Nachweis der Expression von HMGB1 und HMGA2 zur Anwendung in der Tumor- und Pränataldiagnostik

The high mobility group protein AT-hook 2 (HMGA2) is an architectonic transcription factor abundantly expressed during embryonic and fetal development and is associated with the progression of malignant tumors. In this thesis, chromatin immunoprecipitation (ChIP) experiments and bioinformatic methods were used to analyze and characterize DNA-binding sites of the HMGA2 protein. The results show that artificially generated SELEX sequences and short BLAST alignments of the ChIP fragments from living cells possess similarities in their structural organization. In further experiments the expression of HMGB1 and HMGA2 in different body fluids from cancer patients and pregnant women was determined to provide valuable data for further use in tumor and prenatal diagnosis. HMGB1, a so-called danger signaling protein, as well as the protooncogene HMGA2 were found to be highly expressed in human pleural and peritoneal effusions due to cancer and inflammation. The results underline these proteins as possible targets for treatment in advanced cancer as well as in inflammatory diseases. Additionally an improved protocol of the chromatin immunoprecipitation was established, to select and enrich cell-free, fetal DNA from amniotic fluid. The fact that HMGA2 apparently remains to be attached to cell-free DNA suggests interesting new approaches in noninvasive prenatal diagnosis

How does rubber flooring in farrowing pens affect the lying time and lying behaviour of the sow and her time to lie down?

In the farrowing pens the amount of bedding material and the quality of the concrete floor has a huge impact on both the sow and the piglets. In this study imbedding of rubber flooring on the solid area in the farrowing pen was used to see if it had any effects on the sows lying behaviour when compared to concrete. Another important aspect was to evaluate if the rubber floorings had a high enough durability to resist the normal wear in a farrowing pen. Concrete flooring is assumed to have a higher thermally conductive effect then rubber which can affect the sow’s chance to cool down. Therefore the temperature in the farrowing compartment was measured to see if there was a correlation between the sows lying behaviour and the temperature. In total, the study was performed during five farrowing batches, in total about 30 weeks observation period. In each batch, two “rubber” pens and two “concrete” pens were included in the behavioural observations. Three different rubber floorings were included in the study; ProCoat rubber compound, Porca relax, and KKM Porca prototype. Continuous video recordings for the behavioural observations were made twice during the suckling period of five weeks. The video recordings were 24 hours each and took place at about one and three weeks after farrowing. The different behaviours that were noted were standing/walking, lying on the side, lying on the abdomen and sitting. The floor in the farrowing pen was divided into three different zones: solid flooring, slatted flooring and transition zone between solid and slatted flooring. In the behavioural study there was a significant difference one week after farrowing and a trend three weeks after farrowing, that the sows in the rubber pens lay down less than the sows in the concrete pens. This difference was not due to less lying on the solid floor area in the “rubber” pens, but was due to significantly less lying in the transition zone. In contrary, when only looking at the behaviour lying and recalculating the figures for this there was a weak, but not significant, trend that the sows chose to lie more on the solid rubber area than on the solid concrete area in the pen. The highest mean temperature was 21.9 °C and the lowest mean temperature was 15.1 °C. The assumption that sows could be more sensitive to higher temperatures when on the rubber floor, due to less thermal conductivity, could not be confirmed nor disregarded because the temperature during the observation period did not exceed the sows’ thermo neutral zone (15-20 °C) by much. The relation between temperature and lying percent on the slatted area showed a large variation between individual sows. The time it took for the sows to lie down showed no significant difference between the treatments, but a great variation between individual sows could be noted. The good durability of the Porca relax and of the KKM Porca prototype rubber mats were convincing during the whole study. In contrast ProCoat rubber flooring did not sustain the tough rooting behaviour of a sow in a farrowing pen and broke down. In conclusion there were large individual variations in sow behaviour in the study and the sows, in the farrowing pens, choose between different surfaces with different thermal and comfort properties. The use of rubber flooring instead of concrete on the solid area in the farrowing pen did not seem to be a great advantage in this herd. But the study showed that there are now rubber mats on the market, which can sustain the weight and behavioral activity of sows.I grisningsboxar påverkar mängden och kvaliteten strö samt golvets typ och kvalitet både suggan och smågrisarna. I denna studie lades gummimattor alternativt en gummimassa in på grisningsboxens betonggolv för att se om det hade någon inverkan på suggornas liggbeteende jämfört med de suggor som hölls på betong. En annan aspekt som också var viktig att utvärdera var om gummimattorna och gummimassan hade en så pass hög hållbarhet att de kunde motstå påfrestningarna som uppstår i en grisningsbox. Betonggolv har en viss värmeledande effekt som antas vara högre än den hos gummigolv. För att se om det fanns ett samband mellan liggbeteende och temperatur mättes därför också temperaturen i grisningsavdelningen. Studien utfördes under totalt fem grisningsomgångar under sammanlagt ca 30 veckor. I varje omgång av beteendeobservationer ingick två boxar med gummigolv och två med betonggolv. Tre olika sorters gummigolv användes: ProCoat gummimassa, Porca relax och KKM Porca prototyp. Dygnsvisa videoinspelningar gjordes en och tre veckor efter grisning. Dessa inspelningar användes för att observera suggans beteende. De beteende som noterades var står/går, ligger, sidoligger/sidobukligger och sitter. En indelning av golvet i grisningsboxen gjordes också och de olika zonerna var: helt golv, spaltgolv och övergång mellan helt golv och spaltgolv. I beteendestudierna av suggorna var det en signifikant skillnad en vecka efter grisning, och tre veckor efter grisning sågs en trend att suggor i boxar med gummigolv låg mindre än de med betonggolv. Denna skillnad berodde dock inte på att suggorna låg mindre på det hela golvet utan på att de låg signifikant mindre på övergången mellan helt golv och spaltgolv. Då en omräkning av siffrorna gjordes och endast beteendet Ligger studerades fanns en svag, men ej signifikant, trend att suggor valde att ligga mer på det hela gummiområdet än på det hela betongområdet. Den högsta medeltemperaturen var 21.9 °C och den lägsta temperaturen var 15.1° C. Hypotesen att suggor kan vara mer känsliga för högre temperaturer på gummigolv, på grund av sämre värmeledningsförmåga, kunde varken bekräftas eller förkastas eftersom medeltemperaturen inte mer än marginellt översteg den termiska komfort zonen (15-20°C) under observationsperioden. Förhållandet mellan temperatur och liggtiden i procent på spalten visade en stor variation mellan suggorna. Tiden det tog för suggorna att lägga sig ner visade också på en stor variation mellan suggorna, men ingen signifikant skillnad mellan behandlingarna kunde ses. Porca relax och KKM Porca prototyp visade god hållbarhet under hela studien. Däremot kunde inte ProCoat gummimassa stå emot suggans bökande i grisningsboxen utan gick sönder. Slutsatserna av studien var att det fanns en stor variation mellan suggor och att icke fixerade suggor själva kan bestämma vilken yta i boxen med olika komfort och termiska egenskaper som de vill uppehålla sig på. Gummigolv istället för betong på den fasta ytan i grisningsboxen verkade inte vara någon fördel i den här studien. Undersökningen visade att det finns gummimattor på marknaden som kan motstå suggors vikt och bökande beteende i grisningsboxen

