Short Bio

I am a microbial ecologist interested in deciphering the way in which terrestrial communities of microorganisms, on a micro scale, control the cycling of nutrients on landscape scales. In particular, I focus on anaerobic processes in soil aggregates, biological soil crusts and arthropod guts. In the lab, we use stable isotopes labelling and tracing in combination with classical microbiology and modern omics techniques to identify organisms and community interactions that impact ecosystems. Particular attention is given to processes and effects of interest to society such as the turnover of greenhouse gases and response to stress originating from climate change, or from pollution.

Currently I work as a senior scientist at the Biology Centre of the Czech Academy of Sciences in České Budějovice. I received my doctoral degree from the Philipp University of Marburg in Germany, after successfully completing a research project at the Max Planck Institute for Terrestrial Microbiology under the supervision of Prof. Ralf Conrad. Following my doctorate, I stayed for a brief post-doc period in the group of Prof. Conrad and then moved to a second post-doc position at the University of Vienna. Prior to working in Germany I conducted my academic studies in my home country, Israel. I received a bachelor’s degree in life sciences from the Open University of Israel and a Master’s degree from the Ben-Gurion University of the Negev.

Calculating CsCl and GB+DNA volumes to reach a desired density

My rationale is as follows:

I assume no contraction of volume when mixing CsCl (or CsTFA) with GB because they are both aqueous solutions. If there is a volume contraction then this will have to be determined empirically and corrected for (e.g. like for ethanol-water mixture).

So assuming no contraction, the formula is pretty simple:

\begin{equation} \label{eqn:mix1} \label{eqn:mix1}\rho_{CsCl}\cdot V_{CsCl}+\rho_{(GB+DNA)}\cdot V_{(GB+DNA)}=\rho_{mix}\cdot V_{mix}\\ \end{equation}Replace \(V_{(GB+DNA)}\) with \(V_{mix}-V_{CsCl}\)

\begin{equation}
\label{eqn:mix2}
\label{eqn:mix2}\rho_{CsCl}\cdot V_{CsCl}+\rho_{(GB+DNA)}\cdot(V_{mix}-V_{CsCl})=\rho_{mix}\cdot V_{mix}\\
\end{equation}

Open brackets and reorganise sides

\begin{equation}
\label{eqn:mix3}
\label{eqn:mix3}\rho_{CsCl}\cdot V_{CsCl}+\rho_{(GB+DNA)}\cdot V_{mix}-\rho_{(GB+DNA)}\cdot V_{CsCl}=\rho_{mix}\cdot V_{mix}\\
\end{equation}

\begin{equation}
\label{eqn:mix4}
\label{eqn:mix4}V_{CsCl}\cdot(\rho_{CsCl}-\rho_{(GB+DNA)})=V_{mix}\cdot(\rho_{mix}-\rho_{(GB+DNA)})\\
\end{equation}

\begin{equation}
\label{eqn:mix5}
\label{eqn:mix5}V_{CsCl}=V_{mix}\cdot\frac{(\rho_{mix}-\rho_{(GB+DNA)})}{(\rho_{CsCl}-\rho_{(GB+DNA)})}\\
\end{equation}

I haven’t measured the density of GB but according to my quick calculation it should be around 1.023 g ml^{-1} (I cannot determine it precisely because I couldn’t find the density of Tris-HCl). The density of a DNA sample should be very close to 1, even if it’s in TE. Still, even assuming the density of GB+DNA = 1 g ml^{-1} doesn’t change the result by much, so for practical purposes we can even formulate it as follows:

The formula in the paper is for calculating the volume of \(V_{GB}\) but it’s only a matter of reorganising the equation. In any case, using the example in the paper of a total volume of 6 ml my equation would give: 4.89 ml CsCl solution and 1.11 ml GB + DNA (or 4.86 + 1.14 if you use \(\rho=1.023\) for GB+DNA), which is close to 4.8 + 1.2, but still wrong…

For a direct comparison with the Neufeld paper, or the book by Rickwood my formula would look like this (assuming \(\rho_{(GB+DNA)}=1\)):

\begin{equation} \label{eqn:mix6} \label{eqn:mix6}V_{GB}=V_{mix}\cdot(\rho_{CsCl}-\rho_{mix})\cdot\frac{1}{(\rho_{mix}-1)}\\ \end{equation}So instead of \(\frac{1}{(\rho_{mix}-1)}\) he has some factor ”1.52”, which corresponds to a \(\rho_{mix}=1.657895\). Is there anything special about this density? Otherwise I cannot explain this.

I don’t have CsCl at the moment, but we’ve ordered it so I should be able to test it soon.

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