Summarize the function of the human immune system in protecting against disease and in causing some of the damages associated with disease
Audience: Undergraduate

3. Read and analyze data on the health status of populations
Audience: Undergraduate

4. Assess environmental, medical and political strategies for controlling infectious diseases
Audience: Undergraduate

5. Identify the evolutionary processes that lead to adaptation and biological diversity
Audience: Undergraduate

6. Describe the genetic and behavioral reasons why there are increasing numbers of antibiotic resistant infections
Audience: Undergraduate

7. Evaluate global progress toward reaching MD6—to reduce the burden of HIV, TB, Malaria and other diseases
Audience: Undergraduate

8. Critically evaluate and effectively use textbooks, current research literature, online information, as well as information related to scientific and biological issues in the popular press
Audience: Undergraduate

Learning Outcomes: 1. Perform basic command line operations to navigate through an operating system
Audience: Undergraduate

2. Recognize basic sequence data formats, access them through publicly available datasets, and utilize them in bioinformatics applications
Audience: Undergraduate

3. Use sequence analysis programs by downloading and installing them locally on their own computers
Audience: Undergraduate

4. Use publicly available bioinformatics databases
Audience: Undergraduate

5. Create programs in a scientific programming language to conduct basic bioinformatics analyses
Audience: Undergraduate

6. Demonstrate mastery of basic bioinformatics skills by completing a hands-on final project focused on the recovery and analyses of microbial genomes from public databases
Audience: Undergraduate

Learning Outcomes: 1. Perform assigned responsibilities in a professional setting for 80 hrs/credit/semester.
Audience: Undergraduate

2. Identify and employ standards of professionalism at work site.
Audience: Undergraduate

3. Articulate through discussion with faculty mentor how concepts learned in microbiology relate to real work situations.
Audience: Undergraduate

4. Synthesize and apply knowledge from the microbiology curriculum and broader coursework to solve problems on the worksite.
Audience: Undergraduate

5. Create and submit a progress report to a faculty mentor, twice during the semester, one at mid-semester and one at the end of the semester.
Audience: Undergraduate

Learning Outcomes: 1. Build intuition and an ability to predict which kinds of organisms will be found in different ecosystems using quantitative reasoning when possible.
Audience: Undergraduate

2. Gain familiarity with research tools and applications in environmental microbiology, along with an appreciation for their limitations.
Audience: Undergraduate

3. Critically evaluate published research carried out in the field and think creatively about new potential research questions and applications.
Audience: Undergraduate

4. Work collaboratively in a team to enhance learning and solve complex problems.
Audience: Undergraduate

Learning Outcomes: 1. Define the foundational principles of phylogenetics.
Audience: Undergraduate

2. Compare the major phyla within bacteria, archaea and eukaryotic microbes.
Audience: Undergraduate

3. Recognize general properties of viruses and the issues with their phylogenetic classification.
Audience: Undergraduate

4. Define ecology, its domains and distinguish it from other closely related fields.
Audience: Undergraduate

5. Develop a deeper understanding of methods available to characterize microbial communities.
Audience: Undergraduate

6. Explain Darwin’s Theory of Natural Selection and the four postulates of natural selection.
Audience: Undergraduate

7. Describe the concept of adaptation and how over the history of science this concept has changed.
Audience: Undergraduate

8. Identify the major events in the history of microbial life.
Audience: Undergraduate

9. Develop an evolutionary understanding of the 3 domains of life.
Audience: Undergraduate

Learning Outcomes: 1. Use correct nomenclature to describe microbial genetic and molecular processes and experimental approaches.
Audience: Undergraduate

2. Recognize and apply concepts of genetics.
Audience: Undergraduate

3. Describe how the molecular machines in bacterial gene expression function and, how they contribute to final gene-encoded activities.
Audience: Undergraduate

4. Explain the mechanisms by which these molecular machines are regulated.
Audience: Undergraduate

5. Interpret molecular and genetic data in regard to specific experimental questions.
Audience: Undergraduate

6. Apply understanding of microbial genetics and molecular machines to design experimental approaches test research hypotheses.
Audience: Undergraduate

Learning Outcomes: 1. Evaluate the reliability of sources of information about biology
Audience: Both Grad & Undergrad

2. Synthesize key topics/concepts of planetary microbiology, astrobiology, and the molecular history of life
Audience: Both Grad & Undergrad

3. Describe the environments in which life on Earth might have originated, emerged, and persisted over billions of years
Audience: Both Grad & Undergrad

