The Biological Physics Training Laboratory
Projects
and Laser tweezing
Formation
Dynamics
Biology, Mathematics
and Physics Initiative
For further information
contact Applied Mathematics
(520-621-2016)
Biological Physics Teaching Laboratory
Interdisciplinary Biological Training Laboratory
Syllabus: Fall 2002
PHYS 603, Cross listed as MATH 603 - BIOC 603 - BME 603
The goal of the laboratory is to support the IGERT multidisciplinary training program by helping train a new generation of mathematicians, physicists and biologists in ways that will enable them to collaborate productively across traditional disciplinary boundaries.
Course description
This laboratory serves to acquaint students from a variety of disciplines with modern quantitative techniques in biological physics and soft condensed matter physics. Emphasis will be placed upon phenomena at the micron scale, involving biological form and motion, studied through microscopy and micromanipulation. Students will learn about techniques such as optical trapping, micropipette aspiration, and electrophysiological recording methods. They will also learn about phenomena such as the action of motor proteins, the shapes of membrane vesicles, and Brownian fluctuations; about quantification of these observations through image analysis and statistical methods, and about explanation of these phenomena based on the principles of statistical mechanics, continuum mechanics, nonlinear and stochastic dynamics - all linked together through the underlying biology and biochemistry.
Contacts
Class hours
Monday and Wednesday: 1-5 p.m.
Friday: 1-2 p.m.
2002 Schedule of Classes
Structure of the course
During the first several classes of the semester, students will attend a series of lectures in conjunction with the lab experience. The lectures will comprise parts of the Monday and Wednesday lab sessions; the remaining Mon/Wed time will be devoted to the lab. The focus of these shorter-than-normal lab sessions will be participation in a wide variety of experimental observations and discussions. Each student will choose an experimental setup by the 6th class meeting and, during the remainder of the semester,
students
will develop the fundamental skills and knowledge necessary to successfully conduct
a specific experiment(s), acquire and analyze data and investigate all aspects
of that experiment. A major goal of the course is to enhance cross-disciplinary
communication through: Collaboration
Students will work in small groups to develop techniques, conduct experiments, understand phenomena, quantify data and explain results. Inspection of the grading structure for this course (below) will confirm the importance of collaboration and communication in this interdisciplinary setting.
Friday discussions
The Friday sessions are meant to provide the opportunity for students to discuss issues, questions, ideas, and approaches that have arisen during the course of the week's experimental sessions.
The sessions will have an open format and
will include special presentations by the students of work they are doing in other
contexts, e.g., work they are carrying out in their own research. Students are
expected to participate in each Friday session and can expect to lead a part of
several sessions during the semester. Visitors with special expertise may be included
in these sessions to help with unresolved issues. These sessions also provide
the opportunity for students to learn and practice presentation skills. Final exam
Students will organize and present both written and oral material based upon their laboratory experience. The written paper will follow a research paper format with introduction, methods, results, discussion and references. The paper is also expected to contain relevant tables, figures and figure legends where applicable. The oral presentation may be supported by overhead transparencies, video or computer presentations as determined by the student.
Attendance
Regular lecture and laboratory attendance is essential to student success in this course. If you miss a class, you are responsible for getting missed material from a classmate. If you are unable to attend your laboratory section you must contact your lab mentor. If the circumstances warrant, your mentor can arrange for you to attend another lab session. You must have a good reason for missing lab in order to request rescheduling.
Grades
25% Performance in the laboratory & laboratory notebook
25% Participation in weekly discussion sessions
25% Final exam-laboratory report in scientific manuscript format
25% Final exam-oral presentation
Academic Integrity
The U of A Code of Academic Integrity places full responsibility on the student for the content and integrity of all academic performance. It is a violation of this code for a student to represent the work of another as his or her own. Copying another person's work or portions of it is a violation of academic integrity and will be handled according to U of A policy. Under no circumstances should you copy or represent the work of another student as your own. A copy of the UA Code of Academic Integrity can be found here and in the schedule of classes. Take the time to read it.
Faculty statement
We, the teaching faculty, wish you an interesting and challenging semester. Please do not hesitate to contact us (by phone, email, or in person).
