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Institute
- Institut für Biochemie und Biologie (370) (remove)
Sequelae of prematurity triggered by oxidative stress and free radical-mediated tissue damage have coined the term “oxygen radical disease of prematurity”. Caffeine, a potent free radical scavenger and adenosine receptor antagonist, reduces rates of brain damage in preterm infants. In the present study, we investigated the effects of caffeine on oxidative stress markers, anti-oxidative response, inflammation, redox-sensitive transcription factors, apoptosis, and extracellular matrix following the induction of hyperoxia in neonatal rats. The brain of a rat pups at postnatal Day 6 (P6) corresponds to that of a human fetal brain at 28–32 weeks gestation and the neonatal rat is an ideal model in which to investigate effects of oxidative stress and neuroprotection of caffeine on the developing brain. Six-day-old Wistar rats were pre-treated with caffeine and exposed to 80% oxygen for 24 and 48 h. Caffeine reduced oxidative stress marker (heme oxygenase-1, lipid peroxidation, hydrogen peroxide, and glutamate-cysteine ligase catalytic subunit (GCLC)), promoted anti-oxidative response (superoxide dismutase, peroxiredoxin 1, and sulfiredoxin 1), down-regulated pro-inflammatory cytokines, modulated redox-sensitive transcription factor expression (Nrf2/Keap1, and NFκB), reduced pro-apoptotic effectors (poly (ADP-ribose) polymerase-1 (PARP-1), apoptosis inducing factor (AIF), and caspase-3), and diminished extracellular matrix degeneration (matrix metalloproteinases (MMP) 2, and inhibitor of metalloproteinase (TIMP) 1/2). Our study affirms that caffeine is a pleiotropic neuroprotective drug in the developing brain due to its anti-oxidant, anti-inflammatory, and anti-apoptotic properties.
Monoclonal antibodies are universal binding molecules and are widely used in biomedicine and research. Nevertheless, the generation of these binding molecules is time-consuming and laborious due to the complicated handling and lack of alternatives. The aim of this protocol is to provide one standard method for the generation of monoclonal antibodies using hybridoma technology. This technology combines two steps. Step 1 is an appropriate immunization of the animal and step 2 is the fusion of B lymphocytes with immortal myeloma cells in order to generate hybrids possessing both parental functions, such as the production of antibody molecules and immortality. The generated hybridoma cells were then recloned and diluted to obtain stable monoclonal cell cultures secreting the desired monoclonal antibody in the culture supernatant. The supernatants were tested in enzyme-linked immunosorbent assays (ELISA) for antigen specificity. After the selection of appropriate cell clones, the cells were transferred to mass cultivation in order to produce the desired antibody molecule in large amounts. The purification of the antibodies is routinely performed by affinity chromatography. After purification, the antibody molecule can be characterized and validated for the final test application. The whole process takes 8 to 12 months of development, and there is a high risk that the antibody will not work in the desired test system.
Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are hepatic manifestations of the metabolic syndrome. Many currently used animal models of NAFLD/NASH lack clinical features of either NASH or metabolic syndrome such as hepatic inflammation and fibrosis (e.g., high-fat diets) or overweight and insulin resistance (e.g., methionine-choline-deficient diets), or they are based on monogenetic defects (e.g., ob/ob mice). In the current study, a Western-type diet containing soybean oil with high n-6-PUFA and 0.75% cholesterol (SOD + Cho) induced steatosis, inflammation and fibrosis accompanied by hepatic lipid peroxidation and oxidative stress in livers of C57BL/6-mice, which in addition showed increased weight gain and insulin resistance, thus displaying a phenotype closely resembling all clinical features of NASH in patients with metabolic syndrome. In striking contrast, a soybean oil-containing Western-type diet without cholesterol (SOD) induced only mild steatosis but not hepatic inflammation, fibrosis, weight gain or insulin resistance. Another high-fat diet, mainly consisting of lard and supplemented with fructose in drinking water (LAD + Fru), resulted in more prominent weight gain, insulin resistance and hepatic steatosis than SOD + Cho, but livers were devoid of inflammation and fibrosis. Although both LAD + Fru-and SOD + Cho-fed animals had high plasma cholesterol, liver cholesterol was elevated only in SOD + Cho animals. Cholesterol induced expression of chemotactic and inflammatory cytokines in cultured Kupffer cells and rendered hepatocytes more susceptible to apoptosis. In summary, dietary cholesterol in the SOD + Cho diet may trigger hepatic inflammation and fibrosis. SOD + Cho-fed animals may be a useful disease model displaying many clinical features of patients with the metabolic syndrome and NASH.
