Courses of Study 2017-2018 
    
    May 14, 2024  
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Courses of Study 2017-2018 [ARCHIVED CATALOG]

Course Descriptions

 

BIONB—Neurobiology & Behavior
  

  • BIONB 3950 - [Molecular and Genetic Approaches to Neuroscience]


    (PBS-AS)      
    Fall. Next offered 2018-2019 (offered alternate years). 3 credits. Letter grades only.

    Prerequisite: BIONB 2220  or BIOMG 3300  or BIOMG 3320 . Enrollment limited to: 25 students.

    D. L. Deitcher.

    Focuses on how different molecular and genetic approaches have led to major advances in neuroscience.  Lectures, student presentations, and discussions examine original research articles.  Topics include ligand-gated channels, potassium channels, seven membrane spanning receptors, olfaction, pain and cold receptors, neurotransmitter release, neural networks, epilepsy, optogenetics, and circadian rhythms.

    Outcome 1: Demonstrate mastery of reading primary scientific literature in molecular neuroscience

    Outcome 2: Demonstrate ability to present scientific information from primary literature to a broad audience by oral presentation.

    Outcome 3: Demonstrate ability to apply basic scientific principles to formulate hypotheses that explain raw scientific data.

    Outcome 4: Develop a clear understanding of the utility of model genetic organisms in the field of neuroscience.
  

  • BIONB 3960 - Introduction to Sensory Systems


    (PBS-AS)      
    Spring. 3 credits. Student option grading.

    Prerequisite: BIONB 2220  or equivalent. Enrollment limited to: 22 students.

    R. R. Hoy.

    This is a survey course on sensory systems that focuses on how humans and other animals detect and process environmental information that guides adaptive behavioral actions. Sensory function will be tackled from multiple levels of biological organization, from cell and molecular to sensory organs, to sensory systems in the brain, to sensori-motor integration, and finally to behavior. Behavior analysis will include psychophysical viewpoints and the role of behavioral plasticity, including learning.

    Outcome 1: To be able to explain, diagram, or prepare a brief power point presentation that summarizes current knowledge about how any environmental signal or stimulus energy (light/vision; soundwaves/audition; chemical molecule(s)/ olfaction-gustation; or bodily stimulation during action/somatosensation-proprioception) is transduced into bioelectrical signals in sensory organs and sensory pathways in the brain that generates in the subject a sensation, perception, thought, or overt behavioral act.

    Outcome 2: To be able to compare and contrast the different sensory modalities in terms of their adaptive/survival value in humans and other animals in a way that recognizes how natural selection shaped any given sensory system for the animal that possesses it.

    Outcome 3: To be able to explain the process of sensory transduction in sensory organs at the cellular and molecular levels and the way that these organs process excitation into spike codes that represent the output of sensory organs.

    Outcome 4: To be able to explain why the way humans and perhaps other animals perceive the unfolding of natural scenes (such as natural vision or auditory scenes) as involving not only modality-specific information but also behavioral goal-directed actions that need to take into account motor programs that underlie adaptive/appropriate reactions or behavior.
  

  • BIONB 4140 - Principles of Pharmacology

    (crosslisted) BIOAP 4140 , BIOMS 4140  
    (PBS-AS)      
    Spring. 3 credits. Letter grades only.

    Prerequisite: BIOAP 3110  or NS 3410 .

    C. Fewtrell, M. Linder, G. Weiland.

    For description and learning outcomes, see BIOAP 4140 .

  

  • BIONB 4200 - Topics in Neurobiology and Behavior


    (OPHLS-AG)      
    Fall, spring. 1-4 credits, variable (may be repeated for credit). Student option grading.

    Enrollment preference given to: undergraduates. For NBB concentration: these topics courses may be used toward the additional 7 credit requirement, but do not qualify as advanced courses.

    Staff.

    Courses on selected topics in neurobiology and behavior; can include lecture and seminar courses. Topics vary by section.

  

  • BIONB 4220 - [Modeling Behavioral Evolution]


    (PBS-AS)      
    Fall. Next offered 2018-2019 (offered alternate years). 4 credits. Student option grading.

    Prerequisite: BIONB 2210 , one year calculus, course in probability or statistics, or permission of instructor. Enrollment limited to: 25 advanced undergraduates and graduate students.

    H. K. Reeve.

    Intensive lecture and computer lab course on modeling strategies and techniques in the study of behavioral evolution. Population-genetic (including quantitative-genetic), static optimization, dynamic programming, and game-theoretic methods are emphasized. These approaches are illustrated by application to problems in optimal foraging, sexual selection, sex ratio evolution, animal communication, and the evolution of cooperation and conflict within animal social groups. Students learn to critically assess recent evolutionary theories of animal behavior, as well as to develop their own testable models for biological systems of interest or to extend preexisting models in novel directions. The Mathematica software program is used as a modeling tool in the accompanying computer lab.

    Outcome 1: To be able to understand and create single-locus population genetic models of selection.

    Outcome 2: To be able to understand and manipulate the Price equation.

    Outcome 3: To understand and use static and dynamic optimization methods, both constrained and unconstrained, as in models of patch residence time from optimal foraging theory.

    Outcome 4: To understand and create discrete and continuous strategy game theory models and derive ESS’s from them with appropriate checks on stability.

    Outcome 5: To understand and use kin selection theory, using both inclusive fitness and neighbor-modulated methods.
  

  • BIONB 4240 - [Neuroethology: A Comparative Approach to Neural Circuits and Behavior]

    (crosslisted) PSYCH 4240  
    (PBS-AS)      
    Fall. Next offered 2018-2019. 4 credits. Student option grading.

    Prerequisite: BIONB 2220  or equivalent with permission of instructor. Enrollment limited to: 25 students. There is a required discussion section with this course.

    Staff.

    Neuroethology is the comparative study of neural circuits used in behavior. The course will emphasize fundamental principles in neuroscience using comparative examples drawn from invertebrate and vertebrate species. Each case will emphasize a specific behavior and how neural systems are adapted to that specific behavior. This course will emphasize sensory systems: vision, hearing, chemosensing, mechano-sensing and other unusual sensory systems. Students will learn about the natural context of behavior and how sensory and other systems are adapted to solving behavioral problems.

    Outcome 1: Demonstrate mastery of core principles in the field of neuroscience using specific examples drawn from the comparative literature on natural behaviors of animals.

    Outcome 2: Demonstrate knowledge of original papers in neuroscience by making use of bibliographic searches and tools; reading and analyzing original articles; and by making written summaries of key points of original research. Students will demonstrate competence in making oral presentations of neuroscience research.

    Outcome 3: Demonstrate through speech and writing both the power and usefulness of the comparative method in neuroscience by making reference to specific examples from anatomy, physiology, and behavior.

    Outcome 4: Explain in terms of neuronal circuits how some well-studied behaviors are controlled by a particular pattern of neuronal and synaptic connections of neurons with specific cellular properties.

    Outcome 5: Cite and explain examples of neural circuits have undergone changes during evolution.
  

  • BIONB 4260 - Animal Communication


    (PBS-AS)      
    Spring. Offered alternate years. 4 credits. Letter grades only.

    Prerequisite: BIONB 2210 . Enrollment limited to: 48 students. Discussion TBA.

    M. S. Webster.

    Communication is the “glue” that holds societies together. This course examines how and why animals communicate. Topics include the role of the environment in shaping animal signals, whether animals tell the truth to each other, why some bird songs are simple and others complex, and what kinds of signals might be exchanged between species.

    Outcome 1: Demonstrate mastery of the core principles of animal communication.

    Outcome 2: Discuss and explain methodological approaches to studying communication.

    Outcome 3: Describe the mechanistic bases of communication systems, and the function and evolution of animal signals.

    Outcome 4: Formulate hypotheses, predictions and tests in order to investigate active research questions in the field of animal communication.

    Outcome 5: Apply bioacoustic methods to analyze one key modality of communication, acoustic signals.
  

  • BIONB 4300 - Experimental Molecular Neurobiology


    (PBS-AS)      
    Spring. 4 credits. Letter grades only.

    Prerequisite: BIOMG 3300  or BIOMG 3310 . Recommended prerequisite: BIOMG 2801 . Enrollment limited to: 16 students.

    D. L. Deitcher.

    Experiments include PCR, immunoprecipitations, western blots, RNAi, antibody staining, optogenetics, and behavioral assays. Experiments emphasize how molecular techniques can be applied to studying neurobiological problems and will culminate in designing your own experiments.

    Outcome 1: Demonstrate competence in basic molecular biology and protein biochemistry skills in the laboratory and the underlying principles of these techniques.

    Outcome 2: Demonstrate mastery of basic bioinformatics tools such as BLASTN, TBLASTN, and BLASTP and using model organism databases such as FlyBase.

    Outcome 3: Develop a clear understanding of how different laboratory techniques provide complementary information about gene expression.

    Outcome 4: Demonstrate deep understanding of scientific procedures and results through written laboratory reports.
  

  • BIONB 4310 - [Genes and Behavior]


    (PBS-AS)      
    Spring. Next offered 2018-2019 (offered alternate years). 3 credits. Student option grading.

    Prerequisite: BIONB 2220 . Enrollment limited to: 50 students.

    J. R. Fetcho.

    Our genes influence how we behave. This lecture course explores the current understanding of how genes influence the behavior of a variety of animals, including humans. Topics include the genetic basis of hearing, movement, learning, memory, intelligence, sexual behavior, aggression, sleep, and diseases of behavior. The focus is on the unprecedented insight that modern molecular and genetic tools are providing into the genetic basis of behavior.

    Outcome 1: To understand the tools used to identify genes that affect behavior.

    Outcome 2: To understand at an experimental and conceptual level the classic examples of genes that affect behaviors such as learning and memory, social behaviors, and circadian rhythms.

    Outcome 3: To understand the genetic and neuronal substrates for behavioral disorders such as Alzheimer’s, anxiety and depression.

    Outcome 4: To be able to design experimental strategies to both identify genes affecting behavior and bridge the gap between the genes and behavior by tying the genes to alterations in neurons and networks.

    Outcome 5: To critically analyze experiments that claim to tie genes to neurons and behavior to identify problems with experimental design and interpretation and to gain an appreciation for the differences between strong and weak experiments and evidence.
  

  • BIONB 4320 - [Neural Circuits for Motor Control in Health and Disease]


    (PBS-AS)      

    Fall. Next offered 2018-2019 (offered alternate years). 3 credits. Student option grading.

    Prerequisite: BIONB 2220  or ECE 2100  or permission of instructor. Enrollment limited to: 25 students.

