Dual retrieval in conceptual information systems

Conceptual Information Systems provide a multi-dimensional conceptually structured view on data stored in relational databases. On restricting the expressiveness of the retrieval language, they allow the visualization of sets of realted queries in conceptual hierarchies, hence supporting the search of something one does not have a precise description, but only a vague idea of. Information Retrieval is considered as the process of finding specific objects (documents etc.) out of a large set of objects which fit to some description. In some data analysis and knowledge discovery applications, the dual task is of interest: The analyst needs to determine, for a subset of objects, a description for this subset. In this paper we discuss how Conceptual Information Systems can be extended to support also the second task.

Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Pathogens occuring in the winter pea-maize-winter wheat rotation, their host specificity and the potential of compost in suppressing foot and root disease of peas

The overall aim of the work presented was to evaluate soil health management with a specific focus on soil borne diseases of peas. For that purpose field experiments were carried out from 2009 until 2013 to assess crop performance and pathogen occurrence in the rotation winter pea-maize-winter wheat and if the application of composts can improve system performance. The winter peas were left untreated or inoculated with Phoma medicaginis, in the presence or absence of yard waste compost at rate of 5 t dry matter ha-1. A second application of compost was made to the winter wheat. Fusarium ssp. were isolated and identified from the roots of all three crops and the Ascochyta complex pathogens on peas. Bioassays were conducted under controlled conditions to assess susceptibility of two peas to Fusarium avenaceum, F. solani, P. medicaginis and Didymella pinodes and of nine plant species to F. avenaceum. Also, effects of compost applications and temperature on pea diseases were assessed. Application of composts overall stabilized crop performance but it did not lead to significant yield increases nor did it affect pathogen composition and occurrence. Phoma medicaginis was dominating the pathogen complex on peas. F. graminearum, F. culmorum, F. proliferatum, Microdochium nivale, F. crookwellense, F. sambucinum, F. oxysporum, F. avenaceum and F. equiseti were frequently isolated species from maize and winter wheat with no obvious influence of the pre-crop on the Fusarium species composition. The spring pea Santana was considerably more susceptible to the pathogens tested than the winter pea EFB33 in both sterile sand and non-sterilized field soil. F. avenaceum was the most aggressive pathogen, followed by P. medicaginis, D. pinodes, and F. solani. Aggressiveness of all pathogens was greatly reduced in non-sterile field soil. F. avenaceum caused severe symptoms on roots of all nine plant species tested. Especially susceptible were Trifolium repens, T. subterraneum, Brassica juncea and Sinapis alba in addition to peas. Reduction of growing temperatures from 19/16°C day/night to 16/12°C and 13/10°C did not affect the efficacy of compost. It reduced plant growth and slightly increased disease on EFB33 whereas the highest disease severity on Santana was observed at the highest temperature, 19/16°C. Application of 20% v/v of compost reduced disease on peas due to all four pathogens depending on pea variety, pathogen and growing media used. Suppression was also achieved with lower application rate of 3.5% v/v. Tests with γ sterilized compost suggest that the suppression of disease caused by Fusarium spp. is biological in origin, whereas chemical and physical properties of compost are playing an additional role in the suppression of disease caused by D. pinodes and P. medicaginis.

Heat stress response for physiological traits in dairy and dual purpose cattle populations on phenotypic and genetic scales

The main objective of this thesis was to determine the potential impact of heat stress (HS) on physiological traits of lactating cows and semen quality of bulls kept in a temperate climate. The thesis is comprised of three studies. An innovative statistical modeling aspect common to all three studies was the application of random regression methodology (RRM) to study the phenotypic and genetic trajectory of traits in dependency of a continuous temperature humidity index (THI). In the first study, semen quality and quantity traits of 562 Holstein sires kept on an AI station in northwestern Germany were analyzed in the course of THI calculated from data obtained from the nearest weather station. Heat stress was identified based on a decline in semen quality and quantity parameters. The identified general HS threshold (THI = 60) and the thermoneutal zone (THI in the range from 50 to 60) for semen production were lower than detected in studies conducted in tropical and subtropical climates. Even though adult bulls were characterized by higher semen productivity compared to younger bulls, they responded with a stronger semen production loss during harsh environments. Heritabilities (low to moderate range) and additive genetic variances of semen characteristics varied with different levels of THI. Also, based on genetic correlations genotype, by environment interactions were detected. Taken together, these findings suggest the application of specific selection strategies for specific climate conditions. In the second study, the effect of the continuous environmental descriptor THI as measured inside the barns on rectal temperatures (RT), skin temperatures (ST), vaginal temperatures (VT), respiration rates (RR), and pulse rate (PR) of lactating Holstein Friesian (HF) and dual-purpose German black pied cattle (DSN) was analyzed. Increasing HS from THI 65 (threshold) to THI 86 (maximal THI) resulted in an increase of RT by 0.6 °C (DSN) and 1 °C (HF), ST by 3.5 °C (HF) and 8 °C (DSN), VT by 0.3 °C (DSN), and RR by 47 breaths / minute (DSN), and decreased PR by 7 beats / minute (DSN). The undesired effects of rising THI on physiological traits were most pronounced for cows with high levels of milk yield and milk constituents, cows in early days in milk and later parities, and during summer seasons in the year 2014. In the third study of this dissertation, the genetic components of the cow’s physiological responses to HS were investigated. Heat stress was deduced from indoor THI measurements, and physiological traits were recorded on native DSN cows and their genetically upgraded crosses with Holstein Friesian sires in two experimental herds from pasture-based production systems reflecting a harsh environment of the northern part of Germany. Although heritabilities were in a low range (from 0.018 to 0.072), alterations of heritabilities, repeatabilities, and genetic components in the course of THI justify the implementation of genetic evaluations including heat stress components. However, low repeatabilities indicate the necessity of using repeated records for measuring physiological traits in German cattle. Moderate EBV correlations between different trait combinations indicate the potential of selection for one trait to simultaneously improve the other physiological attributes. In conclusion, bulls of AI centers and lactating cows suffer from HS during more extreme weather conditions also in the temperate climate of Northern Germany. Monitoring physiological traits during warm and humid conditions could provide precious information for detection of appropriate times for implementation of cooling systems and changes in feeding and management strategies. Subsequently, the inclusion of these physiological traits with THI specific breeding values into overall breeding goals could contribute to improving cattle adaptability by selecting the optimal animal for extreme hot and humid conditions. Furthermore, the recording of meteorological data in close distance to the cow and visualizing the surface body temperature by infrared thermography techniques might be helpful for recognizing heat tolerance and adaptability in cattle.