Effizienter Austausch and Verarbeitung von semistrukturierten Daten in eingebetteten Systemen

The Internet is a global system of interconnected computers and computer networks where semi-structured data has been successfully applied for exchanging information. In nowadays Internet the huge range of actors, the large diversity of the associated device classes and domains, and the enormous amount of resource-restricted controllers in this system created new requirements and coined also a new term. Internet of Things (IoT), in this regard, refers to identifiable objects (things) and their virtual representations in an Internet-like structure. The fundamental question the thesis tries to answer is whether and how the same semi-structured data can be also applied to the IoT and the embedded domain in spite of resource-limited controllers. In order to discuss this question properties and requirements of embedded networks with regard to the IoT domain have been collected and evaluated. Thereafter the omnipresent semi-structured data exchange format in the Web, the Extensible Markup Language (XML), has been validated. The result was a list of missing requirements such as a compact representation, a representation that can be generated and consumed fast and also allows a small footprint implementation. To address the compiled requirements a binary representation of XML which nowadays is known as W3Cs Efficient XML Interchange (EXI) format has been accomplished which simultaneously optimizes performance and the utilization of computational resources and is designed to be compatible with XML. Moreover, in this work the format has been practically validated and tested. Addressing the needs of the embedded domain one result of this analyzes were optimizations to constrain runtime memory usage and to predict memory growth at runtime. A concept introduced in this thesis is LazyDOM which reduces memory requirements when processing and querying data. By means of a newly proposed code generation technique processing of EXI on ultra-constrained device classes has been enabled and resulting format modifications have been adopted by the W3C standardization. The research work described in this thesis on efficiently exchanging and processing semi-structured data on constrained embedded devices has not only triggered modifications in the W3C EXI format but even is already adopted in domain specific application standards and implementations. The above mentioned optimizations such as predictably limit the memory growth at runtime have been contributed, discussed and evaluated by the W3C experts and become a core part of the EXI specification. Even more significantly from the IoT perspective these optimizations provide the basis for the adoption of this technology in ISO and IEC standardization which is the first time for automotive and power industry to use IoT in the control plane. The implementation of EXI to conduct the evaluation as part of this thesis has become the de-facto open source reference implementation of EXI and became the basis of a number of other reference implementations such as the OpenV2G project that provides the reference implementation of the communication interface in ISO/IEC 15118. In summary the conducted research work has evaluated the options to adapt semi-structured data for the constrained embedded domain, proposed modifications and evaluated those under realistic conditions. This made it relevant for the technology as well as for application standardization despite the short period of this work. As such the research can now be taken as a basis for further challenges in the IoT field namely adopting concepts of the Semantic Web and adapting those to stimulate the quickly expanding eco-system of embedded devices

Thraustochytrids as novel parasitic protists of marine free-living flatworms: Thraustochytrium caudivorum sp. nov. parasitizes Macrostomum lignano

The Labyrinthulomycota are a relatively poorly studied group of heterotrophic unicellular eukaryotes. They comprise three lineages, labyrinthulids, thraustochytrids, and aplanochytrids, which are all primarily marine organisms and considered to be important components of marine microbial communities. Recently a number of Labyrinthulomycota have been implicated as parasites of marine (but also terrestrial) plants and marine molluscs. Here we describe a new species of thraustochytrid, Thraustochytrium caudivorum sp. nov. that we have isolated from laboratory cultures of Macrostomum lignano (Rhabditophora, Macrostomorpha), a marine free-living flatworm. In these worms T. caudivorum can cause lesions, which start at the tip of the tail plate and which can lead to the dissolution of the posterior part of the animal. Although the worms can frequently cure these lesions and regenerate the lost parts, the lesions can also result in the complete dissolution of the animal. We describe this thraustochytrid based on pure agar cultures and infestations in the worm cultures. Moreover, we describe its pathological effects on the worms and its morphology using both light and electron microscopy. In addition, we report a phylogenetic analysis using a partial 18S rDNA sequence that allows us to place this new species within the thraustochytrids. Finally, we outline a protocol that allows to permanently remove the parasites from infested worm cultures. We conclude that thraustochytrids represent a novel group of parasites of free-living flatworm

