Wed Dec 2 12:24:01 2009
| Effective Term: |
New:
1109 - Fall 2010 Old: 1089 - Fall 2008 |
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Catalog Description: |
New:
Fundamentals
of cellular/molecular biology. Chemistry of proteins, lipids, and
nucleic acids. Applications to biomedical engineering.
Function/dynamics of intracellular structures and differentiated animal
cells. Emphasizes application of physical/chemical fundamentals to
modeling cellular/subcellular processes. Lecture/lab. Old: Fundamentals of cellular/molecular biology. Chemistry of proteins, lipids, and nucleic acids. Applications to biomedical engineering. Function/dynamics of intracellular structures and differeniated animal cells. Emphasizes application of physical/chemical fundamentals to modeling cellular/subcellular processes. Lecture/lab. |
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CCE Catalog Description: |
New:
Fundamentals
of cellular/molecular biology. Chemistry of proteins, lipids, and
nucleic acids. Applications to biomedical engineering.
Function/dynamics of intracellular structures and differentiated animal
cells. Emphasizes application of physical/chemical fundamentals to
modeling cellular/subcellular processes. Lecture/lab.
Old: <no text provided> |
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Years most frequently offered: |
New:
Every academic year
Old: Other frequency |
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Term(s) most frequently offered: |
New:
Fall Old: Fall, Spring |
| Component 1: |
New:
LEC (with final exam) Old: LAB (no final exam) |
| Component 2: |
New:
LAB (no final exam) Old: LEC (with final exam) |
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Course Prerequisites for Catalog: |
New:
&CHEM 1022, &MATH 1372, &PHYS 1302 Old: CHEM 1022, MATH 1372, PHYS 1302, [% or @] |
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Enforced Prerequisites: (course-based or non-course-based) |
New:
&CHEM 1022, &MATH 1372, &PHYS 1302 Old: 000021 - Institute of Technology student |
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Faculty Sponsor Name: |
New:
David Odde Old: |
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Faculty Sponsor E-mail Address: |
New:
oddex002@umn.edu Old: |
| Student Learning Outcomes: |
* Student in the course:
- Can identify, define, and solve problems
New:
Please explain briefly how this outcome will be addressed in the course. Give brief examples of class work related to the outcome. Building on examples in class, problems are identified, defined, and solved by students in homework assignments. For example, students use Monte Carlo computer simulations to test hypotheses regarding the role of Brownian motion in living cells. In addition, problems are identified, defined, and, solved in the laboratory. For example, students use live cell digital light microscopy to test models for cytoskeletal filament self-assembly and of bacterium swimming (see example laboratory description ¿lab5.pdf¿ and movie ¿bacterium_swimming.mov¿). How will you assess the students' learning related to this outcome? Give brief examples of how class work related to the outcome will be evaluated. Students are evaluated based on individual and group homework assignments and lab reports requiring mathematical & statistical analysis, physical principles and critical reasoning in the assessment of biological principles/hypotheses. Old: unselected - Have mastered a body of knowledge and a mode of inquiry
New:
Please explain briefly how this outcome will be addressed in the course. Give brief examples of class work related to the outcome. Mastering the body of knowledge and the scientific mode of inquiry is addressed via lectures and textbook reading. For example, the textbook currently in use (Essential Cell Biology by Alberts et al., Garland, www.garlandscience.com/textbooks/0815341296.asp) contains ¿How We Know¿ sections that cover the history and development of scientific knowledge and modes of inquiry in cell biology. In addition, lectures cover how our understanding of basic cellular processes, such as mitosis and apoptosis, has evolved over time. The scientific mode of inquiry is mastered in the laboratories where observations are made to test a biological hypothesis. For example, the worm-like chain model is used to describe the mobility of proteins in solution. Students make predictions based on the worm-like chain model, and then test the predictions experimentally. They conduct a quantitative statistical analysis of the data they collected in order to reach a scientifically based conclusion regarding the applicability of a random coil polymer model. In so doing students learn the physical basis of gel electrophoresis, a major methodology of the scientific approach to biology. How will you assess the students' learning related to this outcome? Give brief examples of how class work related to the outcome will be evaluated. Students are evaluated in terms of their mastery of the body of knowledge by in-class examinations. The mastery of a mode of inquiry is assessed via laboratory reports, where student must demonstrate that they understand how to conduct a scientific laboratory study. Old: unselected |
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Requirement this course fulfills: |
New:
BIOL
- BIOL Biological Sciences
Old: |
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Criteria for Core Courses: |
Describe how the course meets the specific bullet points for the proposed core
requirement. Give concrete and detailed examples for the course syllabus, detailed
outline, laboratory material, student projects, or other instructional materials or method.
