Tropical waves and rainfall over Africa: Variability, mechanisms and potential for forecasting

Excessive rains or prolonged drought can have severe impacts on the economy, agriculture, water resources, spread of diseases and ecosystems in many African countries. As current global numerical weather prediction systems fail to deliver accurate rainfall forecasts over tropical Africa, novel forecasting strategies are needed. Tropical waves are known to modulate precipitation over this region on timescales of a few days to several weeks. The aim of this dissertation is to quantify the influence of all major waves on rainfall variability over Africa, to investigate the involved mechanisms and, to test their potential for forecasting rainfall, with a focus on northern tropical Africa during the extended monsoon season. Despite the importance of rainfall variability for vulnerable societies in tropical Africa, the relative influence of tropical waves for this region is largely unknown. This thesis closes this gap and presents the first systematic comparison of the impact of six wave types on precipitation over northern tropical Africa during the transition and full monsoon seasons, using two satellite products and a dense rain gauge network. Composites of rainfall anomalies based on different datasets show comparable modulation intensities in the West Sahel and at the Guinea Coast, varying from less than 2 to above 7 mm per day depending on the wave type. Tropical disturbances (TDs, including African Easterly Waves, AEWs) and Kelvin waves dominate the 3-hourly to daily timescale and explain 10-30% of precipitation variability locally. On longer timescales (7–20 days), only the Madden-Julian Oscillation (MJO) and Equatorial Rossby (ER) waves remain as modulating factors and explain up to one third of rainfall variability. Eastward inertio-gravity (EIG) waves and mixed Rossby-gravity (MRG) waves are comparatively unimportant. An analysis of wave superposition shows that low-frequency waves (MJO, ER) in their wet phase amplify the activity of high-frequency waves (TD, MRG) and suppress them in the dry phase. Furthermore, this dissertation gives the first systematic comparison of the dynamics and thermodynamics associated with tropical waves affecting rainfall variability over northern tropical Africa: Reanalysis and radiosonde data were analyzed for the period 1981–2013 based on space-time filtering of outgoing longwave radiation. The identified circulation patterns are largely consistent with equatorial shallow water theory. The slow modes, MJO and ER, mainly impact precipitable water, whereas the faster TDs, Kelvin waves, and MRG waves primarily modulate moisture convergence. Monsoonal inflow intensifies during wet phases of the MJO, ER, and MRG waves, associated with a northward shift of the intertropical discontinuity for MJO and ER waves. This study reveals that MRG waves over Africa have a distinct dynamical structure that differs significantly from AEWs. During passages of vertically tilted imbalanced wave modes, such as MJO, TDs, Kelvin, and partly MRG waves, increased vertical wind shear and improved conditions for up- and downdrafts facilitate the organization of mesoscale convective systems. The balanced ER waves are not tilted and rainfall is triggered by large-scale moistening and stratiform lifting. The MJO and ER waves interact with intraseasonal variations of the Indian monsoon and extratropical Rossby wave trains. The latter causes a trough over the Atlas Mountains associated with a tropical plume and rainfall over the Sahara. The presented results unveil which dynamical processes need to be modeled realistically to represent the coupling between tropical waves and rainfall in northern tropical Africa. The potential of tropical waves as predictors for African rainfall was tested. The spatio-temporal correlation patterns of tropical waves highlight their potential for synoptic rainfall forecasting. The observed spatio-temporal properties agree with values predicted by shallow-water theory, with the exception of MRG and EIG waves, which have a strong phase dispersion at low wavenumbers. Unfiltered precipitation fields show correlations patterns that are physically explainable by tropical waves and other atmospheric phenomena such as the position of the tropical rainbelt. These correlations serve as predictors in a logistic regression model. It was shown that this model successfully predicts rainfall occurrence over Africa with a lead time of one day. The statistical model is calibrated and outperforms the climatological forecast and current numerical weather prediction models by about 20%. The fact that tropical waves explain large portions of synoptic to intraseasonal rainfall variability in almost the entire tropics emphasize the potential of the proposed statistical model. This PhD thesis has laid the foundation to exploit this potential and to significantly improve short-term weather forecasts in Africa and throughout the tropics

Expected sensitivity of the AugerPrime Radio Detector to the masses of ultra-high-energy cosmic rays using inclined air showers