    J. H. Goldberg.

    Almost all behaviors-from speech to a cross court forehand-are mediated by the contraction of muscles. This course examines the neural origins of motor behavior, from simple reflexes to complex learned motor sequences. Ascending the motor hierarchy, we will study the neuromuscular junction, spinal cord, brainstem, cerebellum, basal ganglia and cerebral cortex. At each level, we will examine the structure and function of the local microcircuit, as well as diseases-such as myasthenia gravis, stroke, ALS, ataxia and Parkinson’s-that result from that circuit’s dysfunction.

    Each week we will discuss a topic relating to the neurobiology of motor control, with a combination of lectures (both video and real-life) and student-led presentations of relevant research papers. Students will be evaluated on the basis of their participation, their presentations, their final project (a 5 page grant proposal on a research question relevant to the course), and a final exam.

    Outcome 1: To understand the structure and function of the vertebrate motor system, including neural mechanisms of human movement disorders.

    Outcome 2: To critically read and comprehend primary literature.

    Outcome 3: To distill large amounts of information into central concepts of nervous system function, and to articulate these concepts both verbally and in writing.

    Outcome 4: To creatively come up with new ideas and design experiments to test them.
  
  

  • BIONB 4350 - [Animal Cognition]


    (PBS-AS)      
    Spring. Next offered 2018-2019 (offered alternate years). 4 credits. Letter grades only.

    Prerequisite: BIONB 2210 . Enrollment limited to: 25 students.

    T. D. Seeley.

    Examination of the mechanisms by which animals acquire, process, store, and act on information from the environment. Topics to be covered include perception, learning, memory, decision-making, with special attention to spatial cognition, numerical cognition, understanding of tool use, and social cognition.

    Outcome 1: Understanding the classical foundational issues in the study of animal cognition, such as the role of Morgan’s Canon.

    Outcome 2: Understanding the relationship between brain evolution and cognition.

    Outcome 3: Understanding perception, simple forms of learning, and more complex forms of memory and categorization.

    Outcome 4: Understanding physical cognition (space, time, number, and physical causation).

    Outcome 5: Outcome 5. Understanding social cognition (social knowledge, social learning, and communication).
  

  • BIONB 4360 - [Neural Views on Mental Illness]

    (crosslisted) PSYCH 4330  
    (PBS-AS)      
    Fall. Next offered 2018-2019. 3 credits. Student option grading.

    Prerequisite: PSYCH 2230  or BIONB 2220 .

    T. DeVoogd.

    For description, see PSYCH 4330 .

  

  • BIONB 4370 - [Neural Circuits of Motivated Behavior]


    (OPHLS-AG, PBS-AS)      
    Spring. Next offered 2018-2019 (offered alternate years). 3 credits. Letter grades only.

    Prerequisite: BIONB 2220 .  Enrollment limited to: 25 students.

    M. R. Warden.

    This class examines the neural circuits of motivated behavior and reward, and involves the critical reading and discussion of classic and contemporary papers in this subject. Topics include neural processes related to reward, punishment, risk, effort, appetite, aggression, addiction, and depression.

    Outcome 1: To understand the neural circuits mediating reward and motivated behavior and their dysfunction in psychiatric disease.

    Outcome 2: To critically read and comprehend primary literature.

    Outcome 3: To distill large amounts of information into central concepts of nervous system function, and to articulate these concepts both verbally and in writing.

    Outcome 4: To creatively come up with new ideas and design experiments to test them.
  

  • BIONB 4460 - Plant Behavior and Biotic Interactions, Lecture

    (crosslisted) BIOEE 4460 , PLSCI 4460  
    (PBS-AS)      

    Spring. 3 credits. Student option grading.

    Co-meets with BIOEE 4460 /PLSCI 4460 .

    A. Kessler, T. Pawlowska, R. Raguso.

    How do plants respond to antagonists, such as herbivores and pathogens? What are the checks and balances that keep mutualist organisms in their tight interactions? How are symbioses organized on molecular, metabolic and ecological levels? What are the molecular, plant hormonal, and metabolic mechanisms mediating plant biotic interactions with other organisms? What ecological and evolutionary consequences do these interactions have for the fitness of the plants and their interactors? This course provides an overview of plants’ myriad interactions with antagonists and mutualists, from microbes to multicellular organisms, and explains the underlying ecological and evolutionary concepts. It gives an introduction to the study of induced plant responses in the light of a behavioral biology framework.            

    For learning outcomes, see BIOEE 4460 .

  

  • BIONB 4461 - Plant Behavior and Biotic Interactions, Laboratory

    (crosslisted) BIOEE 4461 , PLSCI 4461  
         
    Spring. 1 credit. Student option grading.

    Prerequisite or corequisite: BIOEE 4460 , BIONB 4460  or PLSCI 4460 . Enrollment limited to: 12 students.

    A. Kessler, T. Pawlowska, R. Raguso.

    For descriptions and learning outcomes, see BIOEE 4461 .

  

  • BIONB 4530 - [Speciation: Genetics, Ecology, and Behavior]

    (crosslisted) BIOEE 4530  
    (PBS-AS)      
    Spring. Not offered 2017-2018 (offered alternate years). 4 credits. Student option grading.

    Prerequisite: BIOEE 1780  and BIOMG 2800  or equivalents, or permission of instructor. Enrollment limited to: 40 students.

    K. Shaw.

    For description and learning outcomes, see BIOEE 4530 .

  

  • BIONB 4550 - Molecular and Neural Basis of Decision Making


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: BIONB 2220 . Permission of instructor required.

    N. Yapici.

    This course will examine the neural and molecular mechanisms of decision making across a variety of animal species and humans. The course involves the critical reading and discussion of classic and contemporary papers in this subject. Topics will include the neural mechanisms of motivation, attention, working memory, risk taking and neuroeconomics.

    Outcome 1: Investigate the molecular and neural mechanism regulating decision making in the nervous system.

    Outcome 2: Critically read and comprehend primary literature.

    Outcome 3: Understand general concepts of how the nervous system works and to discuss these concepts verbally.

    Outcome 4: Learn how to design experiments to test scientific hypothesis.
  

  • BIONB 4700 - [Biophysical Methods]

    (crosslisted) AEP 4700 , BME 5700 , VETMM 4700  
    (PBS-AS)      
    Fall. Next Offered 2018-2019. 3 credits. Letter grades only.

    Prerequisite: solid knowledge of basic physics and mathematics through sophomore level. Recommended prerequisite: knowledge of cellular biology.

    Staff.

    For description, see AEP 4700 .

  

  • BIONB 4910 - Principles of Neurophysiology

    (crosslisted) BME 4910 , ECE 4910  
    (OPHLS-AG, PBS-AS)      
    Spring. 4 credits. Student option grading.

    Prerequisite: BIONB 2220  or written permission of instructor. Enrollment limited to: 28 students. Neurobiology and Behavior concentrators must take class for a letter grade.

    B. R. Johnson.

    Laboratory-oriented course designed to teach the concepts and tools of cellular neurophysiology through hands-on experience with extracellular and intracellular electrophysiological techniques, and computer acquisition and analysis of laboratory results. Students explore signal transmission in the nervous system by examining the cellular basis of resting and action potentials, and synaptic transmission. Lecture time is used to review nervous system physiology, introduce laboratory exercises, discuss lab results and primary research papers, and for presentation of additional experimental preparations and methods. Invertebrate preparations are used as model systems. BioNB4910 website

    Outcome 1: Students should understand the contemporary experimental paradigms in modern neurophysiology and become technically competent with the extracellular and intracellular recording techniques used to explore nervous system physiology.

    Outcome 2: Students should deepen their understanding of the ionic mechanisms underlying neuronal excitability and synaptic communication in the nervous system.

    Outcome 3: Students should develop their skills in communicating scientific results effectively through written lab reports and oral presentations.

    Outcome 4: Students should refine their critical reading skills of primary scientific literature.

    Outcome 5: Students should refine their ability to develop testable hypotheses, and develop independent scientific thinking.
  

  • BIONB 4940 - [Special Topics in Neurobiology and Behavior]


         
    Fall, spring. Next offered 2018-2019. 1-4 credits, variable. Student option grading.

    Staff.

    Offerings vary by semester. See course roster for details.

  

  • BIONB 4970 - [The Brain - Its Evolution and Development]


    (OPHLS-AG, PBS-AS)      
    Fall. Next offered 2018-2019 (offered alternate years). 3 credits. Student option grading.

    Prerequisite: BIONB 2220  or equivalent. Enrollment limited to: 50 students. Intended for juniors, seniors, and graduate students.

    A. H. Bass.

    How does the brain evolve? One of the fastest-growing areas of study in neuroscience is the evolution of developmental mechanisms that have shaped the remarkable diversity in brain organization observed among vertebrates. This lecture course will consider the evolutionary and developmental origins (“evo-devo”) of vertebrate brains from phylogenetic, molecular, anatomical, physiological, and behavioral perspectives. Topics include the evo-devo of brain regions such as the cerebral hemispheres and brainstem; sensory systems ranging from olfaction to vision and hearing; motor systems for posture, locomotion and speech; and mechanisms of social and sexual plasticity.

    Outcome 1: Obtain a basic understanding of vertebrate brain organization.

    Outcome 2: Critically evaluate the molecular, anatomical, physiological, and behavioral mechanisms proposed to influence the diversity in vertebrate brain organization.

    Outcome 3: Prepare a bibliography addressing major trends in brain evolution for a single group of vertebrates.

    Outcome 4: Communicate an understanding of vertebrate brain evolution in PowerPoint and essay formats.

    Outcome 5: Work as part of a team to prepare a website outlining the major trends in brain evolution for a single group of vertebrates.
  

  • BIONB 4980 - Teaching Experience


         
    Fall, spring. 1-4 credits, variable. Student option grading.

    Prerequisite: previous enrollment in course to be taught or equivalent.  Permission of instructor required. Students must register using individual study form. Enrollment form can be found here.

    Staff.

    Designed to give qualified undergraduate students teaching experience through actual involvement in planning and assisting in biology courses.  This experience may include supervised participation in a discussion group, assisting in a biology laboratory, assisting in field biology, or tutoring.

  

  • BIONB 7000 - [Introduction to Programming for Research in Neurobiology and Behavior]


         
    Spring. 4 credits. S/U grades only.

    Permission of instructor required. Enrollment limited to: 10 students.

    C. Linster.

    Lab course offering an introduction to programming in Matlab with a focus on neurobiology and behavior. Modeling, data acquisition, signal processing and data analysis.

    Outcome 1: Principles of MatLab programming.

    Outcome 2: Basic signal processing.

