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Fall 2015 Courses

Biology 001 Environment Preservation & Improvement.
(Cross listed as ENV 0091)
Biology 1 is a readings-based seminar that treats current ecological issues as they relate to preserving and improving the environment. This year’s topics are drawn from readings in Frontiers in Ecology and the Environment, a new journal that provides timely and exciting translations of the best environmental science for use by scientists, the science media, the corporate world and political decision makers. Examples of topics include mapping urban growth from space, modern sustainable agriculture, invasive species, climate and conservation biology of whales, and wildlife medicine. Students must attend the first day of class. This course does not count towards the biology major.
Prerequisites: Sophomore standing and Bio 2 or Bio 7 or Bio 10 or Bio 13 or Bio 14.
Dr. Ellmore
Block 6: Tuesday 1:30 – 4:00pm.

Biology 004 Gross Anatomy
(Cross listed as Occupational Therapy 102).
Call Boston School of Occupational Therapy (617-627-5720) for information about this course.

Biology 007 Environmental Biology
(Cross listed as Environmental Studies 007)
A survey of biodiversity conservation, humans and their interface with the environment, and sustainability from both ecosystem and human perspectives.
Drs. Reed & Orians

Block C: T-W-F, 9:30 – 10:20AM.
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Biology 009 Physiology
(Cross listed as Occupational Therapy 101).
Call Boston School of Occupational Therapy (627-5720) for information about this course.

Biology 011 Kinesiology
(Cross listed as Occupational therapy 104)
Call Boston School of Occupational Therapy (627-5720) for information about this course.

Biology 13-01 Cells and Organisms with Lab.
An introductory course primarily for prospective biology majors. This course must be taken with the lab -- enroll in one of the laboratories in Biology 13L A-N below. General biological principles and widely used methods related to current advances in biochemistry, cell and molecular biology, genetics, development and biomedical sciences. Two lectures per week. Four exams + final.
Dr. Koegel
Tues. & Thurs. 10:30 – 11:45am.
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Textbook information >

Biology 13-02 Cells and Organisms with Lab.
An introductory course primarily for prospective biology majors. This course must be taken with the lab -- enroll in one of the laboratories in Biology 13L A-N below. General biological principles and widely used methods related to current advances in biochemistry, cell and molecular biology, genetics, development and biomedical sciences. Two lectures per week. Four exams + final.
Dr. Koegel
Tues. & Thurs. 12:00 – 1:15pm.
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Textbook information >

Biology 13L Laboratory A - N.
Members of the department. This is the laboratory component to Bio. 13L, which meets once every week. Laboratory exercises are designed to reinforce lecture material as well as to present new topics. A good initial exposure to ways of thinking about and working with living organisms. Homework assignments will emphasize scientific writing and data presentation. NOTE: Turnitin.com will be used to monitor originality of assignments.

Barnum 200: Barnum 216:
Lab A M 1:30-4:30 Lab B M 1:30-4:30
Lab C T 1:30-4:30 Lab D T 1:30-4:30
Lab E W 1:30-4:30 Lab F W 1:30-4:30
Lab G Th 1:30-4:30 Lab H Th 1:30-4:30
Lab I M 6:00-9:00 Lab J M 6:00-9:00
Lab K T 6:00-9:00 Lab L T 6:00-9:00
Lab M W 6:00-9:00 Lab N W 6:00-9:00

Optional Recitation: Block Arr: M 4:40-5:30PM.

Biology 40 Bioinformatics.
(Cross listed as Comp 7)
A hands-on introductory course in bioinformatics for students with little or no computer science background. Basic programming skills for data manipulation and analysis. Methods and applications of online tools for sequence alignment, molecular phylogeny, gene expression data analysis, and linking molecular variation to disease.
Prerequisite: Biology 41 or BME 62 or equivalent
Dr. Slonim
Monday & Wednesday, 10:30 – 11:45.

