A pH-based pedotransfer function for scaling saturated hydraulic conductivity reduction: improved estimation of hydraulic dynamics in HYDRUS

Hydraulic conductivity is a key soil property governing agricultural production and is thus an important parameter in hydrologic modeling. The pH scaling factor for saturated hydraulic conductivity (Ks) reduction in the HYDRUS model was reviewed and evaluated for its ability to simulate Ks reduction. A limitation of the model is the generalization of Ks reduction at various levels of electrolyte concentration for different soil types, i.e., it is not soil specific. In this study, a new generalized linear regression model was developed to estimate Ks reduction for a larger set of Australian soils compared with three American soils. A nonlinear pedotransfer function was also produced, using the Levenberg–Marquardt optimization algorithm, by considering the pH and electrolyte concentration of the applied solution as well as the soil clay content. This approach improved the estimation of the pH scaling factor relating to Ks reduction for individual soils. The functions were based on Ks reduction in nine contrasting Australian soils using two sets of treatment solutions with Na adsorption ratios of 20 and 40; total electrolyte concentrations of 8, 15, 25, 50, 100, 250, and 500 mmolc L−1; and pH values of 6, 7, 8, and 9. A comparison of the experimental data and model outputs indicates that the models performed objectively well and successfully described the Ks reduction due to the pH. Further, a nonlinear function provided greater accuracy than the generalized function for the individual soils of Australia and California. This indicates that the nonlinear model provides an improved estimation of the pH scaling factor for Ks reduction in specific soils in the HYDRUS model and should therefore be considered in future HYDRUS developments and applications

Two-photon water splitting and related work for a green hydrogen economy

Herein, discovery of the first mechanism for water splitting that only requires two photons is described. Through detailed kinetic, spectroscopic and computational investigations of a molecular ruthenium complex, it was found that absorption of the first, shorter wavelength photon generates an intermediate capable of absorbing the second, longer wavelength photon. Oxygen and hydrogen can then be released. By only requiring two photons and having the ability to use a wide wavelength range, this mechanism could form the basis for the development of a new class of water splitting catalysts.Diese Arbeit beschreibt die Entdeckung des ersten Mechanismus für Wasserspaltung, welcher lediglich zwei Photonen erfordert. Detaillierte experimentelle und theoretische Studien eines Rutheniumkomplexes haben gezeigt, dass die Absorption des ersten, kurzwelligen Photons ein Intermediat erzeugt, welches das zweite, langwellige Photon absorbieren kann, gefolgt von Sauerstoff und Wasserstoff Freisetzung. Da nur zwei Photonen benötigt werden und ein breiter Wellenlängenbereich genutzt werden kann, könnte dies die Grundlage für eine neue Klasse von Wasserspaltungskatalysatoren bilden

Towards stable nickel catalysts for selective hydrogenation of biomass-based BHMF into THFDM

Selective transformation of BHMF (2,5-bis(hydroxymethyl)furan) to THFDM (tetrahydrofuran-2,5-dimethanol) over a variety of structured Ni/Sx-Z1−x catalysts was investigated. The effects of support, Ni loading, solvent, temperature, pressure, and particle size on the conversion and selectivity were studied. Among them, the 10 wt% Ni catalyst supported on the SiO2:ZrO2 weight ratio of 90:10 (10NiS90Z10) exhibits the best performance in terms of BHMF conversion and THFDM selectivity. Its good performance was attributed to its well-balanced properties, that depend upon the ZrO2 content of the support in combination with SiO2, the active Ni sites-support interaction, and acidity/basicity ratio of each catalyst resulting in different Ni dispersions. Importantly, the 10NiS90Z10 catalyst showed a stable selectivity to THFDM (>94%), with 99.4% conversion of BHMF during 2 h reaction time. Poor catalytic activity resulted from excessive ZrO2 content (>10 wt%). The structural, textural, and acidity properties of NiSi100−y-Zry catalysts, tuned by selectively varying the Ni amount from 5 to 15 wt%, were critically investigated using numerous material characterization techniques. Catalyst recycling experiments revealed that the catalyst could be recycled several times without any measurable loss of catalytic activity