    Outcome 3: Basic neural modeling.
  

  • BIONB 7200 - Advanced Topics in Neurobiology and Behavior


         
    Fall, spring. 1-4 credits, variable (may be repeated for credit). Student option grading.

    Permission of instructor or graduate standing required. For NBB concentration: these topics courses may be used toward the additional 7 credit requirement, but do not qualify as advanced courses.

    Staff.

    Designed to provide several study groups each semester on specialized topics. A group may meet for whatever period is judged adequate to enable coverage of the selected topics. Discussion of current literature is encouraged. See course roster for offerings.

  

  • BIONB 7201 - Research Design in the Study of Animal Social Behavior


         
    Fall, spring. 1 credit (may be repeated for credit). S/U grades only.

    Permission of instructor required for undergraduates. Enrollment limited to: 20 students. Intended for graduate students.

    Staff.

    A weekly journal club-style discussion. Graduate students may be expected to present a summary of their research or a summary of research in the literature related to their thesis once per year.

    Outcome 1: Become exposed to a wide variety of lines of study of animal behavior.

    Outcome 2: Deepen your understanding of how to conduct research on animal behavior.

    Outcome 3: Get to know the various graduate students, postdocs, and faculty studying animal behavior.

    Outcome 4: Get critical, but also encouraging, feedback on your own research project.
  

  • BIONB 7202 - Topics in Neural Basis of Behavior


         
    Fall, spring. 1 credit (may be repeated for credit). S/U grades only.

    Permission of instructor required for undergraduates. Enrollment limited to: 20 students. Intended for graduate students.

    Staff.

    A weekly journal club-style discussion. Graduate students may be expected to present a summary of their research or a summary of research in the literature related to their thesis once per year.

    Outcome 1: To be able to present a scientific paper in a clear and concise manner.

    Outcome 2: To be able to critique and discuss scientific papers with peers and faculty members.

    Outcome 3: To understand scientific methods and their implications.
  

  • BIONB 7210 - Introductory Graduate Survey in Neurobiology and Behavior


         
    Fall, spring. 2 credits. S/U grades only.

    Corequisite: BIONB 2210  (fall) and BIONB 2220  (spring). Requirement for graduate students in Neurobiology and Behavior.

    Staff.

    Designed to assist students in mapping their graduate careers and in choosing and pursuing transformative and tractable thesis topics. The core of the course will be open-ended discussions directed by paired neurobiology and behavioral ecology faculty on novel research frontiers in the study of mechanisms and the evolution of behavior (including in the zone of their conceptual intersection). Occasional laboratory experiences may also be included. Professional development topics will include how to: navigate graduate school, allocate time between reading, thinking creatively, and investing in research, design experiments, write grant proposals, give talks, and publish peer-reviewed papers.

    Outcome 1: To know and understand the current frontiers of both behavioral and neurobiological studies, including which unanswered questions are considered to be the most important ones, and which questions might actually be answerable in a doctoral thesis project or longer term study.

    Outcome 2: To hone critical thinking skills with respect to identifying important questions and designing strategies to address them.

    Outcome 3: To become familiar with the most compelling current tools, both conceptual and experimental, for answering behavioral and neurobiological questions
  

  • BIONB 7640 - Plant-Insect Interactions Seminar

    (crosslisted) BIOEE 7640 , ENTOM 7640  
         
    Fall, spring. 1 credit (may be repeated for credit). S/U grades only.

    Permission of instructor or graduate standing required.

    A. Agrawal, A. Kessler, K. Poveda, R. Raguso, J. Thaler.

    For description and learning outcomes, see BIOEE 7640 .


BIOSM—Shoals Marine Laboratory
  

  • BIOSM 1500 - Investigative Marine Biology Laboratory


    (BIO-AG, BIOLS-AG, PBS-AS)      
    Summer. 3 credits. Student option grading.

    Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    D. Fudge, D. Taylor.

    This course is a 2 week, 3 credit, field intensive marine-based introduction to the scientific method and experimental biology. We take advantage of the unique learning opportunities in the intertidal zone around Appledore Island, Maine at the Shoals Marine Laboratory. The course philosophy is to allow students to learn the scientific method by doing research under the guidance of veteran marine biologists. The course is structured around two research projects that are designed to expose students to diverse research areas within marine biology: Ecomechanics and Ecophysiology.

    Outcome 1: Scientific method. Students will:
    a. appreciate the power and limitations of science as a way of knowing.
    b. understand and apply the structure of the scientific method.
    c. understand and apply principles of good experimental design and data collection.
    d. learn how to carry out statistical testing, analysis, and graphing using R software.

    Outcome 2: 2. Scientific information literacy. Students will:
    a. learn how to use online research tools for scholarly literature and bioinformatics.
    b. learn how to cite sources using proper format.

    Outcome 3: 3. Scientific communication. Students will:
    a. demonstrate understanding of the structure of scientific papers and their relationship to the scientific method via four writing assignments.
    b. demonstrate principles of data analysis, slide design, and oral communication via participation in a scientific symposium at the end of the course.

    Outcome 4: 4. Knowledge of and ability to use equipment in the lab and field. Students will:
    a. understand the importance of measurement to the scientific process
    b. demonstrate proper use of equipment such as pipets, calipers, micrometers, gel electrophoresis rigs, force transducers, and dissolved oxygen probes.
    c. demonstrate proficiency with the use of remote sensing devices such as CTD probes, and HoboTemp temperature probes.
    d. demonstrate proficiency with biological imaging using microscopes and cameras.
    e. demonstrate proficiency with image processing using Image software.

    Outcome 5: 5. Conceptual knowledge pertaining to two laboratory modules. Students will master introductory concepts in two areas:
    a. Marine Ecophysiology
    b. Marine Biomechanics

    Outcome 6: 6. Additional goals. Students will:
    a. be empowered to undertake their own scientific investigations.
    b. practice critical thinking skills as background for MCAT and GRE.
    c. take ownership of the material.
    d. learn how to work cooperatively with others toward a common goal.
  

  • BIOSM 1551 - Field Introductory Oceanography

    (crosslisted) EAS 1551  
    (BIONLS-AG)      
    Summer. 1.5 or 3 credits, variable. Student option grading.

    Offered in Maine at Shoals Marine Laboratory on Appledore Island. Introductory Biology distribution requirement will be fulfilled when combined with BIOEE 1540 /EAS 1540  on campus.

    E. Zettler.

    Students will gain familiarity with the basic concepts and field techniques (and equipment) used by biological oceanographers as we explore the Gulf of Maine waters using the Isles of Shoals as our base. Minimal lecture time, maximum boat time is the theme of this field immersion course.

  

  • BIOSM 1610 - Ecology and the Marine Environment


    (BIO-AG, BIOLS-AG, PBS-AS)      
    Summer. 3 credits. Student option grading.

    Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    J. Factor, J. Sparks.

    This course provides an introduction to ecology, covering interactions between marine organisms and the environment at scales of populations, communities, and ecosystems.

    Outcome 1: Where and why different biomes occur globally as a function of Earth’s climate dynamics.

    Outcome 2: How plants and animals cope with environmental variation through a range of adaptations that modify their respective heat and water balances.

    Outcome 3: Processes of autotrophic and heterotrophic means of energy acquisition, and tradeoffs among these strategies.

    Outcome 4: Fundamental principles of population growth and demography, including application to human populations and population harvest.

    Outcome 5: Introduction to species interactions including predation, parasitism, competition, and mutualism.

    Outcome 6: Overview of community ecology, including factors that control patterns of species distribution, diversity and abundance.

    Outcome 7: Basic understanding of broad biogeographical patterns of species distributions, including hypotheses explaining latitudinal species gradients, species diversity on islands, and the application of island biogeography theory to the design of nature reserves.

    Outcome 8: Threats to biodiversity and key principles of conservation biology.

    Outcome 9: Major pathways and mechanisms of nutrient cycling, including nutrient inputs, acquisition strategies, limitation, and losses, and major human impact on these cycles.

    Outcome 10: Causes, general magnitudes, and likely consequences of human-driven alterations to global cycles of carbon, nutrients, and climate.
  

  • BIOSM 1620 - Marine Environmental Science


    (PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: two year-long high school courses in science, and completion of grades 10, 11 or 12. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    M. Johnson, L. Jordan-Smith.

    This course is aimed at high school students.  This course focuses on issues in environmental science from a marine perspective. Basic scientific research methods, equipment, and group research projects are introduced. Laboratory exercises and fieldwork include work on Appledore Island’s intertidal zone and offshore oceanographic sampling exercises.

    Outcome 1: Identify by characteristics, adaptations, and scientific names 25-30 intertidal organisms that will be included in later studies;

    Outcome 2: Demonstrate an understanding of the characteristics and adaptations of the major phyla associated with the oceans-with in depth concentration on the phyla Mammalia and Aves;

    Outcome 3: Develop the ability to gather data in the field with a number of types of equipment and in a number of different setting;

    Outcome 4: Perform background research, develop a hypothesis, design an experiment, collect data for 7 days and demonstrate an understanding of the results. Each student will demonstrate this understanding by giving a presentation of their work to the class and by writing a technical paper that includes the full scientific method;

    Outcome 5: Develop an understanding of local microhabitats by conducting a comparative study of the physical, chemical, and biological characteristics of the protected and then exposed sides of Appledore island. They will demonstrate this understanding by writing a field report of their comparative study;

    Outcome 6: Demonstrate a detailed understanding of the human impacts associated with a marine environment. Students will be concentrating on the causes, effects, and both global and personal solutions to these issues;

    Outcome 7: Develop the ability to communicate the knowledge they have gained using through public speaking and writing.
  

  • BIOSM 1640 - Introduction to the Biology of Sharks, Skates, and Rays


         
    Summer. 1 credit. Student option grading.

    Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    L. Jordan-Smith.

    Our main objective is to discover the current state of knowledge of elasmobranch (shark, skate & ray) biology and explore areas for future research and conservation initiatives. This includes separating fact from fiction, analyzing various types of media including peer reviewed scientific literature, and exploring experimental methods in both laboratory and field settings for studying sharks, rays, and other marine life.

    Outcome 1: Demonstrate knowledge of elasmobranch (shark, skate & ray) biology.

    Outcome 2: Identify future research questions for elasmobranchs.

    Outcome 3: Identify appropriate elasmobranch conservation initiatives.
  

  • BIOSM 1650 - Marine Mammal Biology


    (BIOLS-AG, PBS-AS)      
    Summer. 3 credits. Student option grading.

    Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    N. Lysiak.