Modeling a secular trend by Monte Carlo simulation of height biased migration in a spatial network
(2017)
Background: In a recent Monte Carlo simulation, the clustering of body height of Swiss military conscripts within a spatial network with characteristic features of the natural Swiss geography was investigated. In this study I examined the effect of migration of tall individuals into network hubs on the dynamics of body height within the whole spatial network. The aim of this study was to simulate height trends. Material and methods: Three networks were used for modeling, a regular rectangular fishing net like network, a real world example based on the geographic map of Switzerland, and a random network. All networks contained between 144 and 148 districts and between 265-307 road connections. Around 100,000 agents were initially released with average height of 170 cm, and height standard deviation of 6.5 cm. The simulation was started with the a priori assumption that height variation within a district is limited and also depends on height of neighboring districts (community effect on height). In addition to a neighborhood influence factor, which simulates a community effect, body height dependent migration of conscripts between adjacent districts in each Monte Carlo simulation was used to re-calculate next generation body heights. In order to determine the direction of migration for taller individuals, various centrality measures for the evaluation of district importance within the spatial network were applied. Taller individuals were favored to migrate more into network hubs, backward migration using the same number of individuals was random, not biased towards body height. Network hubs were defined by the importance of a district within the spatial network. The importance of a district was evaluated by various centrality measures. In the null model there were no road connections, height information could not be delivered between the districts. Results: Due to the favored migration of tall individuals into network hubs, average body height of the hubs, and later, of the whole network increased by up to 0.1 cm per iteration depending on the network model. The general increase in height within the network depended on connectedness and on the amount of height information that was exchanged between neighboring districts. If higher amounts of neighborhood height information were exchanged, the general increase in height within the network was large (strong secular trend). The trend in the homogeneous fishnet like network was lowest, the trend in the random network was highest. Yet, some network properties, such as the heteroscedasticity and autocorrelations of the migration simulation models differed greatly from the natural features observed in Swiss military conscript networks. Autocorrelations of district heights for instance, were much higher in the migration models. Conclusion: This study confirmed that secular height trends can be modeled by preferred migration of tall individuals into network hubs. However, basic network properties of the migration simulation models differed greatly from the natural features observed in Swiss military conscripts. Similar network-based data from other countries should be explored to better investigate height trends with Monte Carlo migration approach.
The aim of the study was to investigate the correlation of heights of conscripts living in neighboring districts in Poland. The study used 10% of a nationally representative sample of 26,178 males 18.5-19.5 years old examined during the National survey of Polish conscripts conducted in 2001. The sample represented all regions and social strata of the country and included 354 different districts within 16 voivodships (provinces). Analyses were performed with the R statistical software. A small but significant correlation (0.24, p < 0.0001) was observed for height between 1st order neighboring districts. Correlations decreased with increased distances between neighboring districts, but remained significant for 7th node neighbors (0.18, p < 0.0001). Regarding voivodships (provinces), average height showed a geographical trend from the northwest (relatively tall) to the southeast (relatively short), and the correlation was stronger for first order neighboring provinces (0.796, p < 0.001). This study revealed clusters of tall people and short people, providing a support for hypothesis of the community effect in height. Small correlations between 1st order neighbors than in another country (Switzerland) may be associated with differences in geography, since in Poland there are no natural barriers (e.g., mountains) and road infrastructure is well-developed.
