Showing papers by "University of Hohenheim published in 2018"

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.

Abstract: Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Abstract: The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

How to Respond to the Fourth Industrial Revolution, or the Second Information Technology Revolution? Dynamic New Combinations between Technology, Market, and Society through Open Innovation

Abstract: Since Klaus Schwab and the World Economic Forum declared the arrival of the Fourth Industrial Revolution, there has been much discussion about it. However, there is no commonly agreed-upon definition of the Fourth Industrial Revolution. Therefore, we attempted to answer the following four research questions. “What is the definition of the Fourth Industrial Revolution?”, “How can we respond to the Fourth Industrial Revolution in terms of institutions?”, “How can we respond to the Fourth Industrial Revolution in terms of technology?”, “How can we respond to the Fourth Industrial Revolution in terms of firm innovation and start-up strategy?” Brainstorming was conducted by 11 scholars from several countries to answer these four research questions. Therefore, this research is not the end product of four research questions, but a kind of advanced template to answer the four research questions for continuing research.

Access to the odor world: olfactory receptors and their role for signal transduction in insects.

Abstract: The sense of smell enables insects to recognize and discriminate a broad range of volatile chemicals in their environment originating from prey, host plants and conspecifics. These olfactory cues are received by olfactory sensory neurons (OSNs) that relay information about food sources, oviposition sites and mates to the brain and thus elicit distinct odor-evoked behaviors. Research over the last decades has greatly advanced our knowledge concerning the molecular basis underlying the reception of odorous compounds and the mechanisms of signal transduction in OSNs. The emerging picture clearly indicates that OSNs of insects recognize odorants and pheromones by means of ligand-binding membrane proteins encoded by large and diverse families of receptor genes. In contrast, the mechanisms of the chemo-electrical transduction process are not fully understood; the present status suggests a contribution of ionotropic as well as metabotropic mechanisms. In this review, we will summarize current knowledge on the peripheral mechanisms of odor sensing in insects focusing on olfactory receptors and their specific role in the recognition and transduction of odorant and pheromone signals by OSNs.

What's normal anyway? Residual plots are more telling than significance tests when checking ANOVA assumptions

Abstract: We consider two questions important for applying analysis of variance (ANOVA): Should normality be checked on the raw data or on the residuals (or is it immaterial which of the two approaches we take)? Should normality and homogeneity of variance be checked using significance tests or diagnostic plots (or both)? Based on two examples, we show that residuals should be used for model checking and that residual plots are better for checking ANOVA assumptions than statistical tests. We also discuss why one should be very cautious when using statistical tests to check the assumptions.

Integrated Reporting and Assurance of Sustainability Information: An Experimental Study on Professional Investors’ Information Processing

Abstract: Sustainability-related non-financial information is increasingly deemed value relevant. Against this background, two recent trends in non-financial reporting are frequently discussed: integrated reporting and assurance of sustainability information. Using an established framework of information acquisition, evaluation, and weighting, this experimental study investigated how the choice of reporting format interacts with the voluntary assurance of sustainability information. The results from a sample of professional investors underline the important role of assurance in the context of voluntary disclosure and illustrate the relevant interaction with the reporting format. Assurance of sustainability information positively affected professional investors’ evaluation of a firm’s sustainability performance, resulted in a higher weighting of this information, and led to higher investment-related judgments. However, this assurance effect was weaker in the case of integrated reporting compared to separate reporting. We attribute this effect to a cognitive bias in decision-making when assured financial performance and non-assured sustainability performance are presented in the same report.

Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome

Abstract: The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics. However, the respective analyses are still at the beginning and currently there is a lack of information in regard to the activity and functional characterization of the gut microbial communities. In the future, the use of multi-omics approaches may enhance research related to chicken production, animal and also public health. Furthermore, combinations with other disciplines such as genomics, immunology and physiology may have the potential to elucidate the definition of a "healthy" gut microbiota.