    Introduction to the biology and conservation of the whales and seals, with a particular focus on species of the Gulf of Maine. Lectures will examine many facets of marine mammal science including: taxonomy and species diversity, morphological and physiological adaptations for life in the sea, foraging ecology and behavior, reproductive cycles, bioacoustics, anthropogenic interactions, and management of threatened species. Land and open-water observations of whale and seal behavior will give students hands-on opportunities to study marine mammals in the field. Laboratory work, including dissections, may also occur pending the availability of samples.

    Outcome 1: Students can identify and explain morphological and physiological adaptations to life in seawater that are specific to marine mammals.

    Outcome 2: Students can explain the evolutionary history of cetacean and pinniped marine mammals.

    Outcome 3: Students understand the ecology of the Gulf of Maine based on seasonal patterns of productivity and resource availability.

    Outcome 4: Students can explain important aspects of the biology and ecology of marine mammals, including foraging habits and reproductive cycles of local species.

    Outcome 5: Students recognize the anthropogenic threats faced by marine mammals, including historic exploitation and current sources of mortality from human interactions.

    Outcome 6: Students can describe current conservation issues and management efforts for local marine mammal species.
  

  • BIOSM 1780 - Evolution and Marine Diversity


    (BIO-AG, BIOLS-AG, PBS-AS)      
    Summer. 4 credits. Student option grading.

    Enrollment limited to: 24 students who are either: a) matriculated students at Cornell, UNH or at any 4-year college or university; or b) incoming freshmen who will arrive at Cornell or UNH in fall. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    W. Allmon.

    Patterns of diversity and processes of evolution. Topics include the diversity of life, the fossil record, macroevolutionary patterns, the genetics and developmental basis of evolutionary change, processes at the population level, evolution by natural selection, modes of speciation, long-term trends in evolution, and human evolution.

    Outcome 1: Students will understand the underlying causal principles of evolutionary diversification.

    Outcome 2: Students will be able to apply these principles to understand historical and contemporary evolutionary scenarios.

    Outcome 3: Students will be able to identify core taxa in the tree of life, their characteristics, and understand the relationships among them.

    Outcome 4: Students will be able to use basic conceptual and analytical tools to describe complex relationships within the tree of life.

    Outcome 5: Students will be familiar with a number of experimental and synthetic approaches to analyzing and discovering evolutionary processes (microevolution) and establishing evolutionary patterns (macroevolution).

    Outcome 6: Students will discuss knowledgeably the dimensions of evolutionary issues that require decisions in our society.
  

  • BIOSM 2500 - Coastal Habitat Field Research Methods


         
    Summer. 1.5 credits. Student option grading.

    Prerequisite: one semester of introductory biology. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    G. Moore.

    An introduction to flora of the Isles of Shoals in the context of island biogeography, mapping of rare plant habitats, and the management of invasive plant species. Through both field and classroom exercises, we will consider the floristic changes the Isles experienced from past and to present, and predict trends into the future to help preserve the Isle’s unique flora.

    Outcome 1: By the end of the class, students will: Become familiar with the flora of Appledore (and possibly Star) and be able to distinguish native vs invasive species, rare species, and harmful (poisonous) species.

    Outcome 2: Know how to conduct plant surveys and apply the appropriate methodology for their intended purpose.

    Outcome 3: Document rare plant(s) using Natural Heritage’s rare species occurrence forms.

    Outcome 4: Map plant habitats using GPS, which may include natural communities, limits of invasive species stands, or location of isolated rare species.

    Outcome 5: Contribute to an ongoing island-wide floral survey and habitat mapping effort.

    Outcome 6: Produce plant habitat map(s) using GIS, Google Earth or other open source software.

    Outcome 7: Understand the factors that lead to habitat stability or floristic change over time on the island.

    Outcome 8: Completed a modest plant collection and prepare a selection of herbarium specimens to to stored at UNH’s Hodgdon Herbarium.
  

  • BIOSM 2770 - Marine Environmental Science and Conservation


    (BIO-AG, PBS-AS)      

    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology. Offered in Maine at Shoals Marine Laboratory on Appledore Island. BIOSM 2770 is not equivalent to BIOSM 1620 .

    J. Seavey.

    Introduction to the topics of environmental science and conservation of marine and coastal ecosystems. This is a critical subject as over 70% of our planet is ocean and 80% of the world’s population and 50% of Americans live in within 50-60 miles of the ocean. High levels of human use of marine and coastal systems often lead to conflict between natural ecosystems and humans. We will focus on the major principles of the biology of marine organisms and their conservation and on methods to bring human communities into a better relationship with the natural resources they enjoy and rely on. We will investigate examples and topics in the Gulf of Maine and beyond. We will explore the following topics: marine ecosystem processes; biodiversity; threats to marine ecosystems; species conservation; relevance of marine biology to current scientific, social, health, and economic arenas; and the conservation of ecosystem function and services. Course projects will revolve around working with a local land manger to construction real world management goals and actions. The overall goal of this course is to provide students with a working understanding of marine and coastal conservation biology.

    The course will include lectures and fieldwork. Lecture will cover the material described in the syllabus. Lectures are designed to include material relevant to the ecological setting of the course and as preparation for fieldwork

    Outcome 1: Understand the major divisions of marine life, and appreciate the diversity of forms, biological processes and evolutionary strategies that occur in the oceans.

    Outcome 2: Understand classic principles of conservation biology and adaptive management.

    Outcome 3: Understand relevance of marine biology to current scientific, social, health, and economic arenas.

    Outcome 4: Be familiar with an array of marine and coastal conservation problems and solutions.
  

  • BIOSM 2800 - Sustainable Fisheries


    (PBS-AS)      
    Summer (two-week session). 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    E. Chapman, E. Fairchild.

    Students will explore the theory and practice of fisheries sustainability through lectures, readings, laboratory exercises, and ground truthing in the “real world” (in the field) by interacting with local fishermen. This course will focus primarily on species harvested in the Gulf of Maine, with an emphasis on fin fish. Topics will include an overview of commercial fisheries in the Gulf of Maine: fish collection and dissections, fishing gear types and modifications, age and growth techniques, quantitative data collection and analysis, current, past and future directions in fisheries management strategies, collaborative research and ‘conservation’ fishing gear, environmental changes, perspectives from different stakeholders, hands-on demonstrations with commercial fishermen from different industries, sustainable seafood and the market-place, human dimensions of sustainable fishing (cultural and socio-economic issues).

    Outcome 1: By the end of the class, students will:
    -Provide their own definition of “sustainable fishery” and be able to discuss differing opinions regarding this term;
    -Define and discuss how fisheries have moved from a volume-based operation to one that tries to support both fishermen and marine ecosystems;
    -Comprehend challenges commercial fishermen face today;
    -Identify GOM finfish and other commercially important species;
    -Know the basic biology, distribution, and ecology of commercially important fishes in the GOM;
    -Have a historical perspective of how the fishing industry and fish stocks have changed over the past 200 years in the GOM; be able to discuss important issues surrounding the future of New England fisheries;
    -Know how fisheries data are collected and used to determine basic stock assessments;
    -Develop an understanding of the importance of “conservation gear” and “collaborative research” in today’s fisheries;
    -Have collected fisheries-related data, analyzed, and interpreted them in small groups;
    -Have researched and written a detailed paper about the changes incurred to one species over time;
    -Understand the impact of fishing on marine ecosystems and the potential influence of climate change on fisheries;
    -Be more aware of the wide range of stakeholders involved in fisheries;
    -Understand market-based factors that influence sustainable fishing and mediate human impacts on marine ecosystems.
  

  • BIOSM 3210 - Anatomy and Function of Marine Vertebrates


    (PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology or equivalent. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    S. Farina.

    Designed to introduce students to a comparative study of the principal organ systems of vertebrates (i.e., fishes, sea turtles, marine birds, marine mammals) that are specifically adapted to the marine environment. Rather than focusing only on description of anatomical structure, the anatomy of structures will be integrated with function, biological role, and evolutionary relationships. Laboratory exercises cover osteology, dissection, behavior and biomechanics.

    Outcome 1: Identify structural adaptations of marine vertebrates from the various anatomical systems.

    Outcome 2: How marine vertebrates cope with extreme environmental stresses with regard to diving, high pressure, and salinity.

    Outcome 3: Examination of sensory modalities associated with the marine environment and depth, including vision, hearing, echolocation, pressure and electroreception.

    Outcome 4: Mechanisms of animal movement by integration of structural mechanics, muscle physiology, kinematics and fluid mechanics.

    Outcome 5: Demonstrate good dissection technique.

    Outcome 6: Show independent thinking through development of a research project.

    Outcome 7: Expose students to biomechanical analysis.

    Outcome 8: Teach data analysis.

    Outcome 9: Examine evolutionary pathways and selective pressures for the development of anatomical systems to function in the marine environment.

    Outcome 10: Identify potential design elements from animals for transition to engineered systems using the biomimetic approach.
  

  • BIOSM 3290 - Field Animal Behavior

    (crosslisted) BIONB 3290  
    (PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology or equivalent. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    W. Kimler, H. Nance, H. Weeks.

    Presents the ecological significance of behaviors of coastal organisms, with emphasis on field and laboratory research methods. Lectures and readings address the major subareas of behavior (communication, orientation, social behavior, foraging, predator avoidance, and sensory mechanisms). Each student engages in short-term behavioral observation and prepares a research proposal for studying a problem within the course subject area.

    Outcome 1: Understand the scientific process as applied to field and/or laboratory investigations of behavior. Demonstrate the ability to design, conduct and present an independent investigation.

    Outcome 2: Be able to explain the role of natural selection and the influences of predictable and unpredictable environmental change in shaping behavioral patterns.

    Outcome 3: Grasp the significance, and be able to provide examples, of quantitative and qualitative measures that illustrate behavioral adaptation.

    Outcome 4: Demonstrate critical thinking in the evaluation of scientific findings.

    Outcome 5: Understand similar selection pressures operate across taxa.
  

  • BIOSM 3650 - Underwater Research


    (PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology or equivalent, recognized SCUBA certification, and approval to SCUBA dive at Shoals. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    J. Coyer, E. Siddon.

    Covers the philosophy of research, hypothesis testing and experimental design, sampling methods, various underwater techniques, diving physics and physiology, and use of dive tables. Emphasizes subtidal ecological research. Requirements include critical evaluation of several journal articles and production of a research proposal.

    Outcome 1: Understanding of basic principles in marine ecology, including competition, predation, and direct and indirect interactions, and how these forces shape the marine ecosystem in the Gulf of Maine.

