Building up a model family for inflammations.

The paper presents an approach for overcoming modeling problems of typical life science applications with partly unknown mechanisms and lacking quantitative data: A model family of reaction-diffusion equations is built up on a mesoscopic scale and uses classes of feasible functions for reaction and taxis terms. The classes are found by translating biological knowledge into mathematical conditions and the analysis of the models further constrains the classes. Numerical simulations allow comparing single models out of the model family with available qualitative information on the solutions from observations.

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations.

Unlabelled: Screening assays are used to test if one or more microbes suppress a pathogen of interest. In the presence of more than one microbe, the screening method must be able to accurately distinguish viable pathogen cells from non-viable and non-target microbes in a sample. Current screening methods are time-consuming and require special reagents to detect viability in mixed microbial communities.

A source of hidden diversity: soil seed bank and aboveground populations of a common herb contain similar levels of genetic variation.

In many landscapes, successful re-establisment of plant populations depends on the presence of diaspores, either near or directly beneath sites to be restored. The soil seed bank is, therefore, an important part of ecosystem resilience and a vital pillar for regeneration of genetic diversity in many plant populations. However, regeneration from the soil seed bank and the siubsequent restoration can only be considered successful when genetic diversity of restored populations is not eroded nor genetic differentiation inflated.

CRISPR-Associated Transposase for Targeted Mutagenesis in Diverse Proteobacteria.

Genome editing tools, through the disruption of an organism's native genetic material or the introduction of non-native DNA, facilitate functional investigations to link genotypes to phenotypes. Transposons have been instrumental genetic tools in microbiology, enabling genome-wide, randomized disruption of genes and insertions of new genetic elements. Due to this randomness, identifying and isolating particular transposon mutants (i.

Functional annotation and importance of marine bacterial transporters of plankton exometabolites.

Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates.

Plasmids for Controlled and Tunable High-Level Expression in E. coli.

Controlled gene expression is crucial for engineering bacteria for basic and applied research. Inducible systems enable tight regulation of expression, wherein a small-molecule inducer causes the transcription factor to activate or repress transcriptional initiation. The T7 expression system is one of the most widely used inducible systems, particularly for high overexpression of proteins.

Efficient and iterative retron-mediated recombineering in .

Recombineering is an important tool in gene editing, enabling fast, precise and highly specific modification of microbial genomes. Oligonucleotide-mediated recombineering via the production of single-stranded DNA can overcome the limitations of traditional recombineering methods that rely on the exogenous delivery of editing templates. By modifying a previously reported plasmid-based system for fully single-stranded DNA recombineering, we demonstrate iterative editing of independent loci by utilizing a temperature-sensitive origin of replication for easy curing of the editing plasmid from recombinant cells.

The impact of environment on genetic and epigenetic variation in populations from two contrasting semi-natural grasslands.

Central European grasslands, such as calcareous grasslands and oat-grass meadows, are characterized by diverse environmental conditions and management regimes. Therefore, we aimed to determine potential differences in genetic and epigenetic variation patterns between the contrasting habitats and to identify the drivers of genetic and epigenetic variation. We investigated the genetic and epigenetic variation of the ecologically variable plant species L.

Generating Single Nucleotide Point Mutations in E. coli with the No-SCAR System.

Genetic manipulation of microbial genomes is highly relevant for studying biological systems and the development of biotechnologies. In E. coli, λ-Red recombineering is one of the most widely used gene-editing methods, enabling site-specific insertions, deletions, and point mutations of any genomic locus.

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes.

Background: CRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing CRISPR-Cas guide RNAs (gRNAs) for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for challenging projects with (i) non-standard Cas enzymes, (ii) non-model organisms, or (iii) projects that need to design a panel of gRNA for genome-wide screens.

Draft Genome Sequences of Actinobacterial and Betaproteobacterial Strains Isolated from the Stratosphere.

Here, we report the genome sequences of three bacterial isolates that were cultured from aerosol samples collected at altitudes of 18 to 29 km above sea level. The isolates tolerate desiccation and shortwave UV radiation and are members of the actinobacterial genera and and the betaproteobacterial genus .

Restoration of species-rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation-Findings of a practical restoration project in southeastern Germany.

Restoration of species-rich grasslands is a key issue of conservation. The transfer of seed-containing local plant material is a proven technique to restore species-rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species and .

A plasmid toolbox for controlled gene expression across the Proteobacteria.

