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Nitrate is an abundant nutrient and electron acceptor throughout Earth’s biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein’s electron transport chain, and elucidate the electron transfer pathways within the complex.
Self-inactivating gammaretroviral vectors for the gene therapy of chronic granulomatous disease
(2008)
Chronic granulomatous disease (CGD) is a rare inherited primary immunodeficiency characterized by defective intracellular oxidative killing of ingested invading microbes by PMN and monocytes. It is caused by mutations in one of the four genes coding for the essential subunits of the NADPH oxidase (gp91phox, p47phox, p67phox and p22phox). Approximately 75% of the CGD cases are due to mutations in the gp91phox gene. If regular care and conventional therapy fail, the recommended therapy is allogeneic bone marrow transplantation (BMT), but only if a matched donor is available. A therapeutic option for patients lacking suitable donors is the genetic modification of autologous hematopoietic stem cells. The gene therapy offers an interesting alternative to BMT since it implies a less invasive treatment and represents a possibly unique curative option for patients with no suitable donor. Gammaretroviral vectors were already used in some gene therapy trials for CGD and other immunodeficiencies showing relevant clinical benefit. However, these trials uncovered an unexpected mutagenic side effect. If the retrovial integration ocurrs near to, or into proto-oncogenes this might lead to clonal dominance or even malignant transformation (Hacein-Bey-Abina et al., 2003a; Ott et al., 2006). Therefore, there was a need to further improve the safety of these vectors and to this end the self-inactivating gammaretroviral vectors were engineered. Non essential sequences for virus infectivity and integration, which might influence the surrounding gene expression, were deleted in these vectors. In the first set of experiments, a series of SIN gamma retroviral vectors was cloned driving the expression of the wild-type gp91phox cDNA under the control of a viral constitutive SFFV promoter. However initial studies with these vectors failed because the titers of the virus produced by transient transfection protocols were extremely low (<5x105 TU/ml). Therefore, a codon optimization of the gp91phox cDNA was considered as an alternative. The codon optimized synthetic gp91phox gene was used to construct a SIN gammaretroviral vector, again under the control of the SFFV promoter (Schambach et al., 2006c). With this vector an increase in titer was observed compared to the native gp91phox sequence, which was due to the improved transcription in 293T transfected cells. The enhancement of the synthetic gp91phox transcription led to a higher internal transcript production and protein expression. An enhanced superoxide production in transduced myelomonocytic X-CGD PLB-985 populations was also detected. All these data indicate that the synthetic gp91phox might represent an excellent alternative to those former constructs expressing the native gp91phox transgene. Since it was postulated that the SFFV promoter could still cause transactivation of neighboring genes due to its strength (Modlich et al., 2006), three different non-viral promoters were tested, one constitutive (the EFs promoter) and two myeloid-specific promoters (the c-fes and MRP8 promoter). The three SIN gammaretroviral vectors were able to generate high titers after transient transfection of 293T packaging cells, to efficiently transduce the X-CGD PLB-985 cell line and to reconstitute the NADPH oxidase activity to a high degree. In mouse transplantation experiments, the EFs promoter showed a high variable transgene expression in the different lineages analyzed, and the c-fes promoter showed also a ubiquitinous expression. In contrast, the MRP8 promoter showed a high myeloid specificity since gp91phox expression in mSca-1+ cells and lymphoid B cells from transplanted mice was extremly low and even absent. However, the lowest levels of transgene expression were observed in the myeloid populations both in bone marrow and peripheral blood with this vector. When the oxidase reconstitution ability of these promoters was tested, the numbers of superoxide producing cells obtained were similar than those observed in the clinical X-CGD trial conducted by the groups of Dr. M. Grez and Prof. R. A. Seger (over 35% in one patient and ~15% in the second), which led to the eradication of therapy refractory infections (Ott et al., 2006). Between the three constructs, the MRP8 promoter was less effective in restoring the NADPH oxidase activity than the EFs and c-fes promoters. The c-fes promoter reached the highest levels of DHR reactive cells in the highest number of mice. Overall, these data showed that between all constructs tested, the c-fes containing construct in combination with the codon optimized gp91phox sequence showed the best performance within the SIN gammaretroviral backbone. It generated the highest titers in combination with a better NADPH oxidase reconstituting ability. One main goal in the development of SIN gammaretroviral vectors is reducing the genotoxic effect due to random vector integration. An improved gene transfer and expression, and a constant performance are also highly desirable. The present study shows that the c-fes SIN vector in combination with the synthetic gp91phox may be considered as an effective gene therapy strategy for the restoration of the NADPH oxidase activity in CGD. It allows the use of a cellular promoter generating adequate physiological levels of the therapeutic protein and reduces the number of vector copies required for a therapeutic effect.