An OPR3-independent pathway uses 4,5-didehydrojasmonate for jasmonate synthesis

Abstract: Biosynthesis of the phytohormone jasmonoyl-isoleucine (JA-Ile) requires reduction of the JA precursor 12-oxo-phytodienoic acid (OPDA) by OPDA reductase 3 (OPR3). Previous analyses of the opr3-1 Arabidopsis mutant suggested an OPDA signaling role independent of JA-Ile and its receptor COI1; however, this hypothesis has been challenged because opr3-1 is a conditional allele not completely impaired in JA-Ile biosynthesis. To clarify the role of OPR3 and OPDA in JA-independent defenses, we isolated and characterized a loss-of-function opr3-3 allele. Strikingly, opr3-3 plants remained resistant to necrotrophic pathogens and insect feeding, and activated COI1-dependent JA-mediated gene expression. Analysis of OPDA derivatives identified 4,5-didehydro-JA in wounded wild-type and opr3-3 plants. OPR2 was found to reduce 4,5-didehydro-JA to JA, explaining the accumulation of JA-Ile and activation of JA-Ile-responses in opr3-3 mutants. Our results demonstrate that in the absence of OPR3, OPDA enters the β-oxidation pathway to produce 4,5-ddh-JA as a direct precursor of JA and JA-Ile, thus identifying an OPR3-independent pathway for JA biosynthesis.

Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities

Abstract: Background: The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (Po) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction. Scope: We asked a group of experts to consider the global issues associated with Po in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the Po cycle, and to set priorities for Po research. Conclusions: We identified seven key opportunities for Po research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of Po in natural and managed systems; the role of microorganisms in controlling Po cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the Po research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.

Effects of civility and reasoning in user comments on perceived journalistic quality

Abstract: Journalists are increasingly concerned that offensive and banal user comments on news websites might alienate readers and damage quality perceptions. To explore such presumed effects, we investigated the impact of civility and reasoning (and lack thereof) in user comments on perceptions of journalistic quality. An experiment revealed that unreasoned comments decrease an article’s perceived informational quality, but only in unknown news brands. Incivility in comments had an unconditionally negative effect on the perceived formal quality of an article. Neither civility nor reasoning improved the assessments of journalistic quality, as compared to a comment-free version. On the contrary, we observed a trend showing that the mere presence of comments deteriorates the perceived quality of an article.

Glyphosate, a chelating agent-relevant for ecological risk assessment?

Abstract: Glyphosate-based herbicides (GBHs), consisting of glyphosate and formulants, are the most frequently applied herbicides worldwide. The declared active ingredient glyphosate does not only inhibit the EPSPS but is also a chelating agent that binds macro- and micronutrients, essential for many plant processes and pathogen resistance. GBH treatment may thus impede uptake and availability of macro- and micronutrients in plants. The present study investigated whether this characteristic of glyphosate could contribute to adverse effects of GBH application in the environment and to human health. According to the results, it has not been fully elucidated whether the chelating activity of glyphosate contributes to the toxic effects on plants and potentially on plant–microorganism interactions, e.g., nitrogen fixation of leguminous plants. It is also still open whether the chelating property of glyphosate is involved in the toxic effects on organisms other than plants, described in many papers. By changing the availability of essential as well as toxic metals that are bound to soil particles, the herbicide might also impact soil life, although the occurrence of natural chelators with considerably higher chelating potentials makes an additional impact of glyphosate for most metals less likely. Further research should elucidate the role of glyphosate (and GBH) as a chelator, in particular, as this is a non-specific property potentially affecting many organisms and processes. In the process of reevaluation of glyphosate its chelating activity has hardly been discussed.

Nitrogen availability regulates topsoil carbon dynamics after permafrost thaw by altering microbial metabolic efficiency.

Abstract: Input of labile carbon may accelerate the decomposition of existing soil organic matter (priming effect), with the priming intensity depending on changes in soil nitrogen availability after permafrost thaw However, experimental evidence for the linkage between the priming effect and post-thaw nitrogen availability is unavailable Here we test the hypothesis that elevated nitrogen availability after permafrost collapse inhibits the priming effect by increasing microbial metabolic efficiency based on a combination of thermokarst-induced natural nitrogen gradient and nitrogen addition experiment We find a negative correlation between the priming intensity and soil total dissolved nitrogen concentration along the thaw sequence The negative effect is confirmed by the reduced priming effect after nitrogen addition In contrast to the prevailing view, this nitrogen-regulated priming intensity is independent of extracellular enzyme activities but associated with microbial metabolic efficiency These findings demonstrate that post-thaw nitrogen availability regulates topsoil carbon dynamics through its modification of microbial metabolic efficiency