Biology 41 General Genetics
Concepts of classical and molecular genetics. A knowledge of basic genetics and cell structure as covered in Bio 13 is essential for Bio 41 students. Grading is based on two tests and an exam (the exam will be at the assigned final exam time), on-line quizzes, and participation in the mandatory recitation.
Prerequisites: Bio 13
Dr. Kate Mirkin
Block – H+TTh: Tuesday & Thursday 1:30-2:45. Mandatory Recitation you must sign up for one: Block K: Wed 4:30-5:20pm. Block I: Monday 3 – 3:50. Block J: Tues 4:30 – 5:20. Wed 3 – 3:50.
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Biology 49-A Experiments in Physiology.
How do animals work? This sequence of laboratory experiments examines physiology at cellular, tissue and organismal levels with an emphasis on hypothesis formation, data analysis and reporting.
Prerequisite is Biology 14 & sophomore standing or equivalent.
Drs. Trimmer & Tytell
Block ARR: Lab - Monday 1:30-5:00PM, Barnum 001; Recitation: Block L: Thurs. 4:30-5:25PM.

Biology 49-B Experiments in Physiology.

How do animals work? This sequence of laboratory experiments examines physiology at cellular, tissue and organismal levels with an emphasis on hypothesis formation, data analysis and reporting.
Prerequisite is Biology 14 & sophomore standing or equivalent.
Drs. Trimmer & Tytell
Block ARR: Lab - Tuesday 1:30-5:00PM, Barnum 001; Recitation: Block L: Thurs. 4:30-5:25PM.
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Biology 51A Experiments in Ecology.
Introduction to ecological research. Emphasis on acquiring skills in taxonomic identification, sampling techniques, hypothesis testing and experimental design, data analysis and interpretation, oral and written communication. Opportunity for student-designed group research projects on ecological questions. One laboratory session per week plus one discussion period. Prerequisites: Biology 14 or equivalent & sophomore standing.
Drs. Pechenik, Ellmore & Lewis
Block ARR: Lab - Wednesday 1:30 – 5:00PM Barnum 208; Recitation -Tuesday 4:30-5:20PM.

Biology 51B Experiments in Ecology.
Introduction to ecological research. Emphasis on acquiring skills in taxonomic identification, sampling techniques, hypothesis testing and experimental design, data analysis and interpretation, oral and written communication. Opportunity for student-designed group research projects on ecological questions. One laboratory session per week plus one discussion period.
Prerequisites
: Biology 14 or equivalent & sophomore standing.
Drs. Pechenik, Ellmore & Chew
Block ARR: Lab - Thursday 1:30 – 5:00PM. Barnum 208; Recitation - Tuesday 4:30-5:20PM.

Biology 54 Molecular Genetics Projects Lab
A discovery-based research experience in the field of molecular genetics, taught at the introductory level. Students will each carry out a related independent research project using modern techniques in genetics and molecular biology to discover gene function, identify proteins that play a role in maintaining genome stability, and develop testable hypotheses. Techniques used will include genetic assays, PCR, gene knockouts, and phenotype analysis.
Prerequisite: Bio 13. The course is appropriate for sophomores and juniors with no prior laboratory experience.
Dr. Freudenreich
Lab – Monday 1:30-4:00 PM, Barnum 208; Recitation Friday 2:30-3:20, Barnum 208
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Biology 61 Biology of Aging.
An introduction to concepts relevant to the biology of aging. Focus on molecular, cellular, and physiological changes that occur during the aging process in humans and other organisms. Major topics include theories of aging, genetic regulation of longevity in model systems, and therapeutic modulation of the aging process. (Group A)
Prerequisites: Bio13 and Bio14 or their equivalent, or consent.
Dr. McVey
Block D+: Tuesday & Thursday, 10:30 – 11:45.
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Biology 75 Comparative Vertebrate Physiology.
A comparative study of vertebrate function. Physiology of selected systems, including circulation, excretion, respiration, temperature regulation and metabolism. Emphasis on physiological adaptations to the environment. Two lectures. (Group B)
Prerequisites: Biology 13/14 or equivalent.
Dr. Bernheim
Block G+: Monday & Wednesday, 1:30-2:45.
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Biology 93 Introduction to Research.
At least 10 hours per week of guided laboratory research, generally including one hour of consultation or seminar with the research sponsor, and a research paper. Details of the individual project to be arranged with the research sponsor. Provides students with an opportunity to participate in biological research - usually at the Tufts campus in Medford or Boston, but sometimes at other institutions by special arrangement. Cannot be counted as one of the eight graded courses required for a biology major. Pass/Fail grading.
Additional Information >