Background: We investigated height of Norwegian conscripts in view of the hypothesis of a "community effect on height" using autocorrelation analysis of district heights within a time-span of 20 years at the end of the 19th century and correlations between neighboring districts at this time. Material and methods: After digitalizing available body height data of Norwegian draftees in 1877-1878, 1880 (averaged as 1878), and 1895-1897 (averaged as 1896) we calculated the magnitude of autocorrelation of body height within the same municipality at different time points. Furthermore, we generated three different neighborhood networks, (1) based on Euclidean distances, (2) a minimum spanning tree build on those distances, (3) a network founded on real world road connections. The networks were used to determine the correlation between body height of neighboring districts depending on the number of edges required to connect two municipalities. Results: The autocorrelation value for body heights was around r = 0.5 (for all p < 0.001) in the years 1878 and 1896. The correlation between neighboring districts varied in the Euclidean distance based network between 0.47 and 0.27 approximately for both years in a sorted order, descending from nearest (0-50 km) to farthest (150-200 km, for all p < 0.001). First order neighbors in the minimum spanning tree network correlation was 0.36 in 1878 and 0.42 in 1896 (for all p < 0.001). The values of neighbor correlation in the road connection based network ranged in 1878 from 0.42 (first order neighbors) to 0.17 (forth order neighbors, for all p < 0.01) and in 1896 from 0.46 (first order neighbors) to 0.12 (forth order neighbors, for all p < 0.05). Conclusion: This initial study of Norwegian conscript height data from the 19th century showed significant medium sized effects for the within district autocorrelation between 1878 and 1896 as well as medium neighborhood correlation, slightly lower in comparison to a recent study regarding Swiss conscripts. Digitalizing more data from other years in this and later time spans as well as using older road and ship connections instead of the actual road data might stabilize and improve those findings.
Plant Hormones
(2017)
This volume aims to present a representative cross-section of modern experimental approaches relevant to Plant Hormone Biology, ranging from relatively simple physiological to highly sophisticated methods. Chapters describe physiological, developmental, microscopy-based techniques, measure hormone contents, and heterologous systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Preface
(2017)
The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.
Preface
(2017)
Drug target miRNA
(2017)
This volume provides a concise and technical discussion of recently developed approaches to overcome challenges in miRNA drug discovery. Drug Target miRNA: Methods and Protocols explores strategies to overcome pharmacodynamics and pharmacokinetics challenges. These strategies cover anti-sense agents targeting miRNA that are applied in advanced formulations or are chemically optimized to increase delivery; small molecule miRNA modulators to overcome anti-sense agents’ limitations; general enhancers of miRNA maturation; and Argonaute 2 protein and its pharmacokinetic parameters. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and thorough, Drug Target miRNA: Methods and Protocols is a valuable resource for anyone interested in the ever-evolving field of miRNA drug discovery.
The ecological benefits of polyploidy are intensely debated. Some authors argue that plants with duplicated chromosome sets (polyploids) are more stress- resistant and superior colonizers and may thus outnumber their low ploidy conspecifics in more extreme habitats. Brachypodium distachyon (sensu lato), for example, a common annual grass in Israel and the entire Mediterranean basin, comprises three cytotypes of differing chromosome numbers that were recently proposed as distinct species. It was suggested that increased aridity increases the occurrence of its polyploid cytotype. Here, we tested at two spatial scales whether polyploid plants of B. distachyon s. l. are more frequently found in drier habitats in Israel. We collected a total of 430 specimens (i) along a largescale climatic gradient with 15 thoroughly selected sites (spanning 114- 954 mm annual rainfall), and (ii) from corresponding Northern (more mesic) and Southern (more arid) hill slopes to assess the micro- climatic difference between contrasting exposures. Cytotypes were then determined via flow cytometry. Polyploid plants comprised 90% of all specimens and their proportion ranged between 0% and 100% per site. However, this proportion was not correlated with aridity along the large- scale gradient, nor were polyploids more frequently found on Southern exposures. Our results show for both spatial scales that increasing aridity is not the principal driver for the distribution of polyploids in B. distachyon s. l. in Israel. Notably, though, diploid plants were restricted essentially to four intermediate sites, while polyploids dominated the most arid and the most mesic sites. This, to some degree, clustered pattern suggests that the distribution of cytotypes is not entirely random and calls for future studies to assess further potential drivers.
The phylogenetic structure of communities (PSC) reveals how evolutionary history affects community assembly processes. However, there are important knowledge gaps on PSC patterns for annual communities and there is a need for studies along environmental gradients in dry ecosystems where several processes shape PSC. Here, we investigated the PSC of annual plants along an aridity gradient in Israel, including eight years, two spatial scales, the effects of shrubs on understory, and the phylogenetic signal of important traits. Increasing drought stress led to overdispersed PSC at the drier end of the gradient, indicating that species were less related than expected by chance. This was supported at a smaller spatial scale, where within the drier sites, communities in open- more arid- habitats were more overdispersed than those under nurse shrubs. Interestingly, some key traits related to drought resistance were not conserved in the phylogeny. Together, our findings suggested that while habitat filtering selected for drought resistance strategies, these strategies evolved independently along multiple contrasting evolutionary lineages. Our comprehensive PSC study provides strong evidence for the interacting effects of habitat filtering and plant- plant interactions, particularly highlighting that the conservative evolution of traits should not be assumed in future interpretations of PSC patterns.