Beyond Genomic Prediction: Combining Different Types of omics Data Can Improve Prediction of Hybrid Performance in Maize

Abstract: The ability to predict the agronomic performance of single-crosses with high precision is essential for selecting superior candidates for hybrid breeding. With recent technological advances, thousands of new parent lines, and, consequently, millions of new hybrid combinations are possible in each breeding cycle, yet only a few hundred can be produced and phenotyped in multi-environment yield trials. Well established prediction approaches such as best linear unbiased prediction (BLUP) using pedigree data and whole-genome prediction using genomic data are limited in capturing epistasis and interactions occurring within and among downstream biological strata such as transcriptome and metabolome. Because mRNA and small RNA (sRNA) sequences are involved in transcriptional, translational and post-translational processes, we expect them to provide information influencing several biological strata. However, using sRNA data of parent lines to predict hybrid performance has not yet been addressed. Here, we gathered genomic, transcriptomic (mRNA and sRNA) and metabolomic data of parent lines to evaluate the ability of the data to predict the performance of untested hybrids for important agronomic traits in grain maize. We found a considerable interaction for predictive ability between predictor and trait, with mRNA data being a superior predictor for grain yield and genomic data for grain dry matter content, while sRNA performed relatively poorly for both traits. Combining mRNA and genomic data as predictors resulted in high predictive abilities across both traits and combining other predictors improved prediction over that of the individual predictors alone. We conclude that downstream "omics" can complement genomics for hybrid prediction, and, thereby, contribute to more efficient selection of hybrid candidates.

A molecular rheostat adjusts auxin flux to promote root protophloem differentiation.

Abstract: Auxin influences plant development through several distinct concentration-dependent effects 1 . In the Arabidopsis root tip, polar auxin transport by PIN-FORMED (PIN) proteins creates a local auxin accumulation that is required for the maintenance of the stem-cell niche2-4. Proximally, stem-cell daughter cells divide repeatedly before they eventually differentiate. This developmental gradient is accompanied by a gradual decrease in auxin levels as cells divide, and subsequently by a gradual increase as the cells differentiate5,6. However, the timing of differentiation is not uniform across cell files. For instance, developing protophloem sieve elements (PPSEs) differentiate as neighbouring cells still divide. Here we show that PPSE differentiation involves local steepening of the post-meristematic auxin gradient. BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) are interacting plasma-membrane-associated, polarly localized proteins that co-localize with PIN proteins at the rootward end of developing PPSEs. Both brx and pax mutants display impaired PPSE differentiation. Similar to other AGC-family kinases, PAX activates PIN-mediated auxin efflux, whereas BRX strongly dampens this stimulation. Efficient BRX plasma-membrane localization depends on PAX, but auxin negatively regulates BRX plasma-membrane association and promotes PAX activity. Thus, our data support a model in which BRX and PAX are elements of a molecular rheostat that modulates auxin flux through developing PPSEs, thereby timing PPSE differentiation.

Forest Soil Phosphorus Resources and Fertilization Affect Ectomycorrhizal Community Composition, Beech P Uptake Efficiency, and Photosynthesis

Abstract: Phosphorus (P) is an important nutrient, whose plant-availability is often low in natural forest ecosystems. Mycorrhizal fungi mine the soil for P and supply their host with this resource. It is unknown how ectomycorrhizal communities respond to changes in P availability. Here, we used young beech (Fagus sylvatica L.) trees in natural forest soil from a P-rich and P-poor site to investigate the impact of P amendment on soil microbes, mycorrhizas, beech P nutrition, and photosynthesis. We hypothesized that addition of P to forest soil increased P availability, thereby, leading to enhanced microbial biomass and mycorrhizal diversity in P-poor but not in P-rich soil. We further expected that P amendment resulted in increased plant P uptake and enhanced photosynthesis in both soil types. Young beech trees with intact soil cores from a P-rich and a P-poor forest were kept in a common garden experiment and supplied once in fall with triple superphosphate. In the following summer, labile P in the organic layer, but not in the mineral top soil, was significantly increased in response to fertilizer treatment. P-rich soil contained higher microbial biomass than P-poor soil. P treatment had no effect on microbial biomass but influenced the mycorrhizal communities in P-poor soil and shifted their composition towards higher similarities to those in P-rich soil. Plant uptake efficiency was negatively correlated with the Shannon diversity of mycorrhizal communities and highest for trees in P-poor soil and lowest for fertilized trees. In both soil types, radioactive P tracing revealed preferential aboveground allocation of new P in fertilized trees, resulting in increased bound P in xylem tissue and enhanced soluble P in bark, indicating increased storage and transport. Fertilized beeches from P-poor soil furthermore showed a strong increase in leaf P concentrations from deficient to luxurious conditions along with increased photosynthesis. Based on the divergent behavior of beech in P-poor and P-rich forest soil, we conclude that acclimation of beech to low P stocks involves dedicated mycorrhizal community structures, low P reserves in storage tissues and photosynthetic inhibition, while storage and aboveground allocation of additional P occurs regardless of the P nutritional status.

Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components.

Abstract: Phenotypic and genetic analysis of six spike and kernel characteristics in wheat revealed geographic patterns as well as long-term trends arising from breeding progress, particularly in regard to spikelet fertility, i.e. the number of kernels per spikelet, a grain yield component that appears to underlie the increase in the number of kernels per spike. Wheat is a staple crop of global relevance that faces continuous demands for improved grain yield. In this study, we evaluated a panel of 407 winter wheat cultivars for six characteristics of spike and kernel development. All traits showed a large genotypic variation and had high heritabilities. We observed geographic patterns for some traits in addition to long-term trends showing a continuous increase in the number of kernels per spike. This breeding progress is likely due to the increase in spikelet fertility, i.e. the number of kernels per spikelet. While the number of kernels per spike and spikelet fertility were significantly positively correlated, both traits showed a significant negative correlation with thousand-kernel weight. Genome-wide association mapping identified only small- and moderate-effect QTL and an effect of the phenology loci Rht-D1 and Ppd-D1 on some of the traits. The allele frequencies of some QTL matched the observed geographic patterns. The quantitative inheritance of all traits with contributions of additional small-effect QTL was substantiated by genomic prediction. Taken together, our results suggest that some of the examined traits were already the basis of grain yield progress in wheat in the past decades. A more targeted exploitation of the available variation, potentially coupled with genomic approaches, may assist wheat breeding in continuing to increase yield levels globally.

The macroeconomic burden of noncommunicable diseases in the United States: Estimates and projections.

Abstract: We develop and calibrate a dynamic production function model to assess how noncommunicable diseases (NCDs) will affect U.S. productive capacity in 2015-2050. In this framework, aggregate output is produced according to a human capital-augmented production function that accounts for the effects of projected disease prevalence. NCDs influence the economy through the following pathways: 1) when working-age individuals die of a disease, aggregate output undergoes a direct loss because physical capital can only partially substitute for the loss of human capital in the production process. 2) If working-age individuals suffer from a disease but do not die from it, then, depending on the condition's severity, they tend to be less productive, might work less, or might retire earlier. 3) Current NCD interventions such as medical treatments and prevention require substantial resources. Part of these resources could otherwise be used for productive investments in infrastructure, education, or research and development. This implies a loss of savings across the population and hampers economy-wide physical capital accumulation. Our results indicate a total loss of USD94.9 trillion (in constant 2010 USD) due to all NCDs. Mental health conditions and cardiovascular diseases impose the highest burdens, followed by cancer, diabetes, and chronic respiratory diseases. In per capita terms, the economic burden of all NCDs in 2015- 2050 is USD265,000. The total NCD burden roughly corresponds to an annual tax rate of 10.8% on aggregate income.

Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management.

