Microbiology Course Catalog
The ecology of major human, plant and animal diseases from the Black Plague to the Irish Potato Blight to AIDS. How microbes, people and other organisms interact in a changing environment, leading to new threats and controls for disease. (Gen.Ed. BS)
Hans Zinnser said, “... infectious disease is merely a disagreeable instance of a widely prevalent tendency of all living creatures to save themselves the bother of building the things they require. The plant does the work with its roots and green leaves. The cow eats the plant. Man eats both of them; and bacteria eat the man....” In the process, these interactions have fundamentally shaped our planet and ourselves. Plagues, outbreaks of diseases, have been a part of the human condition since recorded history and undoubtedly long before. In fact, disease is a part of all life for all organisms. At the same time, human activity, from agriculture to jet travel, interact with microbes and the environment to bring about plagues. Often we think of infectious diseases as the microbes that cause disease. A cold, and the virus that cause it, are thought of as the same thing. But infectious disease really describes an ecological interaction between microscopic organisms and other organisms that they use as a source of energy and nutrients, a pathogen and its host. The honors colloquium is an addendum to Microbiol 140P to further explore diseases and how they have shaped our world, how we attempt to manage them, and how we often inadvertently aid and abet them. Microbiol H140 is a 1 credit weekly discussion of readings taken from recent popular literature and press. Students will be asked to summarize the context of these articles, write a critical synopsis and participate in evaluating these synopses for publication in blog-like reader online.
Not for credit toward major. How cancer and AIDS begin and progress. The roles of individual cells, the immune system, mutations and viruses. How various physical and subtle factors influence one's chances of getting cancer. How to not get AIDS. The principles of vaccine development and why AIDS presents special difficulties. Established and new medical treatments for cancer and AIDS. What cancer and AIDS can teach us about health, healing, disease, living, and dying. (Gen.Ed. BS).
Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 196 – Independent Study. This form is available in the Main Microbiology Office.
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This lab course will cover basic concepts of microbiology with an emphasis on sterile technique, microscopy, isolation and cultivation of microorganisms. Identification of pathogenic organisms, antibiotic susceptibility testing, how pathogens are spread and the detection of microbes in food will be covered. This is a 2 credit course for NON-MAJORS. It is geared for students applying to post-graduate health care programs (physician assistant, nurse practitioner, pharmacy, etc.).
Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 296 – Independent Study. This form is available in the Main Microbiology Office.
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Overview of the microbial world including a survey of the structure, functioning, and diversity of microorganisms. Introduction to the fundamental concepts of microbial physiology, ecology, genetics, and pathogenesis. Chemistry 112 or 250 are strongly encouraged.
This course will introduce Microbiology majors to the extremely diverse and exciting world of microorganisms. The course begins with describing the basics of microorganisms: structure and function, metabolic pathways, physiology, and genetics. These topics are used as a base to discuss more complex microbial systems we study in environmental microbiology, medical microbiology, and applied biotechnology. We will explore the wonderfully extensive diversity of microbes and discuss this diversity within the context of evolution and what `species? means in microbiology. We will explore the interactions between microbes and humans, including the influence of microbiota on the health of humans, plants, animals and the environment. We will also discuss historical and current innovations where microbes have been used to make great advances in research and biotechnology.
This class is an introduction to microorganisms, concentrating on laboratory methods used to study a wide variety of microbes. You will learn basic microbiological methods, including sterile technique, enrichment and isolation, microscopy and preservation of cultures. Once these techniques are learned, you will use them to investigate a variety of different topics, including bacterial motility, endospore formation, oxygen requirements, microbial growth, quorum sensing, antibiotic production, biofilms, and bacteria important in human and veterinary health care. You will explore the diversity of microorganisms by studying fungi and viruses, as well as by isolation organisms from a wide variety of environmental sources. You will use a lab notebook and written discussions and summaries to communicate your experimental results and to link them to fundamental concepts in microbiology. This course will complement and reinforce topics taught in MICROBIO 311.
The main objective of this course is to introduce students to basic concepts of microbial genetics. The course is intended to provide students with a broad exposure to several fundamental aspects of genetics through lectures, in-class discussion, assigned textbook readings, and study groups. Topics covered in this course will include DNA replication and repair, cellular structure and function, transcription, translation, protein secretion and degradation, gene regulation, genetic manipulation and analysis, the transfer of genetic material, and the use of mutations to dissect regulatory networks. This course will provide students with a solid foundation to continue studies in microbiology and related disciplines.