Bopopia, a new monotypic genus of Gesneriaceae (Gesnerioideae, Coronanthereae) from New Caledonia
(2021)
A new genus of Gesneriaceae, Bopopia Munzinger & J.R.Morel gen. nov., is described from New Caledonia. The genus is based on B. parviflora Munzinger & J.R.Morel gen. et sp. nov., a new species collected during an expedition on Mt Katalupaik, in the North Province of New Caledonia’s main island. Originally considered as a species of Coronanthera, our phylogenetic analysis – including 19 species within Coronanthereae and two individuals of B. parviflora gen. et sp. nov., and using three molecular markers (nuclear rDNA ITS, and chloroplast regions trnL-trnF and trnE-trnT) – showed that the new species is not close to Coronanthera in subtribe Coronantherinae, but belongs to subtribe Negriinae where it is sister to Depanthus. From that genus Bopopia gen. nov. differs in floral symmetry (zygomorphic vs actinomorphic) and the number of stamens (4 vs 5). From the other genera of Negriinae the new genus differs in the white corolla and its indeterminate thyrse with 3 to 5 levels of branching. The morphological circumscription of the subtribe Negriinae is amended to include Bopopia gen. nov. Two keys are provided, one to the subtribes in the tribe Coronanthereae, and one to the genera in subtribe Negriinae. Following the IUCN Red List categories and criteria, the conservation status of B. parviflora gen. et sp. nov. is provisionally assessed as Endangered (EN).
Three leptostracan species (Crustacea: Phyllocarida) are reported from mud volcanoes at the Moroccan margin of the Gulf of Cadiz (NE Atlantic). Nebalia strausi Risso, 1826 and N. abyssicola Fage, 1929 were found in experimentally deployed organic substrates in Mercator, Meknès and Darwin mud volcanoes; N. abyssicola was also found among bathymodiolin bivalves and is recorded for the first time in the Atlantic Ocean. The third species was collected from the Gemini mud volcanoes and is described herein as Sarsinebalia ledoyeri sp. nov. The new species is characterised by having the eyes provided with ommatidia and lacking pigment, the ventral margin of the eye is concave along distal half, the antennular scale is more than twice as long as wide, the second article of the mandibular palp bears one seta on lateral surface about 0.5 times as long as the article and one subterminal seta longer than the third article, the distal article of the maxilla II endopod is about 1.8 times as long as the proximal article, the maxilla II exopod is clearly longer than the endopod proximal article, the lateral margin of the pleopod I exopod lacks setae and the posterodorsal border of pleonites VI–VII is provided with rounded to pointed denticles.
We review the properties of the strongly interacting quark-gluon plasma (QGP) at finite temperature T and baryon chemical potential µB as created in heavy-ion collisions at ultrarelativistic energies. The description of the strongly interacting (non-perturbative) QGP in equilibrium is based on the effective propagators and couplings from the Dynamical QuasiParticle Model (DQPM) that is matched to reproduce the equation-of-state of the partonic system above the deconfinement temperature Tc from lattice QCD. Based on a microscopic transport description of heavy-ion collisions, we discuss which observables are sensitive to the QGP creation and its properties.
We study the effect of the chiral symmetry restoration (CSR) on heavy-ion collisions observables in the energy range sNN=3–20GeV within the Parton-Hadron-String Dynamics (PHSD) transport approach. The PHSD includes the deconfinement phase transition as well as essential aspects of CSR in the dense and hot hadronic medium, which are incorporated in the Schwinger mechanism for particle production. Our systematic studies show that chiral symmetry restoration plays a crucial role in the description of heavy-ion collisions at sNN=3–20GeV, realizing an increase of the hadronic particle production in the strangeness sector with respect to the non-strange one. Our results provide a microscopic explanation for the horn structure in the excitation function of the K+/π+ ratio: the CSR in the hadronic phase produces the steep increase of this particle ratio up to sNN≈7GeV, while the drop at higher energies is associated to the appearance of a deconfined partonic medium. Furthermore, the appearance/disappearance of the horn structure is investigated as a function of the system size. We additionally present an analysis of strangeness production in the (T,μB)-plane (as extracted from the PHSD for central Au+Au collisions) and discuss the perspectives to identify a possible critical point in the phase diagram.
