Pick one of the experimental work, computer work or mini-project.
Extraction of DNA from a banana - a home experiment
The aim of this experiment is to extract DNA from banana cells using tools and chemicals in your own kitchen (it is allowed to work in groups).
If you instead would engineer a new protein, or sequence DNA, you would most probably work with bacteria.
The reason is that bacteria apart from the chromosome also contain small accessory replicating DNA molecules called plasmids.
Plasmids are present in defined copy numbers (numbers of copies per cell) and are suitable vectors for cloning as they are easy to purify and work with (modify, amplify, or sequence).
This bring us back to this experiment. The report (max 1 A4) should include answers to: Did it work? How do you know (or how could you prove) its DNA? What are the disadvantages of working with eukaryotic DNA?
The report should be handed in before the end of the course.
Protocol:
1. Mash a half banana using a mixer or a fork.
2. Add a 10% solution of hand-wash soap (preferably YES)
3. Add a few teaspoons of salt. Mix a few seconds in a mixer to obtain a banana purée.
4. Filter the purée in a coffee filter into a pre-cooled glass.
5. Carefully add ice-cold ethanol (e.g. T-röd) via the glass wall to the filtrate in equal volumes ( a bottle of T-röd will be available in Soliden 2050).
6. DNA will appear as bundles of white threads in-between the ethanol and the water.
7. The DNA can be removed using a stick, freeze for storage (there is no need to save the DNA for this course).
Jerk Bjerneld can answer your questions if needed
Game of Life - computer project
Click here for more details about the project.
Tobias Ambjörnsson takes care of your questions and gives instructions for this project
Background reading: a) March of the Biobots (build your own rat), New Scientist pp. 26, 5 December 1998.
b) The Quark and the Jaguar: Adventures in the Simple and the Complex by Murray Gell-Mann,
Paperback Reprint edition (October 1995) W H Freeman & Co.; ISBN: 0716727250
Mini-projects
(choose one and present last week of course. There are four options: oral (15 min.), written (one A4), home-page (one) or 2 OH's
Evolution under physical constraints
make a physical description of factors which can be behind that insects are so small!
Energy landscapes: hidden observables in ensembles of proteins
make a description of how the different conformations of proteins in effect leads to an energy landscape
Vision in insects and humans - what is the difference?
The title explains this project well, consult "Biology" by Campbell for the fundamental difference, then read a recent research article like:
"Multiple stored views and landmark guidance in ants", Nature, vol. 392, pp. 710 (1998) "More than one way to see it move", Proc. Natl. Acad. Sci. USA,
vol. 96, pp. 7611 (1999) "Stabilizing gaze in flying blowflies", Nature, vol. 395, pp. 654, (1998)
Also have a look at the world through the eyes of a bee.
Patterns as spontaneous symmetry breaking
Symmetries are most interesting when they are not symmetries any longer. Can the spontaneous broken symmetry principle of physics
be related to why zebras are striped and not white or black?
Restorable man
Try to formulate the possibility of one day making man completely restorable from spare parts
Trapping and escape of DNA
This project concerns the physical properties of DNA as it enters and goes through pores. Why is this significant in biological systems?
Try to understand these two papers, one by the nobel-prize winner de Gennes "Entropic trapping and escape of long DNA molecules at
submicron size constriction", PRL, vol. 83, pp. 1688, (1999). "Passive entry of a DNA molecule into a small pore", Proc. Natl. Acad. Sci. USA, vol. 96, pp. 7262-7264 (1999)
Proteins under stress: the effect of solvent, temperature, and pressure.
If you want to do something fancy with a protein, you will soon become aware that they are sensitive molecules.
Yet some are remarkably stable over large temperature ranges, so called thermozymes, which has had a tremendous impact on biotechnology.
PCR (polymerase chain reaction) depends on such an enzyme. This project involves reading and giving an account of:
"Thermozymes-review", TIBTECH, vol. 14, pp. 183 (1996), "Effects of high pressure", TIBTECH, vol. 12, pp. 493 (1994),
"Why are enzymes less active in organic solvents than in water?" TIBTECH, vol. 15, pp. 97 (1997).
Single molecules
This is a research topic particulary suitable for biological systems as they often are dominated by molecules few in number.
There is plenty of material in this area available. For e.g.: "Mechanical and chemical unfolding of a single protein, a comparison", Proc. Natl. Acad. Sci. USA, vol. 96, pp. 3694 (1999).
Modelling biological systems
There is a wealth of possible projects under this heading, I like these two articles, both can be studied individually for a project:"Diffusion-assisted aggregation and synchronization in Dictyostelium discoideum", PRL, vol. 80, pp. 4826 (1998) "Robusteness in bacterial chemotaxis", Nature vol. 397, pp. 168 (1999),
Noise in signal systems
This is a hot topic in physics in general, and in biology in particular. For this course I suggest that you focus on one paper,
either in physics or in biology and try to understand it: "Noise driven avalanche behavior in subexcitable media",
Phys. Rev. Lett., vol. 82, pp. 855, (1999). "Neural noise limitations on infant visual sensitivity", Nature, vol. 391, pp. 697, (1998)
Also consider the Arrhenius equation for activation energy in chemical reactions, and whether temperature is noise.
Self-assembly
Give an account of how certain systems actually aggregate themselves without apparent interference from humans
Blood
Red blood cells change their shape while moving along. Discuss the physics of this (there is a movie from
Ulf Bagge 0708-733314/ulf.bagge@anatcell.gu.se which shows this in a nice way)
Conformal Diffusion in Genus 2 vesicles.
- Use the
unit sphere construction
of Liquid Crystals to demonstrate how the director can be found from a geometrical construction (nematic) and give possible biological applications AFM/STM on DNA and friends
Report on the latest advances using atomic force microscopy or scanning tunneling microscopy of mapping interesting biological molecules and structures
Topology and geometry of DNA constrained to a surface
One of the lectures brought up writhe, twist and linking in 3D - how does this change on a surface?
Conformations of linear DNA
To examine the conformations underwound and overwound DNA can take.
Elastic Rod model of a supercoiled DNA molecule
To examine a model of DNA based on elastic aspects.
Something from the last years' issues of Nature
browse through the last year and pick something which looks interesting to you
Something from the last years' issues of Science
browse through the last year and pick something which looks interesting to you
Something from the last years' issues of Physics Today
browse through the last year and pick something which looks interesting to you
Something from the last years' issues of Physical Review E
browse through the last year and pick something which looks interesting to you
(Peter Apell takes care of your questions and gives instructions for this project)