A yeast cell cycle model integrating stress, signaling, and physiology.

The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast.

Sperm migration in the genital tract-In silico experiments identify key factors for reproductive success.

Sperm migration in the female genital tract controls sperm selection and, therefore, reproductive success as male gametes are conditioned for fertilization while their number is dramatically reduced. Mechanisms underlying sperm migration are mostly unknown, since in vivo investigations are mostly unfeasible for ethical or practical reasons. By presenting a spatio-temporal model of the mammalian female genital tract combined with agent-based description of sperm motion and interaction as well as parameterizing it with bovine data, we offer an alternative possibility for studying sperm migration in silico.

Joint recording of contamination status, multi-element dynamics, and source identification on a sub-catchment scale: The example Lahn River (Germany).

Investigations on the enrichment level, binding dynamics, and source identification of contaminants are important objectives of environmental research into surface waters, but are often carried out independently of each other. To simultaneously address these issues an investigative approach is presented that combines multi-element analyses of water and suspended particulate matter (SPM) and is applied on the scale of a sub-catchment, using the Lahn River (Germany) as an example. Analyses of water and SPM comprised phosphorus (P), vanadium (V), chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd), lead (Pb), and uranium (U).

Catchment soils as a factor of trace metal accumulation in sediments of the reservoir Klingenberg (eastern Ore Mountains, Germany).

The release and accumulation dynamics of trace metals in soils and aquatic sediments were exemplarily investigated in the catchment area of the Reservoir Klingenberg (Germany). Catchment soils were examined for mobilizable and total concentrations of arsenic (As), cadmium (Cd), chrome (Cr), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) and compared with trace metal quantities accumulated in riverbed and reservoir sediments. The comparison of all samples showed relatively small variations of Cr (7.

Impacts of dam draining on the mobility of heavy metals and arsenic in water and basin bottom sediments of three studied dams in Germany.

The draining of a dam is a relatively rare event, however, it can have severe consequences for a watercourse connected to that reservoir. In order to understand the effects of the draining on the mobility of pollutants stored in the bottom sediments, the concentrations of heavy metals and arsenic were measured in pore water, river water, and sediments sampled from three emptied reservoirs in Germany. Two of these sites were analyzed immediately after the draining, while the third reservoir was studied one and a half years after the complete discharge of the stored water.

Computational Modeling of Lipid Metabolism in Yeast.

Lipid metabolism is essential for all major cell functions and has recently gained increasing attention in research and health studies. However, mathematical modeling by means of classical approaches such as stoichiometric networks and ordinary differential equation systems has not yet provided satisfactory insights, due to the complexity of lipid metabolism characterized by many different species with only slight differences and by promiscuous multifunctional enzymes. Here, we present an object-oriented stochastic model approach as a way to cope with the complex lipid metabolic network.

Toward Community Standards and Software for Whole-Cell Modeling.

Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.

SBtab: a flexible table format for data exchange in systems biology.

Unlabelled: : SBtab is a table-based data format for Systems Biology, designed to support automated data integration and model building. It uses the structure of spreadsheets and defines conventions for table structure, controlled vocabularies and semantic annotations. The format comes with predefined table types for experimental data and SBML-compliant model structures and can easily be customized to cover new types of data.

Biological monitoring as a useful tool for the detection of a coal-tar contamination in bitumen-exposed workers.

In our research project entitled "Chemical irritative and/or genotoxic effect of fumes of bitumen under high processing temperatures on the airways," 73 mastic asphalt workers exposed to fumes of bitumen and 49 construction nonexposed workers were analyzed and compared with respect to polycyclic aromatic hydrocarbons (PAHs) exposure and exposure-related health effects. In order to assess the internal exposure the monohydroxylated metabolites of pyrene, 1- hydroxypyrene (1-OHP), and phenanthrene, 1-, 2- and 9-, and 3- and 4-hydroxyphenanthrene (OHPH) were determined in pre- and post-shift urinary samples. Significantly higher concentrations 1-OHP and OHPH were detected in the post-shift urine samples of 7 mastic asphalt workers working on the same construction site compared to the reference workers and all other 66 mastic asphalt workers.

Irritative effects of fumes and aerosols of bitumen on the airways: results of a cross-shift study.

Possible health hazards of fumes and aerosols of bitumen are in discussion, and data on their adverse effects on human airways under current exposure conditions are limited. To assess the irritative effects of exposure to fumes and aerosols of bitumen on the airways, a cross-sectional cross-shift study was conducted including external and internal exposure measurements, spirometry and especially non-invasive methods like nasal lavage collection and induction of sputum in order to identify and evaluate more precisely inflammatory process in the upper and lower airways. The cross-shift study comprised 74 mastic asphalt workers who were exposed to fumes and aerosols of bitumen and 49 construction workers without this exposure as reference group.