Die vorliegende Dissertation untersucht die Nichtgleichgewichtsdynamik von relativistischen Schwerionenkollisionen ausgehend von der anfänglichen Produktion von Teilchen durch den Zerfall von Strings, der Bildung eines Quark-Gluon-Plasmas (QGP), dessen kinetische und chemische Äquilibrierung als Funktion der Zeit sowie seine Transporteigenschaften im Gleichgewicht bei endlicher Temperatur und endlichem chemischen Potential. Ein Verständnis der frühen Phase der Schwerionenkollisionen ist insbesondere von großen Interesse, da letztere eine Verbindung zwischen den ersten Nukleon-Nukleon Kollisionen und der Quark-Gluon-Plasma Phase herstellen, die zu einem späteren Zeitpunkt ein gewisses Maß an Thermalisierung zeigt. Allerdings können nur Nichtgleichgewichts-Theorien eine Verbindung zwischen dem anfänglichen QGP und seiner - zumindest partiellen - Thermalisierung herstellen. Um die Dynamik eines stark wechselwirkenden Mediums wie des Quark-Gluon-Plasmas zu beschreiben, reichen übliche Transportgleichungen (basierend auf der Boltzmann-Gleichung) nicht aus und es müssen komplexere Theorien, die auch für stark korrelierte Medien geeignet sind, angewendet werden. Hier kommen hydrodynamische Simulationen oder Transportrechnungen - basierend auf verallgemeinerten Transportgleichungen - zum Einsatz. Solche verallgemeinerte Transportgleichungen, wie die Kadanoff-Baym-Gleichungen, ergeben sich aus der quantenmechanischen Nichtgleichgewichts-Vielteilchentheorie, in der Green’s- Funktionen in Minkowski Raum-Zeit die interessierenden Größen sind, um die Dynamik des betrachteten Mediums zu beschreiben. Mit geeigneten Näherungen kann man so kinetische Transportgleichungen erhalten, die eine einheitliche Behandlung von stabilen und instabilen Teilchen auch außerhalb des Gleichgewichts ermöglichen. Diese Bestandteile bilden die Basis des Transportmodells Parton-Hadron-String Dynamics (PHSD), welches daher ein geeignetes ’Instrument’ ist um die verschiedenen Phasen einer Schwerionenkollision zu analysieren, egal ob die verschiedenen Formen der Materie im Gleichgewicht sind oder nicht.
In dieser Arbeit wird zunächst die Quantenchromodynamik (QCD) vorgestellt und erklärt, wie diese Theorie im Laufe der Jahre entwickelt wurde um ein wichtiger Bestandteil des Standardmodells der Teilchenphysik zu werden. Wir werden weiterhin die verbleibenden Herausforderungen in unserem Verständnis der QCD vorstellen, die sich primär auf das Phasendiagramm der stark wechselwirkenden Materie konzentrieren.
Im zweiten Kapitel untersuchen wir die Nichtgleichgewichts-Feldtheorie und die damit verbundenen Techniken - wie die Keldysh-Kontur - zur Beschreibung der Green’schen Funktionen als wesentlichen Freiheitsgrade. Wir leiten die Evolutionsgleichung für die Green’schen Funktionen her, d. h. die Kadanoff Baym-Gleichungen am Beispiel einer skalaren Feldtheorie.
Im nächsten Kapitel wird das Transportmodell Parton-Hadron-String Dynamics (PHSD), welches die Anwendung der verallgemeinerten Transportgleichungen zur Beschreibung relativistischer Schwerionenkollisionen darstellt, vorgestellt.
Wir beginnen im Kapitel 4 mit der Untersuchung der Nichtgleichgewichtseigenschaften des Quark-Gluon-Plasmas, welches bei relativistischen Schwerionenkollisionen erzeugt wird. Zu diesem Zweck vergleichen wir die Quark-Gluon-Plasmaentwicklung aus dem PHSD mit einem viskosen hydrodynamischen Modell, bei dem ein lokales kinetisches und chemisches Gleichgewicht angenommen wird.
Im Kapitel 5 konzentrieren wir uns auf das frühe Vorgleichgewichtsstadium ultra-relativistischer Schwerionenkollisionen und insbesondere auf die Freiheitsgrade der QGP-Phase in diesem Stadium. Wir untersuchen die Auswirkungen eines QGP, welches anfänglich entweder aus einem System aus massiven Gluonen (Szenario I) oder alternativ aus Quarks und Antiquarks (Szenario II) besteht. Das nächste Kapitel wird ebenfalls die Produktion von Teilchen im Frühstadium von Schwerionenkollisionen behandeln, jedoch bei niedrigeren Kollisionsenergien. Hier wird eine mikroskopische Beschreibung des K+/pi+-Verhältnisses im Vordergrund stehen, d. h. die Erklärung des Maximums in diesem Verhältnis bei etwa 30 A GeV ("Horn") in zentralen Au+Au (oder Pb+Pb) Kollisionen. Insbesonders werden wir die Modifikation des String-Fragmentierungsprozesses (über den Schwinger-Mechanismus) in einer Umgebung mit hoher hadronischer Dichte aufgrund der teilweisen Wiederherstellung der chiralen Symmetrie untersuchen.
