Heterogeneity in pure microbial systems: experimental measurements and modeling

Cellular heterogeneity influences bioprocess performance in ways that until date are not completely elucidated. In order to account for this phenomenon in the design and operation of bioprocesses, reliable analytical and mathematical descriptions are required. We present an overview of the single cell analysis, and the mathematical modeling frameworks that have potential to be used in bioprocess control and optimization, in particular for microbial processes. In order to be suitable for bioprocess monitoring, experimental methods need to be high throughput and to require relatively short processing time. One such method used successfully under dynamic conditions is flow cytometry. Population balance and individual based models are suitable modeling options, the latter one having in particular a good potential to integrate the various data collected through experimentation. This will be highly beneficial for appropriate process design and scale up as a more rigorous approach may prevent a priori unwanted performance losses. It will also help progressing synthetic biology applications to industrial scale

Osmoprotectants play a major role in the Portulaca oleracea resistance to high levels of salinity stress—insights from a metabolomics and proteomics integrated approach

IntroductionPurslane (Portulaca oleracea L.) is a non-conventional food plant used extensively in folk medicine and classified as a multipurpose plant species, serving as a source of features of direct importance to the agricultural and agri-industrial sectors. This species is considered a suitable model to study the mechanisms behind resistance to several abiotic stresses including salinity. The recently achieved technological developments in high-throughput biology opened a new window of opportunity to gain additional insights on purslane resistance to salinity stress—a complex, multigenic, and still not well-understood trait. Only a few reports on single-omics analysis (SOA) of purslane are available, and only one multi-omics integration (MOI) analysis exists so far integrating distinct omics platforms (transcriptomics and metabolomics) to characterize the response of purslane plants to salinity stress.MethodsThe present study is a second step in building a robust database on the morpho-physiological and molecular responses purslane to salinity stress and its subsequent use in attempting to decode the genetics behind its resistance to this abiotic stress. Here, the characterization of the morpho-physiological responses of adult purslane plants to salinity stress and a metabolomics and proteomics integrative approach to study the changes at the molecular level in their leaves and roots is presented.Results and discussionAdult plants of the B1 purslane accession lost approximately 50% of the fresh and dry weight (from shoots and roots) whensubmitted to very high salinity stress (2.0 g of NaCl/100 g of the substrate). The resistance to very high levels of salinity stress increases as the purslane plant matures, and most of the absorbed sodium remains in the roots, with only a part (~12%) reaching the shoots. Crystal-like structures, constituted mainly by Na+, Cl−, and K+, were found in the leaf veins and intercellular space near the stoma, indicating that this species has a mechanism of salt exclusion operating on the leaves, which has its role in salt tolerance. The MOI approach showed that 41 metabolites were statistically significant on the leaves and 65 metabolites on the roots of adult purslane plants. The combination of the mummichog algorithm and metabolomics database comparison revealed that the glycine, serine, and threonine, amino sugar and nucleotide sugar, and glycolysis/gluconeogenesis pathways were the most significantly enriched pathways when considering the total number of occurrences in the leaves (with 14, 13, and 13, respectively) and roots (all with eight) of adult plants; and that purslane plants employ the adaptive mechanism of osmoprotection to mitigate the negative effect of very high levels of salinity stress; and that this mechanism is prevalent in the leaves. The multi-omics database built by our group underwent a screen for salt-responsive genes, which are now under further characterization for their potential to promote resistance to salinity stress when heterologously overexpressed in salt-sensitive plants

Omics Fusion - A Platform for Integrative Analysis of Omics Data

Brink B, Seidel A, Kleinbölting N, Nattkemper TW, Albaum S. Omics Fusion - A Platform for Integrative Analysis of Omics Data. Journal of Integrative Bioinformatics. 2016;13(4: SI): 296

Omics Fusion – A Platform for Integrative Analysis of Omics Data

We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de