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Barley dwarfs acting big in agronomy. Identification of genes and characterization of proteins involved in dwarfism, lodging resistance and crop yield

Barley (Hordeum vulgare) is an important cereal grain which serves as major animal fodder crop as well as basis for malt beverages or staple food. Currently barley is ranked fourth in terms of quantity of cereal crops produced worldwide. In times of a constantly growing world population in conjunction with an unforeseeable climate change and groundwater depletion, the accumulation of knowledge concerning cereal growth and rate of yield gain is important. The Nordic Genetic Resource Center holds a major collection of barley mutants produced by irradiation or chemical treatment. One phenotypic group of barley varieties are dwarf mutants (erectoides, brachytic, semidwarf, uzu). They are characterized by a compact spike and high rate of yield while the straw is short and stiff, enhancing the lodging resistance of the plant. Obviously they are of applied interest, but they are also of scientific interest as virtually nothing is known about the genes behind the development of plant dwarfism. The aim of this project is to identify and isolate the genes carrying the mutations by using state of the art techniques for gene cloning at the Carlsberg Laboratory. The identified genes will be connected with the mutant phenotype to reveal the gene function in general. One or two genes will be overexpressed and the resulting recombinant proteins will be biochemically and structurally characterized. The insights how the mutation effects the protein will display the protein function in particular. Identified genes and their mutant alleles will be tested in the barley breeding program of the Carlsberg brewery.

14C content of specific organic compounds in subsoils

Organic matter (OM) composition and dynamic in subsoils is thought to be significantly different from those in surface soils. This has been suggested by increasing apparent 14C ages of bulk soil OM with depth suggesting that the amount of fresh, more easily degradable components is declining. Compositional changes have been inferred from declining ä13C values and C/N ratios indicative for stronger OM transformation. Beside these bulk OM data more specific results on OM composition and preservation mechanisms are very limited but modelling studies and results from incubation experiments suggest the presence and mineralization of younger, 'reactive carbon pool in subsoils. Less refractory OM components may be protected against degradation by interaction with soil mineral particles and within aggregates as suggested by the very limited number of more specific OM analysis e.g., identification of organic compound in soil fractions. The objective of this project is to characterize the composition, transformation, stabilization and bioavailability of OM in subsurface horizons on the molecular level: 1) major sources and compositional changes with depth will be identified by analysis of different lipid compound classes in surface and subsoil horizons, 2) the origin and stabilization of 'reactive OM will be revealed by lipid distributions and 14C values of soil fractions and of selected plant-specific lipids, and 3) organic substrates metabolized by microbial communities in subsoils are identified by distributional and 14C analysis of microbial membrane lipids. Besides detailed analyses of three soil profiles at the subsoil observatory site (Grinderwald), information on regional variability will be gained from analyses of soil profiles at sites with different parent material.

Redox processes along gradients

The relevance of biogeochemical gradients for turnover of organic matter and contaminants is yet poorly understood. This study aims at the identification and quantification of the interaction of different redox processes along gradients. The interaction of iron-, and sulfate reduction and methanogenesis will be studied in controlled batch and column experiments. Factors constraining the accessibility and the energy yield from the use of these electron acceptors will be evaluated, such as passivation of iron oxides, re-oxidation of hydrogen sulfide on iron oxides. The impact of these constraints on the competitiveness of the particular process will then be described. Special focus will be put on the evolution of methanogenic conditions in systems formerly characterized by iron and sulfate reducing condition. As methanogenic conditions mostly evolve from micro-niches, methods to study the existence, evolution and stability of such micro-niches will be established. To this end, a combination of Gibbs free energy calculations, isotope fractionation and tracer measurements, and mass balances of metabolic intermediates (small pool sizes) and end products (large pool sizes) will be used. Measurements of these parameters on different scales using microelectrodes (mm scale), micro sampling devices for solutes and gases (cm scale) and mass flow balancing (column/reactor scale) will be compared to characterize unit volumes for organic matter degradation pathways and electron flow. Of particular interest will be the impact of redox active humic substances on the competitiveness of involved terminal electron accepting processes, either acting as electron shuttles or directly providing electron accepting capacity. This will be studied using fluorescence spectroscopy and parallel factor analysis (PARAFAC) of the gained spectra. We expect that the results will provide a basis for improving reactive transport models of anaerobic processes in aquifers and sediments.

