79 lines
3.3 KiB
TeX
79 lines
3.3 KiB
TeX
\documentclass[a4paper,12pt,pdftex]{exam}
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\newcommand{\ptitle}{Activation curve}
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\input{../header.tex}
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\firstpagefooter{Supervisor: Lukas Sonnenberg}{}%
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{email: lukas.sonnenberg@student.uni-tuebingen.de}
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\begin{document}
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\input{../instructions.tex}
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%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
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\section{Estimation of activation curves of sodium channels}
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Mutations in genes encoding ion channels can result in a variety of
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neurological diseases like epilepsy, autism, or intellectual
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disability. One way to find a possible treatment is to compare the
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voltage dependent kinetics of the mutated channel with its
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corresponding wild-type (non-mutated channel). Voltage-clamp
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experiments are used to measure and describe the kinetics.
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In the project you will compute and compare the activation curves of
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the Nav1.6 wild-type (WT) channel and the A1622D mutation (the amino
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acid Alanine (A) at the 1622nd position is replaced by Aspartic acid
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(D)) that causes intellectual disability in humans.
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\begin{questions}
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\question In the accompanying datasets you find recordings of both
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wildtype and A1622D transfected cells. The cells were all clamped to
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a holding potential of $-70$\,mV for some time to bring all ion
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channels in the same closed states. Then the channels were activated
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by a step change in the command voltage to a value described in the
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\code{steps} vector. The corresponding recorded current \code{I} (in
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pA) and time \code{t} (in ms) traces are also saved in the files.
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\begin{parts}
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\part Plot all the current traces of a single WT and a single
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A1622D cell in two plots. Because the number of transfected
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channels can vary the peak values have little value. Normalize the
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curves accordingly (what kind of normalization would be
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appropriate?). Can you already spot differences between the cells?
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\part \textbf{I-V curve}: Find the peak values (minimum or maximum)
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for each voltage step and plot them against the steps.
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\part \textbf{Reversal potential}: Use the $I$-$V$-curve to
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estimate the reversal potential $E_\text{Na}$ of the sodium
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current. Consider a linear interpolation to increase the accuracy
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of your estimation.
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\part \textbf{Activation curve}: The activation curve is a
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representation of the voltage dependence of the sodium
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conductivity. It is computed with a variation of Ohm's law:
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\begin{equation}
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g_\text{Na}(V) = \frac{I_{peak}}{V - E_\text{Na}}
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\end{equation}
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\part \textbf{Comparison of the two ion channel types}: To compare
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WT and A1622D activation curves you should first parameterize your
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data. Fit a sigmoidal function
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\begin{equation}
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g_{Na}(V) = \frac{\bar g_\text{Na}}{1 + e^{ - \frac{V-V_{1/2}}{k}}}
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\end{equation}
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to the activation curves. With $\bar g_\text{Na}$ being the
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maximum conductivity, $V_{1/2}$ the half activation voltage and
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$k$ a slope factor (how these parameters influence the
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curve?). Now you can compare the two variants with three simple
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parameters. What do the differences mean? Which differences are
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statistically significant?
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\part \textbf{BONUS question}: Take a closer look at your raw
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data. What other differences can you see between the two types of
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sodium currents? How could you analyze these?
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\end{parts}
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\end{questions}
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\end{document}
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