High-throughput volatilome fingerprint using PTR–ToF–MS shows species-specific patterns in Mortierella and closely related genera

In ecology, Volatile Organic Compounds (VOCs) have a high bioactive and signaling potential. VOCs are not only metabolic products, but are also relevant in microbial cross talk and plant interaction. Here, we report the first large-scale VOC study of 13 different species of Mortierella sensu lato (s.l.) isolated from a range of different alpine environments. Proton Transfer Reaction–Time-of-Flight Mass Spectrometry (PTR–ToF–MS) was applied for a rapid, high-throughput and non-invasive VOC fingerprinting of 72 Mortierella s.l. isolates growing under standardized conditions. Overall, we detected 139 mass peaks in the headspaces of all 13 Mortierella s.l. species studied here. Thus, Mortierellas.l. species generally produce a high number of different VOCs. Mortierella species could clearly be discriminated based on their volatilomes, even if only high-concentration mass peaks were considered. The volatilomes were partially phylogenetically conserved. There were no VOCs produced by only one species, but the relative concentrations of VOCs differed between species. From a univariate perspective, we detected mass peaks with distinctively high concentrations in single species. Here, we provide initial evidence that VOCs may provide a competitive advantage and modulate Mortierella s.l. species distribution on a global scal

The potential of calcium hydroxide to reduce storage losses: A four months monitoring study of spruce wood chip piles at industrial scale

The objective of this study was to investigate the effect of an alkaline additive on the storage of wood chips from Norway spruce forest residues. Piles of untreated and calcium hydroxide treated wood chips (250 m3) were set up and investigated for four months. It was demonstrated that adding Ca(OH)2 to moist wood chips decreased the dry matter loss by 6%. This was attributed to the increase of the pH to a level of 8, rendering the habitat less suitable for fungal colonisation. The results suggest the set-up storage strategy as a potential alternative method for preserving wood chips when long term storage is required

Mycophilic or Mycophobic? Legislation and Guidelines on Wild Mushroom Commerce Reveal Different Consumption Behaviour in European Countries

Mycophiles forage for and pick vast quantities of a wide variety of wild mushroom species. As a result, mushroom intoxications are comparatively frequent in such countries with mycophiles. Thus, national governments are forced to release guidelines or enact legislation in order to ensure the safe commerce of wild mushrooms due to food safety concerns. It is in these guidelines and laws that one can observe whether a country is indeed mycophobic or mycophilic. Furthermore, these laws and guidelines provide valuable information on mushroom preferences and on the consumption habits of each country. As such we were interested in the questions as to whether mushroom consumption behaviour was different within Europe, and if it was possible to discover the typical or distinctive culinary preferences of Slavic or Romanic speaking people, people from special geographical regions or from different zones. This work is based on the analysis of edible mushroom lists available in specific guidelines or legislation related to the consumption and commerce of mushrooms in 27 European countries. The overall diversity of edible mushrooms authorised to be commercialised in Europe is very high. However, only 60 out of a total 268 fungal species can be cultivated. This highlights the importance of guidelines or legislation for the safe commerce of wild mushrooms. The species richness and composition of the mushrooms listed for commerce is very heterogeneous within Europe. The consumption behaviour is not only languagefamily- related, but is strongly influenced by geographical location and neighbouring countries. Indicator species were detected for different European regions ; most of them are widespread fungi, and thus prove culture-specific preferences for these mushrooms. Our results highlight tradition and external input such as trade and cultural exchange as strong factors shaping mushroom consumption behaviour

high resolution glycoform profiling of intact therapeutic proteins by hydrophilic interaction chromatography mass spectrometry