Core courses must meet the following requirements:
New: They explicitly help students understand what liberal education is, how the content and the substance of this course enhance a liberal education, and what this means for them as students and as citizens: Students will be taught what liberal education is by learning the fundamental concepts of cellular and molecular biology, including evolution, energy, forces, molecular recognition, and heredity. These concepts are essential to appreciating biology in its broadest sense, and by extension to understanding how they impact basic human endeavors such as medicine and technology development, both of which are central to biomedical engineering. Understanding these concepts will be conveyed as important for a college education and beyond as citizens by discussing the cellular and molecular basis of current medical treatments. Doing so will allow students to critically evaluate new and emerging biomedical technologies, such as stem cell therapies, which means they will be better informed as engineers and as citizens. The engineering focus of the course provides a natural context for relating the meaning of biological principles to practical applications and societal consequences. They employ teaching and learning strategies that engage students with doing the work of the field, not just reading about it: Students engage with doing the work of the field by conducting laboratory experiments where hypotheses are critically evaluated based on data they themselves collected. For example, students test whether the random-coil model of polymer mechanics provides as adequate description of the spatial segregation of proteins undergoing gel electrophoresis. Students must test the null hypothesis using statistical analysis and critically assess whether the data they have collected are consistent with the model. In doing so, students apply the tools of statistical hypothesis testing and use them to inform their final conclusions They include small group experiences (such as discussion sections or labs) and use writing as appropriate to the discipline to help students learn and reflect on their learning. Wet laboratories are conducted in 4 groups of 3 students each for a total of 12 students in the laboratory at any one time under the supervision of a graduate teaching assistant. Written laboratory reports are submitted for each experiment and require students to critically evaluate a stated hypothesis based on their own data using rigorous statistical methods. Computer simulation labs will be added to complement the wet labs, introducing students to the power and pitfalls of using simulations to assess parametric sensitivity and effect of assumptions on simulation outcomes. They do not (except in rare and clearly justified cases) have prerequisites beyond the University's entrance requirements: The purpose of liberal education approval for BMEn 2501 will be to specifically serve the students in the B.Bm.E. program, who are required to take this course to complete the degree. The course uses an engineering approach to cellular and molecular biology where mathematics, physics, and chemistry are vital to understanding how cells work. To teach the course at this level, students must have already taken, or be taking concurrently, introductory level mathematics, physics, and chemistry (Math 1372, Phys 1302, and Chem 1022). Requiring B.Bm.E. students to take another biology course at the 1000-level, which is not required for the B.Bm.E. degree, would mean that the total credit load for the degree would exceed the 128 total credit limit for bachelor¿s degrees. If students were required to take a 1000-level biological science course, it would mean that the requirement for advanced engineering and science coursework would be dropped from 27 credits to 24 credits. This would in turn weaken the technical preparation of the students who are entering a highly competitive job market where they will be expected to design and fabricate technologically advanced medical devices that are both safe and effective. It is also worth noting that biological principles are vital to all the required B.Bm.E. courses (total of nine courses minimum beyond BMEn 2501 plus Phsl 3063 Physiology with laboratory). Therefore, it would be far more intellectually challenging for the B.Bm.E. students if BMEn 2501 were approved for liberal education, rather than requiring students to take another 