Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells

The mammalian cell cycle is regulated by a well-studied but complex biochemical reaction system. Computational models provide a particularly systematic and systemic description of the mechanisms governing mammalian cell cycle control. By combining both state-of-the-art multiplexed experimental methods and powerful computational tools, this work aims at improving on these models along four dimensions: model structure, validation data, validation methodology and model reusability. We developed a comprehensive model structure of the full cell cycle that qualitatively explains the behaviour of human retinal pigment epithelial-1 cells. To estimate the model parameters, time courses of eight cell cycle regulators in two compartments were reconstructed from single cell snapshot measurements. After optimisation with a parallel global optimisation metaheuristic we obtained excellent agreements between simulations and measurements. The PEtab specification of the optimisation problem facilitates reuse of model, data and/or optimisation results. Future perturbation experiments will improve parameter identifiability and allow for testing model predictive power. Such a predictive model may aid in drug discovery for cell cycle-related disorders

Health and demographics of African buffalo (Syncerus caffer) in Ruaha National Park, Tanzania

Presented at the 9th international wildlife ranching symposium: wildlife - the key to prosperity for rural communities, held on 12-16 September 2016 at Hotel Safari & the Safari Court, Windhoek, Namibia in conjuction with the IUCN 2nd African Buffalo Symposium.The African buffalo (Syncerus caffer) population of Ruaha National Park may be in decline. Seasonal drying of the park's water source due to upstream irrigation may have caused loss of dry season habitat, increased pressure on remaining water sources, and possibly increased contact between wildlife and livestock at the park borders. The Health for Animals and Livelihood Improvement (HALI) project and Ruaha National Park are collaborating to investigate the health and population status of the African buffaloes. Between 2011 and 2015, this partnership resulted in testing 30 young and 25 adult African buffaloes for bovine tuberculosis (2011, 2014-15), conducting 4 dry season demographic surveys and herd level parasite screenings (2011, 2013-15), and conducting one aerial population survey in collaboration with the Tanzania Wildlife Research Institute (2013). In 2014-15, 12 adult female buffaloes were collared with satellite GPS collars to learn more about the seasonal movements, habitat preferences, and herd dynamics of Ruaha's buffalo herds. The research has shown that bovine tuberculosis and brucellosis is present in the buffalo population, that the population number appear to be reduced since the last total count in 2004, that the herd composition and seasonal movements may be influenced by rainfall, and the herd level gastrointestinal parasite counts generally are low. The data generated in this study will be used to inform management and conservation of Ruaha National Park's buffaloes

Orbital fibrosis in a mouse model of Graves' disease induced by genetic immunization of thyrotropin receptor cDNA

The TSH receptor (TSHR) is the critical target for antibody production in Graves' disease (GD). Insulin-like growth factor 1 receptor (IGF1R) has been proposed as a second autoantigen in complications of GD such as orbitopathy. We attempted to induce orbital tissue remodeling in mice undergoing immunizations with plasmids encoding TSHR and IGF1R delivered by in vivo skeletal muscle electroporation, a procedure known to give a sustained, long-term antibody response. Female BALB/c mice were challenged with TSHR A-subunit or IGF1Rα subunit plasmid by injection and electroporation. Mice challenged with TSHR A-subunit plasmid resulted in high frequency (75%) of hyperthyroidism and thyroid-stimulating antibodies. But strikingly, immunization with TSHR A-subunit plasmid also elicited antibody to IGF1Rα subunit. Mice challenged in the same manner with IGF1Rα subunit plasmid produced strong antibody responses to IGF1R, but did not undergo any changes in phenotype. Simultaneous challenge by double antigen immunization with the two plasmids in distant anatomical sites reduced the incidence of hyperthyroidism, potentially as a consequence of antigenic competition. Thyroid glands from the TSHR A-subunit plasmid-challenged group were enlarged with patchy microscopic infiltrates. Histological analysis of the orbital tissues demonstrated moderate connective tissue fibrosis and deposition of Masson's trichrome staining material. Our findings imply that immunization with TSHR A-subunit plasmid leads to generation of IGF1R antibodies, which together with thyroid-stimulating antibodies may precipitate remodeling of orbital tissue, raising our understanding of its close association with GD

PEtab -- interoperable specification of parameter estimation problems in systems biology

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies. Specifications of PEtab, the PEtab Python library, as well as links to examples, and all supporting software tools are available at https://github.com/PEtab-dev/PEtab, a snapshot is available at https://doi.org/10.5281/zenodo.3732958. All original content is available under permissive licenses

Gut microbiome in BALB/c and C57BL/6J mice undergoing experimental thyroid autoimmunity associate with differences in immunological responses and thyroid function