Abstract Glycosylation is considered a critical quality attribute of therapeutic proteins. Protein heterogeneity introduced by glycosylation includes differences in the nature, number and position of the glycans. Whereas analysis of released glycans and glycopeptides provides information about the composition and/or position of the glycan, intact glycoprotein analysis allows assignment of individual proteoforms and co-occurring modifications. Yet, resolving protein glycoforms at the intact level is challenging. We have explored the capacity of hydrophilic liquid chromatography-mass spectrometry (HILIC-MS) for assessing glycosylation patterns of intact pharmaceutical proteins by analyzing the complex glycoproteins interferon-beta-1a (rhIFN-β − 1a) and recombinant human erythropoietin (rhEPO). Efficient glycoform separation was achieved using a superficially-porous amide HILIC stationary phase and trifluoroacetic acid (TFA) as eluent additive. In-source collision-induced dissociation proved to be very useful to minimize protein-signal suppression effects by TFA. Direct injection of therapeutic proteins in aqueous formulation was possible without causing extra band dispersion, provided that the sample injection volume was not larger than 2 μL. HILIC-MS of rhIFN-β − 1a and rhEPO allowed the assignment of, respectively, 15 and 51 glycoform compositions, next to a variety of posttranslational modifications, such as succinimide, oxidation and N-terminal methionine-loss products. MS-based assignments showed that neutral glycan units significantly contributed to glycoform separation, whereas terminal sialic acids only had a marginal effect on HILIC retention. Comparisons of HILIC-MS with the selectivity provided by capillary electrophoresis-MS for the same glycoproteins, revealed a remarkable complementarity of the techniques. Finally it was demonstrated that by replacing TFA for difluoroacetic acid, peak resolution somewhat decreased, but rhEPO glycoforms with relative abundances below 1% could be detected by HILIC-MS, increasing the overall rhEPO glycoform coverage to 72

Optimized isolation of 7,7′-biphyscion starting from Cortinarius rubrophyllus, a chemically unexplored fungal species rich in photosensitizers

Mushrooms such as the dermocyboid Cortinarius rubrophyllus are characterized by strikingly colorful fruiting bodies. The molecular dyes responsible for such colors recently experienced a comeback as photoactive compounds with remarkable photophysical and photobiological properties. One of them-7,7'-biphyscion-is a dimeric anthraquinone that showed promising anticancer effects in the low nanomolar range under blue-light irradiation. Compared to acidic anthraquinones, 7,7'-biphyscion was more efficiently taken up by cells and induced apoptosis after photoactivation. However, seasonal collection of mushrooms producing this compound, low extraction yields, and tricky fungal identification hamper further developments to the clinics. To bypass these limitations, we demonstrate here an alternative approach utilizing a precursor of 7,7'-biphyscion, i.e., the pre-anthraquinone flavomannin-6,6'-dimethyl ether, which is abundant in many species of the subgenus Dermocybe. Controlled oxidation of the crude extract significantly increased the yield of 7,7'-biphyscion by 100%, which eased the isolation process. We also present the mycochemical and photobiological characterization of the yet chemically undescribed species, i.e. C. rubrophyllus. In total, eight pigments (1-8) were isolated, including two new glycosylated anthraquinones (1 and 2). Light-dependent generation of singlet oxygen was detected for the first time for emodin-1-O-beta-D-glucopyranoside (3) [photophysical measurement: Phi(Delta) =0.11 (CD3OD)]. Furthermore, emodin (7) was characterized as promising compound in the photocytotoxicity assay with EC50-values in the low micromolar range under irradiation against cells of the cancer cell lines AGS, A549, and T24.Metals in Catalysis, Biomimetics & Inorganic Material

Ochratoxin A Producing Species in the Genus Penicillium

Ochratoxin A (OTA) producing fungi are members of the genera Aspergillus and Penicillium. Nowadays, there are about 20 species accepted as OTA producers, which are distributed in three phylogenetically related but distinct groups of aspergilli of the subgenus Circumdati and only in two species of the subgenus Penicillium. At the moment, P. verrucosum and P. nordicum are the only OTA producing species accepted in the genus Penicillium. However, during the last century, OTA producers in this genus were classified as P. viridicatum for many years. At present, only some OTA producing species are known to be a potential source of OTA contamination of cereals and certain common foods and beverages such as bread, beer, coffee, dried fruits, grape juice and wine among others. Penicillium verrucosum is the major producer of OTA in cereals such as wheat and barley in temperate and cold climates. Penicillium verrucosum and P. nordicum can be recovered from some dry-cured meat products and some cheeses

Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19(th) century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general