Der Einfluss der SML auf die Spurengasbiogeochemie und den Ozean-Atmosphäre-Gasaustausch

Labor- und Feldstudien zeigen, dass die Oberflächengrenzschicht des Ozeans (â€Ìsurface microlayerâ€Ì, kurz SML) die biogeochemischen Kreisläufe von klimaaktiven und atmosphärisch wichtigen Spurengasen wie Kohlenstoffdioxid (CO2), Kohlenstoffmonoxid (CO), Methan (CH4), Lachgas (N2O) und Dimethylsulfid (DMS) stark beeinflusst: (i) Jüngste Studien aus den PASSME- und SOPRAN-Projekten haben hervorgehoben, dass Anreicherungen von oberflächenaktiven Substanzen (d.h. Tensiden) einen starken (dämpfenden) Effekt sowohl auf die CO2- als auch auf die N2O-Flüsse über die SML/Atmosphären-Grenzfläche hinweg haben und (ii) Spurengase können durch (mikro)biologische oder (photo)chemische Prozesse in der SML produziert und verbraucht werden. Daher kann der oberste Teil des Ozeans, einschließlich der SML, verglichen mit dem Wasser, das in der Mischungsschicht unterhalb der SML zu finden ist, eine bedeutende Quelle oder Senke für diese Gase sein, was von sehr großer Relevanz für die Forschungseinheit BASS ist. Die Konzentrationen von CO2, N2O und anderen gelösten Gasen in der SML (oder den oberen Zentimetern des Ozeans) unterscheiden sich nachweislich von ihren Konzentrationen unterhalb der SML. Typischerweise werden die Nettoquellen und -senken wichtiger atmosphärischer Spurengase mit Konzentrationen berechnet, die in der Mischungsschicht gemessen wurden und mit Gasaustauschgeschwindigkeiten, die die SML nicht berücksichtigen. Diese Diskrepanzen führen zu falsch berechneten Austauschflüssen, die in der Folge zu großen Unsicherheiten in den Berechnungen der Klima-Antrieben und der Luftqualität in Erdsystemmodellen führen können. Durch die Verknüpfung unserer Spurengasmessungen mit Messungen von (i) der Dynamik und den molekularen Eigenschaften der organischen Materie und speziell des organischen Kohlenstoffs (SP1.1; SP1.5), (ii) der biologischen Diversität und der Stoffwechselaktivität (SP1.2), (iii) den optischen Eigenschaften der organischen Materie (SP1.3), (iv) der photochemischen Umwandlung der organischen Materie (SP1.4) und (v) den physikalischen Transportprozessen (SP2.3) werden wir ein umfassendes Verständnis darüber erlangen, wie die SML die Variabilität der Spurengasflüsse beeinflusst.

Schwerpunktprogramm (SPP) 1488: Planetary Magnetism (PlanetMag), Evolution of geomagnetic dipole moment and South Atlantic Anomaly

The geomagnetic field shields our habitat against solar wind and radiation from space. Due to the geometry of the field, the shielding in general is weakest at high latitudes. It is also anomalously weak in a region around the south Atlantic known as South Atlantic Anomaly (SAA), and the global dipole moment has been decreasing by nearly 10 percent since direct measurements of field intensity became possible in 1832. Due to our limited understanding of the geodynamo processes in Earths core, it is impossible to reliably predict the future evolution of both dipole moment and SAA over the coming decades. However, lack of magnetic field shielding as would be a consequence of further weakening of dipole moment and SAA region field intensity would cause increasing problems for modern technology, in particular satellites, which are vulnerable to radiation damage. A better understanding of the underlying processes is required to estimate the future development of magnetic field characteristics. The study of the past evolution of such characteristics based on historical, archeo- and paleomagnetic data, on time-scales of centuries to millennia, is essential to detect any recurrences and periodicities and provide new insights in dynamo processes in comparison to or in combination with numerical dynamo simulations. We propose to develop two new global spherical harmonic geomagnetic field models, spanning 1 and 10 kyrs, respectively, and designed in particular to study how long the uninterrupted decay of the dipole moment has been going on prior to 1832, and if the SAA is a recurring structure of the field.We will combine for the first time all available historical and archeomagnetic data, both directions and intensities, in a spherical harmonic model spanning the past 1000 years. Existing modelling methods will be adapted accordingly, and existing data bases will be complemented with newly published data. We will further acquire some new archeomagnetic data from the Cape Verde islands from historical times to better constrain the early evolution of the present-day SAA. In order to study the long-term field evolution and possible recurrences of similar weak field structures in this region, we will produce new paleomagnetic records from available marine sediment cores off the coasts of West Africa, Brazil and Chile. This region is weakly constrained in previous millennial scale models. Apart from our main aim to gain better insights into the previous evolution of dipole moment and SAA, the models will be used to study relations between dipole and non-dipole field contributions, hemispheric symmetries and large-scale flux patterns at the core-mantle boundary. These observational findings will provide new insights into geodynamo processes when compared with numerical dynamo simulation results.Moreover, the models can be used to estimate past geomagnetic shielding above Earths surface against solar wind and for nuclide production from galactic cosmic rays.

