Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.

Data representing moving objects is rapidly getting more available, especially in the area of wildlife GPS tracking. It is a central belief that information is hidden in large data sets in the form of interesting patterns. One of the most common spatio-temporal patterns sought after is flocks. A flock is a large enough subset of objects moving along paths close to each other for a certain pre-defined time. We give a new definition that we argue is more realistic than the previous ones, and by the use of techniques from computational geometry we present fast algorithms to detect and report flocks. The algorithms are analysed both theoretically and experimentally.

Whole grain cereals have been found to be a good source of nutritionally valuable substances, such as antioxidants, minerals, vitamins, and dietary fiber. A wide range of these compounds is affected by germination. While some compounds, such as beta-glucans are degraded, others, like vitamins can be increased by means of malting. Therefore, germination and malting of cereals is a way not only to produce fermentable extract for the brewing and distilling industries, but can also be a way to produce ingredients enriched with health promoting compounds. Malt extracts have also been shown to be good substrates for the growth and application of probiotic bacteria.

Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by bacteria for carbon and energy storage that also have commercial potential as bioplastics. One promising class of carbon feedstocks for industrial PHA production is plant oils, due to the high carbon content of these compounds. The bacterium Ralstonia eutropha accumulates high levels of PHA and can effectively utilize plant oil. Growth experiments that include plant oil, however, are difficult to conduct in a quantitative and reproducible manner due to the heterogeneity of the two-phase medium. In order to overcome this obstacle, a new culture method was developed in which palm oil was emulsified in growth medium using the glycoprotein gum arabic as the emulsifying agent. Gum arabic did not influence R. eutropha growth and could not be used as a nutrient source by the bacteria. R. eutropha was grown in the emulsified oil medium and PHA production was measured over time. Additionally, an extraction method was developed to monitor oil consumption. The new method described in this study allows quantitative, reproducible R. eutropha experiments to be performed with plant oils. The method may also prove useful for studying growth of different bacteria on plant oils and other hydrophobic carbon sources.

Abstract. Data representing moving objects is rapidly getting more available, especially in the area of wildlife GPS tracking. It is a central belief that information is hidden in large data sets in the form of interesting patterns. One of the most common spatio-temporal patterns sought after is flocks. A flock is a large enough subset of objects moving along paths close to each other for a certain pre-defined time. We give a new definition that we argue is more realistic than the previous ones, and by the use of techniques from computational geometry we present fast algorithms to detect and report flocks. The algorithms are analysed both theoretically and experimentally.

Procyanidins, as important secondary plant metabolites in fruits, berries, and beverages such as cacao and tea, are supposed to have positive health impacts, although their bioavailability is yet not clear. One important aspect for bioavailability is intestinal metabolism. The investigation of the microbial catabolism of A-type procyanidins is of great importance due to their more complex structure in comparison to B-type procyanidins. A-type procyanidins exhibit an additional ether linkage between the flavan-3-ol monomers. In this study two A-type procyanidins, procyanidin A2 and cinnamtannin B1, were incubated in the pig cecum model to mimic the degradation caused by the microbiota. Both A-type procyanidins were degraded by the microbiota. Procyanidin A2 as a dimer was degraded by about 80% and cinnamtannin B1 as a trimer by about 40% within 8 h of incubation. Hydroxylated phenolic compounds were quantified as degradation products. In addition, two yet unknown catabolites were identified, and the structures were elucidated by Fourier transform mass spectrometry.

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