In this class we will learn about how the process of DNA replication is regulated throughout the cell cycle and what happens when DNA replication goes awry. How does the cell know when and where to begin replicating its DNA? How does a cell prevent its DNA from being replicated more than once? How does damaged DNA cause the cell to arrest DNA replication until that damage has been repaired? And how is the duplication of the genome coordinated with other essential processes? We will examine both classical and current papers from the scientific literature to provide answers to these questions and to gain insights into how biologists have approached such problems. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.

This template course was developed from generally available open educational resources (OER) in use at multiple institutions, drawing mostly from a primary work published by OpenStax College Concepts of Biology, but also including additional open works from various sources as noted in attributions on each page of materials.

This material is labwork meant to be used in conjunction with the Candela "Biology II" course.

This course will cover a range of diverse areas of microbiology, including virology, bacteriology, and even applied microbiology. This course will focus on the medical aspects of microbiology, as medical research has been the primary motivator in microbiology research. Upon successful completion of this course, the student will be able to: explain how organisms are classified using taxonomy, focusing on the domains Archaea, Bacteria, and Eukarya; describe the chemical building blocks and metabolic processes important to sustain microbial life; identify the major principles of microbiology and describe the relationship between microbes and other living organisms; discuss pathogenic microbes and their epidemiology; differentiate between microorganisms based on their shape, size, arrangement, staining, and culture characteristics; outline antimicrobial methods including antibiotic use; explain how the human body protects itself; list uses for microbiology in food and beverage preparation and industry. (Biology 307)

This Module is a study of organisms that cannot be seen with the unaided eye unless with the help of a microscope. They are referred to as microorganisms. More commonly they are called microbes. These are bacteria, viruses, protozoa and fungi. Although viruses are strictly not organisms, they too will be discussed under the same title for convenience. Mycology which is the study of fungi includes some groups like the mushrooms with macroscopic fruiting structures, which appear seasonally above the ground. The study of microbes is called microbiology. The module starts with the history of microbiology; the discovery of microbes and the development of sterile culture techniques, and goes on to explore the diversity of microbes, their major biological characteristics and economic importance. Examples of laboratory exercises meant to familiarise the students with microbiological techniques such as, media preparation, isolation, identification, culture maintenance, growth measurements, staining techniques and preservation are presented wherever applicable.

Watson and Crick noted that the size of a viral genome was insufficient to encode a protein large enough to encapsidate it and reasoned, therefore that a virus shell must be composed of multiple, but identical subunits. Today, high resolution structures of virus capsids reveal the basis of this genetic economy as a highly symmetrical structure, much like a geodesic dome composed of protein subunits. Crystallographic structures and cryo-electron microscopy reconstructions combined with molecular data are beginning to reveal how these nano-structures are built. Topics covered in the course will include basic principles of virus structure and symmetry, capsid assembly, strategies for enclosing nucleic acid, proteins involved in entry and exit, and the life cycles of well understood pathogens such as HIV, influenza, polio, and Herpes. A review of cutting edge structural methods is also covered.

This course explores the specific ways by which microbes defeat our immune system and the molecular mechanisms that are under attack (phagocytosis, the ubiquitin/proteasome pathway, MHC I/II antigen presentation). Through our discussion and dissection of the primary research literature, we will explore aspects of host-pathogen interactions. We will particularly emphasize the experimental techniques used in the field and how to read and understand research data. Technological advances in the fight against microbes will also be discussed, with specific examples. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.