Despite enormous efforts in the last several decades, the origin of ultra-high-energy cosmic rays (UHECRs) -- their acceleration sites and acceleration mechanism(s) -- remains unidentified and is subject of active research. The progress made during that time, in particular by the Pierre Auger Observatory, established that significant advances in our understanding of the nature of UHECRs are only achieved with a better knowledge of their mass composition, i.e., through more precise measurements. To this end, the Pierre Auger Observatory is upgrading its large-aperture Surface Detector (SD) to enhance its mass sensitivity for the detection of the highest-energy cosmic rays ($E \gtrsim 4 \times 10^{19}\,$eV). As part of this effort, the AugerPrime Radio Detector (RD) will consist of over 1600 dual-polarized radio antennas mounted on top of each of the SD\u27s water-Cherenkov detector (WCD) stations. The RD will be measuring the electromagnetic radiation in the 30$\,$MHz to 80$\,$MHz frequency band produced by highly inclined air showers with zenith angles $\gtrsim\,$65$^\circ$. Thus, the RD will allow us to determine the cosmic-ray energy by measuring the shower\u27s electromagnetic component, which is largely independent of the cosmic-ray mass. In contrast, since most particles in highly-inclined air showers are absorbed in the atmosphere and do not reach the ground, the WCDs will mainly record muons from the muonic shower component, which is highly correlated to the cosmic-ray mass. The combination of that complementary information allows us to infer the cosmic-ray mass with high precision. With this work, I have laid the foundation to process, reconstruct, and analyze data measured by the RD. To develop a signal and reconstruction model for the radio detection of inclined air showers, I have conducted comprehensive studies of the nature of the radio emission from inclined air showers by utilizing numerical CoREAS simulations. In particular, I have investigated the origin of the radio emission within the extensive particle cascades and studied the correlation between the emission strength and ambient conditions. Furthermore, I have identified and characterized a refractive displacement of the radio-emission footprints at the ground, caused by the propagation of the electromagnetic radiation through the Earth\u27s atmosphere. This causes the radio emission from an 85$^\circ$ air shower to be displaced by about 1.5$\,$km and thus has essential implications for the description of the radio-emission footprint and the interpretation of the reconstructed geometry for very inclined air showers with zenith angles above 80$^\circ$. With that at hand, I have developed a signal model of the 2-dimensional lateral distribution of the radio emission in the 30$\,$MHz to 80$\,$MHz frequency band. This model enables the reconstruction of the (electromagnetic) shower energy with sparse radio-antenna arrays and an intrinsic resolution of below 5\% without taking into account instrumental uncertainties. As the electromagnetic energy can be reconstructed without any dependency on the cosmic-ray mass, this model is suitable to perform precise studies of the mass(-composition) of UHECRs, for example, with RD-SD hybrid detections of the AugerPrime Observatory. In addition, I have evaluated the possibility of improving this mass sensitivity by measuring the slant depth of the shower maximum $X_\mathrm{max}$ with a newly-proposed interferometric reconstruction technique. I have worked out, that the RD does not meet the specifications for an accurate reconstruction of $X_\mathrm{max}$, and that a time synchronization between antenna stations of $\lesssim\,$1$\,$ns and a signal multiplicity of $\gtrsim\,20$ are required to achieve accurate results. With this theoretical framework, I have thoroughly studied the expected performance of the RD to detect and reconstruct inclined air showers and its potential to determine the mass(-composition) of UHECRs with RD-SD hybrid measurements. These studies utilize Monte-Carlo-generated air showers, perform end-to-end simulations of the RD instrumental response including measured noise, and a reconstruction of all relevant air shower observables with the here-developed signal model. I have found that the RD will be fully efficient to detect inclined air showers with zenith angles above 70$^\circ$ and energies above $6.3 \times 10^{18}\,$eV. For a 10-year operation period, the RD will collect over 3900 events with energies above $10^{19}\,$eV and around 570 events for energies above $4 \times 10^{19}\,$eV. An accurate reconstruction of the shower energy with the RD is already possible for air showers measured with 5 radio antennas and zenith angles above 68$^\circ$. For current assumptions on the instrumental response of the RD, I have obtained an expected energy resolution of well below 10\% for energies above $10^{19}\,$eV and find no bias in the reconstructed electromagnetic energy for air showers induced by different primary particles. This study is concluded with an assessment of possible systematic uncertainties. By combining the RD-reconstructed (electromagnetic) energy and the SD-reconstructed number of muons, I assessed the potential discrimination between different primary particle types and to measure the average mass composition of UHECRs. The separation for proton- and iron-induced air showers with zenith angles above 70$^\circ$ and electromagnetic energies above $10^{19}\,$eV is quantified with a figure of merit $\text{FOM} \approx 1.6$. The (simulated) measurements of the mean muon number with the RD and SD were found to reproduce the injected mass compositions. Hence, RD-SD hybrid measurements carry the potential to extend such measurements currently performed with the Fluorescence Detector and SD to higher energies, and thereby, to distinguish between different astrophysical scenarios that could explain the nature of UHECRs. With the reconstruction model and mass-composition analysis developed in this work, the Pierre Auger Observatory is well-prepared for the arrival of experimental data from AugerPrime of inclined air showers

