3 tera-basepairs as a fundamental limit for robust DNA replication

10 p.-2 tab.In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stall errors, we uncover a fundamental constant that describes a trade-off between genome size and architectural complexity of the developing organism. This constant has the approximate value N_U ≈ 3×10^12 basepairs, and depends only on two highly conserved molecular properties of DNA biology. We show that our theory is successful in interpreting a diverse range of data across the Eukaryota.MAM, LA and TJN acknowledge prior support from the Scottish Universities Life Sciences Alliance. JJB acknowledges support from Cancer Research UK (grant C303/A14301) and the Wellcome Trust (grant WT096598MA). TJN acknowledges prior support from the National Institutes of Health (Physical Sciences in Oncology Centers, U54 CA143682).Peer reviewe

A PETRI NET MODEL OF LIVER RESPONSE TO VISCERAL LEISHMANIASIS: SELF-REGULATION AND COMPLEX INTERPLAY IN THE VERTEBRATE IMMUNE SYSTEM

Visceral leishmaniasis (also called "Kala-azar") is a widespread disease, which is usually fatal in the absence of treatment. Characteristic of the liver immune response to leishmaniasis is a type of inflammation (granulomatous inflammation) that leads to the formation of "granulomas". A granuloma provides a very interesting micro-environment, which is maintained by the coordination of many cells of the immune system. Due to the complexity of the immune response, only a limited amount of modeling work exists in the context of granulomatous infection, and most of the current models focus only on the formation stage of granulomas. The primary goal of this thesis is to gain insights into the process of formation and development of a granuloma. To this end, we built a model of the granuloma formation and resolution in the liver using stochastic Petri nets, and performed several in silico experiments to study the nature of the immune response to leishmaniasis, possible therapeutic options, and the role of the cells involved. Additionally, the building of the model is extensively documented, and the most important qualitative and quantitative assumptions are referenced and discussed, with the aim of presenting a \u201cconceptual framework\u201d to be used when facing similar problems. The model is validated against available biological data, and its robustness is assessed using sensitivity analysis

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

To prevent rereplication of genomic segments, the eukaryotic cell cycle is divided into two nonoverlapping phases. During late mitosis and G1 replication origins are "licensed" by loading MCM2-7 double hexamers and during S phase licensed replication origins activate to initiate bidirectional replication forks. Replication forks can stall irreversibly, and if two converging forks stall with no intervening licensed origin-a "double fork stall" (DFS)-replication cannot be completed by conventional means. We previously showed how the distribution of replication origins in yeasts promotes complete genome replication even in the presence of irreversible fork stalling. This analysis predicts that DFSs are rare in yeasts but highly likely in large mammalian genomes. Here we show that complementary strand synthesis in early mitosis, ultrafine anaphase bridges, and G1-specific p53-binding protein 1 (53BP1) nuclear bodies provide a mechanism for resolving unreplicated DNA at DFSs in human cells. When origin number was experimentally altered, the number of these structures closely agreed with theoretical predictions of DFSs. The 53BP1 is preferentially bound to larger replicons, where the probability of DFSs is higher. Loss of 53BP1 caused hypersensitivity to licensing inhibition when replication origins were removed. These results provide a striking convergence of experimental and theoretical evidence that unreplicated DNA can pass through mitosis for resolution in the following cell cycle

Principled simulation of cell proliferation dynamics using the CoSMoS approach

A collaboration between cancer biologists and academic software engineers has been exploring the development of an agent-based simulator to inform and support work on the dynamics of cell proliferation in the study of prostate disorders. The research has influenced and been informed by the CoSMoS project. This paper presents the simulation project (which is not yet complete). We reflect on the reality of following CoSMoS principles; we describe the domain exploration and show how software modelling approaches (here, Petri nets, state diagrams) can be used to express both biological and software models. We explore fitness for purpose and consider ways to present a fitness argument. We consider issues in choosing simulation media and mapping from domain models through to code. The implementation emphasis is on traceability to support reuse and extension of the simulator, as well as demonstrable fitness for purpose. Initial work on calibration is presented. We discuss the calibration results, that both support and challenge the design and assumptions captured in the domain modelling and development activities

Neutron spectroscopy measurements and modeling of neutral beam heating fast ion dynamics

The energy spectrum of the neutron emission from beam-target reactions in fusion plasmas at the Joint European Torus (JET) has been investigated. Different beam energies as well as injection angles were used. Both measurements and simulations of the energy spectrum were done. The measurements were made with the time-of-flight spectrometer TOFOR. Simulations of the neutron spectrum were based on first-principle calculations of neutral beam deposition profiles and the fast ion slowing down in the plasma using the code NUBEAM, which is a module of the TRANSP package. The shape of the neutron energy spectrum was seen to vary significantly depending on the energy of the beams as well as the injection angle and the deposition profile in the plasma. Cross validations of the measured and modeled neutron energy spectra were made, showing a good agreement for all investigated scenarios

Filling gaps in simulation of complex systems: the background and motivation for CoSMoS

Modelling and simulation of complex systems can create scientific research tools that allow the inaccessible dynamic aspects of systems to be explored in ways that are not possible in live systems. In some scientific contexts, there is a need to be able to create and use such simulations to explore and generate hypotheses alongside conventional laboratory research. The principled complex systems modelling and simulation (CoSMoS) approach was created to support these activities, as a response to a perceived gap in the software engineering development process for simulation. The article presents some of the software engineering motivation for CoSMoS, by exploring this perceived gap. Following from this analysis, the article considers the validation of complex systems simulators, especially where these are to be used in ongoing research

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package