Satisfies the Junior Year Writing requirement. Students develop their writing skills while completing a series of short assignments. Each participant will identify a biological topic of their choice to research and write about during the semester.
An introduction to the methodology fundamental to the practice of modern agricultural biotechnology. Techniques covered include establishment and manipulation of plant and animal cell cultures, preparation and analysis of DNA and RNA, production of recombinant protein expression vectors, isolation and characterization of proteins, and use of immunoassays. Major emphasis on the student's performance of laboratory exercises which provide direct experience with each of the techniques mentioned.
A small group tutorial discussion: the role science in society combined with discussions of contemporary societal issues involving microbiology such as emerging infectious diseases and microbial biotechnology.
Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 396 – Independent Study. This form is available in the Main Microbiology Office.
Program participants will undertake an honors section of independent study (research) under the direction of their research sponsor. Beyond the normal expectations for independent study students in the department, the honors section may include preparation of a review of the scientific literature in the field of the research project. (File an Honors Independent Study Contract with Commonwealth College; form may be found on the ComCol website.)
Practicum credits may be earned by undergraduates participating as undergraduate teaching assistants in laboratory and lecture courses. Students interested in being an undergraduate TA should contact the individual instructor for the course. Applications for laboratory TA’s are available at registration time in the Main Microbiology Office. A Microbiology Course Override Form is required for registration in Microbiology 398 – Practicum. This form is available in the Main Microbiology Office.
Advanced lecture course supported by group discussions designed to introduce upper undergraduate students to ranges of microbial life and evolutionary mechanisms to develop and sustain them. Emphasized are linkages between microbial ecology, diversity, and evolution.
Bioconversion of materials is part of the natural cycle for all bio-based materials as well as a key factor in bioenergy production. Biodegradation processes including those employed by fungal, bacterial, insect and marine organisms relative to carbon and nutrient cycling and the production of feedstocks for bioenergy and biomaterials are important to maintaining the ecological balance on earth, and for the development of a sustainable society with renewable and bio-based materials. The course examines aspects of natural degradative systems, and how biomimicry of these systems can be harnessed for sustainable energy and product production. Deterioration and protection of biomaterials including wood, bamboo, and historic materials is also included.
Infectious disease has many effects on the development of society, and likewise, human interactions affect the development of disease. Emerging and reemerging infectious disease is a contemporary global issue of great concern. We live in a time with very militant anti-vaccine movements and disease etiology denialists. This course examines these interactions with a focus on the role of race, class, and economic status in the development of epidemics. The course also covers the germ theory, disease history and ecology, microbial pathogenesis and the immune response, historic plagues, and the biological, environmental, population and social changes that contribute to disease emergence.
To provide knowledge on the various physiological and metabolic features of prokaryotic cells and the underlying biochemical principles that explain them, and to understand factors which explain complex microbial diversity patterns in the environment.
Nearly 70% of Americans are obese or overweight. The distribution of the epidemic correlates strongly with poverty and access to high quality food. Students in this class will engage in directed literature research and discussion. Topics will start by examining risks factors for obesity including genetic, macro genetic/microbiome, societal (commercial, race, poverty). The goal of this course is to examine the obesity pandemic using a multidisciplinary approach with the aim of identifying any evidence for effective approaches to changing obesity rates. Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.
HIV rates in U.S. poverty areas rival those found in Haiti, Burundi, Ethiopia, and Angola. HIV prevalence in high-poverty neighborhoods is more than double that of the nation overall. Within high-poverty neighborhoods, prevalence among people living below the poverty line was double that of those living above it. Blacks disproportionately bear the brunt of the HIV epidemic in the US accounting for over 48% of all new cases of the disease while representing only 12% of the population. The HIV epidemic that was once thought to be a declining problem is now threatening to destroy not only the progress previously made, but also the health, well-being and potential of men and women of all races in poverty areas across the United States. Some important questions therefore need to be answered: Is race, poverty or both the driver of HIV in these communities? What should be done to stem the tide of new HIV infections in these areas of our society? This course satisfies one of the three modules required for the Integrative Experience for BA-MicBio and BS-MicBio majors.