In Kapitel 7 erweitern wir das Parton-Hadron-String Dynamics (PHSD)-Transportmodell im partonischen Sektor, indem wir explizit die totalen und differentiellen partonischen Streuungsquerschnitte als Funktion der Temperatur T und des baryochemischen Potentials μB berechnen auf der Basis der effektiven Propagatoren und Kopplungen des Dynamical QuasiParticle Models (DQPM), welches auch die generelle Zeitentwicklung der partonischen Freiheitsgrade beschreibt. Wir finden nur eine sehr bescheidene Änderung von n/s mit dem baryonchemischen Potential μB in Abhängigkeit von der skalierten Temperatur T/Tc(μB). Dies gilt auch für eine Vielzahl von hadronischen Observablen aus zentralen A+A Kollisionen im Energiebereich von 5 GeV < vsNN < 200 GeV bei der Implementierung der differentiellen Querschnitte in das PHSD-Modell. Da wir in Schwerionen-Observablen nur kleine Spuren einer μB-Abhängigkeit finden - obwohl die effektiven Partonenmassen und Kollisionsbreiten sowie deren Partonenquerschnitte eindeutig von μB abhängen - impliziert dies, dass man eine beträchtliche Partonendichte und ein großes Raum-Zeit-QGP-Volumen zur Untersuchung der Dynamik in der partonischen Phase benötigt. Diese Bedingungen sind nur bei hohen Kollisionsenergien erfüllt, bei denen μB jedoch eher niedrig ist. Wenn andererseits die Kollisionsenergie verringert und somit μB erhöht wird, wird die hadronische Phase dominant und dementsprechend wird es zunehmend schwieriger, Signale aus der Partonendynamik auf der Basis von "Bulk"-Observablen zu extrahieren.
Professionalization of service-learning in higher education – an academic development approach
(2018)
In an attempt to professionalize service-learning in higher education, teachers and their teaching skills are considered a determining factor and require particular attention. To promote the teaching skills necessary for service-learning courses, an academic development approach addressing these specific requirements has been implemented at Goethe University Frankfurt as part of the academic development program for teaching staff. This article presents the particularities of this approach and illustrates one of its central elements, i.e., the concept of a workshop on planning service-learning courses. Both practical and research implications are discussed.
Two species of the genus Fallopia (F. sachalinensis, F. japonica, Polygonaceae) native to Asia, and their hybrid (F. ×bohemica), belong to the most noxious plant invaders in Europe. They impact highly on invaded plant communities, resulting in extremely poor native species richness. The low number of native species in invaded communities points to the possible existence of mechanisms suppressing their germination. In this study we assessed, under laboratory conditions, whether there are phytotoxic effects of the three Fallopia congeners on seed germination of three target species: two native species commonly growing in habitats that are often invaded by Fallopia taxa (Urtica dioica, Calamagrostis epigejos), and Lepidium sativum, a species commonly used in allelopathic bioassays as a control. Since Fallopia taxa form dense stands with high cover, we included varying light conditions as an additional factor, to simulate the effects of shading by leaf canopy on germination. The effects of aqueous extracts (2.5%, 5.0%, and 0% as a control) from dry leaves and rhizomes of the Fallopia congeners on germination of the target species were thus studied under two light regimes, simulating full daylight (white light) and light filtered through canopy (green light), and in dark as a control regime. Rhizome extracts did not affect germination. Light treatments yielded inconclusive results, indicating that poor germination and establishment of species in invaded stands is unlikely to be caused by shading alone. However, we found a pronounced phytotoxic effect of leaf extracts of Fallopia taxa, more so at 5.0% than 2.5% extract concentration. Fallopia sachalinensis exerted the largest negative effect on the germination of Urtica dioica, F. ×bohemica on that of C. epigejos, and F. japonica had invariably the lowest inhibitory effect on all test species. The weak phytotoxic effect of F. japonica corresponds to the results of previous studies that found this species to be generally a weaker competitor than its two congeners. Although these results do not necessarily provide direct evidence for allelopathic effects in the field, we demonstrate the potential phytotoxic effect of invasive Fallopia taxa on the germination of native species. This suggests that allelopathy may play a role in the impact of Fallopia invasion on species diversity of invaded communities.