Abstract: How to sustainably feed a growing global population is a question still without an answer. Particularly farmers, to increase production, tend to apply more fertilizers and pesticides, a trend especially predominant in developing countries. Another challenge is that industrialization and other human activities produce pollutants, which accumulate in soils or aquatic environments, contaminating them. Not only is human well-being at risk, but also environmental health. Currently, recycling, land-filling, incineration and pyrolysis are being used to reduce the concentration of toxic pollutants from contaminated sites, but too have adverse effects on the environment, producing even more resistant and highly toxic intermediate compounds. Moreover, these methods are expensive, and are difficult to execute for soil, water, and air decontamination. Alternatively, green technologies are currently being developed to degrade toxic pollutants. This review provides an overview of current research on microbial inoculation as a way to either replace or reduce the use of agrochemicals and clean environments heavily affected by pollution. Microorganism-based inoculants that enhance nutrient uptake, promote crop growth, or protect plants from pests and diseases can replace agrochemicals in food production. Several examples of how biofertilizers and biopesticides enhance crop production are discussed. Plant roots can be colonized by a variety of favorable species and genera that promote plant growth. Microbial interventions can also be used to clean contaminated sites from accumulated pesticides, heavy metals, polyaromatic hydrocarbons, and other industrial effluents. The potential of and key processes used by microorganisms for sustainable development and environmental management are discussed in this review, followed by their future prospects.

Multimodel ensembles improve predictions of crop-environment-management interactions.

Abstract: A recent innovation in assessment of climate change impact on agricultural production has been to use crop multimodel ensembles (MMEs). These studies usually find large variability between individual models but that the ensemble mean (e-mean) and median (e-median) often seem to predict quite well. However, few studies have specifically been concerned with the predictive quality of those ensemble predictors. We ask what is the predictive quality of e-mean and e-median, and how does that depend on the ensemble characteristics. Our empirical results are based on five MME studies applied to wheat, using different data sets but the same 25 crop models. We show that the ensemble predictors have quite high skill and are better than most and sometimes all individual models for most groups of environments and most response variables. Mean squared error of e-mean decreases monotonically with the size of the ensemble if models are added at random, but has a minimum at usually 2-6 models if best-fit models are added first. Our theoretical results describe the ensemble using four parameters: average bias, model effect variance, environment effect variance, and interaction variance. We show analytically that mean squared error of prediction (MSEP) of e-mean will always be smaller than MSEP averaged over models and will be less than MSEP of the best model if squared bias is less than the interaction variance. If models are added to the ensemble at random, MSEP of e-mean will decrease as the inverse of ensemble size, with a minimum equal to squared bias plus interaction variance. This minimum value is not necessarily small, and so it is important to evaluate the predictive quality of e-mean for each target population of environments. These results provide new information on the advantages of ensemble predictors, but also show their limitations.

Understanding the Effects of Personalization as a Privacy Calculus: Analyzing Self-Disclosure Across Health, News, and Commerce Contexts

Abstract: The privacy calculus suggests that online self-disclosure is based on a cost–benefit trade-off. However, although companies progressively collect information to offer tailored services, the effect of both personalization and context-dependency on self-disclosure has remained understudied. Building on the privacy calculus, we hypothesized that benefits, privacy costs, and trust would predict online self-disclosure. Moreover, we analyzed the impact of personalization, investigating whether effects would differ for health, news, and commercial websites. Results from an online experiment using a representative Dutch sample (N = 1,131) supported the privacy calculus, revealing that it was stable across contexts. Personalization decreased trust slightly and benefits marginally. Interestingly, these effects were context-dependent: While personalization affected outcomes in news and commerce contexts, no effects emerged in the health context.

Nutritional Value of the Duckweed Species of the Genus Wolffia (Lemnaceae) as Human Food.

Abstract: Species of the genus Wolffia are traditionally used as human food in some of the Asian countries. Therefore, all 11 species of this genus, identified by molecular barcoding, were investigated for ingredients relevant to human nutrition. The total protein content varied between 20 and 30% of the freeze-dry weight, the starch content between 10 and 20%, the fat content between 1 and 5%, and the fiber content was ~25%. The essential amino acid content was higher or close to the requirements of preschool-aged children according to standards of the World Health Organization. The fat content was low, but the fraction of polyunsaturated fatty acids was above 60% of total fat and the content of n-3 polyunsaturated fatty acids was higher than that of n-6 polyunsaturated fatty acids in most species. The content of macro- and microelements (minerals) not only depended on the cultivation conditions but also on the genetic background of the species. This holds true also for the content of tocopherols, several carotenoids and phytosterols in different species and even intraspecific, clonal differences were detected in Wolffia globosa and Wolffia arrhiza. Thus, the selection of suitable clones for further applications is important. Due to the very fast growth and the highest yield in most of the nutrients, Wolffia microscopica has a high potential for practical applications in human nutrition.