Biology 103 Developmental Biology
Concepts of animal developmental biology with emphasis on the molecular events underlying the morphological changes that occur going from egg to adult. Examples drawn from several phyla will illustrate developmental mechanisms, patterns of gene expression and gene regulatory networks involved in gametogenesis, fertilization, cell differentiation, cell signaling, cell-cell interactions and organ formation. Topics include issues of human cloning, birth defects, stem cell research, gene therapy, assisted reproduction technologies and evolutionary developmental biology. (Group A)
Prerequisite: Biology 41 or 46 or consent.
Dr. Ernst
Block - C: T-W-F 9:30-10:20.
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Biology 104 Immunology.
Concepts of modern immunology and their importance in biology. Topics include humoral and cellular immune responses, antibody structure and biosynthesis, antigen-antibody interactions, cellular immunology, immunological tolerance, and tumor immunology. (Group A)
Prerequisite: Biology 41 or equivalent.
Dr. Bernheim
Block – J+: Tues. & Thurs 3:00-4:15.
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Biology 110 Endocrinology.
A comprehensive introduction to the chemical and physiological principles of hormonal integration in vertebrates. Topics include: endocrine regulation of metabolism, growth and development, reproduction, neural functions, mineral and water balance, behavior and nutrition. (Group B)
Prerequisites: Biology 13 and 14 or equivalent.
Dr. Romero
Block E+: Mon. & Wed. 10:30-11:45.
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Biology 132 Biostatistics.
Learning how to describe and interpret experimental results and observations is a critical skill in many disciplines. In this course, students will learn statistical methods for summarizing and analyzing experimental data. Topics include descriptive statistics, experimental design, probability, parameter estimation, inference, correlation, regression, analysis of variance, and nonparametric methods. Note: This course is aimed at providing data analysis tools for any students conducting or planning independent research projects in Biology.
Prerequisites: Biology 13 and 14 and one additional Biology course above Bio 14.
Dr. Lewis
Block D+: Tues. & Th 10:30-11:45.
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Biology 142 Population and Community Ecology.
(Cross-listed as Environmental Studies 142.)
Introduction to population dynamics (population structure and growth), species interactions (predator-prey, competition, mutualism), and community structure, adaptations to the physical environment, patterns and processes governing the world’s biomes. (Group C).
Prerequisites: Biology 13 and 14 or equivalent, or permission of instructor.
Dr. Chew
Block W – F: E+. Wednesday & Friday 10:30-11:45am.
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Biology 168 Biotechnology Processing Projects Lab.
(Cross-listed as BME 168 and CHBE 168.)
Laboratory experience with techniques in biotechnology processing: fermentation of recombinant E. coli cells, hybridoma cell culture, purification of proteins and antibodies and related analytical procedures. Laboratories accompanied by lectures and relevant readings to cover the underlying principles. Counts as laboratory course for biology major.
Dr. Hyunmin Yi
Thursday 6 – 9:30pm

Biology 172 Biochemistry II.
(Cross-listed as Chemistry 172.)See Chemistry for details.
Block B+: Tues. & Thurs., 1:30 – 2:45, Pearson 104.