Schwerpunktprogramm (SPP) 1889: Regional Sea Level Change and Society (SeaLevel), Ursachen regionaler Meeresspiegelvariationen auf dekadischen und längeren Zeitskalen (DECVAR)

Die Studie zielt ab auf die Untersuchung von momentanen und vergangenen Meeresspiegeländerungen auf regionaler Skala. Hierbei sollen Ursachen und Mechanismen identifiziert werden, die diese Variationen erklären können; dabei werden freie Klima-Moden ebenso berücksichtigt wie externe Antriebe, einschließlich anthropogene Einflüsse. Dadurch werden Methoden und Wissen entwickelt, mit denen in regionale Meeresspiegelbeobachtungen jeweils natürliche Variationen und anthropogenen Effekten identifiziert werden können. Erzielte Erkenntnisse werden verwendet werden, um Ursachen und Mechanismen von Meeresspiegelvariationen um die zweiten Untersuchungsgebiete des SPP herum (dem westlichen tropischen Pazifik und Indonesischem Archipel ebenso wie der Nordsee) zu analysieren.

Schwerpunktprogramm (SPP) 1889: Regional Sea Level Change and Society (SeaLevel), Die morphologische Reaktion des Wattenmeeres auf den Klimawandel (MOREWACC)

Das Wattenmeer, das sich von Den Helder in den Niederlanden bis nach Skallingen in Dänemark erstreckt, ist ein Prototyp für eine durch den Meeresspiegelanstieg bedrohte Küstenregion. Über 50% des Wattenmeeres besteht aus Wattflächen, die nur während eines Teils des Gezeitenzyklus von Wasser bedeckt sind. Dadurch wird das einzigartige Küsten-Ökosystem des Wattenmeeres geformt, das aufgrund von Akkumulation von Sediment aus der Nordsee den Meeresspiegelanstieg der letzten Jahrhunderte überleben konnte. Angesichts der beobachteten Beschleunigung des Meeresspiegelanstieges stellt sich die Schlüsselfrage, bis zu welcher Rate des Meeresspiegelanstieges diese Sedimentakkumulation für das Überleben des ausreicht. Diese Frage ist hochkomplex, da die Sedimentflüsse in das Wattenmeer selbst von der Rate des Meeresspiegelanstieges sowie von anderen klimatischen Einflüssen und von der Sedimentverfügbarkeit in nicht-linearer Weise abhängen. Es ist bekannt, dass Netto-Sedimentflüsse durch von nicht-linearen Flachwassergezeiten und horizontalen Dichtegradienten (aufgrund von Niederschlag, Süßwasserabfluss und Oberflächen-Wärmeflüssen) bedingten Gezeitenasymmetrien angetrieben werden. Die Nichtlinearität der Gezeiten wiederum hängt vom Meeresspiegelanstieg selbst ab und die horizontalen Dichtegradienten variieren mit klimabedingten Änderungen von Verdunstung/Niederschlag und Abkühlung/Erwärmung. Weiterhin hängen Sedimentflüsse vom Windantrieb ab, der ebenfalls mit dem Klima variiert. Obwohl ein fundiertes Verständnis der zugrundeliegenden Sedimenttransportprozesse im Wattenmeer vorliegt, werden für Projektionen von morphologischen Veränderungen weiterhin einfache vertikal integrierte Modelle verwendet. Die Erkenntnisse, die aus solchen Modellen gewonnen werden, sind daher sehr eingeschränkt. Das wichtigste Ziel dieses Projektes ist daher, mögliche morphologische Reaktionen des Wattenmeeres auf einen beschleunigten Meeresspiegelanstieg und andere Aspekte des Klimawandels sowie Einflüsse von Sedimentverfügbarkeit mit Hilfe eines prozess-basierten Modells zu untersuchen. Dabei werden die wichtigsten Antriebe für Sedimenttransportprozesse in das Wattenmeer berücksichtigt. Zunächst sollen diese Modellsimulationen in systematischer Weise unter Nutzung verschiedener idealisierter Bathymetern durchgeführt werden, um die kritischsten Prozesse morphodynamischer Veränderungen zu erkennen. Mit Hilfe dieser Bathymeter können die Einflüsse des Meeresspiegelanstieges in Kombination mit anderen Einflussfaktoren (Niederschlag/Verdunstung, Abkühlung/Erwärmung, Wind-Wellenantrieb) untersucht werden. In einer zweiten Phase des SPP, unter der Annahme, dass die verfügbaren Computer Ressourcen weiter anwachsen, sollen solche Simulationen für realistische und komplexere Gezeitenbecken im Wattenmeer durchgeführt werden. In beiden Phasen des SPP soll die Dynamik von Salzwiesen explizit mit untersucht werden.