1000-level course, taught at a lower level than BMEn 2501. Since there are at present 13 1000-level courses already approved for the Biological Science requirement, university students already have ample course options available to them and so are not harmed by approval of BMEn 2501 for the Biological Science Liberal Education requirement. They are offered on a regular schedule: BMEn 2501 has been taught annually since 2000, and, since it is required for the Bachelor of Biomedical Engineering (B.Bm.E.) degree, will continue to be offered annually for the foreseeable future. They are taught by regular faculty or under exceptional circumstances by instructors on continuing appointments. Departments proposing instructors other than regular faculty must provide documentation of how such instructors will be trained and supervised to ensure consistency and continuity in courses: BMEn 2501 has been taught by regular faculty members (Profs. David Odde and Jonathan Sachs) and will continue to be for the foreseeable future. The instructors publish regularly in leading cellular and molecular biology journals, and serve as journal referees and editorial board members as well. They have a combined 17 years of tenured/tenure-track faculty experience and have each taught BMEn 2501 multiple times. Old: Students are taught how molecular, cellular, and physiological processes, including disease processes, can be understood by application of fundamental physical principles (i.e. mechanical, chemical, and electrical). For example, to establish the gradients in ion concentration that allow electrical impulses to be generated in the nervous system, the cell must do work against both an electrical field gradient and a concentration gradient. The energy requirements for this transport must be met by some energy source, which turns out to be the hydrolysis of ATP. Theory and experiment are intimately linked in the laboratory component of BMEN 2501 and in the entire BMEN 3701 course. Students in BMEn 2501 conduct experiments where the biological behavior depends directly on the physical processes covered in the lecture component and in the students earlier coursework in physics, chemistry, and mathematics. Students in BMEn 3701 conduct experiments that apply the systems physiology knowledge acquired in Phsl 3061 Principles of Physiology and the bioinstrumentation knowledge acquired in BMEn 3201 Bioelectricity/instrumentation to physiological measurements. Fundamental theories are introduced, often with historical perspective on their development, and integrated into the laboratory experiments, which are designed to show the theories can be validated but have limitations. That the theories used (e.g. Hookes Law, Stokes Law, etc.) are named after specific scientists reinforces to the students that these principles are human constructs. The relationships between simple and complex systems is the essential characteristic of these courses as they attempt to explain to students how the simple principles governing the behavior of individual molecules leads to the amazingly complex behavior exhibited by cells, tissues, and organs. Students learn that scientists approach medical problems systematically by formulating hypotheses, and then testing the predictions of their hypotheses against the observed behavior of living systems. They also learn that the scientific method has enabled a tremendous increase in our understanding, and our technological capability, both of which have a dramatic effect on society in predictable and unpredictable ways. As engineering courses, the primary skills that students are taught is how to identify, formulate, and solve problems. The analysis of biological systems is one of the essential skills of the biomedical engineer, and one that is developed primarily by homework assignments that require quantitative analysis and reasoning. The laboratory components require students to conduct the experiments in a hands-on environment where students make quantitative observations, process the data into a usable form, and then analyze the results by comparison to the expected results predicted by theory. Students are required to explain any discrepancies they may observe in terms of the assumptions made in the development of both the theory and the experiment. |
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Provisional Syllabus: |
Please
provide a provisional syllabus for new courses and courses in which
