Friday, September 21, 2007

Potassium Channel

hi guys, this is a video of the potassium channel i showed you a picture of in class: enjoy!

Questions from Class

hiya guys...i just wanted to follow up with some answers to questions you had in class the other day:

Q: is Hodgkin's Lymphoma named after the same Hodgkin from the Hodgkin and Huxley model?
A: It appears: NO. At least according to Wikipedia:

Hodgkin's lymphoma, also known as Hodgkin's disease, is named for Thomas Hodgkin in 1832, who first described it. However, it was Sir Alan Lloyd Hodgkin, the British physiologist and biophysicist, who won the 1963 Nobel Prize in Physiology or Medicine for his work with Andrew Fielding Huxley on the basis of nerve "action potentials."'s_disease

Q: What were Hodgkin and Huxley's intellectual backgrounds?
A: Again, according to wikipedia, both are/were physiologists and biophysicists.

Q: What is the time window for performing TTX experiments?
A: I don't know, but I did find a study in which the investigators applied it for 4 hours and another applying TTX for 48 hours.

Q: What are Hydropathy Units a measure of?
A: I got this from:
Biro, JC. "Amino acid size, charge, hydropathy indices and matrices for protein structure analysis." Theor Biol Med Model. 2006; 3: 15.

Hydropathy (hydrophobicity vs. hydrophilicity or lipophobicity vs. lipophilicity) is usually characterized by numbers (hydrophobic moments, HM) from -7.5 (Arg) to 3.1 (Ile), whereas hydrophobicity is a measure of how strongly the side chains are pushed out of water. The more positive a number, the more the amino acid residue will tend not to be in an aqueous environment. Negative numbers indicate hydrophilic side chains, with more negative numbers indicating greater affinity for water.

Patch Clamp: "Gigaseal"

This is an excerpt from Neher's Nobel Lecture for 1991 (He won that year's prize for Physiology/Medicine) concerning the "gigaseal"

click here for the full text of his lecture

"When Bert Sakmann and I started measurements by placing pipettes onto the surface of denervated muscle fibres, we soon realized that it was not so easy to obtain a satisfactory 'seal'...our initial attempts failed. Our seal resistances were just about 10-20 MQl, two orders of magnitude lower than desired."
"We made many systematic attempts to overcome the seal problem (manipulating and cleaning cell surfaces, coating pipette surfaces, reversing charges on the glass surface etc.)
with little success. "
"By about 1980 we had almost given up on attempts to improve the seal, when we noticed by chance that the seal suddenly increased by more than two orders of magnitude when slight suction was applied to the pipette. The resulting seal was in the gigaohm range, the so-called 'Gigaseal'. ...Fortunately, Fred Sigworth had just joined the laboratory. With his experience in engineering he improved the electronic amplifiers to match the advances in recording conditions. Thus, several types of ion channels could be characterized rapidly at good amplitude and time resolution."

Saturday, September 15, 2007

Notes from (Plonsey and Barr) Chapter 3

hi guys,

I got a couple of emails about your Chapter 3 reading and I wanted to post my answers for you all to share. I will be posting more as I get more questions so check back often. So, here are some notes:

(1) Relative charge depletion is a way for us to guage how much (if at all) the intracellular and extracellular concentrations are modified by the movement of ions that charge the membrane. We make the assumption that concentrations don't change even after the membrane is charged and calculating relative charge depletion is a good way to test whether this is a valid assumption. There is an example in your (Plonsey and Barr) textbook on page 61 that shows how to calculate it. If you have specific questions about this example please let me know.

(2) the Nernst Potential is the voltage the cell membrane WOULD HAVE TO BE in order for a particular ion to be in equilibrium. As we discussed in class after we computed the different Nernst potentials for different ions, there is no single Nernst potential that would being all ions into equilibrium, since the Nernst potential for Calcium is different than that for Potassium etc. The parallel conductance model helps us make sense of this fact by putting variable conductances into the equation. Vm is the a weighted average of Nernst potentials depending on the conductances of the different ions.

(3) I skipped the section about contributions from Chloride since I don't think it is particularly important and confusing. Basically, the Chloride ion is not very important in determining the membrane potential, but its behavior is interesting to the authors of this book because it tracks that of potassium (which IS very important) and because its intracellular concentration is very small and is much more affected by small amounts of influx or efflux.

(4) About typos, send them onto me, maybe we can compile a lit of erratas together and send them to the publisher at the end of the course.

Thursday, September 13, 2007

diffusion example

this is a nice (although not exactly scientific) illustration of shows the "diffusion" of walmart throughout the united states...enjoy!

Saturday, September 8, 2007


as we discussed in class, the theremin is one of the earliest fully electronic musical instruments out there, and the first meant to be played without even touching it. here's a video of some guy playing the theremin to a gnarls barkley song: crazy. enjoy!

Friday, September 7, 2007


As per your recommendation, I just wanted to let you know that I have placed orders for reserve copies for the following books at the Cooper Library (they should be there soon):

Bioelectricity: A Quantitative Approach
Publisher: Springer; 3rd ed. edition (June 21, 2007)

Medical Physiology, Updated Edition
by Walter F. Boron, Emile L. Boulpaep
Publisher: Saunders; Updated edition (November 19, 2004)

I also wanted to let you know that if you have friends interested in taking the course (who are not sure about the courseload, prerequisites etc) you can let them know that the course will get in full swing this coming Wednesday, so they haven't really missed much in terms of course material (i.e. it is not too late to join).

Tuesday, September 4, 2007

Hi everybody!

hi guys,

This is the blog for the Cooper Union Fall 2007 Bioelectricity course ECE401.1.

I am hoping that this blog can be a space where we can discuss topics related to class in an open fashion and help each other learn as well as ask and answer questions. I invite you to contribute to it!

This is an experiment that I hope will turn out well. Cheers and see you in class!