Biology 181 Tropical Ecology & Conservation.
(Cross-listed as ENV 181.)
This seminar and field trip is designed to provide students with an in depth understanding of tropical ecology and first-hand experience in tropical Central America. Topics to be covered include 1) community ecology, 2) ecosystem ecology, 3) physiological ecology, 4) plant-animal interactions, and 5) conservation biology. In addition to weekly readings, discussions, and writing assignments, students will write a grant proposal and present it to the class. Over winter break we will travel to Costa Rica for an intensive two-week field experience. We will gain hands-on research experience in contrasting habitats and learn about conservation efforts in Costa Rica. A typical 2-day schedule will be a morning orientation hike followed by meetings to design experiments, data collection in the afternoon, an evening lecture or discussion, data collection the next day, and data analysis in the evening. Although the conditions will often be uncomfortable (hot and humid), this is an excellent opportunity to gain first hand research experience in the tropics. Estimated cost of this trip is $1,200 (financial aid is available). This is a HIGH DEMAND course. Fall 2015 and alternate years. (Group C)
Prerequisites: Bio 14 or equivalent and permission of instructor. A completed application and supporting materials must be submitted to Dr. Orians by April 15.
Dr. Orians
Block J+: T & Th., 3:00 – 4:15pm.
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Biology 190 DNA: Structure to Function.
DNA structure and functioning studied through a combination of lectures and discussions of the original papers. DNA is the sine qua non molecule of life. Originally, it was believed to be a uniform right-handed double helix with limited structural flexibility. It has now become clear, however, that DNA structure is highly versatile, and this versatility is central for major genetic processes. The first half of the course will consider DNA secondary and tertiary structures, DNA topology and topoisomerases, the mechanisms of protein-DNA recognition and the structure of the chromatin. The second half of the course will emphasize how the principles of DNA organization are employed in key genetic transactions, including DNA replication, transcription, repair and recombination. (Group A)
Prerequisites: Biology 41 and permission of the instructor.
Dr. Sergei Mirkin
Block F+: Tues &-Thurs. 12:00-1:15pm.
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Biology 193 Independent Research.
The department feels that the 8 biology courses required for the major should be well distributed in the field of biology. Therefore, normally one course in Biology 193, 194 will be accepted as one of these 8. The student may take courses in Biology 193, 194 beyond these limitations and count them for credit toward graduation but not toward the biology major. One course under 193, 194 can be used to fulfill the biology department requirement for laboratory courses. At the semester's end the student must deliver to his/her sponsor and members of the 193/194 review committee (4 faculty members) copies of a paper concerning his or her semester's work. This should follow the format of a scientific paper. During the reading period following the last class of the semester, the student will meet with this same review group to present and discuss his/her work, and they will jointly award the grade for the course. The presentation should be a 10-15 minute review of the work already described in the written summary followed by questions, discussion of details, etc., lasting another 5-10 minutes. The exact time for each session will be posted prior to the end of classes. The oral presentation will be open to all interested faculty and students. Normally 15 hours per week in the laboratory equals one course credit. The grade is based upon the intellectual quality of the work.
Prerequisite: Bio 93 or comparable experience. Bio 93 and consent of Coordinator.
Dr. Chew.
Additional Information >

Biology 196-01 Teaching Biology: Pedagogy and Practice.
Bio 13 undergraduate TAs only.
Monday, 10:30-11:45. 0.5 credit.

Biology 196-03 Plant and Animal Interactions.
This course is restricted to students doing independent research in the research labs of Professor Orians or Crone.
Drs. Crone and Orians.

Biology 196-04 Seminar in Molecular Evolution.
Current topics in molecular evolution. Focus will be on next-generation sequence (NGS) analysis using Tufts High Performance Computing Cluster and on discussion of primary literature. Possible topics include regulatory and protein evolution, adaptation and the neutral theory, population demography, phylogenomics, QTL mapping, and assembly & variant discovery.
Prerequisites: Bio 143 and junior standing or permission of instructor.

Dr. Dopman.
Thursday, 1:30 – 4:00pm.