Studies of the Distinguishing Features of NADPH:2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase, an Atypical Member of the Disulfide/ Oxidoreductase Family of Enzymes

The metabolism of propylene in Xanthobacter autotrophicus occurs via epoxypropane formation and subsequent metabolism by a three-step, four-enzyme pathway, utilizing the atypical cofactor Coenzyme M (CoM) to form acetoacetate. The last step in the epoxide carboxylase pathway is catalyzed by a distinctive member of the disulfide oxidoreductase (DSOR) family of enzymes, NADPH:2-ketopropyl CoM oxidoreductase/carboxylase (2-KPCC). 2-KPCC catalyzes the unorthodox cleavage of a thioether bond and successive carboxylation of the substrate. The focus of the research presented in this dissertation aims to elucidate the details of 2-KPCC that allow it to perform chemistry unconventional for typical DSOR members. Sitedirected mutagenesis was used to mutate specific active site residues and to examine the catalytic properties of 2-KPCC upon these changes. Mutation of His137, the proximal histidine that directly coordinates the water molecule, eliminated essentially all redox-dependent activity of the enzyme while mutation of His84, the distal histidine that coordinates the water molecule through His137, diminished redoxdependent enzymatic activity to approximately 25% that of the wild type enzyme, confirming the respective roles of the histidine residues in stabilizing the enolate intermediate formed upon catalysis. Neither mutation of either histidine residue, nor mutation of either redox active cysteine residue had any negative effect on the rate of the redox-independent reaction catalyzed by 2-KPCC, the decarboxylation of acetoacetate. Mutation of Met140 resulted in an enzyme with drastically altered kinetic parameters and suggests Met140 plays a role in shielding the substrate from undesired electrostatic interactions with the surroundings. The inhibitory properties of the structural CoM analogs, 2- bromoethanesulfonate (BES) and 3-bromopropanesulfonate (BPS), were examined and exploited to provide further detail on the active site microenvironment of 2- KPCC. Modification by BES results in a charge transfer complex between the thiolate of Cys87 and the oxidized flavin. The spectral features of this charge transfer complex have allowed the determination of the pKa of the Cys87 to be significantly higher than the flavin thiol in other DSOR enzymes. BPS has been shown to be a competitive inhibitor of 2-KPCC with an inhibition constant over two orders of magnitude lower than for that of BES

Pyrrolizidine alkaloids in herbal tea and honey: Report on the 2017 Proficiency testing scheme

Pyrrolizidine alkaloids (PAs) and their N-oxides (PANOs) are plant toxins which can enter the food chain through different paths. Two affected foods are herbal infusions and honey. This proficiency testing scheme was executed to assess the capabilities of laboratories to determine PAs. 29 laboratories from nine EU Member States plus Singapore registered. On 04. and 06.09.2017 test items and documentation were dispatched to all of those laboratories. By the dead line of 24.10.2017 26 laboratories had reported back results and filled in a questionnaire. Test item HO (acacia honey) was fortified with six PAs/PANOs (Echimidine, Integerrimine, Intermedine, Senecionine, Seneciphylline-NO, and Senkirkine) and 23 laboratories reported results for this item. The same number of laboratories reported for test item HT (herbal infusion) which was naturally contaminated with four PAs after extraction under reductive conditions (Integerrimine, Retrorsine, Senecionine, and Senecivernine). Laboratories had to report the sums of PA and its respective PANO. Satisfying outcomes could only be registered for Senecionine in test item HT and for Echimidine, Intermedine, and Senkirkine in test item HO with 74 %, 85 %, 85 %, and 91 %, respectively, of reported results having a z'-score smaller or equal to |2|. Only four laboratories reported for Integerrimine in both test items. Contrary to test item HT, Senecionine analysis in test item HO showed very unsatisfactory results. Of the 22 z'-scores calculated for Senecionine nine (41 %) were larger than 3. Senecivernine measurements in test item HT showed a similarly unsatisfying outcome with 47 % of reported results having z'-scores larger than 3. Only three laboratories out of the 26 were able to test for all 10 measurands and only one reported all 10 values with z'-scores smaller or equal to |2|. Overall only five laboratories obtained satisfactory z'-scores (≤ |2|) for all their reported results. There are two groups of three isomeric PAs/PANOs each which apparently caused, for a number of laboratories, problems with quantification. This is an issue which deserves heightened attention. The questionnaire contained queries regarding accreditation and experience, preparation conditions for the two test items, chromatographic separation conditions, detection conditions, calibration approach, and a comments section. The answers were evaluated and for selected questions their correlation to the z'-score of Senecionine in test item HO or Senecivernine in test item HT was analysed. For none of the tested questions a significant influence could be shown.JRC.F.5-Food and Feed Complianc