Untersuchung des antioxidativen Status des Pferdes bei unterschiedlichen Fütterungsprotokollen sowie Prüfungen zur Stabilität antioxidativer Parameter in Blutproben

Ziel der vorliegenden Arbeit war, die Auswirkungen unregelmäßiger Fütterungen auf den antioxidativen Status des Pferdes zu untersuchen. Weiterhin sollte die Stabilität der antioxidativen Parameter TEAC, ACW, GPX und SOD bei unterschiedlicher Aufbereitung bzw. unterschiedlich langer Lagerung vor Aufbereitung der Proben bestimmt werden

SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis : from Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, (CIBB 2010), Palermo, Italy, 16 - 18 September 2010

Background: The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods: Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results: We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions: The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops

Metallo-Supramolecular Complexation Behavior of Terpyridine- and Ferrocene-Based Polymers in Solution—A Molecular Hydrodynamics Perspective

The contribution deals with the synthesis of the poly(methacrylate)-based copolymers, which contain ferrocene and/or terpyridine moieties in the side chains, and the subsequent analysis of their self-assembly behavior upon supramolecular/coordination interactions with Eu 3+ and Pd 2+ ions in dilute solutions. Both metal ions provoke intra and inter molecular complexation that results in the formation of large supra-macromolecular assembles of different conformation/shapes. By applying complementary analytical approaches (i.e., sedimentation-diffusion analysis in the analytical ultracentrifuge, dynamic light scattering, viscosity and density measurements, morphology studies by electron microscopy), a map of possible conformational states/shapes was drawn and the corresponding fundamental hydrodynamic and macromolecular characteristics of metallo-supramolecular assemblies at various ligand-to-ion molar concentration ratios ( M / L ) in extremely dilute polymer solutions ( c [ η ] ≈ 0.006 ) were determined. It was shown that intramolecular complexation is already detected at ( L ≈ 0.1 ), while at M / L > 0.5 solution/suspension precipitates. Extreme aggregation/agglomeration behavior of such dilute polymer solutions at relatively “high” metal ion content is explained from the perspective of polymer-solvent and charge interactions that will accompany the intramolecular complexation due to the coordination interactions

