Tree Recovery by Dynamic Programming.

Tree-like structures are common, naturally occurring objects that are of interest to many fields of study, such as plant science and biomedicine. Analysis of these structures is typically based on skeletons extracted from captured data, which often contain spurious cycles that need to be removed. We propose a dynamic programming algorithm for solving the NP-hard tree recovery problem formulated by (Estrada et al. 2015), which seeks a least-cost partitioning of the graph nodes that yields a directed tree. Our algorithm finds the optimal solution by iteratively contracting the graph via node-merging until the problem can be trivially solved. By carefully designing the merging sequence, our algorithm can efficiently recover optimal trees for many real-world data where (Estrada et al. 2015) only produces sub-optimal solutions. We also propose an approximate variant of dynamic programming using beam search, which can process graphs containing thousands of cycles with significantly improved optimality and efficiency compared with (Estrada et al. 2015).

The plant response to high CO2 levels is heritable and orchestrated by DNA methylation.

Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO2 ) levels has been well studied. However, these investigations are typically limited to plants grown for a single generation in a high CO2 environment while transgenerational studies are rare. We aimed to determine transgenerational growth responses in plants after exposure to high CO2 by investigating the direct progeny when returned to baseline CO2 levels. We found that both the flowering plant Arabidopsis thaliana and seedless nonvascular plant Physcomitrium patens continue to display accelerated growth rates in the progeny of plants exposed to high CO2 . We used the model species Arabidopsis to dissect the molecular mechanism and found that DNA methylation pathways are necessary for heritability of this growth response. More specifically, the pathway of RNA-directed DNA methylation is required to initiate methylation and the proteins CMT2 and CMT3 are needed for the transgenerational propagation of this DNA methylation to the progeny plants. Together, these two DNA methylation pathways establish and then maintain a cellular memory to high CO2 exposure.