20.109(S07): Calcium signaling in vivo

Introduction

Biological systems are complex.

Molecular insights into cell physiology have led to amazing understanding of the factors that influence a cell's behavior. Cells can be described biochemically, using binding constants and reactions rates to calculate expected concentrations of biologically relevant molecules. Cells can be described genetically, using large deletion sets and clever screens to identify critical regions of the genome and phenotypes associated with their malfunction or loss, singularly or in groups. Cells can be described structurally, with powerful microscopes capable of viewing molecules in cells "in action" and through crystalization of cellular components to give an atomic level, three-dimensional picture of cellular proteins and complexes. Often the most compelling and complete story comes from an approach that combines techniques or that asks one questions different ways.

Blind Men and an Elephant, see poemby John Godfrey Saxe

Yet for all the precision with which some aspects of the cell can be described and the volume of data being generated from high throughput analysis and genome sequencing projects, our understanding of a cell is still incomplete. Despite having a good parts list, and a good understanding of what many parts do, we are frustratingly far from "calculating life." Even simple cell like E. coli is hard to model. The great challenge is this: to describe (or better still: to build) a quantitative and predictive model for a cell's dynamic behavior. Wouldn't it be great if we could perturb a "virtual cell" and see it react as a real cell would, even if we haven't ever tried perturbing a real cell in the same way? The possibilities for discovery and engineering expand tremendously when experiments can be correctly simulated.

What is holding us back from this goal? Cell to cell variation for starters, though some efforts to model "noise" and recast it as strategy for evolution are underway, e.g. in the Elowitz lab and in the van Oudenaarden lab. Additionally, the evolution of living systems makes them hard to understand and even harder to model...nature continues to solve environmental demands in clever and novel ways. Finally, existing methods for experimentally testing and measuring the behavior of cells are limited. Measurements of single cells can be particularly noisy and difficult to correlate with bulk measurements made on populations of cells. Moreover, the measurement methods themselves are difficult to correlate with eachother, giving meaningful data in different ranges and with different sensitivities. This last point is what we will explore today, specifically asking how two techniques for measuring Ca2+ in cells compare.

Protocols

Part 1: Modeling Ca2+ signals

With this MATLAB excercise you will make calcium measurements in a model cell.

Introduction

In this exercise, you will study concentration and binding dynamics of calcium in a sim-plified model of a cell. The exercise will be performed in Matlab, using a macro (“m-file” in Matlab terminology) called Ca_kinetics.m. To run the model, you will start Matlab on your computer. When the program opens, you will see a window titled “MATLAB” that looks like this:

The “>>” symbol is the command line prompt. Type “edit Ca_kinetics” at this prompt to open the modeling m-file in the default text editor. You should be able to scroll through the m-file to examine it. Do not edit it in any way yet. At the top of the editor window is a symbol:

Clicking this symbol saves and runs the m-file; click it now. You now should see a new window titled “Figure 1,” that looks like this:

Part 2: Oral presentation instruction

DONE!

For next time

1. Please download the midsemester evaluation form File:Macintosh HD-Users-nkuldell-Desktop-MidsemesterEval 20.109.doc. Complete the questionnaire and then print it out without including your name to turn in next time. If there is something you'd like to see done differently for the rest of the course, this is your chance to lobby for that change. Similarly, if there is something you think the class has to keep doing, let us know that too.
2. Prepare a ten-minute oral presentation of a primary research paper related in topic to the experiments performed in this experimental. Some articles that are suitable for presentation are listed under the link for the next lab. These can be reserved on a first come/first served basis so email your choice as soon as you’ve decided. Alternatively, you’re also welcome to present a research idea stemming from the experiments you have performed in Module 2.