Experimental models of hyperthyroid Graves’ disease (GD) and Graves’ orbitopathy (GO) are efficiently developed by genetic immunisation by electroporation with human thyrotropin hormone receptor (hTSHR) A-subunit plasmid in female BALB/c (H-2d) mice. We investigated susceptibility in C57BL/6 J (H-2b) animals to allow studies on disease mechanisms in transgenic and immune response gene knock-out mice. Higher numbers of female C57BL/6 J were positive for pathogenic thyroid stimulating antibodies, but induced hyperthyroidism remained at a low frequency compared to BALB/c animals. Assessment of hTSHR specific T cells showed reduced proliferation in C57BL/6 J animals accompanied with anti-inflammatory IL-10, with less pro-inflammatory IFN-γ compared to BALB/c. Whilst the orbital tissue from immune BALB/c mice showed inflammation and adipogenesis, in contrast C57BL/6 J animals showed normal pathology. We characterised the gut microbiota using 16 S ribosomal RNA gene sequencing to explore its possible pathogenic role in the model. Despite being housed under identical conditions, we observed significantly different organisation of the microbiota (beta-diversity) in the two strains. Taxonomic differences were also noted, with C57BL/6 J showing an enrichment of Operational Taxonomic Units (OTUs) belonging to the Paludibacter and Allobaculum, followed by Limibacter, Anaerophaga and Ureaplasma genera. A higher number of genera significantly correlating with clinical features was observed in C57BL/6 J compared to BALB/c; for example, Limibacter OTUs correlated negatively with thyroid-stimulating antibodies in C57BL/6 J mice. Thus, our data suggest gut microbiota may play a pivotal immunomodulatory role that differentiates the thyroid function and orbital pathology outcome in these two inbred strains undergoing experimental GO

Linsitinib, an IGF-1R inhibitor, attenuates disease development and progression in a model of thyroid eye disease

IntroductionGraves’ disease (GD) is an autoimmune disorder caused by autoantibodies against the thyroid stimulating hormone receptor (TSHR) leading to overstimulation of the thyroid gland. Thyroid eye disease (TED) is the most common extra thyroidal manifestation of GD. Therapeutic options to treat TED are very limited and novel treatments need to be developed. In the present study we investigated the effect of linsitinib, a dual small-molecule kinase inhibitor of the insulin-like growth factor 1 receptor (IGF-1R) and the Insulin receptor (IR) on the disease outcome of GD and TED.MethodsLinsitinib was administered orally for four weeks with therapy initiating in either the early (“active”) or the late (“chronic”) phases of the disease. In the thyroid and the orbit, autoimmune hyperthyroidism and orbitopathy were analyzed serologically (total anti-TSHR binding antibodies, stimulating anti TSHR antibodies, total T4 levels), immunohistochemically (H&E-, CD3-, TNFa- and Sirius red staining) and with immunofluorescence (F4/80 staining). An MRI was performed to quantify in vivo tissue remodeling inside the orbit.ResultsLinsitinib prevented autoimmune hyperthyroidism in the early state of the disease, by reducing morphological changes indicative for hyperthyroidism and blocking T-cell infiltration, visualized by CD3 staining. In the late state of the disease linsitinib had its main effect in the orbit. Linsitinib reduced immune infiltration of T-cells (CD3 staining) and macrophages (F4/80 and TNFa staining) in the orbita in experimental GD suggesting an additional, direct effect of linsitinib on the autoimmune response. In addition, treatment with linsitinib normalized the amount of brown adipose tissue in both the early and late group. An in vivo MRI of the late group was performed and revealed a marked decrease of inflammation, visualized by 19F MR imaging, significant reduction of existing muscle edema and formation of brown adipose tissue.ConclusionHere, we demonstrate that linsitinib effectively prevents development and progression of thyroid eye disease in an experimental murine model for Graves’ disease. Linsitinib improved the total disease outcome, indicating the clinical significance of the findings and providing a path to therapeutic intervention of Graves’ Disease. Our data support the use of linsitinib as a novel treatment for thyroid eye disease

On the optimal control of contact-cooking processes

In this study, we have considered the design of optimised thermal processes for the preparation of cooked hamburger patties. For this purpose, advanced dynamic optimisation (optimal control) techniques have been used. These techniques make use of predictive mathematical models of heat and mass transfer, previously validated with experimental studies. The generic optimal control problem considered was formulated as the determination of the optimal cooking conditions to obtain the highest quality product with an ensured final level of safety in a minimum time. The obtained optimal policies (dynamic heating temperatures) show significant advantages over nominal constant temperature processes. These optimisation studies provide new information to design the next generation of grills with dynamic controls to improve the product quality and safetyThe authors would like to thank NATO for financial support (Collaborative Research Grant CRG-971581).Peer reviewe

Arnold Schoenberg's approach to text setting in "The Book of the Hanging Gardens".

This study examines the method of setting poetry to music utilised by Arnold Schoenberg in his composition on Stefan George's poetic cycle Das Buch der Hangenden Garten, and compares that method to the one the composer described in his published writings. The compositional process used in Das Buch will be explicated through an examination of the composer's concept sketches and continuity drafts for the eighth movement, Wenn ich heut nicht deinen Leib beruhre, and the fourteenth movement, Sprich nicht immer von dem Laub. In comparing the compositional method Schoenberg claimed to use with his actual compositional process for Das Buch, it will become apparent that he drew on what he called his "definitive method" but did not restrict himself to it. Schoenberg, in his writing, has shown that he wished for purely artistic reasons to place himself in the position of composer of music with text, but in practical application, he combined many sources of inspiration in this transitional work