Biology 196-05 Microbiology of Food.
From the production of raw materials to the digestion of food in our guts, microbes impact what and how we eat. This interdisciplinary course will explore how microbes play critical roles in the production, processing, and consumption of foods. In our farm-to-gut journey, we’ll examine basic principles of microbial diversity, ecology, evolution, physiology, and genetics and learn about the tools that scientists use to study the microbiology of food systems. We'll explore how the impacts of microbes in food systems span many disciplines including economics, political science, international relations, ethics, community health, nutrition, and philosophy. Guest lectures from farmers, chefs, and local food producers will highlight the practical applications of managing food microbes. This course is designed to provide students who are not science majors with the opportunity to develop a core microbial literacy that will serve them in life as well as in their field of study.
Dr. Wolfe
Tuesday 6:30 – 9:00pm.
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Biology 196-06 Seminar in Synthetic Biology.
Introduction to the basics of synthetic biology and the design and development of research proposals, led in part by undergraduate members of Tufts' Synthetic Biology team with faculty guidance. Introduction to essential molecular biology principles, using primary literature and software. Topics may include DNA assembly, protein purification, cell culture, genetic and metabolic engineering, biological circuits and the creation of synthetic life, broader technological and ethical implications of synthetic biology. Design and development of proposals to be implemented in international synthetic biology competition. Pass/Fail.
Monday & Wednesday, 1:30 – 2:45pm. Drs. Mirkin and Nair.
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Biology 0196-07 Selected Topics: Advanced Topics in Biostats.
Exploration of special topics in biology through seminars or guided individual study.
Prerequisite: Consent. Dr. Crone
Friday, 9:00am – 11:30am.

Biology 199 Senior Honors Thesis.
Two semesters of research. Prior consent must be obtained from the Biology 199 course coordinator (Dr. Ernst) at the end of the junior year. In order to register for the course you will also need to see the course coordinator Dr. Ernst. In addition, you must complete the Senior Honors Thesis Candidate form and submit to the Degree Audit Coordinator, Student Services, by October 8. These two steps are essential. Without completing them, you are not registered. See Trunk for additional information and required forms.
Prerequisite
: Bio 193 or 194 and consent. See catalog for other prerequisites.

Biology 243-01 Topics in Molecular/Cellular Biology.
Topics will be drawn from several of the following areas: regulation of gene expression, chromatin structure and epigenetic regulation, mechanisms of chromosome segregation, DNA replication, recombination and repair, genome structure and genome stability, intra- and inter-cellular signaling pathways molecular pathways of tissue regeneration, and developmental biophysics. Students will read and present papers from the current literature. Novel experimental techniques used to answer central questions will be emphasized. (Group A)
Prerequisite: Biology 105 or equivalent; permission of the instructor for undergraduates.
Drs. Fuchs, Ernst & Levin
Block 7+: Wednesday 1:30-4:30PM. 200 Boston Ave., Ste 4747.

Biology 260-01 Teaching Biology: Pedagogy and Practice.
This course aims to enhance the professional development of graduate students by preparing them to teach biological sciences in academic venues that range from community colleges to Research I universities. Graduate student participants will be introduced to issues related to teaching in both lab and lecture settings and will apply effective teaching techniques in their own classrooms. Program participants will learn about pedagogy, gain practical teaching experience, and receive mentoring and formal evaluation of their teaching. The course requirements are designed to be flexible enough to be pursued alongside full-time disciplinary studies, yet ensure that participants are rigorously trained in biology-specific pedagogy.
Drs. McLaughlin and McVey.
Block ARR: Monday 10:30-11:45AM. 1 graded credit. Prerequisite: consent/BIO13L Teaching Assistants. Must also register for Bio 260-02.
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Biology 260-02 Teaching Biology: Pedagogy and Practice.
Dr. Gaudette.
Block 13+: Thursday 6:00-9:00PM.

Biology 291-01 Graduate Seminar.
Dr. Freudenreich.
Block ARR: Thursday 8:30-10:20.

Biology 293-01 Special Topics: Advanced Topics in Ecology and Physiology.
The effects of human alterations of landscapes on species persistence, particularly in birds; Avian ecology and Conservation Biology: population viability, extinction risk, animal behavior as it relates to population biology.
Dr. Reed
Block: ARR