Controlled gene expression is fundamental for the study of gene function and our ability to engineer bacteria. However, there is currently no easy-to-use genetics toolbox that enables controlled gene expression in a wide range of diverse species. To facilitate the development of genetics systems in a fast, easy, and standardized manner, we constructed and tested a plasmid assembly toolbox that will enable the identification of well-regulated promoters in many Proteobacteria and potentially beyond.

Impact of river dynamics on the genetic variation of Gypsophila repens (Caryophyllaceae): a comparison of heath forest and more dynamic gravel bank populations along an alpine river.

Alpine rivers are, despite anthropogenic water flow regulation, still often highly dynamic ecosystems. Plant species occurring along these rivers are subject to ecological disturbance, mainly caused by seasonal flooding. Gypsophila repens typically grows at higher altitudes in the Alps, but also occurs at lower altitudes on gravel banks directly along the river and in heath forests at larger distances from the river.

Habitat matters - Strong genetic and epigenetic differentiation in from dry and wet grasslands.

Plant species differ in their ecological amplitude, with some species occurring in very different habitats under strongly differentiated environmental conditions. We were interested in to what extent the occurrence of in dry calcareous grasslands (Bromion) and wet litter meadows (Molinion), two habitats on opposing ends concerning, for example, moisture level, is reflected on the genetic and epigenetic level. Using AFLP (amplified fragment length polymorphisms) and MSAP (methylation sensitive amplification polymorphisms) analyses, we studied the genetic and epigenetic variation of from calcareous grasslands and litter meadows.

Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study.

Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics.

Clonal diversity and genetic variation of the sedge in an alpine fen depend on soil nutrients.

In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot.

A CRISPR Interference System for Efficient and Rapid Gene Knockdown in Caulobacter crescentus.

CRISPR interference (CRISPRi) is a powerful new tool used in different organisms that provides a fast, specific, and reliable way to knock down gene expression. is a well-studied model bacterium, and although a variety of genetic tools have been developed, it currently takes several weeks to delete or deplete individual genes, which significantly limits genetic studies. Here, we optimized a CRISPRi approach to specifically downregulate the expression of genes in Although the CRISPRi system commonly used in other organisms does not work efficiently in , we demonstrate that a catalytically dead version of Cas9 (dCas9) derived from the type II CRISPR3 module of or from can each be effectively used in We show that these CRISPRi systems can be used to rapidly and inducibly deplete or , two essential well-studied genes in , in either asynchronous or synchronized populations of cells.

Dormancy and endosperm presence influence the conservation potential in central European calcareous grassland plants.

The preservation of plant species under conditions in seed banks strongly depends on seed longevity. However, detailed knowledge on this seed ecological aspect is limited and comparative studies from central European habitats are scarce. Therefore, we investigated the seed longevity of 39 calcareous grassland species in order to assess the prospects of storage of seeds originating from a single, strongly threatened habitat.

Chemotactic effects in reaction-diffusion equations for inflammation.

Predator-prey systems are used to model time-dependent virus and lymphocyte population during a liver infection and to discuss the influence of chemotactic behavior on the chronification tendency of such infections. Therefore, a model family of reaction-diffusion equations is presented, and the long-term behavior of the solutions is estimated by a critical value containing the reaction strength, the diffusion rate, and the extension of the liver domain. Fourier techniques are applied to evaluate the influence of chemotactic behavior of the immune response to the long-term behavior of locally linearized models.

Modeling the Chronification Tendency of Liver Infections as Evolutionary Advantage.

Here, we discuss how the tendency of a liver infection to chronify can be seen as an evolutionary advantage for infected individuals. For this purpose, we present a set of reaction-diffusion equations as a mathematical model of viral liver infections, which allows chronic and acute courses of the liver infection. We introduce a cumulative wealth function, and finally, we show that an immune response favoring the chronification is evolutionary advantageous at the same time.

Species and genetic diversity are not congruent in fragmented dry grasslands.

Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory.

Assay and Analysis of Dimethylsulfoniopropionate Demethylase.

Dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide. This enzyme has been purified and characterized from two marine bacteria from different ecological niches.

LTP or LTD? Modeling the Influence of Stress on Synaptic Plasticity.

In cognitive memory, long-term potentiation (LTP) has been shown to occur when presynaptic and postsynaptic activities are highly correlated and glucocorticoid concentrations are in an optimal (i.e., low normal) range.

A Robust CRISPR Interference Gene Repression System in Pseudomonas.

spp. are widely used model organisms in different areas of research. Despite the relevance of in many applications, the use of protein depletion tools in this host remains limited.