    Outcome 2: Familiarization with subtidal algae, invertebrates, and fishes inhabiting diving depths around the Isles of Shoals, including species identification and life history characteristics.

    Outcome 3: Understanding of hypothesis testing, as well as aspects of experimental design including sampling method, replication, and controls.

    Outcome 4: Understanding of introductory statistics, including student’s t-test, ANOVA, and regression analyses.

    Outcome 5: Experience in designing and implementing an independent research project by observing patterns in the subtidal ecosystem and formulating testable hypotheses to explain the patterns.

    Outcome 6: Experience in analyzing and summarizing collected field data.

    Outcome 7: Experience in writing a formal Research Proposal based on the independent research project (design, data collection, analyses).

    Outcome 8: Experience in critiquing and evaluating original research proposals in an oral presentation and group discussion format.

    Outcome 9: Understanding fundamental principles of diving physics and physiology relevant to a working scientific diver.

    Outcome 10: Becoming certified in fundamental skills in First Aid, O2 administration, and CPR.
  

  • BIOSM 3740 - Field Ornithology


    (OPHLS-AG, PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college-level biology or equivalent; background in ornithology or vertebrate biology is recommended, but not required. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    K. Covino.

    The biology, ecology, and behavior of the avifauna of the Isles of Shoals. Focuses on fieldwork designed to observe and study territoriality, breeding biology, and survivorship. Students learn and apply numerous ornithological field methods including various census techniques, territory mapping, banding, behavioral observations and creating a field notebook.

    Outcome 1: To recognize the birds of the Isles of Shoals by sight and sound.

    Outcome 2: To understand and appreciate the diversity of life-history strategies pursued by these birds.

    Outcome 3: To identify evolutionary adaptations that allow birds to thrive in various environments.

    Outcome 4: To understand the conservation challenges facing bird populations and gain knowledge of approaches used to ensure the long-term persistence of seabird populations.

    Outcome 5: To learn and practice a variety of field techniques used for studying birds including banding, survey methods (point counts, transects, spot mapping), nest monitoring, and behavioral observations.

    Outcome 6: To keep an appropriate and detailed field journal.

    Outcome 7: To develop and test ecological hypotheses through an independent project, to summarize and analyze data, and to present scientific information appropriately in both written and oral form.
  

  • BIOSM 3830 - Field Marine Invertebrate Biology


    (BIO-AG, PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: one semester of college biology. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    J. McAlister.

    An introduction to the biology and diversity of the major marine invertebrate groups, with an emphasis on field and laboratory techniques. Topics and methods include functional morphology through dissection, qualitative and quantitative biotic inventory, intertidal and shallow subtidal collecting (including dredging), zonation, biotic interactions, life histories, and behavior. Mollusks, crustaceans, echinoderms, and worms will be covered in depth; other phyla will be discussed as they are encountered in the field. In addition to field and laboratory assignments, students will develop original short-term research projects that demonstrate skills in research design, data collection and analysis, presentation, and preparation for publication. Appledore Island’s unique location and varied temperate shallow-water habitats provide an excellent venue for the encounter of freshly collected, in situ representatives of more than 200 species during the 2-week course.

    Outcome 1: Through the directed study of selected marine invertebrates in a field setting, and by working as a class, in small groups, and individually in field and laboratory settings, students will develop the skills to design and complete a research project, including defining objectives, designing protocol, making course corrections, analyzing data, and presenting results in oral and written forms; master techniques of documented observation; master techniques of marine animal care in the laboratory; master techniques of field and laboratory experimentation; master techniques in qualitative and quantitative biotic inventory.
  

  • BIOSM 4450 - Field Wildlife Forensics


         
    Summer. 1.5 credits. Student option grading.

    Prerequisite: one semester of college-level biology or equivalent. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    W. Lord, W. Rodriguez, I. Sidor.

    Forensic science represents the unique merging of scientific insight and the law. Forensic Science for Marine Biologists provides a field-oriented introduction to the forensic science domain and the utilization of marine biology within the justice system. Students receive comprehensive instruction concerning the recognition, documentation, collection, and preservation of physical evidence. Additionally, students develop practical incident response, scene management, and forensic teamwork skills.

  

  • BIOSM 4650 - Shark Biology and Conservation


    (PBS-AS)      
    Summer. 3 credits. Student option grading.

    Prerequisite: At least one semester of major-level marine biology or vertebrate biology; e.g. (BIOEE 1780 /BIOSM 1780 ) Intro to Evolutionary Biology and Diversity; (BIOEE 2740 ) The Vertebrates: Comparative Anatomy, Function, and Evolution; (ANSC 3300 /BIOAP 3300 ) Fish Physiology; or similar.  Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    Staff.

    The last 30 years have produced an explosion of new information on the biology of the approximately 1,000 living species of sharks, skates, rays, and chimaeras, which collectively make up the group Chondrichthyes. This course will cover advanced topics in the evolution, diversity, anatomy, functional morphology, neurobiology, sensory systems, behavior, reproduction, development, and conservation of cartilaginous fishes.

    Outcome 1: Outcome 1: Understanding of elasmobranch phylogeny and evolution.

    Outcome 2: Outcome 2: Knowledge of how evolution has resulted in a wide variety of elasmobranch anatomical, physiological and morphological specializations.

    Outcome 3: Outcome 3: Develop a working knowledge of the research methods used to advance understanding of shark biology, ecology and conservation.

    Outcome 4: Outcome 4: Understanding of shark research, objectives and study species in the Gulf of Maine
  

  • BIOSM 4990 - Research in Biology


         
    Summer. 1.5 credits (may be repeated for credit). Student option grading.

    Permission of Assistant Director of Academic Programs required. Offered in Maine at Shoals Marine Laboratory on Appledore Island.

    J. Seavey.

    Section A: Independent Biological Research: Independent study with a member of the Shoals Marine Laboratory core faculty, based on student faculty interest and available facilities. A short proposal of research must be sent with application materials.


BME—Biomedical Engineering
  

  • BME 1110 - Seeing Science in Action


         
    Spring. 1 credit. S/U grades only.

    C. Schaffer.

    The goal of this “Learning Where You Live” course is for students to see and understand the actual practice of scientific research. Too often science is taught as a collection of static facts in a book when science professionals think of it as a highly creative and collaborative process for discovery. Many students leave science degree programs before they even have a chance to see how science really “works,” let alone actually participate. In this course, students will be learning about and seeing cutting-edge research in modern laboratories. Critically, they will see what the practice of science is like. The course will have three modules, each centered on the lab of a different Cornell faculty member. First, there will be a lecture by the STEM faculty member on their research that is targeted to the freshmen audience and emphasizes the importance of work, its application, and the process of discovery and exploration that is intrinsic to the research. During the ~2 weeks following the lecture, students in the course will spend a one day shadowing graduate students and post-docs in the STEM faculty member’s lab. Students will write a short description of what they saw and how it relates to the broader goals of the lab they learned about from the lecture. After all students have shadowed, there will be a second meeting that includes the students, and the scientists they shadowed, and the STEM faculty member. The focus of this second meeting will be discussing the experiments they saw, how they worked, how those measurements connect to the bigger picture goals for the laboratory and the project, as well as the nature of the relationships among the graduate students, post-docs, and faculty that enable this research. Finally, students will read and critically analyze a paper from the faculty member’s lab, with a third and final meeting to discuss how this final scientific product relates to the people, experiments, and process of science they saw in the lab and discussed. These activities will give students incredible insight into how science is done and its inherent excitement.

  

  • BME 1120 - Edible Engineering and Sauteed Science


         
    Fall. 1 credit. S/U grades only.

    N. Nishimura.

    This course is part of the Learning Where You Live initiative. This class will be an investigation into the science of food. We will use a blend of discussing publications and media with hands-on experimenting and tasting to explore scientific and engineering principles encountered in food and in the kitchen. Approximately 5 “labs” held in the Donlon hall kitchen.

  

  • BME 1310 - Introduction to Biomedical Engineering

    (crosslisted) ENGRI 1310  
         
    Spring. 3 credits. Student option grading.

    Enrollment limited to: freshman or sophomore standing.

    I. De Vlaminck.

    For description and learning outcomes, see ENGRI 1310 .

  

  • BME 2000 - Biomedical Transport Phenomena

    (crosslisted) ENGRD 2202  
         
    Fall. 3 credits. Letter grades only.

    Corequisite: mathematics through MATH 2930  (or equivalent).

    P. C. Doerschuk.

    Quantitative analysis of transport phenomena in physiological systems, including fluid mechanics and mass transfer. Fluid statics, mass and momentum conservation, laminar and turbulent flow, microscale and macroscale analytical methods, mass transport with biochemical reactions, applications to transport in tissue and organs.

  

  • BME 2010 - Physiology of Human Health and Disease


         
    Spring. 3 credits. Letter grades only.

    S. Suri.

    Covers essentials of human physiology, with an overview of complementary mechanisms of homeostasis and disease pathogenesis. Topics presented in a modular format incorporating an overview of basic physiological mechanisms and key diseases of specific organ systems susceptible to alterations in that physiological mechanism. Topics include: filtration and renal function, electrophysiology and cardiac arrhythmia, neural transmission and muscular dystrophy, mineral balance and osteoporosis, and lipid transport and atherosclerosis. Course utilizes best pedagogical strategies including engaged learning practices, small group discussion, and lectures by clinicians working in these areas.

  

  • BME 2110 - Biomolecular Thermodynamics


         

    Spring. 3 credits. Letter grades only.

    Prerequisite: BIOMG 1350  (preferred) or BIOG 1440 ; CHEM 2090 ; MATH 2930 ; and BME 2000 /ENGRD 2202  (or equivalent).

    J. Lammerding.

    This course serves as an introduction to thermodynamics and physical chemistry focused on the application to biomolecular systems. Topics include the role of entropy and free energy in determining biological reactions and processes such as enzymatic reactions or molecular interactions, protein folding/unfolding, single molecule mechanics, energy states, and equilibrium distribution of biomolecular and other systems.

    This course serves as the foundation for the Molecular, Cellular, and Systems Engineering (MCSE) concentration as well as the molecular principles of biomedical engineering course.

  

  • BME 2210 - Biomaterials: Foundations and Application in Medicine


         
    Fall. 3 credits. Letter grades only.

    S. Suri.

    This course focuses on the fundamental understanding of implantable materials with respect to their design, analysis and use in human health. The class content includes the fundamentals of materials synthesis/fabrication, methods of characterization/analysis, interactions between materials with tissues, quantitative analysis of material properties and how materials are used to impact human health.

  

  • BME 2310 - Biomedical Signals and Systems


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: CS 1112  or CS 1132 . Corequisite: MATH 2930 , PHYS 2213 .

