Abstract 2085: The evolutionary trajectory of epigenomics in adult glioma

Author(s):  
Indrani Datta ◽  
Tathi Malta ◽  
Thais Sabedot ◽  
Ruicong She ◽  
Antonio Iavarone ◽  
...  
Elements ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. 191-196 ◽  
Author(s):  
Christopher T. Reinhard ◽  
Noah J. Planavsky

The redox state of Earth’s atmosphere has undergone a dramatic shift over geologic time from reducing to strongly oxidizing, and this shift has been coupled with changes in ocean redox structure and the size and activity of Earth’s biosphere. Delineating this evolutionary trajectory remains a major problem in Earth system science. Significant insights have emerged through the application of redox-sensitive geochemical systems. Existing and emerging biogeochemical modeling tools are pushing the limits of the quantitative constraints on ocean–atmosphere redox that can be extracted from geochemical tracers. This work is honing our understanding of the central role of Earth’s biosphere in shaping the long-term redox evolution of the ocean–atmosphere system.


2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Leah L. Weber ◽  
Mohammed El-Kebir

Abstract Background Cancer arises from an evolutionary process where somatic mutations give rise to clonal expansions. Reconstructing this evolutionary process is useful for treatment decision-making as well as understanding evolutionary patterns across patients and cancer types. In particular, classifying a tumor’s evolutionary process as either linear or branched and understanding what cancer types and which patients have each of these trajectories could provide useful insights for both clinicians and researchers. While comprehensive cancer phylogeny inference from single-cell DNA sequencing data is challenging due to limitations with current sequencing technology and the complexity of the resulting problem, current data might provide sufficient signal to accurately classify a tumor’s evolutionary history as either linear or branched. Results We introduce the Linear Perfect Phylogeny Flipping (LPPF) problem as a means of testing two alternative hypotheses for the pattern of evolution, which we prove to be NP-hard. We develop Phyolin, which uses constraint programming to solve the LPPF problem. Through both in silico experiments and real data application, we demonstrate the performance of our method, outperforming a competing machine learning approach. Conclusion Phyolin is an accurate, easy to use and fast method for classifying an evolutionary trajectory as linear or branched given a tumor’s single-cell DNA sequencing data.


Author(s):  
Stefan A. Rensing ◽  
Dolf Weijers

AbstractThe seeds of flowering plants are sexually produced propagules that ensure dispersal and resilience of the next generation. Seeds harbor embryos, three dimensional structures that are often miniatures of the adult plant in terms of general structure and primordial organs. In addition, embryos contain the meristems that give rise to post-embryonically generated structures. However common, flowering plant embryos are an evolutionary derived state. Flowering plants are part of a much larger group of embryo-bearing plants, aptly termed Embryophyta. A key question is what evolutionary trajectory led to the emergence of flowering plant embryos. In this opinion, we deconstruct the flowering plant embryo and describe the current state of knowledge of embryos in other plant lineages. While we are far yet from understanding the ancestral state of plant embryogenesis, we argue what current knowledge may suggest and how the knowledge gaps may be closed.


2020 ◽  
Vol 32 (5) ◽  
pp. 354-366
Author(s):  
Chong Chen ◽  
Katrin Linse

AbstractLush ‘oases’ of life seen in chemosynthetic ecosystems such as hot vents and cold seeps represent rare, localized exceptions to the generally oligotrophic deep ocean floor. Organic falls, best known from sunken wood and whale carcasses, are additional sources of such oases. Kemp Caldera (59°42'S, 28°20'W) in the Weddell Sea exhibits active hydrothermal vents and a natural whale fall in close proximity, where an undescribed cocculinid limpet was found living in both types of chemosynthetic habitats. This represents the first member of the gastropod order Cocculinida discovered from hot vents, and also the first record from the Southern Ocean. Here, we applied an integrative taxonomy framework incorporating traditional dissection, electron microscopy, genetic sequencing and 3D anatomical reconstruction through synchrotron computed tomography in order to characterize this species. Together, our data revealed an unusual member of the genus Cocculina with a highly modified radula for feeding on bacterial film, described herein as Cocculina enigmadonta n. sp. Its phylogenetically derived position within the largely wood-inhabiting Cocculina indicates that it probably evolved from an ancestor adapted to living on sunken wood, providing a compelling case of the ‘stepping stone’ evolutionary trajectory from organic falls to seeps and vents.


2021 ◽  
pp. 1-20
Author(s):  
Michal Placek ◽  
Gabriela Vacekova ◽  
Maria Murray Svidronova ◽  
Juraj Nemec ◽  
Gabriela Korimova

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