The experiments
Experimental workstations have been set up to accommodate a variety of experiments that are representative of the main intellectual and methodological threads that unite the physical, mathematical and biological sciences. The experiments are taken from the recent literature in order that students see the vitality of the field. The students may choose from among the following:
Biophysical Forces
The techniques of video microscopy and optical trapping will be used to quantify several phenomena associated with Brownian motion. A first goal is to learn the principles of optical trapping "laser tweezers", used also in other experiments, and to calibrate traps of varying intensity through measurement of Stokes drag on latex beads of varying sizes. The fluctuations of those beads within the trap will be compared with results of theoretical calculations using the basic principles of statistical mechanics. Observations of Brownian motion in the absence of a trap will be used to determine Avogadro's number from the universal gas constant, along the lines of the original Einstein work on Perrin's results. Fluids of different viscosities and particles of different sizes will be used to check the Stokes-Einstein relation (fluctuation-dissipation theorem). Finally, a double trap has been constructed to examine Kramers' theory, which attempts to characterize a chemical reaction by the rate at which a Brownian particle can move over the energy barrier of a one-dimensional double-well potential. Experimentally, such a potential is readily obtained by using two optical traps positioned closely together. By video-recording the images a glass particle (~500 nm in diameter) jumping from one optical trap into the other, and subsequent Particle tracking using a dedicated image-processing computer, the transition rate can be determined, and Kramers' results can be experimentally verified.
Pattern Formation & Population Dynamics.
Reaction-diffusion phenomena are ubiquitous in biology, from the propagation of electrical impulses in the heart to population dynamics on the scale of kilometers. One of the most important characteristics of reaction-diffusion systems is their ability to support rotating spiral waves. In this module, the formation and dynamics of such waves will be studied in populations of the amoebae Dictyostelium discoideum. When fed sufficient nutrients the individual cells of a population exist essentially independent of the others, but when starved the population self-organizes into a three-dimensional structure of spores supported by a stalk. The cellular motion that leads to this aggregation is controlled by spiral waves of cAMP relayed from cell to cell. These waves can be visualized by dark-field techniques through their effect on cell shape and hence light scattering. Varying simply experimental control parameters results in important competition between spirals and targets controlled by pacemaker cells.
Electrophysiology
The neurophysiology module was designed to introduce students to basic electrophysiological approaches to study of neuronal circuits. Students taking part in this segment will meet three objectives. They will:
a) demonstrate basic knowledge of key concepts in neuronal electrophysiology as defined by contemporary neurobiology, including: generation of resting membrane potential, action potentials, and synaptic potentials; decremental and regenerative modes of voltage spread through axons; voltage- and ligand-gated currents
b) demonstrate the skills and knowledge necessary to set up a standard electrophysiology experiment
c) devise and conduct electrophysiology experiments to explore selected issues that will require formation and testing of hypotheses/models to resolve and that will involve a mathematical approach to data analysis.
This unit requires significant hand skills that can only be learned by experience. Those skills need to be mastered early on, so the student can enjoy the full intellectual experience. For this reason, the first few weeks are spent learning the basics of the experimental preparation, the electrophysiology rig, and the software needed to run the experiments. The preparation is the abdominal portion of the ventral nerve cord of the moth Manduca sexta. Students will learn to dissect the nerve cord, desheathe the ganglia to expose the underlying neurons, and to record from the neurons both extracellularly and intracellularly. In addition, they will learn to prepare the set-up to run an experiment, including making microelectrodes and solutions.
Basic neurophysiology references:
Hille B (2001) Ionic channels of excitable membranes. (Third edition)
Sunderland, MA, Sinauer Associates Inc., Chap. 2: Classical biophysics of the squid giant axon, pp. 23-58. Chap. 6: Ligand-gated channels of fast chemical synapses, pp. 140-169. Chap. 7: Modulation, slow synaptic action, and second messengers, pp. 170-201.
Armstrong CM and Hille B. (1998) Voltage-gated ion channels and electrical excitability. Neuron 20: 371-380.
Moore J and Stuart A (2000) Neurolab. [Note: This is an interactive web-based program that permits simulation of neuronal responses to a variety of stimuli in normal and pathological conditions. Many neuronal parameters that influence responses can be altered, e.g., membrane resistance, ion concentration, neuronal shape.]