    S. Adie.

    Fundamentals of time- and frequency-domain methods to model biomedical signals and systems, within the context of biomedical instrumentation and imaging. Examples covered include the analysis of signals from a pulse oximeter, the reconstruction of ultrasound or MRI images, and the analysis of a control system for robotic surgery. Topics that are covered include the Fourier transform, linear systems, convolution, transfer function, filtering, sampling and aliasing, signal modulation and demodulation, Laplace transforms, circuits and control.

  

  • BME 3010 - Cellular Principles of Biomedical Engineering

    (crosslisted) CHEME 4010  
         
    Fall. 3 credits. Student option grading.

    Prerequisite: course work in basic biology such as BIOMG 1350 ,  BIOG 1440  or BIOG 1445 , BIOMG 3300 , or BIOMI 2900 ; and mathematics through differential equations (e.g. MATH 2930 ). Permission of instructor required if pre-requisites not met.

    S. D. Archer, Y. Wang.

    Integration of mammalian cell biology with engineering modeling principles, put into the context of medical pathology and disease states. Consists of three modules: (1) cell culture techniques/receptor ligand interactions, (2) cellular trafficking, and (3) signal transduction.

  

  • BME 3020 - Molecular Principles of Biomedical Engineering

    (crosslisted) CHEME 4020  
         

    Spring. 3 credits. Student option grading.

    Prerequisite: at least one course from BIOG 1440  or BIOG 1445 , BIOMG 3320 ,  BIOMG 3330 . Instructor’s permission will be required for students who do not meet this requirement.

    S. D. Archer.

    Genomic and proteomic thinking and tools have revolutionized the way scientists study biology and medicine. We are now beginning to understand the molecular level mechanisms that underlie normal and pathologic cellular functions. As a consequence, novel molecular level approaches provide the basis for better diagnostic and therapeutic strategies to effectively treat or prevent human diseases. This course aims to present a broad overview of molecular level techniques that are relevant in many aspects of biomedical engineering.  We will discuss the underlying principles, how to interpret representative data, limitations of current approaches, and engineering challenges for the development of new and improved techniques.

    The lectures will cover existing and emerging technologies and instrumentation critical to molecular - level analysis in biomedical engineering. These will include DNA recombinant technology, design of primers, vectors and gene-modified organisms, gene therapy approaches, DNA sequencing, quantification of RNA expression, fundamentals of protein biochemistry and biophysics, protein structure determination, mass spectrometry, protein purification, thermodynamic principles of biomolecular interactions, enzyme kinetics and modes of inhibition, and design and application of nano- and microtechnologies for diagnosis and therapeutic applications.

    The laboratory work consists of three modules: DNA isolation and sequencing, surface plasmon resonance technique, and design of microfluidic systems for molecular biology applications.

  

  • BME 3030 - Measurement and Instrumentation in Biomedical Engineering


         
    Fall. 3 credits. Letter grades only.

    Prerequisite: BME 2010 , BME 2310 . Permission required if pre-requisites not met.

    C. Schaffer.

    This course aims to help students develop the mindset and skills necessary to produce high-quality measurements of a physiological or biological variable. The emphasis will be on helping students develop a broad perspective on biological and biomedical measurement, including carefully identifying the variables that should be measured to quantify a physiological or biological function, determining an approach to measuring that variable that includes tradeoffs of different approaches and integrates sensor design, designing a system to make the measurement with appropriate controls and calibrations, taking high quality data, processing this data and determining the accuracy and precision of the measurement and the degree to which it reflects the underlying biological or physiological function, and finally interpreting the measurements and describing how they could be used for research or diagnostic purposes. The course will build through increasingly open-ended measurement problems. Examples that emphasize mechanically, electrically, chemically, and optically-based measurements will be explored.

  

  • BME 3110 - Cellular Systems Biology


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: BME 3010  (or equivalent), MATH 2930  (or equivalent), MATH 2940  (or equivalent), and CS 1112  (or equivalent). Corequisite: BME 3020  (or equivalent).  Permission of instructor required if prerequisites not satisifed.

    B. D. Cosgrove.

    The behaviors of cells are increasing appreciated to be governed by a system of regulatory pathways, which processes information often in a multivariate, dynamic and non-linear fashion. The ability to reduce this complexity to predictable models is useful for designing new cancer therapies and genetically engineering cellular “machines”. The course will cover: (1) analysis of dynamic control processes in cell biology, from intracellular pathways to networks to multicellular systems; (2) principles of computational systems biology, including genomic, proteomic, and transcriptomic algorithms; and (3) principles of synthetic biology, including gene circuit design and modeling. Students will learn to solve problems using computationally implemented algorithms and models, involving statistical methods, differential equation systems, multivariate regression, and logic-based approaches. This course is designed for upper-level undergraduate and Master’s students in the biomedical, biological and/or engineering sciences.

  

  • BME 3210 - Multiscale Biomaterial Analysis


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: BME 2210  or equivalent.

    D. A. Putnam.

    The course in advanced biomaterials leads the class through the process of material design and characterization for their development as products in the medical device or pharmaceutical fields. Student teams will apply their fundamental knowledge of chemistry and biology to open-ended design challenges focused on biomaterial mechanics, processability, biocompatibility and federal regulatory requirements. Hands-on technical work in materials characterization will be combined with key knowledge of biomaterials to give the class an integrated understanding of biomaterials design and development. Specific topics to be covered are classes of biomaterials, methods of characterization, the interface of biomaterials and biology, the foreign body response, inflammation, wound healing, biofilms, sterilization methods, FDA-approval guidelines and EU-approval guidelines.

  

  • BME 3300 - [Introduction to Computational Neuroscience]

    (crosslisted) BIONB 3300 , COGST 3300 , PSYCH 3300  
         
    Fall. Next offered 2018-2019 (offered alternate years). 3-4 credits, variable. Student option grading.

    Prerequisite: BIONB 2220  or permission of instructor. Enrollment limited to: 50 students. Four credit option includes lab providing additional computer simulation exercises.

    C. Linster.

    For description and learning outcomes, see BIONB 3300 .

  

  • BME 3310 - Medical and Preclinical Imaging


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: BME 2310  or equivalent. Engineering Core complete.  Permission required if prerequisites not met.

    N. Nishimura.

    This course teaches the fundamentals and applications of medical imaging techniques, including x-ray imaging and computed tomography, nuclear medicine, magnetic resonance imaging, ultrasound, and optical imaging.  Through lecture and demonstration labs, the class provides a rigorous introduction to medical imaging, beginning with the basic physical principles of image formation on to image reconstruction and descriptions and demonstrations of the hardware used in clinical applications.  Concepts covered include resolution, point-spread-functions, modulation transfer functions, signal-to-noise, multi-dimensional Fourier transformation, image filtering in spatial domain and the structure and function of the human visual system.

  

  • BME 3410 - Systems Mechanobiology


         
    Spring. 3 credits. Letter grades only.

    Prerequisite: ENGRD 2020 , MATH 2930 , and BME 3010  (or equivalent). Permission required if prerequisites not met. 

    J. T. Butcher.

    This course analyzes how mechanical forces affect biological responses across biological scales, including molecular, cellular, tissue, organ, and organism level. Theoretical and empirical foundations and engineering approaches to applying, quantifying, and elucidating mechanobiological mechanisms across each scale will be presented. Applications in human health and disease pathogenesis will be emphasized.

  

  • BME 4010 - Biomedical Engineering Analysis of Metabolic and Structural Systems

    (crosslisted) MAE 4660  
         
    Fall. 3 credits. Student option grading.

    Prerequisite: ENGRD 2020  and basic coursework in Biology (e.g. BIOMG 1350  or BIOG 1440 ). Permission required if prerequisites are not satisfied.

    S. D. Archer, L. J. Bonassar.

    This course focuses on applying techniques of engineering analysis to quantify function of human physiologic systems. Topics of study include the cardiovascular, respiratory, musculoskeletal, and renal systems. Emphasis will be placed on relating tissue structure to organ function on micro-and macroscales.

  

  • BME 4020 - Electrical and Chemical Physiology


         
    Spring. 3 credits. Student option grading.

    Prerequisite: MATH 2930 ; and PHYS 2213 ; and BME 2000  (or BME 3310  or CEE 3310  or CHEME 3230  or MAE 3230  or ECE 3030  or ECE 3150  ); and BME 2010  (or BIOG 1440 /BIOG 1445  or BIOMG 1350 ). Permission required if prerequisites are not met.

    S. D. Archer, P. Doerschuk.

    Focuses on understanding how circulating agents and bioelectric activity comprises interorgan and central nervous system communication, and control of the human body. Additional emphasis includes examining medical devices involved in the treatment of human disease.

  

  • BME 4110 - [Science and Technology Approaches to Problems in Human Health]


         

    Fall. 3 credits. Student option grading.

    Enrollment limited to: junior, senior, or graduate standing; sophomores by permission of instructor.

    N. Nishimura.

    BME 4110 will provide an in-depth look at diseases that impact human health along with current scientific research and engineering that is aimed at addressing these problems. Faculty from Weill Cornell Medical College will come to the Cornell campus to discuss the health problems they are currently unable to treat as well as they would like. For each disease discussed, faculty from both Cornell University and Weill will talk about current research aimed at better understanding disease process, developing new treatment strategies, and ultimately improving patient outcomes. Five to six topics will be explored in depth over the course of the term. This course is particularly appropriate for students considering medical school or careers in biomedical science and engineering.

    In addition to the lectures, opportunities for informal interactions with the faculty teaching the course (those from both Weill Cornell Medical College and Cornell University) will be available, including small question and answer sessions after class, as well as lunches with the faculty.

  

  • BME 4190 - Laboratory Techniques for Molecular, Cellular, and Systems Engineering


         
    4 credits. Letter grades only.

    Prerequisite: BME 3010 ; BME 3020 ; and BME 3110  or BME 3210 . Course serves as the MCSE Concentration Practicum Laboratory. BMDD students may also use this course to serve as their practicum lab.

    C. Fischbach-Teschl.

    This class will provide students with the skills needed for the design, fabrication, and characterization of experimental approaches relevant to Molecular, Cellular, and Systems engineering. Lectures will integrate three modules: the first module will focus on stem cell biology, differentiation, and characterization. The second module will provide a thorough understanding of polymeric scaffold design and characterization for tissue engineering applications. The third module will focus on analytic techniques suitable to analyze molecular, cellular, and systems-level signaling changes of cells in response to varied microenvironmental context. All three modules will be taught in a manner that will enable students to design and implement experimental approaches for cell manufacturing, tissue regeneration, and drug testing.