Structural Diversity of Photoswitchable Sphingolipids for Optodynamic Control of Lipid Raft Microdomains

Sphingolipids are a structurally diverse class of lipids predominantly found in the plasma membrane of eukaryotic cells. These lipids can laterally segregate with other saturated lipids and cholesterol into lipid rafts; liquid-ordered (Lo) microdomains that act as organizing centers within biomembranes. Owing the vital role of sphingolipids for lipid segregation, controlling their lateral localization is of utmost significance. Hence, we made use of the light-induced trans-cis isomerization of azobenzene-modified acyl chains, to develop a set of photoswitchable sphingolipids, with different headgroups (hydroxyl, galactosyl, phosphocholine) and backbones (sphingosine, phytosphingosine, tetrahydropyran (THP)-blocked sphingosine), able to shuttle between liquid-ordered (Lo) and liquid-disordered (Ld) regions of model membranes upon irradiation with UV-A (λ = 365 nm) and blue (λ = 470 nm) light, respectively. Using combined high-speed atomic force microscopy, fluorescence microscopy, and force spectroscopy, we investigated how these active sphingolipids laterally remodel supported bilayers upon photo-isomerization, notably in terms of domain area changes, height mismatch, line tension, and membrane piercing. Hereby, we show that all sphingosine-(Azo-β-Gal-Cer, Azo-SM, Azo-Cer) and phytosphingosine-based (Azo-α-Gal-PhCer, Azo-PhCer) photolipids behave similarly, promoting a reduction in Lo domain area when in the UV-adapted cis-isoform. In contrast, azo-sphingolipids having THP groups that block H-bonding at the sphingosine backbone (Azo-THP-SM, Azo-THP-Cer) induce an increase in the Lo domain area when in cis, accompanied by a major rise in height mismatch and line tension. These changes were fully reversible upon blue light-triggered isomerization of the various lipids back to trans, pinpointing the role of interfacial interactions for the formation of stable Lo lipid raft domains

Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage-and sub-assemblage-specific presence–absence variation in protein-coding genes

Giardia duodenalis (syn. G. intestinalis, G. lamblia) is a widespread gastrointestinal protozoan parasite with debated taxonomic status. Currently, eight distinct genetic sub-groups, termed assemblages A–H, are defined based on a few genetic markers. Assemblages A and B may represent distinct species and are both of human public health relevance. Genomic studies are scarce and the few reference genomes available, in particular for assemblage B, are insufficient for adequate comparative genomics. Here, by combining long- and short-read sequences generated by PacBio and Illumina sequencing technologies, we provide nine annotated genome sequences for reference from new clinical isolates (four assemblage A and five assemblage B parasite isolates). Isolates chosen represent the currently accepted classification of sub-assemblages AI, AII, BIII and BIV. Synteny over the whole genome was generally high, but we report chromosome-level translocations as a feature that distinguishes assemblage A from B parasites. Orthologue gene group analysis was used to define gene content differences between assemblage A and B and to contribute a gene-set-based operational definition of respective taxonomic units. Giardia is tetraploid, and high allelic sequence heterogeneity (ASH) for assemblage B vs. assemblage A has been observed so far. Noteworthy, here we report an extremely low ASH (0.002%) for one of the assemblage B isolates (a value even lower than the reference assemblage A isolate WB-C6). This challenges the view of low ASH being a notable feature that distinguishes assemblage A from B parasites, and low ASH allowed assembly of the most contiguous assemblage B genome currently available for reference. In conclusion, the description of nine highly contiguous genome assemblies of new isolates of G. duodenalis assemblage A and B adds to our understanding of the genomics and species population structure of this widespread zoonotic parasite.publishedVersio

Hur fungerar olika gummigolv i grisningsboxen praktiskt och hur är suggans liggbeteende på gummi- jämfört med betonggolv?

Gummigolv på den fasta betongytan installerades i ett antal grisningsboxar med syfte att förbättra djurhälsa och komfort för både smågrisar och suggor. I detta Fakta-blad presenteras erfarenheter från de testade gummigolven samt resultat från suggornas beteende i jämförelse med betonggolv. Totalt testades och jämfördes tre olika gummimaterial i grisningsboxarna under fem grisningsomgångar. Hur lång tid suggorna stod eller låg och var suggorna befann sig i grisningsboxen studerades med hjälp av dygnsvisa videoinspelningar ca 1 vecka respektive 3 veckor efter grisningen. Sammanfattningsvis konstaterades att suggornas liggbeteende inte påverkades negativt av gummimaterialen, snarare tvärtom. Den mjukare gummimattan bedömdes som bäst ur komfortsynpunkt. Hållbarheten hos gummimassabeläggningen var inte tillräckligt bra och den hårdare gummimattan upplevdes som hal vid grisningen för både sugga och personal