A recent whole-genome duplication divides populations of a globally-distributed microsporidian

The Microsporidia are a major group of intracellular fungi and important parasites of animals including insects, fish, and immunocompromised humans. Microsporidian genomes have undergone extreme reductive evolution but there are major differences in genome size and structure within the group: some are prokaryote-like in size and organisation (<3 Mb of gene-dense sequence) while others have more typically eukaryotic genome architectures. To gain fine-scale, population-level insight into the evolutionary dynamics of these tiny eukaryotic genomes, we performed the broadest microsporidian population genomic study to date, sequencing geographically isolated strains of Spraguea, a marine microsporidian infecting goosefish worldwide. Our analysis revealed that population structure across the Atlantic Ocean is associated with a conserved difference in ploidy, with American and Canadian isolates sharing an ancestral whole genome duplication that was followed by widespread pseudogenisation and sorting-out of paralogue pairs. While past analyses have suggested de novo gene formation of microsporidian-specific genes, we found evidence for the origin of new genes from noncoding sequence since the divergence of these populations. Some of these genes experience selective constraint, suggesting the evolution of new functions and local host adaptation. Combining our data with published microsporidian genomes, we show that nucleotide composition across the phylum is shaped by a mutational bias favoring A and T nucleotides, which is opposed by an evolutionary force favoring an increase in genomic GC content. This study reveals ongoing dramatic reorganization of genome structure and the evolution of new gene functions in modern microsporidians despite extensive genomic streamlining in their common ancestor

Improved approaches to ligand growing through fragment docking and fragment-based library design