A Systematic Comparison of Tropical Waves over Northern Africa. Part II: Dynamics and Thermodynamics

This study presents the first systematic comparison of the dynamics and thermodynamics associated with all major tropical wave types causing rainfall modulation over northern tropical Africa: the Madden–Julian oscillation (MJO), equatorial Rossby waves (ERs), tropical disturbances (TDs, including African easterly waves), Kelvin waves, mixed Rossby–gravity waves (MRGs), and eastward inertio-gravity waves (EIGs). Reanalysis and radiosonde data were analyzed for the period 1981–2013 based on space–time filtering of outgoing longwave radiation. The identified circulation patterns are largely consistent with theory. The slow modes, MJO and ER, mainly impact precipitable water, whereas the faster TDs, Kelvin waves, and MRGs primarily modulate moisture convergence. Monsoonal inflow intensifies during wet phases of the MJO, ERs, and MRGs, associated with a northward shift of the intertropical discontinuity for MJO and ERs. This study reveals that MRGs over Africa have a distinct dynamical structure that differs significantly from AEWs. During passages of vertically tilted imbalanced wave modes, such as the MJO, TDs, Kelvin waves, and partly MRG waves, increased vertical wind shear and improved conditions for up- and downdrafts facilitate the organization of mesoscale convective systems. The balanced ERs are not tilted, and rainfall is triggered by large-scale moistening and stratiform lifting. The MJO and ERs interact with intraseasonal variations of the Indian monsoon and extratropical Rossby wave trains. The latter causes a trough over the Atlas Mountains associated with a tropical plume and rainfall over the Sahara. The presented results unveil which dynamical processes need to be modeled realistically to represent the coupling between tropical waves and rainfall in northern tropical Afric

On the proof-theoretic strength of monotone induction in explicit mathematics

AbstractWe characterize the proof-theoretic strength of systems of explicit mathematics with a general principle (MID) asserting the existence of least fixed points for monotone inductive definitions, in terms of certain systems of analysis and set theory. In the case of analysis, these are systems which contain the Σ12-axiom of choice and Π12-comprehension for formulas without set parameters. In the case of set theory, these are systems containing the Kripke-Platek axioms for a recursively inaccessible universe together with the existence of a stable ordinal. In all cases, the exact strength depends on what forms of induction are admitted in the respective systems

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.Fil: Salto, Ileana Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Torres Tejerizo, Gonzalo Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Wibberg, Daniel. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Pühler, Alfred. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Schlüter, Andreas. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Pistorio, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

GEOSITES AS A POTENTIAL FOR THE DEVELOPMENT OF TOURISM – OVERVIEW OF RELEVANT SITES IN ESWATINI (FORMERLY SWAZILAND)

Despite being one of the smallest countries in Africa, the Kingdom of Eswatini (formerly Swaziland) is characterized by many locations, which are due to their geoscientific significance to be termed as geosites, and which are here in an overview presented and briefly explained. Each of them can be assigned to a specific scientific approach, e.g. as a landscape, a geological, a geomorphologic, an archaeological (prehistoric) or a mining heritage site. Eswatini yields remarkable landscapes like the Mahamba Gorge and the Sibebe Monolith, it exhibits worldwide one of the largest in granite formed caves (Gobholo), and possibly the oldest dated rocks in Africa (Piggs Peak gneisses), as well as beautiful and scientifically relevant rock painting sites (Nsangwini, Sandlane and Hholoshini) and three abandoned mines in the Barberton Greenstone Belt (Forbes, Ngwenya and Bulembu). The latter have contributed largely to the infrastructural development of the country. The geotouristic value of the respective sites is evaluated and commented, and it is assumed that in future these and other, here not yet mentioned geosites, may contribute to income generating processes for the country and the local communities

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions

Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars. © 2018 The Author

Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV

Bartholomaeus A, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M. Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV. PLOS ONE. 2016;11(11): e0165965.Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species. Based on the alignment of the conserved RNA-dependent RNApolymerase (RdRp) domain, this viral community included putative members of the families Narnaviridae, Endornaviridae, Partitiviridae and Megabirnaviridae as well as of the order Tymovirales. Furthermore, viruses, which could not be assigned to any existing family or order, but showed similarities to so far unassigned species like Sclerotinia sclerotiorum RNA virus L, Rhizoctonia solani dsRNA virus 1, Aspergillus foetidus slow virus 2 or Rhizoctonia fumigata virus 1, were identified. This is the first report of a fungal isolate infected by 17 different viral species and a valuable study case to explore the diversity of mycoviruses infecting R. solani