Helmholtz Centre for Environmental Research - UFZ

About: Helmholtz Centre for Environmental Research - UFZ is a facility organization based out in Leipzig, Germany. It is known for research contribution in the topics: Population & Species richness. The organization has 3230 authors who have published 9880 publications receiving 394385 citations.

Quantitative profiling of tryptophan metabolites in serum, urine, and cell culture supernatants by liquid chromatography–tandem mass spectrometry

Abstract: A sensitive, selective, and comprehensive method for the quantitative determination of tryptophan and 18 of its key metabolites in serum, urine, and cell culture supernatants was developed. The analytes were separated on a C18 silica column by reversed-phase liquid chromatography and detected by electrospray ionization tandem mass spectrometry in positive ion multiple reaction monitoring (MRM) mode, except for indoxyl sulfate which was measured in negative ion MRM mode in a separate run. The limits of detection and lower limits of quantification were in the range of 0.1–50 and 0.5–100 nM, respectively. Fully 13C isotope-labeled and deuterated internal standards were used to achieve accurate quantification. The applicability of the method to analyze serum, urine, and cell culture supernatants was demonstrated by recovery experiments and the evaluation of matrix effects. Precision for the analysis of serum, urine, and cell culture supernatants ranged between 1.3% and 16.0%, 1.5% and 13.5%, and 1.0% and 17.4%, respectively. The method was applied to analyze changes in tryptophan metabolism in cell culture supernatants from IFN-γ-treated monocytes and immature or mature dendritic cells.

Dynamic Energy Budget theory meets individual‐based modelling: a generic and accessible implementation

Abstract: Summary 1. Dynamic Energy Budget (DEB) theory was designed to understand the dynamics of biological systems from cells to populations and ecosystems via a mass balance approach of individuals. However, most work so far has focused on the level of the individual. To encourage further use of DEB theory in a population context, we developed DEB-IBM, a generic individual-based model (IBM) that is based on DEB theory. 2. The generic IBM is implemented as a computer program using NetLogo, a free software platform that is accessible to biologists with little programming background. The IBM uses DEB to represent assimilation, maintenance, growth and reproduction of individuals. The model description follows the overview, design and details (ODD) protocol, a generic format for describing IBMs, and thereby provides a novel and accessible introduction to DEB theory and how it works in a population context. 3. Dynamic Energy Budget-individual-based model can be used to explore properties of both individual life-history traits and population dynamics, which emerge from the set of DEB parameters of a species, and their interaction with environmental variables such as food density. Furthermore, DEB-IBM can be adapted to address specific research questions, for example by including spatial effects. A user manual explains how this can be done. 4. Dynamic Energy Budget-individual-based model is designed to both facilitate use and testing DEB theory in a population context and to advance individual-based modelling by basing the representation of individuals on well-tested physiological principles.

The intrinsic mean time to extinction: a unifying approach to analysing persistence and viability of populations

Abstract: Analysing the persistence and viability of small populations is a key issue in extinction theory and population viability analysis. However, there is still no consensus on how to quantify persistence and viability. We present an approach to evaluate any simulation model concerned with extinction. The approach is devised from general Markov models of stochastic population dynamics. From these models, we distil insights into the general mathematical structure of the risk of extinction by time t, P 0 (t). From this mathematical structure, we devise a simple but effective protocol - the ln(1-P 0 )-plot - which is applicable for situations including environmental noise or catastrophes. This plot delivers two quantities which are fundamental to the assessment of persistence and viability: the intrinsic mean time to extinction, T m , and the probability c 1 of the population reaching the established phase. The established phase is characterized by typical fluctuations of the population's state variable which can be described by quasi-stationary probability distributions. The risk of extinction in the established phase is constant and given by 1/T m . We show that T m is the basic currency for the assessment of persistence and viability because T m is independent of initial conditions and allows the risk of extinction to be calculated for any time horizon. For situations where initial conditions are important, additionally c 1 has to be considered.