Over 70% of the Earth’s surface is covered with the oceans, and nearly all of the life within the
ocean is microscopic. Some of these microbes are photosynthetic and form most of the base of the marine food web. These in turn are consumed by other small creatures that eventually provide food for the larger animals in the sea. Bacteria are responsible for maintaining certain chemical balances in the oceans, and themselves are food for other microbes. Understanding how life is sustained in our oceans is vital for coastal human populations that rely on the sea for food. Other people turn to marine microbes for new biotechnologies, or hope that by understanding them we might understand our own planet’s climate history and how marine microbes will respond to global warming and ocean acidification. Satisfies one of the three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.
In this class, we will discuss current events in the world related to viral outbreaks. We will discuss typical practices used by the media to cover viral-induced epidemics and reflect on how societal and political factors are influencing our own comprehension and perspective on potential pandemics.
Students will engage in meaningful literature research and dialogue about whether organic standards are meeting the needs of both environmental and community sustainability. We will also consider the benefits of sustainable agriculture, both in the sense of conservation of land and soil as limiting natural resources, as well as the sense of community with the farm and food production as the center of family and local community life. In exploring these wide-ranging issues, students will have the opportunity to reflect on and integrate their Gen Ed learning experience from various courses as well as practice Gen Ed learning objectives at a more advanced level as they seek meaningful solutions to complex and ever evolving societal problems. Students will work in small groups to explore these solutions allowing them to participate in shared learning experiences as they apply prior knowledge from various Gen Ed courses and social experiences to solve challenging real-world problems. Satisfies one of three required modules of the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.
The vast majority of Earth's biodiversity is microbial. Microorganisms are directly involved in the ecosystem services on which all of life depends. They interact intimately with other organisms and yet we know much less about their biodiversity than we do for plants and animals. Our lack of understanding of the interactions and feedbacks of microbial biodiversity is troubling, given the high rates of environmental change that the Earth is currently experiencing, including man-made global climate change. Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.
Neglected tropical diseases (NTDs) are a set of infectious diseases arising from a diverse group of parasitic worms, bacteria, and vector-borne protozoa that affect an estimated 1.4 billion people worldwide. These diseases affect the world’s most vulnerable populations, almost exclusively poor and powerless people living in rural areas and urban slums of low-income countries. NTDs coexist with poverty because they thrive where access to clean water and sanitation are limited and people live without protection from insects that transmit disease. They also contribute to poverty since they can impair intellectual development in children, reduce school enrollment, and hinder economic productivity by limiting the ability of infected individuals to work. Current control efforts focus primarily on mass drug administration (MDA) to treat the seven most common NTDs and has become one of the most cost effective global health programs to treat multiple diseases at once, in large part because major pharmaceutical companies are donating the needed medicines for free. End 7 is a global campaign to deworm the world and bring an end to 7 of the NTDs. Important questions exist related to this global health strategy: what might be the long-term benefits (and possible detriments) to a sustained global deworming effort? What other measures should be implemented in combination with MDA for sustained control? Satisfies one of the three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.
In this course, we will explore the field of quorum sensing and cellular communication, focusing on strategies microbes have developed to sense neighboring cells and regulate biological processes. A specific emphasis will be placed on processes of biomedical importance and environmental relevance as well as effective strategies to manipulate of alter these processes to benefit mankind. Students will develop two presentations. Satisfies one of the three required modules for the Integrative Experience requirement for BS-MicBio majors.In this course, we will explore the field of quorum sensing and cellular communication, focusing on strategies microbes have developed to sense neighboring cells and regulate biological processes. A specific emphasis will be placed on processes of biomedical importance and environmental relevance as well as effective strategies to manipulate of alter these processes to benefit mankind. Students will develop two presentations. Satisfies one of the three required modules for the Integrative Experience requirement for BS-MicBio majors.
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The honors project consists of completing and presenting the original research undertaken. The presentation will include but not be limited to an abstract suitable for publication and a research summary in the form of a poster appropriate for presentation at a scientific meeting. A Departmental Poster Presentation Session will be held at the end of the semester. Honors students are also encouraged to present their results at local or national scientific meetings. Students must also complete the Capstone Manuscript requirement of Commonwealth College. File an Independent Capstone Contract with Commonwealth College.