Die Fragment-basierte Wirkstoffforschung (“fragment-based drug discovery“ – FBDD) hat in den vergangenen zwei Jahrzehnten kontinuierlich an Beliebtheit gewonnen und sich zu einem dominanten Instrument der Erforschung neuer chemischer Moleküle als potentielle bioaktive Modulatoren entwickelt. FBDD ist eng mit Ansätzen zur Fragment-Erweiterung, wie etwa dem Fragment-„growing“, „merging“ oder dem „linking“, verknüpft. Diese Entwicklungsansätze können mit Hilfe von Computerprogrammen oder teilautomatischen Prozessen der „de novo“ Wirkstoffentwicklung beschleunigt werden. Obwohl Computer mühelos Millionen von Vorschlägen generieren können, geschieht dies allerdings oft auf Kosten unsicherer synthetischer Realisierbarkeit der Verbindungen mit einer potentiellen Sackgasse im Optimierungsprozess. Dieses Manuskript beschreibt die Entwicklung zweier computerbasierter Instrumente, PINGUI und SCUBIDOO, mit dem Ziel den FBDD Ausarbeitungs-Zyklus zu fördern. PINGUI ist ein halbautomatischer Arbeitsablauf zur Fragment-Erweiterung basierend auf der Proteinstruktur unter Berücksichtigung der synthetischen Umsetzbarkeit. SCUBIDOO ist eine freizugängliche Datenbank mit aktuell 21 Millionen verfügbaren virtuellen Produkten, entwickelt durch die Kombination kommerziell verfügbarer Bausteine („building blocks“) mit bewährten organischen Reaktionen. Zu jedem erzeugten virtuellen Produkt wird somit eine Synthesevorschrift geliefert. Die entscheidenden Funktionen von PINGUI, wie die Erzeugung abgeleiteter Bibliotheken oder das Anwenden organischer Reaktionen, wurden daraufhin in die SCUBIDOO Webseite integriert. PINGUI als auch SCUBIDOO wurden des Weiteren zur Erforschung Fragment-basierter Liganden („fragment-based ligand discovery“) mit dem β-2 adrenergen Rezeptor (β-2-AR) und der PIM1 Kinase als Zielproteine („targets“) eingesetzt. Im Rahmen einer ersten Studie zum β-2-AR wurden mit PINGUI acht unterschiedliche Erweiterungen für verschiedene Fragment-Treffer („hits“) vorhergesagt (ausgewählt?). Alle acht Verbindungen konnten dabei erfolgreich synthetisiert werden und vier der acht Produkte zeigten im Vergleich zu den Ausgangsfragmenten eine erhöhte Affinität zum target. Eine zweite Studie umfasste die Anwendung von SCUBIDOO zur schnellen Identifikation von Fragmenten und deren möglichen Erweiterungen mit potentieller Bindungsaktivität zur PIM-1 Kinase. Als Ergebnis ergab sich ein Fragment-Treffer mit der dazugehörigen Kristallstruktur. Weitere Folgeprodukte befinden sich derzeit in Synthese. Abschließend wurde SCUBIDOO an eine automatische Roboter- Synthese gekoppelt, wodurch hunderte von Verbindungen effizient parallel synthetisiert werden können. 127 der 240 vorhergesagten Produkte (53%) wurden mit dem Ziel an den β-2-AR zu binden bereits synthetisiert und werden in Kürze weitergehend getestet. Die beiden vorgestellten Computer-Tools könnten zur Verbesserung im Anfangsstadium befindlicher Projekte zur Fragment-basierten Wirkstoffentwicklung, vor allem hinsichtlich der Strategien im Bereich der Fragment Erweiterung, eingesetzt werden. PINGUI zum Beispiel generiert Vorschläge zur Fragment- Erweiterung, die sich mit hoher Wahrscheinlichkeit an die Zielstruktur anlagern, und stellt somit ein nützliches und kreatives Werkzeug zur Untersuchung von Struktur-Wirkungsbeziehungen („structure-activity relationship“ – SAR) dar. SCUBIDOO zeigte sich mit einem bisherigen 53-prozentigen Synthese-Erfolg als zugänglich für die Integration an die effiziente automatisierte Roboter-Synthese. Jede zukünftige Synthese liefert neue Kenntnisse innerhalb der Datenbank und wird somit nach und nach den Synthese-Erfolg erhöhen. Des Weiteren stellen alle synthetisierten Produkte neuartige Verbindungen dar, was umso mehr den möglichen Einfluss SCUBIDOOs bei der Entdeckung neuer chemischer Strukturen hervorhebt

Toward a Computational Archaeology of Fictional Space

In this paper I propose to reconsider theories of diegetic space that rely on explicit framing (i.e., "two people walk into a room" or "in Spain"). Rather than looking for maps, I define space in terms of lexical categories denoting objects. The emphasis on objects leads to a method for literary archaeology, informed by cognitive theory and anthropology. If the universe is made of atoms, a fictional world is also made up of atomic relationships that form basic, stable configurations, or what I call narratological primes. I construct several such basic spatial buildings blocks here—diegetic density and clutter distance. Their application to a well-explored body of nineteenth-century novels challenges several long-standing historical intuitions related to the development of material culture in the nineteenth century