The profits of excludability and transferability in redistributive land reform in central Namibia
(2017)
Policies which redistribute property rights to land can improve the well-being of rural households and can have overall growth effects. In many cases, however, land reforms are driven mainly by politically justified objectives. Under such circumstances, little emphasis is placed on whether and, if so, how property rights can increase productivity. Following 18 years of land reform implementation in Namibia, we evaluated 65 beneficiaries in Namibia. We assess to which degree land rights affects their farm income. The study focuses on Namibia’s two main commercial land reform instruments, namely the Farm Unit Resettlement Scheme and the Affirmative Action Loan Scheme. We find evidence that the majority of land reform projects are not profitable. Further, our study confirms the importance of the right to restrict land access compared with the right to transfer. The long-term leasehold contract seemingly provides sufficient incentives to make productive use of the land.
miRNA Targeting Drugs
(2017)
Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs’ chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.
Enzymes from the xanthine oxidase (XO) family of molybdenum enzymes are generally, with some exceptions, molybdenum iron–sulfur flavin hydroxylases. Mammalian xanthine oxidoreductase and aldehyde oxidase were among the first enzymes to be studied in detail more than 100 years ago and, surprisingly, they continue to be thoroughly studied in molecular detail with many open and unresolved questions remaining. Enzymes of the XO family are characterized by a molybdenum cofactor (Moco) active site with a MoVIOS(OH) ligand sphere where substrate hydroxylation of either aromatic or aliphatic carbon centers is catalyzed. During the reaction, electrons are transferred to the oxidizing substrate, most commonly O2 or NAD+, which react at the FAD site.
Bacterial Molybdoenzymes
(2017)
The biogenesis of molybdoenzymes is a cytoplasmic event requiring both the folded apoenzymes and the matured molybdenum cofactor. The structure and the complexity of the molybdenum cofactor varies in each molybdoenzyme family and consequently different accessory proteins are required for the maturation of the respective enzymes. Thus, for enzymes of both the DMSO reductase and xanthine oxidase families, specific chaperones exist which are dedicated to increase the stability and the folding of specific members of each family. In this review, we describe the role of these chaperones for molybdoenzyme maturation. We present a model which describes step by step the mechanism of the maturation of representative molybdoenzymes from each family.
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes with the exception of nitrogenase, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into three steps in eukaryotes, and four steps in bacteria and archaea: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5′GTP, (ii) in the second step the two sulfur molecules are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into molybdopterin to form Moco and (iv) additional modification of Moco occurs in bacteria and archaea with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review will focus on the biosynthesis of Moco in bacteria, humans and plants.
Fat loads were quantified for 2125 Yellow-browed Warblers Phylloscopus inornatus trapped at a stop-over site in Far East Russia during autumn migration. Flight ranges of 660-820km were estimated for the fattest individuals, suggesting that they would need to stop for refuelling at least six times to reach their wintering areas in South East Asia.
Anthropologists all over the world are discussing influences on individual height including quantity and quality of nutrition. To examine whether a relationship between nutritional components and height can be found this pilot study has been developed. The research samples consisted of 44 children (age 3–6 years) attending two different kindergartens in Germany. Height measurements were taken for each child. Furthermore the parents had to fill out a 24-hour questionnaire to document their children’s eating habits during the weekend. In order to standardize the measured height values z-scores were calculated with reference to the average height of the overall cohort. The results of correlation analysis indicate that height is not significantly related to any of the main nutritional components as protein (r = –0.148), carbohydrates (r = 0.126), fat (r = 0.107), fibre (r = –0.289), vitamin (r = 0.050), calcium (r = 0.110), potassium (r = 0.189) and overall calorie intake (r = 0.302). In conclusion, it can be stated that the quality of nutrition may not have a strong influence on individual height. However, due to the small sample size further research should be provided with a larger cohort of children to verify the present results.