  

  • BME 4390 - Circuits, Signals and Sensors: Instrumentation Laboratory


         
    Fall. 4 credits. Letter grades only.

    Prerequisite: Engineering core math/science courses complete (with CS 1112  or CS 1114  preferred); and BME 2310  (or equivalent). Course serves as the BMII Concentration Practicum Laboratory.

    W. Zipfel.

    This class will provide students with the skills needed for the design and fabrication of biomedical and bioanalytical instrumentation. In lecture cover analog and digital electronics, optoelectronics and programing required for microprocessor use (C/C++). The level of electronics covered is equivalent to PHYS 3600/AEP 3610  (level of Horowitz and Hill) with the addition of exposure to schematic and printed circuit board layout using (CAD) software. Emphasis is on designing and building analog circuitry for sensors (electrochemical, flow, pressure), photodetectors and other measuring devices, analog to digital conversion and interfacing. Basic optics and opto-electronics is covered with a focus on areas relevant to biomedical imaging and bioanalytical device design. Lectures will be coordinated with lab exercises to provide experience with the material being covered in lecture. Lab exercises include hands-on building of circuits and optical set-ups, and exposure to schematic capture/PCB layout software (Eagle CAD) as well as SPICE simulation software. This course serves as an introduction to the array of skills needed by biomedical engineers who chose to focus on instrument design and imaging.

    Outcome 1: Become proficient with analog electronics and analog circuit design at the level required to design and build a various biomedical devices.   (ABET a,k)

    Outcome 2: Become proficient with digital electronics and digital circuit design at the level required to digitize signals and collect data from a biomedical device.   (ABET a,k)

    Outcome 3: Become proficient with hardware programing of microcontrollers in C to implement microcontroller/peripheral device interfacing and microcontroller –PC communications and data transfer. (ABET a,k)
  

  • BME 4440 - Science Policy Bootcamp: Concept to Conclusion


    (CU-CEL)     
    Spring. 3 credits. Letter grades only.

    C. Schaffer.

    Science Policy Bootcamp: Concept to Conclusion, is an interdisciplinary service-learning course where students will explore the trends that shape science and innovation policy, understand core science policy concepts and engage in active policymaking work. This three-credit course will comprise of a three-hour long session that will meet every week. The first hour of each session will be devoted to broadening student’s perspective on science policy. The following two hours will be spent working in groups on the primary activity of the course - a science policy advocacy project that builds over the full semester. Working in small groups, students will identify a key science policy issue. Together, they will thoroughly research the issue and contact key stakeholders, formulate a detailed plan to address the issue, and unique to this course - implement their plan for solving the problem toward the end of the semester. Examples may include drafting legislation, commenting on Federal or State rulemaking procedures, launching public outreach campaigns, or raising press awareness of an issue. This aspect of the course will include both mentored work in developing the idea and advocacy plan, as well as activities to build the skills necessary to be an effective policy advocate. Examples of such activities include mock press interviews and lobbying visits. As a result of the final project - students will have the unique opportunity to address a bona fide policy issue and create a working solution.

  

  • BME 4640 - Orthopaedic Tissue Mechanics

    (crosslisted) MAE 4640  
         
    Spring. 3 credits. Letter grades only.

    Prerequisite: ENGRD 2020 , MAE 2120 , MAE 3250  or permission of instructor. Co-meets with MAE 4641 /MAE 5640 .

    C. Hernandez.

    For description, see MAE 4640 .

  

  • BME 4900 - Independent Undergraduate Project in Biomedical Engineering


    (CU-UGR)     
    Fall, spring. 1-8 credits, variable. Student option grading.

    Staff.

    Research or projects by an individual or a small group of undergraduates.

  

  • BME 4910 - Principles of Neurophysiology

    (crosslisted) BIONB 4910 , ECE 4910  
         
    Spring. 4 credits. Student option grading.

    Prerequisite: BIONB 2220  or written permission of instructor. Enrollment limited to: 28 students. Neurobiology and Behavior concentrators must take class for a letter grade.

    B. R. Johnson.

    For description and learning outcomes, see BIONB 4910 .

  

  • BME 4970 - Undergraduate Teaching in Biomedical Engineering


         
    Fall, spring. 3 credits. Letter grades only.

    Permission of instructor required.

    J. Butcher.

    The student assists in teaching a biomedical engineering course appropriate to their previous training. The student may meet with a discussion or laboratory section, prepare course materials, grade assignments, and regularly discuss objectives and techniques with the faculty member in charge of the course.

  

  • BME 4980 - [Introduction to Systems and Synthetic Biology]

    (crosslisted) ECE 3530  
         
    Fall. 4 credits. Letter grades only.

    Staff.

    For description, see ECE 3530 .

  

  • BME 5010 - Bioengineering Seminar


         

    Fall, spring. 1 credit. S/U grades only.

    Permission of instructor required. Enrollment limited to: M.Eng. students only. BME 5010 is no longer required for the BME minor.

    N. de Faria.

    Students must attend and report on 10 self-selected seminars to fulfill the requirements of the course.

    Self-selected seminars may include topics related to bioengineering, engineering and biology or life science. Seminars offered at other universities or at national scientific meetings may be used as long as the topic is relevant.

    All students must be enrolled in Blackboard. Official course registration through Cornell’s system now automatically enrolls you in Blackboard. All communications about the course and its requirements will be sent through Blackboard. Also, the final report must be downloaded and re-uploaded via Blackboard in order to receive a grade.

    The 10 seminars that you attend must be summarized in the final report found under “Assignments” in Blackboard. Download a copy of the form and rename the file with your name and netID. Give a 2 sentence summary of each seminar along with the date, name and affiliation of the speaker and seminar title and location. We will check for reporting on cancelled seminars. Once completed, your report should be uploaded to Blackboard under the same location in “Assignments” by the first Monday after the last day of classes. Click on the title in bold next to the book icon to find the report submission page.

    REMINDER: Cornell’s Code of Academic Integrity requires that you not misrepresent your attendance at these seminars.

  

  • BME 5030 - [Electronic Bioinstrumentation]

    (crosslisted) ECE 5030  
         
    Spring. 4 credits. Letter grades only.

    Prerequisite: introductory biology, analog design, signal processing, at the level of BIOL 1010, ECE 3150  and ECE 4250  respectively. Permission of instructor required. Enrollment limited to: M.Eng. students only.

    Staff.

    For description, see ECE 5030 .

  

  • BME 5040 - Introduction to Neural Engineering

    (crosslisted) ECE 5040  
         
    Spring. 3 credits. Student option grading.

    Prerequisite: ECE 2200  and ECE 3150 , or permission of instructor.

    M. Shoaran.

    For description, see ECE 5040 .

  

  • BME 5100 - Clinical Preceptorship for Biomedical Engineers


    (CU-CEL)     

    Fall, spring. 2 credits. Student option grading.

    Permission of instructor required. Enrollment limited to: BME M.Eng students.

    N. de Faria, R. Karpman.

    Preceptorship, is a well-known process in healthcare education and described as a short term relationship between a student as novice and an experienced health care professional, who provides individual attention to the student’s learning needs within a clinical environment. The BME 5100 leverages this methodology and enable our students to experience the dynamics of a clinical environment, observe the routine practice of a clinician, identify potential needs, and through a formal process evaluate the merits and provide ideas on how to address these perceived needs. The instructor will educate the students about the clinical environment, dress and behavior code, interaction with hospital staff and patients, as well as monitor and manage each student-preceptor team. The instructor and other engineering faculty will also review the student’s experiences and assist in any assignments the preceptor may have given to the student. The preceptor will guide the student with in depth knowledge of the related anatomy, physiology and pathology associated with his specialty. The preceptor will also provide the student the ability to participate and observe as well as generate weekly assignments. The sponsoring institution and the preceptors are very interested in the identified problems, the ideas resultant of the process, and how these ideas could be addressed by applying principles of engineering. The student will provide feedback in the form of a final report as well as an on-site poster presentation at the end of the academic year. The merited ideas will be placed in the pipeline for the sponsored design projects (BME 5910 , BME 5920 ).

     

  

  • BME 5200 - [Fundamentals of Biomaterials in Science and Engineering]


         
    Fall. 3 credits. Letter grades only.

    Enrollment limited to: seniors and graduate students.

    Staff.

    Introduction to fundamentals of biomaterials science and engineering focusing on biological performance of man-made or modified natural materials: degradation of materials in biological environments and biological effects of materials and their degradation products, locally, systemically and at remote sites.

  

  • BME 5390 - Biomedical Materials and Devices for Human Body Repair

    (crosslisted) FSAD 4390  
         
    Spring. 2-3 credits, variable. Student option grading.

    Prerequisite: college natural science requirement (chemistry or biology). Enrollment limited to: junior or senior standing.

    C. C. Chu.

    For description, see FSAD 4390 .

  

  • BME 5400 - [Biomedical Computation]


         
    Fall. 3 credits. Student option grading.

    Prerequisite: MATH 2930  and MATH 2940  (or equivalent), and introductory computer programming course.

    M. R. King.

    The application of numerical and statistical methods to model biological systems and interpret biological data, using the MATLAB programming language.

  

  • BME 5500 - Innovation and Design of Biomedical Technologies


         
    Fall. 3 credits. Student option grading.

    Enrollment limited to: graduate standing. Requirement for M.Eng in BME.

    N. de Faria.

    This course was designed to addresses the business, regulatory, and technical challenges throughout the many design phases of a biomedical technology product life cycle. It is a required and essential course for the BME Masters of Engineering program and it lays the foundation to the also required BME 5910  (Design Project) and BME 5920  (Performance of Design Project).

  

  • BME 5620 - Biomineralization: The Formation and Properties of Inorganic Biomaterials

    (crosslisted) MSE 5620  
         
    Spring. 3 credits. Letter grades only.

    Prerequisite: MSE 3010  or CHEM 1570  or CHEM 3570 -CHEM 3580  or equivalent or permission of instructor.

    L. Estroff.

    For description, see MSE 5620 .

  

  • BME 5700 - [Biophysical Methods]

    (crosslisted) AEP 4700 , BIONB 4700 , VETMM 4700  
         
    Fall. Next Offered 2018-2019. 3 credits. Letter grades only.

    Prerequisite: solid knowledge of basic physics and mathematics through sophomore level. Recommended prerequistie: some knowledge of cellular biology.

    Staff.

    For description, see AEP 4700 .

  

  • BME 5710 - Analytical Techniques for Material Science

    (crosslisted) MSE 5710  
         
    Fall. 3 credits. Letter grades only.

