Estimating properties of kinetoplast DNA by fragmentation reactions
Estimating properties of kinetoplast DNA by fragmentation reactions
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DOI：
10.1088/1751-8121/aaf15f
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发表时间：
2018-12
期刊：
影响因子：
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通讯作者：
L. Ibrahim;P. Liu;M. Klingbeil;Y. Diao;J. Arsuaga
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作者：
L. Ibrahim;P. Liu;M. Klingbeil;Y. Diao;J. Arsuaga
锥虫的线粒体DNA，称为动基体DNA（kDNA），含有数千个微环，这些微环在拓扑学上连接成一个类似于中世纪锁子甲的单一结构。这种生物链甲的特征在于两个参数：微环之间的连接类型和连接到每个微环的微环的数量（即微环价）。在以前的工作中，提出了一个协议，以确定的平均值的小环价。在这些实验中，从网络中切除微环，并将产物与从破碎理想化结构中获得的产物进行比较。这些理想化的结构假设初始网络的价态分布的变化可以忽略不计。因此，目前尚不清楚当从不同步的细胞或具有沉默的kDNA复制基因的细胞中提取kDNA样本时，这种理论分析在多大程度上捕捉到了kDNA网络的真实拓扑结构。随后的研究提出，在网络形成过程中存在一个临界渗流密度。我们询问是否可以使用碎裂反应来估计该密度。本工作的目标是开发一种数学方法，可以用来估计网络的平均价时，价的方差是不可忽略的。我们首先显示的Crithidia fasciculata的显微镜数据，与原来的实验结果一致，显示非零方差的价态分布。其次，我们使用计算机模拟的网络碎片表明，预测和实际的平均价是不同的时，价分布有非零方差。我们提出了一个更一般的数学公式和计算机模拟的kDNA片段来估计这个值。最后，我们表明，破碎实验可能会导致错误的临界渗流密度的估计，因为崩溃的密度依赖于网络的初始密度，并在破碎反应。
The mitochondrial DNA of trypanosomes, called kinetoplast DNA (kDNA) contains thousands of minicircles that are topologically linked into a single structure that resembles a medieval chainmail. This biological chainmail is characterized by two parameters: the link type between minicircles, and the number of minicircles linked to each minicircle (i.e. the minicircle valence). In previous works, a protocol was proposed to determine the mean value of the minicircle valence. In these experiments, minicircles were excised from the network and the products compared with those obtained from fragmenting idealized structures. These idealized structures assumed a negligible variance in the distribution of valences of the initial network. It is therefore unclear to what extent this theoretical analysis captures the true topology of the kDNA network when kDNA samples are extracted from unsynchronized cells or from cells with silenced kDNA replication genes. Subsequent studies proposed that there is a critical percolation density during network formation. We asked whether this density can be estimated using fragmentation reactions. The goal of this work is to develop a mathematical method that can be used to estimate the mean valence of networks when the variance of the valence is non-negligible. We first show microscopy data on Crithidia fasciculata that, in agreement with the original experimental results, show a distribution of valences with nonzero variance. Second, we use computer simulations of network fragmentation to show that the predicted and actual mean valence are different when the valence distribution has nonzero variance. We propose a more general mathematical formulation and computer simulations of kDNA fragmentation to estimate this value. Last, we show that fragmentation experiments may lead to errors in the estimation of the critical percolation density since the collapsing density depends on the initial density of the network, and on the fragmentation reaction.