4. Analyze and describe the significant molecular innovations that impacted life on Earth
Audience: Both Grad & Undergrad

5. Describe the current origins of life scenarios on Earth and planetary conditions that may give rise to life elsewhere in the universe
Audience: Both Grad & Undergrad

6. Formulate an original hypothesis to guide future research based on a synthesis of current research into the connections between the origins, evolution, and molecular underpinnings of life and corresponding planetary scale changed
Audience: Graduate

Learning Outcomes: 1. Define basic categories and modes of biosignature production and preservation.
Audience: Both Grad & Undergrad

2. Describe the environmental and ecological attributes that enable biosignature preservation.
Audience: Both Grad & Undergrad

3. Articulate how different microenvironments can be present in an extreme environment (i.e., a salt flat), and how different instruments are required to explore these microenvironments at different scales of observation.
Audience: Both Grad & Undergrad

4. Explain the basic chemical drivers of life that exist in different microenvironments.
Audience: Both Grad & Undergrad

5. Hypothesize planetary and stellar conditions likely to lead to the long-term persistence of life on a planet.
Audience: Both Grad & Undergrad

6. Operate each of the main instruments that compose the payload package of the simulated spacecraft, organized in order of scale: Drone/imaging data (km-m); Outcrop scale detection/field microscope and hand lens (m-dm); Molecular characterization/spectrophotometer (mm-nm); Atomic characterization/XRD (nm-fm).
Audience: Both Grad & Undergrad

7. Formulate an original hypothesis to guide future research based on a synthesis of findings from the field experience with current understandings of the origins, evolution and molecular underpinnings of life and corresponding planetary scale changes.
Audience: Graduate

Learning Outcomes: 1. Recognize the chemical logic and fundamental regulatory principles of central metabolism.
Audience: Undergraduate

2. Describe how the fundamental concepts in metabolism relate to real-world problems in areas such as microbiology, biotechnology, and human health.
Audience: Undergraduate

3. Recognize that the same fundamental principles that help us understand microbial metabolism also apply to higher organisms.
Audience: Undergraduate

4. Describe the interconnected nature of metabolism, where pathways work in concert by feeding, draining, and regulating each other.
Audience: Undergraduate

5. Describe the core mechanisms of energy generation in biology and how they impact the diversity of microbial life.
Audience: Undergraduate

Learning Outcomes: 1. Explain the conceptual design of an experiment.
Audience: Undergraduate

2. Given an experimental question, design and effectively execute an experiment that answers a scientific question.
Audience: Undergraduate

3. Find, and use correctly, information in the primary literature relevant to experiments being carried out.
Audience: Undergraduate

4. Properly and critically interpret data including understanding experimental limitations and controls.
Audience: Undergraduate

5. Effectively communicate their scientific findings through writing as well as present data/results clearly and effectively in a professional manner.
Audience: Undergraduate

6. Take complete, effective and detailed lab notes.
Audience: Undergraduate

Learning Outcomes: 1. Attend all lectures on a diverse range of speakers from the Biotechnology sector and related topics.
Audience: Undergraduate

2. Demonstrate an understanding of lectures though lecture evaluation sheets.
Audience: Undergraduate

3. Choose a current topic in Biotechnology and formulate an opinion paper on the challenges and potential utility.
Audience: Undergraduate

Learning Outcomes: 1. Compare classical and modern microbial genetic approaches and explain how their application advanced knowledge in microbial cellular pathways.
Audience: Both Grad & Undergrad

2. Interpret experimental results and demonstrate how misinterpretation can result in erroneous conclusions.
Audience: Both Grad & Undergrad

3. Effectively communicate in writing and by oral communication a microbial process described in an experimental paper.
Audience: Both Grad & Undergrad

4. Evaluate scientific papers and proposals in terms of potential impact, significance and logistics.
Audience: Both Grad & Undergrad

5. Apply microbial genetics to design experiments to test scientific hypotheses.
Audience: Both Grad & Undergrad

6. Apply microbial genetics to design experiments to test scientific hypotheses, then demonstrate the experimental feasibility and potential pitfalls of the experiment.
Audience: Graduate

Learning Outcomes: 1. Access and evaluate original research literature.
Audience: Undergraduate

2. Demonstrate problem solving practices.
Audience: Undergraduate

3. Identify enzyme mechanisms responsible for transcription, translation, gene regulation, and replication in bacteria.
Audience: Graduate