changes in content and/or description and/or credits are proposed that
include the following information: course goals and description;
format/structure of the course (proposed number of instructor contact
hours per week, student workload effort per week, etc.); topics to be
covered; scope and nature of assigned readings (texts, authors,
frequency, amount per week); required course assignments; nature of any
student projects; and how students will be evaluated. The University policy on credits is found under Section 4A of "Standards for Semester Conversion" at http://www.fpd.finop.umn.edu/groups/senate/documents/policy/semestercon.html . Provisional course syllabus information will be retained in this system until new syllabus information is entered with the next major course modification, This provisional course syllabus information may not correspond to the course as offered in a particular semester. New: Instructor: D. Odde, Ph.D. Professor Department of Biomedical Engineering, University of Minnesota Room 7-132, Nils Hasselmo Hall phone: 612-626-9980 oddex002@umn.edu Meeting Time: MWF 1:25-2:15 Meeting Place: Lecture: Tate Laboratory of Physics Room 170, Laboratory: Shepherd Laboratories 462/466 Office Hours: T 11-12, Th 4-5 in BSBE 7th Atrium Web Page: webct.umn.edu TAs: Clarence Chan (chan0659@umn.edu), Keegan Haselkorn (hase0063@umn.edu), Dan Toso (toso0005@umn.edu), office hours TBA on webct. Objectives: 1) Learn basic structure and function of cells and their molecules. 2) Be able to apply fundamentals of physics, chemistry, and mathematics to problems in cellular and molecular biology. Textbook: Alberts et al., Essential Cell Biology, 3nd edition, 2009, Garland. Week Date Topic Laboratory Reading 1 Jan. 18 Introduction to course, Cells Ch. 1 Jan. 20 Microscopy 2 Jan. 23 Chemical components of cells 1: Cell Structures and Microscopy Ch. 2 Jan. 25 Diffusion-r.m.s. displacement, Fick's Law Jan. 27 Diffusion-Fick's Law, Stokes-Einstein 3 Jan. 30 Free energy-G, Go Feb. 1 Free energy/kinetics-K,k1,k-1 Ch. 3 Feb. 3 Computer simulation via Matlab 4 Feb. 6 Diffusion-limited kinetics, Langmuir isotherm 2: Protein Separation Ch. 4 Feb. 8 Forces-gravity, centrifugal, drag, electric Ch. 5 Feb. 10 Forces and energy,M-M kinetics 5 Feb. 13 Exam 1 Feb. 15 DNA replication, repair, and function Ch. 6 Feb. 17 DNA to protein, kinetic modeling Ch. 7 6 Feb. 20 Control of gene expression 3: DNA Restriction Enzyme Reactions Ch. 8 Feb. 22 Control of gene expression Ch. 8 Feb. 24 How genes and genomes evolve Ch. 9 7 Feb. 27 Manipulating genes and cells Ch. 10 Mar. 1 Membrane structure Ch. 11 Mar. 3 Membrane transport Ch. 12 8 Mar. 6 Forces-electric/membrane 4: Quantitative PCR (2 lab periods) Mar. 8 How cells obtain energy from food Ch. 13 Mar. 10 Energy generation Ch. 14 Spring break 9 Mar. 20 Intracellular compartments Ch. 15 Mar. 22 Kinetic modeling Mar. 24 Exam 2 10 Mar. 27 Cell communication Ch. 16 Mar. 29 Cytoskeleton 1 Ch. 17 Mar. 31 Cytoskeleton 2 11 Apr. 3 Forces-mechanical/beam bending Apr. 5 Forces-viscoelasticity Apr. 7 Forces-viscoelasticity 12 Apr. 10 Cell-cycle control and cell death 5: Molecular Rotary Motors Ch. 18 Apr. 12 Cell division Ch. 19 Apr. 14 Cell division Ch. 19 13 Apr. 17 Genetics, meiosis, and heredity Ch. 20 Apr. 19 Tissues and Cancer Ch. 21 Apr. 21 Tissues and Cancer Ch. 21 14 Apr. 24 Exam 3 6: Filopodial kinetics Apr. 26 Special topic 1: Aneuploidy and cancer Apr. 28 Special topic 2: Nerve regeneration 15 May 1 Special topic 3: Drug eluting stents May 3 Special topic 4: Modeling in Cell Biology May 5 Review May 12 Final Exam 8-10 a.m. (room t.b.a.) Course Description Tremendous advances in cellular and molecular biology over the last few decades have advanced the frontiers of medicine and biotechnology. Understanding the basic concepts of how cells and their molecules work is now an important tool for biomedical engineers and a new avenue for advancing medicine through technology. To use this tool requires not only an understanding of the fundamentals of cellular and molecular biology, but also the ability to relate these fundamentals to the physical sciences and mathematics. In doing so engineers can better understand, manipulate, and control cellular and molecular systems for therapy and technology. Grading Policy Exams (15% each) 45% Final Exam 20% Homework 10% Lab reports 25% Final grades will be assigned as follows: 90-100 A 86.7-89.9 A- 83.4-86.6 B+ 80-83.3 B 76.7-79.9 B- 73.4-76.9 