    Prerequisite: MSE 2060 .

    C. Watson.

    For description, see MSE 5710 .

  

  • BME 5740 - [Protocols and Fundamentals of Surgery]


         
    Fall. 3 credits. Letter grades only.

    S. Solomon.

    It has been well established that practical experience enhances didactic learning. The aim of this course is to expose students of engineering to the day to day aspects of working in an Operating Room and to understand the art and science of surgery so that they can better serve the surgical community when working in the medical field upon graduation. The lectures are supplemented with experiential learning in a hands-on, training operating room using synthetic and preserved animal specimens at Cornell’s prestigious School of Veterinary Medicine. Surgical scrub, gowning, gloving, instrumentation, suturing, internal fixation, as well as surgical documentation, pre and post operative protocols, aseptic technique and medical terminology will be explored.

  

  • BME 5780 - [Computer Analysis of Biomed Images]

    (crosslisted) ECE 5780  
         
    Spring. 4 credits. Letter grades only.

    Permission of instructor required.

    A. Reeves.

    For description, see ECE 5780 .

  

  • BME 5810 - Soft Tissue Biomechanics

    (crosslisted) MAE 5680  
         
    Fall. 3 credits. Letter grades only.

    Enrollment limited to: graduate standing; seniors by permission of instructor.

    J. T. Butcher.

    Introduces concepts of biomechanics applied to understanding the material behavior of soft tissues. Topics include finite strain, nonlinearities, constitutive frameworks, and experimental methodologies. Tissues to be modeled include tendons, blood vessels, heart valves, cartilage, and engineered tissues.

  

  • BME 5830 - Cell-Biomaterials Interactions


         
    Spring. 3 credits. Student option grading.

    Prerequisite: BME 3010  and BME 3020  or equivalent, or permission of instructor.

    S. Suri.

    Biological principles underlying biomaterial design and cellular adhesive behavior, incorporating biomechanical analysis across the molecular, cellular and tissue length scales.  We will take an in-depth look at design considerations and biomaterials analysis, incorporating reading from the primary literature as well as the text.

  

  • BME 5850 - Current Practice in Tissue Engineering


         
    Fall. 3 credits. Student option grading.

    Corequisite: BME 3010 , BME 3020 , or BME 4010 .

    S. Suri.

    Covers fundamental biological principles and engineering concepts underlying the field of tissue engineering and describes specific strategies to engineer tissues for clinical use along with examples.

  

  • BME 5875 - Frontiers in Biomedical Research for Teachers


         
    Summer. 3 credits. Letter grades only.

    Permission of instructor required. Enrollment limited to: middle and high school teachers participating in summer research experiences.

    C. Schaffer, J. Butcher.

    The goal of BME 5875 is to help middle and high school science teachers increase their knowledge in key topics of relevance for biomedical science and for them to gain a sense of how new scientific knowledge is generated. This new knowledge and understanding of science topics and the process of science will then enable these teachers to provide better classroom instruction to their students. 

  

  • BME 5910 - Preliminary Study for Design Project


         
    Fall, spring. 2 credits. Student option grading.

    Requirement for M.Eng. students majoring in BME. Students encouraged to register for two semesters as continuing course.

    D. Lipson, staff.

    Design and economic evaluation of a biomedical engineering device or therapeutic strategy. Team projects are encouraged.

  

  • BME 5920 - Performance of Design Project


         
    Fall, spring. 4 credits. Letter grades only.

    Prerequisite: BME 5910 . Requirement for M.Eng. students majoring in BME. Performance of the M.Eng. design project developed in BME 5910 .

    D. Lipson, staff.

    Once a proposal for the project has been approved by the Sponsor or Faculty member, the student must (“deliver on time and under budget”) produce a tangible work product. Scheduling activities, ordering supplies, assembling, testing the device or procedure, and documenting the work and outcomes are the key expectation for the project. 

  

  • BME 5930 - Independent Design Project


         
    Fall, spring. 1-6 credits, variable. Student option grading.

    Corequisite: BME 5910 . Permission of department required. Enrollment limited to: graduate standing.

    D. Lipson, staff.

    Graduate-level, non-thesis research or studies on special projects in biomedical engineering.

  

  • BME 6110 - Stem Cell Bioengineering


         
    Fall. 3 credits. Letter grades only.

    Prerequisite: Cellular biology (BME 3010  or equivalent) and molecular biology (BME 3020  or equivalent), differential equations (MATH 2930  or equivalent), linear algebra (MATH 2940  or equivalent), and computer programming (Matlab preferred: CS 1112  or equivalent). Enrollment limited to: graduate standing or permision of instructor.

    B. Cosgrove.

    This course explores the interface of stem cell biology and bioengineering and will examine how quantitative analysis and modeling approaches inform stem cell-based biotechnologies and medical therapies. The course covers (i) cell and molecular biotechnology concepts, (ii) embryonic and adult stem cell biology fundamentals, (iii) analysis, design, and production of biomolecular therapies to regulate stem cell function, and (iv) generation of biomimetic and bioreactor environments to generate cell biotechnological products, including stem cell derivatives. This course is designed for graduate students in the biological and/or engineering sciences but will be accessible and engaging for Master’s students and advanced undergraduates (with instructor permission), especially those with successful experiences with the pre-requisite material.

  

  • BME 6120 - Precision and Genomic Medicine


         

    Fall. 3 credits. Letter grades only.

    Suggested prerequistes: introductory genetics, introductory probability and statistics, and basic R-programming skills (or a willingness to acquire those skills independently).

    I. De Vlaminck.

    Genomic medicine is gaining momentum across the entire clinical continuum. This class will provide an introduction to the latest advances in genome research and their impact on medicine. This 3-credit graduate level course focuses on quantitative engineering principles and precision measurements.

    The course has a modular structure and tackles a broad range of topics. Course modules will start with a discussion of molecular principles and basic concepts relevant to the module topic, will then proceed with a discussion of contemporary examples and applications, supported by a discussion of recent literature, and will incorporate discussion of relevant computational biology concepts. Topics will include:

    i) Foundational principles of precision medicine, with an introduction to the human genome, a discussion of modern DNA and RNA sequencing technologies, and basic principles of genome analyses;

    ii) A survey of cancer genomes, and an introduction to precision measurements of the genetic diversity within tumors;

    iii) Principles of precision diagnostics, a discussion of omics-enabled prenatal testing, organ transplant monitoring and cancer diagnostics. An in-depth discussion of the structure, function and diversity of the circulating genome.

    iv) Overview of the impact of genomics on Infectious disease. Measurements of viral sequence diversity and the implications for antiviral therapy. Discussion of the concept of viral quasi-species. Brief introduction to the human microbiome, with a focus on measurement principles;

    v) Gene expression in human tissues. Discussion of recent advances in single-cell genomics, with a focus on technologies and applications;

    vi) Principles of immune repertoire sequencing;

    vii) Omics-enabled analyses of the epigenome and the three dimensional structure of the genome.

  

  • BME 6130 - Engineering the Microbiome


         
    Fall. 3 credits. Letter grades only.

    Suggested prerequisites: introduction to genetics, molecular biology/engineering (BME 3020  or equivalent), and computer programming familiarity (python and/or R preferred but not required).

    I. Brito.

    The human microbiome impacts human health in a multitude of ways. To achieve a specific health outcome, we can modify the compositions of the microbiome, the molecules microbes produce, how they interact or how our body interacts with them. Yet, our current toolbox is fairly limited. In this course, we will examine current methods for intervening in the microbiome, but focus primarily on cutting-edge technologies for microbiome-related therapeutics. This will include synthetic biology and genetic engineering approaches. Topics will include: probiotics, antibiotics, drug discovery, live bacterial therapeutics, biosensors, phage therapies, bacterial evolution and engineering immune responses. We will touch on the safety implications of using different biological technologies. This course is designed for graduate students or Masters and advanced undergraduate students (with advanced permission). There will be a computational component to this course, although no prior computational experience is required.

  

  • BME 6180 - Principles of Magnetic Resonance Imaging

    (crosslisted) ECE 5180 , VETCS 6180 
         
    Fall. 3 credits. Letter grades only.

    Prerequisite: calculus based physics and knowledge of Fourier transformation. Three credit enrollment requires functional knowledge and skills of linear algebra, calculus, Fourier transformation, and calculus-based physics. The students will have hands-on experience to scan phantoms at Cornell MRI facility. The students may also attend field trips to the Cornell University Hospital for Animals and Cayuga Medical Center (Weill Cornell Medical Center for students at NYC campus) to observe imaging in clinical practice, pending on hospital courtesies.

    Y. Wang.

    After a brief overview of all major medical modalities: x-ray, CT, MRI, SPECT/PET, and US, this course will focus on the formulations of spatial encoding and image contrasts as exemplified in MRI. The inverse problem between detected signal and image source will be discussed for biomedical applications. The concepts of image resolution, image contrast, SNR, and scan time will be illustrated quantitatively from an engineering point of view.

  

  • BME 6210 - Engineering Principles for Drug Delivery

    (crosslisted) CHEME 6310  
         
    Fall. 3 credits. Student option grading.

    Prerequisite: background in organic and polymer chemistry or permission of instructor. Enrollment limited to: graduate standing.

    D. A. Putnam.

    Application of engineering design principles to problems in drug formulation and delivery. Specific topics include traditional drug formulation, mechanisms and kinetics of pharmaceutical stability, stimuli-sensitive systems, controlled-release devices, prodrugs, targeted drug delivery, transdermal drug delivery, biomaterials, and gene therapy. 

  

  • BME 6260 - Optical Microscopy and Fluorescence Methods for Research


         

    Spring. 3 credits. Student option grading.

    Prerequisite: physics, biology and calculus. You are expected to be able to carry out college level engineering math.

    W. R. Zipfel.

    BME 6260 covers the fundamental optics, photophysics, spectroscopy and instrumentation required for understanding how to apply all modes of modern fluorescence microscopy, bioanalytical methods and single molecule fluorescence techniques for biomedical research and diagnostics. 

    Material covered includes:

    (1) Theory and practical application of lenses, mirrors, dispersive elements, light sources, optical fibers, detectors, interference, nonlinear optical concepts and tissue optics.

    (2) Optical systems analysis concepts such as resolution, optical transfer functions, Fourier optics and convolution.

    (3) Photophysical analysis, such as photochemistry and photon statistics. 

    (4)  Both a lecture based and lab module based survey of the types of light microscopy and fluoresce methodologies used in modern biomedical research.  The lab modules provide the students with hands-on experience with all forms of light microscopy now used in biological and biomedical research.

 

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