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Original microbiological research carried out under the direction of the research sponsor. The honors student will take an active role in the experimental design of the research project. While it is not expected that undergraduate honors student will be fully capable of initiating original research on their own it is hoped that participation in the design and implementation of a research project will help the student acquire the necessary skills to carry out independent research. Independent Capstone Contract and Research Proposal with Commonwealth College; form and proposal information may be found on the ComCol website.
This class concentrates on bacteria that are known to cause disease in humans and animals. We will begin by exploring the concept of virulence factors and how they allow organisms to be more effective pathogens. Pathogenesis mechanisms of immune evasion, attachment and invasion of bacteria to host cells, and the production of toxins will be explored through a variety of molecular, protein, and whole cells assays. After covering virulence factor mechanisms, we explore many of the major disease-causing groups of bacteria. How these organisms initiate disease will be covered, as well as clinical lab identification strategies, and how clinical specimens are processed. The course ends with students using identification tests learned in lab to identify unknown bacteria.
The demand for authentic research experience at UMass greatly outstrips supply. One way to bridge this gap is to offer course-based undergraduate research experiences, or CUREs. Microbio 565 is a CURE that focuses on the cell envelope of mycobacteria. These organisms are technically Gram-positive but have an unusual, complex envelope that in some ways is more reminiscent of Gram-negatives. They grow weirdly, expanding their envelope preferentially from one end of the cell (instead of evenly along its entire length á la Escherichia coli and other well-studied species). In Fall 2018 we will build on work done by Ph.D. student Emily Melzer with the help of then-undergraduate Caralyn Sein. They have shown that the protein DivIVA initiates and stabilizes polar growth in Mycobacterium smegmatis by organizing cell wall peptidoglycan synthesis. We will repeat some of their experiments, then extend this work by asking 1) whether DivIVA organizes peptidoglycan assembly by localizing MurG, a cytoplasmic enzyme required for precursor synthesis and 2) what part(s) of the DivIVA protein contribute to its function. Guided by the literature, in the last, post-Thanksgiving third of the class, we will perform experiments of the students’ choosing. In Microbio 565 we will use genetic depletion and site-directed mutagenesis along with methods from cell and chemical biology to address a real research question. Neither the professor nor the TA knows the answer! This means that some things may not work as hypothesized or may not work at all. The class will puzzle together to figure out whether the hypothesis needs adjusting or whether something went wrong with the execution of the experiment. If the latter, we map out a troubleshooting plan. Besides gaining hands-on experience with modern genetic techniques, students learn how to learn from failure, an essential skill in bench science.
Molecular biology of animal viruses and viral genetic systems; viral disease processes. Emphasis on polio virus, influenza, herpes viruses, the DNA tumor viruses. Prerequisite: background in cell biology, genetics, or biochemistry. Biochem 420 recommended.
This is an advanced elective course for junior/senior students and is designed to provide students with a basic understanding of modern parasitology. Parasites are still an important threat to our global health and economy, and represent an important branch of infectious diseases. It has been stated that there are more kinds of parasites than free-living animals and plants, providing a wealth of biological diversity to study. Once thought of as strange and bizarre, parasites now serve as model organisms in which to study basic biological principles. The course covers a plethora of organisms and a multitude of disciplines. Our discussions will focus primarily on protozoan and metazoan parasites of major medical/veterinary consequence. Topics covered will include basic principles of parasitology, life cycles, host-parasite interactions, epidemiology, and medical treatments. The basic biology, biochemistry and genetics of selected parasites will also be discussed.
This computer laboratory course is intended to give students technical, computational and practical microbial experience in sequencing and analyzing genomes. We will focus on bacterial genomes from recently isolated bacteria, so there is a possibility of discovery of new microbial diversity. By the end of this course, students should be able to describe the structure and function of a genome; write and edit unix- and R-based coee; use computational tools de novo assemble genomes, predict gene presence and function; test a hypothesis using gDNA data; and tell a story about an unknown organism using only the genome sequence, including generating new hypotheses.
Research project under direction of a faculty member. By arrangement.