C+ 70-73.3 C 67.7-69.9 C- 63.4-67.6 D+ 60-63.3 D <60 F Exams will be closed book and closed notes. It is expected that students will behave in a manner consistent with the Regents¿ Student Conduct policy (www1.umn.edu/regents/policies/academic). Unless instructed otherwise, submitted work must be done without assistance from others. Academic misconduct will be grounds for failure in the course. Remember that engineering is a profession that is trusted by society to conduct its work honestly. Laboratory The laboratory component will provide hands-on experience with cellular and molecular systems. The objectives of the laboratory are to learn some of the basic techniques used in cellular and molecular biology (e.g. microscopy, PCR, image processing, etc.) as well as the quantitative analysis and statistical description of experimental data. The experiments are scheduled to approximately match the timing of the topics presented in the lecture. A total of 6 experiments will be conducted during the 2 hour period in groups of 3 students. Students will be given an objective for the laboratory in advance and then will take a prelab quiz, which must be passed in order for the student to conduct the experiment. Written reports will be collected one week after completion of the laboratory. Students with disabilities The instructor will make all reasonable accommodations necessary for students with disabilities. Additional Information on BMEn 2501 and its Role in the B.Bm.E. Curriculum The courses required for the Bachelor of Biomedical Engineering degree program are designed to meet the Program Educational Objectives (PEOs), as defined by the BME Department (BMED), and the Program Outcomes (POs), as defined by the Accreditation Board for Engineering and Technology (ABET). Achieving the PEOs and POs is necessary to maintain program accreditation by ABET. For a full description of the PEOs, the POs, and the accreditation of the program, please refer to the BMED web site (www1.bme.umn.edu). With respect to the BMEN 2501 course, there are two PEOs that the course is meant to partially achieve: PEO1: Learn the scientific and engineering principles underlying the 6 major elements of biomedical engineering (BME): cellular and molecular biology, physiology, biomechanics, bioelectricity/instrumentation, biomedical transport processes, and biomaterials. (italics added) PEO 3: Learn experimental, statistical, and computational techniques in the context of BME. The POs that the BMEn 2501 course is meant to at least partially achieve are that students should have: (a) an ability to apply knowledge of mathematics, science, and engineering (b) an ability to design and conduct experiments, as well as to analyze and interpret data (k) an ability to use the techniques, skills, and modern engineering tools necessary for engineering practice. (l) an understanding of biology and physiology, and the capability to apply advanced mathematics (including differential equations and statistics), science, and engineering to solve problems at the interface of engineering and biology. (m) the ability to make measurements on and interpret data from living systems, addressing the problems associated with the interaction between living and non-living materials and systems. Course Title a b c d e f g h i j k l m BMEn 2501 Cell & Molecular Biology for Biomedical Engineers H M L H M H= High priority M= Medium priority L= Low priority Note: The B.Bm.E. degree program has been reviewed based in part on the criteria outlined above for BMEn 2501, and has received accreditation from ABET, the accrediting body for engineering programs in the United States and Canada, in the field of biomedical engineering. Essential Cell Biology, 3rd Ed., Table of Contents 1. Introduction to Cells 2. Chemical Components of Cells 3. Energy, Catalysis, and Biosynthesis 4. Protein Structure and Function 5. DNA and Chromosomes 6. DNA Replication, Repair, and Recombination 7. From DNA to Protein: How Cells Read the Genome 8. Control of Gene Expression 9. How Genes and Genomes Evolve 10. Manipulating Genes and Cells 11. Membrane Structure 12. Membrane Transport 13. How Cells Obtain Energy from Food 14. Energy Generation in Mitochondria and Chloroplasts 15. Intracellular Compartments and Transport 16. Cell Communication 17. Cytoskeleton 18. The Cell Division Cycle 19. Genetics, Meiosis, and the Molecular Basis of Heredity 20. Tissues and Cancer Old: <no text provided> |