Trophic interactions in the soil of rice-rice and rice-maize cropping systems

Subproject 3 will investigate the effect of shifting from continuously flooded rice cropping to crop rotation (including non-flooded systems) and diversified crops on the soil fauna communities and associated ecosystem functions. In both flooded and non-flooded systems, functional groups with a major impact on soil functions will be identified and their response to changing management regimes as well as their re-colonization capability after crop rotation will be quantified. Soil functions corresponding to specific functional groups, i.e. biogenic structural damage of the puddle layer, water loss and nutrient leaching, will be determined by correlating soil fauna data with soil service data of SP4, SP5 and SP7 and with data collected within this subproject (SP3). In addition to the field data acquired directly at the IRRI, microcosm experiments covering the broader range of environmental conditions expected under future climate conditions will be set up to determine the compositional and functional robustness of major components of the local soil fauna. Food webs will be modeled based on the soil animal data available to gain a thorough understanding of i) the factors shaping biological communities in rice cropping systems, and ii) C- and N-flow mediated by soil communities in rice fields. Advanced statistical modeling for quantification of species - environment relationships integrating all data subsets will specify the impact of crop diversification in rice agro-ecosystems on soil biota and on the related ecosystem services.

Development of a Bayesian estimator for non-stationary Markov transition probabilities and its application to EU farm structural change

The agricultural sector has experienced substantial structural changes in the past and faces continuing adjustments in the future. The implications of structural change are not only relevant for the sector itself but have broader social, economic and environmental consequences for a region. An understanding of this process is required in order to assess how (agricultural-) policy affects or, if a specific social outcome is desired, can influence this development. A common approach to gain understanding of the process is to model structural change as a Markov process. One problem in the analysis of structural change in the EU is that farm level (micro) data is rarely available such that inference about behaviour of individual farms has to be derived from aggregated (macro) data. Recently, the generalized cross entropy estimator gained popularity in this context since it allows considering prior information such that the often underdetermined 'macro data' Markov models can be estimated. However, the way prior information is considered is also the greatest drawback of the approach. Therefore, the project aims to develop a Bayesian framework as an alternative estimator that allows to consider prior information in a more efficient and transparent way. The project will further provide an evaluation of the statistical properties of the estimator as well as an exemplifying application analyzing the effects of single farm payments on agricultural structural change in the EU.

Simulated field environment with combined salt and drought stresses as a platform for phenotyping plant tolerance to salinity

Salinity occurs often simultaneously with drought stress. Therefore, breeding for tolerance to combined both stresses can contribute significantly to crop yield. However, classical selection in salinity has generally been unsuccessful, partly due to high variability of salt stress resulting from the different salinity and drought status. Unfortunately, the use of unrealistic stress protocols for mimicking salinity and drought stress is the norm rather than the exception in biotechnological studies. Therefore, the great challenge is to gain knowledge required to develop plants with enhanced tolerance to field conditions. Our overall hypothesis is that a realistic stress protocol simulating a field environment with combined salt and drought stress as a platform for precision phenotyping of plant tolerance to salinity may solve this problem. This study will demonstrate that highly managed stress environments can be created and key traits of plants can be characterised by using advanced non-destructive sensors that are able to identify relevant traits of plants.

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