Courses

All courses carry 3 credits unless otherwise specified.

542 Immunology Laboratory
This laboratory course is designed to help students become familiar with and proficient in the performance of protocols in cellular immunology, immunochemistry and clinical serology. These experiments are designed to introduce the student to the fundamentals of laboratory work in the field of immunology. The laboratory experience is designed to closely reflect that of a modern immunology lab. Students will also have relevant lectures in these topic areas to assist in learning the principles governing each of these important protocols. This will be accomplished over the course of the semester by antibody isolation and purification using salt precipitation, ion exchange chromatography and dialysis. Purified IgG antibody molecules will be cleaved by specific enzymes in order to study the protein biochemistry of antibodies, and size exclusion or molecular sieving column chromatography will be used to isolate fragments for further analysis. Students will become proficient in the use of spectrophotometers, perform SDS-PAGE, Western blot analysis, immunoprecipitation, enzyme-linked immunosorbent assays, and immunofluorescence staining. The student will also perform comparative proteomics using immunology techniques as well as classic serological assays including the immunodiffusion (Ouchterlony technique) and blood typing. Anatomy of the lymphatic system will be explored using a mouse model. Specifically, student will perform mouse dissection, lymph node examination, and isolation of lymphocytes from the mouse spleen and thymus. In addition students will perform assays to determine protein concentration, and solidify their skills in light and fluorescence microscopy. Finally, the student will be exposed to cellular immunology, including differential leukocyte counts, mammalian histology and immunohistopathology, identification and enumeration of mouse and human leukocytes and Flow Cytometric analysis of lymphocyte subpopulations. We will take a field trip to Baystate Medical Center to visit the transfusion medicine and immunology departments where students will get the opportunity to observe many of the protocols they learned in class in use within a clinical setting and have ample opportunity to interact with the director of transfusion medicine and a transfusion medicine education specialist. Students will be evaluated via quizzes, class participation, competence at the lab bench, demonstrated independence and critical thinking along with lab reports written in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals format with an IMRAD structure, ready to be published.

552 Pathogenic Bacteriology
Laboratory procedures in clinical and diagnostic bacteriology including: i) cultural and physiological characteristics of the pathogenic bacteria; ii) recommended procedures for the cultivation of both the common and rare pathogens isolated from clinical material; iii) conventional and rapid biochemical methods for detection and identification of medically important bacteria; iv) serological procedures on microorganisms of prime medical concern; and v) prescribed tests for the susceptibility of bacteria to antibiotics and antimetabolites.

557 Advanced Topics in Biotechnology
This course covers a detailed analysis of the molecular mechanisms that control the maintenance, expression, and evolution of prokaryotic and eukaryotic genomes. The topics covered in lectures and readings of relevant literature include DNA replication, transcription, gene regulation, genetic recombination, and translation. Class format will include lectures, journal clubs, presentations and group discussions.

562 Environmental Biotechnology
Environmental Biotechnology is a laboratory course supported by lectures and demonstrations. This advanced course is designed to introduce graduate level students to traditional and molecular methods strategically applied to problems related to microbial biotechnology and environmental microbiology. Course topics cover a wide range of subjects from the diversity of microbial life to biodegradation. Seven general areas are emphasized: (1) Statistical sampling and chemical and physical site characterization, (2) biomass determination and cell counts, (3) enrichment techniques, (4) microbial activity measurements, (5) single cell detection in situ, (6) sequence analysis and phylogenetic analysis followed by probe design, and (7) other modern techniques of environmental microbiology.

565 Laboratory in Molecular Genetics
Methodology and principles of modern molecular genetics. Microbial genetics combining classical techniques with bacteriophages and bacteria with modern PCR and recombinant DNA experiments. Introduction to genomic, structural analysis using computer methods and fluorescence microscopy in bacteria. Designed to help students learn techniques and analyze results. Credit, 4

570 Virology
Biology and Molecular biology of viral systems and viral disease processes. Emphasis on diversity of molecular mechanisms of viral replication; viral disease processes, treatment and prevention including polio virus, influenza, rabies, herpes viruses, and hepadna viruses. Prerequisite: background in cell biology, genetics, or biochemistry. This course is taught in Team Based Learning (TBL) format with weekly team assignments.

597B Archaea Journal Club
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. Credit, 1

597E Environmental Microbiology
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.

597N Parasitology & Neglected Tropical Diseases
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.

597Z Medical Zoology Journal Club
This is a literature review style course for advanced undergraduate and graduate students interested in zoonotic disease. Zoonotic diseases are those whose transmission cycles involve non-human animal hosts. Topics within this large framework vary with interests of enrollees, but there tends to be a focus on vector-borne disease including those most often associated with ticks and mosquitoes. Medical Zoology is a transdisciplinary approach to understand disease by incorporating broad disciplinary background (eg. entomology, physiology, genetics, ecology, etc.). The course meets once per week and each student is expected to choose and lead discussion on peer reviewed paper (or set of papers). Aims are to build students’ capacity for searching sources and critically evaluating science literature.

680 Microbial Physiology
Main aspects of microbial growth, energy and biosynthesis pathways, metabolic regulation and integration of pathways into a coherent system. Emphasis on physiological diversity, global control systems governing the adaptation of microorganisms to different environmental conditions, and emerging methodologies. Prerequisite: general background in microbiology and biochemistry.

681S/681F Applied Molecular Biotechnology Lab
This lab 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. Available only to students accepted to the AMB program. Prerequisites: A bachelor's degree from an accredited four year college or university. Candidates must have demonstrated success in several of the following areas during their undergraduate studies including: genetics, biology, biochemistry, molecular biology, cell biology, calculus, organic chemistry, physics, and statistics. Credit, 5

685 Concepts in Molecular Genetics
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.

696 Independent Study
Research under direction of a faculty member. Credit, 1-8

699 Master’s Thesis
Credit, 1-9

791A Departmental Seminar
Reports and discussion of pertinent literature and research. Required of all microbiology graduate majors each semester in residence. Credit, 1

796 Independent Study
Research under direction of a faculty member. Credit, 1-8

797E Microbial Ecology Journal Club
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. Credit, 1

797J Immunology Journal Club
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 include molecular immunology, programmed cell death, virus immunology, infection and defense, cellular immunology and receptor-mediated signaling. Credit, 1

797P Molecular Mechanisms in Pathogenesis
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. Credit, 1

899 Doctoral Dissertation
Credit, 18