4. Compare the structural bases for the mechanisms.
Audience: Graduate

5. Evaluate the experiments that led to our understanding of theses mechanisms.
Audience: Graduate

6. Deconstruct how these enzymes respond to nutritional and environmental signals in cells.
Audience: Graduate

7. Outline the evolutionary basis and selection pressure for these mechanisms in vivo.
Audience: Graduate

Learning Outcomes: 1. Describe the instrumentation and analytical approaches commonly used in mass spectrometry-based metabolomics, lipidomics, and metabolic flux analysis studies.
Audience: Both Grad & Undergrad

2. Explain how isotope tracers are used to measure metabolic flux, elucidate metabolic network structure, and investigate pathway thermodynamics.
Audience: Both Grad & Undergrad

3. Critically evaluate primary scientific literature that utilizes metabolomics, lipidomics, or isotope tracer studies as a key research component.
Audience: Both Grad & Undergrad

4. Argue how fundamental concepts in cellular metabolism relate to real-world problems in areas such as microbiology, biotechnology, and human health.
Audience: Both Grad & Undergrad

5. Analyze and interpret published or unpublished metabolomics and lipidomics data to generate biological insights on microbial and/or cellular metabolism.
Audience: Both Grad & Undergrad

6. Analyze and interpret published or unpublished data from isotope-tracer studies to make inferences on pathway activity and metabolic network structure in microbial and/or mammalian cellular systems.
Audience: Both Grad & Undergrad

7. Formulate experimental designs that incorporate metabolomics and isotope tracers to test specific hypothesis related to cellular metabolism.
Audience: Graduate

Learning Outcomes: 1. Demonstrate use of the Unix/Linux-based operating system using command line.
Audience: Both Grad & Undergrad

2. Download and install sequence analysis programs locally on a computer.
Audience: Both Grad & Undergrad

3. Evaluate the outcomes of sequence data analysis and determine if an analysis is statistically relevant and robust.
Audience: Both Grad & Undergrad

4. Code complex and advanced programs in python that not only facilitate pipeline construction, but also more in-depth parsing of tool output.
Audience: Both Grad & Undergrad

5. Utilize bioinformatics tools to enable comparative genomics analysis that extend the standard use of those tools.
Audience: Both Grad & Undergrad

6. Evaluate primary literature and determine what available tools are most appropriate for solving a specific analysis problem.
Audience: Both Grad & Undergrad

7. Utilize advanced parameters in BLAST to facilitate complex comparisons across sequence data types.
Audience: Graduate

8. Demonstrate the ability to compile a program from source code so as to leverage local environmental variables for installation.
Audience: Graduate

Learning Outcomes: 1. Demonstrate proficient use of PyMol software for visualizing 3D structures.
Audience: Both Grad & Undergrad

2. Evaluate the quality of published structural models for biological macromolecules.
Audience: Both Grad & Undergrad

3. Identify common themes in structural biology which are used when addressing structural biology research questions.
Audience: Both Grad & Undergrad

4. Design and deliver a presentation to communicate scientific results to an audience of their peers.
Audience: Graduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

6. Write an honors thesis that contains an abstract, background, a demonstration of research skills, analysis of the research question, and a summary of the impact of the work.
Audience: Undergraduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

6. Write an honors thesis that contains an abstract, background, a demonstration of research skills, analysis of the research question, and a summary of the impact of the work.
Audience: Undergraduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

6. Write a thesis that contextualizes the work, presents the research question, describes the experiments performed to answer the question, and analyzes the results.
Audience: Undergraduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

6. Write a thesis that contextualizes the work, presents the research question, describes the experiments performed to answer the question, and analyzes the results.
Audience: Undergraduate

Learning Outcomes: 1. Investigate a science topic in conjunction with other investigators to develop a deep understanding of a research problem.
Audience: Undergraduate

2. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Undergraduate

3. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Undergraduate

4. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Undergraduate

5. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Undergraduate

Learning Outcomes: 1. Identify a research problem and develop a series of experiments to test a hypothesis related to the problem under investigation.
Audience: Graduate

2. Carry out designed experiments and collect data related to the research problem under investigation.
Audience: Graduate

3. Analyze the results of experiments and use them to test the validity of the developed hypothesis.
Audience: Graduate

4. Communicate the results of investigations via written and/or oral means to an appropriate audience.
Audience: Graduate

Learning Outcomes: 1. Discuss state-of-the-art research in gene expression and regulation
Audience: Graduate

2. Communicate and critically evaluate experimental results
Audience: Graduate