Examination of all aspects related to the third Domain of life, the Archaea. New and recent papers on the physiology, ecology, biotechnological applications and evolution of archaea are discussed, as well as papers on the application of this information to biogeochemistry, early Earth history, and the search for life beyond Earth. A basic understanding of microbiology is recommended.
How Microorganisms interact with each other and with their environment. Microbial distribution and activities in natural systems, and their importance to ecosystem function and environmental quality. Extreme habitats; habitat-specific forces; microbial activity; microbial transformations and their impact on different environments; species diversity, detection, and control of microorganisms; and associations with higher organisms. Each basic principle followed by applied and environmental case studies. Modern techniques of environmental microbiology graduate students write an independent research proposal.
This course focuses on parasites - pathogens of neglected tropical diseases. The pathogens covered in this course include the ones that cause malaria, African sleeping sickness, river blindness, Chaga's disease, kala-azar, guinea-worm disease, among other tropical diseases. Students will learn the basic principles of parasitology, life cycles of the parasite pathogens, epidemiology, host-parasite interactions, drug treatments and vector control programs, along with information on the basic biology, biochemistry, and genetics of selected parasites. The course is primarily lecture-based, but includes dedicated time for discussion and student-led journal clubs: student's participation is highly encouraged.
The main aspects of bacterial growth, including energy metabolism, biosynthesis of macromolecular precursor materials and their assembly into macromolecules, and the integration of these processes by various regulatory mechanisms. Emphasis on the isolation of mutant bacteria blocked in key cellular functions and on global control systems governing the adaptation of bacteria to different environmental conditions. Prerequisite: general background in microbiology and biochemistry.
The Applied Molecular Biotechnology Laboratory (AMBL) is a requisite course for the MS concentration in Applied Molecular Biology. AMBL combines hands on laboratory training with independent research experience to train students in the latest techniques and concepts of molecular biology and biochemistry. Recombinant DNA technology is the primary focus of the first semester. Topics covered include nucleic acid isolation, genomics, quantitative PCR and RT-PCR, southern and northern blot analysis, and computational biological analyses. Protein expression, purification, and detection are the focus of the second semester. Topics covered include prokaryotic and eukaryotic protein expression systems, column chromatography, proteomics, western blot analysis, enzymatic assay, and microscopic analysis. Throughout the year-long course, students will develop critical thinking skills and gain valuable research experience, all while working on real world problems and preparing for careers in the biotechnology and pharmaceutical industries.
Fundamental and advanced topics in the molecular genetics of micro-organisms covered through lecture and discussion of the literature. Topics vary depending on the instructor. Prerequisites: basic coursework in biochemistry and genetics.
Research project under direction of a faculty member. By arrangement.
A 10 week laboratory work participation. It will occur after the second semester of campus classes (summer). Students are required to actively work in a research or a production laboratory to gain hands on work experience. All work should include some responsibility. It is preferred that students work on a research projects. This can be fulfilled by a traditional internship at a company (paid), at an academic institution (unpaid) or by a full time career based job. Acceptable performance is evaluated by the supervising scientist. A final grade will be assigned by the program director.
Reports and discussion of pertinent literature and research. Required of all microbiology graduate majors each semester in residence. More information.
Research project under direction of a faculty member. By arrangement.
Presentations an discussions of important microbial ecology research papers from the current literature. Fundamental questions in microbial ecology include: what are the drivers of community assembly? How do microbial functions scale? How does mass flow between species, and what factors regulate this? How can we predict or engineer community function? We will discuss microbial communities from a variety of natural and manufactured environments, with emphasis on new strategies to test hypothesis-driven microbial ecology research.
Critical review of the scientific literature is an integral part of scientific research, and both students and faculty benefit greatly from the discussions originating from these reviews. This well organized journal club entails critical review of the scientific literature deemed beneficial and relevant to both students and immunology faculty. Students make one presentation of a journal article from a reputable immunology-related journal with the advice and final approval from an immunology faculty member. Topics may include, but are not limited to molecular immunology, programmed cell death, virus immunology, infection and defense, cellular immunology and receptor-mediated signaling.
Explores through current primary literature some of the complex processes used by microbial pathogens to establish themselves in a host and to gain nutrients, subsequently causing host cell damage and disease, and to evade the host's defense. Includes discussion of the modern molecular biology, genetics, and biochemistry tools to study these processes.